Genome-wide association scan for heterotic quantitative trait loci in multi-breed and crossbred beef cattle 06 Biological Sciences 0604 Genetics

Citation

Akanno, E.C., Chen, L., Abo-Ismail, M.K., Crowley, J.J., Wang, Z., Li, C., Basarab, J.A., MacNeil, M.D., Plastow, G.S. (2018). Genome-wide association scan for heterotic quantitative trait loci in multi-breed and crossbred beef cattle 06 Biological Sciences 0604 Genetics. Genetics Selection Evolution, [online] 50(1), http://dx.doi.org/10.1186/s12711-018-0405-y

Plain language summary

Heterosis is an increase in performance of an offspring as a result of mixing the genetic contributions of its parents. Dominance effects, which refer to one allele or one type of a gene having more effects than the other, have been suggested as a genetic mechanism underlying heterosis. In this study, we performed a genome-wide association analysis using data from purebred and crossbred beef cattle to identify single nucleotide polymorphisms (SNP) that show significant dominance association or effects on growth and carcass traits in a model including independent SNP allele substitution effects. Six SNPs were found to have significant dominant associations for weaning weight (WWT) and marbling score (MBS) on bovine chromosome (BTA) 4, 7, 10 and 16. These SNPs explained 0.002% and 0.17% of the total phenotypic variance for WWT and MBS, respectively, and were mapped to six putative candidate genes underlying these associations. Two of the heterotic SNPs each for WWT and MBS were found within the introns of genes HSPA4 and ICA1, respectively. Although the proportions of total phenotypic variance explained by dominance genetic effects were moderate for those traits investigated, our results suggest that dominance effects are polygenic. The research results will help the beef industry to design better crossbreeding programs to improve heterosis and production performance.

Abstract

Background: Heterosis 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. Methods: Illumina 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. Results: Seven 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. Conclusions: Our 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.

Publication date

2018-10-05

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