Genotyping-by-sequencing-based QTL mapping reveals novel loci for Pepper yellow leaf curl virus (PepYLCV) resistance in Capsicum annuum

• Published in: PloS one 2022-02, Vol.17 (2), p.e0264026-e0264026
• Main Authors: Siddique, Muhammad Irfan, Lee, Joung-Ho, Ahn, Jung-Hwan, Kusumawardhani, Meirina Kartika, Safitri, Ramadhani, Harpenas, Asep, Kwon, Jin-Kyung, Kang, Byoung-Cheorl
• Format: Article
• Language: English
• Subjects: Agriculture; Analysis; Begomovirus - physiology; Biology and Life Sciences; Capsicum; Capsicum - genetics; Capsicum - immunology; Capsicum - virology; Capsicum annuum; Chromosome Mapping; Chromosomes; Chromosomes, Plant - genetics; Cultivars; Disease; Disease resistance; Disease Resistance - genetics; Disease Resistance - immunology; Gene mapping; Genes; Genetic aspects; Genetics; Genomes; Genomics; Genotype; Genotyping; Inoculation; Insecticides; Leaf-curl; Life sciences; Mapping; Markers; Methods; Nucleotides; Pathogens; Peppers; Plant diseases; Plant Diseases - genetics; Plant Diseases - immunology; Plant Diseases - virology; Plant pathology; Plant viruses; Polymorphism; Polymorphism, Single Nucleotide; Population; Quantitative Trait Loci; Research and Analysis Methods; Seeds; Signs and symptoms; Single nucleotide polymorphisms; Single-nucleotide polymorphism; Tropical environments; Vegetables; Virus diseases of plants; Viruses; Yellow leaf
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0264026

Disease caused by Pepper yellow leaf curl virus (PepYLCV) is one of the greatest threats to pepper (Capsicum spp.) cultivation in the tropics and subtropics. Resistance to PepYLCV was previously identified in a few Capsicum accessions, but no resistance QTLs have been mapped. This study aimed to elucidate the genetics of PepYLCV resistance in C. annuum L. Augmented inoculation by the viruliferous whitefly Bemisia tabaci was used to evaluate parental lines and an F2 segregating population derived from a cross between resistant C. annuum line LP97 and susceptible C. annuum line ECW30R. Final evaluation was performed six weeks after inoculation using a standardized 5-point scale (0 = no symptoms to 4 = very severe symptoms). A high-density linkage map was constructed using genotyping-by-sequencing (GBS) to identify single-nucleotide polymorphism (SNP) markers associated with PepYLCV resistance in the F2 population. QTL analysis revealed three QTLs, peplcv-1, peplcv-7, and peplcv-12, on chromosomes P1, P7, and P12, respectively. Candidate genes associated with PepYLCV resistance in the QTL regions were inferred. In addition, single markers Chr7-LCV-7 and Chr12-LCV-12 derived from the QTLs were developed and validated in another F2 population and in commercial varieties. This work thus provides not only information for mapping PepYLCV resistance loci in pepper but also forms the basis for future molecular analysis of genes involved in PepYLCV resistance.