Chickpea: Crop Wild Relatives for Enhancing Genetic Gains

By Mohar Singh

Chickpea: Crop Wild Relatives for Enhancing Genetic Gains explores aspects related to critical analysis on factors responsible for narrow genetic base of chickpea productions including domestication bottleneck, the level of diversity present in different cultivated and wild species, the uniqueness and usefulness of potential gene sources available and maintained in production systems across the globe, the level of genetic erosion both at landrace and species level over time and space etc. Despite considerable international investment in conventional breeding, production of chickpea has not yet been significantly improved beyond that achieved through its normal single domestication event and high self-pollination rate. Total annual pulse production of ~12 million tons (FAO 2016) is far below actual potential. Susceptibility to both biotic and abiotic stresses have created a production level bottleneck whose solution possibly lies in the use of crop wild relatives and other genetic traits cultivated by tailoring novel germplasm.

Presenting options for widening the genetic base of chickpea cultivars by introgression of diverse genes available in distantly related wild Cicer taxa, thus expanding the genetic base and maximize genetic gains from the selection, it is necessary to accumulate other complimentary alleles from CWRs. This review will focus on present status of gene pool and species distribution, germplasm conservation, characterization and evaluation, problems associated with crop production, sources of target traits available in wild species, status of trait introgression in synthesizing new gene pool of chickpea along with progress made in chickpea genomics.

An edited book with contributions from leading scientists, this information will guide and inform chickpea breeders, PGR researchers and crop biologists across the world.

• Presents both conventional and emerging techniques
• Provides insights into gene pyramiding as cytogenic manipulations
• Includes case studies highlighting the impact of improving chickpea production

• Language: English
• Publisher: Academic Press
• Release date: Feb 29, 2020
• ISBN: 9780128183007

Book preview

Chickpea: Crop Wild Relatives for Enhancing Genetic Gains

Edited by

Mohar Singh

Principal Scientist (Plant Breeding), ICAR National Bureau of Plant Genetic Resources, Shimla, Himachal Pradesh, India

Table of Contents

Cover image

Title page

Copyright

Contributors

About the Editor

Preface

Chapter 1. Introduction

1.1. Introduction

1.2. Germplasm characterization and evaluation

1.3. Production-related problems

1.4. Origin, distribution, gene pools

1.5. Chickpea genetic resources: collection, conservation, characterization, and maintenance

1.6. Conventional cytogenetic manipulations

1.7. Embryo rescue and chromosomal manipulations

1.8. Gene pyramiding and multiple character breeding

1.9. Molecular markers and marker-trait associations

1.10. Genetic transformation

1.11. Chickpea economy in India

Chapter 2. Origin, distribution, and gene pools

2.1. Introduction

2.2. Origin and distribution

2.3. Taxonomy

2.4. Gene pools

2.5. Barriers in interspecific hybridization and crossability groups

Chapter 3. Chickpea genetic resources: collection, conservation, characterization, and maintenance

3.1. Introduction

3.2. Species distribution and gene pools

3.3. Germplasm conservation

3.4. Germplasm characterization and evaluation

3.5. Future challenges and prospects

Chapter 4. Conventional cytogenetic manipulations

4.1. Introduction

4.2. Production-related problems

4.3. Narrow genetic bases: a bottleneck for enhancing productivity

4.4. Conventional chickpea breeding strategies

4.5. Cytogenetics and chickpea improvement

4.6. Exploitation of marker-assisted selection

4.7. Generation of additional variability through hybridization

4.8. Generation of variability through mutagenesis

4.9. Wild Cicer species

4.10. Utilization of wild species for crop improvement

4.11. New germplasm/varieties developed through wide hybridization

4.12. Wide hybridization for transfer of resistance to biotic stresses

4.13. Future strategy and conclusions

Chapter 5. Embryo rescue and chromosomal manipulations

5.1. Introduction

5.2. Origin and taxonomy

5.3. Genus cicer

5.4. Gene pools and wide hybridization

5.5. Chromosomal manipulation

5.6. Cytogenetics and distant hybridization

Chapter 6. Gene pyramiding and multiple character breeding

6.1. Introduction

6.2. Genetic resources in chickpea

6.3. Genomic resources

6.4. Speed breeding

6.5. Conclusion

Chapter 7. Molecular markers and marker trait associations

7.1. Introduction

7.2. DNA-based markers for chickpea

7.3. DNA-based markers other than SSRs

7.4. Genotyping-by-sequencing

7.5. Development of linkage maps

7.6. Genetic mapping of disease resistance and agro-morphological traits in chickpea

7.7. Genetic mapping of abiotic stress tolerance

7.8. Marker-assisted breeding

7.9. Genomic selection for prediction of agronomic traits

7.10. Future perspectives

Chapter 8. Genetic transformation

8.1. Introduction

8.2. Genetic base of chickpea

8.3. Constraints to chickpea productivity

8.4. Genetic engineering as complement to plant breeding

8.5. Selectable/scorable markers

8.6. Root transformation

8.7. Conclusion

Chapter 9. Chickpea economy in India

9.1. Introduction

9.2. Global pulse economy: an overview

9.3. Global scenario of chickpea

9.4. Indian pulse scenario

9.5. Per capita availability of pulses in India

9.6. Growth in chickpea area, production, and productivity

9.7. Contribution of chickpea area to the total pulses area in India

9.8. Availability status of pulses

9.9. Availability status of chickpea in India

9.10. Export and import of chickpea

9.11. Trade destination of chickpea

9.12. Import duty on important pulses

9.13. Cost of cultivation of chickpea

9.14. MSP for major pulses

9.15. Prices of chickpea in major domestic markets

9.16. Market segmentation in chickpea market

9.17. Marketing channel of chickpea in India

9.18. Government intervention for chickpea in India

9.19. Conclusion

Index

Copyright

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Contributors

Jamal Ansari,     Division of Plant Biotechnology, ICAR-Indian Institute of Pulses Research, Kanpur, Uttar Pradesh, India

C. Bharadwaj,     ICAR-Indian Agricultural Research Institute, New Delhi, Delhi, India

Shayla Bindra,     Punjab Agricultural University, Ludhiana, Punjab, India

Surinder Singh Chandel,     Department of Agricultural Biotechnology, CSK Himachal Pradesh Agricultural University, Palampur, Himachal Pradesh, India

Rahul Chandora,     ICAR-National Bureau of Plant Genetic Resources, Shimla, Himachal Pradesh, India

S.K. Chaturvedi,     College of Agriculture, RLBCAU, Jhansi, Uttar Pradesh, India

Alok Das,     Division of Plant Biotechnology, ICAR-Indian Institute of Pulses Research, Kanpur, Uttar Pradesh, India

G.P. Dixit,     ICAR-Indian Institute of Pulses Research, Kanpur, Uttar Pradesh, India

P.M. Gaur,     International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Telangana, India

Gayacharan,     ICAR-National Bureau of Plant Genetic Resources, New Delhi, Delhi, India

Soma Gupta,     ICAR-Indian Institute of Seed Science, Mau, Uttar Pradesh, India

Norah Johal,     Punjab Agricultural University, Ludhiana, Punjab, India

Gopal Katna,     Department of Organic Agriculture and Natural Farming, CSK Himachal Pradesh Agricultural University, Palampur, Himachal Pradesh, India

Yogesh Kumar,     Division of Crop Improvement, ICAR-Indian Institute of Pulses Research, Kanpur, Uttar Pradesh, India

Ashutosh Kushwah,     Punjab Agricultural University, Ludhiana, Punjab, India

Nikhil Malhotra,     ICAR-National Bureau of Plant Genetic Resources, Shimla, Himachal Pradesh, India

Biswajit Mondal,     Division of Crop Improvement, ICAR-Indian Institute of Pulses Research, Kanpur, Uttar Pradesh, India

Harsh Nayyar,     Panjab University, Chandigarh, Punjab, India

S.D. Nitesh,     Department of Crop Improvement, CSK Himachal Pradesh Agricultural University, Palampur, Himachal Pradesh, India

Rajeev Rathour,     Department of Agricultural Biotechnology, CSK Himachal Pradesh Agricultural University, Palampur, Himachal Pradesh, India

Aqeel Hasan Rizvi,     Food Legume Breeder, South Asia and China Regional Program, International Center for Agricultural Research in the Dry Areas, New Delhi, India

Samriti,     Department of Social Sciences, Dr YS Parmar University of Horticulture and Forestry, Solan, Himachal Pradesh, India

Ashutosh Sarker,     Regional Coordinator, South Asia and China Regional Program, International Center for Agricultural Research in the Dry Areas, New Delhi, India

Shiv Sewak,     Division of Crop Improvement, ICAR-Indian Institute of Pulses Research, Kanpur, Uttar Pradesh, India

Kamal Dev Sharma,     Department of Agricultural Biotechnology, CSK Himachal Pradesh Agricultural University, Palampur, Himachal Pradesh, India

Ravinder Sharma,     Department of Social Sciences, Dr YS Parmar University of Horticulture and Forestry, Solan, Himachal Pradesh, India

Subhash Sharma,     Department of Social Sciences, Dr YS Parmar University of Horticulture and Forestry, Solan, Himachal Pradesh, India

Neelam Shekhawat,     ICAR-National Bureau of Plant Genetic Resources, Jodhpur, Rajasthan, India

Alok Shukla,     Division of Plant Biotechnology, ICAR-Indian Institute of Pulses Research, Kanpur, Uttar Pradesh, India

Inderjit Singh,     Punjab Agricultural University, Ludhiana, Punjab, India

Mohar Singh,     ICAR-National Bureau of Plant Genetic Resources, Shimla, Himachal Pradesh, India

N.P. Singh,     ICAR-Indian Institute of Pulses Research, Kanpur, Uttar Pradesh, India

Prateek Singh,     Division of Plant Biotechnology, ICAR-Indian Institute of Pulses Research, Kanpur, Uttar Pradesh, India

Sarvjeet Singh,     Punjab Agricultural University, Ludhiana, Punjab, India

Shallu Thakur,     Division of Plant Biotechnology, ICAR-Indian Institute of Pulses Research, Kanpur, Uttar Pradesh, India

Aneeta Yadav,     Faculty of Agriculture and Allied Industries, RAMA University, Kanpur, Uttar Pradesh, India

About the Editor

Dr. Mohar Singh is currently serving as Principal Scientist to the National Bureau of Plant Genetic Resources Regional Station, Shimla, India. He obtained his Doctoral degree in Plant Breeding from Himachal Pradesh Agricultural University, Palampur, India. He has made an outstanding contribution to the management of plant genetic resources for food and agriculture in the country. His research interest reflects a continuum of high-quality basic and strategic research in pulses. He has developed 3 core sets, 2 reference sets, registered 5 genetic stocks, 25 gene sequences, 6 farmer varieties, and 2 lentil varieties developed through distant hybridization for rainfed areas of north-western Indian Himalaya. He has conducted 10 explorations on crop wild relatives (CWRs) and explored >900 wild germplasm of cereals, oilseeds, and pulses. He is instrumental to initiate prebreeding in chickpea and lentil for securing national nutritional demand in India. His pioneer research work on understanding the population structure and diversity assessment of global wild species of lentil and chickpea is very well known. This has led to the identification of most target gene sources in the secondary and tertiary gene pools of chickpea and lentil for biofortification of cultivated varieties including several yield and major biotic and abiotic stress–related traits that were successfully incorporated in cultivated backgrounds of these two important pulse crops. Successful deployment of marker-assisted breeding for introgression of two most promising superior haplotypes with high seed weight and pod number from cultivated and wild species into high yielding varieties of chickpea for improving their overall yield and productivity. Dr. Singh has published more than 60 research articles in international journals of repute viz., DNA Research, Scientific Reports, Plant Breeding, Crop Science, Euphytica, PLoS ONE, Frontiers in Plant Science, Genetic Resources and Crop Evolution, Journal of Genetics, Journal of Genetics and Breeding, Plant Genetic Resources: Cambridge, and Advances in Horticulture Science. He also holds two text books and five edited books to his credit.

Preface

The majority of cultivated grain legume crop species including chickpea have been exploited up to their maximum level of productivity, and there is a projection that by 2050, the world population will be more than 9 plus billion, which require an astonishing increase in food production. To attain further breakthroughs in increasing grain yield and improving stability in future cultivars, new sources of genes and alleles need to be identified in the plant genetic resources (PGR) including crop wild relatives (CWRs) and introgressed into the elite genetic backgrounds so that new plant types for different conditions could be tailored. Furthermore, in the face of climate change, this great resource may prove to be instrumental for future food and nutritional security. Therefore, it is imperative to motivate crop researchers to look into new sources of variation in untapped germplasm including CWRs and identify target traits of interest using appropriate tools and techniques in order to make the selection more efficient and reliable. In view of this context, an effort has been made to bring together the rather scattered research work done in this useful area in the form of an edited collection, a compilation that should be of great value to the chickpea researchers across the globe. The book comprises a total of nine chapters contributed by eminent researchers from various reputed organizations of the world. An introductory chapter describes some key issues linked to bottlenecks and potential of species utilization on current trends of wide hybridization. The subsequent chapters deal with different aspects related to potential resources and techniques for enhancing genetic gains of cultivated gene pool. The editor is extremely thankful to all authors for their significant contributions to this volume. The entire process of preparing the manuscript was marked by cordial collegiality. I am also indebted to the staff of Academic Press for their excellent professional support in the completion of this project. Despite one round of galley proof-reading, the book may still have some scientific, technical, and printing errors. I will appreciate if these omissions are brought to my notice, so that they may be addressed in future editions.

Mohar Singh

Chapter 1

Introduction

Mohar Singh     ICAR-National Bureau of Plant Genetic Resources, Shimla, Himachal Pradesh, India

Abstract

The narrow genetic base of domesticated chickpea has hindered the speed in realizing high genetic gains in chickpea breeding programs. Moreover, various abiotic and biotic stresses are the major obstacles for increasing chickpea productivity. So, there is an urgent need for systematic utilization of agro-economic traits from wild Cicer species including elite cultivated germplasm to tackle the problems associated with reduced crop production and subordinate yields for broadening the cultivated gene pool. Furthermore, advances in chickpea genomics will assist in genomics-assisted selection and facilitate breeding of climate-resilient chickpea cultivars for sustainable agriculture production system. This book is aimed to update the current progress made in genetic improvement of chickpea in context of gene pools and species distribution, germplasm conservation, characterization, evaluation and utilization of wild species along with research breakthroughs accomplished in identification of useful gene sources, wide hybridization including contemporary breeding approaches, and genomic advancements for widening the genetic base of cultivated chickpea varieties.

Keywords

Cicer; Contemporary approaches; Crop wild relatives; Cytogenetic manipulation; Gene pyramiding; Genetic resources; Genomics; Wide hybridization

1.1. Introduction

Chickpea (Cicer arietinum L.) is the third most important grain legume species cultivated in 59 nations contributing to world nutritional security owing to 23% protein content (FAO, 2016). It is a self-pollinating true diploid (2n   =   2x   =   16) belonging to family Fabaceae. The species is grouped into desi and kabuli types: desi chickpeas generally have small, colored seeds, whereas kabulis produce large, creamish colored seeds (Archak et al., 2016). Kabuli chickpea is usually utilized as whole grains, while desi is processed into flour. It is a cool-season annual crop performing suitably in 20–25°C daytime and 15–20°C night temperatures. The crop produces good grain yields in drier conditions, because of having deep tap root system. Chickpea has a moderately sized genome of around 750 Mbp (Varshney et al., 2013) evolved from its immediate wild progenitor C. reticulatum through natural selection. The genus Cicer comprises 44 species and is divided into two subgenera. The cultivated species, C. arietinum is found only in cultivation and cannot colonize successfully without human intervention. The wild species occur in weedy habitats, mountain slopes among rubble, and broad-leaf or pine forests, which can be accommodated into 9 annual and 35 perennial species.

Despite considerable international investment in traditional breeding, productivity of the crop has not yet been significantly enhanced. The reasons underlying marginal improvements are series of biotic and abiotic stresses, which reduce crop yield and its adaptation (Varshney et al., 2012). Nonavailability of genetically improved varieties remains a major bottleneck in achieving higher productivity levels. Furthermore, constraints in breeding of domesticated chickpea include narrow genetic base, because of its single domestication event and a very high self-pollination rate (Abbo et al., 2003). Adequate sources of resistance to prevailing biotic and abiotic stresses including productivity-related traits are often not available within cultivated gene pool, and this has forced to take the interest in crop wild relatives (CWRs) for the genetic improvement of cultivated crop varieties (Mallikarjuna et al., 2007). There are practical evidences available for the use of wild progenitors as donors of productivity alleles in some crops such as rice, tomato, and chickpea. Therefore, to attain further breakthrough for enhanced yield and stability in future crop cultivars, new traits of interest are needed to be identified and incorporated into cultivated varieties for developing novel germplasm. Hence, to meet the dietary requirements of growing world population, the consolidated efforts are needed to increase the nutrition and yield potential of chickpea. So, an immediate thrust is needed to widen the genetic base of chickpea cultivars by introgression of diverse set of genes and alleles available in distantly related wild Cicer taxa. To broaden the genetic base and maximize gains from the selection, it is therefore necessary to accumulate other complementary alleles from CWRs.

Substantial improvement in any crop species depends upon the whole spectrum of genetic diversity available in its germplasm repository. Systematic work on germplasm conservation is prerequisite for any genetic intervention. A lot of interest has recently been developed in CWRs with the notion that they will gain significance as changing climate put both traditional and advanced cultivars under increasing stress, leading to a prerequisite for plant breeding to produce new crop varieties able to grow under the new climatic system. Traditionally, the approach to the conservation of CWRs has been ex situ, while the need to maintain CWRs in their natural habitats as in situ has been supported. Large-scale collection and conservation efforts have been made to protect chickpea biodiversity, and ex situ gene banks have been established for the collection and conservation of useful plant genetic resources. There are a large number of gene banks conserving over 98,000 germplasm accessions of chickpea comprising of landraces, modern cultivars, genetic stocks, mutants, and wild Cicer species. Globally, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, India, has the largest collection comprising 19,959 accessions of cultivated chickpea and 308 accessions of 18 wild Cicer species from about 60 countries. It is followed by the National Bureau of Plant Genetic Resources (NBPGR), New Delhi, India, having a total of 17,053 accessions. Other major gene banks holding chickpea germplasm include International Centre for Agricultural Research in Dry Areas holding 13,818 accessions; Australian Temperate Field Crops Collection Victoria, 8660 accessions; and Washington State University Pullman, 6789 accessions. The important regions for in situ conservation of wild chickpea include Turkey and Syria for C. reticulatum, C. bijugum, C. echinospermum, and C. pinnatifidum; Israel, Jordan, and Lebanon for C. judaicum; and Afghanistan for C. yamashitae. Furthermore, Lahaul and Spiti in North-West Indian Trans-Himalayas is the main region for in situ conservation of C. microphyllum, a perennial wild Cicer species.

1.2. Germplasm characterization and evaluation

It is widely recognized that characterization is the basic step to classify the crop gene pool into distinct phenotypic categories using crop descriptor states, while evaluation is prerequisite to understand the value of genetic resources for its successful utilization against the target traits. A large number of chickpea germplasm accessions have been characterized and evaluated over the years in various institutions across globe. The CWRs provide the broadest range of genetic diversity in grain legumes, including chickpea, and have the ability to provide the wide range of germplasm resources for the incorporation of elite traits of agro-economic importance (Singh et al., 2014a,b). The wild Cicer species not only consists of useful variation for morphological characteristics and protein content but are also rich sources of resistance to various biotic and abiotic stresses (Croser et al., 2003; Sandhu et al., 2006; Singh et al., 2014a,b), biochemical traits (Kaur et al., 2010), and yield components (Singh and Ocampo, 1997; Singh et al., 2014a,b). The studies pertaining to wild Cicer species vis-à-vis agro-morphological traits, biotic and abiotic stresses along with nutritional aspects at ICRISAT, ICARDA, NBPGR, and other institutions across the world have been successful in initiating chickpea improvement programs. It was reported that linkage drag of undesirable traits hampered the efforts of transferring elite traits from wild species to cultivated chickpea. Therefore, Aryamanesh et al. (2010) developed a genetic linkage map of chickpea using an interspecific F2 population between cultivated and C. reticulatum. They identified a closely related marker for plant growth habit and quantitative trait loci (QTLs) for ascochyta blight resistance and flowering time. Thereafter, Singh et al. (2014a,b) have made detailed characterization and evaluation of global wild annual Cicer accessions for useful traits of interest. They identified multiple gene resistant sources for various agronomic traits including prevailing biotic stresses. It was revealed that the frequency distribution of wild Cicer species exhibited a wide range of intraspecific variation for some of the important morphological plant characteristics. Plant pigmentation showed variation in C. reticulatum, C. judaicum, and C. pinnatifidum along with light pubescent leaves, except C. yamashitae, where it was densely pubescent. In most of the Cicer species, seed shape was angular, with the exception of C. bijugum where it was irregular, rounded, and pea shaped. Testa texture was rough in C. reticulatum, C. judaicum, C. pinnatifidum, and C. yamashitae, but appeared tuberculated in C. bijugum and C. echinospermum. Similarly, substantial variation in seed color was observed in C. reticulatum, C. judaicum, and C. pinnatifidum. Although QTLs controlling agro-morphological traits in chickpea were also identified, a genome-wide scanning of wild Cicer accessions was revealed by the studies of Saxena et al. (2014) and Das et al. (2015). Moreover, a comprehensive comparative transcriptome profiling and high-resolution QTL mapping of C. microphyllum revealed molecular machinery regulating agronomic traits in chickpea (Srivastava et al., 2016a,b), which was further followed by detailed analysis of differentially expressed transcripts related to traits ranging from seed growth and metabolic processes to elite traits of interest in chickpea improvement programs (Srivastava et al., 2016a,b; Sagi et al., 2017). The summary of important traits identified in different wild Cicer species has been presented in Table 1.1.

Chickpea is susceptible to various abiotic and biotic stresses; therefore, CWRs can provide the wide range of germplasm resources for their incorporation into the cultivated gene pool, because the narrow genetic base of cultivated chickpea is one of the major limitations in improving chickpea production and productivity worldwide. CWRs are species closely related to crops, including crop progenitors, identified as critical resources which are vital for wealth creation, food security, and environmental stability (Maxted et al., 2008). Systematic screening of wild Cicer collections by ICRISAT, ICARDA, and NBPGR have promoted genetic base broadening flagship activities in chickpea and identified several useful target traits of interest. These institutions have characterized over 400 wild annual Cicer accessions and landraces for various agro-morphological traits and biotic and abiotic stresses. Wild Cicer species have been extensively screened, and several of them have been reported to have very high levels of tolerance to many biotic and abiotic stresses, which includes resistance to ascochyta blight (Pande et al., 2010), botrytis gray mold (BGM; Basandrai et al., 2008), fusarium wilt (Nguyen et al., 2004), multiple disease resistance against ascochyta blight, BGM, root knot nematode (Singh et al., 2014a,b), cold (Toker, 2005), drought, and heat (Canci and Toker, 2009). The transfer of specific genes is frequently associated with the transfer of large alien chromosome segments having undesirable traits. Owing to linkage drag, the genes for primitive or wild traits are often introduced along with desirable traits. Breaking linkages with unwanted type and restoring the genotype associated with accepted agronomic background may take a long time. The first report on interspecific hybridization involving C. arietinum with C. reticulatum and C. cuneatum was published by Ladizinsky and Adler (1976). The cross between C. arietinum and C. reticulatum was achieved successfully. Subsequently, wide hybridization was attempted between C. arietinum and C. echinospermum (Singh and Ocampo, 1993). Due to the use of in vitro technique, success has been made in achieving crosses between C. arietinum and C. bijugum and C. arietinum and C. judaicum. Badami et al. (1997) reported successful hybridization between C. arietinum and C. pinnatifidum using embryo rescue technique. However, Singh et al. (2015, 2018) have also attempted interspecific crosses between C. arietinum × reticulatum and echinospermum and transferred important yield component traits. Further, using various techniques, interspecific hybrids have been produced between C. arietinum × C. cuneatum, C. arietinum × C. judaicum, C. arietinum × C. bijugum, and C. arietinum × C. pinnatifidum (Singh et al., 1999; Mallikarjuna and Jadhav, 2008) to exploit an introgression of desirable alien genes from wild Cicer species into the cultivated gene pool. An attempt has also been made successfully to hybridize two wild annual Cicer species with three cultivated chickpea cultivars which resulted in high level of heterosis for number of pods/plant and seed yield/plant. Cross-combinations of cultivated chickpea cultivars with C. reticulatum and C. echinospermum exhibited higher variability for important yield component traits. Using wild Cicer accessions, promising donors, and popular chickpea cultivars as recipients, introgression of traits in elite material is being pursued by traditional and/or molecular breeding approaches, and the prebreeding populations are being developed for useful traits following simple (C. arietinum × C. reticulatum or C. echinospermum) and/or complex three-way (C. arietinum × [C. reticulatum × C. echinospermum]) crosses as reported by Sharma (2017). These interspecific hybrids have contributed significantly toward the development of genomic resources for chickpea improvement. Chickpea breeding programs are aimed at developing early-maturing cultivars especially to increase the crop adaptation by avoiding abiotic stresses affecting the crop production globally. Wild relatives of chickpea viz. C. reticulatum, C. echinospermum, C. bijugum, and C. pinnatifidum have been shown to possess early flowering and maturity accessions (Singh et al., 2014a,b). The wild Cicer species also harbor beneficial alleles/genes for high seed protein and improvement of agronomic traits in cultivated chickpea. The productivity genes/alleles have been introgressed from C. reticulatum, C. echinospermum, and C. pinnatifidum species (Singh and Ocampo, 1997; Singh et al., 2012). Of the eight annual wild Cicer species, only C. reticulatum is readily crossable with cultivated chickpea resulting in a fertile hybrid, whereas for exploitation of the remaining seven annual wild Cicer species for chickpea improvement, specialized techniques such as application of growth hormones, embryo rescue, ovule culture, and other tissue culture techniques have been suggested by various researchers (Mallikarjuna and Jadhav, 2008). Promising high-yielding lines with good agronomic base and seed traits such as early flowering and 100-seed weight have also been obtained from crosses involving C. reticulatum and C. echinospermum with cultivated chickpea (Singh et al., 2005; Upadhyaya, 2008).

Table 1.1

Reproduced from Singh, M., Bisht, I.S., Dutta, M., Kumar, K., Basandrai, A.K., Kaur, L., Sirari, A., Khan, Z., et al., 2014a. Characterization and evaluation of wild annual Cicer species for agro-morphological traits and major biotic stresses under Northwestern Indian conditions. Crop Sci. 54, 229–239. Singh, S., Singh, I., Kapoor, K., Gaur, P.M., Chaturvedi, S.K., Singh, N.P., Sandhu, J.S., 2014b. Chickpea. In: Singh, M., et al. (Eds.), Broadening the Genetic Base of Grain Legumes. Springer, pp. 51–73.

Furthermore, biotechnological interventions can help to increase chickpea productivity by using the marker-assisted selection (MAS) approach in improvement programs. Recent developments in genomics technology have helped to explain the mechanism of complex traits controlling chickpea productivity and the genetic architecture of traits of economic importance to accelerate breeding programs. The extensive use of molecular markers in chickpea genetics and breeding started only after the development of simple sequence repeat (SSR) markers. Over 2000 SSR markers are available for chickpea molecular analysis. The draft genome sequence of chickpea identified over 48,000 SSRs suitable for PCR primer design for use as genetic markers (Varshney et al., 2013) while a draft sequence of C. reticulatum (PI 489777) measuring 327.07   Mb was assembled to the eight linkage groups with 25,680 protein coding genes (Gupta et al., 2017). A number of marker-trait associations have been identified in chickpea along with the dense genetic maps which have allowed MAS to become a routine in breeding programs. Molecular markers have been identified for the genes/QTLs linked to resistance to several abiotic stresses such as drought and salinity resilience; biotic stresses, viz., fusarium wilt, ascochyta blight, BGM, and yield contributing characteristics in chickpea. Recent advances in the development of markers and identification of molecular markers linked to genes/QTLs controlling elite traits of interest have encouraged applications of marker-assisted backcrossing in chickpea improvement. Moreover, genome-wide selection has been proposed as a potential approach for improving complex traits governed by many genes/QTLs (Bajaj et al., 2015). In this approach, both phenotyping and genotyping data are used to predict genomic estimated breeding values of progenies. Additionally, emerging novel approach of genome editing technologies namely CRISPR/Cas9, transcription activator-like effector nucleases (TALENs), zinc finger nucleases could be potentially used in genomics-assisted selection in chickpea for rapid genetic gain (Bortesi and Fischer, 2015).

1.3. Production-related problems

1.3.1. Fusarium wilt

Chickpea wilt occurs in 32 countries across six continents in the world (Nene et al., 1991; Singh and Sharma, 2002). It is caused by Fusarium oxysporum f. sp. ciceri. The yield losses caused by it vary from 10% to 90% (Jimenez-Diaz et al., 1989; Singh and Reddy, 1991). At present there are eight distinct physiological races of F. oxysporum, viz., 0, 1A, 1B/C, 2, 3, 4, 55, and 6. Out of them four races have been identified as 1, 2, 3, and 4 which are prevalent in India (Haware and Nene, 1982) and race 0, 5, and 6 are reported from Spain (Jimenez-Diaz et al., 1989). Breeding for fusarium wilt is of prime importance because of nature of the pathogen as it can persist in soil year after year even in the absence of the host (Haware et al., 1996). Due to the presence of such a number of races, it is very tedious to breed a variety, which shows stability to the disease across different agro-ecological regions. Most of the resistance against fusarium wilt is of vertical nature (Sharma et al., 2005) as it is mostly governed by a single major gene. Chickpea genotypes differ in the development