A Distinct Genetic Cluster in Cultivated Chickpea as Revealed by Genome‐wide Marker Discovery and Genotyping

Abstract

The accurate description of plant biodiversity is of utmost importance to efficiently address efforts in conservation genetics and breeding. Herein, we report the successful application of a genotyping-by-sequencing (GBS) approach in chickpea (Cicer arietinum L.), resulting in the characterization of a cultivated germplasm collection with 3187 high-quality single nucleotide polymorphism (SNP) markers. Genetic structure inference, principal component analysis, and hierarchical clustering all indicated the identification of a genetic cluster corresponding to black-seeded genotypes traditionally cultivated in Southern Italy. Remarkably, this cluster was clearly distinct at both genetic and phenotypic levels from germplasm groups reflecting commercial chickpea classification into desi and kabuli seed types. Fixation index estimates for individual polymorphisms pointed out loci and genomic regions that might be of significance for the diversification of agronomic and commercial traits. Overall, our findings provide information on genetic relationships within cultivated chickpea and highlight a gene pool of great interest for the scientific community and chickpea breeding, which is limited by the low genetic diversity available in the primary gene pool.

Genotyping-by-Sequencing Reveals Molecular Genetic Diversity in Italian Common Bean Landraces

“…In conclusion, GBS proved to be a valuable tool to study the population genetics and relationships in common bean germplasm, even at local level, as already observed for other crops [67][68][69][70]. In addition, our work is relevant regarding the preservation of local landraces of the common bean from genetic erosion, and could be useful for future studies to tackle the identification of interesting traits relating to plant adaptation for breeding purposes.…”

Integrating genomics for chickpea improvement: achievements and opportunities

“…For example, the GBS approach has been widely used for linkage mapping and QTL detection of ascochyta blight resistance (Deokar et al 2019a), heat tolerance (Paul et al 2018), seed iron and zinc concentrations (Upadhyaya et al 2016) and seed quality (Verma et al 2015) among others, using RIL populations in chickpea (Table 1). This technology has also been used to identify and validate SNPs from cultivated and wild Cicer accessions to study allelic diversity, population structure and linkage disequilibrium patterns in these gene pools Kujur et al 2015;Pavan et al 2017). Interestingly, the GBS approach was used for enhancing marker density within the 'QTL-hotspot' region, which harbours multiple QTLs for drought tolerance.…”

In Vitro and In Vivo Nutraceutical Characterization of Two Chickpea Accessions: Differential Effects on Hepatic Lipid Over-Accumulation

“…Two chickpea accessions, namely MG_13 and PI358934, were selected from the germplasm collections previously characterized, as they belong to distinct genetic clusters and display markedly different phenotypic features [22,23]. For each accession, 40 plants were grown at the experimental farm "P. Martucci" of the University of Bari (41 • 01 22.1 N and 16 • 54 21.0 E) from 2013 to 2014.…”

“…Recent studies on global chickpea germplasm collections reveal a high level of genetic, phenotypic, and compositional diversity [4,21,22]. The present study was carried out to investigate the physiological effect of two genetically and phenotypically diverse chickpea accessions in a cellular and animal model of nonalcoholic fatty liver disease.…”