New world goat populations are a genetically diverse reservoir for future use

Abstract

Western hemisphere goats have European, African and Central Asian origins, and some local or rare breeds are reported to be adapted to their environments and economically important. By-in-large these genetic resources have not been quantified. Using 50 K SNP genotypes of 244 animals from 12 goat populations in United States, Costa Rica, Brazil and Argentina, we evaluated the genetic diversity, population structure and selective sweeps documenting goat migration to the "New World". Our findings suggest the concept of breed, particularly among "locally adapted" breeds, is not a meaningful way to characterize goat populations. The USA Spanish goats were found to be an important genetic reservoir, sharing genomic composition with the wild ancestor and with specialized breeds (e.g. Angora, Lamancha and Saanen). Results suggest goats in the Americas have substantial genetic diversity to use in selection and promote environmental adaptation or product driven specialization. These findings highlight the importance of maintaining goat conservation programs and suggest an awaiting reservoir of genetic diversity for breeding and research while simultaneously discarding concerns about breed designations.

Figure 1

First three principal components using 17 goat populations. Values between parentheses in each axis are the eigenvalues of each component.

Figure 2

Plot of model-based clustering (ADMIXTURE) results from K equal 3 to 10 using 17 goat populations.

Figure 3

Population tree with 17 goat populations from TreeMix software using Capra aegagrus as root and showing six migration events.

Figure 4

Smoothed Fst per SNP for comparison between Angora and Meat (Boer) and Milk (Saanen and LaMancha) specialized breeds and between Angora and all others goat breeds in the analyses. Red line: significant threshold of three standard deviations above the mean. Blue line: threshold of two standard deviations above the mean.

Figure 5

Genome scan for selection in five different scenarios of 16 populations of goat using a haplotype-based (hapFLK) test. 6 groups: Boer/Meat, Argentinean, Brazilian, Milk, Spanish and Angora breeds. 16 populations: Angora_AR, Angora_SA, Angora_USA, Iran, Boer_USA, Argentinean populations, Caninde_BR, Moxoto_BR, LaMancha_USA, Morocco, Saanen_CR, Spanish_USA. 12 populations: 16 populations minus Angora and Iran populations. Angora populations: Angora animals from South Africa, United States and Argentina. Argentinean populations: C. Formosena_AR, C. Llanos_ AR, C. Neuquino_AR, C. Pampeana_AR, C. Riojano_AR.

Figure 6

Group trees (at left) generated using all available SNPs and only 351 SNPs surrounding the hapFLK peak in chromosome 3 analyzing the six groups. Haplotype clusters frequencies (at right) in the region of chromosome 3 for each group used in the test. AR: Argentinean breeds; BR: Brazilian breeds. This peak are used as example here, the others significant regions are showed in supplementary files.

Figure 7

Population trees (at left) generated using all available SNPs and only 150 SNPs surrounding the hapFLK peak in chromosome 23 analyzing only the Angora populations. Haplotype clusters frequencies (at right) in the region of chromosome 23 for each population used in the test.