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31© Springer Nature Switzerland AG 2020
S. S. Gosal, S. H. Wani (eds.), Accelerated Plant Breeding, Volume 3,
https://doi.org/10.1007/978-3-030-47306-8_2
Chapter 2
Advances inChickpea Breeding
andGenomics forVarietal Development
andTrait Improvement inIndia
AshutoshKushwah, ShaylaBindra, InderjitSingh, G.P.Dixit,
PankajSharma, S.Srinivasan, P.M.Gaur, andSarvjeetSingh
2.1 Introduction
Chickpea (Cicer arietinum L.) is a temperate self-pollinated legume crop, origi-
nated from southeastern Turkey (Ladizinsky 1975). It is an annual species having
chromosome number 2n=2x=16 and haploid genome size of 738Mb (Varshney
etal. 2013a). India, Pakistan, Australia, Canada, Turkey and the USA are the major
chickpea-producing countries. India ranks rst in chickpea area as well as produc-
tion with 11.38 million tonnes produced from 10.56 million ha during 2017–2018
(Dixit 2018). The wild progenitor of chickpea is believed to be C. reticulatum L.,
while C. arietinum L. is the only cultivated species of genus Cicer. Broadly chick-
pea has been divided in two distinct types based on seed morphology,desi type with
small seed having brown coat seed colour and kabuli type with large seed having
cream or beige seed coat colour.
Chickpea grains are rich in proteins (20–22%), carbohydrates (∼40%), vitamins
and several minerals such as phosphorus, calcium, manganese, potassium, magnesium,
iron and zinc (Jukanti et al. 2013). It also contains signicant amount of essential
amino acids, viz., leucine, isoleucine, lysine, valine and phenylalanine. Consumption
of chickpea helps in reducing diabetes due to lower glycemic index. Chickpea seed oil
A. Kushwah · S. Bindra · I. Singh · P. Sharma · S. Singh (*)
Department of Plant Breeding and Genetics, Punjab Agricultural University,
Ludhiana, Punjab, India
e-mail: shaylabindra@pau.edu; inderjitpb@pau.edu; pankaj-pbg@pau.edu; sarvjeet62@pau.
edu
G. P. Dixit
ICAR-Indian Institute of Pulses Research, Kanpur, India
S. Srinivasan · P. M. Gaur
International Crops Research Institute for the Semi-Arid Tropics,
Patancheru, Telangana, India
e-mail: s.srinivasan@cgiar.org; p.gaur@cgiar.org
32
contains unsaturated fatty acids such as oleic acid and linoleic acid which are good for
the heart. It also contains various phytosterols such as tocopherols, β-sitosterol, sterols
and tocotrienols which exhibit anti-bacterial, anti- fungal, anti-tumoric and anti-inam-
matory properties. It also contains several bioactive compounds like isoavones, phy-
tates and phenolic compounds, which are associated with potential health benets and
helps in prevention of cardiovascular diseases, blood pressure, cancer and obesity.
Chickpea is consumed as dal prepared from split cotyledons and snacks prepared from
besan (chickpea our) in Indian subcontinent while as soups, stews and salads in
African regions. It is also consumed as roasted, salted, boiled, raw vegetable and fer-
mented forms. In addition to its nutritive benets in human diet, chickpea also xes
atmospheric nitrogen efciently and helps in improving soil health and fertility.
Molecular markers help in accelerating the process of trait improvement by
understanding the genetic basis of the traits (Varshney etal. 2007). Selection of traits
having low heritability which are highly inuenced by the environment can be easily
performed by molecular markers. The molecular markers are also helpful in the
transfer and pyramiding of multiple genes simultaneously, introgression of genes
from wild species into cultivated one with minimum linkage drag, description of any
germplasm, assessment of genetic relatedness amongst accessions and mapping of
several quantitative trait loci (QTLs) governing economically important traits. Thus,
the molecular tools help in speeding up the conventional breeding approaches ef-
ciently and offer the rapid and precise alternative for improvement of quantitative
traits like yield and resistance/tolerance to various biotic and abiotic stresses.
During the past 10years, large-scale genomic resources have been developed for
chickpea improvement. Molecular marker technologies have made it feasible to
locate genomic regions of various quantitative traits for use in marker-assisted selec-
tion (MAS). This further prompted to use molecular breeding approaches, namely,
marker-assisted backcrossing (MABC), marker-assisted recurrent selection (MARS),
advanced backcross quantitative trait loci (AB-QTL) analysis and genomics- assisted
breeding (GAB) in chickpea breeding programmes. Next- generation sequencing
technologies led to rapid development of molecular markers in chickpea on a large
scale. These advanced resources and technologies have been utilized for construction
of dense linkage maps and identication of several molecular markers associated
with agronomically important traits. The chapter describes progress in varietal devel-
opment, availability of genetic and genomic resources and their deployment for mul-
tiple trait breeding and genomics-assisted chickpea breeding.
2.2 Germplasm andGenetic Resources
Chickpea genetic resource comprises of 99,877 accessions including 1476 wild Cicer
accessions at global level. These accessions are safeguarded and maintained amongst
120 national and international gene banks located across 64 countries (Upadhyaya
etal. 2018). The National Bureau of Plant Genetic Resources, India, holds 14,704
chickpea accessions including cultivated and wild species. The International Crop
A. Kushwah et al.
33
Research Institute for the Semi-Arid Tropics (ICRISAT) holds largest chickpea germ-
plasm collection of 20,764 accessions representing 59 countries of origin.
The wild Cicer species consist of useful variation for many desired traits includ-
ing resistance/tolerance to various biotic and abiotic stresses (Croser etal. 2003;
Gaur etal. 2010; Kaur etal. 2013; Singh etal. 2013), productivity traits (Singh and
Ocampo 1997; Singh et al. 2005) and biochemical traits (Kaur et al. 2010).
Availability of passport information on agronomic and nutrition traits and resistance
to biotic and abiotic stresses have been the major challenge for utilization of germ-
plasm in breeding programmes for developing trait-specic genotypes. As many as
16,990 chickpea accessions were evaluated at ICRISAT for 13 traits to form a core
collection comprising 1956 accessions so as to promote signicance of global chick-
pea genetic resources in genomics and breeding (Upadhyaya etal. 2001). Further, a
mini-core collection of 211 chickpea accessions has also been developed (Upadhyaya
and Ortiz 2001). The ICRISAT and ICARDA with their joint efforts have developed
a reference set of 300 lines under the Generation Challenge Program (GCP) of the
Consortium of International Agricultural Research Centres depicting genetic vari-
ability available in the germplasms maintained at the aforementioned institutions
(Upadhyaya et al. 2008). These manageable numbers of accessions representing
mini-core, core and reference sets of germplasm contribute ideal resource for asso-
ciation genetics, gene mapping and cloning, allele mining and applied breeding for
the development of elite cultivars. Long history of breeding efforts made towards few
domesticated traits has inated the crop yields but narrowed the genetic base.
Conventional breeding approaches have made a signicant improvement in
chickpea and contributed towards bringing pulses self-sufciency in India. The
pedigree analysis tracing parents back to 120in desi and 53in kabuli of 138 variet-
ies (103 desi and 33 kabuli) developed through hybridization revealed that IP 58
(27), C 1234 (26), JG 62 (18), S 26 (18) and Chaffa (15) were the frequently utilized
parents in desi (Fig.2.1a) while Rabat (26), Pb 7 (24), Banda Local (14), Etah Bold
(14), Guamchil 2 (14), P 458 (14) and GW 5/6 (14) were involved in development
of kabuli varieties (Fig.2.1b). This clearly indicated that very few genotypes have
been used to develop chickpea varieties released in India as earlier reported by
Kumar etal. (2004). Thus, there is need to involve more and diverse germplasm,
primitive landraces and wild Cicer species in hybridization for cultivar development
(Verma et al. 1990; van Rheenen et al. 1993; Nadarajan and Chaturvedi 2010;
Mishra et al. 2013a, b; Singh et al. 2014). A large number of donors identied
through multi-location screening have been listed in Table2.1.
2.3 Varietal Development
A systematic breeding work on chickpea started in 1905 at Imperial Agricultural
Research Institute, Pusa (Bihar), and subsequently at other centres by mainly con-
centrating towards collection of landraces. In the initial phase of varietal develop-
ment in the 1970s, major emphasis was laid on increasing yield potential over
2 Advances in Chickpea Breeding and Genomics for Varietal Development and Trait…
34
landraces; hence most of the varieties were developed via selection and purication
of existing landraces. Varieties like Dahod yellow, Chaffa, Annegri-1, Ujjain 21, BR
78 and Gwalior 2 are selection from the local germplasm/landraces. During the
1980s, major emphasis was laid on breeding for disease resistance. Systematic
breeding programme led to the identication and development of disease-resistant/
disease-tolerant donors/varieties against major diseases particularity Fusarium wilt
and Ascochyta blight. As a result, varieties like KWR 108, H 82-2, GPF 2, Vijay, JG
11, Vishal, Gujarat Gram 1, Gujarat Gram 2, GNG 663, JG-16, KPG 59, Digvijay,
Rajas, BGM 547, BGD 128, GNG 1581 etc. were evolved exhibiting potential in
minimizing the wilt incidence. In the early 1980s, Ascochyta blight outbreak caused
substantial damage to chickpea crop in northern states like Punjab, Haryana, north-
west Rajasthan and Jammu region. Hence, the emphasis was laid to develop
Fig. 2.1 (a) Per cent utilization of major parents in development of desi chickpea varieties. (b) Per
cent utilization of major parents in development of kabuli chickpea varieties
A. Kushwah et al.
35
Table 2.1 Donors identied for major biotic and abiotic stresses
Trait Donors identied
Fusarium
wilt
AKG 1303, RLBG 2, WR315, Avrodhi, RLBG 3, BDNG 2017-1, RKG18-1,
NBeG 857, ICCV 171105, NBeG 798, PBC 546-18, JG 2017-50, RKG 13-515-1,
H 12-22, GL 14015, Bidhan Chola 1, GAG 1620, H 15-25, PG 221, JG 2018-53,
GNG 2418, BG 4007, RG 2016-133, GNG 2438, JG 2018-54, BDN 9-3, BCP 4,
GL 88341, GL 87079, Phule G 5, Phule G 81-1-1 (Vijay), Phule G 12, Phule
87,207, ICCV 10, ICCV 2, ICCC 37, ICCC 42, KPG 59, H 86-72, IPC 92-37, DCP
92-3, SAKI 8516 (JG 16), BGM 443, JCP 27, BDNG 88, GL 83119, GL 84038,
HC 1, GNG 663, KPG 259-4, GL 86123, KPG 143-1, H 86-18, GPF 2, JG 12, JG
24, HK05-169, JSC 40, JG 2000-04, GJG 0919, GJG 0904, GJG 0814, CSJK 54,
Phule G16111, GJG1603. NBeG 776, RKG 13-55, GNG 2325, PG 209, JG
74315-2, IPC 08-11, PG 211, JG 2017-50, Phule G 0819, JG 2017-49, GJG 0922,
GNG 2391, GL 13037, IPC 07-28, NBeG 779, H 12-63, SCGP-WR 28, BCP 60,
GJG 0814, IPCK 10-134, IPC 17-28, GJG 0921, GJG 1010, SCGP-WR 32, GJG
904, IPC 08-69, CSJK 96
Ascochyta
blight
DKG 964, PBG1, PBG 7, GNG 2207, GNG 2171, E 100Ym, E100Y, PG 82-1, EC
26446, BRG8, ICC7002, GL84038, GL 84099, GL 90169, GL 23094, GLK 24092,
GLK 24096, BG 276, H 82-5, H 86-18, H 75-35, Gaurav, GL 88016, ICC 1069,
BG 267, GNG 469, BG 362, GNG 1581, IPC 79, IPC 129, H03-45, ILC 3279
Botrytis
grey mould
IPC 15-95, IPC 15-202, IPC 15-183, IPC 15-48, IPC 15-113, IPC 16-48, GCP 101,
RVG 202, CSJ 556, GNG 1581, IPC 15-185, ICC 1069, IC 12483, Dhanush,
ICCW 92, ICCV 41, HK 94-134, CSJK 72, GL 10006, GLW 69, GLW 91
Dry root
rot
H14-14, RLBG 3, BDNG 2017-1, ICCV 171117, CSJ 902, BG4001, DBGC-2,
GJG 1607, NBeG 798, PBC 546-181, BG 3091, BG 372, IPC11-30, GJG 1603,
Phule G 15109, RKG 18-4, BDNG 21-1, RKGK 13-499, GNG 2453, MABT
66-266, IG 2018-110, NBeG 786, CSJ 867, IPC 2013-74, RKG 13-223, RKGK
13-223, RKGK 13-159, JH 13-09, BG 3062
Herbicide
tolerance
ICC 1205, ICC 1161, ICC 07110, ICC 1164, ICC 1381, GL 22044, GLK 10103,
NDG 11-24
Wilt + dry
root rot
ICC 8383, ICC 10466, ICC 12237, ICC 12269, GNG 2226, IPC 2007-28, IPC
2010-134, H 86-84, H 86-18
Wilt +
gram pod
borer
ICCL 86102, ICCL 86111, ICCX 730020
Wilt +
Ascochyta
blight
GL 83119, GL 84038, GL 84096, GL 84107, H 83-84, H 83-60, FLIP 82-78-C,
FLIP 83-7-C, FLIP 82-74-C, FLIP 84-43-C, FLIP 84-130-C, ILC 171, GL 91058,
GL 91060, GL 88341, FLIP 96-41, ICCV 89445, ICC 1272, ICC 3137, IC 4074,
IPC 97-1, DKG 964
Drought
tolerance
ICC 4958, ICC 8261
Heat
tolerance
ICCV92944 (JG 14), ICC 15614, JSC 55, JSC 56, ILWC 115, ILWC 21,
EC 556270
Cold
tolerance
GL 26018, GL 28202
Salinity
tolerance
CSG 8962, ICCV 10, JG 62
2 Advances in Chickpea Breeding and Genomics for Varietal Development and Trait…
36
Ascochyta blight-resistant varieties, thereby resulting in the release of landmark
varieties like PBG1, PBG 5, GNG 469, Gaurav, PBG 7 (Fig.2.2) and GNG 2171 for
cultivation in blight-prone areas.
Under All India Coordinated Pulses Improvement Project (AICPIP), the evalua-
tion of genotypes in two separate trials (kabuli and desi) started in 1981–1982. Later
in 1982–1983, desi chickpea trials were bifurcated in two categories– normal sown
and late sown. Subsequently, JG 74 was identied for central and northern India.
‘Bold Seeded’ trial was constituted in 1983–1984 to facilitate the release of high-
yielding and large-seeded desi chickpea varieties. A special trial to screen breeding
lines against Ascochyta blight started in 1982–1983. During the 1990s, major thrust
was given to breed for short-duration, multiple-resistance, drought-tolerant and
high-input responsive varieties. Breeding for short duration (90–110 days) was
directed in the environment where the growing season is short to escape from termi-
nal drought and heat for successfully raising a crop. Development of short-duration
varieties like JG 16, JG 11, Vijay, Vikas, Vishal, JGK 1, KAK 2, ICCV 2, ICCV 10,
etc. helped in expanding chickpea area in southern and central part of the country.
In spite of reduction in duration, the yield potential of these early varieties remained
almost similar to long-duration varieties. Similarly, in states like Uttar Pradesh,
Bihar, parts of Chhattisgarh, Jharkhand, Haryana and Punjab where rice elds are
vacated quite late after the harvest of rice, early-maturing varieties amenable to late
planting like Pusa 372, Udai, RSG 963, BGM 547 and Rajas were developed. In
1991–1992, two special trials for evaluation of genotypes under high input
Fig. 2.2 A high-yielding Ascochyta blight-resistant variety PBG 7
A. Kushwah et al.
37
conditions and for salinity tolerance were constituted. Later in 1995–1996, a trial to
evaluate breeding lines under drought was constituted.
In order to evolve large-seeded desi (>20g/100 seeds) and kabuli (>25g/100
seeds) varieties, coordinated trials were implemented since 1983–1984 and
1995–1996, respectively, and as a result, varieties like Pusa 256, JG 11, Samrat,
Phule G 5, Vishal and BGM 547 were developed in desi group. Similarly, kabuli
varieties such as BG 1003, BG 1053, Haryana Kabuli Chana 1, Haryana Kabuli
Chana 2, KAK 2, JGK 1, Vihar and Virat were developed after considering the con-
sumer’s preference for large-seeded kabuli types(Chaturvedi etal. 2010). A wilt-
resistant variety, DCP 92-3, was released for the areas where high soil moisture or
frequent winter rains or high fertility causes more vegetative growth and subse-
quently causes lodging of the crop. Later, varieties for specic conditions like CSG
8962 for mild salinity conditions of north west plain zone, JG 14 for heat tolerance
for central India and RSG 888 for cultivation in moisture stress or rainfed conditions
of Rajasthan, Haryana and Punjab were developed. In recent years, kabuli varieties
like HK 05-169, L 555 (GLK 26155), GNG 1969, and L 556 (GLK 28127) were
released for north Indian conditions. For north hill region, cold-tolerant kabuli vari-
eties like CSJK 6 and Phule G 0027 were released, whereas varieties like JSC 55
and JSC 56 were released for late sown conditions of central India. Now, emphasis
is being laid on development of extra-large-seeded kabuli chickpea varieties with
seed size more than 50g/100 seeds. Several promising entries are in advance vari-
etal trails, and few varieties like Phule G 0517, PKV 4–1 and MNK-1 have been
developed with seed size more than 50g/100 seeds which fetch premium price in
market. These varieties are being popularized amongst farmers through FLDs and
State Agricultural Department. The farmers of India are now gradually adopting
mechanization of farm operations for improving efciency and reducing cost of
cultivation. The farmers are demanding chickpea cultivars which can be directly
harvested by combine harvesters. Most of the present-day chickpea cultivars are not
well suited to machine harvesting because the plant height and plant architecture are
not suitable for mechanized harvesting. Development of chickpea cultivars with tall
(>55 cm.) and erect growth habit is required. In the recent years, few machine-
harvestable varieties such as NBeG 47, Phule Vikram, RVG 204 and BG 3062 have
been released in India for southern and central India. So far, more than 210 chickpea
varieties have been developed for cultivation in different parts of the country since
the inception of All India Coordinated Research Project on Chickpea (Singh
2014;Dixit 2015). The milestones in chickpea varietal development during the past
100years are given in Table2.2.
At present, the major emphasis of AICRP on chickpea is on collection, evalua-
tion, characterization, and utilization of germplasm for developing improved variet-
ies. Linkages are being established with national and international institutions to
make use of new knowledge in frontier areas like biotechnology, information tech-
nology, etc. There is a need to have dedicated research efforts on development of
cultivars responsive to irrigation and high fertility conditions for rehabilitating
chickpea in northern India. Drought tolerance would continue to be the most impor-
tant trait for two-third of the chickpea area that is rainfed. The programmes need to
2 Advances in Chickpea Breeding and Genomics for Varietal Development and Trait…
38
continue efforts on enhancing resistance/tolerance to abiotic and biotic stresses for
improving yield stability(Malhotra and Saxsena 1993). There is a need to enhance
precision and efciency of breeding programmes. This would include novel
approaches for enhancing genetic base of the breeding populations,
Table 2.2 Milestones in chickpea improvement research during the past 100years
Year Product developed
1926 Varieties developed through selection: NP 17, NP 25, NP 28 and NP 58
1940s Varieties developed through hybridization: C12/34 and type 87
1948 Variety with wide adaptability released: Chaffa
1960s First variety for south India released: Annegiri 1
1960 First wilt-resistant variety released: C 104
First widely adaptable variety for north India C 235 developed
1969 First release through All India Coordinated Pulse Improvement Project (AICPIP):
GNG 114
1970 Bold (large)-seeded variety for central India released: Radhey
1970 Spontaneous Mutant of RS 10 released as RS 11
1976 First kabuli variety released: L 144
1979 First green seeded variety developed: Hare Chhole
1982 First Ascochyta blight-resistant variety released: GL 769
1984 First variety developed through desi x kabuli introgression– Pusa 256
1985 Varieties released through mutation breeding: Pusa 408, Pusa 413, Pusa 417
1985 Russian tall donors used and tall variety developed: Pusa 261
1992 First variety released for late sown condition through AICRP– KPG 59 (Uday)
1993 First short-duration kabuli variety developed– ICCV 2 (Sweta)
1994 First drought-tolerant variety release for rainfed condition– Vijay
1998 For high input condition, rst lodging-resistant variety developed: DCP 92–3
1998 First salinity-tolerant variety released: CSG 8962
1999 First ofcially released Gulabi gram variety: JGG 1
1999 First variety developed through polygon breeding: JG 11
1999 First large-seeded kabuli variety released: KAK 2
2002 First drought-tolerant variety developed: RSG 888
2003 First large-seeded kabuli variety for south India: Vihar
2005 First variety through inter-specic hybridization: Pusa 1088
2008 Large-seeded kabuli variety (IPCK 2002–29) for central India developed
2009 Extra-large-seeded (>50g/100 seed wt.) kabuli varieties MNK 1, Phule G 0517,
IPCK02, PKV 4-1 developed
2011 Heat-tolerant variety JG 14 released
2017 Chickpea varieties amenable to machine harvesting developed for Andhra Pradesh
(NBeG 47), Karnataka (GBM 2) and Maharashtra (PhuleVikram)
2019 Chickpea varieties amenable to machine harvesting developed central India
(Phule G 08108, JG 20016-24, BG 3062)
2019 Release and notication of chickpea varieties evolved through marker-assisted selection
backcrossing (MABC) developed for drought tolerance (BGM 10216) and Fusarium
wilt resistance (MABC WR SA 1)
A. Kushwah et al.
39
genomics- assisted breeding, precision phenotyping, rapid generation turnover and
efcient breeding data management system. Efforts are being made to introgress
desirable traits from wild Cicer species at different institutes. In this endeavour,
PAU, Ludhiana, successfully crossed an elite cultivar GPF 2 with C. judaicum acc.
185 to introgress resistance against Botrytis grey mould. A high-yielding inter-spe-
cic derivative line, GL 13042 (Fig.2.3), possessing moderate level of resistance to
Botrytis grey mould has been identied for released in Punjab state. It will be the
rst variety developed from inter-specic cross with C. judaicum.
2.4 Major Constraints
Chickpea is prone to a large number of biotic (diseases, insect pests, nematodes,
weeds) and abiotic (drought, heat, cold, salinity, alkalinity, etc.) stresses. Abrupt rise
or drop in temperature, terminal soil moisture stress or excess rains during crop
growth result in low productivity. These biotic and abiotic constraints limiting
chickpea yields in different states are listed in Table2.3.
Fig. 2.3 GL 13042– a high-yielding variety having moderate level of resistance to Botrytis grey
mould derived from an inter-specic cross (GPF 2 x Cicer judaicum acc. 185)
2 Advances in Chickpea Breeding and Genomics for Varietal Development and Trait…
40
2.4.1 Biotic Stresses
2.4.1.1 Fusarium Wilt
In 32 countries across 6 continents in the world, chickpea wilt (Nene etal. 1991; Singh
and Sharma 2002) was reported as a major problem causing losses varying from 10 to
90% (Jimenez-Diaz etal. 1989; Singh and Reddy 1991). Chickpea genotypes vary in
the progress of initial symptoms of wilt, indicating different degrees of resistance con-
trolled by a few major genes. Such individual genes that are part of oligogenic resis-
tance mechanism delay the onset of disease symptoms leading to late wilting.
Resistance has been reported against Fusarium wilt in the indigenous chickpea germ-
plasm (Singh etal. 2012). Reliable and efcient screening methods have been estab-
lished for evaluating a large number of genotypes under eld conditions at several
AICRP centres.
2.4.1.2 Ascochyta Blight
It is the most important foliar disease of chickpea in many parts of the world includ-
ing India. It is caused by Ascochyta rabiei resulting in yield losses ranging from
10% to 100% (Nene and Reddy 1987; Singh 1990). Ascochyta rabiei isolates have
been classied into either a two- or three-pathotype system (I, II and III) according
to their levels of virulence (Udupa etal. 1998; Chen etal. 2004; Jayakumar et al.
2005). Under new breeding approach, plant breeders have shifted to gene pyramid-
ing in elite lines instead of incorporating vertical resistance. An alternative strategy
to deploy different lines possessing resistance against different races of the
Table 2.3 Biotic and abiotic stresses to chickpea production in different states of India
States/area Biotic stresses Abiotic stresses
Jammu and Kashmir, Himachal
Pradesh, Uttarakhand
Ascochyta blight,
Fusarium wilt, dry root
rot
Drought, cold, fog, frost
Punjab, Haryana, Himachal
Pradesh, Jammu and Kashmir,
Uttaranchal, North Rajasthan and
western Uttar Pradesh
Fusarium wilt, dry and
wet root rot, Ascochyta
blight, Botrytis grey
mould, stem rot
Drought, heat, cold, fog/frost,
salinity, excess vegetative growth,
poor partitioning of
photosynthates
Eastern Uttar Pradesh, Bihar,
Jharkhand, West Bengal, Assam
Fusarium wilt, dry and
wet root rot, collar rot,
Botrytis grey mould
Drought, temperature extremities,
fog, salinity
Gujarat, Maharashtra, Madhya
Pradesh, Chhattisgarh, part of
Rajasthan
Fusarium wilt, dry root
rot, collar rot, stunt
Drought, heat, salinity, frost in
parts of Madhya Pradesh, less
biomass accumulation (short
growing period)
Andhra Pradesh, Karnataka,
Tamil Nadu
Fusarium wilt, dry root
rot, collar rot, stunt
Drought, heat, less biomass
accumulation (short growing
period)
A. Kushwah et al.
41
pathogen prevalent in different regions can also be effective in order to minimize
yield losses caused by Ascochyta blight.
2.4.1.3 Botrytis Grey Mould
It is the second major foliar disease of chickpea prevalent in 15 countries including
India, Bangladesh, Nepal, Pakistan, Australia, Argentina, Myanmar, Canada,
Columbia, Hungary, Mexico, Spain, Turkey, the USA and Vietnam. Earlier there
was no reliable source known for resistance to BGM in India (Singh and Reddy
1991), but derivative lines from the inter-specic crosses of C. arietinum and C. pin-
natidum, developed at PAU, Ludhiana, exhibited moderate to high level of genetic
resistance against BGM (Kaur etal. 2013) and can be incorporated into elite lines
to develop high-yielding chickpea cultivars with durable resistance.
2.4.1.4 Pod Borer
Pod borer (Helicoverpa armigera) is the major insect pest infesting chickpea crop,
predominantly causing damages across Asia, Africa, Australia and some other
chickpea-growing regions. Being a polyphagous insect, pod borer is known to cause
damage to more than 182 plant species. The development of cultivars resistant or
tolerant to H. armigera could be integrated in the pest management strategy particu-
larly in the developing countries (Fitt 1989; Sharma and Ortiz 2002). More than
14,000 chickpea germplasm accessions screened under eld conditions at ICRISAT
for resistance towards H. armigera (Lateef and Sachan 1990) led to the identica-
tion and release of moderately resistant/tolerant chickpea cultivars (Gowda etal.
1983; Lateef 1985; Lateef and Pimbert 1990). Still complete resistance against pod
borer is far from reach, as different chickpea cultivars express differential inhibition
activity of gut proteinases of H. armigera, indicating that H. armigera is adapted to
a wide range of host protein inhibitors (Singh etal. 2008).
2.4.1.5 Bruchids
Signicant level of storage losses occurs in the Mediterranean region and in India
by storage pest bruchids (Callosobruchus chinensis) where infestation levels
approach 13% (Mookherjee etal. 1970; Dias and Yadav 1988) to total loss (Weigand
and Tahhan 1990). Till date there is no report of resistance in the cultivated chick-
pea, though wild chickpea accessions have shown some resistance to bruchids
(Singh et al. 1994, 1998). Owing to crossing barrier, it has not been possible to
transfer this trait to the cultivated background. Thus, it is advised to go for chemical
control measures (Duke 1981). Recent studies in legume crops indicated that seed
storage in three-layered polythene bag resulted in effective control of bruchids and
their further spread (Vales etal. 2014; Sudini etal. 2015).
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2.4.1.6 Weeds
In addition to other biotic factors, seasonal weeds associated with chickpea crop
such as Phalaris minor (L.Retz), Avena fatua, Lolium temulentun (L), Trifolium
spp., Chenopodium album (L), Melilotus spp., Lathyrus tuberosus (L), Convolvulus
arvensis (L), Anagallis arvensis (L), Asphodelus tenuifolius (cavan), Medicago den-
ticulata (L. wild), Rumex dentatus (L), Fumaria parviora (Lamk), Cirsium arvense
(L.Scop), Cyperus rotundus (L), Cynodon dactylon (L. Pe rs ) etc. are posing serious
threat to chickpea productivity. It is specically observed to be major problem of
concern during winter rains when the weeds become major yield-limiting factor.
Farm labour days are becoming expensive gradually; thus there is a need of
herbicide- tolerant varieties (Sandhu et al. 2010; Gaur et al. 2012a). Systematic
screening of reference set and elite breeding lines exhibited large genetic variations
against post-emergence herbicide (imazethapyr) tolerance in chickpea (Gaur etal.
2013a; Chaturvedi et al. 2014a; Gupta etal. 2018). These have paved a way to
develop post-emergence herbicide-tolerant varieties of chickpea.
2.4.2 Abiotic Stresses
2.4.2.1 Drought
Drought is the most important abiotic stress globally, contributing immensely to the
yield losses in chickpea. Generally, it is terminal drought that has an adverse effect on
the crop productivity (Khanna-Chopra and Sinha 1987). In order to counter drought
stress, cultivation of early maturing cultivars for areas frequently affected by drought
was found promising, as it would help in judicious utilization of the available soil mois-
ture efciently, thereby leading to relatively higher yields. In addition, root traits have
gained more importance in recent years as genotypes with longer root systems have
revealed better drought tolerance by extracting moisture from deeper soil regimes.
Apart from this, wild Cicer species have been screened, and a few accessions of C. pin-
natidum and C. reticulatum were found to be resistant against drought (Toker et al.
2007). In the case of cultivated chickpea, ICC 4958 has been used extensively as a
potential donor for drought tolerance. Chickpea introgression lines with improved
drought tolerance (ICC 4958, used as donor) were found promising in India and Kenya
(Gaur etal. 2012a). However, the introgression lines with improved root traits showed
high G x E interactionwhen tested at several locations in central and southern India.
2.4.2.2 Heat Stress
Chickpea is adapted to cool climatic conditions. In the scenario of climate change
and changing cropping pattern, the crop is being exposed to high temperature
(>35°C) during the reproductive phase, causing severe yield penalty. Reproductive
A. Kushwah et al.
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period was found to be sensitive to heat stress conditions; if temperature rises above
the threshold level, it would affect the pod formation and seed set causing reduced
grain yield (Summereld etal. 1984; Wery etal. 1993;Wang etal. 2006; Basu etal.
2009; Kumar etal. 2013). Moreover, high temperature has been observed to cause
adverse effects on seed germination, respiration, membrane stability, photosynthesis,
hormone level, nutrient absorption, protoplasmic movement, quality of seeds, fruit
maturation, fertilization, materials transport, withering, burning of lower leaves, des-
iccation of poorly developed plants, stunting ower and pod abortion, reduced root
nodulation, nitrogen xation and seed yield (Chen etal. 1982; Saxena et al. 1988;
Kurdali 1996; Wahid and Close 2007). Although chickpea is more tolerant to heat
stress compared to other cool season legume crops (Summereld etal. 1984; Erskine
etal. 1994; McDonald and Paulsen 1997; Patrick and Stoddard 2010), acute heat
stress could lead to high-yield losses and crop failure (Devasirvatham etal. 2012).
Large genetic variations have been observed for heat tolerance in chickpea as
revealed in multi-location screening of reference set against heat stress in India
(Krishnamurthy etal. 2010). A eld screening technique for heat tolerance has been
standardized, and several sources of heat tolerance were identied (Gaur etal. 2014).
A heat-tolerant variety JG 14 was released in India and found promising under both
normal and late planting conditions in central, southern and eastern states.
2.4.2.3 Cold Stress
Typically chickpea grown during winter season is more productive than the tradi-
tionally grown spring season in the Mediterranean region (Singh and Hawtin 1979).
This is particularly due to long growing season and better moisture availability. But
winter season crop experiences problems such as ower drop and pod abortion lead-
ing to major yield loss as soon as mean day temperature falls below 15°C (Savithri
etal. 1980; Srinivasan etal. 1999; Clarke and Siddique 2004; Nayyar etal. 2005).
Studies in Australia have highlighted the complete lack of cold/chilling tolerance in
the domesticated gene pool and demonstrated greater tolerance potential in the
annual wild relatives (Berger and Turner 2007; Berger etal. 2012). Preliminary
studies in Australia demonstrating that the wild relatives that readily cross with
chickpea (C. reticulatum, C. echinospermum) appear to have considerably more
vegetative cold and reproductive chilling tolerance than domestic chickpea. More
efforts are needed for identifying novel sources of cold tolerance and to develop the
breeding population for identifying cold-tolerant genotypes.
2.5 Genomic andTranscriptomic Resources
Genomic studies aim towards the direction of gene/QTL mapping and identication of
metabolic pathways affecting chickpea productivity which accelerates the genetic
advance under selection and enhanced genetic gain. Thus, several international
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platforms have been initiated for developing and further exploiting the chickpea
genomic resources in genomics-assisted breeding. Initially isozymes as biochemical
markers have been utilized in chickpea. Isozymes catalysed the same chemical reaction
but differ in their electrophoretic mobility. Segregation pattern of isozyme markers was
reported in the F2 generation developed from inter-specic crosses of Cicer arietinum
with C. reticulatum and C. echinospermum (Gaur and Slinkard 1990a; b). Based on the
isozyme proling of annual and perennial chickpea accessions, the Cicer species were
classied into four categories (Kazan and Muehlbauer 1991) and were conrmed in
some later studies (Ahmad etal. 1992; Labdi etal. 1996; Tayyar and Waines 1996).
After the development of molecular markers, RFLP markers have been exten-
sively exploited in kabuli and desi type of chickpea for diversity analysis (Udupa
etal. 1993), for identication of centre of genetic diversity (Serret etal. 1997) and
for construction of linkage map (Simon and Muehlbauer 1997). The RAPD markers
have also been employed for polymorphism assessment (Banerjee etal. 1999), trait
mapping (Tullu etal. 1998) and genetic diversity analysis and to identify the phylo-
genetic relationship amongst accessions (Sant etal. 1999; Iruela etal. 2002; Singh
et al. 2003). With the discovery of AFLP markers, they have also been used in
genetic diversity analysis, to nd out the phylogenetic relationship of germplasm
lines (Nguyen etal. 2004; Shan etal. 2005; Talebi etal. 2008) and linkage map
construction (Winter etal. 2000). Microsatellite markers are the highly efcient
markers in chickpea which were developed from sequencing of probe genomic
libraries (Winter etal. 1999; Hüttel et al. 1999), microsatellite-enriched libraries
and bacterial articial chromosome (BAC) clones (Nayak etal. 2010; Thudi etal.
2011). These microsatellite markers have also been utilized in construction of link-
age maps and gene/QTL mapping. DArT (Diversity Arrays Technology) markers
are also used in chickpea excessively for diversity analysis and constructing linkage
maps. ICRISAT has developed the DArT arrays in chickpea with 15,360 clones in
association with DArT Pty Ltd. (Thudi etal. 2011). Similar trend of narrow genetic
diversity has been observed using DArT markers in gene pool of cultivated Cicer
species than in wild Cicer species (Roorkiwal etal. 2014b).
Single-nucleotide polymorphism (SNP) markers are the highly efcient molecu-
lar markers which are profoundly used in chickpea. Facilities for analysis of genetic
diversity, ne mapping of genes, genome-wide association studies, genomic selec-
tion and evolutionary studies are being provided by SNP genotyping platforms.
Ample amount of sequencing data has been generated with the advancement of
next-generation sequencing (NGS) technologies. By using Sanger sequencing tech-
nology, over 20,000 expressed sequence tags (ESTs) have been developed from
drought and salinity stress-challenged tissues at specic stage in chickpea (Varshney
etal. 2009b). Further, extra sequencing data from more than 20 tissues representing
different varietal developmental stages were generated (Hiremath etal. 2011). By
analysing the pooled sequencing data with the help of NGS transcripts and Sanger
ESTs, rst transcript assembly has been generated with 103,215 tentative unique
sequences (TUSs), which further employed for identication of thousands of SNPs.
Several thousand of SNPs were also identied through several sequencing plat-
forms like Illumina sequencing platform (Varshney et al. 2013b), allele-specic
A. Kushwah et al.
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sequencing technique (Gujaria etal. 2011; Roorkiwal etal. 2014a) and 454 tran-
scriptome sequencing platform (Deokar etal. 2014). A high-resolution linkage map
of genomic and transcriptomic SNPs has been constructed containing 6698 SNPs
which were mapped on 8 linkage groups having size of 1083.93cM from an inter-
specic RIL mapping population (Gaur etal. 2015). A high-throughput SNP geno-
typing platform (Axiom Cicer SNP Array) has been developed and used for
constructing high-density linkage maps by using two RIL mapping populations
(Roorkiwal etal. 2017). A total of 13,679 SNPs spanning 1033.67 cM and 7769
SNPs spanning 1076.35cM have been used for constructing linkage map.
Sequence-based trait mapping has been successfully enabled due to advancement
of NGS technologies as it is time- and cost-effective. Several techniques such as skim
sequencing, genotyping by sequencing (GBS) and whole genome re- sequencing pro-
vide large-scale marker data useful for high-resolution sequence- based trait mapping
(Pandey et al. 2016). GBS approach has been employed for renement of QTL-
hotspot (Jaganathan etal. 2015) identied from an intra-specic RIL mapping popu-
lation developed from the cross between ICC 4958 and ICC 1882, whereas skim
sequencing approach has identied 84,963 SNPs by employing the same parental
cross, out of which 76.01% were distributed over eight pseudo- molecules (Kale etal.
2015). Through integrated reference genome-based GBS approach, >40,000 genome-
wide SNPs (Kujur etal. 2015) and through de novo- based GBS approach >80,000
genome-wide SNPs have been identied (Bajaj etal. 2015) using 93 wild and culti-
vated chickpea accessions. These SNP markers are being used in genomics-assisted
breeding programmes at large scale. Various SNP genotyping platforms such as
KASP markers (Hiremath etal. 2012) and VeraCode and GoldenGate (Roorkiwal
etal. 2013) were generated for exploiting the genome- wide large-scale SNP marker
information in chickpea improvement breeding programmes.
The gene/QTLs can also be identied through transcriptomics approach.
Transcriptome proling of various biotic and abiotic stresses challenged specic
plant tissues, and expressed sequence tags (ESTs) have played an instrumental role
for development of functional markers which can be further utilized in chickpea
improvement breeding programmes. Several functional markers have been devel-
oped from ESTs for various biotic and abiotic stresses in chickpea (Buhariwalla
etal. 2005). A total of 177 new EST-SSRs functional markers have been developed
from salinity and drought stress-responsive ESTs (Varshney et al. 2009b).
Development of NGS technologies has played a major role in large-scale transcrip-
tome and genome sequencing. Transcriptome sequencing has led to ample amount
of information about the gene candidate in chickpea. A transcriptome assembly has
been constructed by using a number of 103,215 tentative unique sequences (TUSs)
based on several FLX/454 reads and Sanger ESTs (Hiremath etal. 2011). An array
of 34,760 contigs of transcriptome sequence representing ~35.5 Mb through
Illumina and FLX/454 sequencing and 53,409 contigs of transcriptome sequence
which represents ~28Mb through Illumina sequencing were assembled (Garg etal.
2011a, b). A hybrid assembly has also been constructed using 46,369 contigs of
transcriptome sequence from different developmental stages of plant tissues exposed
to various stresses (Kudapa etal. 2014).
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2.6 Linkage Maps, Physical Maps andFunctional Maps
In the process of various genomics-assisted breeding approaches, discovery of
the specic markers tightly linked with gene/QTL of interest appears as the
initial step(Kumar and van Rheenen 2000). Before the identication of tightly
linked markers, constructions of linkage/genetic maps are prerequisite which
allowed the gene mapping and gene tagging in molecular breeding as well as
characterization of the specic genomic regions and deciphering the gene action
involved in phenotypic expression of these traits of interest (Tanksley 1993).
The closely linked markers thus obtained would serve as nal genomic sequence
for positional cloning of the respective trait of interest(Varshney etal. 2009a).
Construction of linkage maps in chickpea signicantly developed from morpho-
logical markers to sequence-based markers like SNPs, InDels and DArT
(Roorkiwal et al. 2018; Kushwah etal. 2020). Adopting the next-generation
sequencing platforms enabled the large-scale genome- wide SNP discovery
which leads to construction of high-resolution saturated linkage maps in chick-
pea (Deokar etal. 2014; Jaganathan etal. 2015; Kujur etal. 2015) which facili-
tates ne mapping of genes/QTLs as well as positional cloning of these genes/
QTLs to know the underlying candidate genes involved in phenotypic expres-
sion of the trait of interest.
Utilization of large-scale transcriptomic resources as EST-SSRs and EST-
SNPs helps to construct transcript maps in chickpea. These transcript maps
have immense target-specific gene/QTL mapping, positional cloning and iden-
tifying the candidate genes responsible for economically important traits in
chickpea. First large-scale transcript map employing EST-SSRs, EST-SNPs
and intron spanning region has been developed in an inter-specific mapping
population of chickpea spanning about 767cM of the total genome size with
inter-marker distance of 2.5cM (Gujaria etal. 2011). Another transcript map
has been constructed with a different set of EST- derived genic molecular mark-
ers spanning 1498cM of the total genome size having inter-marker distance of
3.7 cM by using the same inter-specific mapping population of chickpea
(Choudhary etal. 2012). Further, by using TOGs (tentative orthologous genes)-
SNPs, a highly saturated large-scale transcript map was constructed spanning
about 788.6cM of the total genome size (Hiremath etal. 2012). Now, this high-
resolution inter-specific transcript map was exploited to develop the first draft
version of whole genome sequences of chickpea variety CDC Frontier
(Varshney etal. 2013a). Further improvement has been done for construction
of highly saturated inter-specific genetic/linkage map spanning map length of
949cM of the total genome size using SSRs and SNPs markers developed from
various transcription factors of specific candidate genes (Saxena etal. 2014).
Now, these SSRs and SNPs markers derived from transcription factors of spe-
cific candidate genes responsible for phenotypic expression of targeted traits
can play an instrumental role in genomics-assisted chickpea improvement
breeding programmes.
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2.7 Trait Mapping forVarious Biotic andAbiotic Stress
Tolerance andYield-Related Traits
The exploitation of DNA-based genetic markers including sequence-based molecu-
lar markers tightly linked to trait of interest helps to dene the genotypic constitu-
tion of crop plants as well as to overcome the confounding effects of genotype x
environment interactions, problems of stage dependency and several operational
difculties. Mapping of several economically important traits responsible for vari-
ous abiotic and biotic stress tolerance and yield improvement traits paves the way
for efcient exploitation of molecular breeding in chickpea. Application of these
molecular markers tightly linked to complex traits has been successfully applied in
various genomics-assisted breeding approaches. Recently, genome-wide associa-
tion study (GWAS) approach is being signicantly utilized for identication of sev-
eral sequence-based molecular markers related to yield and yield-related traits
against various abiotic and biotic stress conditions.
A genomic region on LG4 has been identied as QTL-hotspot for several major
QTLs responsible for drought stress tolerance which explains up to 58% of pheno-
typic expression for various root-related traits under rainfed conditions, and the
estimated size of this QTL-hotspot was 29 cM on the linkage/genetic map and
7.74Mb on the physical map of chickpea genome (Varshney etal. 2014a). Now, this
QTL-hotspot genomic region was further rened by genotyping-by-sequencing
(GBS) approach to 14cM on genetic map from 29cM as well as ~4 Mb on the
physical map from 7.74Mb of chickpea genome and incorporated 49 new SNPs in
this genomic region (Jaganathan etal. 2015). Now this genomic region was again
rened by using a combination of GWAS-based gene enrichment analysis of skim
sequenced data approach and sliding window-based bin mapping approach, and this
QTL-hotspot was split into two sub-genomic regions, i.e., QTL-hotspot-a of size of
139.22Kb and QTL-hotspot-b of size of 153.36 Kb (Kale etal. 2015).
A comprehensive GWAS approach using whole genome sequencing and candi-
date gene-based approach has been exploited for discovery of 312 molecular mark-
ers responsible for drought and heat stress tolerance-related traits in chickpea (Thudi
etal. 2014). Likewise, a total of 25 putative candidate genes harbouring two genomic
regions having four QTLs were identied on LG5 and LG6 which were responsible
for heat tolerance-related traits in chickpea (Paul etal. 2018). Several major QTLs
responsible for salinity tolerance-related traits have also been identied in chickpea.
Several molecular markers closely associated for salinity tolerance- related traits
have been identied on LG1, LG2, LG3 and LG7 using RIL mapping population
developed from the cross between ICC6263 (salinity sensitive) and ICC1431 (salin-
ity tolerance) under salinity conditions (Samineni 2010). In another study, major
QTLs for yield and yield-related traits responsible for salinity tolerance were identi-
ed on LG3 and LG6 by using RIL mapping population derived from a cross
between ICCV2 (salinity sensitive) and JG62 (salinity tolerant) under salinity con-
ditions (Vadez etal. 2012). Further, a total of 46 major QTLs including 19 QTLs for
several phonological traits and 27 QTLs for yield and yield-related traits
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responsible for salinity stress tolerance have been identied using a RIL mapping
population developed from the cross between ICCV 2 (salinity sensitive) and JG 11
(salinity tolerant) which was clustered on LG5, LG7 and LG8 (Pushpavalli
etal. 2015).
Major QTLs responsible for Ascochyta blight (AB) resistance were found to be
located on LG2, LG3, LG4 and LG8 on the chickpea linkage map and validated the
min different genetic backgrounds of chickpea by utilizing different mapping popu-
lations (Kottapalli etal. 2009;Millán etal. 2013). Another major QTL for Ascochyta
blight resistance has been mapped which was located on LG6 on the chickpea
genetic map using the CDC Frontier as a source of AB resistance (Anbessa etal.
2009). In another study, one major QTL for seedling resistance and one minor QTL
for adult plant resistance against Ascochyta blight were identied using RIL map-
ping population (Garg etal. 2018). Recently, Deokar etal. (2019) identied a total
of 11 major QTLs and 6 major QTLs responsible for AB resistance on LG1, LG2,
LG4, LG6 and LG7 using two different RIL mapping populations respectively
through NGS-based bulked segregant analysis (BSA) approach.
The rst gene mapped for Fusarium wilt resistance was H1 (foc 1) providing
resistance to race 1 which was tagged by the RAPD markers (Mayer etal. 1997).
Another group have also found other RAPD markers (UBC-170550, CS-27700)
closely linked with Fusarium wilt resistance gene to race 4 (Tullu etal. 1999). In
another study, ISSR markers (UBC-855500 and CS-27700) have been utilized for
tagging of Fusarium wilt resistance gene to race 4 (Ratnaparkhe etal. 1998). Several
SSR markers, like TR59 and OPJ20600 which were tightly linked to the Fusarium
wilt resistance gene foc 0 (Cobos etal. 2005), TA110 and H3A12 linked to Fusarium
wilt resistance gene foc 1, H3A12 and TA96 linked to Fusarium wilt resistance gene
foc 2 (Gowda etal. 2009), TA96 and TA194 linked to Fusarium wilt resistance gene
foc 3 (Sharma etal. 2004; Gowda etal. 2009), TA96 and CS27 linked to Fusarium
wilt resistance gene foc 4 (Winter etal. 2000; Sharma etal. 2004) and TA59 and
TA96 linked to Fusarium wilt resistance gene foc 5 (Sharma etal. 2005; Cobos
etal. 2009), have been successfully mapped which are responsible for providing
resistance against Fusarium race 0, 1, 2, 3, 4 and 5, respectively. Recently, a total of
ve major QTLs tightly linked to Fusarium wilt resistance gene were detected
which were located on LG2, LG4 and LG6 providing resistance against race 1 of
Fusarium wilt (Garg etal. 2018).
2.8 Genomics-Assisted Breeding (GAB)
forTrait Improvement
GAB involves the integration of genomic tools for enhancing selection efciency
and accuracy in the breeding process. Major strategies which come under the cate-
gory of GAB are genomics, proteomics and transcriptomics for discovery of tightly
linked molecular markers associated with economically important traits that help in
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49
prediction of phenotype from the genotype. Advancement of NGS technologies for
high-throughput genotyping has made possible to develop large-scale genome-wide
markers. Marker-assisted backcrossing (MABC) approach is helpful for requisite
gene pyramiding of several QTLs together in a specic genetic background and
generally used for signicant improvement of breeding traits governed by major
genes/QTLs. Although several economically important traits are polygenic in
nature, MABC has limited applications. Thus for improvement of polygenic char-
acters, marker-assisted recurrent selection (MARS) has been considered as a better
option. Genome-wide selection or genomic selection (GS) approach has emerged as
a powerful approach for selection of desirable progenies obtained from the favour-
able crosses (Jannink etal. 2010). Advanced backcross QTL (AB-QTL) approach
has been exploited for simultaneous identication as well as transfer of desirable
alleles from wild species or wild relatives into elite ones for the development of
improved lines as the wild species accumulates several superior alleles which are
responsible for tolerance to several biotic and abiotic stresses (Tanksley and Nelson
1996). AB-QTL approach has been efciently utilized for introgression of produc-
tivity enhancing traits and resistance traits to diseases from C. reticulatum in chick-
pea (Singh etal. 2005).
AB resistance in chickpea has recessive phenotype in terms of genetics which
shows complex inheritance pattern. MABC approach has been successfully
exploited for introgression QTLs responsible for double podding and QTLs respon-
sible for resistance to AB simultaneously in elite chickpea cultivars through con-
tinuous backcrossing of donors moderately resistant to AB and adapted cultivars
(Tar’an etal. 2013). A stepwise MABC approach has been exploited by Varshney
etal. (2014b) for the development of Fusarium wilt (FW) and AB-resistant lines by
incorporating two QTLs for AB and foc 1 locus for FW into an elite chickpea culti-
var, C 214. Three rounds of backcrosses and three rounds of selng (Varshney
etal.2014b) result into the development of three resistant lines for FW and seven
resistant lines for AB.This approach has also been utilized for introgression of
resistance against two races (foc 2 and foc 4) individually and gene pyramiding of
resistance to two races (foc 1 and foc 3) for FW and two different QTLs providing
resistance to AB in chickpea (Varshney et al. 2014b). Recently, ve germplasm
lines showing resistance against fw race foc 2 have been introgressed in the genetic
background of Pusa 256, an elite chickpea cultivar, using SSR markers (Pratap etal.
2017). Several efforts are in pipeline for introgression of resistance to FW and AB
in several highly promising cultivars in various research institutes like ICAR-Indian
Agricultural Research Institute (New Delhi), Punjab Agricultural University
(Ludhiana) and ICAR-Indian Institute of Pulse Research (Kanpur). Apart from this,
introgression of genomic regions has also been performed for yield. Similarly, for
enhancing drought tolerance in chickpea, QTLs/genomic regions on LG04 labelled
as QTL-hotspot (up to 58% phenotypic variability) for root-related traits were intro-
gressed into JG 11 (Varshney etal.2013b). A set of 20 BC3F4 lines was evaluated at
three locations in India, and several location-specic lines giving signicantly
higher yield than JG 11 were identied (Gaur etal. 2013b). The introgression lines
showed high level of GxE interaction when evaluated at different locations in India.
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Efciency of MARS depends on the total genetic gain achieved by selection
accuracy, marker-trait associations, selection efciency and distribution of desirable
alleles across the parents. In chickpea, MARS has been exploited for accumulation
of desirable set of alleles against drought stress by using crosses ICCV 04112×ICCV
93954 and ICCV 05107×ICCV 94954 (Samineni etal. 2017). The crosses JG 11 x
ICCV 04112 and JG 130 x ICCV 05107 were carried out in chickpea to combine the
desirable alleles for QTLs governing yield using the MARS approach. A total of
188 F3 plants each from two crosses were genotyped using SSR markers, and F3:5
progenies were evaluated at multi-locations. Few major and several minor QTLs
relating to yield and yield component traits have been identied. On the basis of
QTL information on several yield and yield-related parameters in different F5 prog-
enies, four lines from the cross JG 11 x ICCV 04112 and three lines from the cross
JG 130 x ICCV 05107 were selected having several combinations of favourable
alleles for recombination cycle. Now these shortlisted lines were subjected to fur-
ther two recombination cycles, and F1 plants having favourable alleles for yield and
yield-related traits were identied from both the crosses, and those having favour-
able alleles in homozygous condition were grown. Now these shortlisted homozy-
gous F1 plants were advanced to F4 generation for further evaluation. In this way,
numerous recombination cycles in MARS approach help in accumulation of the
frequency of favourable alleles related with economically important traits.
GS approach can be a deployable approach for chickpea yield improvement in
near future due to availability of precise phenotyping of several chickpea breeding
lines, presence of large linkage disequilibrium (LD) blocks in chickpea breeding
populations as well as the availability of large-scale genome-wide marker genotyp-
ing system like DArT and SNP markers. Moving in this direction, ICRISAT has
started efforts for exploitation of this approach in chickpea breeding programme by
using a set of 320 elite chickpea lines which were genotyped by DArT markers.
Precise phenotyping has been carried out at two locations, i.e., Patancheru and New
Delhi, for yield and yield-related traits. Six different statistical GS models have
been employed by utilizing phenotyping and genotyping data which provides prom-
ising results with higher prediction accuracies (up to 0.91) for yield and yield-
related traits (Roorkiwal etal. 2016). Based on the lessons learned from the study, a
new set of training populations is being developed separately for desi and kabuli
types for achieving higher prediction accuracy for yield and yield-related traits. The
selected training populations include promising breeding lines and well-
characterized germplasm lines that have been used in crossing programme in the
past 10 years for developing high-yielding chickpea varieties. Higher prediction
accuracies can be obtained through inclusion of G×E effects by GS approach con-
sidering multiple variables simultaneously in chickpea breeding programmes
(Roorkiwal et al. 2018). Pre-breeding programmes in GS models will be highly
favourable since that will help in screening the accessions for subsequent introgres-
sion (Crossa etal. 2017). Varshney etal. (2018) has been proposed a tentative out-
line of sequence-based breeding using GS approach. According to this, all possible
parental lines of a specic breeding programme have to be sequenced at higher
depth. These founder genotypes can be sequenced to develop GWAS approach or to
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51
develop HapMap that can be further used for selection of suitable parental combina-
tions having higher frequency of favourable alleles. By using higher number of
lines, large number of crosses has to be made followed by early generation selection
with existing ten SNP panels. Now GS approach can be performed on selected lines
from such crosses by using the training model developed from the germplasm set
representing the segregating populations. Best genotyping platform for GS approach
can x SNP array, although this may not be feasible for large-scale breeding pro-
grammes. Thus, segregating populations (F6/F7 generations) can be sequenced at
lower coverage using skim sequencing or 384-plex-based genotyping platform.
High-throughput genotyping data of parental lines and other available germplasm
lines can be used for developing practical haplotype graph (PHG) which will help
in identication of SNP markers. By using sequence-based approaches, these SNP
markers can be evaluated using rhAmp-SNP genotyping technology or DArT-seq
SNP genotyping technology. By this way, GS approach-based breeding programme
can be exploited using these segregating populations, and elite lines and lines hav-
ing higher genomic estimated breeding values (GEBVs) can be selected.
2.9 Rapid Generation Advancement/Speed Breeding
Global food security for ever-growing human population necessitates accelerated
breeding and research programmes so as to meet future food demands. Pace between
time required and development of improved varieties has to be optimum to meet
breeding challenges. Longer generation time required by crops slows down the pro-
gression towards fast-track research and development of improved varieties. Rapid
generation advancement (RGA) or speed breeding methods have been used in
chickpea for advancing three generations per year under eld and greenhouse con-
ditions (Gaur etal. 2007). In 2018, a group of researchers were able to reduce gen-
eration cycle to 5.6 per year in wheat, 5.3in barley, 3.7in canola and 4.5in chickpea
under specially modied glasshouses with sodium vapour lamps (Watson et al.
2018). These protocols involve a sequence of steps such as drying of seeds (5days
at 35 OC), imbibitions of seeds (1day) and chilling treatment (4 OC) to advance a
single generation in chickpea. Further in 2019, a new cost-effective and less cum-
bersome method of RGA/speed breeding has been proposed in chickpea by manipu-
lating photoperiod and temperature (Samineni etal. 2019). The study was conducted
over 2 years using six cultivated chickpea varieties belonging to early, medium and
late maturity groups. Results showed that the mean total number of generations
produced per year was, respectively, 7, 6.2, and 6 in early-, medium-, and late-
maturing genotypes (Samineni etal. 2019). Further,RGA will t well with the GS
model of breeding where no phenotyping is required to select candidate genotypes
in the early generation. Hence, RGA technology has huge scope to implement new
breeding tools to improve the efciency and accuracy of selection in developing
improved varieties.
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2.10 Future Research Priorities
Chickpea being a winter season (rabi) crop does not cope well to warm climate.
With increasing temperature and associated weather uctuations due to climate
change and shift in major chickpea cultivable area from cooler regions of north-
ern India to warmer region of central and southern India, imparting drought and
heat stress resistance in chickpea has become indispensable. Developing early
to extra- early varieties of chickpea with drought and heat tolerance is an impor-
tant objective of AICRP on chickpea. Genomic resources were found promising
for enhancing the efciency of selection in breeding programmes and identica-
tion of genomic regions for several complex traits. Utilizing the molecular
markers, researchers have developed wilt-resistant (Super Annegeri 1) and
drought-tolerant (Pusa 1088) chickpea varieties under ICAR-ICRISAT collabo-
ration. Currently, the crop improvement focuses on using integrated breeding
approaches for the accelerated development of improved breeding materials
with diverse desired traits such as high yield potential, improved resistance/
tolerance to biotic and abiotic stresses, resilience to climate change, labour sav-
ing, market-preferred grain traits and improved quality of produce; deployment
of genomic selection for accelerate genetic gains; bioinformatics; digital data
capture, data management and breeding management system for modernization
of breeding programmes(Chaturvedi et al. 2014b). The major focus areas are
presented below.
2.10.1 Germplasm Characterization
Evaluation of wild species had resulted in identication of genes for resistance to
several biotic stresses such as Botrytis grey mould (C. judaicum and C. pinnati-
dum), Ascochyta blight (C. bijugum, C. pinnatidum and C. yamashitae) and
Fusarium wilt (C. bijugum) (Infantino etal. 1996; Kaur etal. 2013). Two wild
species, C. reticulatum and C. echinospermum, are cross compatible with the
cultivated C. arietinum and are reported to be resistant to several pests (cyst
nematodes, leaf minor and bruchids) and diseases (Fusarium wilt, Ascochyta
blight and phytophthora) and tolerant to cold (Berger etal. 2012). The earlier
studies indicated that C. pinnatidum, a valuable source for several biotic and
abiotic stresses, can be crossed successfully with cultivated chickpea (Fig.2.4)
for the transfer of resistance to Botrytis grey mould and Ascochyta blight (Sandhu
etal. 2005; Kaur et al. 2013). The ICRISAT, Patancheru, has developed core/
mini-core sets of chickpea germplasm. In recent past, more than 14,000 acces-
sions of chickpea have been evaluated and characterized through ICAR-IIPR and
NBPGR collaboration at Mahatma Phule Krishi Vidyapeeth (MPKV), Rahuri, to
add value. Recently, three accessions (ILWC 115, ILWC 21 and EC 556270) of
C. reticulatum have been identied as heat tolerant and are being utilized in
A. Kushwah et al.
53
hybridization (IIPR Annual Report 2014–15). Currently, new diseases such as
dry root rot and collar rot became prominent in several chickpea- growing areas
where high level of resistance was not found in cultivated species. Efforts should
be made for screening of germplasm for these important diseases to develop
resistant varieties.
2.10.2 Trait Identication andGermplasm Enhancement
To reduce vulnerability against environmental uctuations and biotic stresses, there
is need to broaden the genetic base of future chickpea varieties through pre- breeding
efforts. A large number of diverse germplasm lines, primitive landraces and acces-
sions of wild Cicer species are available in gene banks at NBPGR, ICRISAT and
ICARDA which are being supplied from time to time to breeders for use in breeding
programmes.
Fig. 2.4 An inter-specic F1 hybrid between cultivated chickpea and wild Cicer pinnatidum with
prostrate growth habit
2 Advances in Chickpea Breeding and Genomics for Varietal Development and Trait…
54
2.10.3 Regaining Chickpea Area inNorthern India
Tailoring suitable plant types possessing lodging tolerance, Ascochyta blight and
pod borer resistance and response to high inputs are likely to enhance chickpea
yields in northern India. Further, combining tall and erect growth habit will help in
reducing humidity inside crop canopy facilitating better solar light interception. The
erectness of the varieties will make them suitable for mechanical harvesting.
2.10.4 Varieties forVegetable Purpose
Appropriate strategies are required to be adopted to develop high-yielding chickpea
(desi) varieties for green immature grain for vegetable purpose as it has high demand
in the market (Sandhu etal. 2007). This will also help in expanding chickpea culti-
vation in many parts of the country including Punjab, Haryana, western Uttar
Pradesh, Jharkhand, Odisha and parts of West Bengal ensuring supply of protein
through this nutritious pulse. More efforts are required to pyramid genes responsi-
ble for earliness in chickpea so that super early varieties can be developed (Gaur
etal. 2015). In addition of earliness, there is need to incorporate cold tolerance,
greenness in seeds at the time of physiological maturity, large/medium large seed
size and resistance to diseases in high-yielding background for mid-October sowing
so that green pods can be harvested by end of December. However, besides all men-
tioned traits, high temperature tolerance will be required for staggered sowing
(north India) or delayed sowing so that green grains can be supplied for longer dura-
tion as per demand. Development of super early maturing varieties will help in
minimizing losses due to gram pod borer and other stresses as well.
2.10.5 Kabuli Chickpea Varieties forExport
andDomestic Consumption
Extra-large-seeded (>50g 100-seed weight) kabuli genotypes with high resistance
to Fusarium wilt have been identied (Gaur etal. 2006), and several varieties (Phule
G 0517, MNK 1, JGK 5, PKV 4–1) have been developed for cultivation in central
and southern India. The systematic quality seed production of extra-large-seeded
varieties has provided much needed stability in productivity. There is a huge demand
for high-yielding extra-large kabuli varieties having semi-erect/erect growth habit
along with combined resistance to soil-borne diseases in central and southern India.
Similarly, for northern India, ample scope exists to regain area under chickpea
through development and popularization of extra-large seed varieties. Further,
large-seeded kabuli types fetch high premium to farmers in domestic and interna-
tional markets; therefore efforts should continue to improve large-seeded varieties
of kabuli chickpea.
A. Kushwah et al.
55
2.10.6 Machine-Harvestable Chickpea forReducing Cost
ofCultivation
Mechanization of farm operations is essential for improving efciency of agriculture
and reducing cost of cultivation. In many countries such as Australia, Canada, the
USA, Turkey, Syria, etc., chickpea harvesting is fully mechanized. In India, all pulse
crops are largely harvested by hand because the available cultivars are bushy types
which are difcult to harvest using machines. Manual harvesting has become an
expensive eld operation due to labour scarcity and increasing labour costs; hence
Indian farmers are increasingly demanding varieties suitable for machine harvesting.
Since chickpea is grown over ~10 million ha area, development of varieties amena-
ble to mechanical harvesting will attract farmers for chickpea cultivation as cost of
cultivation will also get reduced with the adoption of machine harvesting. The tradi-
tional cultivars are generally having semi-spreading growth habit, and pods at lower
nodes are close to the ground, thus not very much suitable for mechanical harvesting.
Chickpea varieties possessing tall (>55cm crop height) and erect/semi-erect growth
(>600 branch angle from soil surface) and at least with 25cm ground clearance (no
pods up to 25cm crop height) are needed for mechanical harvesting. Such tall and
erect varieties can very well be grown with higher population density in central and
southern India ensuring higher yields. In northern India, where fog and humidity are
major limiting factors to sunlight, tall and erect plant type will have more solar light
penetration which will help in minimizing humidity buildup in chickpea canopy
ensuring minimum damage due to foliar diseases. The release of cultivars suited to
mechanical harvesting will benet farmers by reducing cost of cultivation and
increasing net prot from cultivation of winter season pulse crops. Recently machine-
harvestable varieties (NBeG 47, GBM 2, RVG 204, Phule Vikram, BG 3062) of
chickpea have been released for cultivation in central and southern India.
2.10.7 Herbicide-Tolerant Varieties
Chickpea elds are infested by different types of seasonal weeds causing signicant
yield losses. At present there is no chickpea cultivar possessing tolerance to post-
emergence herbicides, and the manual weeding is a major weed control strategy
which is time-consuming and expensive. Multi-location testing of several germ-
plasm lines identied large genetic variations for post-emergence herbicide (ima-
zethapyr) tolerance in chickpea (Gaur etal. 2013a; Chaturvedi etal. 2014a). A good
number of chickpea genotypes were screened at PAU, Ludhiana, against two post-
emergence herbicides, imazethapyr and carfentrazone-ethyl, to identify tolerant
genotypes. A large genetic variation was observed for tolerance against both the
herbicides (Fig.2.5). In general, genotypes showed more sensitivity to carfentrazone-
ethyl at early growth stage, but at late growth stage, they showed more sensitivity to
imazethapyr. Three genotypes, viz., GLK 10103, NDG 11-24 and GL 22044, were
2 Advances in Chickpea Breeding and Genomics for Varietal Development and Trait…
56
found to be tolerant to both the herbicides, imazethapyr and carfentrazone-ethyl,
and can be used in the chickpea improvement programme (Gupta etal. 2018).
2.10.8 Varieties withBetter Nutrient Acquisition Efciency
Chickpea responds well to application of fertilizers though farmers seldom apply
nutrients. Phosphorus (P) is required for proper growth and development of plants,
and low phosphorus availability in soil affects nodulation adversely. It is also an
established fact that phosphoric fertilizers applied in previous crop get xed in soil
and can be made available to next crop, if varieties with better P acquisition and use
efciency are developed. Development of chickpea varieties having better P acquisi-
tion efciency and ability to grow well on P-decient soils will ensure stable yields.
Cultivation of P acquisition efcient (PAE) varieties in low-input production systems
will help in reducing cost of cultivation by bringing down requirement of ‘P’, thus
saving huge foreign currency as large amount of phosphoric fertilizers are imported
from elsewhere. At ICAR-IIPR, a large number of germplasm lines and elite breed-
ing lines were screened for PAE which revealed large genetic variations. There is
need to have systematic research for identication of gene(s) or QTLs responsible
for PAE and their subsequent transfer to develop better PAE chickpea varieties.
Fig. 2.5 Genetic variation for tolerance to post-emergence herbicide carfentrazone-ethyl in
chickpea
A. Kushwah et al.
57
2.10.9 Nutritionally Rich Varieties
Large variations have been observed in seed protein content of chickpea opening
doors to enhance protein content in future varieties, though trait is governed by
multiple genes. The adoption of high-protein chickpea varieties will ensure higher
order of availability of protein from per gram consumption of chickpea. Further,
there is need to develop chickpea varieties with higher β-carotene (precursor of
vitamin A) levels and micronutrient contents. Limited studies conducted so far on
assessing genetic variability for nutritional quality traits in chickpea germplasm
suggest large genetic variation for β-carotene (0.4–0.1μg per g seed weight), Fe
(35–150ppm) and Zn (25–50ppm). Thus, opportunities exist for developing variet-
ies with enhanced contents of β-carotene, iron and zinc. The only anti-nutritional
factor associated with chickpea is rafnose family of oligosaccharides (RFOs)
which are responsible for causing atulence on consumption. A recent study indi-
cates wide range of RFOs (1.58 to 5.83mmol/100g seed) in chickpea germplasm.
Thus, ample scope exists to develop chickpea varieties with higher contents of pro-
tein, β-carotene, iron and zinc and lower contents of RFOs.
In a preliminary study, 19 popular commercial cultivars of India were analysed
for their Fe and Zn contents in four locations representing different agro-climatic
zone of the country to study the genotypic (G) and genotype X environment (G X
E) interactions on these two mineral micronutrients. In addition, distribution of
phytic acid (PA), an important anti-nutrient that chelates and reduces the mineral
bioavailability, was also analysed. Inuence of other agronomic traits such as days
to owering (DF), plant height (PH) and 100 seed weight (SW) was also analysed
on Fe and Zn content. Fe and Zn content showed positive correlation indicating a
possibility of their co-selection in breeding. RSG44, JG315, Virat and Vihar had
higher Fe (>70ppm) and Zn (>40ppm) at all locations. Such genotypes will be use-
ful in breeding programmes for enhancing the mineral micronutrient content
(Personal Communication Archana Joshi).
2.10.10 Integrated Breeding
Isozyme markers were used in developing the rst linkage map of chickpea (Gaur
and Slinkard 1990b) and establishing phylogenetic relationships amongst annual
Cicer species (Kazan and Muehlbauer 1991; Ahmad etal. 1992). Recently, a large
number of genomic resources have been developed for deployment to improve tar-
geted traits. The year 2013 began by adding a milestone in chickpea genomics as the
draft genome sequence of chickpea genome was reported jointly by the scientists
working at ICRISAT and ICAR institutes (Varshney etal. 2013a). The information
revealed by the draft genome sequence will further boost efforts on development of
genomic resources and their applications in chickpea improvement. Integrated
breeding approaches utilizing conventional and genomics would improve precision
2 Advances in Chickpea Breeding and Genomics for Varietal Development and Trait…
58
and efciency of selection in breeding efforts for developing cultivars better adapted
to diverse growing environments (Gaur et al. 2012b; Varshney et al. 2013b).
Considering the importance of accelerated breeding, ICAR-IIPR has established
Regional Station Cum Off-season Nursery Centre at Dharwad (Karnataka) for rapid
generation turnover to reduce time required to attain homozygosity to develop map-
ping populations and pure line varieties.
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