Dep. of Plant Pathology, Kansas State Univ., 4024 Throckmorton Plant Sciences Center, Manhattan, KS, 66506, USA.
Stakman-Borlaug Center for Sustainable Plant Health, Center for Applied Phenomics, Univ. of Minnesota, 1519 Gortner Avenue, St. Paul, MN, 55108, USA.
Plant Genome. 2021 Jul;14(2):e20089. doi: 10.1002/tpg2.20089. Epub 2021 Apr 26.
The development of perennial grain crops is driven by the vision of simultaneous food production and enhanced ecosystem services. Typically, perennial crops like intermediate wheatgrass (IWG)[Thinopyrum intermedium (Host) Barkworth & D.R Dewey] have low seed yield and other detrimental traits. Next-generation sequencing has made genomic selection (GS) a tractable and viable breeding method. To investigate how an IWG breeding program may use GS, we evaluated 3,658 genets over 2 yr for 46 traits to build a training population. Six statistical models were used to evaluate the non-replicated data, and a model using autoregressive order 1 (AR1) spatial correction for rows and columns combined with the genomic relationship matrix provided the highest estimates of heritability. Genomic selection models were built from 18,357 single nucleotide polymorphism markers via genotyping-by-sequencing, and a 20-fold cross-validation showed high predictive ability for all traits (r > .80). Predictive abilities improved with increased training population size and marker numbers, even with larger amounts of missing data per marker. On the basis of these results, we propose a GS breeding method that is capable of completing one cycle per year compared with a minimum of 2 yr per cycle with phenotypic selection. We estimate that this breeding approach can increase the rate of genetic gain up to 2.6× above phenotypic selection for spike yield in IWG, allowing GS to enable rapid domestication and improvement of this crop. These breeding methods should be transferable to other species with similar long breeding cycles or limited capacity for replicated observations.
多年生粮食作物的发展受到同时生产粮食和增强生态系统服务的愿景的推动。通常，像中间偃麦草（IWG）[Thinopyrum intermedium (Host) Barkworth & D.R. Dewey]这样的多年生作物种子产量低，还有其他有害特性。新一代测序使得基因组选择（GS）成为一种可行的、可行的育种方法。为了研究 IWG 育种计划如何使用 GS，我们在 2 年内对 3658 个品系进行了 46 个性状的评估，以建立一个训练群体。使用六种统计模型来评估非重复数据，并且使用行和列的自回归顺序 1（AR1）空间校正与基因组关系矩阵相结合的模型提供了最高的遗传力估计值。使用通过测序的基因分型获得的 18357 个单核苷酸多态性标记物构建了基因组选择模型，20 倍交叉验证显示所有性状的预测能力都很高（r>.80）。随着训练群体规模和标记数量的增加，预测能力提高，即使每个标记缺失的数据量较大。基于这些结果，我们提出了一种 GS 育种方法，与表型选择相比，每年可以完成一个周期，而表型选择的最小周期为 2 年。我们估计，这种育种方法可以将 IWG 穗产量的遗传增益提高 2.6 倍以上，使 GS 能够实现对这种作物的快速驯化和改良。这些育种方法应该可以转移到其他具有类似长育种周期或有限重复观察能力的物种。
