A whole genome association study to detect additive and dominant single nucleotide polymorphisms for growth and carcass traits in Korean native cattle, Hanwoo

Abstract

ObjectiveA whole genome association study was conducted to identify single nucleotide polymorphisms (SNPs) with additive and dominant effects for growth and carcass traits in Korean native cattle, Hanwoo.MethodsThe data set comprised 61 sires and their 486 Hanwoo steers that were born between spring of 2005 and fall of 2007. The steers were genotyped with the 35,968 SNPs that were embedded in the Illumina bovine SNP 50K beadchip and six growth and carcass quality traits were measured for the steers. A series of lack-of-fit tests between the models was applied to classify gene expression pattern as additive or dominant.ResultsA total of 18 (0), 15 (3), 12 (8), 15 (18), 11 (7), and 21 (1) SNPs were detected at the 5% chromosome (genome) - wise level for weaning weight (WWT), yearling weight (YWT), carcass weight (CWT), backfat thickness (BFT), longissimus dorsi muscle area (LMA) and marbling score, respectively. Among the significant 129 SNPs, 56 SNPs had additive effects, 20 SNPs dominance effects, and 53 SNPs both additive and dominance effects, suggesting that dominance inheritance mode be considered in genetic improvement for growth and carcass quality in Hanwoo. The significant SNPs were located at 33 quantitative trait locus (QTL) regions on 18 Bos Taurus chromosomes (i.e. BTA 3, 4, 5, 6, 7, 9, 11, 12, 13, 14, 16, 17, 18, 20, 23, 26, 28, and 29) were detected. There is strong evidence that BTA14 is the key chromosome affecting CWT. Also, BTA20 is the key chromosome for almost all traits measured (WWT, YWT, LMA).ConclusionThe application of various additive and dominance SNP models enabled better characterization of SNP inheritance mode for growth and carcass quality traits in Hanwoo, and many of the detected SNPs or QTL had dominance effects, suggesting that dominance be considered for the whole-genome SNPs data and implementation of successive molecular breeding schemes in Hanwoo.

Structural Equation Modeling and Whole-Genome Scans Uncover Chromosome Regions and Enriched Pathways for Carcass and Meat Quality in Beef

“…Genomic regions inside or close to the 4w3, 17w4, 20w2, and 27w1 chromosome regions have been previously reported as associated with marbling, fatty acid composition and WBSF ( Cesar et al, 2014 ; Chen et al, 2015 ; Castro et al, 2017 ; Li et al, 2017 ) suggesting that the effect reported on WBSF may be an indirect effect of these genomic regions on meat quality through a direct effect on MARB.…”

“…Proteins such as CASKIN2, CDH11, ENSBTAG00000048046, and OGFRL1 are cell proliferation promoters or cell cycle modulators influencing intramuscular and subcutaneous adipocyte proliferation (MARB and FOR). In this regard, several genomic regions inside or close to 2w4, 8w4, 9w1, 14w2, 19w10, 19w4, and 19w8 are associated with FOR and fatty acid composition ( Ishii et al, 2013 ; Saatchi et al, 2013 ; Chen et al, 2015 ; Li et al, 2017 ; Zhu et al, 2017 ).…”

Genomic partitioning of growth traits using a high-density single nucleotide polymorphism array in Hanwoo (Korean cattle)

“…No gene with a large genetic effect on this trait was observed, but some chromosomes, such as BTA 14, 3, and 19, had moderate genetic effects on the growth traits. Yi et al [ 16 ] performed a GWAS to detect QTLs affecting growth traits. That study found 16 significant SNPs for weaning weight (WWT) and 18 significant SNPs for 365-d yearling weight (YWT) in Hanwoo.…”

Extreme sampling design in genetic association mapping of quantitative trait loci using balanced and unbalanced case-control samples

“…We simulate a wide range of scenarios under dominant, recessive, and multiplicative models to identify situations where extreme selection strategies should profitably be employed. The enhancement in power is also illustrated through two real data application: the methadone doses (MD) in former heroin addicts undergoing methadone maintenance treatment (MMT) in Israel 10 , and the yearling weight in Korean native beef cattle 11 . Our observations offer a practical guide for researchers to choose an appropriate threshold in defining cases and controls.…”