Functional & Integrative Genomics

, Volume 18, Issue 4, pp 457–476 | Cite as

Exploration of miRNAs and target genes of cytoplasmic male sterility line in cotton during flower bud development

  • Hushuai Nie
  • Yumei Wang
  • Ying Su
  • Jinping Hua
Original Article


Cytoplasmic male sterility (CMS) lines provide crucial material to harness heterosis for crop plants, which serves as an important strategy for hybrid seed production. However, the molecular mechanism remains obscure. Although microRNAs (miRNAs) play important roles in vegetative growth and reproductive growth, there are few reports on miRNAs regulating the development of male sterility in Upland cotton. In present study, 12 small RNA libraries were constructed and sequenced for two development stages of flower buds from a CMS line and its maintainer line. Based on the results, 256 novel miRNAs were allocated to 141 new miRNA families, and 77 known miRNAs belonging to 54 conserved miRNA families were identified as well. Comparative analysis revealed that 61 novel and 10 conserved miRNAs were differentially expressed. Further transcriptome analysis identified 232 target genes for these miRNAs, which participated in cellular developmental process, cell death, pollen germination, and sexual reproduction. In addition, expression patterns of typical miRNA and the negatively regulated target genes, such as PPR, ARF, AP2, and AFB, were verified by qRT-PCR in cotton flower buds. These targets were previously reported to be related to reproduction development and male sterility, suggesting that miRNAs might act as regulators of CMS occurrence. Some miRNAs displayed specific expression profiles in special developmental stages of CMS line and its fertile hybrid (F1). Present study offers new information on miRNAs and their related target genes in exploiting CMS mechanism, and revealing the miRNA regulatory networks in Upland cotton.


miRNA Target gene qRT-PCR Flower bud Cytoplasmic male sterility (CMS) Upland cotton 


Author contributions

HN performed bench experiments, assembled and analyzed the sequencing data, and prepared the manuscript. YW maintained the experimental platform, and attended sample collection and bench work. YS attended discussion and bench work. JH designed the experiments, provided research platform, and revised the manuscript. All authors approved the final manuscript.

Funding information

This research was supported in part by the National Key Research and Development Program for Crop Breeding (2016YFD0101407) and the National Natural Science Foundation of China (31671741) to J HUA.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no competing interests.

Supplementary material

10142_2018_606_MOESM1_ESM.jpg (47 kb)
Supplementary Fig. 1 Length distributions of predicted novel miRNAs and known miRNAs in four libraries (JPEG 46 kb)
10142_2018_606_MOESM2_ESM.jpg (162 kb)
Supplementary Fig. 2 The miRNA numbers distributed in cotton conserved miRNA families. (JPEG 161 kb) MiR_1, MiR_2, MiR_3: miRNA family had one member, two and three members, respectively; the others represented cotton conserved miRNA families with multiple members
10142_2018_606_MOESM3_ESM.jpg (4.6 mb)
Supplementary Fig. 3 Analysis of miRNA families of the different expression miRNAs between four flower bud samples. The adjacent miRNAs, which have same colors, belonged to the same family, other individual miRNA on black dotted line belonged to a single family (JPEG 4712 kb)
10142_2018_606_MOESM4_ESM.jpg (1.2 mb)
Supplementary Fig. 4 Differential expressed patterns of miRNAs in CMS line and its maintainer line at different stages. Left: heat map of differently expressed miRNAs from high-throughput sequencing; Right: heat map of differently expressed miRNAs from qRT-PCR, GhUBQ7 and U6 were used as internal control. (JPEG 1182 kb)
10142_2018_606_MOESM5_ESM.jpg (1.9 mb)
Supplementary Fig. 5 KEGG Pathway analyze of the target genes for different expression miRNAs. Including plant-pathogen interaction, plant hormone signal transduction and carbon metabolism, which may be related to CMS occurred. Red squares represent the up-regulated target genes, blue squares represent the down-regulated target genes (JPEG 1977 kb)
10142_2018_606_MOESM6_ESM.jpg (373 kb)
Supplementary Fig. 6 Correlation analyze of expression patterns between miRNAs and their targets. The brown bars represented the miRNAs expression patterns and the gray bars represented its corresponding targets expression abundance from the qRT-PCR results. The primers in this experiment were bare minimum of one set of primers that amplified across the miRNA target site. And the forward primer was located in 5′ end of target site and the reverse primer was located in 3′ end of target site. GhUBQ7 gene as an internal control, and the error bars indicated the standard error of the mean of 2–ΔΔCt (JPEG 373 kb)
10142_2018_606_MOESM7_ESM.jpg (2.5 mb)
Supplementary Fig. 7 The same miRNAs identified in this study with Wei’s GMS result. The study of GMS (Wei et al. 2013) also identified 110 putative novel miRNAs in cotton; The adjacent miRNAs, which have same colors, belong to the same family. And miRNA names beginning with ‘ghr’ represent they are found in present study, beginning with ‘Mar’ are found in the study of GMS.(JPEG 2609 kb)
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Table S1 (XLSX 17 kb)
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Table S9 (DOCX 18 kb)


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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Laboratory of Cotton Genetics, Genomics and Breeding/Beijing Key Laboratory of Crop Genetic Improvement/Key Laboratory of Crop Heterosis and Utilization of Ministry of Education, College of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
  2. 2.Research Institute of Cash CropsHubei Academy of Agricultural SciencesWuhanChina

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