Zhang Tao, Gao Linyu, Zhou Bohan, Xu Qi, Liu Yifan, Li Jinquan, Lv Qi, Zhang Yanjun, Wang Ruijun, Su Rui, Wang Zhiying
College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China.
Grassland Research Institute, Chinese Academy of Agricultural Sciences, Hohhot 010018, China.
Animals (Basel). 2025 Jun 12;15(12):1733. doi: 10.3390/ani15121733.
This study aimed to identify the best model and method for the genomic selection of early growth traits in Inner Mongolian cashmere goats (IMCGs). Using data from 50,728 SNPs, the phenotypes (birth weight, BW; weaning weight, WW; daily weight gain, DWG; and yearling weight, YW) of 2256 individuals, and pedigree information from 14,165 individuals, fixed effects were analyzed using a generalized linear model. Four single-trait animal models with varying combinations of individual and maternal effects were evaluated using the ABLUP, GBLUP, and ssGBLUP methods. The best model was selected based on a likelihood ratio test. Five-fold cross-validation was used to assess the accuracy and reliability of the genomic estimated breeding values (GEBVs). Birth year and herd significantly affected BW ( < 0.05) and WW, DWG, and YW ( < 0.01), while sex, birth type, and dam age had highly significant effects on all traits ( < 0.01). Model 4, incorporating direct and maternal additive genetic effects, maternal environmental effects, and their covariance, was optimal. Additionally, ssGBLUP achieved the highest GEBV accuracy (0.61-0.70), outperforming the GBLUP and ABLUP methods. Thus, ssGBLUP is recommended for enhancing the genetic progress in IMCGs. Under the best method, the heritability estimates for BW, WW, DGW, and YW were 0.11, 0.25, 0.15, and 0.23, respectively.
本研究旨在确定内蒙古白绒山羊早期生长性状基因组选择的最佳模型和方法。利用50728个单核苷酸多态性(SNP)数据、2256只个体的表型(出生体重、断奶体重、日增重和周岁体重)以及14165只个体的系谱信息,采用广义线性模型分析固定效应。使用最佳线性无偏预测(ABLUP)、基因组最佳线性无偏预测(GBLUP)和一步法基因组最佳线性无偏预测(ssGBLUP)方法评估了四种具有不同个体和母体效应组合的单性状动物模型。基于似然比检验选择最佳模型。采用五重交叉验证评估基因组估计育种值(GEBV)的准确性和可靠性。出生年份和群体对出生体重(P<0.05)、断奶体重、日增重和周岁体重有显著影响(P<0.01),而性别、出生类型和母羊年龄对所有性状均有极显著影响(P<0.01)。包含直接和母体加性遗传效应、母体环境效应及其协方差的模型4是最优的。此外,ssGBLUP获得了最高的GEBV准确性(0.61 - 0.70),优于GBLUP和ABLUP方法。因此,推荐使用ssGBLUP来提高内蒙古白绒山羊的遗传进展。在最佳方法下,出生体重、断奶体重、日增重和周岁体重的遗传力估计值分别为0.11、0.25、0.15和0.23。