Two-factor ANOVA of SSH and RNA-seq analysis reveal development-associated Pi-starvation genes in oilseed rape
文献类型： 外文期刊
作者： Zhang, Zhong-Wei 1 ; Feng, Ling-Yang 2 ; Wang, Jian-Hui 3 ; Fu, Yu-Fan 1 ; Cai, Xin 1 ; Wang, Chang-Quan 1 ; Du, Jun-B 1 ;
作者机构： 1.Sichuan Agr Univ, Coll Resources, Chengdu 611130, Sichuan, Peoples R China
2.Sichuan Agr Univ, Coll Agron, Chengdu 611130, Sichuan, Peoples R China
3.Sichuan Acad Agr Sci, Hort Inst, Chengdu 610066, Sichuan, Peoples R China
4.Sichuan Agr Univ, Coll Life Sci, Yaan 625014, Sichuan, Peoples R China
5.Sichuan Agr Univ, Rice Res Inst, Chengdu 611130, Sichuan, Peoples R China
6.Guizhou Acad Agr Sci, Rape Res Inst, Guiyang 550008, Guizhou, Peoples R China
7.Chengdu Acad Agr & Forestry, Rape Res Inst, Chengdu 611130, Sichuan, Peoples R China
8.Mianyang Normal Univ, Res Ctr Ecoenvironm Engn, Mianyang 621000, Sichuan, Peoples R China
关键词： Ethylene signaling; Pi starvation; RNA-Seq; Sugar metabolism; Suppression subtractive hybridization (SSH)
期刊名称：PLANTA （ 影响因子：4.116； 五年影响因子：4.316 ）
ISSN： 0032-0935
年卷期： 2019 年 250 卷 4 期
页码：
收录情况： SCI
摘要： Main conclusion The 5-leaf-stage rape seedlings were more insensitive to Pi starvation than that of the 3-leaf-stage plants, which may be attributed to the higher expression levels of ethylene signaling and sugar-metabolism genes in more mature seedlings. Traditional suppression subtractive hybridization (SSH) and RNA-Seq usually screen out thousands of differentially expressed genes. However, identification of the most important regulators has not been performed to date. Here, we employed two methods, namely, a two-round SSH and two-factor transcriptome analysis derived from the two-factor ANOVA that is commonly used in the statistics, to identify development-associated inorganic phosphate (Pi) starvation-induced genes in Brassica napus. Several of these genes are related to ethylene signaling (such as EIN3, ACO3, ACS8, ERF1A, and ERF2) or sugar metabolism (such as ACC2, GH3, LHCB1.4, XTH4, and SUS2). Although sucrose and ethylene may counteract each other at the biosynthetic level, they may also work synergistically on Pi-starvation-induced gene expression (such as PT1, PT2, RNS1, ACP5, AT4, and IPS1) and root acid phosphatase activation. Furthermore, three new transcription factors that are responsive to Pi starvation were identified: the zinc-finger MYND domain-containing protein 15 (MYND), a Magonashi family protein (MAGO), and a B-box zinc-finger family salt-tolerance protein. This study indicates that the two methods are highly efficient for functional gene screening in non-model organisms.
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