Vol.:(0123456789)
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Plant Cell Reports (2018) 37:947–965
https://doi.org/10.1007/s00299-018-2305-6
REVIEW
Current advances in chickpea genomics: applications and future
perspectives
Uday Chand Jha
1
Received: 22 March 2018 / Accepted: 23 May 2018 / Published online: 2 June 2018
© Springer-Verlag GmbH Germany, part of Springer Nature 2018
Abstract
Chickpea genomics promises to illuminate our understanding of genome organization, structural variations, evolutionary
and domestication-related insights and fundamental biology of legume crops. Unprecedented advancements of next genera-
tion sequencing (NGS) technologies have enabled in decoding of multiple chickpea genome sequences and generating huge
genomic resources in chickpea both at functional and structural level. This review is aimed to update the current progress
of chickpea genomics ranging from high density linkage map development, genome-wide association studies (GWAS),
functional genomics resources for various traits, emerging role of abiotic stress responsive coding and non-coding RNAs
after the completion of draft chickpea genome sequences. Additionally, the current efforts of whole genome re-sequencing
(WGRS) approach of global chickpea germplasm to capture the global genetic diversity existing in the historically released
varieties across the world and increasing the resolution of the previously identified candidate gene(s) of breeding importance
have been discussed. Thus, the outcomes of these genomics resources will assist in genomics-assisted selection and facilitate
breeding of climate-resilient chickpea cultivars for sustainable agriculture.
Keywords Chickpea · NGS · Genomics · QTL · Molecular markers
Introduction
Chickpea remains the second most important grain legume
crop next to dry bean, grown worldwide (FAO 2015). Glob-
ally, chickpea is grown over 14.80 mha areas, contribut-
ing 14.24 million tons to the global food basket annually
(FAOSTAT 2014). As an important member of leguminosae
family, chickpea is capable of fixing atmospheric nitrogen
symbiotically, thus helps in improving soil fertility (Graham
and Vance 2003). Chickpea is prevalently grown in South
Asian countries and in the semi-arid regions across the globe
under rain-fed conditions (Gaur et al. 2012). It also serves as
a cheap source of plant-based dietary protein, micronutrients
and essential mineral elements (Jukanti et al. 2012), thus it
provides nutritional security to the under nourished human
population especially, in the developing countries across
the world. Given the series of ‘genetic bottleneck’ events
that occurred during domestication process caused nar-
rowing down of genetic base of cultivated chickpea (Abbo
et al. 2003a, b). To date efforts of conventional breeding
and intervention of molecular breeding approaches have ena-
bled in increasing chickpea yield from “0.60 t ha
−1
in 1960s
to 0.96 t ha
−1
in 2014” (FAOSTAT 2014; Roorkiwal et al.
2016). However, this progress is not satisfactory to support
the demand of raising global human population. Simultane-
ously, rising incidences of menacing diseases such as fusar-
ium wilt, aschochyta blight and dry root rot (Bohra et al.
2013) and increasing events of abiotic stresses including
drought, high temperature stress and salinity stress (Jha et al.
2014a, b, 2017) prevent it from achieving its potential yield
of 6 ton/ha under optimum conditions (FAOSTAT 2009).
Henceforth, to decipher the genetic basis of various agro-
nomic traits for yield improvement at molecular level, an
accurate genome assembly of chickpea is of utmost impor-
tance for both the basic and applied research. Advances in
NGS technologies have successfully allowed decoding of
chickpea draft genome sequences (Varshney et al. 2013a;
Jain et al. 2013). Afterwards, rapid progress in develop-
ment of ultra dense genetic map, large-scale generation of
Communicated by Neal Stewart.
* Uday Chand Jha
uday_gene@yahoo.co.in
1
ICAR-Indian Institute of Pulses Research (IIPR),
Kanpur 208024, India
@Phil_Robichaud
@deepthiw
@JoseServera