Draft genome sequence ofCicer reticulatumL., the wild progenitor of chickpea provides a resource for agronomic trait improvement

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.

Genome-Enabled Prediction Models for Yield Related Traits in Chickpea

“…With the availability of draft genome sequences (Jain et al, 2013; Varshney et al, 2013a; Ruperao et al, 2014; Gupta et al, 2016) and re-sequencing data for several hundred lines in chickpea, millions of markers have become available now. Ability of GS to address the complex traits and availability of increasing genomic resources enabling the application of emerging markers system like GBS and SNP array for estimating the prediction accuracy, sets the rationale for deployment of this molecular breeding tool for chickpea improvement.…”

“…In addition, very recently draft genome sequences have also become available for kabuli (Varshney et al, 2013a) and desi (Jain et al, 2013; Ruperao et al, 2014) type. In addition, very recently draft genome for wild chickpea ( C. reticulatum ) has also become available (Gupta et al, 2016). …”

Quantitative Trait Loci for Cold Tolerance in Chickpea

“…The vernalization requirement has been well described in C. reticulatum (Abbo et al, 2002;Sharma and Upadhyaya, 2015;van-Oss et al, 2015van-Oss et al, , 2018. A draft genome was published for both CRIL2 parents, which should facilitate this endeavor ( Jain et al, 2013;Gupta et al, 2016). This is a start at candidate gene identification; fine mapping will be necessary to elevate its status.…”

Accelerating genetic gains in legumes for the development of prosperous smallholder agriculture: integrating genomics, phenotyping, systems modelling and agronomy

“…BeadChip (Akond et al, 2013) • SoySNP50K array (Song et al, 2013) • 384 SNP GoldenGate assay (Hyten et al, 2008 (Varshney et al, 2012a) • 292 lines • 20 (crossing parentals of recombinant inbred lines, introgression lines, MAGIC and NAM population; Kumar et al, 2016) • 60K Axiom®Cajanus SNP array (Saxena et al, 2017 and unpublished) (Gupta et al, 2017) • 35 (parental genotypes of mapping populations; Thudi et al, 2016a) • 129 released varieties (Thudi et al, 2016b) • 300 lines (ICRISAT, unpublished) • 3000 lines (ICRISAT, unpublished) • GoldenGate assays based on VeraCode technology (Roorkiwal et al, 2013) • 60K Axiom®Cicer SNP array (Roorkiwal et al, 2017 (Chen et al, 2016) • 11 genotypes including synthetics and their diploid parents (Chen et al, 2016) • 41 diverse genotypes (30 tetraploids and 11 diploids) (Clevenger et al, 2017;Pandey et al, 2017a) • 58K Axiom®Arachis SNP array (Pandey et al, 2017a) •1536 SNP GoldenGate assay (Nagy et al, 2012) Common bean • 80.57% of Phaseolus vulgaris var G19833 genome (587 Mb); 26 279 protein coding genes (Schmutz et al, 2014) • 17 varieties • BARCBean6K_1, BARCBean6K_2 chips, BARCBean6K_3 SNP chips (Song et al, 2013 (Deulvot et al, 2010) • Combines custom-made growth vessels and new image analysis algorithms to non-destructively monitor RSA development over space (2D) and time • Allows information on soil properties (e.g. moisture)…”