Boer goats, as kemp in meat-type goats, are selected and bred from African indigenous goats under a long period of artificial selection. Their advantages in multiple economic traits, particularly their plump growth, have attracted worldwide attention. Here, we displayed the wide-genome selective sweep of South Africa indigenous goat (AF), African Boer (BH), and Australian Boer (AS) to investigate the hereditary basis of artificial selection in different domesticated stages. A total of 18321865 SNPs and 9784 autosomal CNVs were identified, 573 candidate genes are screened by top 5% of both parameters (πrate and FST) for BH vs AF; 502 candidate genes were obtained from AS vs BH based on SNP data. Regarding CNV data, 24 candidate genes were annotated from top 1% CNVs (FST≥0.511719) based on BH vs AF, and 23 were annotated from top 1% (FST≥0.609523) CNVs in AS vs BH. A mount of identified candidate genes was related to reproduction, metabolism, growth, and development according to GO and KEGG annotation. Furthermore, these candidate genes related to the metabolism of fatty acids, minerals, and vitamins confirmed that raising level led to the rapid co-evolution of the metabolism and environment of Boer goats. Specifically, we found a series of non-synonymous mutations from the coding region of NF1 have significant allele frequency different between populations that was related to muscle development. This study provided valuable genomic resources for exploring the evolutionary history of Boer goats and genetic improvement of goats. It also helped us elucidate the genetic basis behind artificial selection in domestic animals.

Breed selection for commercial goat is needed for production efficiency, growth trait alteration, and improved livestock quality. Boer goat is famous for its stable production performance, fast growth rate, and high meat production. Detecting selective signatures in its genome can elucidate selection mechanisms for its economic and adaptive traits. In this study, 1,122,858 InDels were identified based on the whole genomes of 46 Australian Boer goats and 81 worldwide local goats. FST was used to identify the candidate selection signatures in 127 goats. A total of 11229 InDels were obtained from the top1% of all inDels, and 1239 candidate genes were annotated. A total of 1193 and 476 candidate genes were involved in 4726 GO terms and 299 KEGG pathways, respectively. Many genes were related to muscle development (MEF2C, MAPK14, TMOD1 etc.), reproduction (SRD5A1, FBXW11, DMRT1 etc.), immunity (CD200, SGK1, IL17RB etc.) and metabolism (INSR, STXBP3, H6PD etc.). The results provide novel and important insights into the genetic basis of selection in Boer goat and may be useful for goat molecular breeding.

By their paternal transmission, Y-chromosomal haplotypes are sensitive markers of population history and male-mediated introgression. Previous studies identified biallelic single-nucleotide variants in the SRY, ZFY, DDX3Y genes, which in domestic goats identified four major Y-chromosomal haplotypes Y1A, Y1B, Y2A and Y2B with a marked geographic partitioning. Here, we analyze whole-genome sequences of 386 domestic goats from 75 modern breeds and 7 wild goat species that were generated by the VarGoats goat genome project. Phylogenetic analyses indicated domestic haplogroups corresponding to Y1B, Y2A and Y2B, respectively, whereas Y1A is split into Y1AA and Y1AB. All five haplogroups were detected in 26 ancient DNA samples from southeast Europe or Asia. Haplotypes from present-day bezoars are not shared with domestic goats and are attached to deep nodes of the trees and networks. Haplogroup distributions for 180 domestic breeds indicate ancient paternal population bottlenecks and expansions during the migrations into northern Europe, eastern and southern Asia and Africa south of the Sahara. In addition, sharing of haplogroups indicates male-mediated introgressions, most notably an early gene flow from Asian goats into Madagascar and the crossbreeding that in the 19th century resulted in the popular Boer and Anglo-Nubian breeds. More recent introgressions are those from European goats into the native Korean goat population and from Boer goat into Uganda, Kenya, Tanzania, Malawi and Zimbabwe. This study illustrates the power of the Y-chromosomal variants for reconstructing the history of domestic species with a wide geographic range.