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

Li Wen,Christopher A Saski,Don Jones,Matthew West,Michael Smathers,Stephen Parris,Zhigang Li,Wei Li,Shuangxia Jin,John Lawson

doi:10.1186/s12861-020-00230-4

Abstract

BackgroundGenotype 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.ResultsIn 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.ConclusionsThis comparative analysis of NEC and EC transcriptomes gives new insights into the genes involved in somatic embryogenesis in cotton.

Highlights

Genotype independent transformation and whole plant regeneration through somatic embryogenesis relies heavily on the intrinsic ability of a genotype to regenerate
We present and discuss the various classes of genes that are active during the transition from non-embryogenic callus (NEC) to embryogenic callus (EC) cells, and identify several new candidate genes that enhances our knowledge of somatic embryogenesis in upland cotton
Understanding endogenous changes in developmental biology at the molecular level is paramount to developing strategies toward genotype independent transformation and subsequent whole plant regeneration

Summary

Introduction

Genotype independent transformation and whole plant regeneration through somatic embryogenesis relies heavily on the intrinsic ability of a genotype to regenerate. Genome editing through engineered nucleases [6] or CRISPR-Cas systems (spCas9-NG, base editing, xCas, Cpf, Cas, Cas14) [7] are unprecedented technological breakthroughs that behold disruptive potential to precisely edit the genome of living organisms These systems offer biologists the ability to ask precise biological questions; which has led to a new capacity in understanding gene function through targeted knockouts. Agrobacterium-mediated transformation [9] and subsequent whole plant regeneration from a single somatic cell is perhaps the most historic and preferred method to produce plants homoplastic for the transgene [9] This type of whole plant regeneration is generally limited to a narrow range of genotypes within a species, usually with poor agronomic traits and with low efficiency [10,11,12]

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