Santana M H A, Utsunomiya Y T, Neves H H R, Gomes R C, Garcia J F, Fukumasu H, Silva S L, Leme P R, Coutinho L L, Eler J P, Ferraz J B S
Faculdade de Zootecnia e Engenharia de Alimentos, USP - Univ. de São Paulo, Pirassununga, Brazil.
J Anim Breed Genet. 2014 Jun;131(3):210-6. doi: 10.1111/jbg.12084. Epub 2014 Feb 20.
The genome-wide association study (GWAS) results are presented for average daily gain (ADG) in Nellore cattle. Phenotype of 720 male Bos indicus animals with information of ADG in feedlots and 354,147 single-nucleotide polymorphisms (SNPs) obtained from a database added by information from Illumina Bovine HD (777,962 SNPs) and Illumina BovineSNP50 (54,609) by imputation were used. After quality control and imputation, 290,620 SNPs remained in the association analysis, using R package Genome-wide Rapid Association using Mixed Model and Regression method GRAMMAR-Gamma. A genomic region with six significant SNPs, at Bonferroni-corrected significance, was found on chromosome 3. The most significant SNP (rs42518459, BTA3: 85849977, p = 9.49 × 10(-8)) explained 5.62% of the phenotypic variance and had the allele substitution effect of -0.269 kg/day. Important genes such as PDE4B, LEPR, CYP2J2 and FGGY are located near this region, which is overlapped by 12 quantitative trait locus (QTLs) described for several production traits. Other regions with markers with suggestive effects were identified in BTA6 and BTA10. This study showed regions with major effects on ADG in Bos indicus in feedlots. This information may be useful to increase the efficiency of selecting this trait and to understand the physiological processes involved in its regulation.
本文展示了内洛尔牛平均日增重（ADG）的全基因组关联研究（GWAS）结果。研究使用了720头印度瘤牛公牛的表型数据，这些牛在饲养场中有ADG信息，并使用了通过插补从Illumina Bovine HD（777,962个单核苷酸多态性（SNP））和Illumina BovineSNP50（54,609个SNP）数据库添加信息后获得的354,147个SNP。经过质量控制和插补后，使用R包Genome-wide Rapid Association using Mixed Model and Regression method GRAMMAR-Gamma，在关联分析中保留了290,620个SNP。在3号染色体上发现了一个具有六个显著SNP的基因组区域，经Bonferroni校正后具有显著性。最显著的SNP（rs42518459，BTA3: 85849977，p = 9.49 × 10(-8)）解释了5.62%的表型变异，等位基因替代效应为-0.269 kg/天。重要基因如PDE4B、LEPR、CYP2J2和FGGY位于该区域附近，该区域与多个生产性状描述的12个数量性状位点（QTL）重叠。在BTA6和BTA10中还鉴定出了具有提示性效应标记的其他区域。本研究表明了在饲养场中对印度瘤牛ADG有主要影响的区域。这些信息可能有助于提高该性状的选择效率，并了解其调控所涉及的生理过程。
