Bulked-segregant Analysis Identified a Putative Region Related to Short Internode Length in Melon

in HortScience

Short internode length (SIL) is one of the most commercially and important traits in melon varieties (Cucumis melo L.). SIL can result in a compact vining type that promotes concentrated fruit in high-density crops, leading to greater use of light resources for photosynthesis and greater yield per unit area. In our study, two parental melon lines ‘M1-32’ (P1, standard vine) and ‘X090’ (P2, short internodes), and their F1, F2, BC1P1, and BC1P2 progenies were evaluated after being grown in plastic greenhouse conditions in 2017 and 2018. Main stem length (MSL) and internode length (IL) of six melon generations indicated that a single recessive gene (MD7) controlled dwarfism in the ‘X090’ melon line. Whole-genome analysis revealed a genomic region harboring the candidate dwarfism gene on chromosome 7. Six polymorphic cleaved amplified polymorphic sequence (CAPS) markers from chromosome 7 were used to construct a genetic linkage that spanned 30.28 cM. The melon dwarfing locus MD7 responsible for SIL was positioned between markers M7-4 and M7-5, with 3.16 cM of flanking distance. The CAPS markers M7-4 and M7-5 developed have the potential to accelerate the development of dwarf melon varieties, especially in situations when dwarf genotypes are an important breeding goal using marker-assisted selection.

Contributor Notes

Supported by the National Nature Science Foundation of China (no. 31672177), the “Academic Backbone” Project of Northeast Agricultural University (no. 16XG06), the “Young Talents” Project of Northeast Agricultural University (no. 14QC09), and the College Youth Innovation Talent Training Project of Heilongjiang Province (no. UNPYSCT-2016136).

Corresponding author. E-mail: gaopeng_neau@163.com.

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    Differences in plant characteristics between the dwarf melon line ‘X090’ and the standard vining line ‘M1-32’ cultivated in a plastic greenhouse. (A) ‘M1-32’ mature plant with standard vine (behind) and ‘X090’ adult plant with short vine (front). (B) Segregation in F2 progenies, standard-type (left) and dwarf-type (right). (C) Standard-type F2 plant 23 to 25 d after seeding. (D) Dwarf-type F2 plant 23 to 25 d after seeding. (E) CM measurement in dwarf-type F2 plants. (F) CM measurement in standard-type F2 plants. CM represents the height of the entire main vine and the length of the vine between the two adjacent leaves in the middle of the main vine.

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    Comparisons of (A) internode length at the seventh, eighth, and ninth internodes; (B) main stem length, and (C) number of internodes between standard vines and dwarf vines.

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    Calculated single nucleotide polymorphism (SNP) index plots across the whole genome. The x-axis indicates the position of 12 chromosomes in the melon; the y-axis represents the SNP index. The dashed line (green in online figure) is the threshold value calculated by Loess regression (0.5). The circle (red in online figure) on chromosome 7 represents a significant fluctuation peak.

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    Single nucleotide polymorphism index plots across chromosome 7. A candidate gene region is framed with a dashed line (blue in the online figure) ranging from 0 to 1.8 Mb.

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    Position of the dwarf gene on chromosome 7. (A) Linkage map of six markers in the candidate region. The total map distance was 30.28 cM and the average distance between the markers was 5.05 cM. (B) Quantitative trait loci curve of melon MD7. The peak logarithm of the odds (LOD) value of the genetic linkage map between markers M7-4 and M7-5 was 90.7.

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    Frequency distribution of internode lengths (ILs) at the seventh, eighth, and ninth internodes in all F2 progenies examined in 2017 and 2018.

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