Genome-wide analysis reveals divergent patterns of gene expression during zygotic and somatic embryo maturation of Theobroma cacao L., the chocolate tree.

Siela N Maximova,Sergio Florez,Nicolas Niemenak,Mark J Guiltinan,Xiangling Shen,Yufan Zhang,Wayne Curtis

doi:10.1186/1471-2229-14-185

Siela N Maximova, Sergio Florez + Show 5 more

Open Access

https://doi.org/10.1186/1471-2229-14-185

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Abstract

BackgroundTheobroma cacao L. is a tropical fruit tree, the seeds of which are used to create chocolate. In vitro somatic embryogenesis (SE) of cacao is a propagation system useful for rapid mass-multiplication to accelerate breeding programs and to provide plants directly to farmers. Two major limitations of cacao SE remain: the efficiency of embryo production is highly genotype dependent and the lack of full cotyledon development results in low embryo to plant conversion rates. With the goal to better understand SE development and to improve the efficiency of SE conversion we examined gene expression differences between zygotic and somatic embryos using a whole genome microarray.ResultsThe expression of 28,752 genes was determined at 4 developmental time points during zygotic embryogenesis (ZE) and 2 time points during cacao somatic embryogenesis (SE). Within the ZE time course, 10,288 differentially expressed genes were enriched for functions related to responses to abiotic and biotic stimulus, metabolic and cellular processes. A comparison ZE and SE expression profiles identified 10,175 differentially expressed genes. Many TF genes, putatively involved in ethylene metabolism and response, were more strongly expressed in SEs as compared to ZEs. Expression levels of genes involved in fatty acid metabolism, flavonoid biosynthesis and seed storage protein genes were also differentially expressed in the two types of embryos.ConclusionsLarge numbers of genes were differentially regulated during various stages of both ZE and SE development in cacao. The relatively higher expression of ethylene and flavonoid related genes during SE suggests that the developing tissues may be experiencing high levels of stress during SE maturation caused by the in vitro environment. The expression of genes involved in the synthesis of auxin, polyunsaturated fatty acids and secondary metabolites was higher in SEs relative to ZEs despite lack of lipid and metabolite accumulation. These differences in gene transcript levels associated with critical processes during seed development are consistent with the fact that somatic embryos do not fully develop the large storage cotyledons found in zygotic embryos. These results provide insight towards design of improved protocols for cacao somatic embryogenesis.

Highlights

Theobroma cacao L. is a tropical fruit tree, the seeds of which are used to create chocolate
To study cacao embryo development, total RNA was isolated from four biological replicates of six different tissue types and stages of embryo development: zygotic embryo tissues torpedo (T-zygotic embryogenesis (ZE)), early-full (EF-ZE), late-full (LF-ZE) and mature (M-ZE) embryos; and somatic embryos - late torpedo (LT-somatic embryogenesis (SE)) and mature (M-SE) stages
We investigated all genes in these classes that were differentially expressed during zygotic embryo maturation and based on the observation that the two SE developmental stages clustered closest to the M-ZE, we selected to compare the somatic embryo mature stage relative to mature zygotic embryos

Summary

Introduction

Theobroma cacao L. is a tropical fruit tree, the seeds of which are used to create chocolate. Plant embryo development is initiated with the double fertilization of male and female gametes, followed by the process of zygotic embryogenesis (ZE), during which the formation of the embryo occurs by a complex program of lateral, radial and longitudinal growth [2,3]. During SE maturation, cells develop completely outside the maternal context into somatic embryos and by ‘conversion,’ into whole morphologically intact plants [9]. In some plants, this complicated process can be initiated by simple manipulation of hormones, whereas in others, its efficiency is dependent on genotype and explant tissue type, and requires precise control of hormonal and environmental conditions. During zygotic seed development, the embryonic cotyledons expand and accumulate large amounts of lipids, protein, carbohydrates and terpenes, while somatic embryos produce small underdeveloped cotyledons

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