Signatures of positive selection underlying beef production traits in Korean cattle breeds

Abstract

The difference in the breeding programs and population history may have diversely shaped the genomes of Korean native cattle breeds. In the absence of phenotypic data, comparisons of breeds that have been subjected to different selective pressures can aid to identify genomic regions and genes controlling qualitative and complex traits. In this study to decipher genetic variation and identify evidence of divergent selection, 3 Korean cattle breeds were genotyped using the recently developed high-density GeneSeek Genomic Profiler F250 (GGP-F250) array. The three Korean cattle breeds clustered according to their coat color phenotypes and breeding programs. The Heugu breed reliably showed smaller effective population size at all generations considered. Across the autosomal chromosomes, 113 and 83 annotated genes were identified from Hanwoo-Chikso and Hanwoo-Heugu comparisons, respectively of which 16 genes were shared between the two pairwise comparisons. The most important signals of selection were detected on bovine chromosomes 14 (24.39-25.13 Mb) and 18 (13.34-15.07 Mb), containing genes related to body size, and coat color (XKR4, LYN, PLAG1, SDR16C5, TMEM68, CDH15, MC1R, and GALNS). Some of the candidate genes are also associated with meat quality traits (ACSF3, EIF2B1, BANP, APCDD1, and GALM) and harbor quantitative trait locus (QTL) for beef production traits. Further functional analysis revealed that the candidate genes (DBI, ACSF3, HINT2, GBA2, AGPAT5, SCAP, ELP6, APOB, and RBL1) were involved in gene ontology (GO) terms relevant to meat quality including fatty acid oxidation, biosynthesis, and lipid storage. Candidate genes previously known to affect beef production and quality traits could be used in the beef cattle selection strategies.

Genome-wide association study of trypanosome prevalence and morphometric traits in purebred and crossbred Baoulé cattle of Burkina Faso

“…This region harbors the GALM gene involved in glycol-metabolism and meat quality traits in cattle [ 34 ]. This genomic region was also identified to harbor a selection signature for body weight in Korean breeds [ 35 ]. The gene TMEM178A was found to be suggestively associated with loin muscularity in multiple beef cattle breeds [ 36 ].…”

Whole-genome selective sweeps analysis in Pakistani Kamori goat

“…Some examples include ZFPM1 that is under selection in African sheep for milk yield [18]. The ACSF3 gene is reported to be under selection in Korean cattle for meat production [19]. The PIEZO1, CDH15, TDP2, EIF2S2, DUSP15 genes have previously been found…”

Whole Genome Selective Sweeps Analysis in Pakistani Kamori Goat

“…Some examples include ZFPM1 that is under selection in African sheep for milk yield [18]. The ACSF3 gene is reported to be under selection in Korean cattle for meat production [19]. The PIEZO1, CDH15, TDP2, EIF2S2, DUSP15 genes have previously been found under selection in humans for body height trait [20].…”