1. Fine-mapping and identification of a candidate gene controlling seed coat color in melon (Cucumis melo L. var. chinensis Pangalo)
- Author
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Xuemiao Chen, Huaisong Wang, Qiushi Fu, Zhicheng Hu, Aiai Zhang, Jing Zheng, and Xueyin Shi
- Subjects
Genetics ,Candidate gene ,Coat ,education.field_of_study ,Population ,Bulked segregant analysis ,Seed dormancy ,Chromosome Mapping ,food and beverages ,General Medicine ,Biology ,Polymorphism, Single Nucleotide ,Genetic analysis ,Cucurbitaceae ,Phenotype ,Cucumis melo ,Seeds ,Cleaved amplified polymorphic sequence ,education ,Agronomy and Crop Science ,Gene ,Biotechnology - Abstract
Seed coat color is related to flavonoid content which is closely related to seed dormancy. According to the genetic analysis of a six-generation population derived from two parents (IC2508 with a yellow seed coat and IC2518 with a brown seed coat), we discovered that the yellow seed coat trait in melon was controlled by a single dominant gene, named CmBS-1. Bulked segregant analysis sequencing (BSA-Seq) revealed that the gene was located at 11,860,000–15,890,000 bp (4.03 Mb) on Chr 6. The F2 population was genotyped using insertion-deletions (InDels), from which cleaved amplified polymorphic sequence (dCAPS) markers were derived to construct a genetic map. The gene was then fine-mapped to a 233.98 kb region containing 12 genes. Based on gene sequence analysis with two parents, we found that the MELO3C019554 gene encoding a homeobox protein (PHD transcription factor) had a nonsynonymous single nucleotide polymorphism (SNP) mutation in the coding sequence (CDS), and the SNP mutation resulted in the conversion of an amino acid (A→T) at residue 534. In addition, MELO3C019554 exhibited lower relative expression levels in the yellow seed coat than in the brown seed coat. Furthermore, we found that MELO3C019554 was related to 12 flavonoid metabolites. Thus, we predicted that MELO3C019554 is a candidate gene controlling seed coat color in melon. The study lays a foundation for further cloning projects and functional analysis of this gene, as well as marker-assisted selection breeding.
- Published
- 2021
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