Discovery of genes that regulate chickpea seed development and its nutritional quality

Chickpea is an important legume crop because of its seeds which contain significant amounts of proteins, carbohydrates, minerals and micronutrients for human consumption (Verma et al. 2015). Moreover, its seeds also accumulate high amount of value-added products such as secondary metabolites, with ever-expanding applications in health and medicine (Jukanti et al. 2012). Despite the importance of chickpea seed, there has been little discussion on the molecular mechanisms governing its development and yield attributes. Therefore, there is a need to make directed efforts to improve both the quality and quantity of chickpea seeds. This requires an in-depth knowledge of the various regulatory mechanisms that occur during the vital process of seed development.

In the present study, we targeted the maturation stage of seed development. Overall seed development proceeds through three stages.

  1. Embryogenesis
  2. Seed maturation/filling and
  3. Desiccation

From the economic and nutritional point of view, the maturation stage during which a wide range of storage compounds are synthesised and accumulated is the most important. Among storage reserves, seed storage proteins (SSPs) are the primary storage compounds in legumes, including chickpea. The SSPs act as a reservoir of carbon and nitrogen during germination and seedling growth. The SSPs can be classified into different groups based on their solubility in a stream of solvents such as

  • Albumins in water,
  • Prolamins in alcohol/water mixture,
  • Glutelins in dilute acid or alkaline and Globulins in dilute saline

These stored reserves determine the total protein content of the seed and also influence the nutritional quality and end-use properties. Therefore, to manipulate the quality and quantity of seed proteins, it is necessary to explore the regulatory network underlying the synthesis and accumulation of SSPs in chickpea.

To this effect, we scanned the chickpea genome using bioinformatics tools and identified genes that encode SSPs in chickpea (Verma et al. 2019). These genes were analysed for their expression pattern in different chickpea tissues, including leaf, root, flower and seed. This revealed that the maximum SSP encoding genes exhibited higher expression in maturation stages of seed development.

Figure 1. SSPs regulation in Arabidopsis seed.

Expression of a gene is regulated by various transcriptional regulators, amongst which transcription factors (TFs) are the major controllers that influence various regulatory pathways. Further, to identify which TFs regulate their expression and allow SSPs to synthesise and accumulate during maturation, we performed a co-expression analysis. Basically, we analysed the expression profiles of different TFs and SSP encoding genes in different chickpea tissues including seed development stages and subsequently selected those TFs who had the expression pattern similar to the expression pattern of SSPs. This resulted in the identification of 14 TFs belonging to different TF families such as C3H, NAC, bHLH, AP2, B3 and bZIP (Verma et al. 2019). Further, based on extensive literature survey, and co-expression analysis, we selected one candidate TF, i.e. Abscisic acid insensitive3 (ABI3) for further functional characterisation. ABI3 is a member of the B3 domain-containing TF family. Its role during seed development, particularly in the maturation stage has been demonstrated in Arabidopsis (Nambara et al. 1995; Verdier and Thompson 2008). However, very less is known about the molecular mechanisms through which it carries out its functions. Although the ABI3 has been studied in the model plant Arabidopsis, its role in crop plants like chickpea needs to be elucidated.

Figure 2. Over-expression of Chickpea ABI3 in Arabidopsis leads to higher protein content in seeds

Therefore, we generated transgenic Arabidopsis plants by over-expressing the ABI3 gene of chickpea. The seeds of transgenic plants were analysed for seed protein content and seed weight. These experiments revealed that the transgenic expression of chickpea ABI3 in Arabidopsis increased the total seed protein content without substantial changes in seed weight (unpublished). The generation of chickpea mutants and complementation of Arabidopsis mutants with chickpea ABI3 is in progress.

In conclusion, genes encoding SSPs and co-expressing TFs that were identified will be available for studying the various regulatory mechanisms involved in seed development with the overall aim of improving the nutritional qualities of chickpea.

This work was carried out by myself (author of this article) under the supervision of Dr Sabhyata Bhatia at National Institute of Plant Genome Research, New Delhi. Three research articles from this work have been published in peer-reviewed journals (Scientific Reports, Funct Integr Genomics and 3 Biotech).


Additional references:

Jukanti, A. K., Gaur, P. M., Gowda, C. L. L., & Chibbar, R. N. (2012). Nutritional quality and health benefits of chickpea (Cicer arietinum L.): a review. British Journal of Nutrition108(S1), S11-S26.

Nambara E, McCourt P, Naito S (1995) A regulatory role for the ABI3 gene in the establishment of embryo maturation in Arabidopsis thaliana Development (Cambridge, England) 121:629-636

Verma, S., Gupta, S., Bandhiwal, N., Kumar, T., Bharadwaj, C., & Bhatia, S. (2015). High-density linkage map construction and mapping of seed trait QTLs in chickpea (Cicer arietinum L.) using Genotyping-by-Sequencing (GBS). Scientific reports5, 17512.

Verma, S., & Bhatia, S. (2019). Analysis of genes encoding seed storage proteins (SSPs) in chickpea (Cicer arietinum L.) reveals co-expressing transcription factors and a seed-specific promoter. Functional & integrative genomics19(3), 373-390.

Verdier J, Thompson RD (2008) Transcriptional regulation of storage protein synthesis during dicotyledon seed filling Plant & cell physiology 49:1263-1271 doi:10.1093/pcp/pcn116


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