Integrative Analysis of the lncRNA and mRNA Transcriptome Revealed Genes and Pathways Potentially Involved in the Anther Abortion of Cotton (Gossypium hirsutum L.)
by
Yuqing Li 1,2, Tengfei Qin 2, Na Dong 2, Chunyan Wei 2, Yaxin Zhang 2, Runrun Sun 2, Tao Dong 2, Quanjia Chen 1, Ruiyang Zhou 3,* and Qinglian Wang 2,*
Yuqing Li 1,2, Tengfei Qin 2, Na Dong 2, Chunyan Wei 2, Yaxin Zhang 2, Runrun Sun 2, Tao Dong 2, Quanjia Chen 1, Ruiyang Zhou 3,* and Qinglian Wang 2,*
1
Cotton Engineering Research Center of Ministry of Education, College of Agriculture, Xinjiang Agricultural University, Xinjiang Urumqi 830000, China
2
Collaborative Innovation Center of Modern Biological Breeding of Henan Province, Henan Key Laboratory Molecular Ecology and Germplasm Innovation of Cotton and Wheat, School of Life Science and Technology, Henan Institute of Science and Technology, Henan Xinxiang 453003, China
3
Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning 530005, China
*
Authors to whom correspondence should be addressed.
Genes 2019, 10(12), 947; https://doi.org/10.3390/genes10120947 (registering DOI)
Received: 28 September 2019 / Revised: 15 November 2019 / Accepted: 18 November 2019 / Published: 20 November 2019
(This article belongs to the Section Plant Genetics and Genomics)
Cotton plays an important role in the economy of many countries. Many studies have revealed that numerous genes and various metabolic pathways are involved in anther development. In this research, we studied the differently expressed mRNA and lncRNA during the anther development of cotton between the cytoplasmic male sterility (CMS) line, C2P5A, and the maintainer line, C2P5B, using RNA-seq analysis. We identified 17,897 known differentially expressed (DE) mRNAs, and 865 DE long noncoding RNAs (lncRNAs) that corresponded to 1172 cis-target genes at three stages of anther development using gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment of DE mRNAs; and cis-target genes of DE lncRNAs probably involved in the degradation of tapetum cells, microspore development, pollen development, and in the differentiation, proliferation, and apoptosis of the anther cell wall in cotton. Of these DE genes, LTCONS_00105434, LTCONS_00004262, LTCONS_00126105, LTCONS_00085561, and LTCONS_00085561, correspond to cis-target genes Ghir_A09G011050.1, Ghir_A01G005150.1, Ghir_D05G003710.2, Ghir_A03G016640.1, and Ghir_A12G005100.1, respectively. They participate in oxidative phosphorylation, flavonoid biosynthesis, pentose and glucuronate interconversions, fatty acid biosynthesis, and MAPK signaling pathway in plants, respectively. In summary, the transcriptomic data indicated that DE lncRNAs and DE mRNAs were related to the anther development of cotton at the pollen mother cell stage, tetrad stage, and microspore stage, and abnormal expression could lead to anther abortion, resulting in male sterility of cotton.
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Keywords:
cotton; cytoplasmic male sterility; lncRNA; transcriptome; cis-target gene
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MDPI and ACS Style
Li, Y.; Qin, T.; Dong, N.; Wei, C.; Zhang, Y.; Sun, R.; Dong, T.; Chen, Q.; Zhou, R.; Wang, Q. Integrative Analysis of the lncRNA and mRNA Transcriptome Revealed Genes and Pathways Potentially Involved in the Anther Abortion of Cotton (Gossypium hirsutum L.). Genes 2019, 10, 947.
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