title: Small interfering RNAs from bidirectional transcripts of GhMML3_A12 regulate cotton fiber development.
abstract: 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.
authors.affiliation: State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R&D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China.
authors.forename: Qun
authors.initials: Q
authors.lastname: Wan
authors.affiliation: State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R&D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China.
authors.forename: Xueying
authors.initials: X
authors.lastname: Guan
authors.affiliation: State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R&D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China.
authors.forename: Nannan
authors.initials: N
authors.lastname: Yang
authors.affiliation: State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R&D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China.
authors.forename: Huaitong
authors.initials: H
authors.lastname: Wu
authors.affiliation: State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R&D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China.
authors.forename: Mengqiao
authors.initials: M
authors.lastname: Pan
authors.affiliation: State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R&D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China.
authors.forename: Bingliang
authors.initials: B
authors.lastname: Liu
authors.affiliation: State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R&D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China.
authors.forename: Lei
authors.initials: L
authors.lastname: Fang
authors.affiliation: State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R&D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China.
authors.forename: Shouping
authors.initials: S
authors.lastname: Yang
authors.affiliation: State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R&D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China.
authors.forename: Yan
authors.initials: Y
authors.lastname: Hu
authors.affiliation: State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R&D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China.
authors.forename: Wenxue
authors.initials: W
authors.lastname: Ye
authors.affiliation: State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R&D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China.
authors.forename: Hua
authors.initials: H
authors.lastname: Zhang
authors.affiliation: State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R&D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China.
authors.forename: Peiyong
authors.initials: P
authors.lastname: Ma
authors.affiliation: State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R&D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China.
authors.forename: Jiedan
authors.initials: J
authors.lastname: Chen
authors.affiliation: State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R&D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China.
authors.forename: Qiong
authors.initials: Q
authors.lastname: Wang
authors.affiliation: State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R&D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China.
authors.forename: Gaofu
authors.initials: G
authors.lastname: Mei
authors.affiliation: State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R&D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China.
authors.forename: Caiping
authors.initials: C
authors.lastname: Cai
authors.affiliation: National Laboratory of Plant Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China.
authors.forename: Donglei
authors.initials: D
authors.lastname: Yang
authors.affiliation: National Key Laboratory of Plant Molecular Genetics, National Plant Gene Research Center, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China.
authors.forename: Jiawei
authors.initials: J
authors.lastname: Wang
authors.affiliation: State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R&D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China.
authors.forename: Wangzhen
authors.initials: W
authors.lastname: Guo
authors.affiliation: College of Life Sciences, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China.
authors.forename: Wenhua
authors.initials: W
authors.lastname: Zhang
authors.affiliation: National Key Laboratory of Plant Molecular Genetics, National Plant Gene Research Center, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China.
authors.forename: Xiaoya
authors.initials: X
authors.lastname: Chen
authors.affiliation: State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R&D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China.
authors.forename: Tianzhen
authors.initials: T
authors.lastname: Zhang
mesh_terms: D032561:Cotton Fiber; D018506:Gene Expression Regulation, Plant; D003368:Gossypium / Q000235:genetics* / Q000254:growth & development / Q000648:ultrastructure; D059014:High-Throughput Nucleotide Sequencing; D009928:Organ Specificity; D011401:Promoter Regions, Genetic / Q000235:genetics; D059367:RNA Cleavage; D016372:RNA, Antisense / Q000235:genetics*; D018749:RNA, Plant / Q000235:genetics; D034741:RNA, Small Interfering; D012639:Seeds / Q000235:genetics / Q000254:growth & development / Q000648:ultrastructure; D017423:Sequence Analysis, RNA
chemical_list: D016372:RNA, Antisense; D018749:RNA, Plant; D034741:RNA, Small Interfering
keywords: Gossypium hirsutum (cotton); MYBMIXTA-like (MML) transcription factor; epigenetics; fiber development; natural antisense transcripts (NATs); small interfering RNAs (siRNAs)