Selection of Transcripts Affecting Initial Growth Rate of Rice Backcrossed Inbred Lines Using RNA Sequencing Data
Selection of Transcripts Affecting Initial Growth Rate of Rice Backcrossed Inbred Lines Using RNA Sequencing Data
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利用 RNA 测序数据选择影响水稻回交自交系初始生长速率的转录本
DOI：
10.3389/fpls.2018.01880
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发表时间：
2018
影响因子：
5.6
通讯作者：
A. Nagano
中科院分区：
文献类型：
--
作者：
A. Fukuda;T. Hirose;N. Aoki;S. Kondo;M. Yonekura;T. Kataoka;C. Ohto;A. Nagano
秧苗生长是水稻直播的重要因素。然而，参与这一过程的遗传和转录组因素在很大程度上是未知的。在这项研究中，利用来自 20 个回交自交系 (BIL) 及其亲本品种的 RNA 测序 (RNA-Seq) 数据，在水稻 (Oryza sativa L.) 中鉴定了影响芽重的转录本。回归模型的基因选择频率是通过对转录组随机子集的重复分析来确定的。控制低温发芽能力的 qLTG3-1 基因和已知会降低器官伸长的短粒 1 基因 (SG1) 显示出较高的频率。对 BIL 进行的数量性状位点 (QTL) 分析显示，qLTG3-1 包含在苗重 QTL 中，但 SG1 不包含。两个亲本品种的SG1编码区均未发现核苷酸多态性。定量实时 PCR 显示，本研究分析的所有 104 个 BIL 中 SG1 表达与芽重呈负相关。表达 QTL (eQTL) 分析显示，SG1 表达的 eQTL 与芽重 QTL 位于同一区域。然而，在与SG1相同的染色体上没有检测到eQTL，这表明该基因周围的核苷酸多态性不影响其在分析的生长阶段的表达。总体而言，这些结果表明 RNA-Seq 是识别与幼苗生长速率相关的转录本的有用工具。
Seedling growth is an important factor for direct seeding of rice. However, the genetic and transcriptomic factors involved in this process are largely unknown. In this study, transcripts affecting shoot weight were identified in rice (Oryza sativa L.) using RNA sequencing (RNA-Seq) data from 20 backcrossed inbred lines (BILs) and their parental cultivars. The selection frequency of the genes for the regression model was determined using repeated analysis of random subsets of the transcriptome. The qLTG3-1gene, controlling low-temperature germinability, and short grain 1 gene (SG1), known to decrease organ elongation, showed high frequency. The quantitative trait loci (QTLs) analysis performed for BILs revealed that qLTG3-1 was included in the QTLs for shoot weight but SG1 was not. No nucleotide polymorphisms were found in the coding region of SG1 in either of the parental cultivars. Quantitative real-time PCR showed that SG1 expression was negatively correlated with shoot weight for all 104 BILs analyzed in this study. Expression QTL (eQTLs) analysis showed an eQTL for SG1 expression located in the same region as the QTL for shoot weight. However, no eQTLs were detected on the same chromosome as SG1, suggesting that nucleotide polymorphisms around the gene do not affect its expression in analyzed growth stage. Overall, these results indicate that RNA-Seq is a useful tool for identifying transcripts that can be related to seedling growth rate.
影响因子：
5.4
作者：
Abe, Akira;Takagi, Hiroki;Terauchi, Ryohei
通讯作者：
Terauchi, Ryohei