Exploring the genomic landscape of gummy stem blight resistance in watermelon through QTL-Seq

Authors: NATARAJAN, PURUSHOTHAMAN - West Virginia State University; RATHNAGIRI, AKILAN - West Virginia State University; RIVERA-BURGOS, LUIS - North Carolina State University; LOPEZ-ORTIZ, CARLOS - Clemson University; NIMMAKAYALA, PADMA - West Virginia State University; SARI, NEBAHAT - North Carolina State University; WEHNER, TODD, - North Carolina State University; Levi, Amnon; REDDY, UMESH - West Virginia State University

Submitted to: Plant Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/18/2024
Publication Date: 11/27/2024
Citation: Natarajan, P., Rathnagiri, A., Rivera-Burgos, L., Lopez-Ortiz, C., Nimmakayala, P., Sari, N., Wehner, T.T., Levi, A., Reddy, U. 2024. Exploring the genomic landscape of gummy stem blight resistance in watermelon through QTL-Seq. Plant Biology. 24:1129. https://doi.org/10.1186/s12870-024-05839-2.
DOI: https://doi.org/10.1186/s12870-024-05839-2

Interpretive Summary: Watermelon is an important vegetable crop grown in the U.S.A. and throughout the world. Gummy Stem Blight (GSB) is a major watermelon disease, causing significant crop damage and monetary losses to watermelon growers in the USA. GSB is caused by a soil-borne fungus that attacks the upper parts of the plant. Identifying genetic resources and genes conferring resistance to GSB and utilizing them for developing resistant varieties will be a highly effective strategy for managing this disease in watermelon fields. In this study, ARS scientists collaborated with scientists at West Virginia State University and North Carolina State University on developing and evaluating genetic populations and on using advanced genomic technologies to identify genes conferring resistance to GSB in watermelon. This collaboration resulted in identification of several gene loci contributing to GSB-resistance. The genetic material and genomic data developed in this study will beuseful for seed company and public breeders aiming to improve resistance to GSB in elite watermelon cultivars.

Technical Abstract: Watermelon is a nutritionally and economically important crop in the US and globally. Gummy Stem Blight (GSB), caused by three cryptic Stagonosporopsis species, is one of the most devastating diseases affecting watermelon in the US, impacting most of the plant's above-ground parts. This study aimed to identify key Quantitative Trait Variants (QTVs) that include SNPs and In/Dels associated with GSB resistance in selfed derivatives of a MAGIC population derived from intercrosses between the most resistant lines of Citrullus amarus and highly susceptible cultivars of Citrullus lanatus. Resistant and susceptible bulks were created by combining equimolar DNA concentrations from 30 extremely resistant recombinant inbred lines (RILs) and 30 extremely susceptible RILs. These bulks underwent whole-genome sequencing, generating over 1 billion reads per bulk to achieve comprehensive genome coverage. The mapping percentage of the bulks to the parental genomes ranged from 92% to 99%. More than 6 million SNPs and 1 million indels were identified from the resistant parental genome. In comparison, fewer than 2 million SNPs and 0.4 million indels were found using the susceptible parental genome. QTNs associated with GSB resistance were identified using single-nucleotide polymorphism-index and Gprime methods. Statistically significant variants/loci linked to GSB resistance were found on chromosomes 1, 2, 3, 5, 7, 10, and 11. Several important candidate genes were located in these QTV regions, including the Avr9/Cf-9 Rapidly Elicited Protein (CaU07G12990) on chromosome 7. Significant loci associated with GSB resistance were used to develop PACE genotype markers. These findings will aid in the development of GSB-resistant watermelon cultivars.