Legarra A, Baloche G, Barillet F, Astruc J M, Soulas C, Aguerre X, Arrese F, Mintegi L, Lasarte M, Maeztu F, Beltrán de Heredia I, Ugarte E
INRA, UR1388 GenPhySe, CS-52627, F-31326 Castanet-Tolosan, France.
INRA, UR1388 GenPhySe, CS-52627, F-31326 Castanet-Tolosan, France.
J Dairy Sci. 2014 May;97(5):3200-12. doi: 10.3168/jds.2013-7745. Epub 2014 Mar 13.
Genotypes, phenotypes and pedigrees of 6 breeds of dairy sheep (including subdivisions of Latxa, Manech, and Basco-Béarnaise) from the Spain and France Western Pyrenees were used to estimate genetic relationships across breeds (together with genotypes from the Lacaune dairy sheep) and to verify by forward cross-validation single-breed or multiple-breed genetic evaluations. The number of rams genotyped fluctuated between 100 and 1,300 but generally represented the 10 last cohorts of progeny-tested rams within each breed. Genetic relationships were assessed by principal components analysis of the genomic relationship matrices and also by the conservation of linkage disequilibrium patterns at given physical distances in the genome. Genomic and pedigree-based evaluations used daughter yield performances of all rams, although some of them were not genotyped. A pseudo-single step method was used in this case for genomic predictions. Results showed a clear structure in blond and black breeds for Manech and Latxa, reflecting historical exchanges, and isolation of Basco-Béarnaise and Lacaune. Relatedness between any 2 breeds was, however, lower than expected. Single-breed genomic predictions had accuracies comparable with other breeds of dairy sheep or small breeds of dairy cattle. They were more accurate than pedigree predictions for 5 out of 6 breeds, with absolute increases in accuracy ranging from 0.05 to 0.30 points. They were significantly better, as assessed by bootstrapping of candidates, for 2 of the breeds. Predictions using multiple populations only marginally increased the accuracy for a couple of breeds. Pooling populations does not increase the accuracy of genomic evaluations in dairy sheep; however, single-breed genomic predictions are more accurate, even for small breeds, and make the consideration of genomic schemes in dairy sheep interesting.
来自西班牙和法国西比利牛斯地区的6个奶羊品种（包括拉查、马内克和巴斯克 - 贝阿恩斯的细分品种）的基因型、表型和系谱被用于估计品种间的遗传关系（连同拉库纳奶羊的基因型），并通过向前交叉验证来验证单品种或多品种的遗传评估。基因分型的公羊数量在100到1300之间波动，但通常代表每个品种内最后10个经过后代测试的公羊群体。通过基因组关系矩阵的主成分分析以及基因组中给定物理距离处连锁不平衡模式的保守性来评估遗传关系。基于基因组和系谱的评估使用了所有公羊的女儿产奶性能，尽管其中一些没有进行基因分型。在这种情况下，使用伪单步方法进行基因组预测。结果显示，马内克和拉查的白色和黑色品种具有明显的结构，反映了历史交流情况，以及巴斯克 - 贝阿恩斯和拉库纳的隔离情况。然而，任何两个品种之间的亲缘关系低于预期。单品种基因组预测的准确性与其他奶羊品种或小型奶牛品种相当。在6个品种中的5个品种中，它们比系谱预测更准确，准确性的绝对提高范围为0.05至0.30分。通过对候选者进行自助抽样评估，其中2个品种的预测明显更好。使用多个群体进行预测仅略微提高了少数几个品种的准确性。合并群体并不会提高奶羊基因组评估的准确性；然而，单品种基因组预测更准确，即使对于小品种也是如此，这使得考虑奶羊的基因组计划变得很有意义。
