Estimation of linkage disequilibrium levels and haplotype block structure in Chinese Simmental and Wagyu beef cattle using high-density genotypes

• The average LD at the same genetic distance in Chinese Wagyu was higher than that in Simmental.
• LD decayed more slowly on the X chromosome than autosomes in Simmental and Wagyu.
• 50,475 haplotype blocks shared by two populations, 18,440 unique blocks in Chinese Simmental and 15,417 in Wagyu.
• The r2 dropped below 0.2 at distances of 34 kb and 40 kb in Chinese Simmental and Wagyu.

With the advance of high-throughput genotyping technologies, it is possible to estimate the pattern of linkage disequilibrium (LD) and haplotype block structure at genome wide level in farm animals. Understanding LD characteristics and haplotype blocks can provide useful information to guide genome wide association study (GWAS) and genomic selection (GS). In this study, we investigated the LD pattern and haplotype block structure in two beef cattle populations (Chinese Simmental and Wagyu) using the BovineHD BeadChip. We found the average LD measured by r2 in Chinese Wagyu was higher than that in Simmental. We observed LD decayed more slowly on the X chromosome than autosomes for both populations. The persistence of LD phase varied from 0.96 at a distance of <2.5 kb to 0.51 at a distance from 400 kb to 500 kb. The estimated ancestral effective population sizes (Ne) in Chinese Simmental and Wagyu 5 years ago were approximately 74 and 23, respectively. Moreover, we detected 50,475 (991.1 Mb, 69.3%) haplotype blocks shared by two populations, 18,440 (238.9 Mb, 16.7%) unique blocks in Chinese Simmental and 15,417 (199.8 Mb, 14%) in Wagyu. Our study revealed that the r2 dropped below 0.2 at distances of 34 kb and 40 kb in Chinese Simmental and Wagyu, which indicated that the implementation of GS for both populations require at least 77,941 and 66,250 markers, respectively. The pattern of LD mirrored the slightly different selection histories for Chinese Simmental and Wagyu, and our result suggested the shared haplotype blocks may offer valuable insights for the implementation of genome wide association and genomic selection studies based on multi-population.