Oladzad Atena, Roy Jayanta, Mamidi Sujan, Miklas Phillip N, Lee Rian, Clevenger Josh, Myers Zachary, Korani Walid, McClean Phillip E
Genomics Data Scientist II, Sound Agriculture, Emeryville, CA, United States.
Department of Plant Sciences, North Dakota State University, Fargo, ND, United States.
Front Plant Sci. 2023 Jul 31;14:1233285. doi: 10.3389/fpls.2023.1233285. eCollection 2023.
White mold (WM) is a major disease in common bean ( L.), and its complex quantitative genetic control limits the development of WM resistant cultivars. WM2.2, one of the nine meta-QTL with a major effect on WM tolerance, explains up to 35% of the phenotypic variation and was previously mapped to a large genomic interval on Pv02. Our objective was to narrow the interval of this QTL using combined approach of classic QTL mapping and QTL-based bulk segregant analysis (BSA), and confirming those results with Khufu QTL-seq. The phenotypic and genotypic data from two RIL populations, 'Raven'/I9365-31 (R31) and 'AN-37'/PS02-029C-20 (Z0726-9), were used to select resistant and susceptible lines to generate subpopulations for bulk DNA sequencing. The QTL physical interval was determined by considering overlapping interval of the identified QTL or peak region in both populations by three independent QTL mapping analyses. Our findings revealed that meta-QTL WM2.2 consists of three regions, WM2.2a (4.27-5.76 Mb; euchromatic), WM 2.2b (12.19 to 17.61 Mb; heterochromatic), and WM2.2c (23.01-25.74 Mb; heterochromatic) found in both populations. Gene models encoding for gibberellin 2-oxidase 8, pentatricopeptide repeat, and heat-shock proteins are the likely candidate genes associated with WM2.2a resistance. A TIR-NBS-LRR class of disease resistance protein (Phvul.002G09200) and LRR domain containing family proteins are potential candidate genes associated with WM2.2b resistance. Nine gene models encoding disease resistance protein [pathogenesis-related thaumatin superfamily protein and disease resistance-responsive (dirigent-like protein) family protein etc] found within the WM2.2c QTL interval are putative candidate genes. WM2.2a region is most likely associated with avoidance mechanisms while WM2.2b and WM2.2c regions trigger physiological resistance based on putative candidate genes.
白霉病（WM）是菜豆（Phaseolus vulgaris L.）的一种主要病害，其复杂的数量遗传控制限制了抗WM品种的培育。WM2.2是对WM耐受性有主要影响的九个元QTL之一，可解释高达35%的表型变异，此前被定位到Pv02上的一个大基因组区间。我们的目标是使用经典QTL定位和基于QTL的混合分离群体分析（BSA）相结合的方法缩小该QTL的区间，并用Khufu QTL-seq验证这些结果。利用两个重组自交系群体“Raven”/I9365-31（R31）和“AN-37”/PS02-029C-20（Z0726-9）的表型和基因型数据，选择抗性和感病株系以生成用于混合DNA测序的亚群体。通过三个独立的QTL定位分析，考虑两个群体中鉴定出的QTL重叠区间或峰值区域，确定QTL物理区间。我们的研究结果表明，元QTL WM2.2由三个区域组成，在两个群体中均发现了WM2.2a（4.27-5.76 Mb；常染色质）、WM 2.2b（12.19至17.61 Mb；异染色质）和WM2.2c（23.01-25.74 Mb；异染色质）。编码赤霉素2-氧化酶8、五肽重复序列和热休克蛋白的基因模型是与WM2.2a抗性相关的可能候选基因。一类TIR-NBS-LRR抗病蛋白（Phvul.002G09200）和含LRR结构域的家族蛋白是与WM2.2b抗性相关的潜在候选基因。在WM2.2c QTL区间内发现的九个编码抗病蛋白的基因模型[病程相关类thaumatin超家族蛋白和抗病反应蛋白（ dirigent样蛋白）家族蛋白等]是推定的候选基因。WM2.2a区域最有可能与避病机制相关，而WM2.2b和WM2.2c区域基于推定的候选基因引发生理抗性。
