Fathoni Akhmad, Boonkum Wuttigrai, Chankitisakul Vibuntita, Buaban Sayan, Duangjinda Monchai
Department of Animal Science, Faculty of Agriculture, Khon Kaen University, Khon Kaen 40002, Thailand.
Department of Animal Breeding and Reproduction, Faculty of Animal Science, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia.
Animals (Basel). 2025 May 2;15(9):1320. doi: 10.3390/ani15091320.
Understanding the genetic basis of economically important traits is essential for enhancing the productivity, fertility, and health of dairy cattle. This study aimed to identify the pleiotropic genes associated with the 305-day milk yield (MY305), days open (DO), and milk fat-to-protein ratio (FPR) in Thai-Holstein crossbred dairy cattle using a genome-wide association study (GWAS) approach. The dataset included 18,843 records of MY305 and milk FPR, as well as 48,274 records of DO, collected from first-lactation Thai-Holstein crossbred dairy cattle. A total of 868 genotyped animals and 43,284 informative SNPs out of 50,905 were used for the analysis. The single-nucleotide polymorphism (SNP) effects were evaluated using a weighted single-step GWAS (wssGWAS), which estimated these effects based on genomic breeding values (GEBVs) through a multi-trait animal model with single-step genomic BLUP (ssGBLUP). Genomic regions explaining at least 5% of the total genetic variance were selected for candidate gene analysis. Single-step genomic REML (ssGREML) with a multi-trait animal model was used to estimate components of (co)variance. The heritability estimates from additive genetic variance were 0.262 for MY305, 0.029 for DO, and 0.102 for milk FPR, indicating a moderate genetic influence on milk yield and a lower genetic impact on fertility and milk FPR. The genetic correlations were 0.559 (MY305 and DO), -0.306 (MY305 and milk FPR), and -0.501 (DO and milk FPR), indicating potential compromises in genetic selection. wssGBLUP showed a higher accuracy than ssGBLUP, although the improvement was modest. A total of 24, 46, and 33 candidate genes were identified for MY305, DO, and milk FPR, respectively. Pleiotropic effects, identified by SNPs showing significant influence with more than trait, were observed in 14 genes shared among all three traits, 17 genes common between MY305 and DO, 14 genes common between MY305 and milk FPR, and 26 genes common between DO and milk FPR. Overall, wssGBLUP is a promising approach for improving the genomic prediction of economic traits in multi-trait analyses, outperforming ssGBLUP. This presents a viable alternative for genetic evaluation in dairy cattle breeding programs in Thailand. However, further studies are needed to validate these candidate genes and refine marker selection for production, fertility, and health traits in dairy cattle.
了解经济重要性状的遗传基础对于提高奶牛的生产力、繁殖力和健康状况至关重要。本研究旨在采用全基因组关联研究（GWAS）方法，鉴定泰国荷斯坦杂交奶牛中与305天产奶量（MY305）、空怀天数（DO）和乳脂蛋白比（FPR）相关的多效基因。数据集包括从第一胎泰国荷斯坦杂交奶牛收集的18,843条MY305和乳脂率记录，以及48,274条空怀天数记录。在50,905个单核苷酸多态性（SNP）中，共868只基因分型动物和43,284个信息性SNP用于分析。使用加权单步GWAS（wssGWAS）评估SNP效应，该方法通过单步基因组最佳线性无偏预测（ssGBLUP）的多性状动物模型，基于基因组育种值（GEBV）估计这些效应。选择解释至少5%总遗传方差的基因组区域进行候选基因分析。使用多性状动物模型的单步基因组REML（ssGREML）估计（协）方差成分。MY305的加性遗传方差遗传力估计值为0.262，DO为0.029，乳脂率为0.102，表明对产奶量有中等遗传影响，对繁殖力和乳脂率的遗传影响较低。遗传相关系数分别为0.559（MY305和DO）、-0.306（MY305和乳脂率）和-0.501（DO和乳脂率），表明在遗传选择中可能存在权衡。尽管改进幅度不大，但wssGBLUP显示出比ssGBLUP更高的准确性。分别为MY305、DO和乳脂率鉴定出24个、46个和33个候选基因。在所有三个性状共有的14个基因、MY305和DO共有的17个基因、MY305和乳脂率共有的14个基因以及DO和乳脂率共有的26个基因中，观察到由对多个性状有显著影响的SNP所确定的多效性效应。总体而言，wssGBLUP是一种有前景的方法，可用于改进多性状分析中经济性状的基因组预测，优于ssGBLUP。这为泰国奶牛育种计划中的遗传评估提供了一种可行的替代方法。然而，需要进一步研究来验证这些候选基因，并完善奶牛生产、繁殖力和健康性状的标记选择。
