Abstract
BackgroundSingle nucleotide polymorphism (SNP) arrays have facilitated discovery of genetic markers associated with complex traits in domestic cattle; thereby enabling modern breeding and selection programs. Genome-wide association analyses (GWAA) for growth traits were conducted on 10,837 geographically diverse U.S. Gelbvieh cattle using a union set of 856,527 imputed SNPs. Birth weight (BW), weaning weight (WW), and yearling weight (YW) were analyzed using GEMMA and EMMAX (via imputed genotypes). Genotype-by-environment (GxE) interactions were also investigated.ResultsGEMMA and EMMAX produced moderate marker-based heritability estimates that were similar for BW (0.36–0.37, SE = 0.02–0.06), WW (0.27–0.29, SE = 0.01), and YW (0.39–0.41, SE = 0.01–0.02). GWAA using 856K imputed SNPs (GEMMA; EMMAX) revealed common positional candidate genes underlying pleiotropic QTL for Gelbvieh growth traits on BTA6, BTA7, BTA14, and BTA20. The estimated proportion of phenotypic variance explained (PVE) by the lead SNP defining these QTL (EMMAX) was larger and most similar for BW and YW, and smaller for WW. Collectively, GWAAs (GEMMA; EMMAX) produced a highly concordant set of BW, WW, and YW QTL that met a nominal significance level (P ≤ 1e-05), with prioritization of common positional candidate genes; including genes previously associated with stature, feed efficiency, and growth traits (i.e., PLAG1, NCAPG, LCORL, ARRDC3, STC2). Genotype-by-environment QTL were not consistent among traits at the nominal significance threshold (P ≤ 1e-05); although some shared QTL were apparent at less stringent significance thresholds (i.e., P ≤ 2e-05).ConclusionsPleiotropic QTL for growth traits were detected on BTA6, BTA7, BTA14, and BTA20 for U.S. Gelbvieh beef cattle. Seven QTL detected for Gelbvieh growth traits were also recently detected for feed efficiency and growth traits in U.S. Angus, SimAngus, and Hereford cattle. Marker-based heritability estimates and the detection of pleiotropic QTL segregating in multiple breeds support the implementation of multiple-breed genomic selection.
Highlights
Single nucleotide polymorphism (SNP) arrays have facilitated discovery of genetic markers associated with complex traits in domestic cattle; thereby enabling modern breeding and selection programs
Genome-wide association analyses (GWAA) for birth weight (BW), weaning weight (WW), and yearling weight (YW) in U.S Gelbvieh beef cattle The results of our 856K single-marker analyses for BW (GEMMA; EMMAX) [27,28,29] are shown in Fig. 1 and in Figure S1 (Additional File 1), with detailed summary data for quantitative trait loci (QTL) detected by GEMMA and EMMAX described in Table 2 and Table S1, respectively
QTL signals for BW were detected on BTA6, BTA7, BTA14, and BTA20 across both analyses (Table 2, Table S1, Additional File 1), and included an array of positional candidate genes generally involved in diverse aspects of mammalian growth and development (i.e., CCSER1, ST18, RP1/XKR4, SLIT2, STC2, IBSP) as well as bovine growth (i.e., NCAPG, LCORL, KCNIP4, ARRDC3), stature (i.e., PLAG1), and production traits (i.e., IMPAD1/FAM110B, HERC6/PPM1K) [2, 13, 14, 18, 21, 22, 30, 32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60]
Summary
Single nucleotide polymorphism (SNP) arrays have facilitated discovery of genetic markers associated with complex traits in domestic cattle; thereby enabling modern breeding and selection programs. Genome-wide association analyses (GWAA) for growth traits were conducted on 10,837 geographically diverse U.S Gelbvieh cattle using a union set of 856,527 imputed SNPs. Birth weight (BW), weaning weight (WW), and yearling weight (YW) were analyzed using GEMMA and EMMAX (via imputed genotypes). Growth traits are commonly recorded and used as selection criteria within modern beef cattle breeding programs and production systems; primarily because of their correlation with increased overall meat production and other economically important traits [1,2,3,4]. Given the increasing economic importance of growth traits in beef cattle, a number of studies have sought to identify quantitative trait loci (QTL) influencing bovine body weight, growth, and aspects of stature, including both linkage studies and modern genome-wide association analyses [2, 8,9,10,11,12,13]. The results of this study are expected to positively augment current beef cattle breeding programs and production systems, for U.S Gelbvieh cattle, and serve to highlight the increasing potential for eliciting economic impacts from industrysupported research frameworks that were developed for enhancing U.S food security
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