Candidate gene prediction for a petal degeneration mutant, pdm, of the Chinese cabbage (Brassica campestris ssp pekinensis) by using fine mapping and transcriptome analysis
Candidate gene prediction for a petal degeneration mutant, pdm, of the Chinese cabbage (Brassica campestris ssp pekinensis) by using fine mapping and transcriptome analysis
复制标题
利用精细作图和转录组分析预测大白菜（Brassica Campestris ssp. pekinensis）花瓣退化突变体 pdm 的候选基因
DOI：
10.1007/s11032-016-0452-4
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发表时间：
2016-03-01
影响因子：
3.1
通讯作者：
Feng, Hui
中科院分区：
文献类型：
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作者：
Huang, Shengnan;Liu, Zhiyong;Feng, Hui
以大白菜野生型“FT”为材料，经Co-60 γ射线辐射处理和游离小孢子培养，获得了一个稳定遗传的花瓣退化突变体pdm。观察到pdm突变体的花瓣比'FT的花瓣皱缩、退化、不完全展开，并且在开花期颜色更深。pdm突变体的表型由一对隐性核基因控制。为了进行连锁分析和基因定位，对1419个具有pdm表型的F-2代隐性纯合个体进行了调查。结果表明，pdm位于标记Indelhsn 26和SSRhsn 123之间，遗传距离分别为0.04和0.04 cM，连锁群A01。Indelhsn 26和SSRhsn 123这两个最紧密连锁的标记之间的物理距离估计约为285.2 kb。28个基因被预测在目标区域。使用RNA-seq，Bra 040093被预测为最可能的pdm候选基因。基于基因注释，Bra 040093编码过氧化物酶体酰基辅酶A氧化酶1（ACX 1）。比较pdm和'FT'中的序列，发现pdm中存在两个单核苷酸多态性。使用定量实时PCR分析Bra 040093在pdm和'FT'之间的表达模式，并且在'FT'中的表达水平显著高于pdm。这些研究结果为pdm基因的图位克隆、鉴定和功能分析提供了坚实的基础和宝贵的资源，有助于了解大白菜花发育过程。
A stably inherited petal degeneration mutant pdm of the Chinese cabbage was obtained from its wild-type 'FT' by radiation treatment (Co-60 gamma-rays) and isolated microspore culture. Petals of the pdm mutant were observed to be shriveled, degenerated, not fully expanded, and darker at the flowering stage than those of 'FT.' The pdm mutant phenotype was found to be controlled by a single recessive nuclear gene. For linkage analysis and gene mapping, 1419 recessive homozygous individuals with the pdm phenotype of the F-2 generation were investigated as the mapping population. Results showed that the pdm was located between markers Indelhsn26 and SSRhsn123 at a genetic distance of 0.04 and 0.04 cM, respectively, on linkage group A01. Physical distance between Indelhsn26 and SSRhsn123, the two most closely linked markers, was estimated to be approximately 285.2 kb. Twenty-eight genes were predicted in the target region. Using RNA-seq, Bra040093 was predicted to be the most likely candidate gene for pdm. Based on gene annotation, Bra040093 encodes a peroxisomal acyl-coenzyme A oxidase 1 (ACX1). Comparison of the sequences in pdm and 'FT' revealed two single-nucleotide polymorphisms in pdm. Expression patterns of Bra040093 between pdm and 'FT' were analyzed using quantitative real-time PCR, and the expression level was dramatically higher in 'FT' than in pdm. These findings provide a solid foundation and valuable resources for map-based cloning, identification, and functional analysis of pdm and facilitate the understanding of floral development processes in the Chinese cabbage.