Genetic Diversity and Population Structure in South African, French and Argentinian Angora Goats from Genome-Wide SNP Data

Visser, Carina; Lashmar, S.F.; Marle-Köster, E. van; Poli, M. A.; Allain, Daniel

doi:10.1371/journal.pone.0154353

Cited by 63 publications

(66 citation statements)

References 35 publications

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“…The panel was developed from sequence data from Saanen, Alpine, Creole, Boer, Kacang, and Savanna animals (http://www.goatgenome.org/). The genetic diversity measures observed in these nine populations are in agreement with estimates reported in the literature [15, 67, 68]. For instance, Nicoloso et al [15] reported levels of P N , H O , H E and F EH ranging from 0.951 to 0.997, 0.35 to 0.41, 0.35 to 0.41 and −0.06 to 0.070, respectively, for 14 Italian goat breeds using the same SNP chip.…”

Section: Discussionsupporting

confidence: 90%

Genetic diversity and signatures of selection in various goat breeds revealed by genome-wide SNP markers

et al. 2017

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BackgroundThe detection of signatures of selection has the potential to elucidate the identities of genes and mutations associated with phenotypic traits important for livestock species. It is also very relevant to investigate the levels of genetic diversity of a population, as genetic diversity represents the raw material essential for breeding and has practical implications for implementation of genomic selection. A total of 1151 animals from nine goat populations selected for different breeding goals and genotyped with the Illumina Goat 50K single nucleotide polymorphisms (SNP) Beadchip were included in this investigation.ResultsThe proportion of polymorphic SNPs ranged from 0.902 (Nubian) to 0.995 (Rangeland). The overall mean HO and HE was 0.374 ± 0.021 and 0.369 ± 0.023, respectively. The average pairwise genetic distance (D) ranged from 0.263 (Toggenburg) to 0.323 (Rangeland). The overall average for the inbreeding measures FEH, FVR, FLEUT, FROH and FPED was 0.129, −0.012, −0.010, 0.038 and 0.030, respectively. Several regions located on 19 chromosomes were potentially under selection in at least one of the goat breeds. The genomic population tree constructed using all SNPs differentiated breeds based on selection purpose, while genomic population tree built using only SNPs in the most significant region showed a great differentiation between LaMancha and the other breeds. We hypothesized that this region is related to ear morphogenesis. Furthermore, we identified genes potentially related to reproduction traits, adult body mass, efficiency of food conversion, abdominal fat deposition, conformation traits, liver fat metabolism, milk fatty acids, somatic cells score, milk protein, thermo-tolerance and ear morphogenesis.ConclusionsIn general, moderate to high levels of genetic variability were observed for all the breeds and a characterization of runs of homozygosity gave insights into the breeds’ development history. The information reported here will be useful for the implementation of genomic selection and other genomic studies in goats. We also identified various genome regions under positive selection using smoothed FST and hapFLK statistics and suggested genes, which are potentially under selection. These results can now provide a foundation to formulate biological hypotheses related to selection processes in goats.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-3610-0) contains supplementary material, which is available to authorized users.

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Section: Discussionsupporting

confidence: 90%

Genetic diversity and signatures of selection in various goat breeds revealed by genome-wide SNP markers

et al. 2017

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“…); and a variety of Angora goat populations in Argentina, France and South Africa (Visser et al . ).…”

Section: Discussionmentioning

confidence: 97%

Genome‐wide population structure and admixture analysis reveals weak differentiation among Ugandan goat breeds

et al. 2018

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SummaryUganda has a large population of goats, predominantly from indigenous breeds reared in diverse production systems, whose existence is threatened by crossbreeding with exotic Boer goats. Knowledge about the genetic characteristics and relationships among these Ugandan goat breeds and the potential admixture with Boer goats is still limited. Using a medium‐density single nucleotide polymorphism (SNP) panel, we assessed the genetic diversity, population structure and admixture in six goat breeds in Uganda: Boer, Karamojong, Kigezi, Mubende, Small East African and Sebei. All the animals had genotypes for about 46 105 SNPs after quality control. We found high proportions of polymorphic SNPs ranging from 0.885 (Kigezi) to 0.928 (Sebei). The overall mean observed (HO) and expected (HE) heterozygosity across breeds was 0.355 ± 0.147 and 0.384 ± 0.143 respectively. Principal components, genetic distances and admixture analyses revealed weak population sub‐structuring among the breeds. Principal components separated Kigezi and weakly Small East African from other indigenous goats. Sebei and Karamojong were tightly entangled together, whereas Mubende occupied a more central position with high admixture from all other local breeds. The Boer breed showed a unique cluster from the Ugandan indigenous goat breeds. The results reflect common ancestry but also some level of geographical differentiation. admixture and f4 statistics revealed gene flow from Boer and varying levels of genetic admixture among the breeds. Generally, moderate to high levels of genetic variability were observed. Our findings provide useful insights into maintaining genetic diversity and designing appropriate breeding programs to exploit within‐breed diversity and heterozygote advantage in crossbreeding schemes.

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“…Although the Angora breed in France is the result of a second wave of imports during the 1980s from several regions of the world (Canada, Texas, South Africa, Australia and New Zealand; Visser et al . ), it forms a homogeneous cluster of individuals. This is most likely due to the absence of later imports and its management in an efficient breeding program, which generally leads to homogenize within‐breed diversity.…”

Section: Discussionmentioning

confidence: 99%

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

2018

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Summary After domestication 11 000 years ago in Asia Minor, the goat followed human migration to Europe and Asia. It was then introduced in Africa and is now raised all over the world. In this study, we exploited a dataset composed of 54 000 SNP s (Illumina goat DNA chip) to analyze the genetic diversity of 223 individuals belonging to eight French breeds (Alpine, Angora, Corse, Fossés, Poitevine, Provençale, Pyrénées and Saanen). Analyses carried out included individual‐based approaches (principal component analysis and population structure) and population‐based approaches (phylogenetic tree constructions). The results of the genetic diversity analyses revealed that French breeds are clearly differentiated, in particular, the Angora breed that originates from south west Asia. The Provençale breed shows a very original genetic pattern that could be the result of ancient admixture. Then, selection signatures were detected by identifying regions of outlying genetic differentiation between populations. Five genomic regions were detected under selection on chromosomes 5, 6, 11, 13 and 20, revealing mainly soft selective sweeps and a few hard selective sweeps and highlighting candidate genes that had been selected for during the evolutionary history of these breeds. Among them, two coat coloration genes ( ADAMTS 20 and ASIP ) and one gene related to milk composition ( CSN 1S1 ) were involved.

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Genetic Diversity and Population Structure in South African, French and Argentinian Angora Goats from Genome-Wide SNP Data

Cited by 63 publications

References 35 publications

Genetic diversity and signatures of selection in various goat breeds revealed by genome-wide SNP markers

Genetic diversity and signatures of selection in various goat breeds revealed by genome-wide SNP markers

Genome‐wide population structure and admixture analysis reveals weak differentiation among Ugandan goat breeds

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

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