Data_Sheet_1_Associated SNPs, Heritabilities, Trait Correlations, and Genomic Breeding Values for Resistance in Snap Beans (Phaseolus vulgaris L.) to Root Rot Caused by Fusarium solani (Mart.) f. sp. phaseoli (Burkholder).pdf

Root rot is a major constraint to snap bean (Phaseolus vulgaris) production in the United States and around the world. Genetic resistance is needed to effectively control root rot disease because cultural control methods are ineffective, and the pathogen will be present at the end of one season of production on previously clean land. A diversity panel of 149 snap bean pure lines was evaluated for resistance to Fusarium root rot in Oregon. Morphological traits potentially associated with root rot resistance, such as aboveground biomass, adventitious roots, taproot diameter, basal root diameter, deepest root angle, shallowest root angle, root angle average, root angle difference, and root angle geometric mean were evaluated and correlated to disease severity. A genome wide association study (GWAS) using the Fixed and random model Circulating Probability Unification (FarmCPU) statistical method, identified five associated single nucleotide polymorphisms (SNPs) for disease severity and two SNPs for biomass. The SNPs were found on Pv03, Pv07, Pv08, Pv10, and Pv11. One candidate gene for disease reaction near a SNP on Pv03 codes for a peroxidase, and two candidates associated with biomass SNPs were a 2-alkenal reductase gene cluster on Pv10 and a Pentatricopeptide repeat domain on Pv11. Bean lines utilized in the study were ranked by genomic estimated breeding values (GEBV) for disease severity, biomass, and the root architecture traits, and the observed and predicted values had high to moderate correlations. Cross validation of genomic predictions showed slightly lower correlational accuracy. Bean lines with the highest GEBV were among the most resistant, but did not necessarily rank at the very top numerically. This study provides information on the relationship of root architecture traits to root rot disease reaction. Snap bean lines with genetic merit for genomic selection were identified and may be utilized in future breeding efforts.

根腐病是美国乃至全球范围内制约菜豆（Phaseolus vulgaris）生产的主要限制因素。鉴于传统防治手段的无效性以及病原体在连续季节生产后仍可能存在，遗传抗病性对于有效控制根腐病至关重要。在俄勒冈州，一项包含149个菜豆纯系的多样性组面板被评估其对抗真菌性根腐病的抵抗力。与根腐病抗性相关的形态学特征，如地上生物量、不定根、主根直径、基根直径、最深根角、最浅根角、根角平均值、根角差异以及根角几何平均数等，均被评估并与病害严重程度进行相关性分析。利用固定和随机模型循环概率统一（FarmCPU）统计方法进行的全基因组关联研究（GWAS）确定了与病害严重程度相关的五个单核苷酸多态性（SNPs）和与生物量相关的两个SNPs。这些SNPs位于Pv03、Pv07、Pv08、Pv10和Pv11上。位于Pv03的一个与病害反应相关的候选基因编码过氧化物酶，与生物量相关的两个候选基因分别是位于Pv10上的2-烯醛还原酶基因簇和位于Pv11上的戊肽重复结构域。参与研究的豆系按照基因组估计育种值（GEBV）对病害严重程度、生物量和根构型性状进行排名，观察值和预测值表现出高度至中度的相关性。基因组预测的交叉验证显示略低的关联准确性。具有最高GEBV的豆系在抗病性方面表现最为突出，但并不一定在数值排名上位于最前列。本研究揭示了根构型性状与根腐病反应之间的关系，并识别了具有基因组选择遗传优点的菜豆系，这些菜豆系可能被用于未来的育种工作中。