RNA-Seq-Mediated Transcriptome Analysis of a Fiberless Mutant Cotton and Its Possible Origin Based on SNP Markers.
RNA-Seq-Mediated Transcriptome Analysis of a Fiberless Mutant Cotton and Its Possible Origin Based on SNP Markers.
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DOI：
10.1371/journal.pone.0151994
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发表时间：
2016
期刊：
影响因子：
3.7
通讯作者：
Yu S
中科院分区：
文献类型：
--
作者：
Ma Q;Wu M;Pei W;Wang X;Zhai H;Wang W;Li X;Zhang J;Yu J;Yu S
棉花（Gossypium L.）纤维构成研究细胞起始和伸长的经典模型系统。本研究利用高通量转录组测序技术对野生型高地棉（G.获得了代表超过58 Gb序列的约7亿个高质量cDNA读段，导致从13，960个表达基因中鉴定出28，610个SNP，其中17，479个是新的。在这些SNPs中，fl基因50%的SNPs与G. fl突变体可能来源于徐州142与一个未知的G. barbadense基因型在所有检测到的SNPs中，分别有15，555、12，750和305个被归类为非同义、同义和预终止的SNPs。此外，还检测到1，352个插入/缺失多态性（InDels）。在开花后-3天和0天，在胚珠中的WT和fl之间总共鉴定了865个DEG，从这些DEG中选择了302个候选SNP，用于通过高分辨率熔解分析和桑格测序在7个棉花基因型中进行验证。基因型成对多态性的数量从43到302不等，表明所鉴定的SNP是可靠的。这些SNPs可以作为棉花育种和遗传研究的良好资源。
As the longest known single-celled trichomes, cotton (Gossypium L.) fibers constitute a classic model system to investigate cell initiation and elongation. In this study, we used a high-throughput transcriptome sequencing technology to identify fiber-initiation-related single nucleotide polymorphism (SNP) markers and differentially expressed genes (DEGs) between the wild-type (WT) Upland cotton (G. hirsutum) Xuzhou 142 and its natural fuzzless-lintless mutant Xuzhou 142 fl. Approximately 700 million high-quality cDNA reads representing over 58 Gb of sequences were obtained, resulting in the identification of 28,610 SNPs—of which 17,479 were novel—from 13,960 expressed genes. Of these SNPs, 50% of SNPs in fl were identical to those of G. barbadense, which suggests the likely origin of the fl mutant from an interspecific hybridization between Xuzhou 142 and an unknown G. barbadense genotype. Of all detected SNPs, 15,555, 12,750, and 305 were classified as non-synonymous, synonymous, and pre-terminated ones, respectively. Moreover, 1,352 insertion/deletion polymorphisms (InDels) were also detected. A total of 865 DEGs were identified between the WT and fl in ovules at −3 and 0 days post-anthesis, with 302 candidate SNPs selected from these DEGs for validation by a high-resolution melting analysis and Sanger sequencing in seven cotton genotypes. The number of genotypic pairwise polymorphisms varied from 43 to 302, indicating that the identified SNPs are reliable. These SNPs should serve as good resources for breeding and genetic studies in cotton.