Miao Qing, Deng Peng, Saha Sukumar, Jenkins Johnie N, Hsu Chuan-Yu, Abdurakhmonov Ibrokhim Y, Buriev Zabardast T, Pepper Alan, Ma Din-Pow
Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS, United States of America.
Department of Pharmacology, Weill Cornell Medical College of Cornell University, New York, NY, United States of America.
PLoS One. 2017 Jun 14;12(6):e0179381. doi: 10.1371/journal.pone.0179381. eCollection 2017.
Cotton fiber is an important commodity throughout the world. Fiber property determines fiber quality and commercial values. Previous studies showed that silencing phytochrome A1 gene (PHYA1) by RNA interference in Upland cotton (Gossypium hirsutum L. cv. Coker 312) had generated PHYA1 RNAi lines with simultaneous improvements in fiber quality (longer, stronger and finer fiber) and other key agronomic traits. Characterization of the altered molecular processes in these RNAi genotypes and its wild-type controls is a great interest to better understand the PHYA1 RNAi phenotypes. In this study, a total of 77 conserved miRNAs belonging to 61 families were examined in a PHYA1 RNAi line and its parental Coker 312 genotype by using multiplex sequencing. Of these miRNAs, seven (miR7503, miR7514, miR399c, miR399d, miR160, miR169b, and miR2950) were found to be differentially expressed in PHYA1 RNAi cotton. The target genes of these differentially expressed miRNAs were involved in the metabolism and signaling pathways of phytohormones, which included Gibberellin, Auxin and Abscisic Acid. The expression of several MYB transcription factors was also affected by miRNAs in RNAi cotton. In addition, 35 novel miRNAs (novel miR1-novel miR35) were identified in fibers for the first time in this study. Target genes of vast majority of these novel miRNAs were also predicted. Of these, nine novel miRNAs (novel-miR1, 2, 16, 19, 26, 27, 28, 31 and 32) were targeted to cytochrome P450-like TATA box binding protein (TBP). The qRT-PCR confirmed expression levels of several differentially regulated miRNAs. Expression patterns of four miRNAs-targets pairs were also examined via RNA deep sequencing. Together, the results imply that the regulation of miRNA expression might confer to the phenotype of the PHYA1 RNAi line(s) with improved fiber quality.
棉花纤维是一种在全球范围内都很重要的商品。纤维特性决定纤维质量和商业价值。先前的研究表明，通过RNA干扰沉默陆地棉（Gossypium hirsutum L. cv. Coker 312）中的光敏色素A1基因（PHYA1），已产生了PHYA1 RNAi系，其纤维质量（更长、更强且更细的纤维）以及其他关键农艺性状同时得到改善。对这些RNAi基因型及其野生型对照中分子过程变化的表征，对于更好地理解PHYA1 RNAi表型具有重要意义（引起了极大兴趣）。在本研究中，通过多重测序在一个PHYA1 RNAi系及其亲本Coker 312基因型中检测了总共77个属于61个家族的保守miRNA。在这些miRNA中，发现七个（miR7503、miR7514、miR399c、miR399d、miR160、miR169b和miR2950）在PHYA1 RNAi棉花中差异表达。这些差异表达miRNA的靶基因参与了植物激素的代谢和信号通路，其中包括赤霉素、生长素和脱落酸。几种MYB转录因子的表达在RNAi棉花中也受到miRNA的影响。此外，本研究首次在纤维中鉴定出35个新的miRNA（新miR1 - 新miR35）。还预测了这些新miRNA中绝大多数的靶基因。其中，九个新miRNA（新miR1、2、16、19、26、27、28、31和32）靶向细胞色素P450样TATA盒结合蛋白（TBP）。qRT - PCR证实了几种差异调节miRNA的表达水平。还通过RNA深度测序检测了四对miRNA - 靶标的表达模式。总之，结果表明miRNA表达的调节可能赋予了纤维质量得到改善的PHYA1 RNAi系的表型。
