ArticlePlant physiology2003
Mining for single nucleotide polymorphisms and insertions/deletions in maize expressed sequence tag data.
Article in Plant physiology, 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 88 papers.
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Who cites it
88 citing papers in PubMed.
- A comprehensive catalog of single nucleotide polymorphisms (SNPs) from the black pepper (Piper nigrum L.) genome.BMC genomics · 2025Article
- Epistasis and pleiotropy-induced variation for plant breeding.Plant biotechnology journal · 2024Review
- Understanding genetic diversity in drought-adaptive hybrid parental lines in pearl millet.PloS one · 2024Article
- Mapping of quantitative trait loci for the nutritional value of fresh market tomato.Functional & integrative genomics · 2023Article
- Resequencing of 410 Sesame Accessions Identifies SINST1 as the Major Underlying Gene for Lignans Variation.International journal of molecular sciences · 2023Article
- Low-Density Reference Fingerprinting SNP Dataset of CIMMYT Maize Lines for Quality Control and Genetic Diversity Analyses.Plants (Basel, Switzerland) · 2022Article
- Somatic mutations during rapid clonal domestication ofEvolutionary applications · 2022Article
- Exploring Genomic Variations in Nematode-Resistant Mutant Rice Lines.Frontiers in plant science · 2022Article
- Resequencing of global Tartary buckwheat accessions reveals multiple domestication events and key loci associated with agronomic traits.Genome biology · 2021Article
- Field Screen and Genotyping ofInsects · 2021Article
- Prospects of next generation sequencing in lentil breeding.Molecular biology reports · 2020Review
- Genome-Wide Discovery of InDel Markers in Sesame (Plants (Basel, Switzerland) · 2020Article
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- Whole Genome Sequencing and Comparative Genomic Analysis Reveal Allelic Variations Unique to a Purple Colored Rice Landrace (Frontiers in plant science · 2019Article
- Finding invisible quantitative trait loci with missing data.Plant biotechnology journal · 2018Article
- Genome-wide discovery of DNA polymorphisms by whole genome sequencing differentiates weedy and cultivated rice.Scientific reports · 2018Article
- Genomics-Assisted Identification and Characterization of the Genetic Variants Underlying Differential Nitrogen Use Efficiencies in Allotetraploid Rapeseed Genotypes.G3 (Bethesda, Md.) · 2018Article
- Construction of a highly saturated linkage map in Japanese plum (Prunus salicina L.) using GBS for SNP marker calling.PloS one · 2018Article
- Assessment of Genetic Diversity and Population Structure in Iranian Cannabis Germplasm.Scientific reports · 2017Article
28 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We have developed a computer based method to identify candidate single nucleotide polymorphisms (SNPs) and small insertions/deletions from expressed sequence tag data. Using a redundancy-based approach, valid SNPs are distinguished from erroneous sequence by their representation multiple times in an alignment of sequence reads. A second measure of validity was also calculated based on the cosegregation of the SNP pattern between multiple SNP loci in an alignment. The utility of this method was demonstrated by applying it to 102,551 maize (Zea mays) expressed sequence tag sequences. A total of 14,832 candidate polymorphisms were identified with an SNP redundancy score of two or greater. Segregation of these SNPs with haplotype indicates that candidate SNPs with high redundancy and cosegregation confidence scores are likely to represent true SNPs. This was confirmed by validation of 264 candidate SNPs from 27 loci, with a range of redundancy and cosegregation scores, in four inbred maize lines. The SNP transition/transversion ratio and insertion/deletion size frequencies correspond to those observed by direct sequencing methods of SNP discovery and suggest that the majority of predicted SNPs and insertion/deletions identified using this approach represent true genetic variation in maize.
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