Estimation of the Genetic Substitution Rate of Hanwoo and Holstein Cattle Using Whole Genome Sequencing Data

Abstract

Despite the importance of mutation rate, some difficulties exist in estimating it. Next-generation sequencing (NGS) data yields large numbers of single-nucleotide polymorphisms, which can make it feasible to estimate substitution rates. The genetic substitution rates of Hanwoo and Holstein cattle were estimated using NGS data. Our main findings was to calculate the gene’s substitution rates. Through estimation of genetic substitution rates, we found: diving region of altered substitution density exists. This region may indicate a boundary between protected and unprotected genes. The protected region is mainly associated with the gene ontology terms of regulatory genes. The genes that distinguish Hanwoo from Holstein in terms of substitution rate predominantly have gene ontology terms related to blood and circulatory system. This might imply that Hanwoo and Holstein evolved with dissimilar mutation rates and processes after domestication. The difference in meat quality between Hanwoo and Holstein could originate from differential evolution of the genes related to these blood and circulatory system ontology terms.

Whole-genome resequencing of major populations revealed domestication-related genes in yaks

“…SPATA5 (spermatogenesis associated 5) is associated with catalytic activity in Swiss [ 21 ] and meat traits in Hu sheep [ 22 ]. GRHL2 (grainyhead-like transcription factor 2) has a maternal-related effect on the intramuscular fat content in cattle [ 23 ]. Additionally, gene regulation is involved in human and mouse embryo development [ 24 ].…”

Genome-Wide Association Study for Body Weight and Carcass Weight in Sumba Ongole Bulls (Bos indicus)

“…The mouse embryonic fibroblast with a deficiency of CEP63 protein reduces the centriole number and microcephaly (Brown et al, 2013). Lee & Shin (2018) reported that the substitution rate of the CEP63 gene in Hanwoo was higher than in Friesian Holstein cattle (7.49E-11 vs 5.70E-11). The CEP63 gene has been identified as a potential gene for milk phosphorus content (Chen et al, 2018) and feed intake (Salleh et al, 2018) in dairy cattle.…”