**3. Legume genomics**

**1. Introduction**

the reduced nitrogen (NH3

**2. Challenges in chickpea production**

the masses.

Chickpea (*Cicer arietinum* L.) is a diploid (2*n* = 16), self-pollinated plant which is grown in the cool season and has a genome size of 738 Mb [1]. It is the third most produced pulse crop in the world (13.73 million tons) after beans (26.52 million tons) and green pea (17.43 million tons) (FAOSTAT 2014). It is considered to be an ideal crop for the semiarid and arid regions as it exhibits an extensive tap root system. Chickpea seeds are an excellent source of nutrition as they contain ≈40% carbohydrates, ≈6% oil and 20–30% protein and good source of minerals and trace elements such as calcium, magnesium, phosphorus, iron and zinc [2]. Moreover, chickpea contributes to improvement of soil fertility since it has the capability to establish symbiotic association with *Mesorhizobium ciceri* that helps in fixing atmospheric nitrogen to

246 Applications of RNA-Seq and Omics Strategies - From Microorganisms to Human Health

up to 80% of its nitrogen requirement [3]. All these qualities make chickpea an economically important crop as it is an affordable source that can fulfil the dietary protein requirement of

The world average of chickpea productivity is 982.1 kg/ha (FAOSTAT 2014); however, a simulated study showed that potential productivity of chickpea in rain-fed situations ranged from 1390 to 4590 kg/ha [4]. There is a huge yield gap of 408–3608 kg/ha. A number of biotic and abiotic factors affect chickpea plant growth and, therefore, are responsible for poor productivity. Chickpea is mostly raised on conserved soil moisture under rain-fed conditions [5]. Therefore, drought stress generally affects the crop at terminal stage [6] and leads to productivity loss of up to 50% [7]. Drought reduces overall biomass, reproductive growth and seed yield and increases flower abortion, pod abscission and number of empty pods [8]. Soil salinity affects productivity by delaying the flowering leading to decrease in reproductive success of chickpea [9]. Since chickpea is a cool season crop, high temperatures adversely affect the development of the plant [10]. Chander [11] reported a decline in yield of chickpea by about 301 kg/ha per 1°C increase in mean seasonal temperature in India [12, 13]. Biotic factors also adversely affect the yield of chickpea crop. *Fusarium* wilt, caused by *Fusarium oxysporum* f.sp. *ciceri*; *Ascochyta* blight, caused by *Ascochyta rabiei* and *Botrytis* grey mould, caused by *Botrytis cinerea* mainly affect the leaves of chickpea, whereas *Pythium ultimum* causes root and seed rot and is common in the areas where the chickpea growing season is cool and humid [14, 15]. A number of other fungi, such as *Alternaria* sp., *Ascochyta pisi*, *Uromyces* sp., *Botrytis* sp., *Phytophthora medicaginis* and so on, cause considerable damage to chickpea crops. Pod borer (*Helicoverpa armigera* Hubner) is the major pest affecting chickpea worldwide [15–17]. Therefore, improvement in yield, nutritional quality and stress tolerance are the major targets of chickpea research and breeding programmes which may be facilitated by detailed understanding of biological processes occurring in tissue-specific and developmental pathways. Moreover, responses to

various stresses at molecular level also need to be elucidated in detail.

). Chickpea, through symbiotic nitrogen fixation (SNF), can fulfil

With the advent of next-generation sequencing technologies, there has been a rapid increase in the efficiency of DNA and RNA sequencing and decrease in the cost involved. *Leguminosae* is a very important family known due to the economic and nutritional value of its members [18]. The recent years have witnessed a spurt in the number of studies utilizing genomic approaches to understand the biology of several agronomic traits in legumes.

The advances in DNA sequencing have led to whole genome sequencing of important legumes such as *Glycine max* [19], *Medicago truncatula* [20], *Lotus japonicus* [21], *Cajanus cajan* [22], *Phaseolus vulgaris* [23], diploid ancestors of peanut *Arachis duranensis* and *Arachis ipaensis* [24] and *C. arietinum* [1, 25]. Moreover, whole genome resequencing has been carried out for soybean [26, 27], *Medicago* [28] and chickpea [1] in order to understand the genetic variability, evolution and domestication in greater depth. Simultaneously, in order to unravel the functional aspects of legume biology, several NGS-based studies of transcriptomes were carried out. These studies have made significant contributions towards understanding of gene expression, alternative splicing events and small RNA identification. Gene expression atlases have been developed for soybean [29, 30], *Medicago* [31], *L. japonicus* [32] and pigeon pea [33]. Moreover, in chickpea a number of transcriptome studies have been performed. These include exploring the overall transcriptome of various tissues [34–37], specifically understanding of the development of flower [38], seed [39] and root nodule [40]. Transcriptome analysis of chickpea under different abiotic and biotic stresses such as drought, desiccation, salinity, cold and *Fusarium* wilt has also been carried out [41–43].

Next-generation sequencing (NGS)-based plant genomics has also assisted in understanding of genetic variation within and between species mostly through identification of single-nucleotide polymorphisms (SNPs). In chickpea, a number of studies have been performed to identify SNPs and utilized for various applications such as construction of linkage maps, synteny analysis, anchoring of whole genome sequencing and quantitative trait loci (QTL) analysis [44–49]. A CicArVarDB has also been developed which includes SNP and InDel variations in chickpea [50].
