Weighted Single-Step Genome-Wide Association Study for Growth Traits in Chinese Simmental Beef Cattle

Abstract

Improving the genetic process of growth traits is one of the major goals in the beef cattle industry, as it can increase meat production and reduce the cost of raising animals. Although several quantitative trait loci affecting growth traits in beef cattle have been identified, the genetic architecture of these economically important traits remains elusive. This study aims to map single nucleotide polymorphisms (SNPs) and genes associated with birth weight (BW), yearling weight (YW), average daily gain from birth to yearling (BYADG), and body weight at the age of 18 months (18MW) in a Chinese Simmental beef cattle population using a weighted, single-step, genome-wide association study (wssGWAS). Phenotypic and pedigree data from 6022 animals and genotypes from 744 animals (596,297 SNPs) were used for an association analysis. The results showed that 66 genomic windows explained 1.01-20.15% of the genetic variance for the four examined traits, together with the genes near the top SNP within each window. Furthermore, the identified genomic windows (>1%) explained 50.56%, 57.71%, 61.78%, and 37.82% of the genetic variances for BW, YW, BYADG, and 18MW, respectively. Genes with potential functions in muscle development and regulation of cell growth were highlighted as candidates for growth traits in Simmental cattle (SQOR and TBCB for BW, MYH10 for YW, RLF for BYADG, and ARHGAP31 for 18MW). Moreover, we found 40 SNPs that had not previously been identified as being associated with growth traits in cattle. These findings will further advance our understanding of the genetic basis for growth traits and will be useful for the molecular breeding of BW, YW, BYADG, and 18MW in the context of genomic selection in beef cattle.

Genome-Wide Association Study Based on Random Regression Model Reveals Candidate Genes Associated with Longitudinal Data in Chinese Simmental Beef Cattle

“…Bärlocher et al illustrated TBC1D5 could promote the intracellular growth of L. pneumophila [ 63 ]. Notably, Zhuang et al reported TBC1D5 might play a special role in BW at 18 months of age in Chinese Simmental beef cattle [ 11 ]. Consistent with these findings, TBC1D5 was also identified as the functional gene for the bovine BW trait in the present study.…”

“…Buzanskas et al revealed four SNPs significantly associated with the BW trait in Canchim beef cattle [ 10 ]. Zhuang et al performed the weighted single-step GWAS in 744 Chinese Simmental beef cattle with 770K BovineHD SNP BeadChip, concluding TBC1D5 and MYH10 were associated with birth weight at the age of 18 months and YW [ 11 ], respectively, of which MYH10 was also identified to be related to chicken growth traits [ 12 ]. Amounts of candidate genes and significant SNPs relevant to the BW trait have been identified and submitted to Cattle Quantitative Trait Locus Database (Cattle QTLdb) [ 13 ].…”

Key Genes Regulating Skeletal Muscle Development and Growth in Farm Animals

“…NCAPG was also reported to be in linkage disequilibrium with the average daily gain (ADG) in cattle [ 89 ]. Candidate genes for muscle development and growth identified in Simmental beef cattle include MYH10 (associated with yearling weight), RLF (associated with ADG from birth to yearling), SQOR and ARHGAP31 (associated with body weight at the age of 18 months), and TBCB (associated with birth weight) [ 90 ]. TBCB was identified as a candidate gene affecting meat quality in pigs because it is associated with actin and cytoskeleton filament development [ 91 ].…”

Genome-Wide Association Study of Growth Performance and Immune Response to Newcastle Disease Virus of Indigenous Chicken in Rwanda

“…All these candidate genes for Ab response to ND have not been heretofore directly associated with immune response in poultry (Adhikari and Davie, 2018;Elbeltagy et al, 2019). Some of these genes are new genes in the chicken and have mostly been discussed in other species (Zhou et al, 2014;Fleming et al, 2016;Zhuang et al, 2020). Further examination is therefore required to prove these novel genes as putative genes for Ab response to ND in chicken.…”