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Link to original content: https://pubmed.ncbi.nlm.nih.gov/27567261
Draft genome sequence of Cicer reticulatum L., the wild progenitor of chickpea provides a resource for agronomic trait improvement - PubMed Skip to main page content
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. 2017 Feb 1;24(1):1-10.
doi: 10.1093/dnares/dsw042.

Draft genome sequence of Cicer reticulatum L., the wild progenitor of chickpea provides a resource for agronomic trait improvement

Sonal Gupta  1 , Kashif Nawaz  1 , Sabiha Parween, Riti Roy, Kamlesh Sahu, Anil Kumar Pole, Hitaishi Khandal, Rishi Srivastava, Swarup Kumar Parida, Debasis Chattopadhyay
Affiliations

Draft genome sequence of Cicer reticulatum L., the wild progenitor of chickpea provides a resource for agronomic trait improvement

Sonal Gupta et al. DNA Res. .

Abstract

Cicer reticulatum L. is the wild progenitor of the fourth most important legume crop chickpea (C. arietinum L.). We assembled short-read sequences into 416 Mb draft genome of C. reticulatum and anchored 78% (327 Mb) of this assembly to eight linkage groups. Genome annotation predicted 25,680 protein-coding genes covering more than 90% of predicted gene space. The genome assembly shared a substantial synteny and conservation of gene orders with the genome of the model legume Medicago truncatula. Resistance gene homologs of wild and domesticated chickpeas showed high sequence homology and conserved synteny. Comparison of gene sequences and nucleotide diversity using 66 wild and domesticated chickpea accessions suggested that the desi type chickpea was genetically closer to the wild species than the kabuli type. Comparative analyses predicted gene flow between the wild and the cultivated species during domestication. Molecular diversity and population genetic structure determination using 15,096 genome-wide single nucleotide polymorphisms revealed an admixed domestication pattern among cultivated (desi and kabuli) and wild chickpea accessions belonging to three population groups reflecting significant influence of parentage or geographical origin for their cultivar-specific population classification. The assembly and the polymorphic sequence resources presented here would facilitate the study of chickpea domestication and targeted use of wild Cicer germplasms for agronomic trait improvement in chickpea.

Keywords: Cicer reticulatum L. PI489777; annotation; diversity; genome sequence; wild chickpea.

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Figures

Figure 1
Figure 1
Images of field-grown wild (C. reticulatum L.) (left) and cultivated (C. arietinum L.) chickpea (right) plants and seeds. The colour version of the figure is available online.
Figure 2
Figure 2
Syntenic relationship between C. reticulatum (Cr) and Medicago truncatula (Mt) pseudomolecules. Mt pseudomolecules are labelled as Mt1-8. C. reticulatum pseudomolecules are labelled as Cr1-8. Collinear blocks are shown according to the shades of the corresponding Cr pseudomolecules. The colour version of the figure is available online.
Figure 3
Figure 3
Genome-wide sequence diversity between wild and cultivated chickpea. (a) Genome-wide distribution of nucleotide diversity (θπ) within the wild, desi and kabuli chickpea genotypes. RAD sequence reads of 10 accessions of C. reticulatum, 28 accessions each of desi and kabuli chickpeas were mapped on the pseudomolecules of 8 LGs of C. reticulatum. Circular maps show (from periphery to centre) distribution of gene density (in 0.5 Mb) with R gene loci are shown by vertical lines, nucleotide diversities within C. reticulatum, desi and kabuli accessions. A 500 kb bin size with a 50 kb sliding window and the maximum value of 1 for the Y-axis was used to plot nucleotide diversity. (b) Density plot showing distribution of Ks values of the orthologous gene pairs between wild and cultivated (desi-light line, kabuli-dark line) chickpeas. The colour version of the figure is available online (desi-green line, kabuli-red line).
Figure 4
Figure 4
Genome-wide SNP-based molecular diversity among 66 wild and domesticated chickpea accessions. (a) Unrooted phylogram depicting the genetic relationships (Nei’s genetic distance) among 66 wild (R1-10), desi (D1-28) and kabuli (K1-28) chickpea accessions based on genome-wide SNP mapped on C. reticulatum genome assembly. The phylogenetic tree differentiated 66 accessions into three diverse groups. (b) The population genetic structure of the wild and domesticated chickpea accessions. The mapped genetic markers assigned to three distinct desi, kabuli and wild population groups at population number (K = 3). The accessions represented by vertical bars along the horizontal axis were classified into K colour segments based on their estimated membership fraction in each K cluster. The colour version of the figure is available online.
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References

    1. Varshney R. K., Song C., Saxena R. K., et al. 2013, Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement, Nat. Biotechnol., 31, 240–246. - PubMed
    1. Jain M., Misra G., Patel R. K., et al. 2013, A draft genome sequence of the pulse crop chickpea (Cicer arietinum L.), Plant J., 74, 715–729. - PubMed
    1. Parween S., Nawaz K., Roy R., et al. 2015, An advanced draft genome assembly of a desi type chickpea (Cicer arietinum L.), Sci. Rep., 5, 12806. - PMC - PubMed
    1. Abbo S., Berger J., Turner N.C. 2003, Evolution of cultivated chickpea: four bottlenecks limit diversity and constrain adaptation, Funct. Plant Biol., 30, 1081–1087. - PubMed
    1. Harlan J. R. 1971, Agricultural origins: centers and noncenters, Science, 174, 468–474. - PubMed

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