Identification of cultivar-specific candidate genes associated with resistance to the root-knot nematode Meloidogyne incognita in sweetpotato by whole genome resequencing

Abstract

Meloidogyne incognita is a plant-parasitic rootknot nematode (RKN) that decreases the yield and quality of sweetpotato [Ipomoea batatas (L.) Lam.], a root crop. The development of resistant cultivars and molecular markers for the identification of resistance traits is highly desirable. Moreover, whole-genome-based molecular marker profiling of RKN-infected sweetpotato has not been explored to date. In this study, whole-genome resequencing was used to identify single nucleotide polymorphisms (SNPs) in three RKN-susceptible (Dahomi, Shinhwangmi, and Yulmi) and three RKN-resistant (Danjami, Pungwonmi, and Juhwangmi) sweetpotato cultivars in relation to the reference sweetpotato genome. In total, 14,533,720 SNPs were identified, of which 9,895,216 were intergenic and 4,638,504 were genic. Of these, 165 cultivar-specific SNPs were found to be in coding regions. The genes corresponding to these regions might therefore play an important role in RKN resistance and may provide insights into the molecular regulation of RKN resistance in sweetpotato roots.