Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
Theor Appl Genet. 2022 Mar;135(3):803-815. doi: 10.1007/s00122-021-03999-5. Epub 2021 Nov 26.
MELO3C019554 encoding a homeobox protein (PHD transcription factor) is a candidate gene that involved in the formation of seed coat color in melon. 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 is controlled by a single dominant gene, named CmBS-1. Bulked segregant analysis sequencing (BSA-Seq) revealed that the gene is located at 11,860,000-15,890,000 bp (4.03 Mb) on Chr 6. The F 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 is 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.
MELO3C019554 编码同源盒蛋白（PHD 转录因子），是一种参与甜瓜种皮颜色形成的候选基因。种皮颜色与类黄酮含量有关，而类黄酮含量与种子休眠密切相关。根据来自两个亲本（黄色种皮的 IC2508 和棕色种皮的 IC2518）的六代群体的遗传分析，我们发现甜瓜的黄色种皮性状由一个单一的显性基因控制，命名为 CmBS-1。BSA-Seq 揭示该基因位于第 6 号染色体上的 11860000-15890000bp（4.03Mb）处。利用插入缺失（InDels）对 F 群体进行基因分型，从中衍生出切割扩增多态性序列（dCAPS）标记，构建遗传图谱。然后，将该基因精细定位到一个包含 12 个基因的 233.98kb 区域。基于对两个亲本的基因序列分析，我们发现编码同源盒蛋白（PHD 转录因子）的 MELO3C019554 基因在编码序列（CDS）中发生了非同义单核苷酸多态性（SNP）突变，该 SNP 突变导致 534 位氨基酸残基的转换（A→T）。此外，MELO3C019554 在黄色种皮中的相对表达水平低于棕色种皮。此外，我们发现 MELO3C019554 与 12 种类黄酮代谢物有关。因此，我们预测 MELO3C019554 是控制甜瓜种皮颜色的候选基因。本研究为进一步克隆该基因及其功能分析以及标记辅助选择育种奠定了基础。
