Verbyla Klara L, Kube Peter D, Evans Bradley S
CSIRO, Black Mountain Canberra ACT Australia.
Present address: Center for Aquaculture Technology San Diego CA USA.
Evol Appl. 2021 Oct 11;15(4):631-644. doi: 10.1111/eva.13304. eCollection 2022 Apr.
Genomic information was included for the first time in the prediction of breeding values for Atlantic salmon within the Australian Salmon Enterprises of Tasmania Pty Ltd selective breeding program in 2016. The process to realize genomic selection in the breeding program begun in 2014 with the scheme finalized and fully implemented for the first time in 2018. The high potential of within family selection to accelerate genetic gain, something not possible using the traditional pedigree-based approach, provided the impetus for implementation. Efficient and effective genotyping platforms are essential for genomic selection. Genotype data from high density arrays revealed extensive persistence of linkage disequilibrium in the Tasmania Atlantic salmon population, resulting in high accuracies of both imputation and genomic breeding values when using imputed data. Consequently, a low-density novel genotype-by-sequence assay was designed and incorporated into the scheme. Through the use of a static high- and dynamic low-density genotyping platforms, an optimized genotyping scheme was devised and implemented such that all individuals in every year class are genotyped efficiently while maximizing the genetic gains and minimizing costs. The increase in the rates of genetic gain attributed to the implementation of genomic selection is significant across both the breeding programs primary and secondary traits. Substantial improvement in the ability to select parents prior to progeny testing is observed across multiple years. The resultant economic impacts for the industry are considerable based on the increases in genetic gain for traits achieved within the breeding program and the use of genomic selection for commercial production.
2016年，塔斯马尼亚澳大利亚鲑鱼企业私人有限公司的大西洋鲑鱼选择性育种计划首次将基因组信息纳入育种值预测。2014年开始在育种计划中实现基因组选择的过程，该计划于2018年首次最终确定并全面实施。家系内选择在加速遗传进展方面具有很高潜力，这是传统系谱法无法实现的，这为实施该方法提供了动力。高效且有效的基因分型平台对于基因组选择至关重要。高密度芯片的基因型数据显示塔斯马尼亚大西洋鲑鱼种群中连锁不平衡广泛存在，使用推算数据时，推算和基因组育种值的准确性都很高。因此，设计了一种低密度的新型序列基因型检测方法并纳入该计划。通过使用静态高密度和动态低密度基因分型平台，设计并实施了一种优化的基因分型方案，使得每年所有个体都能高效地进行基因分型，同时最大限度地提高遗传进展并降低成本。在育种计划的主要和次要性状方面，基因组选择实施带来的遗传进展速度提升都很显著。多年来，在后代测试之前选择亲本的能力有了大幅提高。基于育种计划中实现的性状遗传进展增加以及基因组选择在商业生产中的应用，对该行业产生的经济影响相当可观。
