scholarly journals Extensive genome-wide association analyses identify genotype-by-environment interactions of growth traits in Simmental cattle

2020 ◽  
Author(s):  
Camila U. Braz ◽  
Troy N. Rowan ◽  
Robert D. Schnabel ◽  
Jared E. Decker
Keyword(s):  
Climate Change ◽  
Birth Weight ◽  
Beef Cattle ◽  
Functional Annotation ◽  
Genetic Basis ◽  
Growth Traits ◽  
Genome Wide Association ◽  
Phenotypic Variance ◽  
Genotype By Environment ◽  
Genome Wide

AbstractBackgroundUnderstanding the genetic basis of genotype-by-environment interactions (GxE) is crucial to understand environmental adaptation in mammals and improve the sustainability of agricultural production. In addition, GxE information could also be useful to predict the vulnerability of populations to climate change.ResultsHere, we present an extensive study investigating the interaction of genome-wide SNP markers with a vast assortment of environmental variables and searching for SNPs controlling phenotypic variance (vQTL) using a large beef cattle dataset. We showed that GxE contribute 10%, 4%, and 3% of the phenotypic variance of birth weight, weaning weight, and yearling weight, respectively. GxE genome-wide association analysis (GWAA) detected a large number of GxE loci affecting growth traits, which the traditional GWAA did not detect, showing that functional loci may have non-additive genetic effects between genotype classes regardless of differences in genotypic means. We also showed that variance-heterogeneity GWAA can detect loci enriched with GxE effects without requiring prior knowledge of the interacting environmental factors. Functional annotation and pathway analysis of GxE genes revealed biological mechanisms by which cattle respond to changes in their environment, such as neural signaling, metabolic, hypoxia-induced, and immune system pathways. Knowledge of these pathways will be important as climate change becomes a burden on animal health and productivity. In addition, ecoregion-specific GxE SNPs detected in this study may play a crucial role in identifying resilient and adapted beef cattle across divergent environments.ConclusionsWe detected novel trait associations with large GxE effects for birth weight, weaning weight, and yearling weight. Functional annotation and pathway analysis uncovered genomic regions involved in response to environmental stimuli. We unraveled the relevance and complexity of the genetic basis of GxE underlying growth traits, providing new insights into how different environmental conditions interact with specific genes influencing adaptation and productivity in beef cattle and potentially across mammals

scholarly journals Genome-wide association analyses identify genotype-by-environment interactions of growth traits in Simmental cattle

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Camila U. Braz ◽  
Troy N. Rowan ◽  
Robert D. Schnabel ◽  
Jared E. Decker
Keyword(s):  
Beef Cattle ◽  
Growth Traits ◽  
Extensive Study ◽  
Snp Markers ◽  
Genome Wide Association ◽  
Phenotypic Variance ◽  
Genotype By Environment Interactions ◽  
Association Analyses ◽  
Genotype By Environment ◽  
Genome Wide

AbstractUnderstanding genotype-by-environment interactions (G × E) is crucial to understand environmental adaptation in mammals and improve the sustainability of agricultural production. Here, we present an extensive study investigating the interaction of genome-wide SNP markers with a vast assortment of environmental variables and searching for SNPs controlling phenotypic variance (vQTL) using a large beef cattle dataset. We showed that G × E contribute 10.1%, 3.8%, and 2.8% of the phenotypic variance of birth weight, weaning weight, and yearling weight, respectively. G × E genome-wide association analysis (GWAA) detected a large number of G × E loci affecting growth traits, which the traditional GWAA did not detect, showing that functional loci may have non-additive genetic effects regardless of differences in genotypic means. Further, variance-heterogeneity GWAA detected loci enriched with G × E effects without requiring prior knowledge of the interacting environmental factors. Functional annotation and pathway analysis of G × E genes revealed biological mechanisms by which cattle respond to changes in their environment, such as neurotransmitter activity, hypoxia-induced processes, keratinization, hormone, thermogenic and immune pathways. We unraveled the relevance and complexity of the genetic basis of G × E underlying growth traits, providing new insights into how different environmental conditions interact with specific genes influencing adaptation and productivity in beef cattle and potentially across mammals.

PSXI-7 Genomic analysis of heterosis in a composite beef cattle breed

2021 ◽  
Vol 99 (Supplement_3) ◽  
pp. 244-244
Author(s):  
El Hamidi Hay ◽  
Andrew Roberts
Keyword(s):  
Birth Weight ◽  
Beef Cattle ◽  
Association Study ◽  
Genome Wide Association Study ◽  
Growth Traits ◽  
Snp Markers ◽  
Genome Wide Association ◽  
Weaning Weight ◽  
Genome Wide ◽  
A Genome

Abstract Crossbreeding is widely used in the beef cattle industry to exploit benefits of heterosis. This study evaluated the effects of heterozygosity on growth traits in an Angus x Hereford cross population. Moreover, a genome wide association study was conducted to detect regions in the genome with significant dominance effects on growth traits contributing to heterosis. A total of 1,530 animals, comprised of pure Line 1 Hereford, Angus and Angus x Line 1 Hereford crosses, were evaluated. Phenotypes included birth weight, weaning weight and yearling weight. All animals were genotyped with GeneSeek GGP LD 50k. Effects of genomic heterozygosity on growth traits were estimated. These effects were -0.76 kg (P < 0.001), 4.67 kg (P < 0.0001), 42.39 kg (P < 0.02) on birth weight, weaning weight and yearling weight respectively. A genome wide association study revealed several SNP markers with significant heterotic effects associated with birth weight, weaning weight and yearling weight. These SNP markers were located on chromosomes 1, 2, 14, 19, 13 and 12. Genes in these regions were reported to be involved in growth and other important physiological mechanisms. Our study revealed several regions associated with dominance effects and contributing to heterosis. These results could be beneficial in optimizing crossbreeding.

scholarly journals Genome-Wide Association for Growth Traits in Canchim Beef Cattle

PLoS ONE ◽  
2014 ◽  
Vol 9 (4) ◽  
pp. e94802 ◽  
Author(s):  
Marcos E. Buzanskas ◽  
Daniela A. Grossi ◽  
Ricardo V. Ventura ◽  
Flávio S. Schenkel ◽  
Mehdi Sargolzaei ◽  
...  
Keyword(s):  
Beef Cattle ◽  
Growth Traits ◽  
Genome Wide Association ◽  
Genome Wide

scholarly journals Genome-wide association mapping in a wild avian population identifies a link between genetic and phenotypic variation in a life-history trait

2015 ◽  
Vol 282 (1806) ◽  
pp. 20150156 ◽  
Author(s):  
Arild Husby ◽  
Takeshi Kawakami ◽  
Lars Rönnegård ◽  
Linnéa Smeds ◽  
Hans Ellegren ◽  
...  
Keyword(s):  
Life History ◽  
Association Mapping ◽  
Genetic Basis ◽  
Snp Array ◽  
Genome Wide Association ◽  
Life History Trait ◽  
Lifetime Reproductive Success ◽  
Phenotypic Variance ◽  
Sexual Antagonism ◽  
Genome Wide

Understanding the genetic basis of traits involved in adaptation is a major challenge in evolutionary biology but remains poorly understood. Here, we use genome-wide association mapping using a custom 50 k single nucleotide polymorphism (SNP) array in a natural population of collared flycatchers to examine the genetic basis of clutch size, an important life-history trait in many animal species. We found evidence for an association on chromosome 18 where one SNP significant at the genome-wide level explained 3.9% of the phenotypic variance. We also detected two suggestive quantitative trait loci (QTLs) on chromosomes 9 and 26. Fitness differences among genotypes were generally weak and not significant, although there was some indication of a sex-by-genotype interaction for lifetime reproductive success at the suggestive QTL on chromosome 26. This implies that sexual antagonism may play a role in maintaining genetic variation at this QTL. Our findings provide candidate regions for a classic avian life-history trait that will be useful for future studies examining the molecular and cellular function of, as well as evolutionary mechanisms operating at, these loci.

scholarly journals Weighted Single-Step Genome-Wide Association Study for Growth Traits in Chinese Simmental Beef Cattle

Genes ◽  
2020 ◽  
Vol 11 (2) ◽  
pp. 189 ◽  
Author(s):  
Zhanwei Zhuang ◽  
Lingyang Xu ◽  
Jie Yang ◽  
Huijiang Gao ◽  
Lupei Zhang ◽  
...  
Keyword(s):  
Beef Cattle ◽  
Association Study ◽  
Muscle Development ◽  
Genome Wide Association Study ◽  
Growth Traits ◽  
Average Daily Gain ◽  
Single Step ◽  
Genome Wide Association ◽  
Meat Production ◽  
Genome Wide

Improving the genetic process of growth traits is one of the major goals in the beef cattle industry, as it can increase meat production and reduce the cost of raising animals. Although several quantitative trait loci affecting growth traits in beef cattle have been identified, the genetic architecture of these economically important traits remains elusive. This study aims to map single nucleotide polymorphisms (SNPs) and genes associated with birth weight (BW), yearling weight (YW), average daily gain from birth to yearling (BYADG), and body weight at the age of 18 months (18MW) in a Chinese Simmental beef cattle population using a weighted, single-step, genome-wide association study (wssGWAS). Phenotypic and pedigree data from 6022 animals and genotypes from 744 animals (596,297 SNPs) were used for an association analysis. The results showed that 66 genomic windows explained 1.01–20.15% of the genetic variance for the four examined traits, together with the genes near the top SNP within each window. Furthermore, the identified genomic windows (>1%) explained 50.56%, 57.71%, 61.78%, and 37.82% of the genetic variances for BW, YW, BYADG, and 18MW, respectively. Genes with potential functions in muscle development and regulation of cell growth were highlighted as candidates for growth traits in Simmental cattle (SQOR and TBCB for BW, MYH10 for YW, RLF for BYADG, and ARHGAP31 for 18MW). Moreover, we found 40 SNPs that had not previously been identified as being associated with growth traits in cattle. These findings will further advance our understanding of the genetic basis for growth traits and will be useful for the molecular breeding of BW, YW, BYADG, and 18MW in the context of genomic selection in beef cattle.

scholarly journals Genome-wide association study for feed efficiency and growth traits in U.S. beef cattle

BMC Genomics ◽  
2017 ◽  
Vol 18 (1) ◽  
Author(s):  
Christopher M. Seabury ◽  
David L. Oldeschulte ◽  
Mahdi Saatchi ◽  
Jonathan E. Beever ◽  
Jared E. Decker ◽  
...  
Keyword(s):  
Beef Cattle ◽  
Association Study ◽  
Feed Efficiency ◽  
Genome Wide Association Study ◽  
Growth Traits ◽  
Genome Wide Association ◽  
Genome Wide

scholarly journals Genome-wide association study of appendicular lean mass in UK Biobank cohort

2019 ◽  
Author(s):  
Yu-Fang Pei ◽  
Yao-Zhong Liu ◽  
Xiao-Lin Yang ◽  
Hong Zhang ◽  
Gui-Juan Feng ◽  
...  
Keyword(s):  
Association Study ◽  
Lean Mass ◽  
Genetic Basis ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Phenotypic Variance ◽  
Uk Biobank ◽  
Appendicular Lean Mass ◽  
Gene Sets ◽  
Genome Wide

AbstractLean body mass (LBM), an important physiological measure, has a strong genetic determination. To clarify its genetic basis, a large-scale genome-wide association study (GWAS) of appendicular lean mass (ALM) was conducted in 450,580 UK Biobank subjects. A total of 717 variants (p<5×10−9) from 561 loci were identified, which were replicated across genders (achieving p<5×10−5 in both genders). The identified variants explained ~11% phenotypic variance, accounting for one quarter of the total ~40% GWAS-attributable heritability. The identified variants were enriched in gene sets related to musculoskeletal and connective tissue development. Of interest are several genes, including ADAMTS3, PAM, SMAD3 and MEF2C, that either contain multiple significant variants or serve as the hub genes of the associated gene sets. Polygenic score prediction based on the associated variants was able to distinguish subjects of high from low ALM. Overall, our results offered significant findings on the genetic basis of lean mass through an extraordinarily large sample GWAS. The findings are important to not only lean mass per se but also other complex diseases, such as type 2 diabetes and fracture, as our Mendelian randomization analysis showed that ALM is a protective factor for these two diseases.

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

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Johanna L. Smith ◽  
Miranda L. Wilson ◽  
Sara M. Nilson ◽  
Troy N. Rowan ◽  
David L. Oldeschulte ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Feed Efficiency ◽  
Growth Traits ◽  
Genome Wide Association ◽  
Positional Candidate ◽  
Genotype By Environment ◽  
Genome Wide ◽  
Nominal Significance ◽  
Pleiotropic Qtl ◽  
Heritability Estimates

Abstract Background 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). Genotype-by-environment (GxE) interactions were also investigated. Results GEMMA 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). Conclusions Pleiotropic 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.

1701-P: Genome-Wide Association Study Identifies Novel Potential Associations with Birth Weight in a Southwestern American Indian Population

Diabetes ◽  
2019 ◽  
Vol 68 (Supplement 1) ◽  
pp. 1701-P
Author(s):  
LAUREN E. WEDEKIND ◽  
WEN-CHI HSUEH ◽  
SAYUKO KOBES ◽  
MUIDEEN T. OLAIYA ◽  
WILLIAM C. KNOWLER ◽  
...  
Keyword(s):  
Birth Weight ◽  
American Indian ◽  
Association Study ◽  
Indian Population ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
American Indian Population ◽  
Genome Wide

scholarly journals Comprehensive Genome-Wide Association Analysis Reveals the Genetic Basis of Root System Architecture in Soybean

2020 ◽  
Vol 11 ◽  
Author(s):  
Waldiodio Seck ◽  
Davoud Torkamaneh ◽  
François Belzile
Keyword(s):  
Root System ◽  
System Architecture ◽  
Phenotypic Variation ◽  
Genetic Basis ◽  
Genome Wide Association Study ◽  
Primary Root ◽  
Root System Architecture ◽  
Genome Wide Association ◽  
Nucleotide Polymorphisms ◽  
Genome Wide

Increasing the understanding genetic basis of the variability in root system architecture (RSA) is essential to improve resource-use efficiency in agriculture systems and to develop climate-resilient crop cultivars. Roots being underground, their direct observation and detailed characterization are challenging. Here, were characterized twelve RSA-related traits in a panel of 137 early maturing soybean lines (Canadian soybean core collection) using rhizoboxes and two-dimensional imaging. Significant phenotypic variation (P &lt; 0.001) was observed among these lines for different RSA-related traits. This panel was genotyped with 2.18 million genome-wide single-nucleotide polymorphisms (SNPs) using a combination of genotyping-by-sequencing and whole-genome sequencing. A total of 10 quantitative trait locus (QTL) regions were detected for root total length and primary root diameter through a comprehensive genome-wide association study. These QTL regions explained from 15 to 25% of the phenotypic variation and contained two putative candidate genes with homology to genes previously reported to play a role in RSA in other species. These genes can serve to accelerate future efforts aimed to dissect genetic architecture of RSA and breed more resilient varieties.

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