Comparative Transcriptome Analysis of SE initial dedifferentiation in cotton of different SE capability

Abstract

Somatic embryogenesis (SE) is a critical transition from vegetative to embryogenic growth in higher plants; however, few studies have investigated the mechanism that regulates SE initial differentiation. Most cotton varieties have not undergone regeneration by SE, so only a few varieties can be used in genetic engineering. Here, two varieties of cotton with different SE capabilities (HD, higher differentiation and LD, lower differentiation) were analyzed by high throughout RNA-Seq at the pre-induction stage (0h) and two induction stages (3h and 3d) under callus-induction medium (CIM). About 1150 million clean reads were obtained from 98.21% raw data. Transcriptomic analysis revealed that “protein kinase activity” and “oxidoreductase activity” were highly represented GO terms during the same and different treatment stages among HD and LD. Moreover, several stress-related transcription factors might play important roles in SE initiation. The SE-related regulation genes (SERKs) showed different expression patterns between HD and LD. Furthermore, the complex auxin and ethylene signaling pathway contributes to initiation of differentiation in SE. Thus, our RNA-sequencing of comparative transcriptome analysis will lay a foundation for future studies to better define early somatic formation in cotton with different SE capabilities.

Dynamic Transcriptome Analysis Reveals Uncharacterized Complex Regulatory Pathway Underlying Dose IBA-Induced Embryogenic Redifferentiation in Cotton

“…Auxin response factor (ARFs) is considered as essential SE genes that are specifically activated during embryogenic differentiation [31][32][33][34]. ARFs bind auxin response promoter elements, mediate transcriptional responses to auxin and regulate auxin-mediated transcriptional activation/repression, together with Aux/IAA [35,36]. Three repetitions of the biological experiments were performed.…”

“…Some of the identified genes have been experimentally demonstrated to play an important role in SE [29,35,43,44]. Somatic embryogenesis receptor kinase (SERK) is involved in the signal transduction pathway during somatic embryogenesis and is a marker gene for the embryotic state.…”

Peer Review #2 of "Transcriptome analysis of the induction of somatic embryogenesis in Coffea canephora and the participation of ARF and Aux/IAA genes (v0.1)"

“…With the release of the C. canephora genome (Denoeud et al, 2014 The RNA-Seq technology has allowed us to have a complete picture of the genes expressed during SE induction. Transcriptomic studies have showed that the most important and determining changes begin at the start of the SE induction stage (1 DAI) and at the beginning of the development of the first structures (21 DAI) or, in other words, at the moment of the shift from a non-embryogenic state to an embryogenic one (Cheng et al, 2016;Shi et al, 2016;Tao et al, 2016;Cao et al, 2017;Chu et al, 2017;Enríquez-Valencia et al, 2019). Cao et al (2017) identified the main regulation phase of SE initiation in cotton to occur between three hours and three days after induction.…”

“…Transcriptomic studies have showed that the most important and determining changes begin at the start of the SE induction stage (1 DAI) and at the beginning of the development of the first structures (21 DAI) or, in other words, at the moment of the shift from a non-embryogenic state to an embryogenic one (Cheng et al, 2016;Shi et al, 2016;Tao et al, 2016;Cao et al, 2017;Chu et al, 2017;Enríquez-Valencia et al, 2019). Cao et al (2017) identified the main regulation phase of SE initiation in cotton to occur between three hours and three days after induction. As is the case in our results, most of the dramatic changes are visualized during the transition from the pre-conditioning stage to the first hours of the induction stage and the 21 DAI where embryogenic structures can be observed.…”

“…Using the RNA-seq approach, it has been possible to identify a set of genes involved in the embryogenic response in species such as cotton (Cheng et al, 2016;Cao et al, 2017), conifers (Yakovlev et al, 2016), papaya (Jamaluddin, Mohd Noor, Goh, 2017), wheat (Chu et al, 2017), and banana (Enríquez-Valencia et al, 2019), among others like Arabidopsis, oil palm, soybean, carrot, grape, alfalfa, and maize (Cetz-Chel & Loyola-Vargas, 2016;Shi et al, 2016;Tao et al, 2016;Góngora-Castillo et al, 2018).…”