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

Weng, Ziqing; Su, Hailin; Saatchi, Mahdi; Lee, J.; Thomas, M. G.; Dunkelberger, Jenelle; Garrick, Dorian J.

doi:10.1016/j.livsci.2015.11.011

Cited by 30 publications

(24 citation statements)

References 46 publications

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“…Two pleiotropic QTL identified in Brangus were located on B. taurus autosomes (BTA) 12 at 88 Mb (weaning and yearling weight, and rib eye area) and BTA 20 at 7–8 Mb (birth, yearling and mature weight) (Weng et al ). These two regions had a high Angus assignment as observed in chromosome painting (Fig.…”

Section: Discussionmentioning

confidence: 99%

Dynamics of genomic architecture during composite breed development in cattle

et al. 2020

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Summary Some livestock breeds face the challenge of reduced genetic variation, increased inbreeding depression owing to genetic drift and selection. Hybridization can reverse these processes and increase levels of productivity and adaptation to various environmental stressors. Samples from American Brangus were used to evaluate the indicine/taurine composition through nine generations (~45 years) after the hybridization process was completed. The purpose was to determine how hybridization alters allelic combinations of a breed over time when genetic factors such as selection and drift are operating. Furthermore, we explored genomic regions with deviations from the expected composition from the progenitor breeds and related these regions to traits under selection. The Brangus composition deviated from the theoretical expectation, defined by the breed association, of 62.5% taurine, showing taurine composition to be 70.4 ± 0.6%. Taurine and indicine proportion were not consistent across chromosomes. Furthermore, these non‐uniform areas were found to be associated with traits that were probably under selection such as intermuscular fat and average daily gain. Interestingly, the sex chromosomes were predominantly taurine, which could be due to the composite being formed particularly in the final cross that resulted in progeny designated as purebred Brangus. This work demonstrated the process of new breed formation on a genomic level. It suggests that factors like genetic drift, selection and complementarity shift the genetic architecture into a uniquely different population. These findings are important to better understand how hybridization and crossbreeding systems shape the genetic architecture of composite populations.

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Section: Discussionmentioning

confidence: 99%

Dynamics of genomic architecture during composite breed development in cattle

et al. 2020

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“…Most of the studies on the genetic evaluation of beef cattle traits using genomic information have focused on the discovery or use of additive genetic effects [ 3 – 5 , 31 , 32 ] because these genetic effects are passed from parents to offspring and are the basis of genetic selection and improvement programs. In the current study, many QTL regions with genome-wide significance for additive genetic effects were identified [see Additional file 1 : Tables S1, S2 and S3].…”

Section: Discussionmentioning

confidence: 99%

Genome-wide association scan for heterotic quantitative trait loci in multi-breed and crossbred beef cattle

et al. 2018

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BackgroundHeterosis has been suggested to be caused by dominance effects. We performed a joint genome-wide association analysis (GWAS) using data from multi-breed and crossbred beef cattle to identify single nucleotide polymorphisms (SNPs) with significant dominance effects associated with variation in growth and carcass traits and to understand the mode of action of these associations.MethodsIllumina BovineSNP50 genotypes and phenotypes for 11 growth and carcass traits were available for 6796 multi-breed and crossbred beef cattle. After performing quality control, 42,610 SNPs and 6794 animals were used for further analyses. A single-SNP GWAS for the joint association of additive and dominance effects was conducted in purebred, crossbred, and combined datasets using the ASReml software. Genomic breed composition predicted from admixture analyses was included in the mixed effect model to account for possible population stratification and breed effects. A threshold of 10% genome-wide false discovery rate was applied to declare associations as significant. The significant SNPs with dominance association were mapped to their corresponding genes at 100 kb.ResultsSeven SNPs with significant dominance associations were detected for birth weight, weaning weight, pre-weaning daily gain, yearling weight and marbling score across the three datasets at a false discovery rate of 10%. These SNPs were located on bovine chromosomes 1, 3, 4, 6 and 21 and mapped to six putative candidate genes: U6atac, AGBL4, bta-mir-2888-1, REPIN1, ICA1 and NXPH1. These genes have interesting biological functions related to the regulation of gene expression, glucose and lipid metabolism and body fat mass. For most of the identified loci, we observed over-dominance association with the studied traits, such that the heterozygous individuals at any of these loci had greater genotypic values for the trait than either of the homozygous individuals.ConclusionsOur results revealed very few regions with significant dominance genetic effects across all the traits studied in the three datasets used. Regarding the SNPs that were detected with dominance associations, further investigation is needed to determine their relevance in crossbreeding programs assuming that dominance effects are the main cause of (or contribute usefully to) heterosis.Electronic supplementary materialThe online version of this article (10.1186/s12711-018-0405-y) contains supplementary material, which is available to authorized users.

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“…Likewise, the extended region on BTA 7 was identified in previous studies in beef cattle for body size-related traits. This region has been significantly associated with birth weight, weaning weight, yearling weight, mature weight, and rib eye area across multiple breeds of beef cattle (Snelling et al, 2010;Saatchi et al, 2014b;Weng et al, 2016).…”

Section: Gwas For Underlying Traitsmentioning

confidence: 99%

The genetic and biological basis of feed efficiency in mid-lactation Holstein dairy cows

Hardie

VandeHaar

Tempelman

et al. 2017

Journal of Dairy Science

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The objective of this study was to identify genomic regions and candidate genes associated with feed efficiency in lactating Holstein cows. In total, 4,916 cows with actual or imputed genotypes for 60,671 single nucleotide polymorphisms having individual feed intake, milk yield, milk composition, and body weight records were used in this study. Cows were from research herds located in the United States, Canada, the Netherlands, and the United Kingdom. Feed efficiency, defined as residual feed intake (RFI), was calculated within location as the residual of the regression of dry matter intake (DMI) on milk energy (MilkE), metabolic body weight (MBW), change in body weight, and systematic effects. For RFI, DMI, MilkE, and MBW, bivariate analyses were performed considering each trait as a separate trait within parity group to estimate variance components and genetic correlations between them. Animal relationships were established using a genomic relationship matrix. Genome-wide association studies were performed separately by parity group for RFI, DMI, MilkE, and MBW using the Bayes B method with a prior assumption that 1% of single nucleotide polymorphisms have a nonzero effect. One-megabase windows with greatest percentage of the total genetic variation explained by the markers (TGVM) were identified, and adjacent windows with large proportion of the TGVM were combined and reanalyzed. Heritability estimates for RFI were 0.14 (±0.03; ±SE) in primiparous cows and 0.13 (±0.03) in multiparous cows. Genetic correlations between primiparous and multiparous cows were 0.76 for RFI, 0.78 for DMI, 0.92 for MBW, and 0.61 for MilkE. No single 1-Mb window explained a significant proportion of the TGVM for RFI; however, after combining windows, significance was met on Bos taurus autosome 27 in primiparous cows, and nearly reached on Bos taurus autosome 4 in multiparous cows. Among other genes, these regions contain β-3 adrenergic receptor and the physiological candidate gene, leptin, respectively. Between the 2 parity groups, 3 of the 10 windows with the largest effects on DMI neighbored windows affecting RFI, but were not in the top 10 regions for MilkE or MBW. This result suggests a genetic basis for feed intake that is unrelated to energy consumption required for milk production or expected maintenance as determined by MBW. In conclusion, feed efficiency measured as RFI is a polygenic trait exhibiting a dynamic genetic basis and genetic variation distinct from that underlying expected maintenance requirements and milk energy output.

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

Cited by 30 publications

References 46 publications

Dynamics of genomic architecture during composite breed development in cattle

Dynamics of genomic architecture during composite breed development in cattle

Genome-wide association scan for heterotic quantitative trait loci in multi-breed and crossbred beef cattle

The genetic and biological basis of feed efficiency in mid-lactation Holstein dairy cows

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