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dc.creatorUdupa, Sripada M.en_US
dc.date2016-12-31en_US
dc.date.accessioned2017-03-08T07:06:18Z
dc.date.available2017-03-08T07:06:18Z
dc.identifierhttp://dx.doi.org/en_US
dc.identifierhttps://mel.cgiar.org/reporting/download/hash/6nCuueJxen_US
dc.identifier.citationSripada M. Udupa. (31/12/2016). Sequencing chickpea genomes: genotyping and high-quality reference genomes for association studies and breeding.en_US
dc.identifier.urihttp://hdl.handle.net/20.500.11766/6328
dc.description.abstractNatural populations of species closely related to cultivated chickpea Cicer arietinum were identified and collected systematically using ecological principles from their native range in southeastern Turkey Collection was focused primarily on C reticulatum wild progenitor of the cultigen and C echinospermum a sister species and with limited coincident collection of the more distantly related species C bijugum and C pinnatifidum Over 1000 wild individuals sampled in 2013 were genotyped using Restriction enzyme Associated DNA Genotyping By Sequencing RADGBS Based on this sequencing allelefrequency based population assignment was conducted for all genotypes leading to the choice of the focal genotypes as donor parents for introgression population development Both the currently available reference genomes for cultivated chickpea are draft assemblies containing several ambiguous regions and whole genome assemblies of wild relatives are currently unavailable To address these limitations focal genotypes for high resolution reference genomes for each of the three species were selected based on i their use in introgression population development ii genetic relationships to genotypes from other sites of the same species and iii likelyhood of longterm stability of the collection site for potential future insitu studies Genotypes CDCFrontier Cari Besev079 C ret and S2Drd065 C ech represent the three species For each genotype sequence data from 60x shortread Illumina and 30x longread PacBio are being integrated with BioNano optical mapping data Assemblies will be assessed via highdensity linkage mapping RADGBS of early generation progenies derived from wild x wild and wild x cultivated crosses In addition 26 wild accessions that represent ecological and molecular variation within the species and serving as potential introgression donors and recipient cultivars were sequenced to 30x coverage via Illumina short read sequencing data that allow for analysis of genomewide signatures of selection and for traitgene associations To identify rare alleles among populations and to calculate linkage disequilibrium and association studies with native site ecological parameters 200 genotypes from the same populations were sequenced to medium depth 10x via Illumina shortread sequencing Together these genome data represent a novel resource for chickpea biology to improve the accuracy and precision of association mapping traitmarker discovery and introgression breedingen_US
dc.languageenen_US
dc.rightsBen_US
dc.subjectBreedingen_US
dc.subjectPlant Breedingen_US
dc.subjectPlant Genetic Resourcesen_US
dc.subjectChickpeaen_US
dc.titleSequencing chickpea genomes genotyping and highquality reference genomes for association studies and breedingen_US
dc.typePosteren_US
cg.contributor.centerThe International Center for Agriculture Research in the Dry Areas (ICARDA)en_US
cg.contributor.crpCRP on Grain Legumes - GLen_US
cg.contributor.funderNot Applicableen_US
cg.contributor.project-lead-instituteThe International Center for Agriculture Research in the Dry Areas (ICARDA)en_US
cg.coverage.regionEastern Africaen_US
cg.coverage.regionen_US
cg.coverage.countryBurkina Fasoen_US
cg.coverage.countryIndiaen_US
cg.coverage.countryKenyaen_US
cg.coverage.countryNigeriaen_US
cg.coverage.countryTanzaniaen_US
cg.coverage.admin-uniten_US
cg.contacts.udupa@cgiar.orgen_US
dc.identifier.statusOpen accessen_US
cg.countryBurkina Fasoen_US
cg.countryGlobalen_US
cg.countryIndiaen_US
cg.countryKenyaen_US
cg.countryNigeriaen_US
cg.countryTanzaniaen_US


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