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A high-density SNP-based linkage map using genotyping-by-sequencing and its utilization for improved genome assembly of chickpea (Cicer arietinum L.)

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Title A high-density SNP-based linkage map using genotyping-by-sequencing and its utilization for improved genome assembly of chickpea (Cicer arietinum L.)
 
Creator Gaur, Rashmi
Verma, Subodh
Pradhan, Seema
Ambreen, Heena
Bhatia, Sabhyata
 
Subject Chickpea
GBS
SNP markers
Linkage map
Genome anchoring
 
Description Accepted date: 18 August 2020
Genotyping-by-sequencing (GBS) allows rapid identification of markers for use in development of linkage maps, which expedite
efficient breeding programs. In the present study, we have utilized GBS approach to identify and genotype single-nucleotide
polymorphism (SNP) markers in an inter-specific RIL population of Cicer arietinum L. X C. reticulatum. A total of 141,639 raw
SNPs were identified using the TASSEL-GBS pipeline. After stringent filtering, 8208 candidate SNPs were identified of which ~
37% were localized in the intragenic regions followed by genic regions (~ 30%) and intergenic regions (~ 27%). We then utilized
6920 stringent selected SNPs from present study and 6714 SNPs and microsatellite markers available from previous studies for
construction of linkage map. The resulting high-density linkage map comprising of eight linkage groups contained 13,590
markers which spanned 1299.14 cM of map length with an average marker density of 0.095 cM. Further, the derived linkage
map was used to improve the available assembly of desi chickpea genome by anchoring 443 previously unplaced scaffolds onto
eight linkage groups. The present efforts have refined anchoring of the desi chickpea genome assembly to 55.57% of the ~
520 Mb of assembled desi genome. To the best of our knowledge, the linkage map generated in the present study represents one
of the most dense linkage map developed for the crop till date. It will serve as a valuable resource for fine mapping and positional
cloning of important quantitative trait loci (QTLs) associated with agronomical traits and also for anchoring and ordering of
future genome sequence assemblies.
This work was financially supported by the Department of
Biotechnology (DBT) under the Next Generation Challenge
Programme on Chickpea Genomics (grant number BT/PR12919/AGR/
02/676/2009).
 
Date 2020-08-31T05:42:46Z
2020-08-31T05:42:46Z
2020
 
Type Article
 
Identifier Functional & Integrative Genomics, 20: 763–773
1438-7948
https://doi.org/10.1007/s10142-020-00751-y
https://link.springer.com/article/10.1007/s10142-020-00751-y
http://223.31.159.10:8080/jspui/handle/123456789/1087
 
Language en_US
 
Format application/pdf
 
Publisher Springer Nature Publishing AG