Sun C, VanRaden P M, O'Connell J R, Weigel K A, Gianola D
National Association of Animal Breeders, Columbia, MO 65205.
J Dairy Sci. 2013;96(12):8014-23. doi: 10.3168/jds.2013-6969. Epub 2013 Oct 11.
Computerized mating programs using genomic information are needed by breed associations, artificial-insemination organizations, and on-farm software providers, but such software is already challenged by the size of the relationship matrix. As of October 2012, over 230,000 Holsteins obtained genomic predictions in North America. Efficient methods of storing, computing, and transferring genomic relationships from a central database to customers via a web query were developed for approximately 165,000 genotyped cows and the subset of 1,518 bulls whose semen was available for purchase at that time. This study, utilizing 3 breeds, investigated differences in sire selection, methods of assigning mates, the use of genomic or pedigree relationships, and the effect of including dominance effects in a mating program. For both Jerseys and Holsteins, selection and mating programs were tested using the top 50 marketed bulls for genomic and traditional lifetime net merit as well as 50 randomly selected bulls. The 500 youngest genotyped cows in the largest herd in each breed were assigned mates of the same breed with limits of 10 cows per bull and 1 bull per cow (only 79 cows and 8 bulls for Brown Swiss). A dominance variance of 4.1 and 3.7% was estimated for Holsteins and Jerseys using 45,187 markers and management group deviation for milk yield. Sire selection was identified as the most important component of improving expected progeny value, followed by managing inbreeding and then inclusion of dominance. The respective percentage gains for milk yield in this study were 64, 27, and 9, for Holsteins and 73, 20, and 7 for Jerseys. The linear programming method of assigning a mate outperformed sequential selection by reducing genomic or pedigree inbreeding by 0.86 to 1.06 and 0.93 to 1.41, respectively. Use of genomic over pedigree relationship information provided a larger decrease in expected progeny inbreeding and thus greater expected progeny value. Based on lifetime net merit, the economic value of using genomic relationships was >$3 million per year for Holsteins when applied to all genotyped females, assuming that each will provide 1 replacement. Previous mating programs required transferring only a pedigree file to customers, but better service is possible by incorporating genomic relationships, more precise mate allocation, and dominance effects. Economic benefits will continue to grow as more females are genotyped.
品种协会、人工授精组织以及农场软件供应商都需要使用基因组信息的计算机化配种程序，但此类软件已经受到关系矩阵规模的挑战。截至2012年10月，北美有超过23万头荷斯坦奶牛获得了基因组预测结果。针对大约16.5万头基因分型奶牛以及当时其精液可供购买的1518头公牛的子集，开发了从中央数据库通过网络查询向客户存储、计算和传输基因组关系的有效方法。本研究利用3个品种，调查了种公牛选择、配对方法、基因组或系谱关系的使用以及在配种程序中纳入显性效应的影响。对于泽西牛和荷斯坦牛，使用按基因组和传统终身净效益排名前50的已上市公牛以及50头随机选择的公牛来测试选择和配种程序。为每个品种中最大牛群的500头最年轻的基因分型奶牛分配同一品种的配偶，每头公牛的母牛数量限制为10头，每头母牛的公牛数量限制为1头（对于瑞士褐牛，只有79头母牛和8头公牛）。使用45187个标记和产奶量的管理组偏差，估计荷斯坦牛和泽西牛的显性方差分别为4.1%和3.7%。种公牛选择被确定为提高预期后代价值的最重要组成部分，其次是控制近亲繁殖，然后是纳入显性效应。在本研究中，荷斯坦牛产奶量的相应百分比增益分别为64%、27%和9%，泽西牛为73%、20%和7%。通过减少基因组或系谱近亲繁殖，分别降低0.86至1.06和0.93至1.41，分配配偶的线性规划方法优于顺序选择。使用基因组关系信息而非系谱关系信息可更大程度地降低预期后代近亲繁殖，从而提高预期后代价值。基于终身净效益，假设每头基因分型母牛都能提供1头后备母牛，对于荷斯坦牛，当将基因组关系应用于所有基因分型母牛时，每年使用基因组关系的经济价值超过300万美元。以前的配种程序只需向客户传输系谱文件，但通过纳入基因组关系、更精确的配偶分配和显性效应，可以提供更好的服务。随着更多母牛进行基因分型，经济效益将持续增长。
