A single-step genomic evaluation for milk production in Egyptian buffalo
A single-step genomic evaluation for milk production in Egyptian buffalo
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DOI：
10.1016/j.livsci.2020.103977
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发表时间：
2020-04-01
影响因子：
1.8
通讯作者：
Abou-Bakr, Samy
中科院分区：
文献类型：
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作者：
Abdel-Shafy, Hamdy;Awad, Mohamed A. A.;Abou-Bakr, Samy
本研究的目的是使用单步法估计埃及水牛的遗传参数并确定产奶的候选基因。使用了 698 头水牛的 174,619 条日产奶量记录。选择具有高偏差和低偏差性能的动物使用 Axiom (R) Buffalo 基因分型阵列 90 K 进行基因分型。使用 AIREMLF90 估计单步 GBLUP 的方差分量。使用预测能力方法计算预测的准确性。计算由每 30 个相邻 SNP 的窗口段解释的遗传方差百分比。选择加性遗传方差前20个窗口片段进行QTL和候选基因检索。每日产奶量的遗传力估计为中等（0.20 +/- 0.03）。预测的准确性（0.61）似乎适合当前的挑战。影响最大的前十个窗口片段位于 1、2、3、4、6、9、11、12 和 16 号染色体上，解释了约 6% 的加性遗传方差。这些基因组区域与之前报道的不同牛品种的QTL相一致，并含有许多有利于产奶的候选基因，例如：6号染色体上的POU2F1基因编码的Oct1蛋白已知对主要乳蛋白基因的表达和乳腺发育具有调节作用。这些结果表明，通过单步基因组评估可以获得小规模群体遗传参数的更可靠估计。所确定的具有最高比例的加性遗传变异的基因组区域包含具有与产奶相关的生物学作用的有前途的候选基因。我们的研究结果为以合理的准确性提高埃及水牛的产奶量提供了坚实的基础，因为传统方法因缺乏足够的谱系信息而受到阻碍。需要进一步的研究，包括更多的动物、记录和基因型来验证我们的发现。
The objectives of this study were to estimate genetic parameters and identify candidate genes for milk production in Egyptian buffalo using single-step method. Daily milk yield of 174,619 records from 698 buffalo cows were used. Animals with high and low deviated performance were selected for genotyping with Axiom (R) Buffalo Genotyping array 90 K. Variance components were estimated using AIREMLF90 for single-step GBLUP. Accuracy of prediction was calculated using predicted ability approach. The percentage of genetic variance explained by a window segment of each 30 adjacent SNPs was calculated. The top 20 window segments for additive genetic variance were chosen for QTL and candidate genes retrieving. Heritability estimate for daily milk yield was moderate (0.20 +/- 0.03). The accuracy of prediction (0.61) seems to be suitable under current challenges. The top ten window segments with largest effects are located on chromosomes 1, 2, 3, 4, 6, 9, 11, 12 and 16 and explained around 6% of additive genetic variance. These genomic regions are coincided with previously reported QTL in different cattle breeds and harbored many propitious candidate genes for milk production, for example: the Oct1 protein encoded by POU2F1 gene on chromosome 6 is known to have a role for the regulation of major milk protein genes expression and development of mammary gland. These results indicated that a more reliable estimation of genetic parameters from population with small size can be obtained with a single-step genomic evaluation. The identified genomic regions with highest proportion of additive genetic variance harbor promising candidate genes with biological roles associated with milk production. Our findings provided a solid basis for improving milk production in Egyptian buffalo with reasonable accuracy, since traditional methods is hindered by the lack of sufficient pedigree information. A further research including more animals, records, and genotypes is required to validate our findings.