背景:可以使用反应规范模型来评估肉牛的基因型与环境的相互作用(GxE),以评估环境敏感性,结合全基因组关联研究(GWAS),绘制与动物适应相关的基因组区域。在反应规范(RN)模型中包括来自全基因组测序的遗传标记,使我们能够通过GWAS识别跨环境梯度的高分辨率候选基因。因此,我们使用全基因组测序数据通过RN方法进行了GWAS,重点定位与Nellore牛繁殖和生长性状表达相关的候选基因。为此,我们使用了第一次产牛年龄的表型数据(AFC),阴囊周长(SC),断奶后体重增加(PWG),和一岁体重(YW)。将总共20,000名男性和7,159名女性的770k基因归入整个序列(29M)。经过质量控制和连锁不平衡(LD)修剪,SC还有~2.41MSNP,PWG,以及亚足联的YW和~5.06MSNP。
结果:对于AFC,在Bostaurus常染色体(BTA)10、11、14、18、19、20、21、24、25和27上以及在BTA4、5和8上鉴定了显着的SNP。对于生长性状,在BTA3、5和20上鉴定了YW和PWG的显著SNP标记。总共为AFC鉴定了56个位置候选基因,9为SC,3用于PWG,24为YW。发现Nellore牛的反应标准系数检测到的显着SNP与生长有关,适应性,和生殖特征。这些候选基因参与与脂质代谢相关的生物学机制,免疫反应,丝裂原活化蛋白激酶(MAPK)信号通路,能量和磷酸盐代谢。
结论:GWAS结果强调了与脂质代谢有关的生理过程的差异,免疫反应,MAPK信号通路,能量和磷酸盐代谢,提供不同环境条件如何与影响动物适应的特定基因相互作用的见解,生产力,和生殖性能。截距和斜率之间的共享基因组区域直接涉及在不同环境条件下饲养的Nellore牛的生长和繁殖性状的调节。
BACKGROUND: The genotype-by-environment interaction (GxE) in beef cattle can be investigated using reaction norm models to assess environmental sensitivity and, combined with genome-wide association studies (GWAS), to map genomic regions related to animal adaptation. Including genetic markers from whole-genome sequencing in reaction norm (RN) models allows us to identify high-resolution candidate genes across environmental gradients through GWAS. Hence, we performed a GWAS via the RN approach using whole-genome sequencing data, focusing on mapping candidate genes associated with the expression of reproductive and growth traits in Nellore cattle. For this purpose, we used phenotypic data for age at first calving (AFC), scrotal circumference (SC), post-weaning weight gain (PWG), and yearling weight (YW). A total of 20,000 males and 7,159 females genotyped with 770k were imputed to the whole sequence (29 M). After quality control and linkage disequilibrium (LD) pruning, there remained ∼ 2.41 M SNPs for SC, PWG, and YW and ∼ 5.06 M SNPs for AFC.
RESULTS: Significant SNPs were identified on Bos taurus autosomes (BTA) 10, 11, 14, 18, 19, 20, 21, 24, 25 and 27 for AFC and on BTA 4, 5 and 8 for SC. For growth traits, significant SNP markers were identified on BTA 3, 5 and 20 for YW and PWG. A total of 56 positional candidate genes were identified for AFC, 9 for SC, 3 for PWG, and 24 for YW. The significant SNPs detected for the reaction norm coefficients in Nellore cattle were found to be associated with growth, adaptative, and reproductive traits. These candidate genes are involved in biological mechanisms related to lipid metabolism, immune response, mitogen-activated protein kinase (MAPK) signaling pathway, and energy and phosphate metabolism.
CONCLUSIONS: GWAS results highlighted differences in the physiological processes linked to lipid metabolism, immune response, MAPK signaling pathway, and energy and phosphate metabolism, providing insights into how different environmental conditions interact with specific genes affecting animal adaptation, productivity, and reproductive performance. The shared genomic regions between the intercept and slope are directly implicated in the regulation of growth and reproductive traits in Nellore cattle raised under different environmental conditions.