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

Azam, Sarwar, Thakur, Vivek, Ruperao, Pradeep, Shah, Trushar, Balaji, Jayashree, Amindala, BhanuPrakash, Farmer, Andrew D., Studholme, David J., May, Gregory D., Edwards, David, Jones, Jonathan D. G. and Varshney, Rajeev K. (2012) 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, 99 2: 186-192. doi:10.3732/ajb.1100419


Author Azam, Sarwar
Thakur, Vivek
Ruperao, Pradeep
Shah, Trushar
Balaji, Jayashree
Amindala, BhanuPrakash
Farmer, Andrew D.
Studholme, David J.
May, Gregory D.
Edwards, David
Jones, Jonathan D. G.
Varshney, Rajeev K.
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
Formatted 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
Journal name American Journal of Botany   Check publisher's open access policy
ISSN 0002-9122
1537-2197
Publication date 2012-02
Sub-type Article (original research)
DOI 10.3732/ajb.1100419
Volume 99
Issue 2
Start page 186
End page 192
Total pages 7
Place of publication St. Louis, MO, United States
Publisher Botanical Society of America
Collection year 2013
Language eng
Formatted 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.
Keyword Chickpea
Cicer arietinum
Fabaceae
Legumes
Molecular breeding
Next-generation sequencing
SNP discovery
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: School of Agriculture and Food Sciences
Official 2013 Collection
 
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