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10.3390/genes11050472
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Article

Comparative Transcriptomic Analysis to Identify the Genes Related to Delayed Gland Morphogenesis in Gossypium bickii

by
Mushtaque Ali
1,
Hailiang Cheng
1,
Mahtab Soomro
1,
Li Shuyan
1,
Muhammad Bilal Tufail
1,
Mian Faisal Nazir
1,
Xiaoxu Feng
1,2,
Youping Zhang
1,
Zuo Dongyun
1,
Lv Limin
1,
Qiaolian Wang
1 and
Guoli Song
1,*
1
State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
2
Plant Genetics, Gambloux Agro Bio Tech, University of Liege, 5030 Gambloux, Belgium
*
Author to whom correspondence should be addressed.
Genes 2020, 11(5), 472; https://doi.org/10.3390/genes11050472
Submission received: 20 March 2020 / Revised: 15 April 2020 / Accepted: 19 April 2020 / Published: 26 April 2020
(This article belongs to the Special Issue Genetics of Plant Organogenesis and Tissue Regeneration)
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Abstract

Cotton is one of the major industrial crops that supply natural fibers and oil for industries. This study was conducted to understand the mechanism of delayed gland morphogenesis in seeds of Gossypium bickii. In this study, we compared glandless seeds of G. bickii with glanded seeds of Gossypium arboreum. High-throughput sequencing technology was used to explore and classify the expression patterns of gland-related genes in seeds and seedlings of cotton plants. Approximately 131.33 Gigabases of raw data from 12 RNA sequencing samples with three biological replicates were generated. A total of 7196 differentially-expressed genes (DEGs) were identified in all transcriptome data. Among them, 3396 genes were found up-regulated and 3480 genes were down-regulated. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) annotations were performed to identify different functions between genes unique to glandless imbibed seeds and glanded seedlings. Co-expression network analysis revealed four modules that were identified as highly associated with the development of glandless seeds. Here the hub genes in each module were identified by weighted gene co-expression network analysis (WGCNA). In total, we have selected 13 genes involved in transcription factors, protein and MYB-related functions, that were differentially expressed in transcriptomic data and validated by quantitative reverse-transcription polymerase chain reaction (qRT-PCR). These selected genes may play an important role for delayed gland morphogenesis. Our study provides comprehensive insight into the key genes related to glandless traits of seeds and plants, and can be further exploited by functional and molecular studies.
Keywords: Gossypium bickii; RNA-seq; DEGs; WGCNA Gossypium bickii; RNA-seq; DEGs; WGCNA

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MDPI and ACS Style

Ali, M.; Cheng, H.; Soomro, M.; Shuyan, L.; Bilal Tufail, M.; Nazir, M.F.; Feng, X.; Zhang, Y.; Dongyun, Z.; Limin, L.; et al. Comparative Transcriptomic Analysis to Identify the Genes Related to Delayed Gland Morphogenesis in Gossypium bickii. Genes 2020, 11, 472. https://doi.org/10.3390/genes11050472

AMA Style

Ali M, Cheng H, Soomro M, Shuyan L, Bilal Tufail M, Nazir MF, Feng X, Zhang Y, Dongyun Z, Limin L, et al. Comparative Transcriptomic Analysis to Identify the Genes Related to Delayed Gland Morphogenesis in Gossypium bickii. Genes. 2020; 11(5):472. https://doi.org/10.3390/genes11050472

Chicago/Turabian Style

Ali, Mushtaque, Hailiang Cheng, Mahtab Soomro, Li Shuyan, Muhammad Bilal Tufail, Mian Faisal Nazir, Xiaoxu Feng, Youping Zhang, Zuo Dongyun, Lv Limin, and et al. 2020. "Comparative Transcriptomic Analysis to Identify the Genes Related to Delayed Gland Morphogenesis in Gossypium bickii" Genes 11, no. 5: 472. https://doi.org/10.3390/genes11050472

APA Style

Ali, M., Cheng, H., Soomro, M., Shuyan, L., Bilal Tufail, M., Nazir, M. F., Feng, X., Zhang, Y., Dongyun, Z., Limin, L., Wang, Q., & Song, G. (2020). Comparative Transcriptomic Analysis to Identify the Genes Related to Delayed Gland Morphogenesis in Gossypium bickii. Genes, 11(5), 472. https://doi.org/10.3390/genes11050472

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