Ancient Genomes Reveal the Evolutionary History and Origin of Cashmere-Producing Goats in China.

Goats are one of the most widespread farmed animals across the world; however, their migration route to East Asia and local evolutionary history remain poorly understood. Here, we sequenced 27 ancient Chinese goat genomes dating from the Late Neolithic period to the Iron Age. We found close genetic affinities between ancient and modern Chinese goats, demonstrating their genetic continuity. We found that Chinese goats originated from the eastern regions around the Fertile Crescent, and we estimated that the ancestors of Chinese goats diverged from this population in the Chalcolithic period. Modern Chinese goats were divided into a northern and a southern group, coinciding with the most prominent climatic division in China, and two genes related to hair follicle development, FGF5 and EDA2R, were highly divergent between these populations. We identified a likely causal de novo deletion near FGF5 in northern Chinese goats that increased to high frequency over time, whereas EDA2R harbored standing variation dating to the Neolithic. Our findings add to our understanding of the genetic composition and local evolutionary process of Chinese goats.

Genomic analysis of indigenous goats in Southwest Asia reveals evidence of ancient adaptive introgression related to desert climate.

Understanding how evolutionary pressures related to climate change have shaped the current genetic background of domestic animals is a fundamental pursuit of biology. Here, we generated whole-genome sequencing data from native goat populations in Iraq and Pakistan. Combined with previously published data on modern, ancient (Late Neolithic to Medieval periods), and wild Capra species worldwide, we explored the genetic population structure, ancestry components, and signatures of natural positive selection in native goat populations in Southwest Asia (SWA). Results revealed that the genetic structure of SWA goats was deeply influenced by gene flow from the eastern Mediterranean during the Chalcolithic period, which may reflect adaptation to gradual warming and aridity in the region. Furthermore, comparative genomic analysis revealed adaptive introgression of the KITLG locus from the Nubian ibex ( C. nubiana) into African and SWA goats. The frequency of the selected allele at this locus was significantly higher among goat populations located near northeastern Africa. These results provide new insights into the genetic composition and history of goat populations in the SWA region.

Genetic variants in the TORC2 gene promoter and their association with body measurement and carcass quality traits in Qinchuan cattle.

The TORC2 gene is responsible for nutrient metabolism, gluconeogenesis, myogenesis and adipogenesis through the PI3K-Akt, AMPK, glucagon and insulin resistance signaling pathways. Sequencing of PCR amplicons explored three novel SNPs at loci g.16534694G>A, g.16535011C>T, and g.16535044A>T in the promoter region of the TORC2 gene in the Qinchuan breed of cattle. Allelic and genotypic frequencies of these SNPs deviated from Hardy-Weinberg equilibrium (HWE) (P < 0.05). SNP1 genotype GG, SNP2 genotype CT and SNP3 genotype AT showed significantly (P <0.05) larger body measurement and improved carcass quality traits. Haplotype H1 (GCA) showed significantly (p<0.01) higher transcriptional activity (51.44%) followed by H4 (ATT) (34.13%) in bovine preadipocytes. The diplotypes HI-H3 (GG-CC-AT), H1-H2 (GG-CT-AT) and H3-H4 (GA-CT-TT) showed significant (P<0.01) associations with body measurement and improved carcass quality traits. Analysis of the relative mRNA expression level of the TORC2 gene in different tissues within two different age groups revealed a significant increase (P<0.01) in liver, small intestine, muscle and fat tissues with growth from calf stage to adult stage. We can conclude that variants mapped within TORC2 can be used in marker-assisted selection for carcass quality and body measurement traits in breed improvement programs of Qinchuan cattle.

Genome Analysis Reveals Genetic Admixture and Signature of Selection for Productivity and Environmental Traits in Iraqi Cattle.

The Near East cattle are adapted to different agro-ecological zones including desert areas, mountains habitats, and humid regions along the Tigris and Euphrates rivers system. The region was one of the earliest and most significant areas of cattle husbandry. Currently, four main breeds of Iraqi cattle are recognized. Among these, the Jenoubi is found in the southern more humid part of Iraq, while the Rustaqi is found in the middle and drier region of the country. Despite their importance, Iraqi cattle have up to now been poorly characterized at the genome level. Here, we report at a genome-wide level the diversity and signature of positive selection in these two breeds. Thirty-five unrelated Jenoubi cattle, sampled in the Maysan and Basra regions, and 60 Rustaqi cattle, from around Baghdad and Babylon, were genotyped using the Illumina Bovine HD BeadChip (700K). Genetic population structure and diversity level were studied using principal component analysis (PCA), expected heterozygosity (He), observed heterozygosity (Ho), and admixture. Signatures of selection were studied using extended haplotype homozygosity (EHH) (iHS and Rsb) and inter-population Wright's Fst. The results of PCA and admixture analysis, including European taurine, Asian indicine, African indicine, and taurine indicate that the two breeds are crossbreed zebu × taurine, with more zebu background in Jenoubi cattle compared with Rustaqi. The Rustaqi has the greatest mean heterozygosity (He = 0.37) among all breeds. iHS and Rsb signatures of selection analyses identify 68 candidate genes under positive selection in the two Iraqi breeds, while Fst analysis identifies 220 candidate genes including genes related to the innate and acquired immunity responses, different environmental selection pressures (e.g., tick resistance and heat stress), and genes of commercial interest (e.g., marbling score).