SNP of AHSA2 gene in three cattle breeds using snapshot technology.

Droughtmaster is a tropical breed of beef cattle that can survive in hot climates and easily adapt to torrid environments. These traits are important in livestock breeding. In this study, we genotyped five single-nucleotide polymorphisms (SNPs) of the AHSA2 gene from 190 cattle belonging to three different breeds (Droughtmaster, Angus and Simmental) by using snapshot technology. This work aimed to identify the valuable molecular marker of heat resistance in cattle. Results showed that Droughtmaster exhibited higher expected heterozygosity and polymorphic information content compared with the two other breeds. The AHSA2-1 locus deviated from the Hardy-Weinberg equilibrium in the Droughtmaster breed (P < 0.05). Two SNPs in Droughtmaster diverged significantly from Angus and Simmental. The SNPs were identified as AHSA2-3 and AHSA2-4, which were closely linked to the three breeds based on pair-wise FST. AHSA2-4 involved a missense mutation. In summary, the GG genotypes in AHSA2-3 and AHSA2-4 may be candidate genotypes associated with heat resistance traits and may serve as valuable genetic markers for breeding of heat-tolerant beef cattle in the future.

Genome-wide selective sweep analysis of the high-altitude adaptability of yaks by using the copy number variant.

The domestic yak (Bos grunniens) from the Qinghai-Tibet Plateau is an important animal model in high-altitude adaptation studies. Here, we performed the genome-wide selective sweep analysis to identify the candidate copy number variation (CNV) for the high-altitude adaptation of yaks. A total of 531 autosomal CNVs were determined from 29 yak genome-wide resequencing data (15 high- and 14 low-altitude distributions) by using a CNV caller with a CNV identification interval > 5 kb, CNV silhouette score > 0.7, and minimum allele frequency > 0.05. Most high-frequency CNVs were located at the exonic (44.63%) and intergenic (46.52%) regions. In accordance with the results of the selective sweep analysis, 7 candidate CNVs were identified from the interaction of the top 20 CNVs with highest divergence from the F ST and V ST between the low (LA) and high (HA) altitudes. Five genes (i.e., GRIK4, IFNLR1, LOC102275985, GRHL3, and LOC102275713) were also annotated from the seven candidate CNVs and their upstream and downstream ranges at 300 kb. GRIK4, IFNLR1, and LOC102275985 were enriched in five known signal pathways, namely, glutamatergic synapse, JAK-STAT signaling pathway, cytokine-cytokine receptor interaction, neuroactive ligand-receptor interaction, and olfactory transduction. These pathways are involved in the environmental adaptability and various physiological functions of animals, especially the physiological regulation under a hypoxic environment. The results of this study advanced the understanding of CNV as an important genomic structure variant type that contributes to HA adaptation and helped further explain the molecular mechanisms underlying the altitude adaptability of yaks.

Whole-genome scanning for the heat-resistance-associated genes in the Droughtmaster breed (Bos taurus).

The Droughtmaster is a tropical breed of beef cattle developed in North Queensland that exhibits a combination of heat resistance and parasitic resistance from long-term artificial selection. Therefore, we used next-generation sequencing technology to screen the chromosomal regions and genes related to heat-resistance in cattle to provide data for improving cattle breeding. A total of 15,569,067 variants including 14,249,316 SNPs were obtained from two mixed pools by genome-wide resequencing. According to the results of the selective sweep analysis of the Droughtmaster pool compared to the nonheat resistant breeds pool, 81 candidate genes under selection in Droughtmaster were identified by combining Z HP and F ST analyses with a threshold standard of the top 1%, including SLC7A11, GYPC, and GYPC. In addition, 40 GO terms and 44 pathways were annotated from newly identified candidate genes. These signaling pathways were involved in environmental information processing, organismal systems, and metabolism. A majority of these genes have not been implicated in the previous studies of heat resistance. This study explored the genomic changes that result from long-term artificial selection, our findings help to explain the molecular mechanism of heat resistance in cattle.