Dataset Information

Identification and profiling of upland cotton microRNAs at fiber initiation stage under exogenous IAA application.

ABSTRACT:

Background

Cotton is the most essential textile crop worldwide, and phytohormones are critical for cotton fiber development. One example is the role of auxin in fiber initiation, but we know little molecular basis. MicroRNAs (miRNAs) have a significant function in cotton development; nevertheless their role in fiber initiation remains unclear. Here, exogenous IAA was applied to cotton plant before anthesis. Utilizing small RNA sequencing, the mechanism underlying miRNA-mediated regulation of fiber initiation under exogenous IAA treatment was investigated.

Results

With exogenous IAA application, the endogenous IAA and GA contents of IAA treated (IT) ovules were higher than control (CK) ovules at the fiber initiation stage, while endogenous ABA content was lower in IT than CK. Using scanning electron microscopy, we found the fiber number and size were significantly promoted in IT at 0 DPA. Fiber quality analysis showed that fiber length, uniformity, strength, elongation, and micronaire of IT were higher than CK, though not statistically significant, while lint percent was significantly higher in IT. We generated six small RNA libraries using -?3, 0, and 3 DPA ovules of IT and CK, and identified 58 known miRNAs and 83 novel miRNAs together with the target genes. The differential expressed miRNAs number between IT and CK at -?3, 0, 3 DPA was 34, 16 and 24, respectively. Gene ontology and KEGG pathway enrichment analyses for the target genes of the miRNAs expressed in a differential manner showed that they were significantly enriched in 30 terms and 8 pathways. QRT-PCR for those identified miRNAs and the target genes related to phytohormones and fiber development was performed, and results suggested a potential role of these miRNAs in fiber initiation.

Conclusions

The exogenous IAA application affected the relative phytohormone contents in ovule and promoted fiber initiation in cotton. Identification and profiling of miRNAs and their targets at the fiber initiation stage provided insights for miRNAs' regulation function of fiber initiation. These findings not only shed light on the regulatory network of fiber growth but also offer clues for cotton fiber amelioration strategies in cotton.

SUBMITTER: Zhao T

PROVIDER: S-EPMC6537205 | biostudies-literature | 2019 May

REPOSITORIES: biostudies-literature

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Publications

Identification and profiling of upland cotton microRNAs at fiber initiation stage under exogenous IAA application.

Zhao Tianlun T Xu Xiaojian X Wang Min M Li Cheng C Li Cong C Zhao Rubing R Zhu Shuijin S He Qiuling Q Chen Jinhong J

BMC genomics 20190528 1

<h4>Background</h4>Cotton is the most essential textile crop worldwide, and phytohormones are critical for cotton fiber development. One example is the role of auxin in fiber initiation, but we know little molecular basis. MicroRNAs (miRNAs) have a significant function in cotton development; nevertheless their role in fiber initiation remains unclear. Here, exogenous IAA was applied to cotton plant before anthesis. Utilizing small RNA sequencing, the mechanism underlying miRNA-mediated regulatio ...[more]

PMID: 31138116

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Project description:We constructed cDNA library from 0-10 day post anthesis cotton fibers when fiber cells begin to initiate and elongate throughout this peroid. We randomly sequenced over 95,000 ESTs from this library, and with request of upland cotton ESTs from other laboratories, we acquired a gene pool of more than 30,000 UniESTs. The cotton UniESTs were then PCR-amplified and printed onto microarray. This array is comprised of about 29,000 high-quality cotton cDNAs (each sequence length>400bp, average length > 600bp) and external controls. Data for 8 replicate experiments performed with biologically independent samples. Cy3 and Cy5 dyes were used as follows: Set 1: wt0-Cy5 wt-3-Cy3 Set 1 (dye swap): wt-3-Cy3 wt0-Cy5 Set 2: wt0-Cy5 wt-3-Cy3 Set 2 (dye swap): wt-3-Cy3 wt0-Cy5 Set 3: wt0-Cy5 wt-3-Cy3 Set 3 (dye swap): wt-3-Cy3 wt0-Cy5 Set 4: wt0-Cy5 wt-3-Cy3 Set 4 (dye swap): wt-3-Cy3 wt0-Cy5 GSM209619, GSM209620, GSM209621, GSM209622, GSM209623, GSM209624, GSM209625, GSM209626, Data for 8 replicate experiments performed with biologically independent samples. Cy3 and Cy5 dyes were used as follows: Set 1: wt+1-Cy5 wt-3-Cy3 Set 1 (dye swap): wt-3-Cy3 wt+1-Cy5 Set 2: wt+1-Cy5 wt-3-Cy3 Set 2 (dye swap): wt-3-Cy3 wt+1-Cy5 Set 3: wt+1-Cy5 wt-3-Cy3 Set 3 (dye swap): wt-3-Cy3 wt+1-Cy5 Set 4: wt+1-Cy5 wt-3-Cy3 Set 4 (dye swap): wt-3-Cy3 wt+1-Cy5 GSM209627, GSM209628, GSM209629, GSM209630, GSM209631, GSM209632, GSM209633, GSM209634, Data for 8 replicate experiments performed with biologically independent samples. Cy3 and Cy5 dyes were used as follows: Set 1: wt+2-Cy5 wt-3-Cy3 Set 1 (dye swap): wt-3-Cy3 wt+2-Cy5 Set 2: wt+2-Cy5 wt-3-Cy3 Set 2 (dye swap): wt-3-Cy3 wt+2-Cy5 Set 3: wt+2-Cy5 wt-3-Cy3 Set 3 (dye swap): wt-3-Cy3 wt+2-Cy5 Set 4: wt+2-Cy5 wt-3-Cy3 Set 4 (dye swap): wt-3-Cy3 wt+2-Cy5 GSM209635, GSM209636, GSM209637, GSM209638, GSM209639, GSM209640, GSM209641, GSM209642, Data for 8 replicate experiments performed with biologically independent samples. Cy3 and Cy5 dyes were used as follows: Set 1: wt+3-Cy5 wt-3-Cy3 Set 1 (dye swap): wt-3-Cy3 wt+3-Cy5 Set 2: wt+3-Cy5 wt-3-Cy3 Set 2 (dye swap): wt-3-Cy3 wt+3-Cy5 Set 3: wt+3-Cy5 wt-3-Cy3 Set 3 (dye swap): wt-3-Cy3 wt+3-Cy5 Set 4: wt+3-Cy5 wt-3-Cy3 Set 4 (dye swap): wt-3-Cy3 wt+3-Cy5 GSM209643, GSM209644, GSM209645, GSM209646, GSM209647, GSM209648, GSM209649, GSM209650, Data for 6 replicate experiments performed with biologically independent samples. Cy3 and Cy5 dyes were used as follows: Set 1: fl+3-Cy5 wt-3-Cy3 Set 1 (dye swap): wt-3-Cy3 fl+3-Cy5 Set 2: fl+3-Cy5 wt-3-Cy3 Set 2 (dye swap): wt-3-Cy3 fl+3-Cy5 Set 3: fl+3-Cy5 wt-3-Cy3 Set 3 (dye swap): wt-3-Cy3 fl+3-Cy5 GSM209455, GSM209456, GSM209608, GSM209609, GSM209610, GSM209612, Data for 6 replicate experiments performed with biologically independent samples. Cy3 and Cy5 dyes were used as follows: Set 1: fl-3-Cy5 wt-3-Cy3 Set 1 (dye swap): wt-3-Cy3 fl-3-Cy5 Set 2: fl-3-Cy5 wt-3-Cy3 Set 2 (dye swap): wt-3-Cy3 fl-3-Cy5 Set 3: fl-3-Cy5 wt-3-Cy3 Set 3 (dye swap): wt-3-Cy3 fl-3-Cy5 GSM209613, GSM209614, GSM209615, GSM209616, GSM209617, GSM209618

Dataset Information

Identification and profiling of upland cotton microRNAs at fiber initiation stage under exogenous IAA application.

Background

Results

Conclusions

Publications

Identification and profiling of upland cotton microRNAs at fiber initiation stage under exogenous IAA application.

Similar Datasets

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