Genetic diversity analysis of French goat populations reveals selective sweeps involved in their differentiation

Oget, Claire; Servin, Bertrand; Palhière, Isabelle

doi:10.1111/age.12752

Cited by 26 publications

(17 citation statements)

References 46 publications

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“…Indigenous domestic populations (often referred to as native breeds) are typically unmanaged genetically, or managed through traditional husbandry. These native breed generally show high levels of phenotypic variation [3][4][5][6][7] and are better adapted to local environments than specialised dairy and beef breeds, which are mostly of European taurine origin [8][9][10]. Indigenous populations have been reported for the major livestock species, including sheep, goat, pig, and cattle [7,[11][12][13].…”

Section: Introductionmentioning

confidence: 99%

A genetically unique Chinese cattle population shows evidence of common ancestry with wild species when analysed with a reduced ascertainment bias SNP panel

et al. 2020

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In Hong Kong, there is a cattle population of~1,200 individuals of uncertain origin and genetic diversity. This population shows heterogeneous morphology, both in body type and pigmentation. Once used as draught animals by the local farmers, they were abandoned around the 1970s due to changes in the economy, and since then have lived as feral populations. To explore the origins of these cattle, we analysed~50k genotype data of 21 Hong Kong feral cattle, along with data from 703 individuals of 36 cattle populations of European, African taurine, and Asian origin, the wild x domestic hybrid gayal, plus two wild bovine species, gaur and banteng. To reduce the effect of ascertainment bias~4k loci that are polymorphic in the two wild species were selected for further analysis. The stringent SNP selection we applied resulted in increased heterozygosity across all populations studies, compared with the full panel of SNP, thus reducing the impact of ascertainment bias and facilitating the comparison of divergent breeds of cattle. Our results showed that Hong Kong feral cattle have relatively high levels of genetic distinctiveness, possibly due to the low level of artificial selection, and a likely common ancestry with wild species. We found signs of a putative taurine introgression, probably dating to the import of north European breeds during the British colonialism of Hong Kong. We showed that Hong Kong feral cattle, are distinct from Bos taurus and Bos indicus breeds. Our results highlight the distinctiveness of Hong Kong feral cattle and stress the conservation value of this indigenous breed that is likely to harbour adaptive genetic variation, which is a fundamental livestock resource in the face of climate change and diversifying market demands.

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Section: Introductionmentioning

confidence: 99%

A genetically unique Chinese cattle population shows evidence of common ancestry with wild species when analysed with a reduced ascertainment bias SNP panel

et al. 2020

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“…An increasing number studies focusing on the relationship between ROH and phenotype, especially in human disease, have been conducted to shed light on the genetic architecture of complex traits in the past two decades (Ceballos et al 2018). Recently, ROH was introduced to analyze the genetic diversity of cross breeds, and to screen functional genes responsible for productive trait in goats (Guo et al 2019;Islam et al 2019;Oget et al 2019). Nonetheless, studies focusing on the patterns of ROH and reproduction in goats are scarce, but interesting.…”

Section: Introductionmentioning

confidence: 99%

Combined approaches to reveal genes associated with litter size in Yunshang black goats

Lin

Jiang

et al. 2020

Animal Genetics

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Intensive artificial selection has been imposed in Yunshang black goats, the first black specialist mutton goat breed in China, with a breeding object of improving reproductive performance, which has contributed to reshaping of the genome including the characterization of SNP, ROH and haplotype. However, variation in reproductive ability exists in the present population. A WGS was implemented in two subpopulations (polytocous group, PG, and monotocous group, MG) with evident differences of litter size. Following the mapping to reference genome, and SNP calling and pruning, three approaches-GWAS, ROH analysis and detection of signatures of selectionwere employed to unveil candidate genes responsible for litter size. Consequently, 12 candidate genes containing OSBPL8 with the minimum P-value were uncovered by GWAS. Differences were observed in the pattern of ROH between two subpopulations that shared similar low inbreeding coefficients. Two ROH hotspots and 12 corresponding genes emerged from ROH pool association analysis. Based on the nS L statistic, 15 and 61 promising genes were disclosed under selection for MG and PG respectively. Of them, some promising genes participate in ovarian function (PPP2R5C, CDC25A, ESR1, RPS26 and SERPINBs), seasonal reproduction (DIO3, BTG1 and CRYM) and metabolism (OSBPL8, SLC39A5 and SERPINBs). Our study pinpointed some novel promising genes influencing litter size, provided a comprehensive insight into genetic makeup of litter size and might facilitate selective breeding in goats.

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“…At the individual level, this reduction can be detected in persistent genomic signatures of selective sweeps such as those associated with human evolution (reviewed by 2 , 3 ), animal e.g. 4 , 5 and crop domestication e.g. 6 , 7 .…”

Section: Introductionmentioning

confidence: 99%

High gene flow maintains genetic diversity following selection for high EPSPS copy number in the weed kochia (Amaranthaceae)

Martin

Benedict

Wei

et al. 2020

Sci Rep

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Kochia, a major weed species, has evolved resistance to four herbicide modes of action. Herbicide resistance appears to spread quickly, which could result in diminished standing genetic variation, reducing the ability of populations to adapt further. Here we used double digest restriction enzyme associated sequencing to determine the level of gene flow among kochia populations and whether selection for glyphosate resistance reduces genetic variation. Canadian Prairie populations show little to no genetic differentiation (FST = 0.01) and no correlation between genetic and geographic distance (r2 = − 0.02 p = 0.56), indicating high gene flow and no population structure. There is some evidence that kochia populations are genetically depauperate compared to other weed species, but genetic diversity did not differ between glyphosate susceptible and resistant populations or individuals. The inbreeding coefficients suggest there are 23% fewer heterozygotes in these populations than expected with random mating, and no variation was found within the chloroplast. These results indicate that any alleles for herbicide resistance can be expected to spread quickly through kochia populations, but there is little evidence this spread will reduce the species’ genetic variation or limit the species’ ability to respond to further selection pressure.

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Genetic diversity analysis of French goat populations reveals selective sweeps involved in their differentiation

Cited by 26 publications

References 46 publications

A genetically unique Chinese cattle population shows evidence of common ancestry with wild species when analysed with a reduced ascertainment bias SNP panel

A genetically unique Chinese cattle population shows evidence of common ancestry with wild species when analysed with a reduced ascertainment bias SNP panel

Combined approaches to reveal genes associated with litter size in Yunshang black goats

High gene flow maintains genetic diversity following selection for high EPSPS copy number in the weed kochia (Amaranthaceae)

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