Screening, identification of root-knot nematode resistance sources using multivariate analysis and validation of molecular markers linked to Me genes in chilli (Capsicum annuum L.)

The root-knot nematode infestation is a significant challenge in chilli cultivation, necessitating the development of resistant cultivars. This study aimed to screen 200 chilli germplasm lines and identify resistant sources for root-knot nematode using multivariate analysis at ICAR-Indian Institute of Horticultural Research, Bangalore. The parameters such as shoot length, root length, shoot weight, root weight, shoot girth were assessed, and nematode infestation was quantified by counting galls and egg masses. The germplasm lines were categorized based on gall index and egg mass index into highly resistant, resistant, moderately resistant, moderately susceptible, susceptible, and highly susceptible groups. The analysis of variance revealed substantial variation among the germplasm lines. The Pearson correlation analysis revealed significant positive associations between nematode infestation and growth parameters. The cluster analysis identified three distinct groups of genotypes based on root knot nematode tolerance. The factor analysis 1 is associated with nematode infestation, and factor analysis 2 is related to growth parameters. The multi-trait ideotype genotype distance index analysis integrated multiple traits to identify top-performing genotypes. The germplasm lines EC771549-A, IHR3226 and IHR3575 showed high resistance, while Pusa Sadabahar was susceptible. The PCR-specific markers were used for validation of Me genes for root-knot nematode resistance. The simple sequence repeat (SSR) marker GPMS 171 and sequence characterized amplified region (SCAR) marker SCAR_CD showed clear polymorphism, correlating with phenotypic resistance. The germplasm line EC771549-A, is consistently resistant at phenotypic, molecular and selected based on multi-trait ideotype genotype distance index values, while Pusa Sadabahar was confirmed as susceptible. This study highlights the effectiveness of integrating molecular marker analysis with phenotypic evaluation and multivariate analysis to identify root-knot nematode resistant sources. The findings provide valuable insights into the genetic architecture of root-knot nematode resistance in chilli and candidate lines for breeding programme aimed at developing resistant cultivars, thereby contributing to sustainable chilli production and nematode management.