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

Abstract

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.

Pepper (<i>Capsicum annuum</i>) Plants Harboring the Begomovirus Resistance Gene <i>pepy-1</i> Show Delayed Symptom Progress and High Productivity Under Natural Field Conditions

“…In contrast, there are not yet any commercial cultivars carrying begomovirus resistance in Capsicum (Kenyon et al, 2014b). The need for adequate resistance materials is underlined by the progress in screening and the study of begomovirus resistance in Capsicum (Adluri et al, 2017;Anaya-López et al, 2003;Barchenger et al, 2019;Kenyon et al, 2014a;Mori et al, 2022;Rai et al, 2014;Retes-Manjarrez et al, 2017Siddique et al, 2022;Singh et al, 2016;Srivastava et al, 2017;Thakur et al, 2019). Despite these germplasms being very important for breeding begomovirus resistance in commercial pepper cultivars, begomovirus resistance genes in Capsicum have only ever been identified from C. annuum BaPep-5 and PG-1 (Koeda et al, 2021(Koeda et al, , 2022, and none of these cultivars has been tested for its capacity to mitigate natural infection and minimize the damage due to yield loss under production scale.…”

CRISPR/Cas9-mediated gene editing to confer turnip mosaic virus (TuMV) resistance in Chinese cabbage (Brassica rapa)

“…Extenuation of these losses by incorporating viral resistance into existing elite verities is a promising approach to achieving global food production goals. Exploiting genetic resistance in crops is the most endurable strategy to manage virus infection (Kang et al 2005a; [ 31 , 32 ]). Modern innovative plant biotechnology and molecular breeding approaches can assist as preferable substitutes for traditional breeding.…”

Quantitative Trait Loci Mapping for Bacterial Wilt Resistance and Plant Height in Tomatoes

“…This software also obtained the additive effect and the proportion of the phenotypic variation (R 2 -value) for each QTL. A 1000 permutation option was selected to define the likelihood of an odd (LOD) score threshold to ascertain the presence of QTLs [ 61 , 62 ]. The AUDPC values and PH mean values were used for the QTL analysis.…”