Development of ESTs from chickpea roots and their use in diversity analysis of the Cicergenus

Buhariwalla, H K and Jayashree, B and Eshwar, K and Crouch, J H (2005) Development of ESTs from chickpea roots and their use in diversity analysis of the Cicergenus. BMC Plant Biology, 5 (16). 01-14. ISSN 14712229

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Abstract Background Chickpea is a major crop in many drier regions of the world where it is an important protein-rich food and an increasingly valuable traded commodity. The wild annual Cicer species are known to possess unique sources of resistance to pests and diseases, and tolerance to environmental stresses. However, there has been limited utilization of these wild species by chickpea breeding programs due to interspecific crossing barriers and deleterious linkage drag. Molecular genetic diversity analysis may help predict which accessions are most likely to produce fertile progeny when crossed with chickpea cultivars. While, trait-markers may provide an effective tool for breaking linkage drag. Although SSR markers are the assay of choice for marker-assisted selection of specific traits in conventional breeding populations, they may not provide reliable estimates of interspecific diversity, and may lose selective power in backcross programs based on interspecific introgressions. Thus, we have pursued the development of gene-based markers to resolve these problems and to provide candidate gene markers for QTL mapping of important agronomic traits. Results An EST library was constructed after subtractive suppressive hybridization (SSH) of root tissue from two very closely related chickpea genotypes (Cicer arietinum). A total of 106 EST-based markers were designed from 477 sequences with functional annotations and these were tested on C. arietinum. Forty-four EST markers were polymorphic when screened across nine Cicer species (including the cultigen). Parsimony and PCoA analysis of the resultant EST-marker dataset indicated that most accessions cluster in accordance with the previously defined classification of primary (C. arietinum, C. echinospermum and C. reticulatum), secondary (C. pinnatifidum, C. bijugum and C. judaicum), and tertiary (C. yamashitae, C. chrossanicum and C. cuneatum) gene-pools. A large proportion of EST alleles (45%) were only present in one or two of the accessions tested whilst the others were represented in up to twelve of the accessions tested. Conclusion Gene-based markers have proven to be effective tools for diversity analysis in Cicer and EST diversity analysis may be useful in identifying promising candidates for interspecific hybridization programs. The EST markers generated in this study have detected high levels of polymorphism amongst both common and rare alleles. This suggests that they would be useful for allele-mining of germplasm collections for identification of candidate accessions in the search for new sources of resistance to pests / diseases, and tolerance to abiotic stresses.

Item Type: Article
Divisions: RP-Grain Legumes
CRP: CGIAR Research Program on Grain Legumes
Uncontrolled Keywords: Chickpea roots, Cicer genus, EST database
Subjects: Mandate crops > Chickpea
Depositing User: Mr Ramesh K
Date Deposited: 23 Sep 2016 09:04
Last Modified: 23 Sep 2016 09:04
Official URL:
Acknowledgement: This work was supported by ICRISAT core funds including earmarked unrestricted grants from the governments of UK, Japan and the European Union. The authors would like to thank Dr HC Sharma for providing access to chickpea material, Pratibha R. for technical assistance with initial EST marker screening, Dr HD Upadhyaya for provision of gene-bank passport data for accessions used in this study, Seetha K for lab management, PVNS Prasad and KDV Prasad for assistance with figures and to Drs R Serraj and R Folkertsma for helpful suggestions during manuscript development. We greatly appreciate suggestions from an anonymous reviewer concerning this manuscript.
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