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.

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

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 250 Genome wide Association analyses for meat quality traits in multibreed and crossbred beef cattle.

2018 ◽  
Vol 96 (suppl_3) ◽  
pp. 84-84
Author(s):  
M Abo-Ismail ◽  
J Crowley ◽  
E Akanno ◽  
C Li ◽  
P Stothard ◽  
...  
Keyword(s):  
Beef Cattle ◽  
Meat Quality ◽  
Genome Wide Association ◽  
Quality Traits ◽  
Association Analyses ◽  
Meat Quality Traits ◽  
Genome Wide

scholarly journals Genome-wide association for heifer reproduction and calf performance traits in beef cattle

Genome ◽  
2015 ◽  
Vol 58 (12) ◽  
pp. 549-557 ◽  
Author(s):  
Everestus C. Akanno ◽  
Graham Plastow ◽  
Carolyn Fitzsimmons ◽  
Stephen P. Miller ◽  
Vern Baron ◽  
...  
Keyword(s):  
Beef Cattle ◽  
Genome Wide Association Study ◽  
Average Daily Gain ◽  
Snp Markers ◽  
Genome Wide Association ◽  
Research Centre ◽  
Genome Wide ◽  
A Genome ◽  
Starting Point ◽  
And Performance

The aim of this study was to identify SNP markers that associate with variation in beef heifer reproduction and performance of their calves. A genome-wide association study was performed by means of the generalized quasi-likelihood score (GQLS) method using heifer genotypes from the BovineSNP50 BeadChip and estimated breeding values for pre-breeding body weight (PBW), pregnancy rate (PR), calving difficulty (CD), age at first calving (AFC), calf birth weight (BWT), calf weaning weight (WWT), and calf pre-weaning average daily gain (ADG). Data consisted of 785 replacement heifers from three Canadian research herds, namely Brandon Research Centre, Brandon, Manitoba, University of Alberta Roy Berg Kinsella Ranch, Kinsella, Alberta, and Lacombe Research Centre, Lacombe, Alberta. After applying a false discovery rate correction at a 5% significance level, a total of 4, 3, 3, 9, 6, 2, and 1 SNPs were significantly associated with PBW, PR, CD, AFC, BWT, WWT, and ADG, respectively. These SNPs were located on chromosomes 1, 5–7, 9, 13–16, 19–21, 24, 25, and 27–29. Chromosomes 1, 5, and 24 had SNPs with pleiotropic effects. New significant SNPs that impact functional traits were detected, many of which have not been previously reported. The results of this study support quantitative genetic studies related to the inheritance of these traits, and provides new knowledge regarding beef cattle quantitative trait loci effects. The identification of these SNPs provides a starting point to identify genes affecting heifer reproduction traits and performance of their calves (BWT, WWT, and ADG). They also contribute to a better understanding of the biology underlying these traits and will be potentially useful in marker- and genome-assisted selection and management.

scholarly journals Genome-wide association study reveals candidate genes for flowering time in cowpea (Vigna unguiculata [L.] Walp)

2021 ◽  
Author(s):  
Dev Paudel ◽  
Rocheteau Dareus ◽  
Julia Rosenwald ◽  
Maria Munoz-Amatriain ◽  
Esteban Rios
Keyword(s):  
Flowering Time ◽  
Candidate Genes ◽  
Vigna Unguiculata ◽  
Association Studies ◽  
Snp Markers ◽  
Genome Wide Association ◽  
Human Consumption ◽  
Phenotypic Variance ◽  
Genome Wide Association Studies ◽  
Genome Wide

Cowpea (Vigna unguiculata [L.] Walp., diploid, 2n = 22) is a major crop used as a protein source for human consumption as well as a quality feed for livestock. It is drought and heat tolerant and has been bred to develop varieties that are resilient to changing climates. Plant adaptation to new climates and their yield are strongly affected by flowering time. Therefore, understanding the genetic basis of flowering time is critical to advance cowpea breeding. The aim of this study was to perform genome-wide association studies (GWAS) to identify marker trait associations for flowering time in cowpea using single nucleotide polymorphism (SNP) markers. A total of 367 accessions from a cowpea mini-core collection were evaluated in Ft. Collins, CO in 2019 and 2020, and 292 accessions were evaluated in Citra, FL in 2018. These accessions were genotyped using the Cowpea iSelect Consortium Array that contained 51,128 SNPs. GWAS revealed seven reliable SNPs for flowering time that explained 8-12% of the phenotypic variance. Candidate genes including FT, GI, CRY2, LSH3, UGT87A2, LIF2, and HTA9 that are associated with flowering time were identified for the significant SNP markers. Further efforts to validate these loci will help to understand their role in flowering time in cowpea, and it could facilitate the transfer of some of this knowledge to other closely related legume species.

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 analyses of plant growth traits during the stem elongation phase in wheat

2018 ◽  
Vol 16 (12) ◽  
pp. 2042-2052 ◽  
Author(s):  
Zifeng Guo ◽  
Guozheng Liu ◽  
Marion S. Röder ◽  
Jochen C. Reif ◽  
Martin W. Ganal ◽  
...  
Keyword(s):  
Plant Growth ◽  
Growth Traits ◽  
Stem Elongation ◽  
Genome Wide Association ◽  
Association Analyses ◽  
Genome Wide ◽  
Elongation Phase

scholarly journals Genome-wide association analyses for carcass quality in crossbred beef cattle

BMC Genetics ◽  
2013 ◽  
Vol 14 (1) ◽  
pp. 80 ◽  
Author(s):  
Duc Lu ◽  
Mehdi Sargolzaei ◽  
Matthew Kelly ◽  
Gordon Vander Voort ◽  
Zhiquan Wang ◽  
...  
Keyword(s):  
Beef Cattle ◽  
Genome Wide Association ◽  
Carcass Quality ◽  
Association Analyses ◽  
Genome Wide

Genome-wide association analyses of common wheat (Triticum aestivum L.) germplasm identifies multiple loci for aluminium resistanceThis article is one of a selection of papers from the conference “Exploiting Genome-wide Association in Oilseed Brassicas: a model for genetic improvement of major OECD crops for sustainable farming”

Genome ◽  
2010 ◽  
Vol 53 (11) ◽  
pp. 957-966 ◽  
Author(s):  
Harsh Raman ◽  
Benjamin Stodart ◽  
Peter R. Ryan ◽  
Emmanuel Delhaize ◽  
Livinus Emebiri ◽  
...  
Keyword(s):  
Triticum Aestivum ◽  
Association Mapping ◽  
Common Wheat ◽  
Acid Soils ◽  
Triticum Aestivum L ◽  
Genome Wide Association ◽  
Phenotypic Variance ◽  
Association Analyses ◽  
Genome Wide ◽  
Genomic Regions

Aluminium (Al3+) toxicity restricts productivity and profitability of wheat ( Triticum aestivum L.) crops grown on acid soils worldwide. Continued gains will be obtained by identifying superior alleles and novel Al3+ resistance loci that can be incorporated into breeding programs. We used association mapping to identify genomic regions associated with Al3+ resistance using 1055 accessions of common wheat from different geographic regions of the world and 178 polymorphic diversity arrays technology (DArT) markers. Bayesian analyses based on genetic distance matrices classified these accessions into 12 subgroups. Genome-wide association analyses detected markers that were significantly associated with Al3+ resistance on chromosomes 1A, 1B, 2A, 2B, 2D, 3A, 3B, 4A, 4B, 4D, 5B, 6A, 6B, 7A, and 7B. Some of these genomic regions correspond to previously identified loci for Al3+ resistance, whereas others appear to be novel. Among the markers targeting TaALMT1 (the major Al3+-resistance gene located on chromosome 4D), those that detected alleles in the promoter explained most of the phenotypic variance for Al3+ resistance, which is consistent with this region controlling the level of TaALMT1 expression. These results demonstrate that genome-wide association mapping cannot only confirm known Al3+-resistance loci, such as those on chromsomes 4D and 4B, but they also highlight the utility of this technique in identifying novel resistance 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.

Sign in / Sign up

Export Citation Format

Share Document