Using Transcriptome Analysis to Screen for Key Genes and Pathways Related to Cytoplasmic Male Sterility in Cotton (Gossypium hirsutum L.)

Abstract

Cotton (Gossypium hirsutum L.) is one of the most important cash crops worldwide. Cytoplasmic male sterility (CMS) is an excellent breeding system for exploitation of heterosis, which has great potential to increase crop yields. To understand the molecular mechanism of CMS in cotton, we compared transcriptome, cytomorphological, physiological and bioinformatics data between the CMS line C2P5A and its maintainer line C2P5B. By using high-throughput sequencing technology, 178,166 transcripts were assembled and 2013 differentially expression genes (DEGs) were identified at three different stages of C2P5A anther development. In this study, we identified DEGs associated with reactive oxygen species (ROS), peroxisomes, aldehyde dehydrogenases (ALDH), cytochrome oxidase subunit VI, and cytochrome P450, and DEGs associated with tapetum development, Jojoba acyl-CoA reductase-related male sterility protein, basic helix-loop-helix (bHLH) and MYB transcription factors. The abnormal expression of one of these genes may be responsible for the CMS C2P5A line. In gene ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment, DEGs were mainly related to carbohydrate metabolism, amino acid metabolism, transport and catabolism, and signal transduction. Carbohydrate metabolism provides energy for anther development, starch and sucrose metabolism, fatty acid biosynthesis and metabolism and ascorbate and aldarate metabolism. These results showed that numerous genes and multiple complex metabolic pathways regulate cotton anther development. Weighted correlation network analysis (WGCNA) indicated that three modules, ‘turquoise,’ ‘blue,’ and ‘green,’ were specific for the CMS C2P5A line. The ‘turquoise’ and ‘blue’ modules were mainly related to carbohydrate metabolism, amino acid metabolism, energy metabolism, peroxisomes, pyruvate metabolism as well as fatty acid degradation. The ‘green’ module was mainly related to energy metabolism, carbon metabolism, translation, and lipid metabolism. RNA-sequencing and WGCNA polymerization modules were screened for key genes and pathways related to CMS in cotton. This study presents a new perspective for further research into the metabolic pathways of pollen abortion in the CMS C2P5A line and also provides a theoretical basis for its breeding and production.

Integrated Methylome and Transcriptome Analysis between the CMS-D2 Line ZBA and Its Maintainer Line ZB in Upland Cotton

“…This demonstrates that a ROS burst may occur during anther development in the CMS-D2 line ZBA. This finding is consistent with other cotton sterile lines, such as Zhong41A (CMS-D8) [9] and C2P5A [24]. A decrease in ATP but excessive ROS accumulation was found in a transformant expressing the rice CMS-associated gene orfH79 [89].…”

“…Furthermore, numerous differentially expressed genes (DEGs) were identified in the CMS line H276A ( Gossypium barbadense L.) through a comparative transcriptome analysis, most of which were associated with energy-related metabolic pathways (e.g., the tricarboxylic acid (TCA) cycle, respiratory electron transfer, and oxidative phosphorylation), pentatricopeptide repeat (PPR) proteins, and MYB (v-myb avian myeloblastosis vira I oncogene homolog) transcription factors [11]. Recently, transcriptome sequencing was also used to investigate the cotton CMS line C2P5A, which revealed that genes associated with ROS detoxification enzymes, tapetum proteins, transcription factors, vital metabolic pathways including starch and sucrose metabolism, galactose metabolism, ascorbate and aldarate metabolism, glutathione metabolism, and pyruvate metabolism were differentially expressed in anthers [24]. Although some cotton mitochondrial genomes have been reported so far [25,26], relatively little progress has been achieved in terms of CMS-associated genes in cotton.…”

Transcriptome and MiRNAomics Analyses Identify Genes Associated with Cytoplasmic Male Sterility in Cotton (Gossypium hirsutum L.)

“…The main abortion stages of the Jin A cotton CMS line are the sporogenic cell and microspore mother cell, and the main characteristic is that the sporogenic cells cannot divide normally [ 44 ]. Pollen abortion for the cotton CMS lines H276A [ 22 ], LD6A [ 25 ], and C2P5A [ 27 ] occurs at the tetrad stage. Pollen abortion for the cotton CMS line J4A evaluated in the present study occurred during meiosis in the microspore mother cell stage, as the tapetum cells did not undergo programmed cell apoptosis during the entire developmental process, and the anthers ultimately had an insufficient energy supply and underwent abortion.…”

“…Altered metabolic pathways influence the biological processes leading to CMS [ 7 ]. With the development of the technology for high-throughput sequencing and bioinformatics, CMS-related genes are discovered through the construction of transcription regulatory networks, which are related to the tricarboxylic acid (TCA) cycle, oxidative phosphorylation, respiratory electron transport chain, toxic proteins, and carbohydrate metabolism [ 22 , 23 , 24 , 25 , 26 , 27 , 28 , 29 , 30 , 31 ]. Besides, miRNA also plays an important role in flower development in plants [ 32 ].…”

Deficiencies in the formation and regulation of anther cuticle and tryphine contribute to male sterility in cotton PGMS line

“…Understanding the molecular mechanisms controlling anther development and male sterility is of great importance for heterosis utilization in many crop species, including cotton. In recent years, male sterility lines have been widely studied by transcriptomic analysis in different species, such as wheat [56,57], maize [58], eggplant [59] and cotton [60][61][62][63]. However, most studies tend to carry out extensive enrichment of DEGs without systematic classi cation analysis based on different development stages.…”