Transcriptome analysis identified aberrant gene expression in pollen developmental pathways leading to CGMS in cotton (<i>Gossypium hirsutum L</i>.)

Male sterility (induced or natural) is a potential tool for commercial hybrid seed production in different crops. Despite numerous endeavors to understand the physiological, hereditary, and molecular cascade of events governing CMS in cotton, the exact biological process controlling sterility and fertility reconstruction remains obscure. During current study, RNA-Seq using Ion Torrent S5 platform is carried out to identify ‘molecular portraits’ in floral buds among the Cytoplasmic Genic Male Sterility (CGMS) line, its near-isogenic maintainer, and restorer lines. A total of 300, 438 and 455 genes were differentially expressed in CGMS, Maintainer, and Restorer lines respectively. The functional analysis using AgriGo revealed suppression in the pathways involved in biogenesis and metabolism of secondary metabolites which play an important role in pollen and anther maturation. Enrichment analysis showed dearth related to pollen and anther’s development in sterile line, including anomalous expression of genes and transcription factors that have a role in the development of the reproductive organ, abnormal cytoskeleton formation, defects in cell wall formation. The current study found aberrant expression of DYT1, AMS and cytochrome P450 genes involved in tapetum formation, pollen development, pollen exine and anther cuticle formation associated to male sterility as well as fertility restoration of CGMS. In the current study, more numbers of DEGs were found on Chromosome D05 and A05 as compared to other chromosomes. Expression pattern analysis of fourteen randomly selected genes using qRT-PCR showed high concurrence with gene expression profile of RNA-Seq analysis accompanied by a strong correlation of 0.82. The present study provides an important support for future studies in identifying interaction between cyto-nuclear molecular portraits, to accelerate functional genomics and molecular breeding related to cytoplasmic male sterility studies in cotton.人工诱导或自然产生的雄性不育，是各类作物商业化杂交种子生产的潜在技术手段。尽管学界已开展大量研究，以解析棉花细胞质雄性不育（Cytoplasmic Male Sterility, CMS）相关的生理、遗传及分子调控级联事件，但控制雄性不育与育性恢复的精确生物学过程仍不明确。本研究采用Ion Torrent S5测序平台开展RNA测序（RNA-Seq），以鉴定细胞质核互作雄性不育（Cytoplasmic Genic Male Sterility, CGMS）系、其近等基因保持系及恢复系的花蕾‘分子特征谱’。CGMS系、保持系与恢复系中分别鉴定出300、438和455个差异表达基因（Differentially Expressed Genes, DEGs）。通过AgriGo数据库进行功能分析发现，参与次生代谢物生物合成与代谢的通路受到抑制，而这些通路对花粉及花药成熟至关重要。富集分析显示，不育系中与花粉及花药发育相关的通路存在显著缺失，包括生殖器官发育相关基因与转录因子的异常表达、细胞骨架形成异常以及细胞壁发育缺陷。本研究发现，与绒毡层形成、花粉发育、花粉外壁及花药角质层构建相关的DYT1、AMS以及细胞色素P450基因出现异常表达，这些基因既与雄性不育相关，也参与CGMS的育性恢复过程。本研究还发现，相较于其他染色体，D05与A05染色体上的DEGs数量更多。通过实时定量聚合酶链反应（qRT-PCR）对14个随机筛选的基因进行表达模式分析，结果显示其表达谱与RNA-Seq分析得到的基因表达谱高度一致，二者相关性达0.82。本研究为未来鉴定核质互作分子特征谱之间的相互作用、加速棉花细胞质雄性不育相关功能基因组学与分子育种研究提供了重要支撑。