Integrating de novo QTL‐seq and linkage mapping to identify quantitative trait loci conditioning physiological resistance and avoidance to white mold disease in dry bean

• Published in: The plant genome Vol. 16; no. 4; pp. e20380 - n/a
• Main Authors: Roy, Jayanta, Soler‐Garzón, Alvaro, Miklas, Phillip N., Lee, Rian, Clevenger, Josh, Myers, Zachary, Korani, Walid, McClean, Phillip E.
• Format: Journal Article
• Language: English
• Published: United States John Wiley & Sons, Inc 01.12.2023; Wiley
• Subjects: Architecture; Beans; Chromosome Mapping - methods; Chromosomes; Chromosomes, Plant; Cultivars; Disease management; Disease resistance; Disease Resistance - genetics; Gene mapping; Genomes; Genomics; Genotype & phenotype; Gibberellins; Inbreeding; Kinases; Marker-assisted selection; Phenotype; Physiology; Polymorphism; Quantitative Trait Loci; White mold
• ISSN: 1940-3372; 1940-3372
• DOI: 10.1002/tpg2.20380

White mold (WM), caused by the ubiquitous fungus Sclerotinia sclerotiorum, is a devastating disease that limits production and quality of dry bean globally. In the present study, classic linkage mapping combined with QTL‐seq were employed in two recombinant inbred line (RIL) populations, “Montrose”/I9365‐25 (M25) and “Raven”/I9365‐31 (R31), with the initial goal of fine‐mapping QTL WM5.4 and WM7.5 that condition WM resistance. The RILs were phenotyped for WM reactions under greenhouse (straw test) and field environments. The general region of WM5.4 and WM7.5 were reconfirmed with both mapping strategies within each population. Combining the results from both mapping strategies, WM5.4 was delimited to a 22.60–36.25 Mb interval in the heterochromatic regions on Pv05, while WM7.5 was narrowed to a 0.83 Mb (3.99–4.82 Mb) region on the Pv07 chromosome. Furthermore, additional QTL WM2.2a (3.81–7.24 Mb), WM2.2b (11.18–17.37 Mb, heterochromatic region), and WM2.2c (23.33–25.94 Mb) were mapped to a narrowed genomic interval on Pv02 and WM4.2 in a 0.89 Mb physical interval at the distal end of Pv04 chromosome. Gene models encoding gibberellin 2‐oxidase proteins regulating plant architecture are likely candidate genes associated with WM2.2a resistance. Nine gene models encoding a disease resistance protein (quinone reductase family protein and ATWRKY69) found within the WM5.4 QTL interval are putative candidate genes. Clusters of 13 and 5 copies of gene models encoding cysteine‐rich receptor‐like kinase and receptor‐like protein kinase‐related family proteins, respectively, are potential candidate genes associated with WM7.5 resistance and most likely trigger physiological resistance to WM. Acquired knowledge of the narrowed major QTL intervals, flanking markers, and candidate genes provides promising opportunities to develop functional molecular markers to implement marker‐assisted selection for WM resistant dry bean cultivars. Core Ideas Meta‐QTL WM5.4 and WM7.5, have major effects on white mold (WM) resistance in dry bean. Combining the newly developed pipeline Khufu de novo QTL‐seq and classic QTL mapping, we validated WM5.4 and WM7.5 QTL in two mapping populations. WM5.4 was delimited to 22.60–36.25 Mb in the heterochromatic regions, whereas WM7.5 was fine‐mapped to a 0.83 Mb genomic interval. Strong candidate genes conferring WM resistance were narrowed down for WM5.4 and WM7.5 meta‐QTL. Additionally, we reduced the genomic interval of WM2.2 meta‐QTL and fine‐mapped QTL WM4.2 (0.89 Mb interval).