Journal article
Coverage-based consensus calling (CbCC) of short sequence reads and comparison of CbCC results to identify SNPs in chickpea (Cicer arietinum; Fabaceae), a crop species without a reference genome
American Journal of Botany, Vol.99(2), pp.186-192
2012
Abstract
• Premise of the study: Next-generation sequencing (NGS) technologies are frequently used for resequencing and mining of single nucleotide polymorphisms (SNPs) by comparison to a reference genome. In crop species such as chickpea (Cicer arietinum) that lack a reference genome sequence, NGS-based SNP discovery is a challenge. Therefore, unlike probability-based statistical approaches for consensus calling and by comparison with a reference sequence, a coverage-based consensus calling (CbCC) approach was applied and two genotypes were compared for SNP identification.
• Methods: A CbCC approach is used in this study with four commonly used short read alignment tools (Maq, Bowtie, Novoalign, and SOAP2) and 15.7 and 22.1 million Illumina reads for chickpea genotypes ICC4958 and ICC1882, together with the chickpea trancriptome assembly (CaTA).
• Key results: A nonredundant set of 4543 SNPs was identified between two chickpea genotypes. Experimental validation of 224 randomly selected SNPs showed superiority of Maq among individual tools, as 50.0% of SNPs predicted by Maq were true SNPs. For combinations of two tools, greatest accuracy (55.7%) was reported for Maq and Bowtie, with a combination of Bowtie, Maq, and Novoalign identifying 61.5% true SNPs. SNP prediction accuracy generally increased with increasing reads depth.
• Conclusions: This study provides a benchmark comparison of tools as well as read depths for four commonly used tools for NGS SNP discovery in a crop species without a reference genome sequence. In addition, a large number of SNPs have been identified in chickpea that would be useful for molecular breeding.
Details
- Title
- Coverage-based consensus calling (CbCC) of short sequence reads and comparison of CbCC results to identify SNPs in chickpea (Cicer arietinum; Fabaceae), a crop species without a reference genome
- Authors/Creators
- S. Azam (Author/Creator)V. Thakur (Author/Creator)P. Ruperao (Author/Creator)T. Shah (Author/Creator)J. Balaji (Author/Creator)B.P. Amindala (Author/Creator)A.D. Farmer (Author/Creator)D.J. Studholme (Author/Creator)G.D. May (Author/Creator)D. Edwards (Author/Creator)J.D.G. Jones (Author/Creator)R.K. Varshney (Author/Creator)
- Publication Details
- American Journal of Botany, Vol.99(2), pp.186-192
- Publisher
- Wiley
- Identifiers
- 991005541282407891
- Copyright
- © 2012 Botanical Society of America
- Murdoch Affiliation
- Murdoch University
- Language
- English
- Resource Type
- Journal article
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Source: InCites
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- Collaboration types
- Domestic collaboration
- International collaboration
- Citation topics
- 3 Agriculture, Environment & Ecology
- 3.4 Crop Science
- 3.4.96 QTL
- Web Of Science research areas
- Plant Sciences
- ESI research areas
- Plant & Animal Science