India is the largest milk producer globally, with the largest proportion of cattle milk production coming from smallholder farms with an average herd size of less than two milking cows. These cows are mainly undefined multi-generation crosses between exotic dairy breeds and indigenous Indian cattle, with no performance or pedigree recording. Therefore, implementing genetic improvement based on genetic evaluation has not yet been possible. We present the first results from a large smallholder performance recording program in India, using single nucleotide polymorphism (SNP) genotypes to estimate genetic parameters for monthly test-day (TD) milk records and to obtain and validate genomic estimated breeding values (GEBV). The average TD milk yield under the high, medium, and low production environments were 9.64, 6.88, and 4.61 kg, respectively. In the high production environment, the usual profile of a lactation curve was evident, whereas it was less evident in low and medium production environments. There was a clear trend of an increasing milk yield with an increasing Holstein Friesian (HF) proportion in the high production environment, but no increase above intermediate grades in the medium and low production environments. Trends for Jersey were small but yield estimates had a higher standard error than HF. Heritability estimates for TD yield across the lactation ranged from 0.193 to 0.250, with an average of 0.230. The additive genetic correlations between TD yield at different times in lactation were high, ranging from 0.846 to 0.998. The accuracy of phenotypic validation of GEBV from the method that is believed to be the least biased was 0.420, which was very similar to the accuracy obtained from the average prediction error variance of the GEBV. The results indicate strong potential for genomic selection to improve milk production of smallholder crossbred cows in India. The performance of cows with different breed compositions can be determined in different Indian environments, which makes it possible to provide better advice to smallholder farmers on optimum breed composition for their environment.

中文翻译：

---

印度小农杂交乳制品生产系统产奶量的基因组评估


印度是全球最大的牛奶生产国，最大比例的牛奶产量来自平均牛群规模不到两头奶牛的小农场。这些奶牛主要是外来奶牛品种和印度本土牛之间未定义的多代杂交，没有性能或谱系记录。因此，基于遗传评价实施遗传改良尚不可能。我们展示了印度大型小农绩效记录计划的第一个结果，该计划使用单核苷酸多态性 (SNP) 基因型来估计每月测试日 (TD) 牛奶记录的遗传参数，并获取和验证基因组估计育种值 (GEBV)。高、中、低生产环境下的平均TD产奶量分别为9.64、6.88和4.61公斤。在高产量环境中，泌乳曲线的通常特征是明显的，而在中低产量环境中则不太明显。在高产环境中，随着荷斯坦弗里斯兰（HF）比例的增加，产奶量有明显的增加趋势，但在中低产环境中，中等等级以上的产奶量没有增加。泽西岛的趋势较小，但产量估计的标准误差高于 HF。整个哺乳期 TD 产量的遗传力估计范围为 0.193 至 0.250，平均值为 0.230。哺乳期不同时间TD产量之间的加性遗传相关性较高，范围为0.846至0.998。据认为偏差最小的方法对 GEBV 表型验证的准确度为 0.420，这与根据 GEBV 平均预测误差方差获得的准确度非常相似。 结果表明，基因组选择在提高印度小农杂交奶牛产奶量方面具有巨大潜力。具有不同品种组成的奶牛的生产性能可以在不同的印度环境中确定，这使得可以为小农户提供关于适合其环境的最佳品种组成的更好建议。