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Sequencing chickpea genomes: genotyping and high-quality reference genomes for association studies and breeding

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Title Sequencing chickpea genomes: genotyping and high-quality reference genomes for association studies and breeding
 
Creator Udupa, Sripada M.
 
Description Natural 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 co-incident collection
of the more distantly related species C. bijugum and C. pinnatifidum.
Over 1,000 wild individuals sampled in 2013 were genotyped using Restriction- enzyme
Associated DNA Genotyping By Sequencing (RAD-GBS). 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 long-term stability of the collection site for
potential future in-situ studies. Genotypes CDCFrontier (C.ari), Besev_079 (C. ret) and
S2Drd_065 (C. ech) represent the three species. For each genotype, sequence data from
~60x short-read Illumina and ~30x long-read PacBio are being integrated with BioNano
optical mapping data. Assemblies will be assessed via high-density 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 genome-wide signatures of selection and for trait-gene 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 short-read sequencing.
Together these genome data represent a novel resource for chickpea biology, to improve
the accuracy and precision of association mapping, trait-marker discovery and introgression
breeding
 
Date 2016-12-31
2017-03-08T07:06:18Z
2017-03-08T07:06:18Z
 
Type Poster
 
Identifier https://mel.cgiar.org/reporting/download/hash/6nCuueJx
Sripada M. Udupa. (31/12/2016). Sequencing chickpea genomes: genotyping and high-quality reference genomes for association studies and breeding.
https://hdl.handle.net/20.500.11766/6328
Open access
 
Language en
 
Rights CC-BY-NC-4.0
 
Format PDF