Journal articles: 'Genome architecture mapping'

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McKay, Daniel J., Alexis V. Stutzman, and Jill M. Dowen. "Advancements in mapping 3D genome architecture." Methods 170 (January 2020): 75–81. http://dx.doi.org/10.1016/j.ymeth.2019.06.002.

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Chowdhary, Surabhi, Amoldeep S. Kainth, and David S. Gross. "Methods for mapping three-dimensional genome architecture." Methods 170 (January 2020): 1–3. http://dx.doi.org/10.1016/j.ymeth.2019.10.011.

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Feng, Yi, Leslie Y. Beh, Wei-Jen Chang, and Laura F. Landweber. "SIGAR: Inferring Features of Genome Architecture and DNA Rearrangements by Split-Read Mapping." Genome Biology and Evolution 12, no. 10 (2020): 1711–18. http://dx.doi.org/10.1093/gbe/evaa147.

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Abstract Ciliates are microbial eukaryotes with distinct somatic and germline genomes. Postzygotic development involves extensive remodeling of the germline genome to form somatic chromosomes. Ciliates therefore offer a valuable model for studying the architecture and evolution of programed genome rearrangements. Current studies usually focus on a few model species, where rearrangement features are annotated by aligning reference germline and somatic genomes. Although many high-quality somatic genomes have been assembled, a high-quality germline genome assembly is difficult to obtain due to its smaller DNA content and abundance of repetitive sequences. To overcome these hurdles, we propose a new pipeline, SIGAR (Split-read Inference of Genome Architecture and Rearrangements) to infer germline genome architecture and rearrangement features without a germline genome assembly, requiring only short DNA sequencing reads. As a proof of principle, 93% of rearrangement junctions identified by SIGAR in the ciliate Oxytricha trifallax were validated by the existing germline assembly. We then applied SIGAR to six diverse ciliate species without germline genome assemblies, including Ichthyophthirius multifilii, a fish pathogen. Despite the high level of somatic DNA contamination in each sample, SIGAR successfully inferred rearrangement junctions, short eliminated sequences, and potential scrambled genes in each species. This pipeline enables pilot surveys or exploration of DNA rearrangements in species with limited DNA material access, thereby providing new insights into the evolution of chromosome rearrangements.

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Danchin, Antoine, Pascale Guerdoux-Jamet, Ivan Moszer, and Patrick Nitschké. "Mapping the bacterial cell architecture into the chromosome." Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences 355, no. 1394 (2000): 179–90. http://dx.doi.org/10.1098/rstb.2000.0557.

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A genome is not a simple collection of genes. We propose here that it can be viewed as being organized as a ;‘celluloculus’ similar to the homunculus of preformists, but pertaining to the category of programmes (or algorithms) rather than to that of architectures or structures: a significant correlation exists between the distribution of genes along the chromosome and the physical architecture of the cell. W e review here data supporting this observation, stressing physical constraints operating on the cell's architecture and dynamics, and their consequences in terms of gene and genome structure. If such a correlation exists, it derives from some selection pressure: simple and general physical principles acting at the level of the cell structure are discussed. As a first case in point we see the piling up of planar modules as a stable, entropy–driven, architectural principle that could be at the root of the coupling between the architecture of the cell and the location of genes at specific places in the chromosome. W e propose that the specific organization of certain genes whose products have a general tendency to form easily planar modules is a general motor for architectural organization in the bacterial cell. A second mechanism, operating at the transcription level, is described that could account for the efficient building up of complex structures. As an organizing principle we suggest that exploration by biological polymers of the vast space of possible conformation states is constrained by anchoring points. In particular, we suggest that transcription does not always allow the 5 ′ –end of the transcript to go free and explore the many conformations available, but that, in many cases, it remains linked to the transcribing RNA polymerase complex in such a way that loops of RNA, rather than threads with a free end, explore the surrounding medium. In bacteria, extension of the loops throughout the cytoplasm would therefore be mediated by the de novo synthesis of ribosomes in growing cells. Termination of transcription and mRNA turnover would accordingly be expected to be controlled by sequence features at both the 3 ′ – and 5 ′ –ends of the molecule. These concepts are discussed taking into account in vitro analysis of genome sequences and experimental data about cell compartmentalization, mRNA folding and turnover, as well as known structural features of protein and membrane complexes.

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Schmitt, Anthony D., Ming Hu, and Bing Ren. "Genome-wide mapping and analysis of chromosome architecture." Nature Reviews Molecular Cell Biology 17, no. 12 (2016): 743–55. http://dx.doi.org/10.1038/nrm.2016.104.

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Beagrie, Robert A., Antonio Scialdone, Markus Schueler, et al. "Complex multi-enhancer contacts captured by genome architecture mapping." Nature 543, no. 7646 (2017): 519–24. http://dx.doi.org/10.1038/nature21411.

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Ramani, Vijay, Darren A. Cusanovich, Ronald J. Hause, et al. "Mapping 3D genome architecture through in situ DNase Hi-C." Nature Protocols 11, no. 11 (2016): 2104–21. http://dx.doi.org/10.1038/nprot.2016.126.

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Maluszynska, J., and J. S. Heslop-Harrison. "Physical mapping of rDNA loci in Brassica species." Genome 36, no. 4 (1993): 774–81. http://dx.doi.org/10.1139/g93-102.

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The number of major rDNA loci (the genes coding for 18S–5.8S–26S rRNA) was investigated in the economically important Brassica species and their wild relatives by in situ hybridization of an rDNA probe to metaphase chromosomes and interphase nuclei. The diploid species B. nigra (B genome) has two major pairs of rDNA loci, B. oleracea (C genome) has two major pairs and one minor pair of loci, while B. campestris (A genome) has five pairs of loci. Among the three tetraploid species arising from these three diploid ancestors, B. carinata (BBCC genomes) has four loci, B. juncea (AABB genomes) has five major pairs and one minor pair of loci, and B. napus (AACC genomes) has six pairs of loci, indicating that the number of loci has been reduced during evolution. The complexity of the known rDNA restriction fragment length polymorphism patterns gave little indication of number of rDNA loci. It is probable that chromosome rearrangements have occurred during evolution of the amphidiploid species. The data will be useful for physical mapping of genes relative to rDNA loci, micro- and macro-evolutionary studies and analysis of aneuploids including addition and substitution lines used in Brassica breeding programs.Key words: Brassica, centromeric DNA, genetic maps, nuclear architecture, ribosomal DNA, evolution, Brassicaceae, Cruciferae, gene mapping.

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Burridge, James D., Hannah M. Schneider, Bao-Lam Huynh, Philip A. Roberts, Alexander Bucksch, and Jonathan P. Lynch. "Genome-wide association mapping and agronomic impact of cowpea root architecture." Theoretical and Applied Genetics 130, no. 2 (2016): 419–31. http://dx.doi.org/10.1007/s00122-016-2823-y.

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Thoen, Manus P. M., Nelson H. Davila Olivas, Karen J. Kloth, et al. "Genetic architecture of plant stress resistance: multi-trait genome-wide association mapping." New Phytologist 213, no. 3 (2016): 1346–62. http://dx.doi.org/10.1111/nph.14220.

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Jaroszewicz, Artur, and Jason Ernst. "An integrative approach for fine-mapping chromatin interactions." Bioinformatics 36, no. 6 (2019): 1704–11. http://dx.doi.org/10.1093/bioinformatics/btz843.

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Abstract Motivation Chromatin interactions play an important role in genome architecture and gene regulation. The Hi-C assay generates such interactions maps genome-wide, but at relatively low resolutions (e.g. 5-25 kb), which is substantially coarser than the resolution of transcription factor binding sites or open chromatin sites that are potential sources of such interactions. Results To predict the sources of Hi-C-identified interactions at a high resolution (e.g. 100 bp), we developed a computational method that integrates data from DNase-seq and ChIP-seq of TFs and histone marks. Our method, χ-CNN, uses this data to first train a convolutional neural network (CNN) to discriminate between called Hi-C interactions and non-interactions. χ-CNN then predicts the high-resolution source of each Hi-C interaction using a feature attribution method. We show these predictions recover original Hi-C peaks after extending them to be coarser. We also show χ-CNN predictions enrich for evolutionarily conserved bases, eQTLs and CTCF motifs, supporting their biological significance. χ-CNN provides an approach for analyzing important aspects of genome architecture and gene regulation at a higher resolution than previously possible. Availability and implementation χ-CNN software is available on GitHub (https://github.com/ernstlab/X-CNN). Supplementary information Supplementary data are available at Bioinformatics online.

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ZENG, ZHAO-BANG, CHEN-HUNG KAO, and CHRISTOPHER J. BASTEN. "Estimating the genetic architecture of quantitative traits." Genetical Research 74, no. 3 (1999): 279–89. http://dx.doi.org/10.1017/s0016672399004255.

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Understanding and estimating the structure and parameters associated with the genetic architecture of quantitative traits is a major research focus in quantitative genetics. With the availability of a well-saturated genetic map of molecular markers, it is possible to identify a major part of the structure of the genetic architecture of quantitative traits and to estimate the associated parameters. Multiple interval mapping, which was recently proposed for simultaneously mapping multiple quantitative trait loci (QTL), is well suited to the identification and estimation of the genetic architecture parameters, including the number, genomic positions, effects and interactions of significant QTL and their contribution to the genetic variance. With multiple traits and multiple environments involved in a QTL mapping experiment, pleiotropic effects and QTL by environment interactions can also be estimated. We review the method and discuss issues associated with multiple interval mapping, such as likelihood analysis, model selection, stopping rules and parameter estimation. The potential power and advantages of the method for mapping multiple QTL and estimating the genetic architecture are discussed. We also point out potential problems and difficulties in resolving the details of the genetic architecture as well as other areas that require further investigation. One application of the analysis is to improve genome-wide marker-assisted selection, particularly when the information about epistasis is used for selection with mating.

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Wang, Jiachi, Andy Pang, Karl Hong, Jill Lai, Dipa Roychoudhury, and Joyce L. Murata-Colllins. "Integrative structural variant and breakpoint detection using optical genome mapping in a patient with a transformed diffuse large B-cell lymphoma from chronic lymphocytic leukemia." Journal of Clinical Oncology 39, no. 15_suppl (2021): e19511-e19511. http://dx.doi.org/10.1200/jco.2021.39.15_suppl.e19511.

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e19511 Background: The finding of complex karyotypes has been a clinically significant finding in cancers of advanced stage or during cancer progression. Conventional cytogenetic and FISH analyses have been limited by the low-resolution of chromosomes and the number of FISH probes which can be implemented in one assay. Recent study revealed the potential of using optical genome mapping to decipher the architecture of cancer genome at nucleotide level. Methods: Karyotyping, FISH and optical genome mapping of bone marrow specimen. Results: We reported on a 63-year-old female with chronic lymphocytic leukemia for nine years and transformed to diffuse large B-cell lymphoma (DLBCL). The karyotype revealed a hypodiploid chromosomal complement: 42,X,-X,der(2)t(2;?;8)(p25;?;q11.2),t(2;9)(q3?5;p2?2),der(4)t(4;?;8)(p16;?;q11.2)t(4;15)(q35;q15),-8,-15,dic(17;21)(p11.2;p11.2),der(18)t(8;18)(q21.2;p11.32)[12]/46,XX[8]. FISH analysis showed loss of TP53, monosomy 8 with 3-5 copies of the Myc genes. Optical genome mapping analysis revealed 12 insertions, 29 deletions, 8 duplications, 6 intrachromosomal translocations and 12 interchromosomal translocations. Whole genome analysis identified multiple gains of 2p, 8p and 8q, losses of 9p, 15q and 17p. The breakpoints of two unbalanced translocation and one complex chromosomal rearrangement have been narrowed down to nucleotide resolution: ogm[GRCh37] t(2;9)(q34;p21.2) g.[chr2:211,281,003::chr9:26,532,620], ogm t(2;8)(p25.3;p23.3) g.[chr2:15,924::chr8:215,177] and ogm der(4)t(8q24.3→8q21.13→2p24.2→2q34→4p15.2→4q34.3→15q15.1) g.[chr8:80,461,191::chr2:18,079,530→chr2:211,274,379::chr4:26,381,729→chr4:180,989,408::chr15:42,404,514]. Conclusions: Integrative analysis using conventional cytogenetic and molecular cytogenomic methodologies unveil the complex architectural alterations of caner genome. The resolution achieved by optical genome mapping would potentially lead to discovery of carcinogenic mechanisms, new fusion genes, prognostic and therapeutic markers.

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Lee, Ling Sze, Beatriz M. Navarro-Domínguez, Zhiqiang Wu, et al. "Karyotypic Evolution of Sauropsid Vertebrates Illuminated by Optical and Physical Mapping of the Painted Turtle and Slider Turtle Genomes." Genes 11, no. 8 (2020): 928. http://dx.doi.org/10.3390/genes11080928.

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Recent sequencing and software enhancements have advanced our understanding of the evolution of genomic structure and function, especially addressing novel evolutionary biology questions. Yet fragmentary turtle genome assemblies remain a challenge to fully decipher the genetic architecture of adaptive evolution. Here, we use optical mapping to improve the contiguity of the painted turtle (Chrysemys picta) genome assembly and use de novo fluorescent in situ hybridization (FISH) of bacterial artificial chromosome (BAC) clones, BAC-FISH, to physically map the genomes of the painted and slider turtles (Trachemys scripta elegans). Optical mapping increased C. picta’s N50 by ~242% compared to the previous assembly. Physical mapping permitted anchoring ~45% of the genome assembly, spanning 5544 genes (including 20 genes related to the sex determination network of turtles and vertebrates). BAC-FISH data revealed assembly errors in C. picta and T. s. elegans assemblies, highlighting the importance of molecular cytogenetic data to complement bioinformatic approaches. We also compared C. picta’s anchored scaffolds to the genomes of other chelonians, chicken, lizards, and snake. Results revealed a mostly one-to-one correspondence between chromosomes of painted and slider turtles, and high homology among large syntenic blocks shared with other turtles and sauropsids. Yet, numerous chromosomal rearrangements were also evident across chelonians, between turtles and squamates, and between avian and non-avian reptiles.

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Tian, Feng, Peter J. Bradbury, Patrick J. Brown, et al. "Genome-wide association study of leaf architecture in the maize nested association mapping population." Nature Genetics 43, no. 2 (2011): 159–62. http://dx.doi.org/10.1038/ng.746.

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Zurek, Paul R., Christopher N. Topp, and Philip N. Benfey. "Quantitative Trait Locus Mapping Reveals Regions of the Maize Genome Controlling Root System Architecture." Plant Physiology 167, no. 4 (2015): 1487–96. http://dx.doi.org/10.1104/pp.114.251751.

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Yu, Kang, Dongcheng Liu, Yong Chen, et al. "Unraveling the genetic architecture of grain size in einkorn wheat through linkage and homology mapping and transcriptomic profiling." Journal of Experimental Botany 70, no. 18 (2019): 4671–88. http://dx.doi.org/10.1093/jxb/erz247.

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Genome-wide linkage and homology mapping revealed 17 genomic regions harboring 42 QTLs affecting grain size in einkorn wheat. Transcriptomic analysis identified 20 genes involved in grain development and starch biosynthesis with differential expression between two parental lines.

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Lee, Tong Geon, Samuel F. Hutton, and Reza Shekasteband. "Fine Mapping of the brachytic Locus on the Tomato Genome." Journal of the American Society for Horticultural Science 143, no. 4 (2018): 239–47. http://dx.doi.org/10.21273/jashs04423-18.

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Mechanization of farm work is increasingly demanded for the current system of fresh-market tomato (Solanum lycopersicum) production. One essential element for the adoption of mechanical harvest of fresh-market tomatoes is modification of plant architecture so that the crop can be grown without staking. To address this in the current production system, the stem length should be reduced. The tomato brachytic (br) locus has been shown to be a primary source of reducing stem length. To improve the effectiveness of marker-assisted selection (MAS) for the br-mediated trait and to provide resources for cloning this gene, we fine-mapped br to the tomato genome. Fine mapping of br to chromosome 1 was initiated by a survey of genome-wide single-nucleotide polymorphisms (SNPs) shown to be polymorphic between the br phenotype and normal using the tomato array, identifying the interval that harbors br. Genetic markers that flank the locus further permitted saturation of the interval. Twenty-six fixed homozygous recombinant lines were identified together in two different populations and tested with those markers. These efforts resulted in the first report that the br is fine-mapped to a 763-kb physical interval of tomato reference genome. The identified markers close to the br in the present study will be significant resources for MAS and gene cloning research.

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Seda, Ondrej, Frantisek Liska, Drahomira Krenova, et al. "Dynamic genetic architecture of metabolic syndrome attributes in the rat." Physiological Genomics 21, no. 2 (2005): 243–52. http://dx.doi.org/10.1152/physiolgenomics.00230.2004.

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The polydactylous rat strain (PD/Cub) is a highly inbred (F > 90) genetic model of metabolic syndrome. The aim of this study was to analyze the genetic architecture of the metabolic derangements found in the PD/Cub strain and to assess its dynamics in time and in response to diet and medication. We derived a PD/Cub × BN/Cub (Brown Norway) F2 intercross population of 149 male rats and performed metabolic profiling and genotyping and multiple levels of genetic linkage and statistical analyses at five different stages of ontogenesis and after high-sucrose diet feeding and dexamethasone administration challenges. The interval mapping analysis of 83 metabolic and morphometric traits revealed over 50 regions genomewide with significant or suggestive linkage to one or more of the traits in the segregating PD/Cub × BN/Cub population. The multiple interval mapping showed that, in addition to “single” quantitative train loci, there are more than 30 pairs of loci across the whole genome significantly influencing the variation of particular traits in an epistatic fashion. This study represents the first whole genome analysis of metabolic syndrome in the PD/Cub model and reveals several new loci previously not connected to the genetics of insulin resistance and dyslipidemia. In addition, it attempts to present the concept of “dynamic genetic architecture” of metabolic syndrome attributes, evidenced by shifts in the genetic determination of syndrome features during ontogenesis and during adaptation to the dietary and pharmacological influences.

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Ungerer, Mark C., Solveig S. Halldorsdottir, Jennifer L. Modliszewski, Trudy F. C. Mackay, and Michael D. Purugganan. "Quantitative Trait Loci for Inflorescence Development in Arabidopsis thaliana." Genetics 160, no. 3 (2002): 1133–51. http://dx.doi.org/10.1093/genetics/160.3.1133.

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Abstract Variation in inflorescence development patterns is a central factor in the evolutionary ecology of plants. The genetic architectures of 13 traits associated with inflorescence developmental timing, architecture, rosette morphology, and fitness were investigated in Arabidopsis thaliana, a model plant system. There is substantial naturally occurring genetic variation for inflorescence development traits, with broad sense heritabilities computed from 21 Arabidopsis ecotypes ranging from 0.134 to 0.772. Genetic correlations are significant for most (64/78) pairs of traits, suggesting either pleiotropy or tight linkage among loci. Quantitative trait locus (QTL) mapping indicates 47 and 63 QTL for inflorescence developmental traits in Ler × Col and Cvi × Ler recombinant inbred mapping populations, respectively. Several QTL associated with different developmental traits map to the same Arabidopsis chromosomal regions, in agreement with the strong genetic correlations observed. Epistasis among QTL was observed only in the Cvi × Ler population, and only between regions on chromosomes 1 and 5. Examination of the completed Arabidopsis genome sequence in three QTL regions revealed between 375 and 783 genes per region. Previously identified flowering time, inflorescence architecture, floral meristem identity, and hormone signaling genes represent some of the many candidate genes in these regions.

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Yang, Fangping, Jindong Liu, Ying Guo, et al. "Genome-Wide Association Mapping of Adult-Plant Resistance to Stripe Rust in Common Wheat (Triticum aestivum)." Plant Disease 104, no. 8 (2020): 2174–80. http://dx.doi.org/10.1094/pdis-10-19-2116-re.

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Stripe rust, caused by Puccinia striiformis f. sp. tritici, is a globally devastating disease of common wheat (Triticum aestivum L.), resulting in substantial economic losses. To identify effective resistance genes, a genome-wide association study was conducted on 120 common wheat lines from different wheat-growing regions of China using the wheat 90K iSelect SNP array. Seventeen loci were identified, explaining 9.5 to 21.8% of the phenotypic variation. Most of these genes were detected in the A (seven) and B (seven) genomes, with only three in the D genome. Among them, 11 loci were colocated with known resistance genes or quantitative trait loci reported previously, whereas the other six are likely new resistance loci. Annotation of flanking sequences of significantly associated SNPs indicated the presence of three important candidate genes, including E3 ubiquitin-protein ligase, F-box repeat protein, and disease resistance RPP13-like protein. This study increased our knowledge in understanding the genetic architecture for stripe rust resistance and identified wheat varieties with multiple resistance alleles, which are useful for improvement of stripe rust resistance in breeding.

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Ma, Yu, Afef Marzougui, Clarice J. Coyne, et al. "Dissecting the Genetic Architecture of Aphanomyces Root Rot Resistance in Lentil by QTL Mapping and Genome-Wide Association Study." International Journal of Molecular Sciences 21, no. 6 (2020): 2129. http://dx.doi.org/10.3390/ijms21062129.

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Lentil (Lens culinaris Medikus) is an important source of protein for people in developing countries. Aphanomyces root rot (ARR) has emerged as one of the most devastating diseases affecting lentil production. In this study, we applied two complementary quantitative trait loci (QTL) analysis approaches to unravel the genetic architecture underlying this complex trait. A recombinant inbred line (RIL) population and an association mapping population were genotyped using genotyping by sequencing (GBS) to discover novel single nucleotide polymorphisms (SNPs). QTL mapping identified 19 QTL associated with ARR resistance, while association mapping detected 38 QTL and highlighted accumulation of favorable haplotypes in most of the resistant accessions. Seven QTL clusters were discovered on six chromosomes, and 15 putative genes were identified within the QTL clusters. To validate QTL mapping and genome-wide association study (GWAS) results, expression analysis of five selected genes was conducted on partially resistant and susceptible accessions. Three of the genes were differentially expressed at early stages of infection, two of which may be associated with ARR resistance. Our findings provide valuable insight into the genetic control of ARR, and genetic and genomic resources developed here can be used to accelerate development of lentil cultivars with high levels of partial resistance to ARR.

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Heckel, D. G., L. J. Gahan, J. C. Daly, and S. Trowell. "A genomic approach to understanding Heliothis and Helicoverpa resistance to chemical and biological insecticides." Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences 353, no. 1376 (1998): 1713–22. http://dx.doi.org/10.1098/rstb.1998.0323.

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Genomics is the comparative study of the structure and function of entire genomes. Although the complete sequencing of the genome of any insect pest is far in the future, a genomic approach can be useful in the study of mechanisms of insecticide resistance. We describe this strategy for Heliothis and Helicoverpa , two of the most destructive genera of pest moths (Lepidoptera) worldwide. Genome–wide linkage mapping provides the location of major and minor resistance genes. Positional cloning identifies novel resistance genes, even when the mechanisms are poorly understood, as with resistance to Bacillus thuringiensis toxins. Anchor loci provide the reference points for comparing the genomes and the genetic architecture of resistance mechanisms among related species. Collectively, these tools enable the description of the evolutionary response of related, but independent, genomes to the common selective pressure of insecticides in the environment. They also provide information that is useful for targeted management of specific resistance genes, and may even speed the search for families of novel insecticidal targets in Lepidoptera.

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Zhang, Ning, and Xueqing Huang. "Mapping quantitative trait loci and predicting candidate genes for leaf angle in maize." PLOS ONE 16, no. 1 (2021): e0245129. http://dx.doi.org/10.1371/journal.pone.0245129.

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Leaf angle of maize is a fundamental determinant of plant architecture and an important trait influencing photosynthetic efficiency and crop yields. To broaden our understanding of the genetic mechanisms of leaf angle formation, we constructed a F3:4 recombinant inbred lines (RIL) population to map QTL for leaf angle. The RIL was derived from a cross between a model inbred line (B73) with expanded leaf architecture and an elite inbred line (Zheng58) with compact leaf architecture. A sum of eight QTL were detected on chromosome 1, 2, 3, 4 and 8. Single QTL explained 4.3 to 14.2% of the leaf angle variance. Additionally, some important QTL were confirmed through a heterogeneous inbred family (HIF) approach. Furthermore, twenty-four candidate genes for leaf angle were predicted through whole-genome re-sequencing and expression analysis in qLA02-01and qLA08-01 regions. These results will be helpful to elucidate the genetic mechanism of leaf angle formation in maize and benefit to clone the favorable allele for leaf angle. Besides, this will be helpful to develop the novel maize varieties with ideal plant architecture through marker-assisted selection.

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Kooke, Rik, Willem Kruijer, Ralph Bours, et al. "Genome-Wide Association Mapping and Genomic Prediction Elucidate the Genetic Architecture of Morphological Traits in Arabidopsis." Plant Physiology 170, no. 4 (2016): 2187–203. http://dx.doi.org/10.1104/pp.15.00997.

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Resende, Rafael T., Marcos Deon V. de Resende, Camila F. Azevedo, et al. "Genome-Wide Association and Regional Heritability Mapping of Plant Architecture, Lodging and Productivity in Phaseolus vulgaris." G3: Genes|Genomes|Genetics 8, no. 8 (2018): 2841–54. http://dx.doi.org/10.1534/g3.118.200493.

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Schödel, Johannes, Spyros Oikonomopoulos, Jiannis Ragoussis, Christopher W. Pugh, Peter J. Ratcliffe, and David R. Mole. "High-resolution genome-wide mapping of HIF-binding sites by ChIP-seq." Blood 117, no. 23 (2011): e207-e217. http://dx.doi.org/10.1182/blood-2010-10-314427.

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Abstract Hypoxia-inducible factor (HIF) regulates the major transcriptional cascade central to the response of all mammalian cells to alterations in oxygen tension. Expression arrays indicate that many hundreds of genes are regulated by this pathway, controlling diverse processes that in turn orchestrate both oxygen delivery and utilization. However, the extent to which HIF exerts direct versus indirect control over gene expression together with the factors dictating the range of HIF-regulated genes remains unclear. Using chromatin immunoprecipitation linked to high throughput sequencing, we identify HIF-binding sites across the genome, independently of gene architecture. Using gene set enrichment analysis, we demonstrate robust associations with the regulation of gene expression by HIF, indicating that these sites operate over long genomic intervals. Analysis of HIF-binding motifs demonstrates sequence preferences outside of the core RCGTG-binding motif but does not reveal any additional absolute sequence requirements. Across the entire genome, only a small proportion of these potential binding sites are bound by HIF, although occupancy of potential sites was enhanced approximately 20-fold at normoxic DNAse1 hypersensitivity sites (irrespective of distance from promoters), suggesting that epigenetic regulation of chromatin may have an important role in defining the response to hypoxia.

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Jowhar, Ziad, Sigal Shachar, Prabhakar R. Gudla, et al. "Effects of human sex chromosome dosage on spatial chromosome organization." Molecular Biology of the Cell 29, no. 20 (2018): 2458–69. http://dx.doi.org/10.1091/mbc.e18-06-0359.

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Sex chromosome aneuploidies (SCAs) are common genetic syndromes characterized by the presence of an aberrant number of X and Y chromosomes due to meiotic defects. These conditions impact the structure and function of diverse tissues, but the proximal effects of SCAs on genome organization are unknown. Here, to determine the consequences of SCAs on global genome organization, we have analyzed multiple architectural features of chromosome organization in a comprehensive set of primary cells from SCA patients with various ratios of X and Y chromosomes by use of imaging-based high-throughput chromosome territory mapping (HiCTMap). We find that X chromosome supernumeracy does not affect the size, volume, or nuclear position of the Y chromosome or an autosomal chromosome. In contrast, the active X chromosome undergoes architectural changes as a function of increasing X copy number as measured by a decrease in size and an increase in circularity, which is indicative of chromatin compaction. In Y chromosome supernumeracy, Y chromosome size is reduced suggesting higher chromatin condensation. The radial positioning of chromosomes is unaffected in SCA karyotypes. Taken together, these observations document changes in genome architecture in response to alterations in sex chromosome numbers and point to trans-effects of dosage compensation on chromosome organization.

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Demetci, Pinar, Wei Cheng, Gregory Darnell, Xiang Zhou, Sohini Ramachandran, and Lorin Crawford. "Multi-scale inference of genetic trait architecture using biologically annotated neural networks." PLOS Genetics 17, no. 8 (2021): e1009754. http://dx.doi.org/10.1371/journal.pgen.1009754.

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In this article, we present Biologically Annotated Neural Networks (BANNs), a nonlinear probabilistic framework for association mapping in genome-wide association (GWA) studies. BANNs are feedforward models with partially connected architectures that are based on biological annotations. This setup yields a fully interpretable neural network where the input layer encodes SNP-level effects, and the hidden layer models the aggregated effects among SNP-sets. We treat the weights and connections of the network as random variables with prior distributions that reflect how genetic effects manifest at different genomic scales. The BANNs software uses variational inference to provide posterior summaries which allow researchers to simultaneously perform (i) mapping with SNPs and (ii) enrichment analyses with SNP-sets on complex traits. Through simulations, we show that our method improves upon state-of-the-art association mapping and enrichment approaches across a wide range of genetic architectures. We then further illustrate the benefits of BANNs by analyzing real GWA data assayed in approximately 2,000 heterogenous stock of mice from the Wellcome Trust Centre for Human Genetics and approximately 7,000 individuals from the Framingham Heart Study. Lastly, using a random subset of individuals of European ancestry from the UK Biobank, we show that BANNs is able to replicate known associations in high and low-density lipoprotein cholesterol content.

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Kitony, Justine K., Hidehiko Sunohara, Mikako Tasaki, et al. "Development of an Aus-Derived Nested Association Mapping (Aus-NAM) Population in Rice." Plants 10, no. 6 (2021): 1255. http://dx.doi.org/10.3390/plants10061255.

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A genetic resource for studying genetic architecture of agronomic traits and environmental adaptation is essential for crop improvements. Here, we report the development of a rice nested association mapping population (aus-NAM) using 7 aus varieties as diversity donors and T65 as the common parent. Aus-NAM showed broad phenotypic variations. To test whether aus-NAM was useful for quantitative trait loci (QTL) mapping, known flowering genes (Ehd1, Hd1, and Ghd7) in rice were characterized using single-family QTL mapping, joint QTL mapping, and the methods based on genome-wide association study (GWAS). Ehd1 was detected in all the seven families and all the methods. On the other hand, Hd1 and Ghd7 were detected in some families, and joint QTL mapping and GWAS-based methods resulted in weaker and uncertain peaks. Overall, the high allelic variations in aus-NAM provide a valuable genetic resource for the rice community.

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Martin, Anke, Paula Moolhuijzen, Yongfu Tao, et al. "Genomic Regions Associated with Virulence in Pyrenophora teres f. teres Identified by Genome-Wide Association Analysis and Biparental Mapping." Phytopathology® 110, no. 4 (2020): 881–91. http://dx.doi.org/10.1094/phyto-10-19-0372-r.

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Net form net blotch (NFNB), caused by the fungal pathogen Pyrenophora teres f. teres, is an important foliar disease present in all barley-producing regions of the world. This fungus is a hemibiotrophic and heterothallic ascomycete, where sexual recombination can lead to changes in disease expression in the host. Knowledge of the genetic architecture and genes involved in virulence is vital to increase the durability of NFNB resistance in barley cultivars. We used a genome-wide association mapping approach to characterize P. teres f. teres genomic regions associated with virulence in Australian barley cultivars. One hundred eighty-eight P. teres f. teres isolates collected across five Australian states were genotyped using Diversity Arrays Technology sequence markers and phenotyped across 20 different barley genotypes. Association mapping identified 14 different genomic regions associated with virulence, with the majority located on P. teres f. teres chromosomes 3 and 5 and one each present on chromosomes 1, 6, and 9. Four of the regions identified were confirmed by quantitative trait loci (QTL) mapping. The QTL regions are discussed in the context of their genomic architecture together with examination of their gene contents, which identified 20 predicted effectors. The number of QTL shown in this study at the population level clearly illustrates a complex genetic basis of P. teres f. teres virulence compared with pure necrotrophs, such as the wheat pathogens Parastagonospora nodorum and Parastagonospora tritici-repentis.

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Dutta, Anik, Fanny E. Hartmann, Carolina Sardinha Francisco, Bruce A. McDonald, and Daniel Croll. "Mapping the adaptive landscape of a major agricultural pathogen reveals evolutionary constraints across heterogeneous environments." ISME Journal 15, no. 5 (2021): 1402–19. http://dx.doi.org/10.1038/s41396-020-00859-w.

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AbstractThe adaptive potential of pathogens in novel or heterogeneous environments underpins the risk of disease epidemics. Antagonistic pleiotropy or differential resource allocation among life-history traits can constrain pathogen adaptation. However, we lack understanding of how the genetic architecture of individual traits can generate trade-offs. Here, we report a large-scale study based on 145 global strains of the fungal wheat pathogen Zymoseptoria tritici from four continents. We measured 50 life-history traits, including virulence and reproduction on 12 different wheat hosts and growth responses to several abiotic stressors. To elucidate the genetic basis of adaptation, we used genome-wide association mapping coupled with genetic correlation analyses. We show that most traits are governed by polygenic architectures and are highly heritable suggesting that adaptation proceeds mainly through allele frequency shifts at many loci. We identified negative genetic correlations among traits related to host colonization and survival in stressful environments. Such genetic constraints indicate that pleiotropic effects could limit the pathogen’s ability to cause host damage. In contrast, adaptation to abiotic stress factors was likely facilitated by synergistic pleiotropy. Our study illustrates how comprehensive mapping of life-history trait architectures across diverse environments allows to predict evolutionary trajectories of pathogens confronted with environmental perturbations.

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Raj, Towfique, Lori B. Chibnik, Cristin McCabe, et al. "Genetic architecture of age-related cognitive decline in African Americans." Neurology Genetics 3, no. 1 (2016): e125. http://dx.doi.org/10.1212/nxg.0000000000000125.

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Objective:To identify genetic risk factors associated with susceptibility to age-related cognitive decline in African Americans (AAs).Methods:We performed a genome-wide association study (GWAS) and an admixture-mapping scan in 3,964 older AAs from 5 longitudinal cohorts; for each participant, we calculated a slope of an individual's global cognitive change from neuropsychological evaluations. We also performed a pathway-based analysis of the age-related cognitive decline GWAS.Results:We found no evidence to support the existence of a genomic region which has a strongly different contribution to age-related cognitive decline in African and European genomes. Known Alzheimer disease (AD) susceptibility variants in the ABCA7 and MS4A loci do influence this trait in AAs. Of interest, our pathway-based analyses returned statistically significant results highlighting a shared risk from lipid/metabolism and protein tyrosine signaling pathways between cognitive decline and AD, but the role of inflammatory pathways is polarized, being limited to AD susceptibility.Conclusions:The genetic architecture of aging-related cognitive in AA individuals is largely similar to that of individuals of European descent. In both populations, we note a surprising lack of enrichment for immune pathways in the genetic risk for cognitive decline, despite strong enrichment of these pathways among genetic risk factors for AD.

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Chen, Shaolong, and Miquel Angel Senar. "Exploring efficient data parallelism for genome read mapping on multicore and manycore architectures." Parallel Computing 87 (September 2019): 11–24. http://dx.doi.org/10.1016/j.parco.2019.04.014.

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Wu, Zhiqiang, Jocelyn M. Cuthbert, Douglas R. Taylor, and Daniel B. Sloan. "The massive mitochondrial genome of the angiosperm Silene noctiflora is evolving by gain or loss of entire chromosomes." Proceedings of the National Academy of Sciences 112, no. 33 (2015): 10185–91. http://dx.doi.org/10.1073/pnas.1421397112.

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Across eukaryotes, mitochondria exhibit staggering diversity in genomic architecture, including the repeated evolution of multichromosomal structures. Unlike in the nucleus, where mitosis and meiosis ensure faithful transmission of chromosomes, the mechanisms of inheritance in fragmented mitochondrial genomes remain mysterious. Multichromosomal mitochondrial genomes have recently been found in multiple species of flowering plants, including Silene noctiflora, which harbors an unusually large and complex mitochondrial genome with more than 50 circular-mapping chromosomes totaling ∼7 Mb in size. To determine the extent to which such genomes are stably maintained, we analyzed intraspecific variation in the mitochondrial genome of S. noctiflora. Complete genomes from two populations revealed a high degree of similarity in the sequence, structure, and relative abundance of mitochondrial chromosomes. For example, there are no inversions between the genomes, and there are only nine SNPs in 25 kb of protein-coding sequence. Remarkably, however, these genomes differ in the presence or absence of 19 entire chromosomes, all of which lack any identifiable genes or contain only duplicate gene copies. Thus, these mitochondrial genomes retain a full gene complement but carry a highly variable set of chromosomes that are filled with presumably dispensable sequence. In S. noctiflora, conventional mechanisms of mitochondrial sequence divergence are being outstripped by an apparently nonadaptive process of whole-chromosome gain/loss, highlighting the inherent challenge in maintaining a fragmented genome. We discuss the implications of these findings in relation to the question of why mitochondria, more so than plastids and bacterial endosymbionts, are prone to the repeated evolution of multichromosomal genomes.

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Onogi, Akio. "Connecting mathematical models to genomes: joint estimation of model parameters and genome-wide marker effects on these parameters." Bioinformatics 36, no. 10 (2020): 3169–76. http://dx.doi.org/10.1093/bioinformatics/btaa129.

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Abstract Motivation Parameters of mathematical models used in biology may be genotype-specific and regarded as new traits. Therefore, an accurate estimation of these parameters and the association mapping on the estimated parameters can lead to important findings regarding the genetic architecture of biological processes. In this study, a statistical framework for a joint analysis (JA) of model parameters and genome-wide marker effects on these parameters was proposed and evaluated. Results In the simulation analyses based on different types of mathematical models, the JA inferred the model parameters and identified the responsible genomic regions more accurately than the independent analysis (IA). The JA of real plant data provided interesting insights into photosensitivity, which were uncovered by the IA. Availability and implementation The statistical framework is provided by the R package GenomeBasedModel available at https://github.com/Onogi/GenomeBasedModel. All R and C++ scripts used in this study are also available at the site. Supplementary information Supplementary data are available at Bioinformatics online.

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Jordan, Katherine W., Shichen Wang, Fei He, et al. "The genetic architecture of genome‐wide recombination rate variation in allopolyploid wheat revealed by nested association mapping." Plant Journal 95, no. 6 (2018): 1039–54. http://dx.doi.org/10.1111/tpj.14009.

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Li, Zhaoling, Peng Liu, Xiaoxiang Zhang, et al. "Genome‐wide association studies and QTL mapping uncover the genetic architecture of ear tip‐barrenness in maize." Physiologia Plantarum 170, no. 1 (2020): 27–39. http://dx.doi.org/10.1111/ppl.13087.

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Topp, C. N., A. S. Iyer-Pascuzzi, J. T. Anderson, et al. "3D phenotyping and quantitative trait locus mapping identify core regions of the rice genome controlling root architecture." Proceedings of the National Academy of Sciences 110, no. 18 (2013): E1695—E1704. http://dx.doi.org/10.1073/pnas.1304354110.

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Zhou, Hao, and Brian Steffenson. "Genome-wide association mapping reveals genetic architecture of durable spot blotch resistance in US barley breeding germplasm." Molecular Breeding 32, no. 1 (2013): 139–54. http://dx.doi.org/10.1007/s11032-013-9858-4.

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Chapman, Carol, Matthew Henry, Kimberly A. Bishop-Lilly, et al. "Scanning the Landscape of Genome Architecture of Non-O1 and Non-O139 Vibrio cholerae by Whole Genome Mapping Reveals Extensive Population Genetic Diversity." PLOS ONE 10, no. 3 (2015): e0120311. http://dx.doi.org/10.1371/journal.pone.0120311.

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Alomari, Dalia, Kai Eggert, Nicolaus von Wirén, et al. "Whole-Genome Association Mapping and Genomic Prediction for Iron Concentration in Wheat Grains." International Journal of Molecular Sciences 20, no. 1 (2018): 76. http://dx.doi.org/10.3390/ijms20010076.

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Malnutrition of iron (Fe) affects two billion people worldwide. Therefore, enhancing grain Fe concentration (GFeC) in wheat (Triticum aestivum L.) is an important goal for breeding. Here we study the genetic factors underlying GFeC trait by genome-wide association studies (GWAS) and the prediction abilities using genomic prediction (GP) in a panel of 369 European elite wheat varieties which was genotyped with 15,523 mapped single-nucleotide polymorphism markers (SNP) and a subpanel of 183 genotypes with 44,233 SNP markers. The resulting means of GFeC from three field experiments ranged from 24.42 to 52.42 μg·g−1 with a broad-sense heritability (H2) equaling 0.59 over the years. GWAS revealed 41 and 137 significant SNPs in the whole and subpanel, respectively, including significant marker-trait associations (MTAs) for best linear unbiased estimates (BLUEs) of GFeC on chromosomes 2A, 3B and 5A. Putative candidate genes such as NAC transcription factors and transmembrane proteins were present on chromosome 2A (763,689,738–765,710,113 bp). The GP for a GFeC trait ranged from low to moderate values. The current study reported GWAS of GFeC for the first time in hexaploid wheat varieties. These findings confirm the utility of GWAS and GP to explore the genetic architecture of GFeC for breeding programs aiming at the improvement of wheat grain quality.

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Luo, Z. W., Chung-I. Wu, and M. J. Kearsey. "Precision and High-Resolution Mapping of Quantitative Trait Loci by Use of Recurrent Selection, Backcross or Intercross Schemes." Genetics 161, no. 2 (2002): 915–29. http://dx.doi.org/10.1093/genetics/161.2.915.

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Abstract Dissecting quantitative genetic variation into genes at the molecular level has been recognized as the greatest challenge facing geneticists in the twenty-first century. Tremendous efforts in the last two decades were invested to map a wide spectrum of quantitative genetic variation in nearly all important organisms onto their genome regions that may contain genes underlying the variation, but the candidate regions predicted so far are too coarse for accurate gene targeting. In this article, the recurrent selection and backcross (RSB) schemes were investigated theoretically and by simulation for their potential in mapping quantitative trait loci (QTL). In the RSB schemes, selection plays the role of maintaining the recipient genome in the vicinity of the QTL, which, at the same time, are rapidly narrowed down over multiple generations of backcrossing. With a high-density linkage map of DNA polymorphisms, the RSB approach has the potential of dissecting the complex genetic architecture of quantitative traits and enabling the underlying QTL to be mapped with the precision and resolution needed for their map-based cloning to be attempted. The factors affecting efficiency of the mapping method were investigated, suggesting guidelines under which experimental designs of the RSB schemes can be optimized. Comparison was made between the RSB schemes and the two popular QTL mapping methods, interval mapping and composite interval mapping, and showed that the scenario of genomic distribution of QTL that was unlocked by the RSB-based mapping method is qualitatively distinguished from those unlocked by the interval mapping-based methods.

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Dickel, D. E., A. Visel, and L. A. Pennacchio. "Functional anatomy of distant-acting mammalian enhancers." Philosophical Transactions of the Royal Society B: Biological Sciences 368, no. 1620 (2013): 20120359. http://dx.doi.org/10.1098/rstb.2012.0359.

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Transcriptional enhancers are a major class of functional element embedded in the vast non-coding portion of the human genome. Acting over large genomic distances, enhancers play critical roles in the tissue and cell type-specific regulation of genes, and there is mounting evidence that they contribute to the aetiology of many human diseases. Methods for genome-wide mapping of enhancer regions are now available, but the functional architecture contained within human enhancer elements remains unclear. Here, we review recent approaches aimed at understanding the functional anatomy of individual enhancer elements, using systematic qualitative and quantitative assessments of mammalian enhancer variants in cultured cells and in vivo . These studies provide direct insight into common architectural characteristics of enhancers including the presence of multiple transcription factor-binding sites and the mixture of both transcriptionally activating and repressing domains within the same enhancer. Despite such progress in understanding the functional composition of enhancers, the inherent complexities of enhancer anatomy continue to limit our ability to predict the impact of sequence changes on in vivo enhancer function. While providing an initial glimpse into the mutability of mammalian enhancers, these observations highlight the continued need for experimental enhancer assessment as genome sequencing becomes routine in the clinic.

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Ren, Bing. "Organization and Regulation of the Human Genome." Blood 128, no. 22 (2016): SCI—16—SCI—16. http://dx.doi.org/10.1182/blood.v128.22.sci-16.sci-16.

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Abstract The 3-dimensional (3D) chromatin organization plays a critical role in gene regulation. Great strides have been made recently to characterize and identify cis regulatory elements from epigenome profiles in different cell types and tissues, but efforts have just begun to functionally characterize these long-range control elements. Mapping interactions between enhancers and promoters, and understanding how the 3D landscape of the genome constrains such interactions is fundamental to our understanding of genome function. I will present recent findings related to 3D genome organization in mammalian cells, with a particular focus on how chromatin organization contributes to transcriptional regulation. I will describe higher-order organizational features that are observed at the level of both the whole chromosome and individual loci. I will highlight changes in genome organization that occur during the course of differentiation, and discuss the functional relationship between chromatin architecture and gene regulation. Taken together, mounting evidence now shows that the genome organization plays an essential role in orchestrating the lineage-specific gene expression programs through modulating long- range interactions between enhancers and target genes. Disclosures Ren: Arima Genomics, Inc.: Equity Ownership, Patents & Royalties; Eli Lilly: Employment.

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Yuan, Ruizhi, Neng Zhao, Babar Usman, et al. "Development of Chromosome Segment Substitution Lines (CSSLs) Derived from Guangxi Wild Rice (Oryza rufipogon Griff.) under Rice (Oryza sativa L.) Background and the Identification of QTLs for Plant Architecture, Agronomic Traits and Cold Tolerance." Genes 11, no. 9 (2020): 980. http://dx.doi.org/10.3390/genes11090980.

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Common wild rice contains valuable resources of novel alleles for rice improvement. It is well known that genetic populations provide the basis for a wide range of genetic and genomic studies. In particular, chromosome segment substitution lines (CSSLs) ais a powerful tool for fine mapping of quantitative traits, new gene discovery and marker-assisted breeding. In this study, 132 CSSLs were developed from a cultivated rice (Oryza sativa) cultivar (93-11) and common wild rice (Oryza rufipogon Griff. DP30) by selfing-crossing, backcrossing and marker-assisted selection (MAS). Based on the high-throughput sequencing of the 93-11 and DP30, 285 pairs of Insertion-deletions (InDel) markers were selected with an average distance of 1.23 Mb. The length of this DP30-CSSLs library was 536.4 cM. The coverage rate of substitution lines cumulatively overlapping the whole genome of DP30 was about 91.55%. DP30-CSSLs were used to analyze the variation for 17 traits leading to the detection of 36 quantitative trait loci (QTLs) with significant phenotypic effects. A cold-tolerant line (RZ) was selected to construct a secondary mapping F2 population, which revealed that qCT2.1 is in the 1.7 Mb region of chromosome 2. These CSSLs may, therefore, provide powerful tools for genome wide large-scale gene discovery in wild rice. This research will also facilitate fine mapping and cloning of QTLs and genome-wide study of wild rice. Moreover, these CSSLs will provide a foundation for rice variety improvement.

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Darrow, Emily M., Miriam H. Huntley, Olga Dudchenko, et al. "Deletion of DXZ4 on the human inactive X chromosome alters higher-order genome architecture." Proceedings of the National Academy of Sciences 113, no. 31 (2016): E4504—E4512. http://dx.doi.org/10.1073/pnas.1609643113.

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During interphase, the inactive X chromosome (Xi) is largely transcriptionally silent and adopts an unusual 3D configuration known as the “Barr body.” Despite the importance of X chromosome inactivation, little is known about this 3D conformation. We recently showed that in humans the Xi chromosome exhibits three structural features, two of which are not shared by other chromosomes. First, like the chromosomes of many species, Xi forms compartments. Second, Xi is partitioned into two huge intervals, called “superdomains,” such that pairs of loci in the same superdomain tend to colocalize. The boundary between the superdomains lies near DXZ4, a macrosatellite repeat whose Xi allele extensively binds the protein CCCTC-binding factor. Third, Xi exhibits extremely large loops, up to 77 megabases long, called “superloops.” DXZ4 lies at the anchor of several superloops. Here, we combine 3D mapping, microscopy, and genome editing to study the structure of Xi, focusing on the role of DXZ4. We show that superloops and superdomains are conserved across eutherian mammals. By analyzing ligation events involving three or more loci, we demonstrate that DXZ4 and other superloop anchors tend to colocate simultaneously. Finally, we show that deleting DXZ4 on Xi leads to the disappearance of superdomains and superloops, changes in compartmentalization patterns, and changes in the distribution of chromatin marks. Thus, DXZ4 is essential for proper Xi packaging.

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Wang, Yuanyuan, Guirong Li, Xinlei Guo, et al. "Dissecting the genetic architecture of seed-cotton and lint yields in Upland cotton using genome-wide association mapping." Breeding Science 69, no. 4 (2019): 611–20. http://dx.doi.org/10.1270/jsbbs.19057.

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Famoso, Adam N., Keyan Zhao, Randy T. Clark, et al. "Genetic Architecture of Aluminum Tolerance in Rice (Oryza sativa) Determined through Genome-Wide Association Analysis and QTL Mapping." PLoS Genetics 7, no. 8 (2011): e1002221. http://dx.doi.org/10.1371/journal.pgen.1002221.

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LI, C. Q., N. J. AI, Y. J. ZHU, et al. "Association mapping and favourable allele exploration for plant architecture traits in upland cotton (Gossypium hirsutum L.) accessions." Journal of Agricultural Science 154, no. 4 (2015): 567–83. http://dx.doi.org/10.1017/s0021859615000428.

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SUMMARYAssociation mapping based on linkage disequilibrium (LD) is a promising tool to identify genes responsible for quantitative variations underlying complex traits. The present paper presents an association mapping panel consisting of 172 upland cotton (Gossypium hirsutum L.) accessions. The panel was phenotyped for five cotton plant architecture traits across multiple environments and genotyped using 386 simple sequence repeat (SSR) markers. Of these markers, 101 polymorphic SSR markers were used in the final analysis. There were abundant phenotypic variations within this germplasm panel and a total of 267 alleles ranging from two to seven per locus were identified in all collections. The threshold of LD decay was set to r2 = 0·1 and 0·2, and the genome-wide LD extended up to about 13–14 and 6–7 cM, respectively, providing the potential for association mapping of agronomically important traits in upland cotton. A total of 66 marker–trait associations were detected based on a mixed linear model, of which 35 were found in more than one environment. The favourable alleles from 35 marker loci can be used in marker-assisted selection of target traits. Both the synergistic alleles and the negative alleles for some traits, especially plant height and fruit branch angle, can be utilized in plant architecture breeding programmes according to specific breeding objectives.

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Journal articles on the topic 'Genome architecture mapping'

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