AUTHOR=Shrestha Swati , Fu Yuqing , Michael Vincent Njung’e , Meru Geoffrey 

TITLE=Whole Genome Re-sequencing and Bulk Segregant Analysis Reveals Chromosomal Location for Papaya Ringspot Virus W Resistance in Squash

JOURNAL=Frontiers in Plant Science

VOLUME=13

YEAR=2022

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2022.848631

DOI=10.3389/fpls.2022.848631

ISSN=1664-462X

ABSTRACT=<p>Squash (<italic>Cucurbita moschata</italic>) is among the most important cucurbit crops grown worldwide. Plant pathogen, Papaya ringspot virus W (PRSV-W) causes significant yield loss in commercial squash production globally. The development of virus-resistant cultivars can complement integrated disease management and mitigate losses due to viral infections. However, the genetic loci and molecular markers linked to PRSV-W resistance that could facilitate marker-assisted selection (MAS) for accelerated cultivar development are unknown. In this study, quantitative trait loci (QTL), molecular markers, and candidate genes associated with PRSV-W resistance in squash were identified in an F<sub>2</sub> population (<italic>n</italic> = 118) derived from a cross between Nigerian Local accession (resistant) and Butterbush cultivar (susceptible). Whole genome re-sequencing-based bulked segregant analysis (QTLseq method; <italic>n</italic> = 10 for each bulk) and non-parametric interval mapping were used to identify a major QTL associated with PRSV-W resistance on chromosome 9 (<italic>QtlPRSV-C09</italic>) (<italic>p</italic> &lt; 0.05) of <italic>C. moschata</italic>. <italic>QtlPRSV-C09</italic> extended from 785,532 to 5,093,314 bp and harbored 12,245 SNPs among which 94 were high-effect variants. To validate <italic>QtlPRSV-C09</italic>, 13 SNP markers were assayed as Kompetitive allele-specific PCR (KASP) markers in the F<sub>2</sub> population and tested for the association with PRSV-W resistance. Among these, two KASP markers (Ch09_2080834 and Ch09_5023865-1) showed significant association with PRSV-W resistance (<italic>p</italic> &lt; 0.05). The two SNPs were located within exons of putative disease-resistant genes encoding the clathrin assembly family and actin cytoskeleton-regulatory complex proteins, which are implicated in disease resistance across plant species. The findings of this study will facilitate MAS for PRSV-W resistance in squash and allow further understanding of the functional mechanisms underlying potyvirus resistance in <italic>Cucurbita</italic> species.</p>