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Journal articles on the topic 'Polymorphism (genetics)'

Author: Grafiati

Published: 4 June 2021

Last updated: 6 February 2022

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1

O'hUigin, Colm, Yoko Satta, Anja Hausmann, Roger L. Dawkins, and Jan Klein. "The Implications of Intergenic Polymorphism for Major Histocompatibility Complex Evolution." Genetics 156, no. 2 (2000): 867–77. http://dx.doi.org/10.1093/genetics/156.2.867.

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Abstract A systematic survey of six intergenic regions flanking the human HLA-B locus in eight haplotypes reveals the regions to be up to 20 times more polymorphic than the reported average degree of human neutral polymorphism. Furthermore, the extent of polymorphism is directly related to the proximity to the HLA-B locus. Apparently linkage to HLA-B locus alleles, which are under balancing selection, maintains the neutral polymorphism of adjacent regions. For these linked polymorphisms to persist, recombination in the 200-kb interval from HLA-B to TNF must occur at a low frequency. The high d

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2

Kreitman, M., and R. R. Hudson. "Inferring the evolutionary histories of the Adh and Adh-dup loci in Drosophila melanogaster from patterns of polymorphism and divergence." Genetics 127, no. 3 (1991): 565–82. http://dx.doi.org/10.1093/genetics/127.3.565.

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Abstract The DNA sequences of 11 Drosophila melanogaster lines are compared across three contiguous regions, the Adh and Adh-dup loci and a noncoding 5' flanking region of Adh. Ninety-eight of approximately 4750 sites are segregating in the sample, 36 in the 5' flanking region, 38 in Adh and 24 in Adh-dup. Several methods are presented to test whether the patterns and levels of polymorphism are consistent with neutral molecular evolution. The analysis of within- and between-species polymorphism indicates that the region is evolving in a nonneutral and complex fashion. A graphical analysis of t

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3

Richter, Brent, Manyuan Long, R. C. Lewontin, and Eiji Nitasaka. "Nucleotide Variation and Conservation at the dpp Locus, a Gene Controlling Early Development in Drosophila." Genetics 145, no. 2 (1997): 311–23. http://dx.doi.org/10.1093/genetics/145.2.311.

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A study of polymorphism and species divergence of the dpp gene of Drosophila has been made. Eighteen lines from a population of D. melanogaster were sequenced for 5200 bp of the Hin region of the gene, coding for the dpp polypeptide. A comparison was made with sequence from D. simulans. Ninety-six silent polymorphisms and three amino acid replacement polymorphisms were found. The overall silent polymorphism (0.0247) is low, but haplotype diversity (0.0066 for effectively silent sites and 0.0054 for all sites) is in the range found for enzyme loci. Amino acid variation is absent in the N-termin

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4

Anderson, J. A., G. A. Churchill, J. E. Autrique, S. D. Tanksley, and M. E. Sorrells. "Optimizing parental selection for genetic linkage maps." Genome 36, no. 1 (1993): 181–86. http://dx.doi.org/10.1139/g93-024.

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Genetic linkage maps based on restriction fragment length polymorphisms are useful for many purposes; however, different populations are required to fulfill different objectives. Clones from the linkage map(s) are subsequently probed onto populations developed for special purposes such as gene tagging. Therefore, clones contained on the initial map(s) must be polymorphic on a wide range of genotypes to have maximum utility. The objectives of this research were to (i) calculate polymorphism information content values of 51 low-copy DNA clones and (ii) use the resulting values to choose potentia

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5

Gimelfarb, A. "Pleiotropy and multilocus polymorphisms." Genetics 130, no. 1 (1992): 223–27. http://dx.doi.org/10.1093/genetics/130.1.223.

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Abstract It is demonstrated that systems of two pleiotropically related characters controlled by additive diallelic loci can maintain under Gaussian stabilizing selection a stable polymorphism in more than two loci. It is also shown that such systems may have multiple stable polymorphic equilibria. Stabilizing selection generates negative linkage disequilibrium, as a result of which the equilibrium phenotypic variances are quite low, even though the level of allelic polymorphisms can be very high. Consequently, large amounts of additive genetic variation can be hidden in populations at equilib

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6

Dietrich, W., H. Katz, S. E. Lincoln, et al. "A genetic map of the mouse suitable for typing intraspecific crosses." Genetics 131, no. 2 (1992): 423–47. http://dx.doi.org/10.1093/genetics/131.2.423.

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Abstract We report the construction of a genetic linkage map of the mouse, consisting entirely of genetic markers that can be rapidly typed by polymerase chain reaction and that show a high degree of polymorphism among inbred laboratory strains. Specifically, the map contains 317 simple sequence length polymorphisms at an average spacing of 4.3 cM and is detectably linked to approximately 99% of the mouse genome. In typical crosses between inbred laboratory strains, about 50% of the markers are polymorphic, making it straightforward to follow inheritance in almost any cross.

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7

Woeste, Keith, Gale H. McGranahan, and Robert Bernatzky. "Randomly Amplified Polymorphic DNA Loci from a Walnut Backcross [(Juglans hindsii × J. regia) × J. regia]." Journal of the American Society for Horticultural Science 121, no. 3 (1996): 358–61. http://dx.doi.org/10.21273/jashs.121.3.358.

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Twenty-five random decamer primers were used to evaluate the level of polymorphism between Persian walnut and the Northern California black walnut. Sixty-six randomly amplified polymorphic DNA (RAPD) markers were identified using an interspecific walnut backcross population [(Juglans hindsii × J. regia) × J. regia]. Segregation data from these polymorphisms were joined to a previously published set of restriction fragment-length polymorphism (RFLP) marker data to expand the genetic map of walnut to 107 markers in 15 linkage groups.

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8

Gaut, B. S., and M. T. Clegg. "Nucleotide polymorphism in the Adh1 locus of pearl millet (Pennisetum glaucum) (Poaceae)." Genetics 135, no. 4 (1993): 1091–97. http://dx.doi.org/10.1093/genetics/135.4.1091.

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Abstract We investigated nucleotide polymorphism in the Adh1 locus of pearl millet (Pennisetum glaucum) (Poaceae) by determining the DNA sequence of 20 alleles from 10 individuals. The individuals were sampled from throughout pearl millet's indigenous range and represent both wild and cultivated accessions. Our results indicated that there is little nucleotide polymorphism in the Adh1 locus. Estimates of per site nucleotide polymorphism did not differ significantly between cultivated and wild millet accessions. We compared nucleotide polymorphism in pearl millet Adh1 with nucleotide polymorphi

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9

Escalante, Ananias A., Altaf A. Lal, and Francisco J. Ayala. "Genetic Polymorphism and Natural Selection in the Malaria Parasite Plasmodium falciparum." Genetics 149, no. 1 (1998): 189–202. http://dx.doi.org/10.1093/genetics/149.1.189.

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Abstract We have studied the genetic polymorphism at 10 Plasmodium falciparum loci that are considered potential targets for specific antimalarial vaccines. The polymorphism is unevenly distributed among the loci; loci encoding proteins expressed on the surface of the sporozoite or the merozoite (AMA-1, CSP, LSA-1, MSP-1, MSP-2, and MSP-3) are more polymorphic than those expressed during the sexual stages or inside the parasite (EBA-175, Pfs25, PF48/45, and RAP-1). Comparison of synonymous and nonsynonymous substitutions indicates that natural selection may account for the polymorphism observe

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10

Kumar, Sanjay. "Studies on efficiency of RAPD primers in developing molecular profiles for genetic purity studies in soybean (Glycine max L.) cultivars." Genetika 46, no. 3 (2014): 681–92. http://dx.doi.org/10.2298/gensr1403681k.

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Major advances have recently been made in our understanding of soybean genetics and of the application of new technologies to soybean improvement. Estimates of genetic relationships on the basis of the enzymes and molecular markers have been shown to be consistent with expectations based on origin and pedigree information. To identify efficient markers, that are to be used for genetic purity studies, polymorphism is the basic criterion. RAPD has been found to be an effective and efficient tool to evaluate and reveal genetic polymorphism in several crop species. In present study a total of 80 R

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11

Holland, J. B., S. J. Helland, N. Sharopova, and D. C. Rhyne. "Polymorphism of PCR-based markers targeting exons, introns, promoter regions, and SSRs in maize and introns and repeat sequences in oat." Genome 44, no. 6 (2001): 1065–76. http://dx.doi.org/10.1139/g01-110.

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Sequence databases could be efficiently exploited for development of DNA markers if it were known which gene regions reveal the most polymorphism when amplified by PCR. We developed PCR primer pairs that target specific regions of previously sequenced genes from Avena and Zea species. Primers were targeted to amplify 40 introns, 24 exons, and 23 promoter regions within 54 maize genes. We surveyed 48 maize inbred lines (previously assayed for simple-sequence repeat (SSR) polymorphism) for amplification-product polymorphism. We also developed primers to target 14 SSRs and 12 introns within 18 Av

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12

Riley, M. A., M. E. Hallas, and R. C. Lewontin. "Distinguishing the forces controlling genetic variation at the Xdh locus in Drosophila pseudoobscura." Genetics 123, no. 2 (1989): 359–69. http://dx.doi.org/10.1093/genetics/123.2.359.

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Abstract Fifty-eight isochromosomal lines sampled from two natural populations of Drosophila pseudoobscura in California and one from Bogota, Colombia, were examined using four-cutter restriction mapping. A 4.6-kb region of the xanthine dehydrogenase locus was probed and 66 of 135 restriction sites scored were polymorphic. This predicts that on average every 12th bp would be polymorphic in this region for the genes surveyed if polymorphism occurred randomly along the coding region. In addition, there were 12 insertion/deletion polymorphisms. Forty-nine distinct haplotypes were recognized in th

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13

Alvarez, Gonzalo, and Carlos Zapata. "Conditions for Protected Inversion Polymorphism Under Supergene Selection." Genetics 146, no. 2 (1997): 717–22. http://dx.doi.org/10.1093/genetics/146.2.717.

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Conditions for protected inversion polymorphism under the operation of both karyotype and supergene selection in a viability model have been analytically determined. When supergene selection (the effect of recombination in homokaryotypes lowering the mean fitness of their offspring) is acting on gene arrangements and there is no karyotype selection, it is demonstrated that a polymorphic stable equilibrium is reached by the population, which is a function of only the recombination effects in homokaryotypes. Under both supergene and karyotype selection the degree of dominance (h) of karyotype se

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14

Laurie, C. C., and L. F. Stam. "The effect of an intronic polymorphism on alcohol dehydrogenase expression in Drosophila melanogaster." Genetics 138, no. 2 (1994): 379–85. http://dx.doi.org/10.1093/genetics/138.2.379.

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Abstract Several lines of evidence indicate that natural selection controls the frequencies of an allozyme polymorphism at the alcohol dehydrogenase (Adh) locus in Drosophila melanogaster. However, because of associations among sequence polymorphisms in the Adh region, it is not clear whether selection acts directly (or solely) on the allozymic site. This problem has been approached by using in vitro mutagenesis to distinguish among the effects on Adh expression of individual polymorphisms. This study shows that a polymorphism within the first Adh intron (delta 1) has a significant effect on t

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15

Verrelli, Brian C., and Walter F. Eanes. "Clinal Variation for Amino Acid Polymorphisms at thePgmLocus inDrosophila melanogaster." Genetics 157, no. 4 (2001): 1649–63. http://dx.doi.org/10.1093/genetics/157.4.1649.

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AbstractClinal variation is common for enzymes in the glycolytic pathway for Drosophila melanogaster and is generally accepted as an adaptive response to different climates. Although the enzyme phosphoglucomutase (PGM) possesses several allozyme polymorphisms, it is unique in that it had been reported to show no clinal variation. Our recent DNA sequence investigation of Pgm found extensive cryptic amino acid polymorphism segregating with the allozyme alleles. In this study, we characterize the geographic variation of Pgm amino acid polymorphisms at the nucleotide level along a latitudinal clin

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16

Tian, Ruizheng, Cunhuan Zhang, Yixiao Huang, Xin Guo, and Maohua Chen. "A Novel Software and Method for the Efficient Development of Polymorphic SSR Loci Based on Transcriptome Data." Genes 10, no. 11 (2019): 917. http://dx.doi.org/10.3390/genes10110917.

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Traditional methods for developing polymorphic microsatellite loci without reference sequences are time-consuming and labor-intensive, and the polymorphisms of simple sequence repeat (SSR) loci developed from expressed sequence tag (EST) databases are generally poor. To address this issue, in this study, we developed a new software (PSSRdt) and established an effective method for directly obtaining polymorphism details of SSR loci by analyzing diverse transcriptome data. The new method includes three steps, raw data processing, PSSRdt application, and loci extraction and verification. To test

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17

Laurie, C. C., J. T. Bridgham, and M. Choudhary. "Associations between DNA sequence variation and variation in expression of the Adh gene in natural populations of Drosophila melanogaster." Genetics 129, no. 2 (1991): 489–99. http://dx.doi.org/10.1093/genetics/129.2.489.

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Abstract A large part of the genetic variation in alcohol dehydrogenase (ADH) activity level in natural populations of Drosophila melanogaster is associated with segregation of an amino acid replacement polymorphism at nucleotide 1490, which generates a difference in electrophoretic mobility. Part of the allozymic difference in activity level is due to a catalytic efficiency difference, which is also caused by the amino acid replacement, and part is due to a difference in the concentration of ADH protein. A previous site-directed in vitro mutagenesis experiment clearly demonstrated that the am

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18

Game, A. Y., and J. G. Oakeshott. "Associations between restriction site polymorphism and enzyme activity variation for esterase 6 in Drosophila melanogaster." Genetics 126, no. 4 (1990): 1021–31. http://dx.doi.org/10.1093/genetics/126.4.1021.

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Abstract Thirty-five nucleotide polymorphisms were found in a 21.5-kbp region including the Est6 locus among 42 isoallelic lines extracted from a single natural population of Drosophila melanogaster. The heterozygosity per nucleotide pair was estimated to be 0.010 overall, but was lower in sequences hybridizing to transcripts than in those not hybridizing to transcripts. Eleven of 36 pairwise comparisons among the nine most common polymorphisms showed significant gametic disequilibrium. Four of these polymorphisms were also significantly associated with the major EST6-F/EST6-S allozyme polymor

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Peng, T. X., A. Moya, and F. J. Ayala. "Two modes of balancing selection in Drosophila melanogaster: overcompensation and overdominance." Genetics 128, no. 2 (1991): 381–91. http://dx.doi.org/10.1093/genetics/128.2.381.

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Abstract Overdominance is often invoked to account for the extensive polymorphisms found in natural populations of organisms; overcompensation, however, may be equally or more important. Overcompensation occurs when limiting resources are better exploited by a genetically mixed than by a uniform population, and is often causally related to frequency-dependent selection. We have designed experiments to test whether overcompensation occurs in Drosophila melanogaster, using the Sod locus as a marker. Tests are made at each of two densities and two temperatures for cultures with desired genetic co

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20

Dong, J., and D. B. Wagner. "Paternally inherited chloroplast polymorphism in Pinus: estimation of diversity and population subdivision, and tests of disequilibrium with a maternally inherited mitochondrial polymorphism." Genetics 136, no. 3 (1994): 1187–94. http://dx.doi.org/10.1093/genetics/136.3.1187.

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Abstract We have surveyed a chloroplast DNA restriction fragment length polymorphism in 745 individuals, distributed rangewide in eight allopatric natural populations of jack pine (Pinus banksiana Lamb.) and eight allopatric natural populations of lodgepole pine (Pinus contorta Dougl.). The polymorphic region of the chloroplast genome is located near duplicated psbA genes. Fourteen length variants were found in the survey, and these variants distinguished the two species qualitatively. Variant diversities were high in both species (hes = 0.43 in jack pine; hes = 0.44 in lodgepole pine). Popula

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Schmid, Karl J., Loredana Nigro, Charles F. Aquadro, and Diethard Tautz. "Large Number of Replacement Polymorphisms in Rapidly Evolving Genes of Drosophila: Implications for Genome-Wide Surveys of DNA Polymorphism." Genetics 153, no. 4 (1999): 1717–29. http://dx.doi.org/10.1093/genetics/153.4.1717.

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AbstractWe present a survey of nucleotide polymorphism of three novel, rapidly evolving genes in populations of Drosophila melanogaster and D. simulans. Levels of silent polymorphism are comparable to other loci, but the number of replacement polymorphisms is higher than that in most other genes surveyed in D. melanogaster and D. simulans. Tests of neutrality fail to reject neutral evolution with one exception. This concerns a gene located in a region of high recombination rate in D. simulans and in a region of low recombination rate in D. melanogaster, due to an inversion. In the latter case

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22

Verrelli, Brian C., and Walter F. Eanes. "Extensive Amino Acid Polymorphism at the Pgm Locus Is Consistent With Adaptive Protein Evolution in Drosophila melanogaster." Genetics 156, no. 4 (2000): 1737–52. http://dx.doi.org/10.1093/genetics/156.4.1737.

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Abstract PGM plays a central role in the glycolytic pathway at the branch point leading to glycogen metabolism and is highly polymorphic in allozyme studies of many species. We have characterized the nucleotide diversity across the Pgm gene in Drosophila melanogaster and D. simulans to investigate the role that protein polymorphism plays at this crucial metabolic branch point shared with several other enzymes. Although D. melanogaster and D. simulans share common allozyme mobility alleles, we find these allozymes are the result of many different amino acid changes at the nucleotide level. In a

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Gra, O., Zh Kozhekbaeva, O. Makarova, E. Samochatova, and T. Nasedkina. "Polymorphism of Biotransformation Genes and Risk of Relapse in Childhood Acute Leukemia." Balkan Journal of Medical Genetics 12, no. 1 (2009): 21–35. http://dx.doi.org/10.2478/v10034-009-0008-6.

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Polymorphism of Biotransformation Genes and Risk of Relapse in Childhood Acute LeukemiaLeukemia is a hematological malignancy that involves bone marrow. Polymorphism of biotransformation genes plays an important role in primary childhood leukemia and affects the incidence and character of acute leukemia relapse. A biochip designed to assess some polymorphisms of biotransformation genes was used to determine the frequency of the polymorphic variants ofCYP1A1, CYP2D6, GSTT1, GSTM1, MTHFR, MTRR, NQO1, CYP2C9, CYP2C19andNAT2in 332 children with acute lymphoblastic leukemia (ALL) and 71 children wi

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Takahata, N., and M. Nei. "Allelic genealogy under overdominant and frequency-dependent selection and polymorphism of major histocompatibility complex loci." Genetics 124, no. 4 (1990): 967–78. http://dx.doi.org/10.1093/genetics/124.4.967.

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Abstract To explain the long-term persistence of polymorphic alleles (trans-specific polymorphism) at the major histocompatibility complex (MHC) loci in rodents and primates, a computer simulation study was conducted about the coalescence time of different alleles sampled under various forms of selection. At the same time, average heterozygosity, the number of alleles in a sample, and the rate of codon substitution were examined to explain the mechanism of maintenance of polymorphism at the MHC loci. The results obtained are as follows. (1) The coalescence time for neutral alleles is too short

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Spencer, H. G., and R. W. Marks. "The maintenance of single-locus polymorphism. I. Numerical studies of a viability selection model." Genetics 120, no. 2 (1988): 605–13. http://dx.doi.org/10.1093/genetics/120.2.605.

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Abstract The ability of viability selection to maintain single-locus polymorphism is investigated with two models in which the population is bombarded with a series of mutations with random fitnesses. In the first model, the population is allowed to reach equilibrium before mutation resumes; in the second the iterations and mutation occur simultaneously. Monte Carlo simulations of these models show that viability selection is easily able to maintain stable 6- or 7-allele polymorphisms and that monomorphisms and diallelic polymorphisms are uncommon. The question of how monomorphisms arise is al

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Hasson, Esteban, and Walter F. Eanes. "Contrasting Histories of Three Gene Regions Associated With In(3L)Payne of Drosophila melanogaster." Genetics 144, no. 4 (1996): 1565–75. http://dx.doi.org/10.1093/genetics/144.4.1565.

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In the present report, we studied nucleotide variation in three gene regions of Drosophila melanogaster, spanning &gt;5 kb and showing different degrees of association with the cosmopolitan inversion In(3-L)Payne. The analysis of sequence variation in the regions surrounding the breakpoints and the heat shock 83 (Hsp83) gene locus, located close to the distal breakpoint, revealed the absence of shared polymorphisms and the presence of a number of fixed differences between arrangements, indicating absence of genetic exchange. In contrast, for the esterase-6 gene region, located in the cente

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Labate, J., and W. F. Eanes. "Direct measurement of in vivo flux differences between electrophoretic variants of G6PD from Drosophila melanogaster." Genetics 132, no. 3 (1992): 783–87. http://dx.doi.org/10.1093/genetics/132.3.783.

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Abstract Demonstrating that naturally occurring enzyme polymorphisms significantly impact metabolic pathway flux is a fundamental step in examining the possible adaptive significance of such polymorphisms. In earlier studies of the glucose-6-phosphate dehydrogenase (G6PD) polymorphism in Drosophila melanogaster, we used two different methods, exploiting both genotype-dependent interactions with the 6Pgd locus, and conventional steady-state kinetics to examine activity differences between the two common allozymes. In this report we use 1-14C- and 6-14C-labeled glucose to estimate directly genot

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Ravel, Catherine, Sébastien Praud, Alain Murigneux, et al. "Single-nucleotide polymorphism frequency in a set of selected lines of bread wheat (Triticum aestivum L.)." Genome 49, no. 9 (2006): 1131–39. http://dx.doi.org/10.1139/g06-067.

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Information on single-nucleotide polymorphisms (SNPs) in hexaploid bread wheat is still scarce. The goal of this study was to detect SNPs in wheat and examine their frequency. Twenty-six bread wheat lines from different origins worldwide were used. Specific PCR-products were obtained from 21 genes and directly sequenced. SNPs were discovered from the alignment of these sequences. The overall sequence polymorphism observed in this sample appears to be low; 64 single-base polymorphisms were detected in ~21.5 kb (i.e., 1 SNP every 335 bp). The level of polymorphism is highly variable among the di

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Aidinidou, L., A. Chatzikyriakidou, A. Giannopoulos, et al. "Association of NFKB1, NKX2-5, GATA4 and RANKL gene polymorphisms with sporadic congenital heart disease in Greek patients." Balkan Journal of Medical Genetics 24, no. 1 (2021): 15–20. http://dx.doi.org/10.2478/bjmg-2021-0014.

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Abstract Congenital heart disease (CHD) is a group of structural defects of the heart and the great vessels, and one of the leading causes of death among infants and young adults. Several gene variants are involved in diverse mechanisms of cardiac and vessel development and could thus be considered candidate mutated genes for a congenital heart defect or a specific variant could predispose a person to CHD. In the present study, variants in four such genes are investigated for the first time in a group of young Greek CHD patients: the NFKB1 gene polymorphism (–94ins/ delATTG), rs28362491, NKX2-

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Janssen, Kirstin, Jan Ove Bustnes, and Nicholas I. Mundy. "Variation in Genetic Mechanisms for Plumage Polymorphism in Skuas (Stercorarius)." Journal of Heredity 112, no. 5 (2021): 430–35. http://dx.doi.org/10.1093/jhered/esab038.

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Abstract Coloration is evolutionarily labile and so provides an excellent trait for examining the repeatability of evolution. Here, we investigate the repeatability of the evolution of polymorphic variation in ventral plumage coloration in skuas (Stercorarius: Stercorariidae). In 2 species, arctic (S. parasiticus) and pomarine skuas (S. pomarinus), plumage polymorphism was previously shown to be associated with coding changes at the melanocortin-1 receptor (MC1R) locus. Here, we show that polymorphism in a third species, the south polar skua (S. maccormicki), is not associated with coding vari

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Misawa, Kazuharu, and Fumio Tajima. "Estimation of the Amount of DNA Polymorphism When the Neutral Mutation Rate Varies Among Sites." Genetics 147, no. 4 (1997): 1959–64. http://dx.doi.org/10.1093/genetics/147.4.1959.

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Abstract Knowing the amount of DNA polymorphism is essential to understand the mechanism of maintaining DNA polymorphism in a natural population. The amount of DNA polymorphism can be measured by the average number of nucleotide differences per site (π), the proportion of segregating (polymorphic) site (s) and the minimum number of mutations per site (s*). Since the latter two quantities depend on the sample size, θ is often used as a measure of the amount of DNA polymorphism, where θ = 4Nμ, N is the effective population size and μ is the neutral mutation rate per site per generation. It is kn

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Timmermans, Marja C. P., O. Prem Das, and Joachim Messing. "Characterization of a Meiotic Crossover in Maize Identified by a Restriction Fragment Length Polymorphism-Based Method." Genetics 143, no. 4 (1996): 1771–83. http://dx.doi.org/10.1093/genetics/143.4.1771.

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Abstract Genetic map lengths do not correlate directly with genome size, suggesting that meiotic recombination is not uniform throughout the genome. Further, the abundance of repeated sequences in plant genomes requires that crossing over is restricted to particular genomic regions. We used a physical mapping approach to identify these regions without the bias introduced by phenotypic selection. This approach is based on the detection of nonparental polymorphisms formed by recombination between polymorphic alleles. In an F2 population of 48 maize plants, we identified a crossover at two of the

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Long, Anthony D., Richard F. Lyman, Alison H. Morgan, Charles H. Langley, and Trudy F. C. Mackay. "Both Naturally Occurring Insertions of Transposable Elements and Intermediate Frequency Polymorphisms at the achaete-scute Complex Are Associated With Variation in Bristle Number in Drosophila melanogaster." Genetics 154, no. 3 (2000): 1255–69. http://dx.doi.org/10.1093/genetics/154.3.1255.

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Abstract A restriction enzyme survey of a 110-kb region including the achaete scute complex (ASC) examined 14 polymorphic molecular markers in a sample of 56 naturally occurring chromosomes. Large insertions as a class were associated with a reduction in both sternopleural and abdominal bristle number, supporting deleterious mutation-selection equilibrium models for the maintenance of quantitative genetic variation. Two polymorphic sites were independently associated with variation in bristle number measured in two genetic backgrounds as assessed by a permutation test. A 6-bp deletion near sc

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Li, Ximei, Daojun Yuan, Hantao Wang, et al. "Increasing cotton genome coverage with polymorphic SSRs as revealed by SSCP." Genome 55, no. 6 (2012): 459–70. http://dx.doi.org/10.1139/g2012-032.

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Simple sequence repeat (SSR) markers are widely used in plant genetics and breeding. However, there are many SSR markers that do not reveal polymorphism in cotton. Traditional SSR genotyping methods only provide information on product sizes. This leaves many marker polymorphism undetected, thus, lowering the utility of SSRs. In the present study, monomorphic SSRs between two mapping parents, ‘Emian22’ and 3-79, were subjected to single-strand conformation polymorphism (SSCP) analysis to reveal polymorphism. Of the 4194 monomorphic SSR primer pairs, 158 pairs (3.77%) showed polymorphism and rev

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Balakirev, Evgeniy S., and Francisco J. Ayala. "Nucleotide Variation in the tinman and bagpipe Homeobox Genes of Drosophila melanogaster." Genetics 166, no. 4 (2004): 1845–56. http://dx.doi.org/10.1093/genetics/166.4.1845.

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Abstract The tinman (tin) and bagpipe (bap) genes are members of the NK homeobox gene family of Drosophila, so that tin occupies a higher position than bap in the regulatory hierarchy. Little is known about the level and pattern of genetic polymorphism in homeobox genes. We have analyzed nucleotide polymorphism in 27 strains of Drosophila melanogaster and one each of D. simulans and D. sechellia, within two closely linked regions encompassing a partial sequence of tin and the complete sequence of bap. The two genes exhibit different levels and patterns of nucleotide diversity. Two sets of shar

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Grauke, L. J., T. E. Thompson, and A. S. Reddy. "AFLPs in Pecan Genetics Research." HortScience 33, no. 3 (1998): 527b—527. http://dx.doi.org/10.21273/hortsci.33.3.527b.

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Procedures were refined for extraction and amplification of DNA from pecan [Carya illinoinensis (Wangenh.) K. Koch] leaf tissue. Genomic DNA was extracted from leaf tissue from multiple inventories of `Wichita' and `Pawnee' and processed for Amplified Fragment Length Polymorphism (AFLPs). Using only four AFLP primers, 26 polymorphisms were identified, verifying the reproducibility and consistency of amplification. The application and limitation of the procedure for separating genotypes will be discussed. Twenty-four cultivars and seedlings representing the geographic range of the species were

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Kesseli, R. V., I. Paran, and R. W. Michelmore. "Analysis of a detailed genetic linkage map of Lactuca sativa (lettuce) constructed from RFLP and RAPD markers." Genetics 136, no. 4 (1994): 1435–46. http://dx.doi.org/10.1093/genetics/136.4.1435.

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Abstract A detailed genetic map has been constructed from the F2 population of a single intraspecific cross of Lactuca sativa (n = 9). It comprises 319 loci, including 152 restriction fragment length polymorphism (RFLP), 130 random amplified polymorphic DNA (RAPD), 7 isozyme, 19 disease resistance, and 11 morphological markers. Thirteen major, four minor linkage groups and several unlinked markers are identified for this genome which is estimated to be approximately 1950 cM. RFLP and RAPD markers show similar distributions throughout the genome and identified similar levels of polymorphism. RA

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Verrelli, Brian C., and Walter F. Eanes. "The Functional Impact ofPgmAmino Acid Polymorphism on Glycogen Content inDrosophila melanogaster." Genetics 159, no. 1 (2001): 201–10. http://dx.doi.org/10.1093/genetics/159.1.201.

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AbstractEarlier studies of the common PGM allozymes in Drosophila melanogaster reported no in vitro activity differences. However, our study of nucleotide variation observed that PGM allozymes are a heterogeneous mixture of amino acid polymorphisms. In this study, we analyze 10 PGM protein haplotypes with respect to PGM activity, thermostability, and adult glycogen content. We find a twofold difference in activity among PGM protein haplotypes that is associated with a threefold difference in glycogen content. The latitudinal clines for several Pgm amino acid polymorphisms show that high PGM ac

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Rosenzweig, R. F., R. R. Sharp, D. S. Treves, and J. Adams. "Microbial evolution in a simple unstructured environment: genetic differentiation in Escherichia coli." Genetics 137, no. 4 (1994): 903–17. http://dx.doi.org/10.1093/genetics/137.4.903.

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Abstract Populations of Escherichia coli initiated with a single clone and maintained for long periods in glucose-limited continuous culture, become polymorphic. In one population, three clones were isolated and by means of reconstruction experiments were shown to be maintained in stable polymorphism, although they exhibited substantial differences in maximum specific growth rates and in glucose uptake kinetics. Analysis of these three clones revealed that their stable coexistence could be explained by differential patterns of the secretion and uptake of two alternative metabolites acetate and

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Verloop, Herman, Olaf M. Dekkers, Robin P. Peeters, Jan W. Schoones, and Johannes W. A. Smit. "GENETICS IN ENDOCRINOLOGY: Genetic variation in deiodinases: a systematic review of potential clinical effects in humans." European Journal of Endocrinology 171, no. 3 (2014): R123—R135. http://dx.doi.org/10.1530/eje-14-0302.

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Iodothyronine deiodinases represent a family of selenoproteins involved in peripheral and local homeostasis of thyroid hormone action. Deiodinases are expressed in multiple organs and thyroid hormone affects numerous biological systems, thus genetic variation in deiodinases may affect multiple clinical endpoints. Interest in clinical effects of genetic variation in deiodinases has clearly increased. We aimed to provide an overview for the role of deiodinase polymorphisms in human physiology and morbidity. In this systematic review, studies evaluating the relationship between deiodinase polymor

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Levi, Amnon, Claude E. Thomas, M. Newman, O. U. K. Reddy, X. Zhang, and Y. Xu. "ISSR and AFLP Markers Differ among American Watermelon Cultivars with Limited Genetic Diversity." Journal of the American Society for Horticultural Science 129, no. 4 (2004): 553–58. http://dx.doi.org/10.21273/jashs.129.4.0553.

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Wide phenotypic diversity exists among American heirloom cultivars of watermelon (Citrullus lanatus var. lanatus). However, in published studies, low or no polymorphism was revealed among those heirlooms using isozyme or randomly amplified polymorphic DNA (RAPD) markers. In this study, experiments with inter-simple sequence repeat (ISSR) [also known as simple sequence repeat-(SSR-) anchored primers] and amplified fragment-length polymorphism (AFLP) markers produced high polymorphisms among watermelon heirloom cultivars. ISSR (111) and AFLP (118) markers (229 total) identified 80.2% to 97.8% ge

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Broughton, Richard E., and Richard G. Harrison. "Nuclear Gene Genealogies Reveal Historical, Demographic and Selective Factors Associated With Speciation in Field Crickets." Genetics 163, no. 4 (2003): 1389–401. http://dx.doi.org/10.1093/genetics/163.4.1389.

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Abstract Population genetics theory predicts that genetic drift should eliminate shared polymorphism, leading to monophyly or exclusivity of populations, when the elapsed time between lineage-splitting events is large relative to effective population size. We examined patterns of nucleotide variation in introns at four nuclear loci to relate processes affecting the history of genes to patterns of divergence among natural populations and species. Ancestral polymorphisms were shared among three recognized species, Gryllus firmus, G. pennsylvanicus, and G. ovisopis, and genealogical patterns sugg

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Kado, Tomoyuki, Hiroshi Yoshimaru, Yoshihiko Tsumura, and Hidenori Tachida. "DNA Variation in a Conifer,Cryptomeria japonica(Cupressaceae sensu lato)." Genetics 164, no. 4 (2003): 1547–59. http://dx.doi.org/10.1093/genetics/164.4.1547.

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AbstractWe investigated the nucleotide variation of a conifer, Cryptomeria japonica, and the divergence between this species and its closest relative, Taxodium distichum, at seven nuclear loci (Acl5, Chi1, Ferr, GapC, HemA, Lcyb, and Pat). Samples of C. japonica were collected from three areas, Kantou-Toukai, Hokuriku, and Iwate. No apparent geographic differentiation was found among these samples. However, the frequency spectrum of the nucleotide polymorphism revealed excesses of intermediate-frequency variants, which suggests that the population was not panmictic and a constant size in the p

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Aguadé, Montserrat. "Positive Selection Drives the Evolution of the Acp29AB Accessory Gland Protein in Drosophila." Genetics 152, no. 2 (1999): 543–51. http://dx.doi.org/10.1093/genetics/152.2.543.

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Abstract Nucleotide sequence variation at the Acp29AB gene region has been surveyed in Drosophila melanogaster from Spain (12 lines), Ivory Coast (14 lines), and Malawi (13 lines) and in one line of D. simulans. The ∼1.7-kb region studied encompasses the Acp29AB gene that codes for a male accessory gland protein and its flanking regions. Seventy-seven nucleotide and 8 length polymorphisms were detected. Nonsynonymous polymorphism was an order of magnitude lower than synonymous polymorphism, but still high relative to other non-sex-related genes. In D. melanogaster variation at this region reve

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Yao, Jianbo, Samuel E. Aggrey, David Zadworny, J. Flan Hayes, and Urs Kühnlein. "Sequence Variations in the Bovine Growth Hormone Gene Characterized by Single-Strand Conformation Polymorphism (SSCP) Analysis and Their Association with Milk Production Traits in Holsteins." Genetics 144, no. 4 (1996): 1809–16. http://dx.doi.org/10.1093/genetics/144.4.1809.

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Sequence variations in the bovine growth hormone (GH) gene were investigated by single strand conformation polymorphism (SSCP) analysis of seven amplified fragments covering almost the entire gene (2.7 kb). SSCPs were detected in four of these fragments and a total of six polymorphisms were found in a sample of 128 Holstein bulls. Two polymorphisms, a T→C transition in the third intron (designated GH4.1) and an A→C transversion in the fifth exon (designated GH6.2), were shown to be associated with milk production traits. GH4.1c/GH4.1c bulls had higher milk yield than GH4.1c/GH4.1t (P ≤ 0.005)

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King, Lynn Mertens. "The Role of Gene Conversion in Determining Sequence Variation and Divergence in the Est-5 Gene Family in Drosophila pseudoobscura." Genetics 148, no. 1 (1998): 305–15. http://dx.doi.org/10.1093/genetics/148.1.305.

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Abstract Nucleotide sequences of eight Est-5A and Est-5C genes corresponding to previously sequenced Est-5B genes in Drosophila pseudoobscura were determined to compare patterns of polymorphism and divergence among members of this small gene family. The three esterase genes were also sequenced from D. persimilis and D. miranda for interspecific comparisons. The data provide evidence that gene conversion between loci contributes to polymorphism and to the homogenization of the Est-5 genes. For Est-5B, which encodes one of the most highly polymorphic proteins in Drosophila, 12% of the segregatin

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SINGH, PRANVEER, and B. N. SINGH. "Population genetics of Drosophila ananassae: genetic differentiation among Indian natural populations at the level of inversion polymorphism." Genetical Research 89, no. 4 (2007): 191–99. http://dx.doi.org/10.1017/s0016672307008890.

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SummaryThe present study, which is one of the longest temporal (two decades) and largest spatial (different parts of India covered) investigations on inversion polymorphism in natural populations of D. ananassae, was undertaken to understand the dynamics of inversion polymorphism in a broad and comprehensive manner. Forty-five natural populations from different ecogeographic regions of the country (covering the regions from Kashmir to Kanniyakumari and Gujarat to Nagaland) were analysed for chromosomal inversions. All the populations show the presence of the three cosmopolitan inversions, freq

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Sousa, João Adriano, Maria Isabel Mendonça, Marco Serrão, et al. "Epicardial Adipose Tissue: The Genetics Behind an Emerging Cardiovascular Risk Marker." Clinical Medicine Insights: Cardiology 15 (January 2021): 117954682110292. http://dx.doi.org/10.1177/11795468211029244.

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Evidence points epicardial adipose tissue (EAT) as an emerging cardiovascular risk marker. Whether genetic polymorphisms linked with atherosclerosis are associated with higher EAT is still unknown. We aim to assess the role of genetic burden of atherosclerosis and its association to EAT in a cohort of asymptomatic individuals without coronary disease. A total of 996 participants were prospectively enrolled in a single Portuguese center. EAT volume was measured by Cardiac Computed Tomography and participants were distributed into 2 groups, above and below median EAT. SNPs were genotyped and lin

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Aguade, M. "Restriction map variation at the adh locus of Drosophila melanogaster in inverted and noninverted chromosomes." Genetics 119, no. 1 (1988): 135–40. http://dx.doi.org/10.1093/genetics/119.1.135.

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Abstract Restriction map variation among 39 Standard and 40 In(2L)t chromosomes extracted from a Spanish natural population of Drosophila melanogaster was investigated for a 2.7-kb region encompassing the Adh locus with ten four-cutter restriction enzymes. A total of 20 polymorphisms were detected, representing 15 restriction site polymorphisms, 4 length polymorphisms and the allozyme polymorphism. Variation at the DNA level was compared among St-Adh(F), St-Adh(S) and t-Adh(S) chromosomes. t-Adh(S) chromosomes show a higher level of variation than St-Adh(F) chromosomes. This suggests that In(2

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Vadva, Larsen, Propp, Trautwein, Alford, and Alper. "A New Pedigree-Based SNP Haplotype Method for Genomic Polymorphism and Genetic Studies." Cells 8, no. 8 (2019): 835. http://dx.doi.org/10.3390/cells8080835.

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Single nucleotide polymorphisms (SNPs) are usually the most frequent genomic variants. Directly pedigree-phased multi-SNP haplotypes provide a more accurate view of polymorphic population genomic structure than individual SNPs. The former are, therefore, more useful in genetic correlation with subject phenotype. We describe a new pedigree-based methodology for generating non-ambiguous SNP haplotypes for genetic study. SNP data for haplotype analysis were extracted from a larger Type 1 Diabetes Genetics Consortium SNP dataset based on minor allele frequency variation and redundancy, coverage ra

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