Genome wide association studies for body conformation traits in the Chinese Holstein cattle population

BMC Genomics
Xiaoping WuDongxiao Sun

Abstract

Genome-wide association study (GWAS) is a powerful tool for revealing the genetic basis of quantitative traits. However, studies using GWAS for conformation traits of cattle is comparatively less. This study aims to use GWAS to find the candidates genes for body conformation traits. The Illumina BovineSNP50 BeadChip was used to identify single nucleotide polymorphisms (SNPs) that are associated with body conformation traits. A least absolute shrinkage and selection operator (LASSO) was applied to detect multiple SNPs simultaneously for 29 body conformation traits with 1,314 Chinese Holstein cattle and 52,166 SNPs. Totally, 59 genome-wide significant SNPs associated with 26 conformation traits were detected by genome-wide association analysis; five SNPs were within previously reported QTL regions (Animal Quantitative Trait Loci (QTL) database) and 11 were very close to the reported SNPs. Twenty-two SNPs were located within annotated gene regions, while the remainder were 0.6-826 kb away from known genes. Some of the genes had clear biological functions related to conformation traits. By combining information about the previously reported QTL regions and the biological functions of the genes, we identified DARC, GAS1, MTPN, HTR2A...Continue Reading

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Citations

Sep 16, 2015·BMC Genetics·Johanna K HöglundGoutam Sahana
Jun 20, 2015·Genetics, Selection, Evolution : GSE·Fuping ZhaoDonagh P Berry
May 4, 2015·BMC Genetics·Goutam SahanaMogens S Lund
Jan 26, 2017·Genetics, Selection, Evolution : GSE·Thu H LeGoutam Sahana
Jan 2, 2018·Journal of Dairy Science·Sebastian MuchaJoanne Conington
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Feb 8, 2019·Scientific Reports·Tiago do Prado PaimHarvey D Blackburn
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May 4, 2021·Frontiers in Genetics·Shaolei ShiShengli Zhang
Aug 21, 2021·Frontiers in Genetics·Bruno SerranitoAnne Da Silva
Aug 28, 2021·Animals : an Open Access Journal From MDPI·Ismail Mohamed AbdallaZhangping Yang

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Methods Mentioned

BETA
chip
chips

Software Mentioned

RunGE
LASSO
SMMA
Beagle

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