Genomic selection for improving watermelon cultivars (citrullus lanatus) with the polygenic trait of Root-knot Nematode (RKN)-Resistance that exist in Citron watermelon (Citrullus amarus)

Authors: BISWAS, ANJU - Oak Ridge Institute For Science And Education (ORISE); REGMI, HOMAN - Oak Ridge Institute For Science And Education (ORISE); Waldo, Benjamin; BRANHAM, SANDRA - Clemson University; WECHTER, WILLIAM - Clemson University; Kousik, Chandrasekar; Levi, Amnon; Rutter, William

Submitted to: The Plant Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/14/2026
Publication Date: N/A
Citation: N/A
DOI: https://doi.org/10.1002/tpg2.70203

Interpretive Summary: Watermelon is an important vegetable crop grown in 44 states in the U.S.A. Root-knot nematodes (RKN) are major plant parasites affecting watermelon production. Developing resistant varieties is the most effective strategy in reducing RKN-impact in watermelon fields. ARS scientists utilized an advanced approach named 'Genomic Selection (GS)' to evaluate the ARS watermelon collection and select these genotypes having the highest RKN-resistance. The resistant genotypes selected in this study are a viable source for ARS scientists in improving RKN-resistance in watermelon cultivars. The GS data and genetic material developed in this study will be useful to seed companies and public researchers and breeders aiming to improve RKN-resistance in elite watermelon cultivars.

Technical Abstract: Meloidogyne enterolobii is a virulent root-knot nematode (RKN) species posing a threat to the watermelon crop. The USDA, ARS, Plant Introduction (PI) collection of Citrullus amarus, a wild relative of cultivated watermelon (Citrullus lanatus) contains RKN-resistance. However, incorporating RKN-resistance into watermelon cultivars is challenging since the resistance is a polygenic trait, reflected in the broad-sense heritability (ratio of all genetic factors, including dominance, gene-gene interactions, and additive genetic variance to total phenotypic variance) versus the narrow-sense heritability (ratio of additive genetic variance to total phenotypic variance; H² = 0.44 versus h² = 0.41 for galling and 0.20 for eggs per gram of root for both, broad and narrow sense heritability). Here, a genomic selection (GS) approach was used to evaluated 108 C. amarus PIs (S3 inbred lines) for RKN-resistance based on two criteria: 1) root galling percentage, and 2) eggs per gram of root. All PIs were re-sequenced, resulting in 2.1 million single nucleotide polymorphic (SNP) markers. Genomic prediction models, including genomic best linear unbiased prediction (gBLUP), sparse GBLUP, and RKHS-regression were tested using a subset of 10,000 versus the 2.1 million SNPs. The RKHS models based on 10,000 SNPs reached the highest prediction ability for galling (PA = 0.42) and for eggs per gram of root (PA = 0.40). Candidate PIs common to the best linear unbiased estimates (BLUEs) and genome estimated breeding values (GEBVs) under different selection intensities (10%, 20%, and 30%) were selected and used in our breeding program aimed to enhance RKN-resistance in watermelon cultivars.