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1
Barton, N. H. "Pleiotropic models of quantitative variation." Genetics 124, no. 3 (March 1, 1990): 773–82. http://dx.doi.org/10.1093/genetics/124.3.773.
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Abstract It is widely held that each gene typically affects many characters, and that each character is affected by many genes. Moreover, strong stabilizing selection cannot act on an indefinitely large number of independent traits. This makes it likely that heritable variation in any one trait is maintained as a side effect of polymorphisms which have nothing to do with selection on that trait. This paper examines the idea that variation is maintained as the pleiotropic side effect of either deleterious mutation, or balancing selection. If mutation is responsible, it must produce alleles which are only mildly deleterious (s approximately 10(-3)), but nevertheless have significant effects on the trait. Balancing selection can readily maintain high heritabilities; however, selection must be spread over many weakly selected polymorphisms if large responses to artificial selection are to be possible. In both classes of pleiotropic model, extreme phenotypes are less fit, giving the appearance of stabilizing selection on the trait. However, it is shown that this effect is weak (of the same order as the selection on each gene): the strong stabilizing selection which is often observed is likely to be caused by correlations with a limited number of directly selected traits. Possible experiments for distinguishing the alternatives are discussed.
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Burrow, H. M., S. S. Moore, D. J. Johnston, W. Barendse, and B. M. Bindon. "Quantitative and molecular genetic influences on properties of beef: a review." Australian Journal of Experimental Agriculture 41, no. 7 (2001): 893. http://dx.doi.org/10.1071/ea00015.
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The scientific literature is reviewed to identify quantitative and molecular genetic influences on quantity and quality of beef. Genetic variation between breeds is of similar magnitude to genetic variation within breeds for many economically important traits. Differences between breeds are significant and large for most carcass and beef quality attributes, including beef tenderness, although differences for sensory juiciness and flavour are of little practical importance. For traits such as beef tenderness, between-breed differences may be more easily exploited than within-breed differences, because exceptional breeds are easier to identify than exceptional animals. Effects of heterosis on carcass and beef quality attributes are relatively small (3% or less), with most effects mediated through heterotic effects on weight. Carcass composition traits (e.g. carcass weight, fat thickness and marbling) are moderately to highly heritable. Most estimates of retail beef yield percentage are highly heritable, offering good potential for within-breed selection for the trait, although a moderate to strong antagonistic relationship exists between yield and marbling. This relationship needs to be considered in within-breed selection programs for yield percentage. Early estimates of heritability of objective measures of beef tenderness (Warner Bratzler shear force values) indicated tenderness was moderately to highly heritable. Recent estimates using larger numbers of carcasses and more discriminatory methods of analysis indicate that beef tenderness is lowly heritable in Bos taurus breeds and moderately heritable inBos indicus and Bos indicus-derived breeds. Within breeds, measures of 24-h calpastatin activity are genetically strongly correlated with shear force values but are more heritable. However, phenotypic correlations between shear force values and 24-h calpastatin activities are low. There are also inconsistencies in relationships between these measurements across breeds. Low correlations between tenderness in different muscles, low to moderate heritabilities and inconsistent variation within- and between-breeds for traits such as 24-h calpastatin activity suggest that genetic improvement in beef tenderness may be difficult. The possibility exists that significant mitochondrial genetic effects occur for some carcass and beef quality attributes. A major gene for muscular hypertrophy in cattle significantly affects carcass and beef quality characteristics. Genome-wide screening of DNA markers indicates a number of putative Quantitative Trait Loci (QTL) associated with carcass and meat quality characteristics. Published data for these QTL are summarised. Strategies to combine quantitative and molecular genetic information to maximise genetic progress are discussed.
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Bayele, Henry K., and Surjit K. S. Srai. "Regulatory variation in hepcidin expression as a heritable quantitative trait." Biochemical and Biophysical Research Communications 384, no. 1 (June 2009): 22–27. http://dx.doi.org/10.1016/j.bbrc.2009.04.032.
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Pavlicev, Mihaela, James M. Cheverud, and Günter P. Wagner. "Evolution of adaptive phenotypic variation patterns by direct selection for evolvability." Proceedings of the Royal Society B: Biological Sciences 278, no. 1713 (November 24, 2010): 1903–12. http://dx.doi.org/10.1098/rspb.2010.2113.
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A basic assumption of the Darwinian theory of evolution is that heritable variation arises randomly. In this context, randomness means that mutations arise irrespective of the current adaptive needs imposed by the environment. It is broadly accepted, however, that phenotypic variation is not uniformly distributed among phenotypic traits, some traits tend to covary, while others vary independently, and again others barely vary at all. Furthermore, it is well established that patterns of trait variation differ among species. Specifically, traits that serve different functions tend to be less correlated, as for instance forelimbs and hind limbs in bats and humans, compared with the limbs of quadrupedal mammals. Recently, a novel class of genetic elements has been identified in mouse gene-mapping studies that modify correlations among quantitative traits. These loci are called relationship loci, or relationship Quantitative Trait Loci (rQTL), and affect trait correlations by changing the expression of the existing genetic variation through gene interaction. Here, we present a population genetic model of how natural selection acts on rQTL. Contrary to the usual neo-Darwinian theory, in this model, new heritable phenotypic variation is produced along the selected dimension in response to directional selection. The results predict that selection on rQTL leads to higher correlations among traits that are simultaneously under directional selection. On the other hand, traits that are not simultaneously under directional selection are predicted to evolve lower correlations. These results and the previously demonstrated existence of rQTL variation, show a mechanism by which natural selection can directly enhance the evolvability of complex organisms along lines of adaptive change.
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Linder, Robert A., Fabian Seidl, Kimberly Ha, and Ian M. Ehrenreich. "The complex genetic and molecular basis of a model quantitative trait." Molecular Biology of the Cell 27, no. 1 (January 2016): 209–18. http://dx.doi.org/10.1091/mbc.e15-06-0408.
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Quantitative traits are often influenced by many loci with small effects. Identifying most of these loci and resolving them to specific genes or genetic variants is challenging. Yet, achieving such a detailed understanding of quantitative traits is important, as it can improve our knowledge of the genetic and molecular basis of heritable phenotypic variation. In this study, we use a genetic mapping strategy that involves recurrent backcrossing with phenotypic selection to obtain new insights into an ecologically, industrially, and medically relevant quantitative trait—tolerance of oxidative stress, as measured based on resistance to hydrogen peroxide. We examine the genetic basis of hydrogen peroxide resistance in three related yeast crosses and detect 64 distinct genomic loci that likely influence the trait. By precisely resolving or cloning a number of these loci, we demonstrate that a broad spectrum of cellular processes contribute to hydrogen peroxide resistance, including DNA repair, scavenging of reactive oxygen species, stress-induced MAPK signaling, translation, and water transport. Consistent with the complex genetic and molecular basis of hydrogen peroxide resistance, we show two examples where multiple distinct causal genetic variants underlie what appears to be a single locus. Our results improve understanding of the genetic and molecular basis of a highly complex, model quantitative trait.
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Bell, R. L., and Jules Janick. "Quantitative Genetic Analysis of Fruit Quality in Pear." Journal of the American Society for Horticultural Science 115, no. 5 (September 1990): 829–34. http://dx.doi.org/10.21273/jashs.115.5.829.
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Narrow-sense heritability estimates were computed for five fruit quality characteristics and their weighted total index. Grit content and skin russeting were moderately heritable traits, while flesh texture, flavor, appearance, and the weighted total score were of relatively low heritability. Within sub-populations of crosses, defined by the species ancestry of the parents, the relative magnitudes of heritabilities for each trait varied, but were in general agreement with those for the entire population. The general combining ability variances were 4.5 to 12.0 times those for specific combining ability, although both were statistically significant for all traits and the weighted quality index. The species ancestry of a parent had no effect on its general combining ability rank. While selection of individual seedlings on the basis of their own phenotype will result in genetic improvement for grit and russet, selection based on a combination of full-sib family means and individual phenotypes is recommended for flavor, texture, appearance, and overall fruit quality.
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Chapco, William. "Genetic variation in three subspecies of Melanoplus sanguinipes (F.). I. Morphometric traits." Genome 29, no. 5 (October 1, 1987): 793–801. http://dx.doi.org/10.1139/g87-133.
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Samples of three subspecies of Melanoplus sanguinipes (M. s. sanguinipes, M. s. vulturnus, and M. s. defectus), raised under the same laboratory conditions, differ significantly in a number of morphometric traits. The heritable nature of these differences was explored by performing intersubspecific crosses, hybrid crosses, and backcrosses. On the whole, the genetics underlying each trait was complex, with the presence or absence of heterosis, of genic interaction, and of maternal effects being dependent on the strains compared and the sex of the insects. Key words: Melanoplus sanguinipes, Acrididae, quantitative genetics, morphometric traits.
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Blanckenhorn, Wolf, and Claudia Mühlhäuser. "The quantitative genetics of sexual selection in the dung fly Sepsis cynipsea." Behaviour 141, no. 3 (2004): 327–41. http://dx.doi.org/10.1163/156853904322981888.
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AbstractIn the common dung or black scavenger fly Sepsis cynipsea (Diptera: Sepsidae) several morphological and behavioural male and female traits interact during mating. Previous studies show that males attempt to mount females without courtship, females use vigorous shaking behaviour in response to male mounting, the duration of shaking is an indicator of both direct and indirect female choice and sexual conflict, and larger males enjoy a mating advantage. We conducted a quantitative genetic paternal half sib study to investigate the genetic underpinnings of these traits, notably body size (the preferred trait) and the associated female preference, and to assess the relative importance of various models generally proposed to account for the evolution of sexually selected traits. Several morphological traits and female shaking duration were heritable, thus meeting a key requirement of all sexual selection models. In contrast, two traits indicative of male persistence in mating were not. Male longevity was also heritable and negatively correlated with his mating effort, suggesting a mating cost. However, the crucial genetic correlation between male body size and female shaking duration, predicted to be negative by both 'good genes' and Fisherian models and positive by the sexual conflict (or chase-away) model, was zero. This could be because of low power, or because of constraints imposed by the genetic correlation structure. Based on our rsults we conclude that discriminating sexual selection models by sole means of quantitative genetics is difficult, if not impossible.
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Wales, R., K. W. Siggens, M. J. T. van Eijk, B. Brugmans, A. Archibald, C. S. Haley, and G. S. Plastow. "Is a linkage map and a pedigree structure required to detect useful DNA markers (QTL) in the pig?" Proceedings of the British Society of Animal Science 1999 (1999): 44. http://dx.doi.org/10.1017/s175275620000199x.
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The heritable components of many traits in which livestock producers strive for improvement comprise a number of genetic loci. Many workers have now reported the identification of such quantitative trait loci (QTL) using model crosses between divergent breeds or lines in combination with whole genome scans using mapped DNA markers. Such methods rely on two or three generation pedigrees in order to be able to trace the inheritance of markers and the QTL. However, it is not yet clear if such QTL have application in commercial pig populations. The AFLP™ technology is a very efficient method for identifying markers segregating in any population. We have previously reported the successful use of the AFLP™technology and bulk segregant analysis (BSA) for the detection of markers associated with pig coat colour, a monogenic trait (Plastow et al 1998). We set out to determine whether these methods could be used for the detection of loci associated with quantitative traits directly in commercial populations.
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Mihai, G., I. Mirancea, and C. Duta. "Variation of the quantitative traits in a progeny test of Abies alba (Mill.) at the nursery stage." Silvae Genetica 63, no. 1-6 (December 1, 2014): 275–84. http://dx.doi.org/10.1515/sg-2014-0035.
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AbstractFifty-one full-sib families were created using 11 parents in a silver fir seed orchard and a half-diallel mating design. The seeds of control-pollinated families were sown in a nursery in autumn 2007. Growth and branches traits were measured during nursery testing, and genetic parameters were estimated at the ages of 3, 4, 5, and 6 years. The additive and dominance genetic variances were major sources of genetic variance. Dominance variance was greater than additive variance at these early ages for all traits. However, the ratio of SCA/GCA variance decreased from 23 to 14 for total height and from 36 to 19 for root collar diameter. Broadsense family heritability is higher than individual heritability. Height and root collar diameter are the most heritable traits in silver fir. The time trend of the five heritability estimates for total height increased with age. Significant trait-trait genetic correlations were obtained. Age-age genetic correlations were very high, and they displayed increasing trends with age. The selection of the most valuable parents and most valuable individuals within the best families could maximise genetic gain in the second breeding generation of silver fir.
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Knoll, A. T., K. Jiang, and P. Levitt. "Quantitative trait locus mapping and analysis of heritable variation in affiliative social behavior and co-occurring traits." Genes, Brain and Behavior 17, no. 5 (December 6, 2017): e12431. http://dx.doi.org/10.1111/gbb.12431.
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Ulrich, Anna, Pablo Otero-Núñez, John Wharton, Emilia M. Swietlik, Stefan Gräf, Nicholas W. Morrell, Dennis Wang, et al. "Expression Quantitative Trait Locus Mapping in Pulmonary Arterial Hypertension." Genes 11, no. 11 (October 22, 2020): 1247. http://dx.doi.org/10.3390/genes11111247.
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Expression quantitative trait loci (eQTL) can provide a link between disease susceptibility variants discovered by genetic association studies and biology. To date, eQTL mapping studies have been primarily conducted in healthy individuals from population-based cohorts. Genetic effects have been known to be context-specific and vary with changing environmental stimuli. We conducted a transcriptome- and genome-wide eQTL mapping study in a cohort of patients with idiopathic or heritable pulmonary arterial hypertension (PAH) using RNA sequencing (RNAseq) data from whole blood. We sought confirmation from three published population-based eQTL studies, including the GTEx Project, and followed up potentially novel eQTL not observed in the general population. In total, we identified 2314 eQTL of which 90% were cis-acting and 75% were confirmed by at least one of the published studies. While we observed a higher GWAS trait colocalization rate among confirmed eQTL, colocalisation rate of novel eQTL reported for lung-related phenotypes was twice as high as that of confirmed eQTL. Functional enrichment analysis of genes with novel eQTL in PAH highlighted immune-related processes, a suspected contributor to PAH. These potentially novel eQTL specific to or active in PAH could be useful in understanding genetic risk factors for other diseases that share common mechanisms with PAH.
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Lynch, Rachel M., Sudhir Naswa, Gary L. Rogers, Stephen A. Kania, Suchita Das, Elissa J. Chesler, Arnold M. Saxton, Michael A. Langston, and Brynn H. Voy. "Identifying genetic loci and spleen gene coexpression networks underlying immunophenotypes in BXD recombinant inbred mice." Physiological Genomics 41, no. 3 (May 2010): 244–53. http://dx.doi.org/10.1152/physiolgenomics.00020.2010.
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The immune system plays a pivotal role in the susceptibility to and progression of a variety of diseases. Due to a strong genetic basis, heritable differences in immune function may contribute to differential disease susceptibility between individuals. Genetic reference populations, such as the BXD (C57BL/6J × DBA/2J) panel of recombinant inbred (RI) mouse strains, provide unique models through which to integrate baseline phenotypes in healthy individuals with heritable risk for disease because of the ability to combine data collected from these populations across both multiple studies and time. We performed basic immunophenotyping (e.g., percentage of circulating B and T lymphocytes and CD4+and CD8+T cell subpopulations) in peripheral blood of healthy mice from 41 BXD RI strains to define the immunophenotypic variation in this strain panel and to characterize the genetic architecture that underlies these traits. Significant QTL models that explained the majority (50–77%) of phenotypic variance were derived for each trait and for the T:B cell and CD4+:CD8+ratios. Combining QTL mapping with spleen gene expression data uncovered two quantitative trait transcripts, Ptprk and Acp1, as candidates for heritable differences in the relative abundance of helper and cytotoxic T cells. These data will be valuable in extracting genetic correlates of the immune system in the BXD panel. In addition, they will be a useful resource for prospective, phenotype-driven model selection to test hypotheses about differential disease or environmental susceptibility between individuals with baseline differences in the composition of the immune system.
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Kanaga, Megan K., Ronald J. Ryel, Karen E. Mock, and Michael E. Pfrender. "Quantitative-genetic variation in morphological and physiological traits within a quaking aspen (Populus tremuloides) population." Canadian Journal of Forest Research 38, no. 6 (June 2008): 1690–94. http://dx.doi.org/10.1139/x08-012.
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Genetic diversity within populations is an important component of adaptive evolution, and recent research has demonstrated that genetic variation within plant populations can have important ecological effects. In this study, we investigate quantitative-genetic variation in several traits within a quaking aspen ( Populus tremuloides Michx.) population. A common garden experiment was planted with replicates of 13 aspen genotypes collected from wet and dry sites within a population in southern Utah, USA. Ten growth, leaf, physiological, and structural traits were measured. There were significant, heritable phenotypic differences among genotypes in every measured trait and differences in 4 of the 10 traits among genotypes originating from wet and dry collection sites. The data were compared with other published studies, showing that aspen heritability (H2) estimates and coefficients of genetic variation (CVG) were comparable or higher than other Populus species and hybrid F1 Populus genotypes, indicating a large amount of quantitative-genetic variation in aspen.
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Edwin, Deepa, Timothy S. Fenske, Christine McMahon, Vikram Mathews, Molly Bogue, Michael Province, James Cheverud, Howard McLeod, and Timothy A. Graubert. "Susceptibility to Alkylator-Induced Cancer Is a Heritable Trait." Blood 106, no. 11 (November 16, 2005): 3266. http://dx.doi.org/10.1182/blood.v106.11.3266.3266.
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Abstract Secondary malignancies are a serious adverse consequence of alkylator chemotherapy treatment. The incidence of secondary hematopoietic malignancies (t-MDS/AML) exceeds 11% in several recent reports. Secondary solid tumors (lung, breast) also occur after alkylator exposure. While patient age, primary diagnosis, and chemotherapy dose are established risk factors, there is increasing evidence that germline genetic factors are also important in determining risk. The genetic basis of susceptibility to alkylator-induced secondary neoplasms is poorly understood. Most studies have focused on genes in drug metabolic pathways. A limited number of genetic polymorphisms with modest impact on risk for alkylator-induced cancer have been reported. We hypothesize that other genetic contributors to alkylator-induced cancer susceptibility have not yet been identified. To screen genome-wide for novel heritable susceptibility factors, we established a mouse model of alkylator-induced malignancy. In collaboration with the Mouse Phenome Project, we exposed mice from 20 inbred strains to the prototypical alkylating agent, N-nitroso-N-ethylurea (ENU). Mice (n=12 per strain) received two doses of ENU (100mg/kg, IP) or no treatment (n=12 per strain) at 9 and 10 weeks of age. ENU was a potent carcinogen in many of the strains tested, inducing 140 tumors in 240 ENU-treated mice (66% incidence of at least one tumor in evaluable mice), compared to a background incidence of 8% spontaneous tumors in 240 strain, age, and sex-matched control mice (relative risk = 8.4, p< 0.0001). A wide variety of tumor histologies were noted, including epithelial carcinomas, soft tissue sarcomas, and hematopoietic tumors. Cancer susceptibility was a heritable trait for the most common tumor types, lung adenocarcinoma (H2 = 0.25, implying that 25% of cancer risk is heritable), T-cell lymphoma (H2 = 0.19), and myeloid malignancies (H2 = 0.10). The development of hematopoietic tumors (either lymphoid or myeloid) was negatively associated with the likelihood of developing gastrointestinal or lung adenocarcinoma. In silico quantitative trait locus (QTL) mapping was used to identify genomic intervals associated with cancer susceptibility. Strains were segregated by haplotype using a panel of 10,900 single nucleotide polymorphisms (SNPs). Differences in cancer susceptibility between haplotypes were assessed by ANOVA. After correcting for false detection, genomic intervals significantly associated with specific cancer phenotypes were identified. Preliminary analysis linked lung cancer susceptibility to four intervals on chromosomes 1,2,6, and 12. The latter interval contains Ahr, a highly polymorphic gene encoding the aryl hydrocarbon receptor previously implicated in carcinogenicity of environmental toxins. Lymphoma susceptibility was linked to two regions on chromosomes 3 and 18. The latter contains a member of the frizzled family of Wnt receptors. This novel mouse model recapitulates many features of human alkylator-associated cancer and supports the hypothesis that susceptibility to this syndrome is influenced by inherited polymorphisms that could be used to inform clinical treatment decisions.
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Jowett, Jeremy B., Vincent P. Diego, Navaratnam Kotea, Sudhir Kowlessur, Pierrot Chitson, Thomas D. Dyer, Paul Zimmet, and John Blangero. "Genetic Influences on Type 2 Diabetes and Metabolic Syndrome Related Quantitative Traits in Mauritius." Twin Research and Human Genetics 12, no. 1 (February 1, 2009): 44–52. http://dx.doi.org/10.1375/twin.12.1.44.
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AbstractEpidemiological studies report a high prevalence of type 2 diabetes and metabolic syndrome in the island nation of Mauritius. The Mauritius Family Study was initiated to examine heritable factors that contribute to these high rates of prevalence and consists of 400 individuals in 24 large extended multigenerational pedigrees. Anthropometric and biochemical measurements relating to the metabolic syndrome were undertaken in addition to family and lifestyle based information for each individual. Variance components methods were used to determine the heritability of the type 2 diabetes and metabolic syndrome related quantitative traits. The cohort was made up of 218 females (55%) and 182 males with 22% diagnosed with type 2 diabetes and a further 30% having impaired glucose tolerance or impaired fasting glucose. Notably BMI was not significantly increased in those with type 2 diabetes (P= .12), however a significant increase in waist circumference was observed in these groups (P= .02). The heritable proportion of trait variance was substantial and greater than values previously published for hip circumference, LDL and total cholesterol, diastolic and systolic blood pressure and serum creatinine. Height, weight and BMI heritabilities were all in the upper range of those previously reported. The phenotypic characteristics of the Mauritius family cohort are similar to those previously reported in the Mauritian population with a high observed prevalence rate of type 2 diabetes. A high heritability for key type 2 diabetes and metabolic syndrome related phenotypes (range 0.23 to 0.68), suggest the cohort will have utility in identifying genes that influence these quantitative traits.
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Castelbaum, Lauren, Chad M. Sylvester, Yi Zhang, Qiongru Yu, and John N. Constantino. "On the Nature of Monozygotic Twin Concordance and Discordance for Autistic Trait Severity: A Quantitative Analysis." Behavior Genetics 50, no. 4 (December 18, 2019): 263–72. http://dx.doi.org/10.1007/s10519-019-09987-2.
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AbstractThe characterizing features of autism spectrum disorder (ASD) are continuously distributed in nature; however, prior twin studies have not systematically incorporated this knowledge into estimations of concordance and discordance. We conducted a quantitative analysis of twin–twin similarity for autistic trait severity in three existing data sets involving 366 pairs of uniformly-phenotyped monozygotic (MZ) twins with and without ASD. Probandwise concordance for ASD was 96%; however, MZ trait correlations differed markedly for pairs with ASD trait burden below versus above the threshold for clinical diagnosis, with R2s on the order of 0.6 versus 0.1, respectively. Categorical MZ twin discordance for ASD diagnosis is rare and more appropriately operationalized by standardized quantification of twin–twin differences. Here we provide new evidence that although ASD itself is highly heritable, variation-in-severity of symptomatology above the diagnostic threshold is substantially influenced, in contrast, by non-shared environmental factors which may identify novel targets of early ASD amelioration.
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Dapas, Matthew, Ryan Sisk, Richard S. Legro, Margrit Urbanek, Andrea Dunaif, and M. Geoffrey Hayes. "Family-Based Quantitative Trait Meta-Analysis Implicates Rare Noncoding Variants in DENND1A in Polycystic Ovary Syndrome." Journal of Clinical Endocrinology & Metabolism 104, no. 9 (April 30, 2019): 3835–50. http://dx.doi.org/10.1210/jc.2018-02496.
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AbstractContextPolycystic ovary syndrome (PCOS) is among the most common endocrine disorders of premenopausal women, affecting 5% to15% of this population depending on the diagnostic criteria applied. It is characterized by hyperandrogenism, ovulatory dysfunction, and polycystic ovarian morphology. PCOS is highly heritable, but only a small proportion of this heritability can be accounted for by the common genetic susceptibility variants identified to date.ObjectiveThe objective of this study was to test whether rare genetic variants contribute to PCOS pathogenesis.Design, Patients, and MethodsWe performed whole-genome sequencing on DNA from 261 individuals from 62 families with one or more daughters with PCOS. We tested for associations of rare variants with PCOS and its concomitant hormonal traits using a quantitative trait meta-analysis.ResultsWe found rare variants in DENND1A (P = 5.31 × 10−5, adjusted P = 0.039) that were significantly associated with reproductive and metabolic traits in PCOS families.ConclusionsCommon variants in DENND1A have previously been associated with PCOS diagnosis in genome-wide association studies. Subsequent studies indicated that DENND1A is an important regulator of human ovarian androgen biosynthesis. Our findings provide additional evidence that DENND1A plays a central role in PCOS and suggest that rare noncoding variants contribute to disease pathogenesis.
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Cowley, D. E., and W. R. Atchley. "Quantitative Genetics of Drosophila Melanogaster. II. Heritabilities and Genetic Correlations between Sexes for Head and Thorax Traits." Genetics 119, no. 2 (June 1, 1988): 421–33. http://dx.doi.org/10.1093/genetics/119.2.421.
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Abstract A quantitative genetic analysis is reported for traits on the head and thorax of adult fruit flies, Drosophila melanogaster. Females are larger than males, and the magnitude of sexual dimorphism is similar for traits derived from the same imaginal disc, but the level of sexual dimorphism varies widely across discs. The greatest difference between males and females occurs for the dimensions of the sclerotized mouthparts of the proboscis. Most of the traits studied are highly heritable with heritabilities ranging from 0.26 to 0.84 for males and 0.27 to 0.81 for females. In general, heritabilities are slightly higher for males, possibly reflecting the effect of dosage compensation on X-linked variance. The X chromosome contributes substantially to variance for many of these traits, and including results reported elsewhere, the variance for over two-thirds of the traits studied includes X-linked variance. The genetic correlations between sexes for the same trait are generally high and close to unity. Coupled with the small differences in the traits between sexes for heritabilities and phenotypic variances, these results suggest that selection would be very slow to change the level of sexual dimorphism in size of various body parts.
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Thio, Chris H. L., Anna Reznichenko, Peter J. van der Most, Zoha Kamali, Ahmad Vaez, Johannes H. Smit, Brenda W. J. H. Penninx, et al. "Genome-Wide Association Scan of Serum Urea in European Populations Identifies Two Novel Loci." American Journal of Nephrology 49, no. 3 (2019): 193–202. http://dx.doi.org/10.1159/000496930.
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Background: Serum urea level is a heritable trait, commonly used as a diagnostic marker for kidney function. Genome-wide association studies (GWAS) in East-Asian populations identified a number of genetic loci related to serum urea, however there is a paucity of data for European populations. Methods: We performed a two-stage meta-analysis of GWASs on serum urea in 13,312 participants, with independent replication in 7,379 participants of European ancestry. Results: We identified 6 genome-wide significant single nucleotide polymorphisms (SNPs) in or near 6 loci, of which 2 were novel (POU2AF1 and ADAMTS9-AS2). Replication of East-Asian and Scottish data provided evidence for an additional 8 loci. SNPs tag regions previously associated with anthropometric traits, serum magnesium, and urinary albumin-to-creatinine ratio, as well as expression quantitative trait loci for genes preferentially expressed in kidney and gastro-intestinal tissues. Conclusions: Our findings provide insights into the genetic underpinnings of urea metabolism, with potential relevance to kidney function.
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Thumma, Bala R., Bronwyn A. Matheson, Deqiang Zhang, Christian Meeske, Roger Meder, Geoff M. Downes, and Simon G. Southerton. "Identification of a Cis-Acting Regulatory Polymorphism in a Eucalypt COBRA-Like Gene Affecting Cellulose Content." Genetics 183, no. 3 (September 7, 2009): 1153–64. http://dx.doi.org/10.1534/genetics.109.106591.
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Populations with low linkage disequilibrium (LD) offer unique opportunities to study functional variants influencing quantitative traits. We exploited the low LD in forest trees to identify functional polymorphisms in a Eucalyptus nitens COBRA-like gene (EniCOBL4A), whose Arabidopsis homolog has been implicated in cellulose deposition. Linkage analysis in a full-sib family revealed that EniCOBL4A is the most strongly associated marker in a quantitative trait locus (QTL) region for cellulose content. Analysis of LD by genotyping 11 common single-nucleotide polymorphisms (SNPs) and a simple sequence repeat (SSR) in an association population revealed that LD declines within the length of the gene. Using association studies we fine mapped the effect of the gene to SNP7, a synonymous SNP in exon 5, which occurs between two small haplotype blocks. We observed patterns of allelic expression imbalance (AEI) and differential binding of nuclear proteins to the SNP7 region that indicate that SNP7 is a cis-acting regulatory polymorphism affecting allelic expression. We also observed AEI in SNP7 heterozygotes in a full-sib family that is linked to heritable allele-specific methylation near SNP7. This study demonstrates the potential to reveal functional polymorphisms underlying quantitative traits in low LD populations.
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LAUGEN, ANE T., LOESKE E. B. KRUUK, ANSSI LAURILA, KATJA RÄSÄNEN, JONATHAN STONE, and JUHA MERILÄ. "Quantitative genetics of larval life-history traits in Rana temporaria in different environmental conditions." Genetical Research 86, no. 3 (November 25, 2005): 161–70. http://dx.doi.org/10.1017/s0016672305007810.
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The degree to which genetic variation in a given trait varies among different populations of the same species and across different environments has seldom been quantified in wild vertebrate species. We investigated the expression of genetic variability and maternal effects in three larval life-history traits of the amphibian Rana temporaria. In a factorial laboratory experiment, five widely separated populations (max. 1600 km) were subjected to two different environmental treatments. Animal model analyses revealed that all traits were heritable (h2≈0·20) in all populations and under most treatment combinations. Although the cross-food treatment genetic correlations were close to unity, heritabilities under a restricted food regime tended to be lower than those under an ad libitum food regime. Likewise, maternal effects (m2≈0·05) were detected in most traits, and they tended to be most pronounced under restricted food conditions. We detected several cross-temperature genetic and maternal effects correlations that were lower than unity, suggesting that genotype–environment interactions and maternal effect–environment interactions are a significant source of phenotypic variation. The results reinforce the perspective that although the expression of genetic and maternal effects may be relatively homogeneous across different populations of the same species, local variation in environmental conditions can lead to significant variation in phenotypic expression of quantitative traits through genotype–environment and maternal effect–environment interactions.
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Rameeh, Valiollah. "Combining ability of phenological traits and seed yield in spring rapeseed genotypes." Plant Breeding and Seed Science 71, no. 1 (December 1, 2015): 47–56. http://dx.doi.org/10.1515/plass-2015-0021.
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Abstract Six parents and their 15 F2 diallel progenies, totally 21 genotypes, were evaluated for genetic parameters of quantitative characteristics. The traits of interest were growing degree days (GDDs) from sowing to the flowering (DDF), to end of flowering (DDE), flowering period (DFP), to maturity (DDM) and seed yield (SY). Significant mean squares of general combining ability (GCA) was exhibited for DDF, DDE, DFP, DDM and seed yield indicating significant differences of GCA effects of parents for these traits. Significant mean squares of specific combining ability (SCA) for all the traits exhibited the importance of non additive genetic effects for the traits. Significant ratio of MS(GCA)/MS(SCA) and high narrow sense heritability estimates for DDF, DDE, DDM indicating the prime importance of additive genetic effects for controlling these traits. DFP was also less heritable than the other phonological traits, so the efficiency of selection for this trait will be low. All of the combinations with significant negative SCA effects for DDM had at least one parent with significant negative GCA effect for this trait. PF7045/91 with significant positive GCA effect of SY, was best combiner for improving SY. Significant positive correlation between DDM and each of two traits including DDF and DDE, indicating these traits can be used as indirect selection criteria for improving DDM.
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Yu, Weiqun, Cheryl Ackert-Bicknell, John D. Larigakis, Bryce MacIver, William D. Steers, Gary A. Churchill, Warren G. Hill, and Mark L. Zeidel. "Spontaneous voiding by mice reveals strain-specific lower urinary tract function to be a quantitative genetic trait." American Journal of Physiology-Renal Physiology 306, no. 11 (June 1, 2014): F1296—F1307. http://dx.doi.org/10.1152/ajprenal.00074.2014.
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Lower urinary tract (LUT) symptoms become prevalent with aging and affect millions; however, therapy is often ineffective because the etiology is unknown. Existing assays of LUT function in animal models are often invasive; however, a noninvasive assay is required to study symptom progression and determine genetic correlates. Here, we present a spontaneous voiding assay that is simple, reproducible, quantitative, and noninvasive. Young female mice from eight inbred mouse strains (129S1/SvImJ, A/J, C57BL/6J, NOD/ShiLtJ, NZO/H1LtJ, CAST/EiJ, PWK/PhJ, and WSB/EiJ) were tested for urination patterns on filter paper. Repeat testing at different times of the day showed minimal within-individual and within-strain variations, but all parameters (spot number, total volume, percent area in primary void, corner voiding, and center voiding) exhibited significant variations between strains. Calculation of the intraclass correlation coefficient, an estimate of broad-sense heritability, for each time of day and for each voiding parameter revealed highly significant heritability [spot number: 61%, percent urine in primary void: 90%, and total volume: 94% (afternoon data)]. Cystometrograms confirmed strong strain-specific urodynamic characteristics. Behavior-voiding correlation analysis showed no correlation with anxiety phenotypes. Diagnostically, the assay revealed LUT symptoms in several systems, including a demonstration of voiding abnormalities in older C57BL/6J mice (18–24 mo), in a model of protamine sulfate-induced urothelial damage and in a model of sucrose-induced diuresis. This assay may be used to derive pathophysiological LUT readouts from mouse models. Voiding characteristics are heritable traits, opening the way for genetic studies of LUT symptoms using outbred mouse populations.
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Cai, Guowen, Shelley A. Cole, Nancy F. Butte, V. Saroja Voruganti, and Anthony G. Comuzzie. "A Quantitative Trait Locus on Chromosome 13q Affects Fasting Glucose Levels in Hispanic Children." Journal of Clinical Endocrinology & Metabolism 92, no. 12 (December 1, 2007): 4893–96. http://dx.doi.org/10.1210/jc.2007-1695.
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Abstract Objective: The prevalence of childhood obesity has increased dramatically in the United States. Early presentation of type 2 diabetes has been observed in children and adolescents, especially in the Hispanic population. The genetic contribution of glucose homeostasis related to childhood obesity is poorly understood. The objective of this study was to localize quantitative trait loci influencing fasting serum glucose levels in Hispanic children participating in the Viva La Familia Study. Design: Subjects were 1030 children ascertained through an overweight child from 319 Hispanic families. Fasting serum glucose levels were measured enzymatically, and genetic linkage analyses were conducted using SOLAR software. Results: Fasting glucose was heritable, with a heritability of 0.62 ± 0.08 (P < 0.01). Genome-wide scan mapped fasting serum glucose to markers D13S158–D13S173 on chromosome 13q (LOD score of 4.6). A strong positional candidate gene is insulin receptor substrate 2, regulator of glucose homeostasis and a candidate gene for obesity. This region was reported previously to be linked to obesity- and diabetes-related phenotypes. Conclusions: A quantitative trait locus on chromosome 13q contributes to the variation in fasting serum glucose levels in Hispanic children at high risk for obesity.
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Green, Delbert A., and Cassandra G. Extavour. "Insulin signalling underlies both plasticity and divergence of a reproductive trait in Drosophila." Proceedings of the Royal Society B: Biological Sciences 281, no. 1779 (March 22, 2014): 20132673. http://dx.doi.org/10.1098/rspb.2013.2673.
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Phenotypic plasticity is the ability of a single genotype to yield distinct phenotypes in different environments. The molecular mechanisms linking phenotypic plasticity to the evolution of heritable diversification, however, are largely unknown. Here, we show that insulin/insulin-like growth factor signalling (IIS) underlies both phenotypic plasticity and evolutionary diversification of ovariole number, a quantitative reproductive trait, in Drosophila . IIS activity levels and sensitivity have diverged between species, leading to both species-specific ovariole number and species-specific nutritional plasticity in ovariole number. Plastic range of ovariole number correlates with ecological niche, suggesting that the degree of nutritional plasticity may be an adaptive trait. This demonstrates that a plastic response conserved across animals can underlie the evolution of morphological diversity, underscoring the potential pervasiveness of plasticity as an evolutionary mechanism.
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Matisons, Roberts, Volker Schneck, Diāna Jansone, Endijs Bāders, Stefānija Dubra, Pauls Zeltiņš, and Āris Jansons. "South-Eastern Baltic Provenances of Scots Pine Show Heritable Weather-Growth Relationships." Forests 12, no. 8 (August 18, 2021): 1101. http://dx.doi.org/10.3390/f12081101.
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The productivity of forests has been linked to the sensitivity of tree growth to meteorological conditions and their fluctuations, hence moderation of tree sensitivity is one of the goals for climate-smart forest management. For this, tree breeding is among the most effective means, particularly if breeding populations are supplemented with genotypes (provenances) adapted to the expected climates. Nonetheless, heritability of traits is essential for their improvement by breeding. In this study, heritability of growth sensitivity of south-eastern Baltic provenances of Scots pine differing by field performance to meteorological conditions was assessed combining methods of quantitative genetics and dendrochronology. Five parallel provenance trials within the south-eastern Baltic region were investigated. The effects of regional weather drivers of growth (moisture regime in summer, temperature regime in preceding summer and in the dormancy period) were estimated, yet their strengths differed among the provenances, indicating local specialization of metapopulations of Scots pine. The heritability of growth sensitivity to these factors ranged from low to moderate, similarly as observed for the morphometric traits within the region; however, the provenance (genetic) variation appeared to be higher. The differences in heritability of responses, however, indicated uneven adaptive significance of weather conditions. Although the estimates were based on a limited set of genotypes implying caution in the extrapolation of results, the weather-growth relationships and their heritability indicate that sensitivity of growth is a complementary trait aiding breeding of forest reproductive material best suited for future climates. Heritable weather-growth relationships also imply a high potential for forest breeding to moderate the sensitivity of the trees.
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Darcey, Ellie, Nina McCarthy, Eric K. Moses, Christobel Saunders, Gemma Cadby, and Jennifer Stone. "Is Mammographic Breast Density an Endophenotype for Breast Cancer?" Cancers 13, no. 15 (August 3, 2021): 3916. http://dx.doi.org/10.3390/cancers13153916.
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Mammographic breast density (MBD) is a strong and highly heritable predictor of breast cancer risk and a biomarker for the disease. This study systematically assesses MBD as an endophenotype for breast cancer—a quantitative trait that is heritable and genetically correlated with disease risk. Using data from the family-based kConFab Study and the 1994/1995 cross-sectional Busselton Health Study, participants were divided into three status groups—cases, relatives of cases and controls. Participant’s mammograms were used to measure absolute dense area (DA) and percentage dense area (PDA). To address each endophenotype criterion, linear mixed models and heritability analysis were conducted. Both measures of MBD were significantly associated with breast cancer risk in two independent samples. These measures were also highly heritable. Meta-analyses of both studies showed that MBD measures were higher in cases compared to relatives (β = 0.48, 95% CI = 0.10, 0.86 and β = 0.41, 95% CI = 0.06, 0.78 for DA and PDA, respectively) and in relatives compared to controls (β = 0.16, 95% CI = −0.24, 0.56 and β = 0.16, 95% CI = −0.21, 0.53 for DA and PDA, respectively). This study formally demonstrates, for the first time, that MBD is an endophenotype for breast cancer.
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Carson, M. L., C. W. Stuber, and M. L. Senior. "Quantitative Trait Loci Conditioning Resistance to Phaeosphaeria Leaf Spot of Maize Caused by Phaeosphaeria maydis." Plant Disease 89, no. 6 (June 2005): 571–74. http://dx.doi.org/10.1094/pd-89-0571.
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Phaeosphaeria leaf spot (PLS) is a potentially important disease of maize (Zea mays) that has appeared in winter breeding nurseries in southern Florida. Inbred lines related to B73 are particularly susceptible to Phaeosphaeria leaf spot, whereas inbreds related to Mo17 are highly resistant. A previous study of the inheritance of resistance to Phaeosphaeria leaf spot in the cross B73 × Mo17 found that resistance is highly heritable and controlled by mostly additive gene action at three or four loci. In this study, we used 158 recombinant inbred (RI) lines derived from the cross B73 × Mo17 to map quantitative trait loci (QTL) governing resistance. The RI lines along with the parent inbred lines and the F1 were evaluated for PLS resistance in replicated trials over two winter growing seasons in southern Florida. Using the composite interval mapping (CIM) function of PLABQTL software, five QTL on four different chromosomes were found to control PLS resistance in Mo17. In addition, the × additive interaction between two of these QTL was found to be significant. Our results are in close agreement with the previous study, where generation mean analysis was used to study the inheritance of resistance to PLS.
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Dugué, Pierre-Antoine, Chenglong Yu, Timothy McKay, Ee Ming Wong, Jihoon Eric Joo, Helen Tsimiklis, Fleur Hammet, et al. "VTRNA2-1: Genetic Variation, Heritable Methylation and Disease Association." International Journal of Molecular Sciences 22, no. 5 (March 3, 2021): 2535. http://dx.doi.org/10.3390/ijms22052535.
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VTRNA2-1 is a metastable epiallele with accumulating evidence that methylation at this region is heritable, modifiable and associated with disease including risk and progression of cancer. This study investigated the influence of genetic variation and other factors such as age and adult lifestyle on blood DNA methylation in this region. We first sequenced the VTRNA2-1 gene region in multiple-case breast cancer families in which VTRNA2-1 methylation was identified as heritable and associated with breast cancer risk. Methylation quantitative trait loci (mQTL) were investigated using a prospective cohort study (4500 participants with genotyping and methylation data). The cis-mQTL analysis (334 variants ± 50 kb of the most heritable CpG site) identified 43 variants associated with VTRNA2-1 methylation (p < 1.5 × 10−4); however, these explained little of the methylation variation (R2 < 0.5% for each of these variants). No genetic variants elsewhere in the genome were found to strongly influence VTRNA2-1 methylation. SNP-based heritability estimates were consistent with the mQTL findings (h2 = 0, 95%CI: −0.14 to 0.14). We found no evidence that age, sex, country of birth, smoking, body mass index, alcohol consumption or diet influenced blood DNA methylation at VTRNA2-1. Genetic factors and adult lifestyle play a minimal role in explaining methylation variability at the heritable VTRNA2-1 cluster.
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NAGY, ZSUZSANNA, ANDREAS BUSJAHN, SYLVIA BÄHRING, HANS-DIETER FAULHABER, HANS-RÜDIGER GOHLKE, HANS KNOBLAUCH, MAGDA ROSENTHAL, BERTRAM MÜLLER-MYHSOK, HERBERT SCHUSTER, and FRIEDRICH C. LUFT. "Quantitative Trait Loci for Blood Pressure Exist Near the IGF-1, the Liddle Syndrome, the Angiotensin II-Receptor Gene and the Renin Loci in Man." Journal of the American Society of Nephrology 10, no. 8 (August 1999): 1709–16. http://dx.doi.org/10.1681/asn.v1081709.
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Abstract. Blood pressure (BP) is heritable and finding quantitative trait loci that influence BP is an important step in identifying genes responsible for BP regulation. Sixty-six pairs of dizygotic (DZ) twin subjects and their parents were used in a sib-pair analysis to look for linkage of selected candidate genes to the quantitative trait BP. Microsatellite markers were tested in the vicinity of the gene loci for insulin-like growth factor-1 (IGF-1), Liddle syndrome, autosomal-dominant hypertension with brachydactyly, angiotensinogen, angiotensin II type 1 receptor, angiotensin-converting enzyme, renin, and lipoprotein lipase. BP was measured in a standardized manner. Heart size was determined echocardiographically. Significant linkage was found at the IGF-1, Liddle syndrome, and AT1 receptor gene for systolic BP. Linkage for diastolic BP was found at the autosomal-dominant hypertension with brachydactyly locus. Both systolic and diastolic BP were linked to the renin gene locus. The linkage was most consistent for the IGF-1 gene locus and systolic BP. Linkage was also found between the IGF-1 gene locus and posterior cardiac wall thickness, septal thickness, and left ventricular mass index. It is suggested that these quantitative trait loci may be important for the subsequent detection of allelic variants for elevated BP. Furthermore, these results linking the IGF-1 gene locus to both BP and cardiac dimensions underscore the importance of the IGF-1 gene as a candidate gene for cardiovascular disease.
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Feng, Helian, Nicholas Mancuso, Alexander Gusev, Arunabha Majumdar, Megan Major, Bogdan Pasaniuc, and Peter Kraft. "Leveraging expression from multiple tissues using sparse canonical correlation analysis and aggregate tests improves the power of transcriptome-wide association studies." PLOS Genetics 17, no. 4 (April 8, 2021): e1008973. http://dx.doi.org/10.1371/journal.pgen.1008973.
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Transcriptome-wide association studies (TWAS) test the association between traits and genetically predicted gene expression levels. The power of a TWAS depends in part on the strength of the correlation between a genetic predictor of gene expression and the causally relevant gene expression values. Consequently, TWAS power can be low when expression quantitative trait locus (eQTL) data used to train the genetic predictors have small sample sizes, or when data from causally relevant tissues are not available. Here, we propose to address these issues by integrating multiple tissues in the TWAS using sparse canonical correlation analysis (sCCA). We show that sCCA-TWAS combined with single-tissue TWAS using an aggregate Cauchy association test (ACAT) outperforms traditional single-tissue TWAS. In empirically motivated simulations, the sCCA+ACAT approach yielded the highest power to detect a gene associated with phenotype, even when expression in the causal tissue was not directly measured, while controlling the Type I error when there is no association between gene expression and phenotype. For example, when gene expression explains 2% of the variability in outcome, and the GWAS sample size is 20,000, the average power difference between the ACAT combined test of sCCA features and single-tissue, versus single-tissue combined with Generalized Berk-Jones (GBJ) method, single-tissue combined with S-MultiXcan, UTMOST, or summarizing cross-tissue expression patterns using Principal Component Analysis (PCA) approaches was 5%, 8%, 5% and 38%, respectively. The gain in power is likely due to sCCA cross-tissue features being more likely to be detectably heritable. When applied to publicly available summary statistics from 10 complex traits, the sCCA+ACAT test was able to increase the number of testable genes and identify on average an additional 400 additional gene-trait associations that single-trait TWAS missed. Our results suggest that aggregating eQTL data across multiple tissues using sCCA can improve the sensitivity of TWAS while controlling for the false positive rate.
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Mortenson, John S., Blair L. Waldron, Steve R. Larson, Kevin B. Jensen, Lee R. DeHaan, Michael D. Peel, Paul G. Johnson, and J. Earl Creech. "Quantitative Trait Loci (QTL) for Forage Traits in Intermediate Wheatgrass When Grown as Spaced-Plants versus Monoculture and Polyculture Swards." Agronomy 9, no. 10 (September 25, 2019): 580. http://dx.doi.org/10.3390/agronomy9100580.
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It has been hypothesized that the genetic control of forage traits, especially biomass, for grass plants growing as spaced-plants versus swards is different. Likewise, the genetic control of compatibility in grass–legume polyculture mixtures is assumed to be different than for forage production in a grass monoculture. However, these hypotheses are largely unvalidated, especially at the DNA level. This study used an intermediate wheatgrass mapping population to examine the effect of three competition environments (spaced-plants, polyculture, and monoculture) on classical quantitative genetic parameters and quantitative trait loci (QTL) identification for biomass, morphology, and forage nutritive value. Moderate to high heritable variation was observed for biomass, morphological traits, and nutritive value within all three environments (H ranged from 0.50 to 0.87). Genetic correlations (rG) among environments for morphology and nutritive value were predominantly high, however, were moderately-low (0.30 to 0.48) for biomass. Six biomass QTL were identified, including three on linkage groups (LG) 1, 6, and 15 that were only expressed in the monoculture environment. Moreover, three biomass QTL on LG 10, 14, and 15 exhibited significant QTL by environment interactions. This study verified that the genetic control of grass biomass in a monoculture versus a grass–legume mixture is only partially the same, with additional genes expressed in monoculture, and that biomass in widely spaced-plants versus swards is predominantly under different genetic control. These results indicate that selection for improved grass biomass will be most successful when conducted within the targeted monoculture or polyculture sward environment per se.
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Erickson, Priscilla A., Andrew M. Glazer, Phillip A. Cleves, Alyson S. Smith, and Craig T. Miller. "Two developmentally temporal quantitative trait loci underlie convergent evolution of increased branchial bone length in sticklebacks." Proceedings of the Royal Society B: Biological Sciences 281, no. 1788 (August 7, 2014): 20140822. http://dx.doi.org/10.1098/rspb.2014.0822.
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In convergent evolution, similar phenotypes evolve repeatedly in independent populations, often reflecting adaptation to similar environments. Understanding whether convergent evolution proceeds via similar or different genetic and developmental mechanisms offers insight towards the repeatability and predictability of evolution. Oceanic populations of threespine stickleback fish, Gasterosteus aculeatus , have repeatedly colonized countless freshwater lakes and streams, where new diets lead to morphological adaptations related to feeding. Here, we show that heritable increases in branchial bone length have convergently evolved in two independently derived freshwater stickleback populations. In both populations, an increased bone growth rate in juveniles underlies the convergent adult phenotype, and one population also has a longer cartilage template. Using F 2 crosses from these two freshwater populations, we show that two quantitative trait loci (QTL) control branchial bone length at distinct points in development. In both populations, a QTL on chromosome 21 controls bone length throughout juvenile development, and a QTL on chromosome 4 controls bone length only in adults. In addition to these similar developmental profiles, these QTL show similar chromosomal locations in both populations. Our results suggest that sticklebacks have convergently evolved longer branchial bones using similar genetic and developmental programmes in two independently derived populations.
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Liu, Xiaobing, Bingjie Tu, Qiuying Zhang, and Stephen J. Herbert. "Physiological and molecular aspects of pod shattering resistance in crops." Czech Journal of Genetics and Plant Breeding 55, No. 3 (June 17, 2019): 87–92. http://dx.doi.org/10.17221/104/2018-cjgpb.
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Pod shattering resistance is a trait acquired by crops in the process of evolution. Manipulation of physiological and molecular processes is fundamental for the improvement of shattering resistance in crops. In this review we discuss several enzymes, key hormones and their possible roles or relationships involved in pod shattering, and highlight responsible genes, quantitative traits loci (QTLs) and their implications for increased pod shattering resistance. Cell wall degrading enzymes, particularly β-glucanases and endopolygalacturonases play an important role in the process of pod dehiscence. It is not clear how and to what extent a specific hormone regulates the dehiscence zone differentiation and the dehiscence process is not clear. Resistance to shattering is highly heritable and is not controlled by a single gene. Several QTLs associated to dehiscence have been identified in crops, while the underlying genetic functions of these QTLs deserve further investigation. Further physiological analyses of the pod wall will help to understand better the pod dehiscence.
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Laboni, Sonia Akter, SM Ahsan, Shepon Chandra Ghosh, Eftekhar Mahmud, Mostafizur Rahman Talukder, Soleh Akram, Sayeed Shahriyar, and Abdulla Al Asif. "Segregation pattern and inbreeding depression in F2 generation of some hybrid okra varieties." Asian Journal of Medical and Biological Research 1, no. 2 (November 23, 2015): 316–35. http://dx.doi.org/10.3329/ajmbr.v1i2.25627.
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An experiment was conducted in randomized complete block design (RCBD) with three replications in the experimental field of Regional Horticulture Research Station (RHRS), Bangladesh Agriculture Research Institute (BARI), Lebukhali, Patuakhali during April, 2014 to October, 2014 for assessing the inbreeding depression, genetic parameters, gene action and segregation pattern of Okra [Abelmoschusesculentus (L.) Moench]. The experiment was comprised of five commercial hybrid Okra genotypes such as Tara sonali, Bimala, Juboraj, Suvo 1and Noor, their respective F2 progenies along with a check variety named as BARI Dherosh 1. Results of the experiment indicated that there were considerable variability among the F1 and their F2. The yield were in-between 14.81 to 7.92 Kg plot-1in case of F1 generation, which deteriorate to 10.32 to 5.32 Kg plot-1 in F2 generation. Broad sense heritability computed through variance component method showed that all the quantitative traits were moderate to highly heritable. The trait yield per plot exhibited 68.83% broad sense heritability coupled with 50.96% genetic advance suggesting the existence of sufficient amount of genetic variability for improvement of this trait and also indicates that the trait is more amenable to selection and could be improved easily. In case of segregation pattern, plant height and pod pubescence content exhibit as polygenic trait. Leaf shape, fruit base shape and branching pattern showed complete dominance and fruit color displayed incomplete dominance. The present investigation thus provide information about the nature and magnitude of genetic variation, segregation pattern and inbreeding depression for yield and its components in okra so as to formulate suitable breeding strategy and isolate potential parents and promising crosses for further breeding program.Asian J. Med. Biol. Res. June 2015, 1(2): 316-335
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Staub, Jack E., and Juan Zalapa. "THE INCORPORATION OF THE FRACTAL GROWTH HABIT INTO WESTERN SHIPPING MELON." HortScience 40, no. 3 (June 2005): 889f—890. http://dx.doi.org/10.21273/hortsci.40.3.889f.
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Plant improvement incorporating quantitatively inherited yield component traits is technically difficult, time consuming, and resource demanding. In melon (Cucumis melo L.), the inheritance of yield components is poorly understood. A unique highly branched fractal melon plant type has been developed by the U.S. Department of Agriculture (USDA) from exotic germplasm to improve yield of U.S. Western Shipping type melons (Group Cantalupensis). In order to more effectively develop useful germplasm for commercial use the genetic of components of yield must be clearly understood. Thus, the genetics of branching, an important yield component, was investigated. Melon progeny derived (F1, F2, F3, BC1P1, and BC1P2) derived from a cross between USDA line 846-1 (P1) and Top-Mark (P2) were used to evaluated in two locations (Wisconsin and California) to estimate of components of variance, and narrow-sense (h2N) and broad-sense (h2B) sense heritabilities. Lateral branch numbers among 71 to 119 F3 families were significantly different (P ¾ 0.01) regardless of test environment. Covariance analyses indicates that branching is moderately heritable (h2B = 0.62 to 0.76, h2N = 0.43 to 0.48), and conditioned by several additive factors (perhaps 2 to 4) that are highly additive. Although environment plays an important role in lateral branch development, family rankings over environments were relatively consistent, indicating that effective selection for this trait should be useful for incorporating the fractal plant habit into Western Shipping melon. The significant additive component underlying lateral branch number indicates that quantitative trait loci (QTL) conditioning this yield component might be identified for use in marker-assisted selection.
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van Oers, Kees, Bernice Sepers, William Sies, Fleur Gawehns, Koen J. F. Verhoeven, and Veronika N. Laine. "Epigenetics of Animal Personality: DNA Methylation Cannot Explain the Heritability of Exploratory Behavior in a Songbird." Integrative and Comparative Biology 60, no. 6 (November 12, 2020): 1517–30. http://dx.doi.org/10.1093/icb/icaa138.
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Synopsis The search for the hereditary mechanisms underlying quantitative traits traditionally focused on the identification of underlying genomic polymorphisms such as single-nucleotide polymorphisms. It has now become clear that epigenetic mechanisms, such as DNA methylation, can consistently alter gene expression over multiple generations. It is unclear, however, if and how DNA methylation can stably be transferred from one generation to the next and can thereby be a component of the heritable variation of a trait. In this study, we explore whether DNA methylation responds to phenotypic selection using whole-genome and genome-wide bisulfite approaches. We assessed differential erythrocyte DNA methylation patterns between extreme personality types in the Great Tit (Parus major). For this, we used individuals from a four-generation artificial bi-directional selection experiment and siblings from eight F2 inter-cross families. We find no differentially methylated sites when comparing the selected personality lines, providing no evidence for the so-called epialleles associated with exploratory behavior. Using a pair-wise sibling design in the F2 intercrosses, we show that the genome-wide DNA methylation profiles of individuals are mainly explained by family structure, indicating that the majority of variation in DNA methylation in CpG sites between individuals can be explained by genetic differences. Although we found some candidates explaining behavioral differences between F2 siblings, we could not confirm this with a whole-genome approach, thereby confirming the absence of epialleles in these F2 intercrosses. We conclude that while epigenetic variation may underlie phenotypic variation in behavioral traits, we were not able to find evidence that DNA methylation can explain heritable variation in personality traits in Great Tits.
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Ling, Ashley, and Romdhane Rekaya. "PSVIII-26 Gene editing of complex traits." Journal of Animal Science 97, Supplement_3 (December 2019): 259–60. http://dx.doi.org/10.1093/jas/skz258.529.
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Abstract Gene editing (GE) is a form of genetic engineering in which DNA is removed, inserted or replaced. For simple monogenic traits, the technology has been successfully implemented to create heritable modifications in animals and plants. The benefits of these niche applications are undeniable. For quantitative traits the benefits of GE are hard to quantify mainly because these traits are not genetic enough (low to moderate heritability) and their genetic architecture is often complex. Because its impact on the gene pool through the introduction of heritable modifications, the potential gain from GE must be evaluated within reasonable production parameters and in comparison, with available tools used in animal selection. A simulation was performed to compare GE with genomic selection (GS) and QTN-assisted selection (QAS) under four experimental factors: 1) heritability (0.1 or 0.4), 2) number of QTN affecting the trait (1000 or 10000) and their effect distribution (Gamma or uniform); 3) Percentage of selected females (100% or 33%); and 4) fixed or variable number of edited QTNs. Three models GS (M1), GS and GE (M2), and GS and QAS (M3) were implemented and compared. When the QTN effects were sampled from a Gamma distribution, all females were selected, and non-segregating QTNs were replaced, M2 clearly outperformed M1 and M3, with superiority ranging from 19 to 61%. Under the same scenario, M3 was 7 to 23% superior to M1. As the complexity of the genetic model increased (10000 QTN; uniform distribution), only one third of the females were selected, and the number of edited QTNs was fixed, the superiority of M2 was significantly reduced. In fact, M2 was only slightly better than M3 (2 to 6%). In all cases, M2 and M3 were better than M1. These results indicate that under realistic scenarios, GE for complex traits might have only limited advantages.
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Bijma, P. "The Price equation as a bridge between animal breeding and evolutionary biology." Philosophical Transactions of the Royal Society B: Biological Sciences 375, no. 1797 (March 9, 2020): 20190360. http://dx.doi.org/10.1098/rstb.2019.0360.
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The genetic response to selection is central to both evolutionary biology and animal and plant breeding. While Price's theorem (PT) is well-known in evolutionary biology, most breeders are unaware of it. Rather than using PT, breeders express response to selection as the product of the intensity of selection ( i ), the accuracy of selection ( ρ ) and the additive genetic standard deviation ( σ A ); R = iρσ A . In contrast to the univariate ‘breeder's equation’, this expression holds for multivariate selection on Gaussian traits. Here, I relate R = iρσ A to PT, and present a generalized version, R = i w ρ A , w σ A , valid irrespective of the trait distribution. Next, I consider genotype–environment covariance in relation to the breeder's equation and PT, showing that the breeder's equation may remain valid depending on whether the genotype–environment covariance works across generations. Finally, I consider the response to selection in the prevalence of an endemic infectious disease, as an example of an emergent trait. The result shows that disease prevalence has much greater heritable variation than currently believed. The example also illustrates that the indirect genetic effect approach moves elements of response to selection from the second to the first term of PT, so that changes acting via the social environment come within the reach of quantitative genetics. This article is part of the theme issue ‘Fifty years of the Price equation’.
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FOSTER, R., H. S. POONI, and I. J. MACKAY. "Quantitative analysis of Linum usitatissimum crosses for dual-purpose traits." Journal of Agricultural Science 131, no. 3 (November 1998): 285–92. http://dx.doi.org/10.1017/s0021859698005917.
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The commercial future of Linum usitatissimum is intrinsically linked to its cultivation as a dual-purpose crop for producing increased seed and fibre yields. The present study evaluates 36 F1 crosses derived from nine linseed/flax accessions for their potential as dual-purpose cultivars and/or their suitability for extracting new recombinants producing high seed yield as well as increased fibre output. The quantitative analysis indicated that variation between the F1 families is largely but not exclusively due to the additive and non-additive (dominance) effects of genes. Dominance is high for plant height (H1), height at maturity (HMT), number of branches (NBr) and seed weight (SdWt) while 100 seed weight (Wt100) displays no dominance at all. The repeatability estimates representing the heritability of each trait, vary from low (0·20) for number of branches (NBr) to high (0·71) for height at flowering time (HFT). The dual-purpose traits such as seed weight (SdWt) and straw weight (StWt) were only moderately inherited while flowering time (FT) and various heights were rather highly heritable. A moderate and positive correlation (r=0·57) between StWt and SdWt, and a completely independent inheritance of Wt100 suggested that there are good chances of combining these traits into a single genotype. The phenotypic performance of the crosses also confirmed this trend and at least four crosses showed superior performance for both SdWt and StWt compared to their parental lines. All these crosses involved a linseed line (B3) as a common parent and the second parent was either another linseed line (A1 and A3) or a flax accession (K3 and L2); none of the flax×flax crosses showed good potential for seed yield. While all four crosses possess the potential to become highly productive, dual-purpose, hybrid varieties, the extraction of desirable inbred lines from them, however, may prove difficult because the superior performance of the hybrids seems largely due to strong unidirectional dominance and high SCA effects.
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Stern, Emily N., Samuel Lessard, Patrick G. Schupp, Falak Sher, Guillaume Lettre, and Daniel E. Bauer. "An Essential Erythroid-Specific Enhancer of ATP2B4 Associated with Red Blood Cell Traits and Malaria Susceptibility." Blood 128, no. 22 (December 2, 2016): 1250. http://dx.doi.org/10.1182/blood.v128.22.1250.1250.
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Abstract Genome-wide association studies (GWASs) have identified thousands of common genetic variants associated with human traits and disease susceptibility. Given that the majority of GWAS-identified SNPs are located within non-coding regions of the genome, the mechanisms of these trait associations are frequently unknown. Here we investigate the biological underpinnings of common trait-associated genetic variation at ATP2B4, a gene on chromosome 1q32 that encodes a major plasma membrane calcium ATPase (also known as PMCA4). Genetic variation within this locus is associated with several phenotypes including various red blood cell traits (mean corpuscular hemoglobin concentration and red cell distribution width) as well as susceptibility to severe malaria infection. We conducted an expression quantitative trait loci (eQTL) mapping analysis in human erythroblasts and identified a set of SNPs associated with ATP2B4 gene expression in cis. These included the same genetic variants found by GWAS to be associated with RBC traits and malaria susceptibility. Furthermore, these SNPs overlap an intronic erythroid DNase I hypersensitive site at ATP2B4. An analysis of the ENCODE database showed that this element was erythroid specific in that it lacked DNase I hypersensitivity in >30 queried non-erythroid cell types. We used the CRISPR/Cas9 genome editing system to delete this element in HUDEP-2 immortalized human erythroid precursor cells. We observed that cells bearing a 927 bp biallelic deletion of this noncoding element displayed near complete loss of ATP2B4 expression (3% residual gene expression), while cells bearing heterozygous deletions showed an intermediate gene expression phenotype. We identified a core element that encompassed 3 of the highly trait associated SNPs and 5 GATA1-binding motifs. Biallelic deletion of this 98 bp core led to 83% reduction in ATP2B4 expression. Disruption of individual GATA1-binding motifs resulted in partial reduction of gene expression, suggesting the contribution of multiple binding sites to appropriate gene expression. Overall, this study suggests that variation within an essential erythroid-specific enhancer of ATP2B4 underlies the association of ATP2B4 with RBC traits and malaria susceptibility. Furthermore these results encourage combined analyses of gene expression, chromatin state, and prospective genetic perturbation as a means to explore the variants, elements and genes responsible for heritable blood phenotypes. Disclosures No relevant conflicts of interest to declare.
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Henriksen, Rie, Andrey Höglund, Jesper Fogelholm, Robin Abbey-Lee, Martin Johnsson, Niels J. Dingemanse, and Dominic Wright. "Intra-Individual Behavioural Variability: A Trait under Genetic Control." International Journal of Molecular Sciences 21, no. 21 (October 29, 2020): 8069. http://dx.doi.org/10.3390/ijms21218069.
Full textAbstract:
When individuals are measured more than once in the same context they do not behave in exactly the same way each time. The degree of predictability differs between individuals, with some individuals showing low levels of variation around their behavioural mean while others show high levels of variation. This intra-individual variability in behaviour has received much less attention than between-individual variability in behaviour, and very little is known about the underlying mechanisms that affect this potentially large but understudied component of behavioural variation. In this study, we combine standardized behavioural tests in a chicken intercross to estimate intra-individual behavioural variability with a large-scale genomics analysis to identify genes affecting intra-individual behavioural variability in an avian population. We used a variety of different anxiety-related behavioural phenotypes for this purpose. Our study shows that intra-individual variability in behaviour has a direct genetic basis that is largely unique compared to the genetic architecture for the standard behavioural measures they are based on (at least in the detected quantitative trait locus). We identify six suggestive candidate genes that may underpin differences in intra-individual behavioural variability, with several of these candidates having previously been linked to behaviour and mental health. These findings demonstrate that intra-individual variability in behaviour appears to be a heritable trait in and of itself on which evolution can act.
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Collins Kimutai, Manje Gowda, and Oliver Kiplagat. "Trait-QTL-heritability of grain yield and other agronomic traits under low nitrogen conditions in bi-parental maize populations." International Journal of Biological and Pharmaceutical Sciences Archive 2, no. 1 (August 30, 2021): 096–116. http://dx.doi.org/10.53771/ijbpsa.2021.2.1.0072.
Full textAbstract:
Limited or low Nitrogen is a wanting abiotic stress in maize mainly in Sub-Sahara Africa, affecting yields and quality development of maize crop. As an approach to getting a breeding solution; mapping of QTLs and understanding the heritability factor can provide useful information and guide for breeders in developing low nitrogen resilient maize. QTL mapping which is a molecular breeding component forms an actual basis in estimation of genomic regions associated to the expression of quantitative traits, and how heritable are such traits. Conducting a selection for Low N-tolerance is challenging due to its complex nature with strong interaction between genotypes and environments; therefore, marker assisted breeding is key to improving such complex traits, but at the same time requires markers associated with the trait of interest. In this study, three bi-parental populations were subjected to either or both low and optimum N conditions to detect and determine the QTLs heritability for grain yield and other agronomic traits. Essential to the study; genotype by environmental interaction, significance and heritability was examined for each population with most traits expressing low (<0.2) and moderate to high heritabilities (0.3>). These QTLs with high heritabilities across environments will be of great value for rapid introgression into maize populations using marker assisted selection approach. The study was a preliminary and therefore require further validation on heritability and fine mapping for them to be useful in MAS.
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Pearse, Devon E., Michael R. Miller, Alicia Abadía-Cardoso, and John Carlos Garza. "Rapid parallel evolution of standing variation in a single, complex, genomic region is associated with life history in steelhead/rainbow trout." Proceedings of the Royal Society B: Biological Sciences 281, no. 1783 (May 22, 2014): 20140012. http://dx.doi.org/10.1098/rspb.2014.0012.
Full textAbstract:
Rapid adaptation to novel environments may drive changes in genomic regions through natural selection. Such changes may be population-specific or, alternatively, may involve parallel evolution of the same genomic region in multiple populations, if that region contains genes or co-adapted gene complexes affecting the selected trait(s). Both quantitative and population genetic approaches have identified associations between specific genomic regions and the anadromous (steelhead) and resident (rainbow trout) life-history strategies of Oncorhynchus mykiss . Here, we use genotype data from 95 single nucleotide polymorphisms and show that the distribution of variation in a large region of one chromosome, Omy5, is strongly associated with life-history differentiation in multiple above-barrier populations of rainbow trout and their anadromous steelhead ancestors. The associated loci are in strong linkage disequilibrium, suggesting the presence of a chromosomal inversion or other rearrangement limiting recombination. These results provide the first evidence of a common genomic basis for life-history variation in O. mykiss in a geographically diverse set of populations and extend our knowledge of the heritable basis of rapid adaptation of complex traits in novel habitats.
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Warburton, Marilyn L., Dan Jeffers, Jessie Spencer Smith, Carlos Scapim, Renan Uhdre, Adam Thrash, and William Paul Williams. "Comparative Analysis of Multiple GWAS Results Identifies Metabolic Pathways Associated with Resistance to A. flavus Infection and Aflatoxin Accumulation in Maize." Toxins 14, no. 11 (October 28, 2022): 738. http://dx.doi.org/10.3390/toxins14110738.
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Aflatoxins are carcinogenic secondary metabolites produced by several species of Aspergillus, including Aspergillus flavus, an important ear rot pathogen in maize. Most commercial corn hybrids are susceptible to infection by A. flavus, and aflatoxin contaminated grain causes economic damage to farmers. The creation of inbred lines resistant to Aspergillus fungal infection or the accumulation of aflatoxins would be aided by knowing the pertinent alleles and metabolites associated with resistance in corn lines. Multiple Quantitative Trait Loci (QTL) and association mapping studies have uncovered several dozen potential genes, but each with a small effect on resistance. Metabolic pathway analysis, using the Pathway Association Study Tool (PAST), was performed on aflatoxin accumulation resistance using data from four Genome-wide Association Studies (GWAS). The present research compares the outputs of these pathway analyses and seeks common metabolic mechanisms underlying each. Genes, pathways, metabolites, and mechanisms highlighted here can contribute to improving phenotypic selection of resistant lines via measurement of more specific and highly heritable resistance-related traits and genetic gain via marker assisted or genomic selection with multiple SNPs linked to resistance-related pathways.
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Rouet, Cindy, Joseph O’Neill, Travis Banks, Karen Tanino, Elodie Derivry, Daryl Somers, and Elizabeth A. Lee. "Mapping Winterhardiness in Garden Roses." Journal of the American Society for Horticultural Science 147, no. 4 (July 2022): 216–38. http://dx.doi.org/10.21273/jashs05189-22.
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Field winterhardiness is a critical trait in rose cultivars (Rosa ×hybrida) grown in northern climates. Although the molecular basis of cold hardiness has been well documented in model organisms such as Arabidopsis thaliana, little is known about the genetics and mechanisms underlying winterhardiness in roses. This research aims to explore the genetic control of winterhardiness for application in breeding programs using quantitative trail loci (QTL) analysis in two biparental rose populations derived from cold-hardy roses of the Canadian Explorer Series Collection. Field winterhardiness was assessed as a complex trait with winter damage and regrowth recorded in multiyear and multilocation trials in Ontario and Saskatchewan, Canada. In addition, this research explored the relationship between field measurements and electrolyte leakage recorded under artificial conditions. Electrolyte leakage had limited utility for application in rose breeding programs as a substitute for field evaluation, but did enable identification of QTL associated with potential cold hardiness candidate genes. A QTL for electrolyte leakage mapped to a genomic region that harbors a CBF1-like transcription factor. A total of 14 QTLs associated with field winter damage and regrowth were discovered, and they explained between 11% and 37% of the observed phenotypic variance. Two QTL associated with winter damage and regrowth overlapped with a known QTL for black spot (Diplocarpon rosae) disease resistance, Rdr1, in an environment under high disease pressure. Due to the complexity of field winterhardiness and its direct reliance on intertwined factors, such as overall plant health, moisture status, snow cover, and period of prolonged sub-zero temperatures, field trials are the ultimate measurement of field winterhardiness. Transgressive segregation was observed for all traits, and it was most likely due to complementary gene action. Field winter damage and regrowth were highly heritable in single environments, but they were subject to genotype × environment interaction resulting from pest pressure and severe climatic conditions.
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Diego, V. P., L. Almasy, D. L. Rainwater, M. C. Mahaney, A. G. Comuzzie, S. A. Cole, R. P. Tracy, M. P. Stern, J. W. MacCluer, and J. Blangero. "A Quantitative Trait Locus on Chromosome 5p Influences D-Dimer Levels in the San Antonio Family Heart Study." International Journal of Vascular Medicine 2010 (2010): 1–6. http://dx.doi.org/10.1155/2010/490241.
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Background. D-dimer is associated with increasing severity of atherosclerosis and with increased risk of a cardiovascular disease (CVD).Methods and Results. To better understand this risk factor, we performed a genome scan on 803 (301 males and 502 females) Mexican Americans in the San Antonio Family Heart Study (SAFHS). The SAFHS is ideal for the discovery of quantitative trait loci (QTLs) influencing CVD because CVD risk factors are prevalent in Mexican Americans of San Antonio and because the study design involves large families, which is optimal for QTL discovery. D-dimer levels were normalized in our study. We found that D-dimer levels were heritable, at about 23% heritability (P≈.00001). In a linkage analysis employing 432 microsatellite markers, we found strong evidence of a QTL on chromosome 5p with a lod score of 3.32 at 21 centiMorgans (cM). We also found suggestive evidence of a QTL on chromosome 2q with a lod score of 2.33 at 207 cM.Conclusions. To our knowledge, the putative QTL on chromosome 5p is novel. The possible QTL on chromosome 2q is discussed in relation to a recent report of linkage of a related hemostatic factor to the same location. These results warrant further investigation.
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Cook, Melloni N., Jessica A. Baker, Scott A. Heldt, Robert W. Williams, Kristin M. Hamre, and Lu Lu. "Identification of candidate genes that underlie the QTL on chromosome 1 that mediates genetic differences in stress-ethanol interactions." Physiological Genomics 47, no. 8 (August 2015): 308–17. http://dx.doi.org/10.1152/physiolgenomics.00114.2014.
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Alcoholism, stress, and anxiety are strongly interacting heritable, polygenetic traits. In a previous study, we identified a quantitative trait locus (QTL) on murine chromosome (Chr) 1 between 23.0 and 31.5 Mb that modulates genetic differences in the effects of ethanol on anxiety-related phenotypes. The goal of the present study was to extend the analysis of this locus with a focus on identifying candidate genes using newly available data and tools. Anxiety-like behavior was evaluated with an elevated zero maze following saline or ethanol injections (1.8 g/kg) in C57BL/6J, DBA2J, and 72 BXD strains. We detected significant effects of strain and treatment and their interaction on anxiety-related behaviors, although surprisingly, sex was not a significant factor. The Chr1 QTL is specific to the ethanol-treated cohort. Candidate genes in this locus were evaluated using now standard bioinformatic criteria. Collagen 19a1 ( Col19a1) and family sequence 135a ( Fam135a) met most criteria but have lower expression levels and lacked biological verification and, therefore, were considered less likely candidates. In contrast, two other genes, the prenylated protein tyrosine phosphate family member Ptp4a1 (protein tyrosine phosphate 4a1) and the zinc finger protein Phf3 (plant homeoDomain finger protein 3) met each of our bioinformatic criteria and are thus strong candidates. These findings are also of translational relevance because both Ptp4a1 and Phf3 have been nominated as candidates genes for alcohol dependence in a human genome-wide association study. Our findings support the hypothesis that variants in one or both of these genes modulate heritable differences in the effects of ethanol on anxiety-related behaviors.
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Sacchi, Roberto, Marco Mangiacotti, Stefano Scali, Michele Ghitti, Beatrice Bindolini, and Marco A. L. Zuffi. "Genetic and phenotypic component in head shape of common wall lizard Podarcis muralis." Amphibia-Reptilia 37, no. 3 (2016): 301–10. http://dx.doi.org/10.1163/15685381-00003058.
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Head shape in lizards correlates with a wide range of environmental pressures, supporting the hypothesis that patterns of phenotypic change represent adaptive responses to selective processes. However, natural selection promotes evolutionary adaptation only if the trait under selection has enough heritable variation. In this study we used geometric morphometrics and quantitative genetics to assess the heritability patterns of the head shape and size of common wall lizards (Podarcis muralis). Genetic and phenotypic components were estimated using animal models, which showed that more than half of the variation in head morphology is inheritable. Furthermore, at least five independent patterns of genetically determined phenotypic change were detected. These outcomes confirm that morphological differentiation in common wall lizards may reliably be regarded as the result of adaptive processes driven by natural selection.