Sadohara Rie, Long Yunfei, Izquierdo Paulo, Urrea Carlos A, Morris Daniel, Cichy Karen
Dep. of Plant, Soil and Microbial Sciences, Michigan State Univ., 1066 Bogue St., East Lansing, MI, 48824, USA.
Dep. of Electrical and Computer Engineering, Michigan State Univ., 428 S Shaw Ln., East Lansing, MI, 48824, USA.
Plant Genome. 2022 Mar;15(1):e20173. doi: 10.1002/tpg2.20173. Epub 2021 Nov 24.
Common bean (Phaseolus vulgaris L.) is consumed worldwide, with strong regional preferences for seed appearance characteristics. Colors of the seed coat, hilum ring, and corona are all important, along with susceptibility to postharvest darkening, which decreases seed value. This study aimed to characterize a collection of 295 yellow bean genotypes for seed appearance and postharvest darkening, evaluate genotype × environment (G × E) effects and map those traits via genome-wide association analysis. Yellow bean germplasm were grown for 2 yr in Michigan and Nebraska and seed were evaluated for Lab* color values, postharvest darkening, and hilum ring and corona colors. A model to exclude the hilum ring and corona of the seeds, black background, and light reflection was developed by using machine learning, allowing for targeted and efficient Lab* value extraction from the seed coat. The G × E effects were significant for the color values, and Michigan-grown seeds were darker than Nebraska-grown seeds. Single-nucleotide polymorphisms (SNPs) were associated with L* and hilum ring color on Pv10 near the J gene involved in mature seed coat color and hilum ring color. A SNP on Pv07 associated with L*, a*, postharvest darkening, and hilum ring and corona colors was near the P gene, the ground factor gene for seed coat color expression. The machine-learning-aided model used to extract color values from the seed coat, the wide variability in seed morphology traits, and the associated SNPs provide tools for future breeding and research efforts to meet consumers' expectations for bean seed appearance.
菜豆（Phaseolus vulgaris L.）在全球范围内都有消费，人们对种子外观特征有强烈的区域偏好。种皮颜色、脐环颜色和种阜颜色都很重要，同时收获后种子变黑的易感性也很关键，因为这会降低种子价值。本研究旨在对295个黄菜豆基因型的种子外观和收获后变黑情况进行表征，评估基因型×环境（G×E）效应，并通过全基因组关联分析对这些性状进行定位。黄菜豆种质在密歇根州和内布拉斯加州种植了两年，对种子的Lab颜色值、收获后变黑情况以及脐环和种阜颜色进行了评估。利用机器学习开发了一个模型，用于排除种子的脐环和种阜、黑色背景和光反射的影响，从而能够从种皮中靶向高效地提取Lab值。颜色值的G×E效应显著，在密歇根州种植的种子比在内布拉斯加州种植的种子颜色更深。单核苷酸多态性（SNP）与位于参与成熟种皮颜色和脐环颜色的J基因附近的Pv10上的L和脐环颜色相关。位于Pv07上与L、a*、收获后变黑情况以及脐环和种阜颜色相关的一个SNP靠近P基因，P基因是种皮颜色表达的基础因子基因。用于从种皮中提取颜色值的机器学习辅助模型、种子形态性状的广泛变异性以及相关的SNP为未来的育种和研究工作提供了工具，以满足消费者对菜豆种子外观的期望。
