Transcriptome Analyses in Legumes: A Resource for Functional Genomics

Legumes represent an important family of flowering plants in terms of providing human nutrition and capacity to fix atmospheric N for agricultural sustainability. The recent availability of genome sequence of several legume plants has helped boosting genomics research. Study of the transcriptome at a global level can provide insights into the gene space, gene function, transcriptional programs, and molecular basis of various cellular processes in legumes, even in the absence of genome sequence. Transcriptome analysis has been realized as an essential step for basic and applied research in any organism. Considering the importance of transcriptome analyses, a few studies have been performed in legumes, such as soybean [Glycine max (L.) Merr.], Medicago truncatula Gaertn., Lotus corniculatus L. var. japonicus Regel [syn. Lotus japonicus (Regel) K. Larsen], and chickpea (Cicer arietinum L.), to uncover the overall and specific transcriptional activity of genes across various tissues and/or organs and developmental stages. Several candidate genes putatively involved in important agronomic traits, such as nodule, flower, and seed development, have been identified. The availability of these transcriptome data and future investigations will enable a variety of functional genomic studies to characterize these genes and define their function in legumes. Legumes (Leguminosae) are the third largest family of flowering plants. They are important to humans not only as food and fodder but also for oil, fiber, and green manure. Legumes are the important source of dietary proteins especially in developing countries, which complement cereals. Legumes also play an important role in sustainable agricultural practices, because of their ability to fix atmospheric N in symbiotic association with rhizobia. The legume family includes important food plants, such as common bean (Phaseolus vulgaris L.), soybean [Glycine max (L.) Merr.], pea (Pisum sativum L.), chickpea (Cicer arietinum L.), and pigeonpea [Cajanus cajan (L.) Huth], and important forage species, such as alfalfa (Medicago sativa L.) and clover (Trifolium L.). Despite their importance, crop improvement programs in legumes lagged behind those of cereals (Graham and Vance, 2003). One of the major reasons for this lag has been the nonavailability of enough genomic resources. However, with the recent availability of cost-effective and high-throughput technologies, the scenario has changed to much extent and legumes are also the focus of numerous genomics projects now (Cannon et al., 2009; Varshney et al., 2009). Currently, the genome sequence of five legume plants, including soybean, Lotus japonicus, Medicago truncatula, pigeonpea, and chickpea, are available (Sato et al., 2008; Schmutz et al., 2010; Young et al., 2011; Varshney et al., 2012, 2013; Jain et al., 2013). However, the next question that needs to be addressed is “how to make sense of the genome sequence data to translate it into meaningful information for crop improvement?” There is a great need to understand the relationship between genome sequence and molecular Published in The Plant Genome 6 doi: 10.3835/plantgenome2013.04.0011 © Crop Science Society of America 5585 Guilford Rd., Madison, WI 53711 USA An open-access publication All rights reserved. No part of this periodical may be reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopying, recording, or any information storage and retrieval system, without permission in writing from the publisher. Permission for printing and for reprinting the material contained herein has been obtained by the publisher. National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi110067, India. Received 26 Apr. 2013. *Corresponding author ([email protected]). Abbreviations: DAP, days after pollination; LjGEA, Lotus japonicus Gene Expression Atlas; MtGEA, Medicago truncatula Gene Expression Atlas; NGS, next generation sequencing; RNA-seq, ribonucleic acid sequencing. Published August 5, 2013