Quantitative Trait Loci Analysis on 17 Nonproduction Traits in the New Zealand Dairy Population

Spelman, R. J.; Huisman, A.E.; Singireddy, Shreya; Coppieters, R; Arranz, Juan José; Georges, Michel; Garrick, Dorian J.

doi:10.3168/jds.s0022-0302(00)74890-9

Cited by 7 publications

(7 citation statements)

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“…The most significant peak identified by DCMS was located on BTA14 in the Swedish Holstein-Friesian breed (BTA14:24.42-25.11; Mb; q-value (most significant SNP) = 2.2E − 10). Previous studies have reported that the regions around this location contain numerous genes and QTL that affect cattle stature and related traits [43][44][45][46][47]. The genes that we identified within this region, including PLAG1, CHCHD7, MOS, RPS20, and LYN, are known as major genes with a role in both human height and cattle stature [44,46,[48][49][50][51][52].…”

Section: Signatures Of Potential Human-mediated Selectionmentioning

confidence: 65%

Signatures of selection reveal candidate genes involved in economic traits and cold acclimation in five Swedish cattle breeds

et al. 2020

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Background: Thousands of years of natural and artificial selection have resulted in indigenous cattle breeds that are well-adapted to the environmental challenges of their local habitat and thereby are considered as valuable genetic resources. Understanding the genetic background of such adaptation processes can help us design effective breeding objectives to preserve local breeds and improve commercial cattle. To identify regions under putative selection, GGP HD 150 K single nucleotide polymorphism (SNP) arrays were used to genotype 106 individuals representing five Swedish breeds i.e. native to different regions and covering areas with a subarctic cold climate in the north and mountainous west, to those with a continental climate in the more densely populated south regions. Results: Five statistics were incorporated within a framework, known as de-correlated composite of multiple signals (DCMS) to detect signatures of selection. The obtained p-values were adjusted for multiple testing (FDR < 5%), and significant genomic regions were identified. Annotation of genes in these regions revealed various verified and novel candidate genes that are associated with a diverse range of traits, including e.g. high altitude adaptation and response to hypoxia (DCAF8,

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Section: Signatures Of Potential Human-mediated Selectionmentioning

confidence: 65%

Signatures of selection reveal candidate genes involved in economic traits and cold acclimation in five Swedish cattle breeds

et al. 2020

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“…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, 8–13]. Several recent studies have also established moderate heritability estimates for bovine growth traits in U.S. beef cattle including BW, WW, and YW [14–17], with a number of relevant QTL and positional candidate genes identified to date, including orthologous genes that affect both human and bovine height [2, 18–22].…”

Section: Introductionmentioning

confidence: 99%

Genome-wide association and genotype by environment interactions for growth traits in U.S. Gelbvieh cattle

et al. 2019

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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.

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“…Recent studies have focused on detection of QTL affecting conformation and functional traits (Spelman et al, 1999;Schrooten et al, 2000;Boichard et al, 2003;Hiendleder et al, 2003). Although the benefits of identifying QTL for conformation traits are less obvious, significant genetic correlations between them and production and health traits have been found.…”

Section: Introductionmentioning

confidence: 99%

Detection of Quantitative Trait Loci Influencing Conformation Traits and Calving Ease in Holstein-Friesian Cattle

Ashwell

Heyen

Weller

et al. 2005

Journal of Dairy Science

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An extension of our previous genome scan of a North American Holstein-Friesian population was conducted to identify quantitative trait loci (QTL) affecting conformation traits. Resource families consisted of 1404 sons of 10 elite sires. Genome coverage was estimated to be 2713.5 cM (90%) for 406 markers using a granddaughter design. Regression interval mapping was used to detect QTL affecting 22 conformation traits, including body, udder, feet and legs, and dairy conformation as well as calving ease. Analysis of the families jointly identified 41 chromosome-wise significant QTL influencing conformation traits and 3 significant QTL influencing calving ease on 20 chromosomes. The false discovery rate method was used to account for multiple testing and 3/4 of the suggestive and 5/6 of significant QTL should be real effects. Fourteen of the 44 QTL were significant at the genome-wise level. Comparison of these results with other published reports identifies common QTL affecting conformation traits. Regions on 10 chromosomes appear to affect multiple traits, including conformation, milk production, and somatic cell score, within these particular US Holstein families. Additional work is needed to determine the precise locations of the QTL and select positional candidate genes influencing these traits.

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Quantitative Trait Loci Analysis on 17 Nonproduction Traits in the New Zealand Dairy Population

Cited by 7 publications

References 0 publications

Signatures of selection reveal candidate genes involved in economic traits and cold acclimation in five Swedish cattle breeds

Signatures of selection reveal candidate genes involved in economic traits and cold acclimation in five Swedish cattle breeds

Genome-wide association and genotype by environment interactions for growth traits in U.S. Gelbvieh cattle

Detection of Quantitative Trait Loci Influencing Conformation Traits and Calving Ease in Holstein-Friesian Cattle

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