Transcriptomic profiles of non-embryogenic and embryogenic callus cells in a highly regenerative upland cotton line ( Go
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RESEARCH ARTICLE
Open Access
Transcriptomic profiles of non-embryogenic and embryogenic callus cells in a highly regenerative upland cotton line (Gossypium hirsutum L.) Li Wen1,2, Wei Li1, Stephen Parris1, Matthew West1, John Lawson1, Michael Smathers1, Zhigang Li1, Don Jones3, Shuangxia Jin4 and Christopher A. Saski1*
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. Keywords: Gossypium hirsutum L, Somatic embryogenesis, Callus, embryo
Background The domain of plant transformation has enabled foundational discoveries in plant biology over the last 30 years. Plant genetic engineering has facilitated fundamental knowledge about gene function, trait genetics, and established critical linkages between the genome structure * Correspondence: [email protected] 1 Department of Plant and Environmental Sciences, Clemson University, Clemson, SC, USA Full list of author information is available at the end of the article
and function. Transgenic approaches have been widely used in the improvement and breeding of many crops, such as soybean, rice, and maize [1–4]. The rapid pace of genome sequencing has delivered genome maps of major domesticated crop plants and many non-model and wild species that have led to deep understandings of domestication and genetic diversity, gene function, and the development of tools for precise plant breeding [5]. However, the rate of genome characterization has far
© The Author(s). 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and rep
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