Genomic analysis of claw lesions in Holstein cows: Opportunities for genomic selection, quantitative trait locus detection, and gene identification
Genomic analysis of claw lesions in Holstein cows: Opportunities for genomic selection, quantitative trait locus detection, and gene identification
复制标题
DOI：
10.3168/jds.2018-15979
复制
发表时间：
2019-07-01
影响因子：
3.5
通讯作者：
Ducrocq, Vincent
中科院分区：
文献类型：
--
作者：
Croue, Iola;Michenet, Alexis;Ducrocq, Vincent
在奶牛中，爪病是继乳腺炎和生殖障碍之后的第三大健康问题，基因组选择是长期改善爪健康的关键组成部分。本研究的目的是评估法国荷斯坦奶牛爪健康基因组评估的可行性，探索提高评估准确性的可能性，并更好地了解爪健康性状的遗传决定论。该数据集包括48,685头修剪过的荷斯坦奶牛，其中9,646头进行了基因分型；还使用了478种基因分型的品种。使用BLUP、基因组BLUP、BayesC和单步基因组BLUP评估7个爪伤特征，并通过验证研究测量这些方法获得的准确性。采用贝叶斯方法，根据贝叶斯因子检测与7个个体性状（指皮炎、足跟角糜烂、指间增生、限定性足底出血、弥漫性足底出血、足底溃疡和白线裂）相关的数量性状位点（QTL）。报道了这些区域上的注释基因。基因组评估方法一般不允许比BLUP更高的准确性，除了单步基因组BLUP。准确性中等，但最好和最差的验证动物被正确区分，并显示出病变频率的显著差异。共鉴定出192个QTL区域，其中有主要证据或涉及2个性状的QTL区域13个。大量的基因存在于这些区域，其中一些具有与腹膜系统相关的功能。特别是，EPYC基因位于指间皮炎抗性的主要证据QTL附近，该QTL也是指间增生的QTL（在5号染色体上，约20.9 MB），并且与牛的ehers - danlos综合征有关。基因组选择可用于提高对单个爪损的抵抗力，并且存在几种可能性来提高基因组评估的准确性。
Claw lesions are the third most important health issue in dairy cattle, after mastitis and reproductive disorders, and genomic selection is a key component for long-term improvement of claw health. The objectives of this study were to assess the feasibility of a genomic evaluation for claw health in French Holstein cows, explore possibilities to increase evaluation accuracy, and gain a better understanding of the genetic determinism of claw health traits. The data set consisted of 48,685 trimmed Holstein cows, including 9,646 that were genotyped; 478 genotyped sires were also used. Seven claw lesion traits were evaluated using BLUP, genomic BLUP, BayesC, and single-step genomic BLUP, and the accuracies obtained using these approaches were measured through a validation study. The Bayese approach was used to detect quantitative trait locus (QTL) regions associated with the 7 individual traits (digital dermatitis, heel horn erosion, interdigital hyperplasia, sole hemorrhage circumscribed, sole hemorrhage diffused, sole ulcer, and white line fissure) based on their Bayes factor. Annotated genes on these regions were reported. Genomic evaluation approaches generally did not allow for greater accuracies than BLUP, except for single-step genomic BLUP. Accuracies were moderate, but best and worst validation animals were correctly discriminated and showed significant differences in lesion frequencies. A total of 192 QTL regions were identified, including 13 with major evidence or involved for 2 of the traits. A high number of genes were present on these regions, and several had functions associated with the ininnine system. In particular, the EPYC gene is located close to a major evidence QTL for resistance to digital dermatitis that is also a QTL for interdigital hyperplasia (on chromosome 5, around 20.9 MB) and has been associated with Ehlers-Danlos syndrome in cattle. Genomic selection can be used to improve resistance to individual claw lesions, and several possibilities exist to improve accuracies of genomic evaluations.