Small interfering RNAs from bidirectional transcripts of GhMML3_A12 regulate cotton fiber development

• Published in: The New phytologist Vol. 210; no. 4; pp. 1298 - 1310
• Main Authors: Wan, Qun, Guan, Xueying, Yang, Nannan, Wu, Huaitong, Pan, Mengqiao, Liu, Bingliang, Fang, Lei, Yang, Shouping, Hu, Yan, Ye, Wenxue, Zhang, Hua, Ma, Peiyong, Chen, Jiedan, Wang, Qiong, Mei, Gaofu, Cai, Caiping, Yang, Donglei, Wang, Jiawei, Guo, Wangzhen, Zhang, Wenhua, Chen, Xiaoya, Zhang, Tianzhen
• Format: Journal Article
• Language: English
• Published: England New Phytologist Trust 01-06-2016; Wiley Subscription Services, Inc
• Subjects: Cotton Fiber; epigenetics; fiber development; Gene Expression Regulation, Plant; Gossypium - genetics; Gossypium - growth & development; Gossypium - ultrastructure; Gossypium hirsutum (cotton); High-Throughput Nucleotide Sequencing; MYBMIXTA‐like (MML) transcription factor; natural antisense transcripts (NATs); Organ Specificity; Promoter Regions, Genetic - genetics; RNA Cleavage; RNA, Antisense - genetics; RNA, Plant - genetics; RNA, Small Interfering; Seeds - genetics; Seeds - growth & development; Seeds - ultrastructure; Sequence Analysis, RNA; small interfering RNAs (siRNAs); MYBMIXTA-like (MML) transcription factor; small interfering RNAs (siRNAs); natural antisense transcripts (NATs); Gossypium hirsutum (cotton); epigenetics; fiber development
• ISSN: 0028-646X; 1469-8137
• DOI: 10.1111/nph.13860

Natural antisense transcripts (NATs) are commonly observed in eukaryotic genomes, but only a limited number of such genes have been identified as being involved in gene regulation in plants. In this research, we investigated the function of small RNA derived from a NAT in fiber cell development.
Using a map-based cloning strategy for the first time in tetraploid cotton, we cloned a naked seed mutant gene (N1
) encoding a MYBMIXTA-like transcription factor 3 (MML3)/GhMYB25-like in chromosome A12, GhMML3_A12, that is associated with fuzz fiber development.
The extremely low expression of GhMML3_A12 in N1 is associated with NAT production, driven by its 3′ antisense promoter, as indicated by the promoter-driven histochemical staining assay. In addition, small RNA deep sequencing analysis suggested that the bidirectional transcriptions of GhMML3_A12 form double-stranded RNAs and generate 21–22 nt small RNAs. Therefore, in a fiber-specific manner, small RNA derived from the GhMML3_A12 locus can mediate GhMML3_A12 mRNA self-cleavage and result in the production of naked seeds followed by lint fiber inhibition in N1 plants.
The present research reports the first observation of gene-mediated NATs and siRNA directly controlling fiber development in cotton.