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

Sonika Kumar,Zhigang Li,Clayton Grosse,Christopher Saski,Matthew Bates,Jane Grimwood,Thomas Tyson,Alora Mazarakis,Ashleigh Ruggles,David Reed,Sam Logan,Jeremy Schmutz

doi:10.3390/plants10091775

Abstract

Somatic embryogenesis-mediated plant regeneration is essential for the genetic manipulation of agronomically important traits in upland cotton. Genotype specific recalcitrance to regeneration is a primary challenge in deploying genome editing and incorporating useful transgenes into elite cotton germplasm. In this study, transcriptomes of a semi-recalcitrant cotton (Gossypium hirsutum L.) genotype ‘Coker312’ were analyzed at two critical stages of somatic embryogenesis that include non-embryogenic callus (NEC) and embryogenic callus (EC) cells, and the results were compared to a non-recalcitrant genotype ‘Jin668’. We discovered 305 differentially expressed genes in Coker312, whereas, in Jin668, about 6-fold more genes (2155) were differentially expressed. A total of 154 differentially expressed genes were common between the two genotypes. Gene enrichment analysis of the upregulated genes identified functional categories, such as lipid transport, embryo development, regulation of transcription, sugar transport, and vitamin biosynthesis, among others. In Coker312 EC cells, five major transcription factors were highly upregulated: LEAFY COTYLEDON 1 (LEC1), WUS-related homeobox 5 (WOX5), ABSCISIC ACID INSENSITIVE3 (ABI3), FUSCA3 (FUS3), and WRKY2. In Jin668, LEC1, BABY BOOM (BBM), FUS3, and AGAMOUS-LIKE15 (AGL15) were highly expressed in EC cells. We also found that gene expression of these embryogenesis genes was typically higher in Jin668 when compared to Coker312. We conclude that significant differences in the expression of the above genes between Coker312 and Jin668 may be a critical factor affecting the regenerative ability of these genotypes.

Highlights

IntroductionPlant somatic embryogenesis (SE) is a unique developmental process that leads to the regeneration of a whole plant from single or multiple somatic cells [1]
Differential gene expression analysis revealed a total of 196 genes upregulated and 109 genes downregulated, respectively, in Coker312 embryogenic callus (EC) when compared to Coker312 non-embryogenic callus cells (NEC), with at least 2-fold abundance difference and an adjusted p-value of 0.001, Supplemental Table S1
Functional enrichment of the upregulated genes in Coker312 EC cells identified the biological processes involved in the biosynthesis of vitamins, such as thiamine; the transport of sucrose, copper, and lipids; and genes involved in embryo development, as shown in Figure 1 and Supplemental Table S2

Summary

Introduction

Plant somatic embryogenesis (SE) is a unique developmental process that leads to the regeneration of a whole plant from single or multiple somatic cells [1]. This process involves sophisticated cellular reprogramming events that are controlled by gene expression programs and signaling pathways that direct callus cells to dedifferentiate, reprogram, and begin differentiation into polarized structures that eventually become a viable embryo [2,3,4,5]. Form non-embryogenic callus cells (NEC) that can be described as unorganized, dedifferentiated, continuously dividing cell masses These cells are responsive to the components in the growth medium and signals from the environment, such as light and temperature

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