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Seyedsharifi R, Badbarin S, Seifdavati J, Hedayat-Evrigh N, Mariezcurrena-Berasain MA, Salem AZ. Influence of quantitative trait loci on growth traits of chromosome 1 in Sanjabi lambs during the first year of growth. Small Rumin Res 2021. [DOI: 10.1016/j.smallrumres.2020.106280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Conserved Genetic Architecture Underlying Individual Recombination Rate Variation in a Wild Population of Soay Sheep (Ovis aries). Genetics 2016; 203:583-98. [PMID: 27029733 PMCID: PMC4858801 DOI: 10.1534/genetics.115.185553] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 03/11/2016] [Indexed: 02/06/2023] Open
Abstract
Meiotic recombination breaks down linkage disequilibrium (LD) and forms new haplotypes, meaning that it is an important driver of diversity in eukaryotic genomes. Understanding the causes of variation in recombination rate is important in interpreting and predicting evolutionary phenomena and in understanding the potential of a population to respond to selection. However, despite attention in model systems, there remains little data on how recombination rate varies at the individual level in natural populations. Here we used extensive pedigree and high-density SNP information in a wild population of Soay sheep (Ovis aries) to investigate the genetic architecture of individual autosomal recombination rates. Individual rates were high relative to other mammal systems and were higher in males than in females (autosomal map lengths of 3748 and 2860 cM, respectively). The heritability of autosomal recombination rate was low but significant in both sexes (h2 = 0.16 and 0.12 in females and males, respectively). In females, 46.7% of the heritable variation was explained by a subtelomeric region on chromosome 6; a genome-wide association study showed the strongest associations at locus RNF212, with further associations observed at a nearby ∼374-kb region of complete LD containing three additional candidate loci, CPLX1, GAK, and PCGF3. A second region on chromosome 7 containing REC8 and RNF212B explained 26.2% of the heritable variation in recombination rate in both sexes. Comparative analyses with 40 other sheep breeds showed that haplotypes associated with recombination rates are both old and globally distributed. Both regions have been implicated in rate variation in mice, cattle, and humans, suggesting a common genetic architecture of recombination rate variation in mammals.
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Castaño-Sánchez C, Fuji K, Ozaki A, Hasegawa O, Sakamoto T, Morishima K, Nakayama I, Fujiwara A, Masaoka T, Okamoto H, Hayashida K, Tagami M, Kawai J, Hayashizaki Y, Okamoto N. A second generation genetic linkage map of Japanese flounder (Paralichthys olivaceus). BMC Genomics 2010; 11:554. [PMID: 20937088 PMCID: PMC3091703 DOI: 10.1186/1471-2164-11-554] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2010] [Accepted: 10/11/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Japanese flounder (Paralichthys olivaceus) is one of the most economically important marine species in Northeast Asia. Information on genetic markers associated with quantitative trait loci (QTL) can be used in breeding programs to identify and select individuals carrying desired traits. Commercial production of Japanese flounder could be increased by developing disease-resistant fish and improving commercially important traits. Previous maps have been constructed with AFLP markers and a limited number of microsatellite markers. In this study, improved genetic linkage maps are presented. In contrast with previous studies, these maps were built mainly with a large number of codominant markers so they can potentially be used to analyze different families and populations. RESULTS Sex-specific genetic linkage maps were constructed for the Japanese flounder including a total of 1,375 markers [1,268 microsatellites, 105 single nucleotide polymorphisms (SNPs) and two genes]; 1,167 markers are linked to the male map and 1,067 markers are linked to the female map. The lengths of the male and female maps are 1,147.7 cM and 833.8 cM, respectively. Based on estimations of map lengths, the female and male maps covered 79 and 82% of the genome, respectively. Recombination ratio in the new maps revealed F:M of 1:0.7. All linkage groups in the maps presented large differences in the location of sex-specific recombination hot-spots. CONCLUSIONS The improved genetic linkage maps are very useful for QTL analyses and marker-assisted selection (MAS) breeding programs for economically important traits in Japanese flounder. In addition, SNP flanking sequences were blasted against Tetraodon nigroviridis (puffer fish) and Danio rerio (zebrafish), and synteny analysis has been carried out. The ability to detect synteny among species or genera based on homology analysis of SNP flanking sequences may provide opportunities to complement initial QTL experiments with candidate gene approaches from homologous chromosomal locations identified in related model organisms.
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Affiliation(s)
- Cecilia Castaño-Sánchez
- Faculty of Marine Science, Tokyo University of Marine Science and Technology, Minato, Tokyo, Japan
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Wong AK, Ruhe AL, Dumont BL, Robertson KR, Guerrero G, Shull SM, Ziegle JS, Millon LV, Broman KW, Payseur BA, Neff MW. A comprehensive linkage map of the dog genome. Genetics 2010; 184:595-605. [PMID: 19966068 PMCID: PMC2828735 DOI: 10.1534/genetics.109.106831] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2009] [Accepted: 11/30/2009] [Indexed: 12/15/2022] Open
Abstract
We have leveraged the reference sequence of a boxer to construct the first complete linkage map for the domestic dog. The new map improves access to the dog's unique biology, from human disease counterparts to fascinating evolutionary adaptations. The map was constructed with approximately 3000 microsatellite markers developed from the reference sequence. Familial resources afforded 450 mostly phase-known meioses for map assembly. The genotype data supported a framework map with approximately 1500 loci. An additional approximately 1500 markers served as map validators, contributing modestly to estimates of recombination rate but supporting the framework content. Data from approximately 22,000 SNPs informing on a subset of meioses supported map integrity. The sex-averaged map extended 21 M and revealed marked region- and sex-specific differences in recombination rate. The map will enable empiric coverage estimates and multipoint linkage analysis. Knowledge of the variation in recombination rate will also inform on genomewide patterns of linkage disequilibrium (LD), and thus benefit association, selective sweep, and phylogenetic mapping approaches. The computational and wet-bench strategies can be applied to the reference genome of any nonmodel organism to assemble a de novo linkage map.
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Affiliation(s)
- Aaron K. Wong
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, California 95616, Applied Biosystems, Foster City, California 94404, Department of Biostatistics and Medical Informatics and Laboratory of Genetics, University of Wisconsin, Madison, Wisconsin 53706
| | - Alison L. Ruhe
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, California 95616, Applied Biosystems, Foster City, California 94404, Department of Biostatistics and Medical Informatics and Laboratory of Genetics, University of Wisconsin, Madison, Wisconsin 53706
| | - Beth L. Dumont
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, California 95616, Applied Biosystems, Foster City, California 94404, Department of Biostatistics and Medical Informatics and Laboratory of Genetics, University of Wisconsin, Madison, Wisconsin 53706
| | - Kathryn R. Robertson
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, California 95616, Applied Biosystems, Foster City, California 94404, Department of Biostatistics and Medical Informatics and Laboratory of Genetics, University of Wisconsin, Madison, Wisconsin 53706
| | - Giovanna Guerrero
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, California 95616, Applied Biosystems, Foster City, California 94404, Department of Biostatistics and Medical Informatics and Laboratory of Genetics, University of Wisconsin, Madison, Wisconsin 53706
| | - Sheila M. Shull
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, California 95616, Applied Biosystems, Foster City, California 94404, Department of Biostatistics and Medical Informatics and Laboratory of Genetics, University of Wisconsin, Madison, Wisconsin 53706
| | - Janet S. Ziegle
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, California 95616, Applied Biosystems, Foster City, California 94404, Department of Biostatistics and Medical Informatics and Laboratory of Genetics, University of Wisconsin, Madison, Wisconsin 53706
| | - Lee V. Millon
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, California 95616, Applied Biosystems, Foster City, California 94404, Department of Biostatistics and Medical Informatics and Laboratory of Genetics, University of Wisconsin, Madison, Wisconsin 53706
| | - Karl W. Broman
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, California 95616, Applied Biosystems, Foster City, California 94404, Department of Biostatistics and Medical Informatics and Laboratory of Genetics, University of Wisconsin, Madison, Wisconsin 53706
| | - Bret A. Payseur
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, California 95616, Applied Biosystems, Foster City, California 94404, Department of Biostatistics and Medical Informatics and Laboratory of Genetics, University of Wisconsin, Madison, Wisconsin 53706
| | - Mark W. Neff
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, California 95616, Applied Biosystems, Foster City, California 94404, Department of Biostatistics and Medical Informatics and Laboratory of Genetics, University of Wisconsin, Madison, Wisconsin 53706
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A domestic cat X chromosome linkage map and the sex-linked orange locus: mapping of orange, multiple origins and epistasis over nonagouti. Genetics 2009; 181:1415-25. [PMID: 19189955 DOI: 10.1534/genetics.108.095240] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A comprehensive genetic linkage map of the domestic cat X chromosome was generated with the goal of localizing the genomic position of the classic X-linked orange (O) locus. Microsatellite markers with an average spacing of 3 Mb were selected from sequence traces of the cat 1.9x whole genome sequence (WGS), including the pseudoautosomal region 1 (PAR1). Extreme variation in recombination rates (centimorgans per megabase) was observed along the X chromosome, ranging from a virtual absence of recombination events in a region estimated to be >30 Mb to recombination frequencies of 15.7 cM/Mb in a segment estimated to be <0.3 Mb. This detailed linkage map was applied to position the X-linked orange gene, placing this locus on the q arm of the X chromosome, as opposed to a previously reported location on the p arm. Fine mapping placed the locus between markers at positions 106 and 116.8 Mb in the current 1.9x-coverage sequence assembly of the cat genome. Haplotype analysis revealed potential recombination events that could reduce the size of the candidate region to 3.5 Mb and suggested multiple origins for the orange phenotype in the domestic cat. Furthermore, epistasis of orange over nonagouti was demonstrated at the genetic level.
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Gutiérrez-Gil B, El-Zarei M, Alvarez L, Bayón Y, de la Fuente L, San Primitivo F, Arranz J. Quantitative Trait Loci Underlying Udder Morphology Traits in Dairy Sheep. J Dairy Sci 2008; 91:3672-81. [DOI: 10.3168/jds.2008-1111] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Beraldi D, McRae AF, Gratten J, Slate J, Visscher PM, Pemberton JM. Development of a linkage map and mapping of phenotypic polymorphisms in a free-living population of Soay sheep (Ovis aries). Genetics 2006; 173:1521-37. [PMID: 16868121 PMCID: PMC1526682 DOI: 10.1534/genetics.106.057141] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An understanding of the determinants of trait variation and the selective forces acting on it in natural populations would give insights into the process of evolution. The combination of long-term studies of individuals living in the wild and better genomic resources for nonmodel organisms makes achieving this goal feasible. This article reports the development of a complete linkage map in a pedigree of free-living Soay sheep on St. Kilda and its application to mapping the loci responsible for three morphological polymorphisms for which the maintenance of variation demands explanation. The map was derived from 251 microsatellite and four allozyme markers and covers 3350 cM (approximately 90% of the sheep genome) at approximately 15-cM intervals. Marker order was consistent with the published sheep map with the exception of one region on chromosome 1 and one on chromosome 12. Coat color maps to chromosome 2 where a strong candidate gene, tyrosinase-related protein 1 (TYRP1), has also been mapped. Coat pattern maps to chromosome 13, close to the candidate locus Agouti. Horn type maps to chromosome 10, a location similar to that previously identified in domestic sheep. These findings represent an advance in the dissection of the genetic diversity in the wild and provide the foundation for QTL analyses in the study population.
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Affiliation(s)
- Dario Beraldi
- Institute of Evolutionary Biology, University of Edinburgh, UK.
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McRae AF, Pemberton JM, Visscher PM. Modeling linkage disequilibrium in natural populations: the example of the Soay sheep population of St. Kilda, Scotland. Genetics 2005; 171:251-8. [PMID: 15965254 PMCID: PMC1456516 DOI: 10.1534/genetics.105.040972] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2005] [Accepted: 05/19/2005] [Indexed: 11/18/2022] Open
Abstract
The use of linkage disequilibrium to localize the genes underlying quantitative traits has received considerable attention in the livestock genetics community over the past few years. This has resulted in the investigation of linkage disequilibrium structures of several domestic livestock populations to assess their potential use in fine-mapping efforts. However, the linkage disequilibrium structure of free-living populations has been less well investigated. As the direct evaluation of linkage disequilibrium can be both time consuming and expensive the use of simulations that include as many aspects of population history as possible is advocated as an alternative. A simulation of the linkage disequilibrium structure of the Soay sheep population of St. Kilda, Scotland, is provided as an example. The simulated population showed significant decline of linkage disequilibrium with genetic distance and low levels of background linkage disequilibrium, indicating that the Soay sheep population is a viable resource for linkage disequilibrium fine mapping of quantitative trait loci.
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Affiliation(s)
- Allan F McRae
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3JT, United Kingdom.
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Chistiakov DA, Hellemans B, Haley CS, Law AS, Tsigenopoulos CS, Kotoulas G, Bertotto D, Libertini A, Volckaert FAM. A microsatellite linkage map of the European sea bass Dicentrarchus labrax L. Genetics 2005; 170:1821-6. [PMID: 15937133 PMCID: PMC1449790 DOI: 10.1534/genetics.104.039719] [Citation(s) in RCA: 104] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2004] [Accepted: 04/25/2005] [Indexed: 11/18/2022] Open
Abstract
A genetic linkage map of the European sea bass (Dicentrarchus labrax) was constructed from 174 microsatellite markers, including 145 new markers reported in this study. The mapping panel was derived from farmed sea bass from the North Adriatic Sea and consisted of a single family including both parents and 50 full-sib progeny (biparental diploids). A total of 162 microsatellites were mapped in 25 linkage groups. Eleven loci represent type I (coding) markers; 2 loci are located within the peptide Y (linkage group 1) and cytochrome P450 aromatase (linkage group 6) genes. The sex-averaged map spans 814.5 cM of the sea bass genome. The female map covers 905.9 cM, whereas the male map covers only 567.4 cM. The constructed map represents the first linkage map of European sea bass, one of the most important aquaculture species in Europe.
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Affiliation(s)
- Dimitry A Chistiakov
- Laboratory of Aquatic Ecology, Katholieke Universiteit Leuven, B-3000 Leuven, Belgium
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Samollow PB, Kammerer CM, Mahaney SM, Schneider JL, Westenberger SJ, VandeBerg JL, Robinson ES. First-generation linkage map of the gray, short-tailed opossum, Monodelphis domestica, reveals genome-wide reduction in female recombination rates. Genetics 2004; 166:307-29. [PMID: 15020427 PMCID: PMC1470690 DOI: 10.1534/genetics.166.1.307] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The gray, short-tailed opossum, Monodelphis domestica, is the most extensively used, laboratory-bred marsupial resource for basic biologic and biomedical research worldwide. To enhance the research utility of this species, we are building a linkage map, using both anonymous markers and functional gene loci, that will enable the localization of quantitative trait loci (QTL) and provide comparative information regarding the evolution of mammalian and other vertebrate genomes. The current map is composed of 83 loci distributed among eight autosomal linkage groups and the X chromosome. The autosomal linkage groups appear to encompass a very large portion of the genome, yet span a sex-average distance of only 633.0 cM, making this the most compact linkage map known among vertebrates. Most surprising, the male map is much larger than the female map (884.6 cM vs. 443.1 cM), a pattern contrary to that in eutherian mammals and other vertebrates. The finding of genome-wide reduction in female recombination in M. domestica, coupled with recombination data from two other, distantly related marsupial species, suggests that reduced female recombination might be a widespread metatherian attribute. We discuss possible explanations for reduced female recombination in marsupials as a consequence of the metatherian characteristic of determinate paternal X chromosome inactivation.
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Affiliation(s)
- Paul B Samollow
- Department of Genetics, Southwest Foundation for Biomedical Research, San Antonio, Texas, 78245-0549, USA.
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Slate J, Visscher PM, MacGregor S, Stevens D, Tate ML, Pemberton JM. A genome scan for quantitative trait loci in a wild population of red deer (Cervus elaphus). Genetics 2002; 162:1863-73. [PMID: 12524355 PMCID: PMC1462362 DOI: 10.1093/genetics/162.4.1863] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Recent empirical evidence indicates that although fitness and fitness components tend to have low heritability in natural populations, they may nonetheless have relatively large components of additive genetic variance. The molecular basis of additive genetic variation has been investigated in model organisms but never in the wild. In this article we describe an attempt to map quantitative trait loci (QTL) for birth weight (a trait positively associated with overall fitness) in an unmanipulated, wild population of red deer (Cervus elaphus). Two approaches were used: interval mapping by linear regression within half-sib families and a variance components analysis of a six-generation pedigree of >350 animals. Evidence for segregating QTL was found on three linkage groups, one of which was significant at the genome-wide suggestive linkage threshold. To our knowledge this is the first time that a QTL for any trait has been mapped in a wild mammal population. It is hoped that this study will stimulate further investigations of the genetic architecture of fitness traits in the wild.
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Affiliation(s)
- J Slate
- AgResearch, Invermay Agricultural Centre, Mosgiel, New Zealand.
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Slate J, Van Stijn TC, Anderson RM, McEwan KM, Maqbool NJ, Mathias HC, Bixley MJ, Stevens DR, Molenaar AJ, Beever JE, Galloway SM, Tate ML. A deer (subfamily Cervinae) genetic linkage map and the evolution of ruminant genomes. Genetics 2002; 160:1587-97. [PMID: 11973312 PMCID: PMC1462045 DOI: 10.1093/genetics/160.4.1587] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Comparative maps between ruminant species and humans are increasingly important tools for the discovery of genes underlying economically important traits. In this article we present a primary linkage map of the deer genome derived from an interspecies hybrid between red deer (Cervus elaphus) and Père David's deer (Elaphurus davidianus). The map is approximately 2500 cM long and contains >600 markers including both evolutionary conserved type I markers and highly polymorphic type II markers (microsatellites). Comparative mapping by annotation and sequence similarity (COMPASS) was demonstrated to be a useful tool for mapping bovine and ovine ESTs in deer. Using marker order as a phylogenetic character and comparative map information from human, mouse, deer, cattle, and sheep, we reconstructed the karyotype of the ancestral Pecoran mammal and identified the chromosome rearrangements that have occurred in the sheep, cattle, and deer lineages. The deer map and interspecies hybrid pedigrees described here are a valuable resource for (1) predicting the location of orthologs to human genes in ruminants, (2) mapping QTL in farmed and wild deer populations, and (3) ruminant phylogenetic studies.
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Affiliation(s)
- Jon Slate
- AgResearch, Invermay Agricultural Centre, Mosgiel, New Zealand.
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McRae AF, McEwan JC, Dodds KG, Wilson T, Crawford AM, Slate J. Linkage disequilibrium in domestic sheep. Genetics 2002; 160:1113-22. [PMID: 11901127 PMCID: PMC1462013 DOI: 10.1093/genetics/160.3.1113] [Citation(s) in RCA: 119] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The last decade has seen a dramatic increase in the number of livestock QTL mapping studies. The next challenge awaiting livestock geneticists is to determine the actual genes responsible for variation of economically important traits. With the advent of high density single nucleotide polymorphism (SNP) maps, it may be possible to fine map genes by exploiting linkage disequilibrium between genes of interest and adjacent markers. However, the extent of linkage disequilibrium (LD) is generally unknown for livestock populations. In this article microsatellite genotype data are used to assess the extent of LD in two populations of domestic sheep. High levels of LD were found to extend for tens of centimorgans and declined as a function of marker distance. However, LD was also frequently observed between unlinked markers. The prospects for LD mapping in livestock appear encouraging provided that type I error can be minimized. Properties of the multiallelic LD coefficient D' were also explored. D' was found to be significantly related to marker heterozygosity, although the relationship did not appear to unduly influence the overall conclusions. Of potentially greater concern was the observation that D' may be skewed when rare alleles are present. It is recommended that the statistical significance of LD is used in conjunction with coefficients such as D' to determine the true extent of LD.
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Affiliation(s)
- A F McRae
- AgResearch, Invermay Agricultural Centre, Mosgiel, New Zealand
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