Genetic and Haplotypic Structure in 14 European and African Cattle Breeds

Gautier, Mathieu; Faraut, Thomas; Moazami‐Goudarzi, Katayoun; Navratil, Vincent; Foglio, Mario; Grohs, Cécile; Boland, Anne; Garnier, Jean-Guillaume; Boichard, Didier; Lathrop, G.M.; Gut, Ivo; Eggen, Andre A.

doi:10.1534/genetics.107.075804

Cited by 139 publications

(183 citation statements)

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“…LD is conserved over an extremely long range in the Chillingham cattle, which contrasts with other cattle breeds, for which high values of LD are typically detected only over much shorter distances (<10 kb) and LD drops below r 2 = 0.20 from~200 kb (Gautier et al 2007; Porto-Neto et al 2014). However, the strong LD observed in the Chillingham population is consistent with the high level of monomorphic loci, which means recombination events may go undetected.…”

Section: Discussionmentioning

confidence: 95%

Inbreeding and purging at the genomic Level: the Chillingham cattle reveal extensive, non‐random SNP heterozygosity

et al. 2015

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SummaryLocal breeds of livestock are of conservation significance as components of global biodiversity and as reservoirs of genetic variation relevant to the future sustainability of agriculture. One such rare historic breed, the Chillingham cattle of northern England, has a 350-year history of isolation and inbreeding yet shows no diminution of viability or fertility. The Chillingham cattle have not been subjected to selective breeding. It has been suggested previously that the herd has minimal genetic variation. In this study, high-density SNP genotyping with the 777K SNP chip showed that 9.1% of loci on the chip are polymorphic in the herd, compared with 62-90% seen in commercial cattle breeds. Instead of being homogeneously distributed along the genome, these loci are clustered at specific chromosomal locations. A high proportion of the Chillingham individuals examined were heterozygous at many of these polymorphic loci, suggesting that some loci are under balancing selection. Some of these frequently heterozygous loci have been implicated as sites of recessive lethal mutations in cattle. Linkage disequilibrium equal or close to 100% was found to span up to 1350 kb, and LD was above r 2 = 0.25 up to more than 5000 kb. This strong LD is consistent with the lack of polymorphic loci in the herd. The heterozygous regions in the Chillingham cattle may be the locations of genes relevant to fitness or survival, which may help elucidate the biology of local adaptation in traditional breeds and facilitate selection for such traits in commercial cattle.

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Section: Discussionmentioning

confidence: 95%

Inbreeding and purging at the genomic Level: the Chillingham cattle reveal extensive, non‐random SNP heterozygosity

et al. 2015

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“…Haplotype blocks have been studied in other species as well, both model organisms, including the mouse and rat 22 , and domesticated species, including cows 23 and dogs 24 . The isolation of strains and breeds in these species results in much longer block lengths than are found in humans.…”

Section: Ld At More Than Two Locimentioning

confidence: 99%

Linkage disequilibrium — understanding the evolutionary past and mapping the medical future

2008

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Linkage disequilibrium -the nonrandom association of alleles at different loci -is a sensitive indicator of the population genetic forces that structure a genome. Because of the explosive growth of methods for assessing genetic variation at a fine scale, evolutionary biologists and human geneticists are increasingly exploiting linkage disequilibrium in order to understand past evolutionary and demographic events, to map genes that are associated with quantitative characters and inherited diseases, and to understand the joint evolution of linked sets of genes. This article introduces linkage disequilibrium, reviews the population genetic processes that affect it and describes some of its uses. At present, linkage disequilibrium is used much more extensively in the study of humans than in non-humans, but that is changing as technological advances make extensive genomic studies feasible in other species.Linkage disequilibrium (LD) is one of those unfortunate terms that does not reveal its meaning. As every instructor of population genetics knows, the term is a barrier not an aid to understanding. LD means simply a nonrandom association of alleles at two or more loci, and detecting LD does not ensure either linkage or a lack of equilibrium. The term was first used in 1960 by Lewontin and Kojima 1 and it persists because LD was initially the concern of population geneticists who were not picky about terminology as long as the mathematical definition was clear. At first, there were few data with which to study LD, and its importance to evolutionary biology and human genetics was unrecognized outside of population genetics. However, interest in LD grew rapidly in the 1980s once the usefulness of LD for gene mapping became evident and large-scale surveys of closely linked loci became feasible. By then, the term was too well established to be replaced.LD is of importance in evolutionary biology and human genetics because so many factors affect it and are affected by it. LD provides information about past events and it constrains the potential response to both natural and artificial selection. LD throughout the genome reflects the population history, the breeding system and the pattern of geographic subdivision, whereas LD in each genomic region reflects the history of natural selection, gene conversion, mutation and other forces that cause gene-frequency evolution. How these factors affect LD between a particular pair of loci or in a genomic region depends on local recombination rates. The population genetics theory of LD is well developed and is being widely used to provide insight into evolutionary history and as the basis for mapping genes in humans and in other species. HHS Public AccessAuthor manuscript Nat Rev Genet. Author manuscript; available in PMC 2016 November 27. Author Manuscript Author ManuscriptAuthor Manuscript Author ManuscriptIn this article, I will review the definitions of LD and the problems with assessing it, then outline the basic population genetics of LD that tells us how natural select...

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“…To date, Bangladeshi cattle populations have not been subjected to thorough molecular investigation; however, limited study of the Red Chittagong population has been conducted using mtDNA (Bhuiyan et al, 2007). With the development of next-generation sequencing technology, single-nucleotide polymorphisms (SNPs) are among the most important molecular markers and are now routinely employed for inference of population history and studies of genetic diversity and genome-wide association (Brumfield et al, 2003;Gautier et al, 2007). Genome-wide comparison of populations from different geographical regions can also detect potential candidate genes associated with ecological adaptations (Edea et al, 2014).…”

Section: Introductionmentioning

confidence: 99%

Genome-wide genetic diversity, population structure and admixture analysis in African and Asian cattle breeds

Edea

Bhuiyan

Dessie³

et al. 2015

Animal

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Knowledge about genetic diversity and population structure is useful for designing effective strategies to improve the production, management and conservation of farm animal genetic resources. Here, we present a comprehensive genome-wide analysis of genetic diversity, population structure and admixture based on 244 animals sampled from 10 cattle populations in Asia and Africa and genotyped for 69 903 autosomal single-nucleotide polymorphisms (SNPs) mainly derived from the indicine breed. Principal component analysis, STRUCTURE and distance analysis from high-density SNP data clearly revealed that the largest genetic difference occurred between the two domestic lineages (taurine and indicine), whereas Ethiopian cattle populations represent a mosaic of the humped zebu and taurine. Estimation of the genetic influence of zebu and taurine revealed that Ethiopian cattle were characterized by considerable levels of introgression from South Asian zebu, whereas Bangladeshi populations shared very low taurine ancestry. The relationships among Ethiopian cattle populations reflect their history of origin and admixture rather than phenotype-based distinctions. The high within-individual genetic variability observed in Ethiopian cattle represents an untapped opportunity for adaptation to changing environments and for implementation of within-breed genetic improvement schemes. Our results provide a basis for future applications of genome-wide SNP data to exploit the unique genetic makeup of indigenous cattle breeds and to facilitate their improvement and conservation.

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Genetic and Haplotypic Structure in 14 European and African Cattle Breeds

Cited by 139 publications

References 45 publications

Inbreeding and purging at the genomic Level: the Chillingham cattle reveal extensive, non‐random SNP heterozygosity

Inbreeding and purging at the genomic Level: the Chillingham cattle reveal extensive, non‐random SNP heterozygosity

Linkage disequilibrium — understanding the evolutionary past and mapping the medical future

Genome-wide genetic diversity, population structure and admixture analysis in African and Asian cattle breeds

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