Genetic Gain and Inbreeding from Genomic Selection in a Simulated Commercial Breeding Program for Perennial Ryegrass
Genetic Gain and Inbreeding from Genomic Selection in a Simulated Commercial Breeding Program for Perennial Ryegrass
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DOI：
10.3835/plantgenome2015.06.0046
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发表时间：
2016-03-01
期刊：
影响因子：
4.2
通讯作者：
Daetwyler, Hans D.
中科院分区：
文献类型：
--
作者：
Lin, Zibei;Cogan, Noel O. I.;Daetwyler, Hans D.
基因组选择（GS）为加速多年生黑麦草（Lolium perenne L.）改良提供了一个有吸引力的选择，因为目前大多数育种计划的周期都很长。本研究采用模拟方法比较了GS育种策略与传统育种策略在关键性状（持久性、产量和开花时间）上的遗传增益和近交水平。在有效种群规模为1万的情况下，通过随机交配6万代来模拟基本种群基因组。将所得群体的连锁不平衡程度（LD）与实证研究结果进行了比较。模拟了初始亲本品种，以匹配当前商品品种的多样性。基因组选择被设计成适合公司育种计划在育种周期的两个选择点（间隔植物和小块）。生产力性状的基因组估计育种值（GEBVs）用小区的表型和基因型进行训练。单株持久性和单株产量的gebv精度分别为0.24和0.36，而地块的gebv精度较低（分别为0.17和0.19）。gebv对开花时间的精度较高（高达0.7），部分原因是克隆行期的参考群体规模较大。gebv的可用性使周期时间缩短了4年，这使得持久性和产量的遗传增益分别比传统方案增加了至少一倍和三倍。然而，也观察到GS策略的品种间每周期的近交率较高。
Genomic selection (GS) provides an attractive option for accelerating genetic gain in perennial ryegrass (Lolium perenne L.) improvement given the long cycle times of most current breeding programs. The present study used simulation to investigate the level of genetic gain and inbreeding obtained from GS breeding strategies compared with traditional breeding strategies for key traits (persistency, yield, and flowering time). Base population genomes were simulated through random mating for 60,000 generations at an effective population size of 10,000. The degree of linkage disequilibrium (LD) in the resulting population was compared with that obtained from empirical studies. Initial parental varieties were simulated to match diversity of current commercial cultivars. Genomic selection was designed to fit into a company breeding program at two selection points in the breeding cycle (spaced plants and miniplot). Genomic estimated breeding values (GEBVs) for productivity traits were trained with phenotypes and genotypes from plots. Accuracy of GEBVs was 0.24 for persistency and 0.36 for yield for single plants, while for plots it was lower (0.17 and 0.19, respectively). Higher accuracy of GEBVs was obtained for flowering time (up to 0.7), partially as a result of the larger reference population size that was available from the clonal row stage. The availability of GEBVs permit a 4-yr reduction in cycle time, which led to at least a doubling and trebling genetic gain for persistency and yield, respectively, than the traditional program. However, a higher rate of inbreeding per cycle among varieties was also observed for the GS strategy.