Genome-wide association mapping and genomic predictions for bacterial fruit blotch resistance in the USDA Citrullus amarus collection

Authors: GANAPARTHI, ENKAT - Clemson University; WECHTER, WILLIAM - Clemson University; Katawczik, Melanie; Levi, Amnon; BRANHAM, SANDRA - Clemson University

Submitted to: Plant Disease
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/8/2025
Publication Date: 5/13/2025
Citation: Ganaparthi, E., Wechter, W., Katawczik, M.L., Levi, A., Branham, S. 2025. Genome-wide association mapping and genomic predictions for bacterial fruit blotch resistance in the USDA Citrullus amarus collection. Plant Disease. https://doi.org/10.1094/PDIS-12-24-2665-RE.
DOI: https://doi.org/10.1094/PDIS-12-24-2665-RE

Interpretive Summary: Watermelon is an important vegetable crop grown in 44 states in the U.S.A. Bacterial fruit blotch (BFB) is a devastating disease of watermelon, causing significant crop damage and monetary losses to growers and producers in the USA and throughout the world. Identifying genetic resources and genes conferring resistance to BFB should be useful for developing resistant varieties and in reducing the impact of this disease on the watermelon industry. ARS scientists collaborated with scientists at Clemson University on evaluating a collection of USDA watermelon accessions collected in Africa for resistance to BFB. The scientists also employed advanced genomic technologies to identify gene loci associated with resistance to BFB. The accessions showing highest levels of resistance to BFB and the gene loci identified in this study should be useful for seed company and public breeders in their efforts to improve resistance to BFB in elite watermelon cultivars.

Technical Abstract: Acidovorax citrulli infects seedlings, adult plants and fruits, causing bacterial fruit blotch (BFB) in watermelon (Citrullus lanatus) and most other cucurbits. Host resistance would provide an effective and economical management option for BFB but there are currently no resistant watermelon cultivars. Several resistant accessions were previously identified in the USDA Citrullus amarus (citron melon) collection. Identifying the genetic basis of this resistance would allow the development of BFB-resistant cultivars through introgression from this crop wild relative. Genome-wide association studies (GWAS) are an excellent tool for dissecting the genetic architecture of a trait. The USDA Citrullus amarus collection (N=127 accessions) was genotyped with whole genome resequencing, resulting in 2,126,759 SNP markers, which were used for GWAS of seedling resistance to A. citrulli. Four models were used for GWAS in R with the GAPIT package. MLM and MLMM analysis did not identify any significant marker associations. FarmCPU identified three quantitative trait nucleotides (QTN) on chromosomes 2, 4, and 8. BLINK identified only one significant QTN on chromosome 8. The three significant QTNs explained 65.1% of the phenotypic variance using a linear regression model. Putative candidate genes within the linkage disequilibrium blocks of significant SNPs code proteins relevant to biotic resistance, such as Patellin-6, macrophage migration inhibitory factor homolog, PRA1 family protein and trichome birefringence-like family proteins. The predictive ability of six genomic prediction models (gBLUP, rrBLUP, BayesB, BayesC, BL and BayesRR) for A. citrulli seedling resistance ranged from 0.45 to 0.75. Along with identifying genomic regions associated with BFB seedling resistance, this study observed moderate to high predictive abilities across genomic prediction models.