Abstract
Simple SummaryEvaluation of the population structure and linkage disequilibrium can offer important insights to fully understand the genetic diversity and population history of cattle, which can enable us to appropriately design and implement GWAS and GS in cattle. In this study, we characterized the extent of genome-wide LD and the haplotype block structure, and estimated the persistence of phase of Chinese indigenous cattle with Illumina BovineHD BeadChip. According to our study, 58K, 87K, 95K, 52K, and 52K markers would be necessary for SCHC, NCC, SWC, SIM, and WAG, respectively, in the implementation of GWAS and GS and combining a multipopulation with high persistence of phase is feasible for the implication of genomic selection for Chinese beef cattle.Understanding the linkage disequilibrium (LD) across the genome, haplotype structure, and persistence of phase between breeds can enable us to appropriately design and implement the genome-wide association (GWAS) and genomic selection (GS) in beef cattle. We estimated the extent of genome-wide LD, haplotype block structure, and the persistence of phase in 10 Chinese cattle population using high density BovinHD BeadChip. The overall LD measured by r2 between adjacent SNPs were 0.60, 0.67, 0.58, 0.73, and 0.71 for South Chinese cattle (SCHC), North Chinese cattle (NCC), Southwest Chinese cattle (SWC), Simmental (SIM), and Wagyu (WAG). The highest correlation (0.53) for persistence of phase across groups was observed for SCHC vs. SWC at distances of 0–50 kb, while the lowest correlation was 0.13 for SIM vs. SCHC at the same distances. In addition, the estimated current effective population sizes were 27, 14, 31, 34, and 43 for SCHC, NCC, SWC, SIM, and WAG, respectively. Our result showed that 58K, 87K, 95K, 52K, and 52K markers were required for implementation of GWAS and GS in SCHC, NCC, SWC, SIM, and WAG, respectively. Also, our findings suggested that the implication of genomic selection for multipopulation with high persistence of phase is feasible for Chinese cattle.
Highlights
High-throughput genotype technology has revolutionized genome-scale studies and offers an effective strategy to investigate population structure and genetic diversity [1]
quality control (QC), a analysis, we found that SIM and WAG were separated from other Chinese indigenous cattle
As selection can change the level of linkage disequilibrium (LD), our result indicated that Southwest Chinese cattle (SWC) and North Chinese cattle (NCC) may be under moderate selection compared with South Chinese cattle (SCHC) [38]
Summary
High-throughput genotype technology has revolutionized genome-scale studies and offers an effective strategy to investigate population structure and genetic diversity [1] This technology provides new opportunities to analyze linkage disequilibrium (LD) at a genome-wide level. The detection of high resolution LD pattern and characterization of haplotype block structure of the bovine genome can provide important insights into understanding economically important traits, which are under selection for different agricultural purposes [7]. Evaluation of the extent of genome-wide LD can offer important insights to understanding the cattle genetic diversity and population history. We characterized the extent of genome-wide LD patterns and haplotype blocks in Chinese cattle (10 Chinese indigenous cattle populations and two imported breeds) using Illumina. BovineHD BeadChip (Illumina, Inc., San Diego, CA), and the persistence of phase between breeds was estimated to evaluate the feasibility of multibreed genomic prediction for these populations
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
