Abstract
Understanding developmental processes, especially in non-model crop plants, is extremely important in order to unravel unique mechanisms regulating development. Chickpea (C. arietinum L.) seeds are especially valued for their high carbohydrate and protein content. Therefore, in order to elucidate the mechanisms underlying seed development in chickpea, deep sequencing of transcriptomes from four developmental stages was undertaken. In this study, next generation sequencing platform was utilized to sequence the transcriptome of four distinct stages of seed development in chickpea. About 1.3 million reads were generated which were assembled into 51,099 unigenes by merging the de novo and reference assemblies. Functional annotation of the unigenes was carried out using the Uniprot, COG and KEGG databases. RPKM based digital expression analysis revealed specific gene activities at different stages of development which was validated using Real time PCR analysis. More than 90% of the unigenes were found to be expressed in at least one of the four seed tissues. DEGseq was used to determine differentially expressing genes which revealed that only 6.75% of the unigenes were differentially expressed at various stages. Homology based comparison revealed 17.5% of the unigenes to be putatively seed specific. Transcription factors were predicted based on HMM profiles built using TF sequences from five legume plants and analyzed for their differential expression during progression of seed development. Expression analysis of genes involved in biosynthesis of important secondary metabolites suggested that chickpea seeds can serve as a good source of antioxidants. Since transcriptomes are a valuable source of molecular markers like simple sequence repeats (SSRs), about 12,000 SSRs were mined in chickpea seed transcriptome and few of them were validated. In conclusion, this study will serve as a valuable resource for improved chickpea breeding.
Highlights
Chickpea (Cicer arietinum L.) is one of the earliest annual pulse crops to be cultivated by man and consumed as a source of vegetable protein and the third most important food legume in the world
SEQUENCING AND ASSEMBLY OF CHICKPEA SEED TRANSCRIPTOME cDNA libraries were prepared using the mRNA isolated from four stages of seed development i.e., 10 days after anthesis (DAA), 20 DAA, 30 DAA and 40 DAA
BLASTX comparison with protein sequences of Arabidopsis, Oryza, Glycine, Lotus japonicus and Medicago downloaded from Phytozome v 9.1 showed that the chickpea seed transcriptome showed highest similarity with G. max (64.7%) and M. truncatula (60.6%) as compared to L. japonicus (59.8%), A. thaliana (57.6%) and O. sativa (53.7%)
Summary
Chickpea (Cicer arietinum L.) is one of the earliest annual pulse crops to be cultivated by man and consumed as a source of vegetable protein and the third most important food legume in the world. 0.33 million tons comprises the seeds (FAOSTAT, 20121, http://faostat3.fao.org/faostat-gateway/go/to/ download/Q/QC/E). Chickpea is a self-pollinating diploid (2n = 16) annual crop with a genome size of 738.09 Mbp (Varshney et al, 2013). The seeds are an important source of protein for millions of people in the developing countries. In addition to having high protein content (20–23%), chickpea seeds are rich in carbohydrates (41.1–47.42%), fiber (6% crude fiber), minerals (phosphorus, calcium, magnesium, iron and zinc) and β-carotene (Friedman, 1996; Abbo et al, 2005; Iqbal et al, 2006). Apart from all the obvious dietary attributes, improving the yield and quality of chickpeas is economically desirable keeping in mind the
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