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Protocols in ecological and environmental plant physiology

 

Open Access Article << Previous     |     Next >>   Contents Vol 41(11)

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


 
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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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Upadhyaya HD, Kashiwagi J, Varshney RK, Gaur PM, Saxena KB, Krishnamuthy L, Gowda CLL, Pundir RPS, Basu PS, Singh IP (2012) Phenotyping chickpeas and pigeonpea for adaptation to drought. Frontiers in Physiology 3, 179
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Vadez V, Krishnamurthy L, Thudi M, Colmer TD, Turner NC, Siddique KHM, Gaur PM, Varshney RK (2012) Assessment of ICCV 2 × JG 62 chickpea progenies shows sensitivity of reproduction to salt stress and reveals QTLs for seed yield and seed number. Molecular Breeding 30, 9–21.
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Valente F, Gauthier F, Bardol N, Blanc G, Joets J, Charcosset A, Moreau L (2013) OptiMAS: a decision support tool for marker-assisted assembly of diverse alleles. The Journal of Heredity 104, 586–590.
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Varshney RK, Graner A, Sorrells ME (2005) Genomics-assisted breeding for crop improvement. Trends in Plant Science 10, 621–630.
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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.
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Varshney RK, Glaszmann J-C, Leung H, Ribaut JM (2010a) More genomic resources for less-studied crops. Trends in Biotechnology 28, 452–460.
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Varshney RK, Thudi M, May GD, Jackson SA (2010b) Legume genomics and breeding. Plant Breeding Reviews 33, 257–304.

Varshney RK, Kudapa H, Roorkiwal M, Thudi M, Pandey KM, Saxena RK, Chamarthi SK, Murali Mohan S, Mallikarjuna N, Upadhyaya HD, Gaur PM, Krishnamurthy L, Saxena KB, Nigam SN, Pande S (2012a) Advances in genetics and molecular breeding of three legume crops of semi-arid tropics using next-generation sequencing and high-throughput genotyping technologies. Journal of Biosciences 37, 811–820.
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Varshney RK, Luo M-C, Bhatia S, Tyagi A (2012b) A physical map of chickpea genome. (International Crop Research Institute for the Semiarid Tropics: Patancheru, India). Available online at: http://probes.pw.usda.gov:8080/chickpea/ [Verified 6 June 2014].

Varshney RK, Ribaut J-M, Buckler ES, Tuberosa R, Rafalski JA, Langridge P (2012c) Can genomics boost productivity of orphan crops? Nature Biotechnology 30, 1172–1176.
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Varshney RK, Gaur PM, Chamarthi SK, Krishnamurthy L, Tripathi S, Kashiwagi J, Samineni S, Singh VK, Thudi M, Jaganathan D (2013a) Fast-track introgression of ‘QTL-hotspot’ for root traits and other drought tolerance traits in JG 11, an elite and leading variety of chickpea. The Plant Genome 6,
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Varshney RK, Song C, Saxena RK, Azam S, Yu S, Sharpe A, Cannon S, Baek J, Rosen BD, Tar’an B, Milláan T, Zhang X, Ramsay LD, Iwata A, Wang Y, Nelson W, Farmer AD, Gaur PM, Soderlund C, Penmetsa RV, Xu C, Bharti AK, He W, Winter P, Zhao S, Hane JK, Garcia NC, Condie JA, Upadhyaya HD, Luo MC, Thudi M, Gowda CLL, Singh NP, Lichtenzveig J, Gali KK, Rubio J, Nadarajan N, Dolezel J, Bansal KC, Xu X, Edwards D, Zhang G, Kahl G, Gil J, Singh KB, Datta SK, Jackson SA, Wang J, Cook DR (2013b) Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement. Nature Biotechnology 31, 240–246.
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Varshney RK, Mir RR, Bhatia S, Thudi M, Hu Y, Azam S, Zhang Y, Jaganathan D, You FM, Gao J, Riera-Lizarazu O, Luo M-C (2014a) Integrated physical, genetic and genome map of chickpea (Cicer arietinum L.). Functional & Integrative Genomics 14, 59–73.
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Varshney RK, Thudi M, Nayak SN, Gaur PM, Kashiwagi J, Krishnamurthy L, Jaganathan D, Koppolu J, Bohra A, Tripathi S, Rathore A, Jukanti AK, Jayalakshmi V, Vemula A, Singh S, Yasin M, Sheshshayee MS, Viswanatha KP (2014b) Genetic dissection of drought tolerance in chickpea (Cicer arietinum L.). Theoretical and Applied Genetics 127, 445–462.
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Xu YB, Crouch JH (2008) Marker-assisted selection in plant breeding: from publications to practice. Crop Science 48, 391–407.
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Zhao Y, Gowda M, Liu W, Würschum T, Maurer HP, Longin FH, Ranc N, Reif JC (2012) Accuracy of genomic selection in European maize elite breeding populations. Theoretical and Applied Genetics 124, 769–776.
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