Genome-wide comparative transcriptome analysis of CMS-D2 and its maintainer and restorer lines in upland cotton

Jianyong Wu,Meng Zhang,Tingxiang Qi,Hailin Wang,Liping Guo,Bingbing Zhang,Chaozhu Xing,Xuexian Zhang,Jinfa Zhang

doi:10.1186/s12864-017-3841-0

Abstract

BackgroundCytoplasmic male sterility (CMS) conferred by the cytoplasm from Gossypium harknessii (D2) is an important system for hybrid seed production in Upland cotton (G. hirsutum). The male sterility of CMS-D2 (i.e., A line) can be restored to fertility by a restorer (i.e., R line) carrying the restorer gene Rf1 transferred from the D2 nuclear genome. However, the molecular mechanisms of CMS-D2 and its restoration are poorly understood.ResultsIn this study, a genome-wide comparative transcriptome analysis was performed to identify differentially expressed genes (DEGs) in flower buds among the isogenic fertile R line and sterile A line derived from a backcross population (BC8F1) and the recurrent parent, i.e., the maintainer (B line). A total of 1464 DEGs were identified among the three isogenic lines, and the Rf1-carrying Chr_D05 and its homeologous Chr_A05 had more DEGs than other chromosomes. The results of GO and KEGG enrichment analysis showed differences in circadian rhythm between the fertile and sterile lines. Eleven DEGs were selected for validation using qRT-PCR, confirming the accuracy of the RNA-seq results.ConclusionsThrough genome-wide comparative transcriptome analysis, the differential expression profiles of CMS-D2 and its maintainer and restorer lines in Upland cotton were identified. Our results provide an important foundation for further studies into the molecular mechanisms of the interactions between the restorer gene Rf1 and the CMS-D2 cytoplasm.

Highlights

Cytoplasmic male sterility (CMS) conferred by the cytoplasm from Gossypium harknessii (D2) is an important system for hybrid seed production in Upland cotton (G. hirsutum)
Plant materials In our previous study [14], the sterile line ZBA with the CMS-D2 cytoplasm was crossed with the restorer line Zhonghui46, and the maintainer B line with the normal fertile Upland cotton (AD1) cytoplasm was used as the recurrent male parent to backcross with the F1 plants to construct a BC8F1 population
The results demonstrated that ‘sesquiterpene synthase activity’ and ‘(+)-delta-cadinene synthase activity’ were the two major GO terms with the highest enrichment ratios, while ‘sesquiterpenoid and triterpenoid biosynthesis’, ‘protein processing in endoplasmic reticulum’ and ‘carotenoid biosynthesis’ were the three major pathways identified in KEGG enrichment analysis

Summary

Introduction

Cytoplasmic male sterility (CMS) conferred by the cytoplasm from Gossypium harknessii (D2) is an important system for hybrid seed production in Upland cotton (G. hirsutum). As a powerful tool for studying global transcriptional networks, transcriptome sequencing provides high-resolution data and has been widely used in many crops. It has been used to study boll development [16], fiber development [17,18,19], leaf senescence [20], gland morphogenesis [21], abiotic stress responses [22,23,24], biotic stress responses [25, 26], RNA editing in relation to CMS-D8 [27], and genic male sterility [28]. That the genome sequences of G. raimondii [31, 32], G arboreum [33], and G hirsutum [34, 35] have been published, gene annotation can be better performed, which will improve genome-wide transcriptome sequencing and analysis in cotton

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Discussion

Conclusion