title: Identification of miRNAs and their targets by high-throughput sequencing and degradome analysis in cytoplasmic male-sterile line NJCMS1A and its maintainer NJCMS1B of soybean.
abstract: BACKGROUND
  Cytoplasmic male sterility (CMS) provides crucial breeding materials that facilitate hybrid seed production in various crops, and thus plays an important role in the study of hybrid vigor (heterosis), in plants. However, the CMS regulatory network in soybean remains unclear. MicroRNAs (miRNAs) play crucial roles in flower and pollen development by targeting genes that regulate their expression in plants. To identify the miRNAs and their targets that exist in the soybean CMS line NJCMS1A and its maintainer NJCMS1B, high-throughput sequencing and degradome analysis were conducted in this study.
  
  
  RESULTS
  Two small RNA libraries were constructed from the flower buds of the soybean CMS line NJCMS1A and its maintainer NJCMS1B. A total of 105 new miRNAs present on the other arm of known pre-miRNAs, 23 new miRNA members, 158 novel miRNAs and 160 high-confidence soybean miRNAs were identified using high-throughput sequencing. Among the identified miRNAs, 101 differentially expressed miRNAs with greater than two-fold changes between NJCMS1A and NJCMS1B were discovered. The different expression levels of selected miRNAs were confirmed by stem-loop quantitative real-time PCR. A degradome analysis showed that 856 targets were predicted to be targeted by 296 miRNAs, including a squamosa promoter-binding protein-like transcription factor family protein, a pentatricopeptide repeat-containing protein, and an auxin response factor, which were previously shown to be involved in floral organ or anther development in plants. Additionally, some targets, including a MADS-box transcription factor, NADP-dependent isocitrate dehydrogenase and NADH-ubiquinone oxidoreductase 24 kDa subunit, were identified, and they may have some relationship with the programmed cell death, reactive oxygen species accumulation and energy deficiencies, which might lead to soybean male sterility.
  
  
  CONCLUSIONS
  The present study is the first to use deep sequencing technology to identify miRNAs and their targets in the flower buds of the soybean CMS line NJCMS1A and its maintainer NJCMS1B. The results revealed that the miRNAs might participate in flower and pollen development, which could facilitate our understanding of the molecular mechanisms behind CMS in soybean.
authors.affiliation: Soybean Research Institute, National Center for Soybean Improvement, MOA Key Laboratory of Biology and Genetic Improvement of Soybean (General), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China. xlding2012@163.com.
authors.forename: Xianlong
authors.initials: X
authors.lastname: Ding
authors.affiliation: Soybean Research Institute, National Center for Soybean Improvement, MOA Key Laboratory of Biology and Genetic Improvement of Soybean (General), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China. lijia6862@163.com.
authors.forename: Jiajia
authors.initials: J
authors.lastname: Li
authors.affiliation: Soybean Research Institute, National Center for Soybean Improvement, MOA Key Laboratory of Biology and Genetic Improvement of Soybean (General), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China. haozhang1223@163.com.
authors.forename: Hao
authors.initials: H
authors.lastname: Zhang
authors.affiliation: Soybean Research Institute, National Center for Soybean Improvement, MOA Key Laboratory of Biology and Genetic Improvement of Soybean (General), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China. 2013201059@njau.edu.cn.
authors.forename: Tingting
authors.initials: T
authors.lastname: He
authors.affiliation: Soybean Research Institute, National Center for Soybean Improvement, MOA Key Laboratory of Biology and Genetic Improvement of Soybean (General), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China. 2012101008@njau.edu.cn.
authors.forename: Shaohuai
authors.initials: S
authors.lastname: Han
authors.affiliation: Soybean Research Institute, National Center for Soybean Improvement, MOA Key Laboratory of Biology and Genetic Improvement of Soybean (General), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China. 2013101108@njau.edu.cn.
authors.forename: Yanwei
authors.initials: Y
authors.lastname: Li
authors.affiliation: Soybean Research Institute, National Center for Soybean Improvement, MOA Key Laboratory of Biology and Genetic Improvement of Soybean (General), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China. spyung@126.com.
authors.forename: Shouping
authors.initials: S
authors.lastname: Yang
authors.affiliation: Soybean Research Institute, National Center for Soybean Improvement, MOA Key Laboratory of Biology and Genetic Improvement of Soybean (General), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China. sri@njau.edu.cn.
authors.forename: Junyi
authors.initials: J
authors.lastname: Gai
mesh_terms: D003593:Cytoplasm / Q000235:genetics* / Q000378:metabolism; D042967:Electron Transport Complex I / Q000235:genetics; D035264:Flowers / Q000235:genetics* / Q000254:growth & development; D018506:Gene Expression Regulation, Plant; D059014:High-Throughput Nucleotide Sequencing; D035683:MicroRNAs / Q000235:genetics*; D051479:Plant Infertility / Q000235:genetics*; D011058:Pollen / Q000235:genetics; D020871:RNA Stability / Q000235:genetics; D012639:Seeds / Q000235:genetics; D013025:Glycine max / Q000235:genetics* / Q000254:growth & development
chemical_list: D035683:MicroRNAs; D042967:Electron Transport Complex I