GWAS Reveals a Novel Candidate Gene CmoAP2/ERF in Pumpkin (Cucurbita moschata) Involved in Resistance to Powdery Mildew

Abstract

Pumpkin (Cucurbita moschata Duchesne ex Poir.) is a multipurpose cash crop rich in antioxidants, minerals, and vitamins; the seeds are also a good source of quality oils. However, pumpkin is susceptible to the fungus Podosphaera xanthii, an obligate biotrophic pathogen, which usually causes powdery mildew (PM) on both sides of the leaves and reduces photosynthesis. The fruits of infected plants are often smaller than usual and unpalatable. This study identified a novel gene that involves PM resistance in pumpkins through a genome-wide association study (GWAS). The allelic variation identified in the CmoCh3G009850 gene encoding for AP2-like ethylene-responsive transcription factor (CmoAP2/ERF) was proven to be involved in PM resistance. Validation of the GWAS data revealed six single nucleotide polymorphism (SNP) variations in the CmoAP2/ERF coding sequence between the resistant (IT 274039 [PMR]) and the susceptible (IT 278592 [PMS]). A polymorphic marker (dCAPS) was developed based on the allelic diversity to differentiate these two haplotypes. Genetic analysis in the segregating population derived from PMS and PMR parents provided evidence for an incomplete dominant gene-mediated PM resistance. Further, the qRT-PCR assay validated the elevated expression of CmoAP2/ERF during PM infection in the PMR compared with PMS. These results highlighted the pivotal role of CmoAP2/ERF in conferring resistance to PM and identifies it as a valuable molecular entity for breeding resistant pumpkin cultivars.

Exploring genomic regions involved in bread wheat resistance to leaf rust at seedling/adult stages by using GWAS analysis

“…The uncovering of QTLs in such populations leads to high mapping resolution since they harness all historical recombination events [ 12 ]. Various characteristics in wheat, including agro-morphological traits [ 14 ], resistance to stripe rust [ 15 ], stem rust [ 16 ], powdery mildew [ 17 ], and fusarium head blight [ 18 ] have been dissected successfully by association mapping. There are some reports on mapping QTL/genes involved in bread wheat resistance to leaf rust [ 9 , 19 – 23 ], with a potential to marker-assisted selection (MAS).…”

Analyzing genomic variation in cultivated pumpkins and identification of candidate genes controlling seed traits

“…GWASs can identify candidate genomic regions harboring genes significantly associated with target trait variations attributed to historical recombination events (Alqudah et al., 2020). In pumpkin, the GWAS approach has recently been used to identify novel genes associated with powdery mildew resistance (Alavilli et al., 2022) and dwarfism (the bush phenotype) in C. pepo (Hernandez et al., 2023). Thus, a GWAS could be an effective approach to study seed size traits in pumpkin.…”