High density linkage mapping of genomic and transcriptomic SNPs for synteny analysis and anchoring the genome sequence of chickpea.

Seema Pradhan,Shefali Gupta,Mukesh Jain,Niraj Shah,Debasis Chattopadhyay,Rashmi Gaur,Akhilesh K Tyagi,Ganga Jeena,Sabhyata Bhatia

doi:10.1038/srep13387

Seema Pradhan, Shefali Gupta + Show 7 more

Open Access

https://doi.org/10.1038/srep13387

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Journal: Scientific reports	Publication Date: Aug 25, 2015
Citations: 42	License type: CC BY 4.0

Affiliation: National Institute of Plant Genome Research

Abstract

This study presents genome-wide discovery of SNPs through next generation sequencing of the genome of Cicer reticulatum. Mapping of the C. reticulatum sequenced reads onto the draft genome assembly of C. arietinum (desi chickpea) resulted in identification of 842,104 genomic SNPs which were utilized along with an additional 36,446 genic SNPs identified from transcriptome sequences of the aforementioned varieties. Two new chickpea Oligo Pool All (OPAs) each having 3,072 SNPs were designed and utilized for SNP genotyping of 129 Recombinant Inbred Lines (RILs). Using Illumina GoldenGate Technology genotyping data of 5,041 SNPs were generated and combined with the 1,673 marker data from previously published studies, to generate a high resolution linkage map. The map comprised of 6698 markers distributed on eight linkage groups spanning 1083.93 cM with an average inter-marker distance of 0.16 cM. Utility of the present map was demonstrated for improving the anchoring of the earlier reported draft genome sequence of desi chickpea by ~30% and that of kabuli chickpea by 18%. The genetic map reported in this study represents the most dense linkage map of chickpea , with the potential to facilitate efficient anchoring of the draft genome sequences of desi as well as kabuli chickpea varieties.

Highlights

For single nucleotide polymorphisms (SNPs) identification, the C. reticulatum reads were aligned to the published draft reference assembly of the desi chickpea (ICC4958)[32]
This resulted in the detection of a total of 8,42,104 unique SNPs at non-repetitive sites between ICC4958 and PI489777 genome sequences
The advent of NGS technologies has enabled the development of sequence-based markers by comparison of two or more genome sequences

Summary

Introduction

Recent advancements in chickpea have reported the large scale discovery and genotyping of SNPs in chickpea[29,30,31]. These advancements were complemented with the release of the draft genome sequences of two major chickpea types i.e. desi [Cicer arietinum ICC4958]32 and kabuli [C. arietinum CDC Frontier]33. For improving the percentage of the anchored genome of desi cultivar, there was an urgent need to develop and utilize a high density linkage map of chickpea. The SNP resources were used to construct the most advanced high-density linkage map of chickpea with increased genome coverage and marker density. The utility of the present map was established for improving the anchoring of scaffolds from the draft chickpea genome sequence[32,33]

Methods

Results

Conclusion