Agronomy Dep., Univ. of Florida, Gainesville, FL, 32611, USA.
Horticultural Sciences Dep., Univ. of Florida, Gainesville, FL, 32611, USA.
Plant Genome. 2022 Sep;15(3):e20235. doi: 10.1002/tpg2.20235. Epub 2022 Jul 11.
Genomic selection (GS) has proven to be an effective method to increase genetic gain rates and accelerate breeding cycles in many crop species. However, its implementation requires large investments to phenotype of the training population and for routine genotyping. Alfalfa (Medicago sativa L.) is one of the major cultivated forage legumes, showing high-quality nutritional value. Alfalfa breeding is usually carried out by phenotypic recurrent selection and is commonly done at the family level. The application of GS in alfalfa could be simplified and less costly by genotyping and phenotyping families in bulks. For this study, an alfalfa reference population composed of 142 full-sib and 35 half-sib families was bulk-genotyped using target enrichment sequencing and phenotyped for dry matter yield (DMY) and canopy height (CH) in Florida, USA. Genotyping of the family bulks with 17,707 targeted probes resulted in 114,945 single-nucleotide polymorphisms. The markers revealed a population structure that matched the mating design, and the linkage disequilibrium slowly decayed in this breeding population. After exploring multiple prediction scenarios, a strategy was proposed including data from multiple harvests and accounting for the G×E in the training population, which led to a higher predictive ability of up to 38 and 24% for DMY and CH, respectively. Although this study focused on the implementation of GS in alfalfa families, the bulk methodology and the prediction schemes used herein could guide future studies in alfalfa and other crops bred in bulks.
基因组选择 (GS) 已被证明是一种在许多作物物种中提高遗传增益率和加速育种周期的有效方法。然而，其实施需要对训练群体进行表型和常规基因型鉴定方面的大量投资。紫花苜蓿（Medicago sativa L.）是主要栽培的饲料豆科作物之一，具有很高的营养价值。紫花苜蓿的选育通常通过表型轮回选择进行，通常在家庭水平上进行。通过对大量的家庭进行批量基因型鉴定和表型鉴定，可以简化和降低 GS 在紫花苜蓿中的应用成本。在这项研究中，使用目标富集测序对由 142 个全同胞和 35 个半同胞家系组成的紫花苜蓿参考群体进行批量基因型鉴定，并在美国佛罗里达州对干物质产量（DMY）和冠层高度（CH）进行表型鉴定。用 17707 个靶向探针对家系进行批量基因型鉴定，共获得 114945 个单核苷酸多态性。这些标记揭示了与交配设计相匹配的群体结构，并且在这个育种群体中连锁不平衡缓慢衰减。在探索了多种预测方案后，提出了一种包括多个收获数据和考虑训练群体中 G×E 的策略，这导致了高达 38%和 24%的 DMY 和 CH 的更高预测能力。尽管这项研究侧重于在紫花苜蓿家系中实施 GS，但此处使用的批量方法和预测方案可以指导未来在紫花苜蓿和其他批量选育的作物中的研究。
