Abstract

The aim of this study was to test the feasibility of genomic selection in the Italian Mediterranean water buffalo, which is farmed mainly in the south Italy for milk, and mozzarella, production. A total of 498 animals were genotyped at 49,164 loci. Test day records (80,417) of milk (MY), fat (FY) and protein (PY) yields from 4127 cows, born between 1975 and 2009, were analysed in a three-trait model. Cows born in 2008 and 2009 with phenotypes and genotypes were selected as validation animals (n = 50). Variance components (VC) were estimated with BLUP and ssGBLUP. Heritabilities for BLUP were 0.25 ± 0.02 (MY), 0.16 ± 0.01 (FY) and 0.25 ± 0.01 (PY). Breeding values were computed using BLUP and ssGBLUP, using VC estimated from BLUP. ssGBLUP was applied in five scenarios, each with a different number of genotypes available: (A) bulls (35); (B) validation cows (50); (C) bulls and validation cows (85); (D) all genotyped cows (463); (E) all genotypes (498). Model validation was performed using the LR method: correlation, accuracy, dispersion, and bias statistics were calculated. Average correlations were 0.71 ± 0.02 and 0.82 ± 0.01 for BLUP and ssGBLUP-E, respectively. Accuracies were also higher in ssGBLUP-E (0.75 ± 0.03) compared to BLUP (0.57 ± 0.03). The best dispersions (i.e. closer to 1) were found for ssGBLUP-C. The use of genotypes only for the 35 bulls did not change the validation values compared to BLUP. Results of the present study, even if based on small number of animals, showed that the inclusion of genotypes of females can improve breeding values accuracy in the Italian Buffalo.

• Highlights

• The genotypes of males did not improve the predictions.

• Genotypes of females improve breeding values accuracy.

• Slight increase in prediction accuracy with weighted ssGBLUP.

摘要

这项研究的目的是检验在意大利地中海水牛中进行基因组选择的可行性，该水牛主要在意大利南部养殖以生产牛奶和马苏里拉奶酪。在49,164个基因座上对498只动物进行了基因分型。在三性状模型中分析了1975年至2009年之间出生的4127头母牛的牛奶（MY），脂肪（FY）和蛋白质（PY）产量的测试日记录（80,417）。选择2008年和2009年出生的具有表型和基因型的母牛作为验证动物（n = 50）。方差分量（VC）用BLUP和ssGBLUP估算。BLUP的遗传力为0.25±0.02（MY），0.16±0.01（FY）和0.25±0.01（PY）。使用BLUP和ssGBLUP，使用从BLUP估计的VC来计算育种值。ssGBLUP被应用于五个场景，每个场景具有不同数量的可用基因型：（A）公牛（35）；（B）确认母牛（50头）；（C）公牛和验证牛（85）；（D）所有基因型奶牛（463）；（E）所有基因型（498）。使用LR方法执行模型验证：计算相关性，准确性，离散度和偏差统计量。BLUP和ssGBLUP-E的平均相关性分别为0.71±0.02和0.82±0.01。与BLUP（0.57±0.03）相比，ssGBLUP-E的准确性也更高（0.75±0.03）。发现ssGBLUP-C的最佳分散度（即接近1）。与BLUP相比，仅对35头公牛使用基因型不会改变验证值。即使基于少量动物，本研究的结果表明，将雌性基因型包括在内可以提高意大利水牛城的育种值准确性。

• 强调

• 男性的基因型没有改善预测。

• 雌性的基因型提高了育种值的准确性。

• 加权ssGBLUP可以略微提高预测准确性。