Y-SNPs Haplotype Diversity in Four Chinese Cattle Breeds

DGAT1 K232A polymorphism is associated with milk production traits in Chinese cattle

The production traits of cattle, especially milk trait, are of great significance to human life. A quantitative trait loci (QTL) associated with milk fat content was detected in the centromeric region of cattle chromosome 14. This QTL harbors a strong candidate gene called DGAT1 responsible for the milk quality. A non-conservative substitution of lysine by alanine (K232A) was found in DGAT1 gene producing a strong effect on milk composition and yield. The lysine (K allele) is associated with increased milk fat content, while the decreased milk fat content is linked to the alanine (A allele) amino acid. To estimate the frequencies of the DGAT1 K232A polymorphism in Chinese cattle breeds, PCR and DNA sequencing methods were used to investigate the polymorphism of DGAT1 K232A in a total of 682 individuals, including 655 Chinese cattle and 27 Holstein cattle. The results demonstrated that the frequency of K allele gradually elevated from the northern group to the southern group of native Chinese cattle, whereas the frequency of A allele showed a contrary pattern, displaying a significant geographical difference across native Chinese cattle breeds. Our results confirm that the southern cattle group has higher milk fat content than that of the northern group.

Genome-Wide SNPs and InDels Characteristics of Three Chinese Cattle Breeds

Simple Summary

Whole-genome resequencing is an important tool to reveal the in-depth genomic characteristics of a genome. Adaptability traits are key to the survival of the south Chinese zebu cattle. However, the potential genetic information behind these remarkable traits still remains uncertain and needs to be addressed. In the current study, we utilized a total of 15 local south Chinese cattle samples (Leiqiong (LQ), Wannan (WN), Wenshan (WS)) from one of our previous studies mapped to the old reference genome (Btau_5.0.1) and remapped them to the latest reference genome (ARS-UCD1.2) to explore potential single nucleotide polymorphisms (SNPs) and insertions-deletions (InDels) responsible for some important immune related traits. The present study emphasizes and illustrates the genetic diversity, extending our previous study. The InDel annotation show that WS cattle had more enriched genes associated with immune functions than the other two breeds. Our findings provide valuable resources for further investigation of the functions of SNP- and InDels-related genes and help to determine the molecular basis of adaptive mutations in Chinese zebu cattle.

Abstract

We report genome characterization of three native Chinese cattle breeds discovering ~34.3 M SNPs and ~3.8 M InDels using whole genome resequencing. On average, 10.4 M SNPs were shared amongst the three cattle breeds, whereas, 3.0 M, 4.9 M and 5.8 M were specific to LQ, WN and WS breeds, respectively. Gene ontology (GO)analysis revealed four immune response-related GO terms were over represented in all samples, while two immune signaling pathways were significantly over-represented in WS cattle. Altogether, we found immune related genes (PGLYRP2, ROMO1, FYB2, CD46, TSC1) in the three cattle breeds. Our study provides insights into the genetic basis of Chinese indicine adaptation to the tropic and subtropical environment, and provides a valuable resource for further investigations of genetic characteristics of the three breeds.

Genetic diversity of Chinese cattle revealed by Y-SNP and Y-STR markers

With its vast territory and complex natural environment, China boasts rich cattle genetic resources. To gain the further insight into the genetic diversity and paternal origins of Chinese cattle, we analyzed the polymorphism of Y-SNPs (UTY19 and ZFY10) and Y-STRs (INRA189 and BM861) in 34 Chinese cattle breeds/populations, including 606 males representative of 24 cattle breeds/populations collected in this study as well as previously published data for 302 bulls. Combined genotypic data identified 14 Y-chromosome haplotypes that represented three haplogroups. Y2-104-158 and Y2-102-158 were the most common taurine haplotypes detected mainly in northern and central China, whereas the indicine haplotype Y3-88-156 predominates in southern China. Haplotypes Y2-108-158, Y2-110-158, Y2-112-158 and Y3-92-156 were private to Chinese cattle. The population structure revealed by multidimensional scaling analysis differentiated Tibetan cattle from the other three groups of cattle. Analysis of molecular variance showed that the majority of the genetic variation was explained by the genetic differences among groups. Overall, our study indicates that Chinese cattle retain high paternal diversity (H = 0.607 ± 0.016) and probably much of the original lineages that derived from the domestication center in the Near East without strong admixture from commercial cattle carrying Y1 haplotypes.