Discovery of Genomic Characteristics and Selection Signatures in Southern Chinese Local Cattle

Abstract

Chinese local cattle with a high level of genetic diversity mainly originate from two subspecies; the cattle in northern China are primarily Bos Taurus, and the cattle in southern China are primarily Bos indicus. Cattle from southern China are characterized by a specific phenotype and adapted to the local environment. This study explored the genetic diversity, degree of admixture, and selection signature in eight local cattle breeds in southern China. The lowest level of heterozygosity was found in Hainan and Nandan cattle from Hainan and Guangxi province, respectively, whereas the highest level of heterozygosity was detected in Zhaotong cattle from Yunnan province. A neighbor-joining phylogenetic tree analysis clearly separated Lufeng cattle from other breeds, whereas Leiqiong and Hainan cattle have some crossover. Based on linkage disequilibrium-filtered single nucleotide polymorphisms (SNPs), the admixture analysis revealed two clusters corresponding to the taurine and indicine cattle lineages, and the local cattle breeds from southern China showed a certain degree of admixture. When K = 4 and 9, we found a slight separation among Leiqiong, Lufeng, and Hainan cattle. Meanwhile, we performed a selection signature analysis in Hainan, Leiqiong, and Lufeng cattle distributed in the extreme south of China, using the integrated haplotype score (iHS), Rsb statistic, and BayeScan software. Using the iHS approach, we identified 251, 270, and 256 candidate regions in Lufeng, Leiqiong, and Hainan cattle, respectively. Moreover, we identified 184, 174, and 146 candidate regions in pairwise comparisons of Leiqiong vs. Lufeng, Leiqiong vs. Hainan, and Hainan vs. Lufeng cattle using the Rsb approach. In addition, we identified 76 loci with a total of 48 genes under selection, based on the FST approach. Several candidate genes under selection were found to be related to meat quality, immunity, and adaptation to the local environment in southern China. Our results provide significant information about the genetic differences among the cattle breeds from southern China and the possible cause of difference in breed-specific characteristics. Selection signature analysis identified a few candidate SNPs and genes related to certain important traits of these cattle. In general, our results provide valuable insights into the genetic basis of specific traits under selection in certain local cattle breeds.

Whole-Genome Resequencing of Xiangxi Cattle Identifies Genomic Diversity and Selection Signatures

“…In the present study, the genomic variation parameters of the populations all had a similar trend. We ranked all breeds according to their nucleotide diversity (Chinese indicine > Xiangxi cattle > Qinchuan cattle > Indian indicine > taurine cattle), which was consistent with the previous study ( Liu et al, 2020 ). By contrasting the two Chinese breeds, it was found that the genetic diversity of Xiangxi cattle exceeded the Qinchuan cattle, possibly because of the fact that Xiangxi cattle contained more Chinese indicine cattle lineage.…”

Assessing the Genetic Background and Selection Signatures of Huaxi Cattle Using High-Density SNP Array

“…We also applied the norm module of selscan to normalize the iHS score, and calculated the average |iHS| score in 100 kb non-overlapping windows across the autosomes. Regions at the top 1% with the highest average |iHS| score and SNP numbers greater than 10 were regarded as candidate regions of positive selection [ 42 ]. For the CLR test, we employed the software SweeD v3.2.1 ( , accessed on 10 October 2021) to calculate the CLR values for sites every 20 kb across each chromosome of the genome [ 43 ].…”

Whole-Genome Analyses Reveal Genomic Characteristics and Selection Signatures of Lincang Humped Cattle at the China–Myanmar Border

“…Yunnan province in China is traversed by the Tropic of Cancer, which is mainly a tropical and subtropical climate zone. Recent studies have identified the complex genetic diversity and admixture patterns of cattle breeds in Yunnan province ( Chen et al, 2018 ; R.; Li et al, 2019 ; Liu et al, 2020 ). Lincang humped cattle is the more primitive regional livestock breed mainly distributed in the southern part of Lincang and Pu’er cities in Yunnan province bordering Myanmar ( Gan, 2011 ).…”