Functional Plant Biology Functional Plant Biology Society
Plant function and evolutionary biology
REVIEW (Open Access)

Genomics-assisted breeding for drought tolerance in chickpea

Mahendar Thudi A , Pooran M. Gaur A , Lakshmanan Krishnamurthy A , Reyazul R. Mir A , Himabindu Kudapa A , Asnake Fikre B , Paul Kimurto C , Shailesh Tripathi D , Khela R. Soren E , Richard Mulwa C , Chellapilla Bharadwaj D , Subhojit Datta E , Sushil K. Chaturvedi E and Rajeev K. Varshney A F

A International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad 502 324, India.

B Ethiopian Institute of Agricultural Research (EIAR), Debre Zeit, PO Box 2003, Ethiopia.

C Egerton University (EU), Egerton 20115, Kenya.

D Indian Agricultural Research Institute (IARI), New Delhi 110 012, India.

E Indian Institute of Pulses Research (IIPR), Kanpur 208 024, India.

F Corresponding author. Email: r.k.varshney@cgiar.org

This paper originates from a presentation at the Interdrought IV Conference, Perth, Australia, 26 September 2013.

Functional Plant Biology 41(11) 1178-1190 http://dx.doi.org/10.1071/FP13318
Submitted: 30 October 2013  Accepted: 23 May 2014   Published: 22 July 2014

Abstract

Terminal drought is one of the major constraints in chickpea (Cicer arietinum L.), causing more than 50% production losses. With the objective of accelerating genetic understanding and crop improvement through genomics-assisted breeding, a draft genome sequence has been assembled for the CDC Frontier variety. In this context, 544.73 Mb of sequence data were assembled, capturing of 73.8% of the genome in scaffolds. In addition, large-scale genomic resources including several thousand simple sequence repeats and several million single nucleotide polymorphisms, high-density diversity array technology (15 360 clones) and Illumina GoldenGate assay genotyping platforms, high-density genetic maps and transcriptome assemblies have been developed. In parallel, by using linkage mapping approach, one genomic region harbouring quantitative trait loci for several drought tolerance traits has been identified and successfully introgressed in three leading chickpea varieties (e.g. JG 11, Chefe, KAK 2) by using a marker-assisted backcrossing approach. A multilocation evaluation of these marker-assisted backcrossing lines provided several lines with 10–24% higher yield than the respective recurrent parents.Modern breeding approaches like marker-assisted recurrent selection and genomic selection are being deployed for enhancing drought tolerance in chickpea. Some novel mapping populations such as multiparent advanced generation intercross and nested association mapping populations are also being developed for trait mapping at higher resolution, as well as for enhancing the genetic base of chickpea. Such advances in genomics and genomics-assisted breeding will accelerate precision and efficiency in breeding for stress tolerance in chickpea.

Additional keywords: backcrossing, Cicer arietinum, genome sequence, quantitative trait loci, yield.


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Sabbavarapu MM, Sharma M, Chamarthi SK, Swapna N, Rathore A, Thudi M, Gaur PM, Pande S, Singh S, Kaur L, Varshney RK (2013) Molecular mapping of QTLs for resistance to Fusarium wilt (race 1) and Ascochyta blight in chickpea (Cicer arietinum L.). Euphytica 193, 121–133.
Molecular mapping of QTLs for resistance to Fusarium wilt (race 1) and Ascochyta blight in chickpea (Cicer arietinum L.).CrossRef | open url image1

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Characterization and genetic diversity analysis of selected chickpea cultivars of nine countries using simple sequence repeat (SSR) markers.CrossRef | open url image1

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Thudi M, Bohra A, Nayak SN, Varghese N, Shah TM, Penmetsa RV, Nepolean T, Srivani G, Gaur PM, Kulwal PL, Upadhyaya HD, KaviKishor PB, Winter P, Kahl G, Town CD, Kilian A, Cook DR, Varshney RK (2011) Novel SSR markers from BAC-end sequences, DArT arrays and a comprehensive genetic map with 1,291 marker loci for chickpea (Cicer arietinum L.). PLoS ONE 6, e27275
Novel SSR markers from BAC-end sequences, DArT arrays and a comprehensive genetic map with 1,291 marker loci for chickpea (Cicer arietinum L.).CrossRef | 1:CAS:528:DC%2BC3MXhsFynur%2FI&md5=f13b260fbe8ec4ca1e236d7f47b6a0dfCAS | 22102885PubMed | open url image1

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A mini core subset for capturing diversity and promoting utilization of chickpea genetic resources in crop improvement.CrossRef | open url image1

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Assessment of ICCV 2 × JG 62 chickpea progenies shows sensitivity of reproduction to salt stress and reveals QTLs for seed yield and seed number.CrossRef | open url image1

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Varshney RK, Hoisington DA, Upadhyaya HD, Gaur PM, Nigam SN, Saxena K, Vadez V, Sethy NK, Bhatia S, Aruna R, Gowda MVC, Singh NK (2007) Molecular genetics and breeding of grain legume crops for the semi-arid tropics. In ‘Genomics-assisted crop improvement. Vol II. Genomics applications in crops’. (Eds RK Varshney, R Tuberosa) pp. 207–242. (Springer: The Netherlands)

Varshney RK, Hiremath PJ, Lekha PT, Kashiwagi J, Balaji J, Deokar AA, Vadez V, Xiao Y, Srinivasan R, Gaur PM, Siddique KHM, Town CD, Hoisington DA (2009a) A comprehensive resource of drought- and salinity-responsive ESTs for gene discovery and marker development in chickpea (Cicer arietinum L.). BMC Genomics 10, 523
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Varshney RK, Nayak SN, May GD, Jackson SA (2009b) Next generation sequencing technologies and their implications for crop genetics and breeding. Trends in Biotechnology 27, 522–530.
Next generation sequencing technologies and their implications for crop genetics and breeding.CrossRef | 1:CAS:528:DC%2BD1MXhtVeitbbE&md5=af4fea38dd2e039e341521760f511de3CAS | 19679362PubMed | open url image1

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More genomic resources for less-studied crops.CrossRef | 1:CAS:528:DC%2BC3cXhtVKisr%2FN&md5=afd5cc34feb158a671e530c3ba408c4aCAS | 20692061PubMed | open url image1

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Advances in genetics and molecular breeding of three legume crops of semi-arid tropics using next-generation sequencing and high-throughput genotyping technologies.CrossRef | 1:CAS:528:DC%2BC38XhslCksrzO&md5=4b525a7e62ea4c686696d0d470f6b0e2CAS | 23107917PubMed | open url image1

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Can genomics boost productivity of orphan crops?CrossRef | 1:CAS:528:DC%2BC38Xhsl2lurjO&md5=cc7d1c07df5ada47ff00ee03011df4f2CAS | 23222781PubMed | open url image1

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Fast-track introgression of ‘QTL-hotspot’ for root traits and other drought tolerance traits in JG 11, an elite and leading variety of chickpea.CrossRef | open url image1

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Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement.CrossRef | 1:CAS:528:DC%2BC3sXhsVymtrY%3D&md5=53a8300621ee0433e826dbdbf93b9565CAS | 23354103PubMed | open url image1

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Integrated physical, genetic and genome map of chickpea (Cicer arietinum L.).CrossRef | 1:CAS:528:DC%2BC2cXjslOntLs%3D&md5=844a6e200e8097da0618a8fabfcf432eCAS | open url image1

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Genetic dissection of drought tolerance in chickpea (Cicer arietinum L.).CrossRef | 1:CAS:528:DC%2BC3sXhvFelurrE&md5=58030c925e3504503b1732d17add5608CAS | 24326458PubMed | open url image1

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Marker-assisted selection in plant breeding: from publications to practice.CrossRef | open url image1

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Accuracy of genomic selection in European maize elite breeding populations.CrossRef | 22075809PubMed | open url image1


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