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Comparative analysis of kabuli chickpea transcriptome with desi and wild chickpea provides a rich resource for development of functional markers.

ABSTRACT: Chickpea (Cicer arietinum L.) is an important crop legume plant with high nutritional value. The transcriptomes of desi and wild chickpea have already been sequenced. In this study, we sequenced the transcriptome of kabuli chickpea, C. arietinum (genotype ICCV2), having higher commercial value, using GS-FLX Roche 454 and Illumina technologies. The assemblies of both Roche 454 and Illumina datasets were optimized using various assembly programs and parameters. The final optimized hybrid assembly generated 43,389 transcripts with an average length of 1065 bp and N50 length of 1653 bp representing 46.2 Mb of kabuli chickpea transcriptome. We identified a total of 5409 simple sequence repeats (SSRs) in these transcript sequences. Among these, at least 130 and 493 SSRs were polymorphic with desi (ICC4958) and wild (PI489777) chickpea, respectively. In addition, a total of 1986 and 37,954 single nucleotide polymorphisms (SNPs) were predicted in kabuli/desi and kabuli/wild genotypes, respectively. The SNP frequency was 0.043 SNP per kb for kabuli/desi and 0.821 SNP per kb for kabuli/wild, reflecting very low genetic diversity in chickpea. Further, SSRs and SNPs present in tissue-specific and transcription factor encoding transcripts have been identified. The experimental validation of a selected set of polymorphic SSRs and SNPs exhibited high intra-specific polymorphism potential between desi and kabuli chickpea, suggesting their utility in large-scale genotyping applications. The kabuli chickpea gene index assembled, and SSRs and SNPs identified in this study will serve as useful genomic resource for genetic improvement of chickpea.

SUBMITTER: Agarwal G

PROVIDER: S-EPMC3531472 | biostudies-literature | 2012

REPOSITORIES: biostudies-literature

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Comparative analysis of kabuli chickpea transcriptome with desi and wild chickpea provides a rich resource for development of functional markers.

Agarwal Gaurav G Jhanwar Shalu S Priya Pushp P Singh Vikash K VK Saxena Maneesha S MS Parida Swarup K SK Garg Rohini R Tyagi Akhilesh K AK Jain Mukesh M

PloS one 20121227 12

Chickpea (Cicer arietinum L.) is an important crop legume plant with high nutritional value. The transcriptomes of desi and wild chickpea have already been sequenced. In this study, we sequenced the transcriptome of kabuli chickpea, C. arietinum (genotype ICCV2), having higher commercial value, using GS-FLX Roche 454 and Illumina technologies. The assemblies of both Roche 454 and Illumina datasets were optimized using various assembly programs and parameters. The final optimized hybrid assembly ...[more]

PMID: 23300670

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Project description:Pakistan is among top three chickpea producing countries but the crop is usually grown on marginal lands without irrigation and fertilizer application which significantly hampers its yield. Soil fertility and inoculation with beneficial rhizobacteria play a key role in nodulation and yield of legumes. Four kabuli and six desi chickpea genotypes were, therefore, evaluated for inoculation response with IAA-producing Ochrobactrum ciceri Ca-34(T) and nitrogen fixing Mesorhizobium ciceri TAL-1148 in single and co-inoculation in two soils. The soil type 1 was previously unplanted marginal soil having low organic matter, P and N contents compared to soil type 2 which was a fertile routinely legume-cultivated soil. The effect of soil fertility status was pronounced and fertile soil on average, produced 31% more nodules, 62% more biomass and 111% grain yield than marginal soil. Inoculation either with O. ciceri alone or its co-inoculation with M. ciceri produced on average higher nodules (42%), biomass (31%), grains yield (64%) and harvest index (72%) in both chickpea genotypes over non-inoculated controls in both soils. Soil 1 showed maximum relative effectiveness of Ca-34(T) inoculation for kabuli genotypes while soil 2 showed for desi genotypes except B8/02. Desi genotype B8/02 in soil type 1 and Pb-2008 in soil type 2 showed significant yield increase as compared to respective un-inoculated controls. Across bacterial inoculation treatments, grain yield was positively correlated to growth and yield contributing parameters (r = 0.294(*) to 0.838(***) for desi and r = 0.388(*) to 0.857(**) for kabuli). PCA and CAT-PCA analyses clearly showed a site-specific response of genotype x bacterial inoculation. Furthermore, the inoculated bacterial strains were able to persist in the rhizosphere showing colonization on root and within nodules. Present study shows that plant growth promoting rhizobacteria (PGPR) inoculation should be integrated with national chickpea breading program in Pakistan especially for marginal soils. Furthermore, the study shows the potential of phytohormone producing strain Ca-34(T) as promising candidate for development of biofertilizer alongwith nodulating strains to get sustainable yield of kabuli and desi chickpea with minimum inputs at marginal land.

Project description:The concept of 'crop ideotype' is coined as a desirable plant model expected to better perform for seed yield, oils and other useful characteristics when developed as a cultivar, and it consists of two major approaches, namely, (i) 'defect elimination', that is, integration of disease resistance to a susceptible genotype from a resistant genotype and (ii) 'selection for yield' by improving yield after crosses between desirable parents. For consideration of these approaches, here we introduced an ideotype in kabuli chickpea (Cicer arietinum L.) which is high-yielding, extra-large-seeded, and double- or multi-podded, has high plant height and imparipinnate-leafed traits, and is heat tolerant and resistant to ascochyta blight [Ascochyta rabiei (Pass.) Labr.], which causes considerable yield losses, via marker-assisted selection. F3 and F4 lines were evaluated for agro-morphological traits divided into six classes, namely, (i) imparipinnate-leafed and single-podded progeny, (ii) imparipinnate-leafed and double-podded progeny, (iii) imparipinnate-leafed and multi-podded progeny, (iv) unifoliolate-leafed and single-podded progeny, (v) unifoliolate-leafed and double-podded progeny, (vi) unifoliolate-leafed and multi-podded progeny. F3:4 lines having 100-seed weight ≥ 45 g and double- or multi-podded traits were additionally assessed for resistance to ascochyta blight using molecular markers including SCY17590 and CaETR-1. Superior lines having higher values than their best parents were determined for all studied traits indicating that economic and important traits including yield and seed size in chickpea could be improved by crossing suitable parents. Imparipinnate-leafed and multi-podded plants had not only the highest number of pods and seeds per plant but also the highest yield. On the other hand, imparipinnate-leafed and single podded progeny had the largest seed size, followed by imparipinnate-leafed and double-podded progeny. Multi-podded plants produced 23% more seed yield than that of single-podded plants, while multi-podded plants attained 7.6% more seed yield than that of double-podded plants. SCY17590 and CaETR-1 markers located on LG4 related to QTLAR2 and QTLAR1 were found in 14 lines among 152 F3:4 lines. Six superior lines were selected for being double- or multi-podded, imparipinnate-leafed, suitable for combine harvest, heat-tolerant, and resistant to ascochyta blight, and having both of two resistance markers and extra-large seeds as high as 50-60 g per 100-seed weight. Resistance alleles from two different backgrounds for resistance to ascochyta blight were integrated with double- or multi-podded kabuli chickpea lines having high yield, extra-large seeds, high plant height, imparipinnate-leaves and high heat tolerance, playing a crucial role for future demands of population and food security. These approaches seem to be applicable in ideotype breeding for other important crop plants.

Dataset Information

Comparative analysis of kabuli chickpea transcriptome with desi and wild chickpea provides a rich resource for development of functional markers.

Publications

Comparative analysis of kabuli chickpea transcriptome with desi and wild chickpea provides a rich resource for development of functional markers.

Similar Datasets

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