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Simple Summary: We performed a genome-wide association study of 100 sheep genomes to investigate the hereditary basis of the four-horn phenotype (FHP) in sheep. The results revealed that a total of 3 InDels (e.g., CHR2: g.133,742,709delA and g.133,743,215insC) and 14 SNPs (e.g., CHR2: g.133,727,513C > T and CHR16: g.40,351,378G > A) in CHR2 and CHR16 were significantly associated with the four-horn trait. Furthermore, HOXD1 and ADAMTS12 annotated from both CHR sequences were the key candidate gene loci contributing to FHP in sheep. This study provided a novel understanding of the Mendelian genetic basis for four horns in sheep. Horns are an important breeding trait for sheep. However, no widely recognized viewpoint on the regulatory genes and mechanisms of horns is available, and the genetic basis of the four-horn phenotype (FHP) is unclear. This work conducted a genome-wide association study with 100 sheep genomes from multiple breeds to investigate the genetic basis of the FHP. The results revealed three significant associations (corrected as p < 1.64 × 10−8) of the InDels (CHR2: g.133,742,709delA, g.133,743,215insC, and g.133,743,940delT) for FHP in the intergenic sequence (IGS) between the MTX2 and the LOC105609047 of CHR2. Moreover, 14 significant associations (corrected as p < 1.42 × 10−9) of SNPs with the FHP phenotype were identified in CHR2 and CHR16, including five (e.g., CHR16: g.40,351,378G > A and g.40,352,577G > A) located in the intron of the ADAMTS12 gene, eight (e.g., CHR2: g.133,727,513C > T and g.133,732,145T > G) in the IGS between MTX2 and LOC105609047, and only one (CHR2: g.133,930,761A > G) in the IGS between HOXD1 and MTX2. Obvious divergence was also observed in genotype patterns between the FHP and others (two horns and hornless) in the HOXD1 and ADAMTS12 gene regions. An extremely significant linkage also occurred between Loci I and Loci II within 100 individuals (LD = −156.02186, p < 0.00001). In summary, our study indicated that the genomic sequences from CHR2 and CHR16 contributed to the FHP in sheep, specifically the key candidate genes HOXD1 and ADAMTS12. These results improved our understanding of the Mendelian genetic basis of the FHP in sheep. [ABSTRACT FROM AUTHOR]

Simple Summary: In this study, genome-wide selective analysis of 371 publicly available genomes from worldwide domestic pigs and wild boars was conducted via FST and XPEHH methods to understand their genetic differences. Some common genes under selection in Eurasian domestic pigs suggest that domestication of pigs worldwide has undergone parallel selection in physiological phenotypes, such as reproduction, metabolism, growth, and development. As important livestock species, pigs provide essential meat resources for humans, so understanding the genetic evolution behind their domestic history could help with the genetic improvement of domestic pigs. This study aimed to investigate the evolution of convergence and divergence under selection in European and Asian domestic pigs by using public genome-wide data. A total of 164 and 108 candidate genes (CDGs) were obtained from the Asian group (wild boar vs. domestic pig) and the European group (wild boar vs. domestic pig), respectively, by taking the top 5% of intersected windows of a pairwise fixation index (FST) and a cross population extended haplotype homozygosity test (XPEHH). GO and KEGG annotated results indicated that most CDGs were related to reproduction and immunity in the Asian group. Conversely, rich CDGs were enriched in muscle development and digestion in the European group. Eight CDGs were subjected to parallel selection of Eurasian domestic pigs from local wild boars during domestication. These CDGs were mainly involved in olfactory transduction, metabolic pathways, and progesterone-mediated oocyte maturation. Moreover, 36 and 18 haplotypes of INPP5B and TRAK2 were identified in this study, respectively. In brief, this study did not only improve the understanding of the genetic evolution of domestication in pigs, but also provides valuable CDGs for future breeding and genetic improvement of pigs. [ABSTRACT FROM AUTHOR]

Simple Summary: In this study, the pairwise fixation index (FST) and π ratio (case/control) genetic parameters were used to identify the genes that influence the body size of pigs and analyze the genetic basis of pig body size formation. The results of candidate gene (CG) annotation showed that a series of CGs (MSTN, LTBP4, PDPK1, PKMYT1, ASS1, and STAT6) was enriched into the gene ontology terms. Moreover, molecular pathways, such as the PI3K-Akt, HIF-1, and AMPK signaling pathways, were verified to be related to body development. These findings will help us further understand the genetic basis of animal body-size determination. This study aimed to identify the genes related to the body size of pigs by conducting genome-wide selection analysis (GWSA). We performed a GWSA scan on 50 pigs belonging to four small-bodied pig populations (Diannan small-eared pig, Bama Xiang pig, Wuzhishan pig, and Jeju black pig from South Korea) and 124 large-bodied pigs. We used the genetic parameters of the pairwise fixation index (FST) and π ratio (case/control) to screen candidate genome regions and genes related to body size. The results revealed 47,339,509 high-quality SNPs obtained from 174 individuals, while 280 interacting candidate regions were obtained from the top 1% signal windows of both parameters, along with 187 genes (e.g., ADCK4, AMDHD2, ASPN, ASS1, and ATP6V0C). The results of the candidate gene (CG) annotation showed that a series of CGs (e.g., MSTN, LTBP4, PDPK1, PKMYT1, ASS1, and STAT6) was enriched into the gene ontology terms. Moreover, molecular pathways, such as the PI3K-Akt, HIF-1, and AMPK signaling pathways, were verified to be related to body development. Overall, we identified a series of key genes that may be closely related to the body size of pigs, further elucidating the heredity basis of body shape determination in pigs and providing a theoretical reference for molecular breeding. [ABSTRACT FROM AUTHOR]

Simple Summary: Boer goat is a world-famous meat-type goat breed that underwent long-term artificial selection from African indigenous animals. The current study displayed the genome-wide selection signature analyses of South African indigenous goat (AF), African Boer (BH), and Australian Boer (AS), to investigate the hereditary basis of artificial selection in different stages. Moreover, the θπ, FST, and XP-CLR methods were used to search for the candidate signatures of positive selection in Boer goats. Ten genes (e.g., BMPR1B, DNER, ITGAL, and KIT) under selection in both groups were identified and are potentially responsible for reproduction, metabolism, growth, and development. This study provided a comprehensive overview of genomic variations in Boer goat, which may provide a basis for further resource protection and improvement of this breed. 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. The current study displayed the genome-wide selection signature analyses of South African indigenous goat (AF), African Boer (BH), and Australian Boer (AS) to investigate the hereditary basis of artificial selection in different stages. Four methods (principal component analysis, nucleotide diversity, linkage disequilibrium decay, and neighbor-joining tree) implied the genomic diversity changes with different artificial selection intensities in Boer goats. In addition, the θπ, FST, and XP-CLR methods were used to search for the candidate signatures of positive selection in Boer goats. Consequently, 339 (BH vs. AF) and 295 (AS vs. BH) candidate genes were obtained from SNP data. Especially, 10 genes (e.g., BMPR1B, DNER, ITGAL, and KIT) under selection in both groups were identified. Functional annotation analysis revealed that these genes are potentially responsible for reproduction, metabolism, growth, and development. This study used genome-wide sequencing data to identify inheritance by artificial selection. The results of the current study are valuable for future molecular-assisted breeding and genetic improvement of goats. [ABSTRACT FROM AUTHOR]