Genome-wide association mapping and genomic prediction of Fusarium wilt race 2 resistance in the USDA Citrullus amarus collection

Authors: GANAPARTHI, VENKATA RAO - Clemson University; RENNBERGER, GABRIEL - Clemson University; WECHTER, PATRICK - Clemson University; Levi, Amnon; BRANHAM, SANDRA - Clemson University

Submitted to: Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/23/2023
Publication Date: 11/28/2023
Citation: Ganaparthi, V., Rennberger, G., Wechter, P., Levi, A., Branham, S.E. 2023. Genome-wide association mapping and genomic prediction of Fusarium wilt race 2 resistance in the USDA Citrullus amarus collection. Theoretical and Applied Genetics. 107:3649-4037. https://apsjournals.apsnet.org/doi/10.1094/PDIS-02-23-0400-RE.
DOI: https://doi.org/10.1094/PDIS-02-23-0400-RE

Interpretive Summary: Watermelon is an important vegetable crop in the United States and around the world. Fusarium wilt (FW) is the major disease of watermelon in the U.S as well as in other cucurbits growing areas around the world. New sources of resistance and molecular markers are needed to control the spread of the FW pathogen in watermelon. To date, there is no a watermelon variety fully resistant to Fusarium wilt race 2. In this research, we screened the USDA-ARS citron watermelon (close relative of the cultivated sweet watermelon) collection for resistance to a virulent isolate of FW race 2 and identified several plant introductions with resistance to this FW pathogen. Using a genetic mapping technique called genome-wide association study, we identified genomic markers and candidate genes linked to resistance to FW race 2. These new molecular markers and resistant USDA plant introductions should be useful for public and seed company breeders aiming to enhance FW race 2-resistance in watermelon varieties .

Technical Abstract: Fusarium wilt caused by Fusarium oxysporum f. sp. niveum (Fon) race 2 is a serious disease in watermelon and can reduce yields by 80%. Genome-wide association studies (GWAS) are a valuable tool in dissecting the genetic basis of traits. Citrullus amarus accessions (N=120) from the USDA germplasm collection were genotyped with whole-genome resequencing, resulting in 2,126,759 single nucleotide polymorphisms (SNPs) that were utilized for GWAS. Three models were used for GWAS with the R package GAPIT. MLM analysis did not identify any significant marker associations. FarmCPU identified four quantitative trait nucleotides (QTN) on chromosomes 1, 5 and 9, and BLINK identified one QTN on chromosome 10 as significantly associated with Fon race 2 resistance. FarmCPU identified four QTN that explained 60% of Fon race 2 resistance, and the single QTN from BLINK explained 27%. Relevant candidate genes were found within the LD blocks of these significant SNPs, including genes encoding aquaporins, expansins, 2S albumins, and glutathione S-transferases which have been shown to be involved in imparting resistance to Fusarium spp. Genomic predictions (GP) for Fon race 2 resistance using all 2,126,759 SNPs resulted in mean prediction accuracy of 0.08 with five-fold cross-validation employing gBLUP or rrBLUP. Mean prediction accuracy with gBLUP leave-one-out cross-validation was 0.48. Thus, along with identifying genomic regions associated with Fon race 2 resistance among the accessions, this study observed prediction accuracies that were strongly influenced by population size.