Abstract
As a notable illustration of totipotency and plant regeneration, somatic embryogenesis (SE) is the developmental reprogramming of somatic cells toward the embryogenesis pathway, the key step for genetic engineering. Investigations examining the totipotency process are of great fundamental and practical importance in crop biotechnology. However, high-frequency regeneration of cotton via SE has been limited due to genotype-dependent response. The molecular basis deciphering SE genotype recalcitrance remains largely unexplored in cotton. In the current study, to comprehensively investigate the dynamic transcriptional profiling and gene regulatory patterns involved in SE process, a genome-wide RNA sequencing analysis was performed in two cotton genotypes with distinct embryogenic abilities, the highly embryogenic genotype Yuzao 1 (YZ) and the recalcitrant genotype Lumian 1 (LM). Three typical developmental staged cultures of early SE—hypocotyls (HY), nonembryogenic calli (NEC) and primary embryogenic calli (PEC)—were selected to establish the transcriptional profiles. Our data revealed that a total of 62,562 transcripts were present amongst different developmental stages in the two genotypes. Of these, 18,394 and 26,514 differentially expressed genes (DEGs) were identified during callus dedifferentiation (NEC-VS-HY) and embryogenic transdifferentiation (PEC-VS-NEC), respectively in the recalcitrant genotype, 21,842 and 22,343 DEGs in the highly embryogenic genotype. Furthermore, DEGs were clustered into six expression patterns during cotton SE process in the two genotypes. Moreover, functional enrichment analysis revealed that DEGs were significantly enriched in fatty acid, tryptophan and pyruvate metabolism in the highly embryogenic genotype and in DNA conformation change otherwise in the recalcitrant genotype. In addition, critical SE-associated expressed transcription factors, as well as alternative splicing events, were notably and preferentially activated during embryogenic transdifferentiation in the highly embryogenic genotype compared with the recalcitrant genotype. Taken together, by systematically comparing two genotypes with distinct embryogenic abilities, the findings in our study revealed a comprehensive overview of the dynamic gene regulatory patterns and uncharacterized complex regulatory pathways during cotton SE genotype-dependent response. Our work provides insights into the molecular basis and important gene resources for understanding the underlying genotype recalcitrance during SE process and plant regeneration, thereby holding great promise for accelerating the application of biotechnology to cotton for improving its breeding efficiency.
Highlights
Somatic embryogenesis (SE) is a powerful tool for plant genetic improvement when used in combination with traditional agricultural techniques, and it is an important technique to understand the different processes that occur during the development of plant embryogenesis [1]
To comprehensively analyze the gene regulatory patterns involved in SE process, we performed a genome-wide analysis of transcripts using the high throughput RNA-seq technology in two cotton genotypes with distinct embryogenic abilities, Yuzao 1 (YZ) with a high embryogenic ability and Lumian 1 (LM) with a very low ability
The quantitative expression levels for total 62,562 transcripts were calculated as Fragments Per Kilobase Million (FPKM) based on the number of uniquely mapped reads that overlapped with exon regions [45] (Table S2)
Summary
Somatic embryogenesis (SE) is a powerful tool for plant genetic improvement when used in combination with traditional agricultural techniques, and it is an important technique to understand the different processes that occur during the development of plant embryogenesis [1]. The ability to regenerate whole plants from cells, tissues, or organs cultured in vitro has long been known, the question of how a somatic cell can differentiate into a whole plant has been considered to be one of the most important questions facing science over the quarter-century [32,33]. Two cotton varieties with different SE capabilities were analyzed by high throughout RNA sequencing at three callus dedifferentiation induction stages during SE [16]. A genome-wide transcriptome sequencing (RNA-seq) was performed to comprehensively investigate the dynamic transcriptomic profiles and gene regulatory patterns involved in the process of cotton somatic embryogenesis in two genotypes with distinct embryogenic abilities. Our work provides an important molecular basis and gene resources for elucidating the SE genotype recalcitrance during cell totipotency and further expanding crop genetic engineering
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