Transcriptomic profiles of non-embryogenic and embryogenic callus cells in a highly regenerative upland cotton line (Gossypium hirsutum L.)

Abstract

Background Genotype independent transformation and whole plant regeneration through somatic embryogenesis relies heavily on the intrinsic ability of a genotype to regenerate. The critical genetic architecture of non-embryogenic callus (NEC) cells and embryogenic callus (EC) cells in a highly regenerable cotton genotype is unknown. Results In this study, gene expression profiles of a highly regenerable Gossypium hirsutum L. cultivar, Jin668, were analyzed at two critical developmental stages during somatic embryogenesis, non-embryogenic callus (NEC) cells and embryogenic callus (EC) cells. The rate of EC formation in Jin668 is 96%. Differential gene expression analysis revealed a total of 5333 differentially expressed genes (DEG) with 2534 genes upregulated and 2799 genes downregulated in EC. A total of 144 genes were unique to NEC cells and 174 genes were unique to EC. Clustering and enrichment analysis identified genes upregulated in EC that function as transcription factors/DNA binding, phytohormone response, oxidative reduction, and regulators of transcription; while genes categorized in methylation pathways were downregulated. Four key transcription factors were identified based on their sharp upregulation in EC tissue; LEAFY COTYLEDON 1 (LEC1), BABY BOOM (BBM), FUSCA (FUS3) and AGAMOUS-LIKE15 with distinguishable subgenome expression bias. Conclusions This comparative analysis of NEC and EC transcriptomes gives new insights into the genes involved in somatic embryogenesis in cotton.

Comparative Transcriptomics of Non-Embryogenic and Embryogenic Callus in Semi-Recalcitrant and Non-Recalcitrant Upland Cotton Lines

“…We compared the gene expression profiles of the semi-recalcitrant genotype, Coker312, to the previous transcriptomic study of a non-recalcitrant genotype, Jin668 [ 26 ]. Comparative analysis of the differentially expressed genes with at least a two-fold change profile and an error corrected p -value of 0.001 identified 151 unique genes in Coker312 and 2001 unique genes in Jin668 ( Figure 2 ), with a total of 305 and 2155 differentially expressed genes in Coker312 and Jin668, respectively ( Figure 2 ).…”

“…In the Coker312, the highest upregula gene was LEC1, followed by WOX5, ABSCISIC ACID INSENSITIVE (ABI3), FUS3, a WRKY2. In Jin668, LEC1, BBM, FUS3, and AGAMOUS-LIKE15 (AGL15) were the hig expressed genes, and their expression was several times higher in comparison We also examined the expression profiles of genes known to have a role in somatic embryogenesis, such as BBM, WUS, LEC1, WUSCHEL-RELATED HOMEOBOX 5 (WOX5), FUSCA3 (FUS3), and several other genes [26]. The genes with the sharpest fold changes were Gohir.D13G136000.1(LEC1−1), Gohir.A13G132600.1(LEC1−2), Gohir.D07G237600.1(FUS3−2), Gohir.D08G035600.1(LEC1−3), and Gohir.A07G230400.1(FUS3_1) in Coker312 EC and Jin668 EC, although the expression was higher in Jin668 EC in comparison of Coker312 EC, as shown in Figure 5.…”

“…More recently, a non-recalcitrant genotype, named Jin668, was described, which has a high frequency of embryo formation (~96%) with only a short duration of 45–60 days from callus initiation to the formation of ball-shaped structures [ 25 ]. Our group recently determined and characterized the global gene expression profiles of this elite regeneration line at two primary developmental stages (NEC and EC) [ 26 ]. We discovered significant transcriptome-wide differences between the two developmental stages and sharp upregulation of the key transcription factors identified in EC cells that may have a primary role in reprogramming in this genotype during SE [ 26 ].…”

“…Our group recently determined and characterized the global gene expression profiles of this elite regeneration line at two primary developmental stages (NEC and EC) [ 26 ]. We discovered significant transcriptome-wide differences between the two developmental stages and sharp upregulation of the key transcription factors identified in EC cells that may have a primary role in reprogramming in this genotype during SE [ 26 ].…”

“…In the present study, we analyzed the transcriptional profiles of NEC and EC cells harvested from the semi-recalcitrant genotype Coker312 and compared these data to the non-recalcitrant genotype Jin668 [ 26 ]. Our objectives were to determine the gene expression profile differences and similarities between Jin668 and Coker312 that fall into the following categories: (i) genes uniquely expressed in each genotype, (ii) genes with similar expression profiles, and (iii) genes with different expression profiles between the two genotypes.…”