ArticleBMC genomics2011
Single-nucleotide polymorphism discovery by high-throughput sequencing in sorghum.
Article in BMC genomics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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Who cites it
41 citing papers in PubMed.
- New methods for sorghum transformation in temperate climates.AoB PLANTS · 2023Review
- Discovery of SNP Molecular Markers and Candidate Genes Associated with Sacbrood Virus Resistance inInternational journal of molecular sciences · 2023Article
- Recent advancements in the breeding of sorghum crop: current status and future strategies for marker-assisted breeding.Frontiers in genetics · 2023Review
- Assembly of the 373k gene space of the polyploid sugarcane genome reveals reservoirs of functional diversity in the world's leading biomass crop.GigaScience · 2019Article
- Gigwa v2-Extended and improved genotype investigator.GigaScience · 2019Article
- Development and validation of an SNP genotyping array and construction of a high-density linkage map in castor.Scientific reports · 2019Article
- Construction of a highly saturated Genetic Map for Vitis by Next-generation Restriction Site-associated DNA Sequencing.BMC plant biology · 2018Article
- Mapping a male-fertility restoration locus for the ABMC plant biology · 2018Article
- Article
- Validation of QTL mapping and transcriptome profiling for identification of candidate genes associated with nitrogen stress tolerance in sorghum.BMC plant biology · 2017Article
- Forward Genetics by Sequencing EMS Variation-Induced Inbred Lines.G3 (Bethesda, Md.) · 2017Article
- Toward Identification of Black Lemma and Pericarp GeneFrontiers in plant science · 2017Article
- SNP-Discovery by RAD-Sequencing in a Germplasm Collection of Wild and Cultivated Grapevines (V. vinifera L.).PloS one · 2017Article
- Transcriptome analysis in switchgrass discloses ecotype difference in photosynthetic efficiency.BMC genomics · 2016Article
- Plant cytochrome P450s: nomenclature and involvement in natural product biosynthesis.Protoplasma · 2016Review
- Using Genotyping by Sequencing to Map Two Novel Anthracnose Resistance Loci in Sorghum bicolor.G3 (Bethesda, Md.) · 2016Article
- Molecular Approaches to Understand Nutritional Potential of Coarse Cereals.Current genomics · 2016Article
- SorGSD: a sorghum genome SNP database.Biotechnology for biofuels · 2016Article
- Article
- Enrichment of an intraspecific genetic map of upland cotton by developing markers using parental RAD sequencing.DNA research : an international journal for rapid publication of reports on genes and genomes · 2015Article
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundEight diverse sorghum (Sorghum bicolor L. Moench) accessions were subjected to short-read genome sequencing to characterize the distribution of single-nucleotide polymorphisms (SNPs). Two strategies were used for DNA library preparation. Missing SNP genotype data were imputed by local haplotype comparison. The effect of library type and genomic diversity on SNP discovery and imputation are evaluated.
resultsAlignment of eight genome equivalents (6 Gb) to the public reference genome revealed 283,000 SNPs at ≥82% confirmation probability. Sequencing from libraries constructed to limit sequencing to start at defined restriction sites led to genotyping 10-fold more SNPs in all 8 accessions, and correctly imputing 11% more missing data, than from semirandom libraries. The SNP yield advantage of the reduced-representation method was less than expected, since up to one fifth of reads started at noncanonical restriction sites and up to one third of restriction sites predicted in silico to yield unique alignments were not sampled at near-saturation. For imputation accuracy, the availability of a genomically similar accession in the germplasm panel was more important than panel size or sequencing coverage.
conclusionsA sequence quantity of 3 million 50-base reads per accession using a BsrFI library would conservatively provide satisfactory genotyping of 96,000 sorghum SNPs. For most reliable SNP-genotype imputation in shallowly sequenced genomes, germplasm panels should consist of pairs or groups of genomically similar entries. These results may help in designing strategies for economical genotyping-by-sequencing of large numbers of plant accessions.
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