ArticleMolecular genetics and genomics : MGG2015
Next-generation transcriptome sequencing, SNP discovery and validation in four market classes of peanut, Arachis hypogaea L.
Article in Molecular genetics and genomics : MGG, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Genetic Diversity Analysis and Core Collection Construction of AncientInternational journal of molecular sciences · 2024Article
- Article
- Genome-wide association studies reveal novel loci for resistance to groundnut rosette disease in the African core groundnut collection.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2023Article
- Use of Targeted Amplicon Sequencing in Peanut to Generate Allele Information on Allotetraploid Sub-Genomes.Genes · 2020Article
- Combining High Oleic Acid Trait and Resistance to Late Leaf Spot and Rust Diseases in Groundnut (Frontiers in genetics · 2020Article
- Genetics, genomics and breeding of groundnut (Plant breeding = Zeitschrift fur Pflanzenzuchtung · 2019Review
- Assessment of low-coverage nanopore long read sequencing for SNP genotyping in doubled haploid canola (Brassica napus L.).Scientific reports · 2019Article
- SNP genotyping reveals major QTLs for plant architectural traits between A-genome peanut wild species.Molecular genetics and genomics : MGG · 2018Article
- Comparative analysis of microsatellite, SNP, and InDel markers in fourBreeding science · 2018Article
- Gene-based SNP identification and validation in soybean using next-generation transcriptome sequencing.Molecular genetics and genomics : MGG · 2018Article
- Transcriptomic analysis and discovery of genes in the response of Arachis hypogaea to drought stress.Molecular biology reports · 2018Article
- Article
- Transcriptome Sequencing of Diverse Peanut (Arachis) Wild Species and the Cultivated Species Reveals a Wealth of Untapped Genetic Variability.G3 (Bethesda, Md.) · 2016Article
- Construction of a high-density genetic map and QTL mapping for pearl quality-related traits in Hyriopsis cumingii.Scientific reports · 2016Article
- Article
- Comparisons of de novo transcriptome assemblers in diploid and polyploid species using peanut (Arachis spp.) RNA-Seq data.PloS one · 2014Article
Corrections and comments
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Authors and funding
10 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Single-nucleotide polymorphisms, which can be identified in the thousands or millions from comparisons of transcriptome or genome sequences, are ideally suited for making high-resolution genetic maps, investigating population evolutionary history, and discovering marker-trait linkages. Despite significant results from their use in human genetics, progress in identification and use in plants, and particularly polyploid plants, has lagged. As part of a long-term project to identify and use SNPs suitable for these purposes in cultivated peanut, which is tetraploid, we generated transcriptome sequences of four peanut cultivars, namely OLin, New Mexico Valencia C, Tamrun OL07 and Jupiter, which represent the four major market classes of peanut grown in the world, and which are important economically to the US southwest peanut growing region. CopyDNA libraries of each genotype were used to generate 2 × 54 paired-end reads using an Illumina GAIIx sequencer. Raw reads were mapped to a custom reference consisting of Tifrunner 454 sequences plus peanut ESTs in GenBank, compromising 43,108 contigs; 263,840 SNP and indel variants were identified among four genotypes compared to the reference. A subset of 6 variants was assayed across 24 genotypes representing four market types using KASP chemistry to assess the criteria for SNP selection. Results demonstrated that transcriptome sequencing can identify SNPs usable as selectable DNA-based markers in complex polyploid species such as peanut. Criteria for effective use of SNPs as markers are discussed in this context.
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