Application of next generation sequencing for developing large-scale genomic resource in chickpea (Cicer arietinum L.)
Material type:
TextPublication details: 2010Description: p. 225Summary: Chickpea, an important semi-arid legume crop is seriously challenged by abiotic stresses- drought and salinity. Enhancing genomic resources (molecular markers and candidate genes) is a pre-requisite to facilitate breeding for improving tolerance against these stresses. In this context, a set of 20,162 drought- and salinity-responsive ESTs from four genotypes using Sanger sequencing and 435,018 transcript reads from a normalized cDNA pool derived from 30 different tissues/stages of chickpea cultivar ICC 4958 using 454/FLX sequencing have been generated. Cluster analysis of these sequence data has provided a set of 103,215 tentative unique sequences (TUSs) that is being used for functional annotation, gene structure prediction and genomic synteny exploration. Furthermore, with an objective to develop large scale SNP marker resources in chickpea, mRNA for four parental genotypes of two mapping populations (ICC 4958 x ICC 1882 and ICC 506 x ICCC 37) has been sequenced by using Illumina/Solexa sequencing approach. As a result, a total of 118.9 million reads of 36-bp length have been generated. These reads are being aligned with the TUSs of chickpea and > 10,000 SNPs have been identified across the parental genotypes of mapping populations. These resources will be used to develop large scale Illumina GoldenGate assays that would supplement the recently developed pilot GoldenGate assay detecting 768 SNPs based on conserved gene orthologs. In summary, these transcriptomic resources open new avenues for functional genomics in chickpea and comparative genomics across the legume species.
| Item type | Current library | Collection | Call number | Status | Date due | Barcode | Item holds | |
|---|---|---|---|---|---|---|---|---|
| Conference proceedings | CIMMYT Knowledge Center: John Woolston Library | CIMMYT Staff Publications Collection | CIS-6177 (Browse shelf(Opens below)) | Available |
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Abstract only
Chickpea, an important semi-arid legume crop is seriously challenged by abiotic stresses- drought and salinity. Enhancing genomic resources (molecular markers and candidate genes) is a pre-requisite to facilitate breeding for improving tolerance against these stresses. In this context, a set of 20,162 drought- and salinity-responsive ESTs from four genotypes using Sanger sequencing and 435,018 transcript reads from a normalized cDNA pool derived from 30 different tissues/stages of chickpea cultivar ICC 4958 using 454/FLX sequencing have been generated. Cluster analysis of these sequence data has provided a set of 103,215 tentative unique sequences (TUSs) that is being used for functional annotation, gene structure prediction and genomic synteny exploration. Furthermore, with an objective to develop large scale SNP marker resources in chickpea, mRNA for four parental genotypes of two mapping populations (ICC 4958 x ICC 1882 and ICC 506 x ICCC 37) has been sequenced by using Illumina/Solexa sequencing approach. As a result, a total of 118.9 million reads of 36-bp length have been generated. These reads are being aligned with the TUSs of chickpea and > 10,000 SNPs have been identified across the parental genotypes of mapping populations. These resources will be used to develop large scale Illumina GoldenGate assays that would supplement the recently developed pilot GoldenGate assay detecting 768 SNPs based on conserved gene orthologs. In summary, these transcriptomic resources open new avenues for functional genomics in chickpea and comparative genomics across the legume species.
English
CIMMYT Staff Publications Collection
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