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. 2022 Sep 2:13:968811.
doi: 10.3389/fpls.2022.968811. eCollection 2022.

Fine mapping a quantitative trait locus underlying seedling resistance to gummy stem blight using a residual heterozygous lines-derived strategy in cucumber

Jianan Han  1 , Shaoyun Dong  1 , Xiaoping Liu  1 , Yanxia Shi  1 , Diane M Beckles  2 , Xingfang Gu  1 , Han Miao  1 , Shengping Zhang  1
Affiliations

Fine mapping a quantitative trait locus underlying seedling resistance to gummy stem blight using a residual heterozygous lines-derived strategy in cucumber

Jianan Han et al. Front Plant Sci. .

Abstract

Gummy stem blight (GSB), caused by Didymella bryoniae, is one of the most devastating diseases that severely reduces cucumber production. Developing resistant varieties would be an effective strategy to control GSB. Although several GSB-resistant QTLs have been reported, causal genes for GSB resistance have not yet been identified in cucumber. A novel loci gsb3.1 for seedling GSB resistance from the "PI 183967" genotype was previously identified in a 1.7-Mb interval on chromosome 3. In this study, we developed a residual heterozygous line-derived strategy from Recombinant Inbred Lines to perform fine mapping, and with this approach, the gsb3.1 locus was narrowed to a 38 kb interval. There were six predicted genes at the gsb3.1 locus, four of which differed in expression in the GSB-resistant compared to the susceptible lines after fungal inoculation. These candidate genes (Csa3G020050, Csa3G020060, Csa3G020090, and Csa3G020590) within the gsb3.1 locus could be helpful for the genetic study of GSB resistance and marker-assisted selection in cucumber. Phylogenetic analyses indicated that the resistant gsb3.1 allele may uniquely exist in the wild species present in the Indian group, and that nucleotide diversity was significantly reduced in cultivated accessions. Therefore, the gsb3.1 allele could be introgressed into existing commercial cultivars and combined with other resistance QTLs to provide broad-spectrum and robust GSB resistance in cucumber.

Keywords: Cucumis sativus L.; candidate genes; fine-mapping; gummy stem blight; residual heterozygous line (RHL)-derived strategy.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

Figure 1
Figure 1
The disease rating scale of leaves at the seedling stage after infection with Didymella bryoniae.
Figure 2
Figure 2
Genetic map of gsb3.1 on Chromosome 3. Mapping of the gsb3.1 QTL associated with GSB resistance at the seedling stage of cucumber. The dashed line curve indicates the LOD score relative to the physical position of genetic markers.
Figure 3
Figure 3
Genetic map and distribution of reported QTLs for GSB resistance at the seedling stage in cucumber. The gsb3.1 QTL in this study is indicated in red.
Figure 4
Figure 4
Fine mapping of the gsb3.1 QTL in cucumber. (A) Genetic mapping of gsb3.1, using key recombinants from the F2 segregated population, i.e., “LM34” and “LM116.” The 38 kb region of gsb3.1 was narrowed in two phases of fine-mapping. The numbers below the markers indicate the physical position of markers. (B) Six annotated genes located in the 38 kb region according to the cucumber “9930”_v2 reference genome. R, resistant; S, susceptible; S (H), susceptible (dominant heterozygous).
Figure 5
Figure 5
Gene structures and nonsynonymous variations of Csa3G020050 (A), Csa3G020070 (B), Csa3G020090 (C), and Csa3G020590 (D) between LM116 and LM34. Nonsynonymous variations are labeled in red font. “STOP” indicates premature translation termination codons.
Figure 6
Figure 6
Relative expression levels of candidate genes in “PI 183967” and “931” after inoculation with at 12, 48, and 96 hpi. The Y-axis represents the relative expression level of candidate genes at 12, 48, and 96 hpi, compared with 0 hpi. Asterisks indicate significant differences as determined by ANOVA (**p < 0.01).
Figure 7
Figure 7
Distribution of nucleotide diversity (π) of four geographic groups. The region of gsb3.1 on Chr. Three overlaps with a large domestication sweep region showing reduced.
Figure 8
Figure 8
Phylogenetic analysis for gsb3.1 locus. A dendrogram of 113 cucumber accessions analyzed using 333 SNPs derived from Qi et al. (2013) within the delimited 38-kb gsb3.1 region.
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