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A High-Density EST-SSR-Based Genetic Map and QTL Analysis of Dwarf Trait in Cucurbita Pepo L

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A High-Density EST-SSR-Based Genetic Map and QTL Analysis of Dwarf Trait in Cucurbita Pepo L

Chenggang Xiang et al. Int J Mol Sci.

Abstract

As one of the earliest domesticated species, Cucurbita pepo (including squash and pumpkin) is rich in phenotypic polymorphism and has huge economic value. In this research, using 1660 expressed sequence tags-simple sequence repeats (EST-SSRs) and 632 genomic simple sequence repeats (gSSRs), we constructed the highest-density EST-SSR-based genetic map in Cucurbita genus, which spanned 2199.1 cM in total and harbored 623 loci distributed in 20 linkage groups. Using this map as a bridge, the two previous gSSR maps were integrated by common gSSRs and the corresponding relationships around chromosomes in three sets of genomes were also collated. Meanwhile, one large segmental inversion that existed between our map and the C. pepo genome was detected. Furthermore, three Quantitative Trait Loci (QTLs) of the dwarf trait (gibberellin-sensitive dwarf type) in C. pepo were located, and the candidate region that covered the major QTL spanned 1.39 Mb, which harbored a predicted gibberellin 2-β-oxidase gene. Considering the rich phenotypic polymorphism, the important economic value in the Cucurbita genus species and several advantages of the SSR marker were identified; thus, this high-density EST-SSR-based genetic map will be useful in Pumpkin and Squash breeding work in the future.

Keywords: Cucurbita pepo; EST-SSR; dwarf; genetic map; gibberellin (GA); quantitative trait locus (QTL); tetraploid.

Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
The linkage map of C. pepo constructed in this research. Blue, red, and yellow bars indicated the EST-SSR marker, gSSR marker developed from Cucurbita and gSSR marker developed from the cucumber genome, respectively. The scaleplate on the left indicated genetic distance (centimorgan as unit, abbreviated cM). LGs represented linkage groups, from LG1 to LG20.
Figure 2
Figure 2
Collinearity between genetic map and physic map of C. pepo. (A) Collinearity between genetic map (blue) and physic map (gray) of C. pepo. The inversion existed in between LG4 and Cp4.1LG04 was indicated by a red pentagram; (B) collinearity between LG4 and LGp12, LG4 and Cp4.1LG04 (C. pepo genome), LG4 and CmoChr11 (C. moschata genome). The common gSSRs between LG4 and LGp12 were represented by grey broken lines. The in order hits between LG4 and Cp4.1LG04, CmoChr11 were represented by grey line and disorder hits were represented by the dark green line. EST-SSRs are represented by the blue bars and gSSRs by red bars in LG4; (C) collinearity between Cp4.1LG04 and CmoChr11. In order and disorder hits were represented by grey and dark green lines respectively. The disorder regions were marked according to the alignment result.
Figure 3
Figure 3
Mapping of quantitative trait loci (QTLs) controlling dwarf traits in the young (top) and mature (bottom) developmental stages. Curve in plot indicates the LOD score. The boxes inside showed the zoom-in view of the peak on LG20. The molecular markers located in the genetic map were represented by red dots.
Figure 4
Figure 4
Alignment result with watermelon genome and the pairwise relationship around linkage groups. (A) Dot plots represent the alignment results between C. pepo and the watermelon genomes. The horizontal axis shows the genetic position of 20 C. pepo LGs, while the vertical axis shows the physical position of the 11 watermelon chromosomes. Each dot corresponds to a single marker and represents one tBLASTx hit between C. pepo LGs and watermelon chromosomes; (B) circos plots that reveal the presence of three categories on the basis of syntenic relationships between C. pepo and watermelon. The LGs in this figure are shown with colored bars while the chromosomes of watermelon are shown with grey bars. The outside scale bars refer to cM in the case of LGs and Mb in the case of chromosomes, respectively. Category A includes twelve LGs (LG20 and LG18, LG5 and LG14, LG16 and LG12, LG17 and LG3, LG2 and LG6, and LG7 and LG9) that show roughly two-to-one relationships with chromosomes of watermelon, melon, and cucumber. Category B includes three LGs (LG4, LG8, and LG15). The front region of LG4 corresponds with LG8 while the backend region of LG4 corresponds to LG15. No syntenic region is shared between LG8 and LG15 in the three genomes. Category C includes five LGs (LG1, LG10, LG11, LG13, and LG19). The backend region of LG11 corresponds to LG19 while the front region of LG11 corresponds to the middle region of LG1. The front region of LG1 corresponds to LG10 and the backend region of LG1 corresponds to LG13.
Figure 4
Figure 4
Alignment result with watermelon genome and the pairwise relationship around linkage groups. (A) Dot plots represent the alignment results between C. pepo and the watermelon genomes. The horizontal axis shows the genetic position of 20 C. pepo LGs, while the vertical axis shows the physical position of the 11 watermelon chromosomes. Each dot corresponds to a single marker and represents one tBLASTx hit between C. pepo LGs and watermelon chromosomes; (B) circos plots that reveal the presence of three categories on the basis of syntenic relationships between C. pepo and watermelon. The LGs in this figure are shown with colored bars while the chromosomes of watermelon are shown with grey bars. The outside scale bars refer to cM in the case of LGs and Mb in the case of chromosomes, respectively. Category A includes twelve LGs (LG20 and LG18, LG5 and LG14, LG16 and LG12, LG17 and LG3, LG2 and LG6, and LG7 and LG9) that show roughly two-to-one relationships with chromosomes of watermelon, melon, and cucumber. Category B includes three LGs (LG4, LG8, and LG15). The front region of LG4 corresponds with LG8 while the backend region of LG4 corresponds to LG15. No syntenic region is shared between LG8 and LG15 in the three genomes. Category C includes five LGs (LG1, LG10, LG11, LG13, and LG19). The backend region of LG11 corresponds to LG19 while the front region of LG11 corresponds to the middle region of LG1. The front region of LG1 corresponds to LG10 and the backend region of LG1 corresponds to LG13.

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