Dynamic Transcriptome Analysis Reveals Uncharacterized Complex Regulatory Pathway Underlying Genotype-Recalcitrant...

Area of Science:

• Plant Biotechnology
• Molecular Biology
• Genetics

Background:

• Somatic embryogenesis (SE) is crucial for plant regeneration and genetic engineering.
• Cotton SE exhibits genotype-dependent recalcitrance, hindering efficient crop improvement.
• Understanding the molecular basis of this recalcitrance is vital for advancing cotton biotechnology.

Purpose of the Study:

• To comprehensively investigate dynamic transcriptional profiling and gene regulatory patterns in cotton SE.
• To compare gene expression between a highly embryogenic and a recalcitrant cotton genotype.
• To identify molecular factors underlying genotype-dependent SE response in cotton.

Main Methods:

• Genome-wide RNA sequencing was performed on two cotton genotypes (highly embryogenic Yuzao 1 and recalcitrant Lumian 1).
• Transcriptional profiles were analyzed across three developmental stages: hypocotyls (HY), nonembryogenic calli (NEC), and primary embryogenic calli (PEC).
• Differential gene expression analysis, clustering, and functional enrichment analysis were conducted.

Main Results:

• A total of 62,562 transcripts were identified across developmental stages and genotypes.
• Significant numbers of differentially expressed genes (DEGs) were found during callus dedifferentiation and embryogenic transdifferentiation in both genotypes.
• Functional enrichment revealed distinct metabolic pathways (fatty acid, tryptophan, pyruvate) in the highly embryogenic genotype and DNA conformation changes in the recalcitrant genotype. Critical SE-associated transcription factors and alternative splicing events were preferentially activated in the highly embryogenic genotype.

Conclusions:

• This study provides a comprehensive overview of gene regulatory patterns during cotton SE genotype-dependent response.
• Key molecular insights into the basis of SE genotype recalcitrance were revealed.
• The findings offer valuable gene resources for understanding and improving cotton plant regeneration and breeding efficiency through biotechnology.