Aug 26, 2014

Genome wide SNP identification in chickpea for use in development of a high density genetic map and improvement of chickpea reference genome assembly

BMC Genomics
Amit DeokarB Tar'an

Abstract

In the whole genome sequencing, genetic map provides an essential framework for accurate and efficient genome assembly and validation. The main objectives of this study were to develop a high-density genetic map using RAD-Seq (Restriction-site Associated DNA Sequencing) genotyping-by-sequencing (RAD-Seq GBS) and Illumina GoldenGate assays, and to examine the alignment of the current map with the kabuli chickpea genome assembly. Genic single nucleotide polymorphisms (SNPs) totaling 51,632 SNPs were identified by 454 transcriptome sequencing of Cicer arietinum and Cicer reticulatum genotypes. Subsequently, an Illumina GoldenGate assay for 1,536 SNPs was developed. A total of 1,519 SNPs were successfully assayed across 92 recombinant inbred lines (RILs), of which 761 SNPs were polymorphic between the two parents. In addition, the next generation sequencing (NGS)-based GBS was applied to the same population generating 29,464 high quality SNPs. These SNPs were clustered into 626 recombination bins based on common segregation patterns. Data from the two approaches were used for the construction of a genetic map using a population derived from an intraspecific cross. The map consisted of 1,336 SNPs including 604 RAD recombination bins...Continue Reading

  • References58
  • Citations38

References

Mentioned in this Paper

Inbred Strain
Chromosome Map
Genome Assembly Sequence
Recombination, Genetic
Genetic Markers
Lathyrus sativus homeopathic preparation
Genome Mapping
Cicer
Sequencing
Massively-Parallel Sequencing

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