QTL Mapping for Gummy Stem Blight Resistance in Watermelon (Citrullus spp.)

Exploring the genomic landscape of gummy stem blight resistance in watermelon through QTL-Seq

BACKGROUND

Watermelon is a nutritionally and economically significant crop in the US and globally. Gummy Stem Blight (GSB), caused by three cryptic Stagonosporopsis species, is one of the most devastating diseases affecting watermelon in the US, impacting most of the plant's above-ground parts. This study aimed to identify key Quantitative Trait Variants (QTVs) that include SNPs and In/Dels associated with GSB resistance in selfed derivatives of advanced multicross interspecific derivatives population derived from intercrosses between the most resistant lines of Citrullus amarus and highly susceptible cultivars of Citrullus lanatus.

RESULTS

Resistant and susceptible bulks were created by combining equimolar DNA concentrations from 30 extremely resistant derivatives and 30 extremely susceptible lines. These bulks underwent whole-genome sequencing, generating over 1 billion reads per bulk to achieve comprehensive genome coverage. The mapping percentage of the bulks to the parental genomes ranged from 92 to 99%. More than 6 million SNPs and 1 million indels were identified from the resistant parental genome, compared to fewer than 2 million SNPs and 0.4 million indels from the susceptible parental genome. QTNs associated with GSB resistance were identified using single-nucleotide polymorphism-index and Gprime methods. Statistically significant variants/loci linked to GSB resistance were found on chromosomes 1, 2, 3, 5, 7, 10, and 11. Notably, the genes Lipase class 3 family protein, Ribosome hibernation promotion factor (CaU02G00010), Ubiquitin-like-specific protease 1D (CaU03G04260), and Zinc finger CCCH domain-containing 15 (CaU03G10970) harbored the highest delta SNPs. Several previously published genes, including Avr9/Cf-9 Rapidly Elicited Protein (CaU07G12990) on chromosome 7, were also identified.

CONCLUSIONS

Identifying significant loci associated with GSB resistance has facilitated the development of PACE assays, which will aid in breeding GSB-resistant watermelon cultivars. These findings provide critical insights into the genetic basis of GSB resistance and represent a significant step towards improving the resilience of watermelon crops against this devastating disease.

Genotyping by Sequencing (GBS)-Based QTL Mapping for Bacterial Fruit Blotch (BFB) in Watermelon

Watermelon (Citrullus lanatus), an economically important and nutritionally rich Cucurbitaceous crop grown worldwide, is severely affected by bacterial fruit blotch (BFB). Development of resistant cultivar is the most eco-friendly, cost-effective, and sustainable way to tackle this disease. This requires wider understanding of the genetics of resistance to BFB. In this study, we identified quantitative trait loci (QTLs) associated with BFB resistance in an F₂ mapping population developed from BFB-resistant 'PI 189225' (Citrullus amarus) and -susceptible 'SW 26' (C. lanatus) genotypes based on the polymorphic markers identified by genotyping by sequencing (GSB). A linkage map covering a total genetic distance of 3377.1 cM was constructed. Two QTLs for BFB resistance, namely, ClBFB10.1 and ClBFB10.2, both located on chromosome 10 explaining 18.84 and 15.41% of the phenotypic variations, respectively, were identified. Two SNP-based high-resolution melting (HRM) markers WmBFB10.1 and WmBFB10.2 having high positive correlation with resistance vs. susceptible alleles were developed. The efficacy of the markers was validated in another F₂ population derived from SW34 × PI 189225. The highest phenotypic variation was found in the locus ClBFB10.2, which also contains three putative candidate genes for resistance to BFB. These findings will accelerate the development of BFB-resistant watermelon varieties via molecular breeding.

QTL associated with resistance to Stagonosporopsis citrulli in Citrullus amarus

Gummy stem blight (GSB) is a fungal disease affecting cucurbit crops, including watermelon (Citrullus lanatus), leading to significant yield losses. The disease is caused by three Stagonosporopsis species, of which Stagonosporopsis citrulli is the most common in the southeastern United States. Currently no gummy stem blight-resistant watermelon cultivars are available to growers. In this study, QTL-seq in an interspecific population developed from Sugar Baby × PI 189225 (Citrullus amarus) identified QTL on chromosomes 2, 5, 9 and 11. A novel QTL on chromosome 5 (Qgsb5.2) associated with resistance to S. citrulli (PVE = 13.3%) was confirmed by genetic mapping. KASP marker assays were developed for selection of Qgsb5.2 to allow breeders to track the allele contributing resistance to GSB, reducing the need for laborious phenotyping. Pyramiding different GSB resistance QTL could be a useful strategy to develop GSB resistant watermelon cultivars.

QTL associated with Gummy Stem Blight (GSB) resistance in watermelon

Background

Gummy stem blight (GSB), caused by Didymella bryoniae (syn. Stagonosporopsis cucurbitacearum), produces devastating symptoms on whole plants of watermelon (Citrullus lanatus) and other cucurbits, significantly reducing yield and quality. Identification of genetic determinants and sources of resistance to this devastating GSB disease in watermelon is essential for developing resistant varieties.

Results

In this study, we aimed at identifying quantitative trait loci (QTLs) linked to GSB resistance in melon. We identified the genome-wide single nucleotide polymorphisms (SNPs) by genotyping by sequencing (GBS) of an F₂ population developed from C. lanatus lines, ‘PI 279461’ (resistant) ✕ ‘PI 223764’ (susceptible). Inheritance analysis indicated that resistance to GSB is a multi-genic trait in this population. Three QTLs namely, ClGSB1.1, ClGSB10.1, and ClGSB11.1 associated with GSB resistance, explaining approximately 10% of the phenotypic variation, were identified. Among these, the QTL ClGSB1.1 on chromosome 1 is identified as a major QTL harboring five candidate genes associated with GSB resistance including two RLKs (ClC01G014900 and ClC01G015010), two WRKY transcription factors (ClC01G014910 and ClC01G014990), and one AvrRpt-cleavage domain protein (ClC01G015130).

Conclusion

Two high resolution melting (HRM) markers, WmGSB1.1–2 and WmGSB1.1–7 having a high positive correlation with the phenotypic variations, were developed. Five potential candidate genes were predicted to be associated with GSB resistance. These findings will help breeders to develop watermelon cultivars resistant to GSB.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08849-2.