Assessing genomic diversity and signatures of selection in Jiaxian Red cattle using whole-genome sequencing data

Abstract

Background Native cattle breeds are an important source of genetic variation because they might carry alleles that enable them to adapt to local environment and tough feeding conditions. Jiaxian Red, a Chinese native cattle breed, is reported to have originated from crossbreeding between taurine and indicine cattle; their history as a draft and meat animal dates back at least 30 years. Using whole-genome sequencing (WGS) data of 30 animals from the core breeding farm, we investigated the genetic diversity, population structure and genomic regions under selection of Jiaxian Red cattle. Furthermore, we used 131 published genomes of world-wide cattle to characterize the genomic variation of Jiaxian Red cattle. Results The population structure analysis revealed that Jiaxian Red cattle harboured the ancestry with East Asian taurine (0.493), Chinese indicine (0.379), European taurine (0.095) and Indian indicine (0.033). Three methods (nucleotide diversity, linkage disequilibrium decay and runs of homozygosity) implied the relatively high genomic diversity in Jiaxian Red cattle. We used θπ, CLR, FST and XP-EHH methods to look for the candidate signatures of positive selection in Jiaxian Red cattle. A total number of 171 (θπ and CLR) and 17 (FST and XP-EHH) shared genes were identified using different detection strategies. Functional annotation analysis revealed that these genes are potentially responsible for growth and feed efficiency (CCSER1), meat quality traits (ROCK2, PPP1R12A, CYB5R4, EYA3, PHACTR1), fertility (RFX4, SRD5A2) and immune system response (SLAMF1, CD84 and SLAMF6). Conclusion We provide a comprehensive overview of sequence variations in Jiaxian Red cattle genomes. Selection signatures were detected in genomic regions that are possibly related to economically important traits in Jiaxian Red cattle. We observed a high level of genomic diversity and low inbreeding in Jiaxian Red cattle. These results provide a basis for further resource protection and breeding improvement of this breed.

Assessing Genomic Diversity and Productivity Signatures in Dianzhong Cattle by Whole-Genome Scanning

“…Genomic features may reflect a variety of multifarious historical events, including climate change, species introduction, and artificial selection (Chen et al, 2021). The characteristics of population genetic diversity are essential for assessing the genetic potential of breeds as well as for the utilization and protection of cattle breed resources (Xia et al, 2021). In this study, three underlying ancestors of Dianzhong cattle were selected as reference groups to explore the genetic information of Dianzhong cattle.…”

“…Dianzhong cattle, belonging to hybrid cattle, obtained more abundant genetic information from multiple genetic sources, while Chinese zebu had high nucleotide diversity which may be due to previous reception of introgression from Banteng (Bos javanicus) Chen et al, 2018). The monotonous environment and high degree of breeding may be the reasons why the nucleotide diversity of Yanbian cattle is lower than that of indicine and hybrid cattle (Singh et al, 2021;Xia et al, 2021). In addition, more 2-4 MB and 1-2 MB ROHs and more rapid LD decayed in Yanbian cattle confirmed this once again.…”

“…The LD decay for each group was measured using PopLDdecay (Zhang et al, 2019) with default parameters. Runs of homozygosity (ROHs) were identified using the Runs of Homozygosity program implemented in PLINK, which slides a window of 50 SNPs (-homozyg-window-snp 50) across the genome in estimating homozygosity (Xia et al, 2021). The following settings were performed for ROH identification: -homozyg-density 50 -homozyg-window-het 1 -homozygwindow-missing 2.…”

“…Based on whole-genome sequencing, many studies initially focused on the genetic architecture and economic traits under positive selection in commercial breeds (Bovine et al, 2009;Stothard et al, 2011), and then the focus gradually shifted to the adaptation of indigenous breeds, such as climate tolerance and disease resistance (Kim et al, 2017;Taye et al, 2017;Kim et al, 2020). With the development of next-generation sequencing technology and the enrichment of re-sequencing databases, genome-wide genetic analysis studies play an increasingly powerful role in the investigation of germplasm resources of landraces, such as cold tolerance of Yanbian cattle (Shen et al, 2020), excellent meat quality of Mongolian cattle (Chen et al, 2021), heat tolerance and parasite resistance of African cattle (Kim et al, 2017), and growth rate and feed conversion of Jiaxian red cattle (Xia et al, 2021). An earlier study on Dianzhong cattle using Illumina BovineHD BeadChip (777K) demonstrated that Dianzhong cattle contained mainly indicine ancestry mixed with taurine ancestry.…”

Assessing Genomic Diversity and Selective Pressures in Bohai Black Cattle Using Whole-Genome Sequencing Data

“…All of these pathways had p -values less than 0.05. In particular, some overlapped candidate genes were strongly selected in Bohai Black cattle and related to muscle development ( ITGA9 , ENAH , CAPG , ABI2 , and ISLR ) [ 39 , 40 ], fat deposition ( TBC1D1 , CYB5R4 , TUSC3 , and EPS8 ) [ 41 , 42 , 43 ], reproduction traits ( SPIRE2 , KHDRBS2 , and FANCA ) [ 44 , 45 ], and immune system ( CD84 , SLAMF6 , SLAMF1 , and CDK10 ) [ 46 , 47 , 48 ] in Bohai Black cattle ( Tables S9 and S10 , Figure 4 a). Interestingly, the selection signal was found on BTA3 (3:9070076-9175511) and contained the CD84 and SLAMF6 genes from the two tests ( Figure 4 b,c).…”