Bayesian genome-wide association analysis of growth and yearling ultrasound measures of carcass traits in Brangus heifers

Abstract

Data from developing Brangus heifers (3/8 Brahman-Bos indicus × 5/8 Angus-Bos taurus; n ≈ 802 from 67 sires) registered with International Brangus Breeders Association were analyzed to detect QTL associated with growth traits and ultrasound measures of carcass traits. Genotypes were from BovineSNP50 (Infinium BeadChip, Illumina, San Diego, CA; 53,692 SNP). Phenotypes included BW collected at birth and ∼205 and 365 d of age, and yearling ultrasound assessment of LM area, percent intramuscular fat, and depth of rib fat. Simultaneous association of SNP windows with phenotype were undertaken with Bayes C analyses, using GenSel software. The SNP windows were ≈ 5 SNP in length. Analyses fitted a mixture model that treated SNP effects as random, with an assumed fraction pi = 0.999 having no effect on phenotype. Bootstrap analyses were used to obtain significance values for the SNP windows with the greatest contribution to observed variation. The SNP windows with P < 0.01 were considered as QTL associated with a trait in which case their location was queried from dbSNP and the presence of a previously reported QTL in that location was checked in CattleQTLdb. For 9 traits, QTL were mapped to 139 regions on 25 chromosomes. Forty-one of these QTL were already described in CattleQTLdb, so 98 are new additions. The SNP windows on chromosomes 1, 3, and 6 were associated with multiple traits (i.e., 205- and 365- d BW, and ADG from birth to 205 and 365 d of age). Several chromosomes harbored regions associated with multiple traits; however, the SNP that comprised the window often varied among traits (i.e., chromosomes 1, 3, 4, 5, 6, 7, 9, 10, 11, 13, 14, 15, 16, 20, 21, 22, 24, 28, and 29). Results from whole genome association of SNP with growth and ultrasound carcass traits in developing Brangus heifers confirmed several published QTL and detected several new QTL.

Whole genome association of SNP with newborn calf cannon bone length

“…Australian investigators reported 75 SNP associations with hip height (using the BovineSNP50 array) in cattle detected at a threshold of P o0.001 in their preliminary investigations (Bolormaa and Goddard, 2009). Proportions of variance explained by markers in the present study (0.58 and 0.74, for analyses of cannon bone length or breeding value, respectively) were much larger than the range (0.11-0.28) reported for weight, growth, and ultrasound measured traits of Brangus heifers (Peters et al, 2012).…”

Genome-wide association study of growth and body composition traits in Brangus beef cattle

“…Of these 18 QTL, 7 were common to all traits studied, and the other 11 were trait-specific. Compared to previous studies, Peters et al (2012) and Saatchi et al (2014), four novel pleiotropic QTL and two novel trait-specific QTL were identified in Brangus beef cattle in this study. These four novel pleiotropic QTL, which located on BTA5 at 47-48 Mb, BTA10 at 33 Mb, BTA12 at 88 Mb, and BTA 20 at 7-8 Mb, were found to influence direct birth weight, weaning weight, yearling weight, mature weight, intramuscular fat, and/or rib eye muscle area in Brangus beef cattle.…”

“…Both genes are evolved in biological process including cellular macromolecule localization and cellular protein localization (Table S1). Peters et al (2012) detected QTL associated with longissimus muscle (GV% ¼1.3%), 365-d weight (GV%¼ 0.14%), and average daily gain (GV%¼ 0.62%), located on BTA20 at 6-8 Mb in Brangus using 50K SNP genotypes with Bayesian C approach.…”

“…QTL mapping using Brangus might identify QTL that are segregating in both Angus and Brahman. Peters et al (2012) and Saatchi et al (2014) mapped QTL for growth traits using the lower density BovineSNP50 in two subsets (835 heifers and 1328 cattle) of this same dataset of U.S. Brangus cattle, respectively. However, GWAS of Brangus using high density of SNP genotypes have not been fully addressed.…”

Genetic parameters and predictions for direct and maternal growth traits in a multibreed Angus–Brahman cattle population using genomic–polygenic and polygenic models

“…Multibreed animals genotyped with the Illumina3k chip were imputed to Illumina50k (Illumina, 2011b) with software findhap2 (VanRaden, 2011) using a reference population (RP) of 828 Brangus heifers previously genotyped with version 1 of the Illumina50k chip (Fortes et al, 2012;Peters et al, 2012). Animal relationships within the RP and MAB subpopulations were available.…”