Genomic selection of root‐knot nematode ( <i>Meloidogyne enterolobii</i> ) resistance in watermelon wild relatives ( <i>Citrullus amarus</i> )

Meloidogyne enterolobii is a virulent root-knot nematode (RKN) species posing a significant threat to watermelon production across the United States. 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. Genomic selection could be a useful strategy for improving RKN resistance in watermelon as it is a polygenic trait primarily controlled through additive gene action, as indicated by the broad-sense heritability being close or equal to the narrow-sense heritability: H² = 0.69, h² = 0.23 for galling and H² = 0.47, h² = 0.46 for eggs per gram of root. Here, a genomic selection approach was used to evaluate 97 C. amarus PIs (S3 inbred lines) for RKN resistance based on two criteria: (1) root galling percentage and (2) eggs per gram of root. Variants from whole-genome resequencing (2.1 million SNPs) of PIs were used here. Genomic prediction (GP) models, including genomic best linear unbiased prediction (GBLUP), sparse GBLUP, and the reproducing kernel Hilbert space (RKHS) regression, were tested. The RKHS model based on 2.1 million SNPs had the highest prediction ability for galling (0.42) and for eggs per gram of root (0.50). The most resistant PIs (galling: PI_596692, PI_532664, PI_288316, PI_271767, and PI_542118; eggs per gram root: PI_271775, PI_485584, and PI_299379) based on both best linear unbiased estimates and genome estimated breeding values under 10% selection intensity were selected and are being used in our breeding program to enhance RKN resistance in watermelon cultivars.