ArticleTAG. Theoretical and applied genetics. Theoretische und angewandte Genetik2012
Development and mapping of SNP assays in allotetraploid cotton.
Article in TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 61 papers.
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Who cites it
61 citing papers in PubMed.
- Genetic diversity and population structure analysis of cotton (Gossypium hirsutum L.) genotypes using DArTseq technology.BMC genomics · 2026Article
- Genetic diversity and population structure analysis of 418 tomato cultivars based on single nucleotide polymorphism markers.Frontiers in plant science · 2024Article
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- KASP-IEva: an intelligent typing evaluation model for KASP primers.Frontiers in plant science · 2023Article
- Construction of SNP fingerprint and population genetic analysis of honeysuckle germplasm resources in China.Frontiers in plant science · 2023Article
- Construction of an SNP fingerprinting database and population genetic analysis of 329 cauliflower cultivars.BMC plant biology · 2022Article
- Genome wide study of cysteine rich receptor like proteins in Gossypium sp.Scientific reports · 2022Article
- Mining Grapevine Downy Mildew Susceptibility Genes: A Resource for Genomics-Based Breeding and Tailored Gene Editing.Biomolecules · 2021Article
- Construction of a SNP Fingerprinting Database and Population Genetic Analysis of Cigar Tobacco Germplasm Resources in China.Frontiers in plant science · 2021Article
- Article
- Genetic Analysis of the Transition from Wild to Domesticated Cotton (G3 (Bethesda, Md.) · 2020Article
- ddRAD sequencing-based identification of inter-genepool SNPs and association analysis in Brassica juncea.BMC plant biology · 2019Article
- Article
- Development of EST-based SSR and SNP markers in3 Biotech · 2019Article
- QTL analysis for yield and fibre quality traits using three sets of introgression lines developed from three Gossypium hirsutum race stocks.Molecular genetics and genomics : MGG · 2019Article
- SNP genotyping reveals major QTLs for plant architectural traits between A-genome peanut wild species.Molecular genetics and genomics : MGG · 2018Article
- Dissection of complicate genetic architecture and breeding perspective of cottonseed traits by genome-wide association study.BMC genomics · 2018Article
- Practical considerations for plant phylogenomics.Applications in plant sciences · 2018Review
- Genetic dissection of the fuzzless seed trait in Gossypium barbadense.Journal of experimental botany · 2018Article
- Maximization of Markers Linked in Coupling for Tetraploid Potatoes via Monoparental Haploids.Frontiers in plant science · 2018Article
1 more citing papers are in PubMed but not listed here.
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5 authors.
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No grant is acknowledged in the PubMed record.
Abstract
A narrow germplasm base and a complex allotetraploid genome have made the discovery of single nucleotide polymorphism (SNP) markers difficult in cotton (Gossypium hirsutum). To generate sequence for SNP discovery, we conducted a genome reduction experiment (EcoRI, BafI double digest, followed by adapter ligation, biotin-streptavidin purification, and agarose gel separation) on two accessions of G. hirsutum and two accessions of G. barbadense. From the genome reduction experiment, a total of 2.04 million genomic sequence reads were assembled into contigs with an N(50) of 508 bp and analyzed for SNPs. A previously generated assembly of expressed sequence tags (ESTs) provided an additional source for SNP discovery. Using highly conservative parameters (minimum coverage of 8× at each SNP and 20% minor allele frequency), a total of 11,834 and 1,679 non-genic SNPs were identified between accessions of G. hirsutum and G. barbadense in genome reduction assemblies, respectively. An additional 4,327 genic SNPs were also identified between accessions of G. hirsutum in the EST assembly. KBioscience KASPar assays were designed for a portion of the intra-specific G. hirsutum SNPs. From 704 non-genic and 348 genic markers developed, a total of 367 (267 non-genic, 100 genic) mapped in a segregating F(2) population (Acala Maxxa × TX2094) using the Fluidigm EP1 system. A G. hirsutum genetic linkage map of 1,688 cM was constructed based entirely on these new SNP markers. Of the genic-based SNPs, we were able to identify within which genome ('A' or 'D') each SNP resided using diploid species sequence data. Genetic maps generated by these newly identified markers are being used to locate quantitative, economically important regions within the cotton genome.
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