ArticleBMC genomics2014
Development of EST-based SNP and InDel markers and their utilization in tetraploid cotton genetic mapping.
Article in BMC genomics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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14 citing papers in PubMed, 33 citations in OpenAlex.
- CSSL-based GWAS identifies SNPs and candidate genes associated with Verticillium wilt resistance in cotton.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- Effects of Genetic Variation of the Sorting Nexin 29 (Animals : an open access journal from MDPI · 2022Article
- Development and Utilization of Functional Kompetitive Allele-Specific PCR Markers for Key Genes Underpinning Fiber Length and Strength inFrontiers in plant science · 2022Article
- GBS-SNP and SSR based genetic mapping and QTL analysis for drought tolerance in upland cotton.Physiology and molecular biology of plants : an international journal of functional plant biology · 2021Article
- Agarose-resolvable InDel markers based on whole genome re-sequencing in cucumber.Scientific reports · 2021Article
- Development of Whole-Genome Agarose-Resolvable LInDel Markers in Rice.Rice (New York, N.Y.) · 2020Article
- Identification of candidate genes for fiber length quantitative trait loci through RNA-Seq and linkage and physical mapping in cotton.BMC genomics · 2017Article
- Identification of genes related to salt stress tolerance using intron-length polymorphic markers, association mapping and virus-induced gene silencing in cotton.Scientific reports · 2017Article
- Diversity analysis of cotton (Gossypium hirsutum L.) germplasm using the CottonSNP63K Array.BMC plant biology · 2017Article
- Development, genetic mapping and QTL association of cotton PHYA, PHYB, and HY5-specific CAPS and dCAPS markers.BMC genetics · 2016Article
- A comparative transcriptome analysis of two sets of backcross inbred lines differing in lint-yield derived from a Gossypium hirsutum × Gossypium barbadense population.Molecular genetics and genomics : MGG · 2016Article
- Structure, evolution, and comparative genomics of tetraploid cotton based on a high-density genetic linkage map.DNA research : an international journal for rapid publication of reports on genes and genomes · 2016Article
- Assessment of Functional EST-SSR Markers (Sugarcane) in Cross-Species Transferability, Genetic Diversity among Poaceae Plants, and Bulk Segregation Analysis.Genetics research international · 2016Article
- Sequence-based ultra-dense genetic and physical maps reveal structural variations of allopolyploid cotton genomes.Genome biology · 2015Article
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Authors and funding
6 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundAvailability of molecular markers has proven to be an efficient tool in facilitating progress in plant breeding, which is particularly important in the case of less researched crops such as cotton. Considering the obvious advantages of single nucleotide polymorphisms (SNPs) and insertion-deletion polymorphisms (InDels), expressed sequence tags (ESTs) were analyzed in silico to identify SNPs and InDels in this study, aiming to develop more molecular markers in cotton.
resultsA total of 1,349 EST-based SNP and InDel markers were developed by comparing ESTs between Gossypium hirsutum and G. barbadense, mining G. hirsutum unigenes, and analyzing 3' untranslated region (3'UTR) sequences. The marker polymorphisms were investigated using the two parents of the mapping population based on the single-strand conformation polymorphism (SSCP) analysis. Of all the markers, 137 (10.16%) were polymorphic, and revealed 142 loci. Linkage analysis using a BC1 population mapped 133 loci on the 26 chromosomes. Statistical analysis of base variations in SNPs showed that base transitions accounted for 55.78% of the total base variations and gene ontology indicated that cotton genes varied greatly in harboring SNPs ranging from 1.00 to 24.00 SNPs per gene. Sanger sequencing of three randomly selected SNP markers revealed discrepancy between the in silico predicted sequences and the actual sequencing results.
conclusionsIn silico analysis is a double-edged blade to develop EST-SNP/InDel markers. On the one hand, the designed markers can be well used in tetraploid cotton genetic mapping. And it plays a certain role in revealing transition preference and SNP frequency of cotton genes. On the other hand, the developmental efficiency of markers and polymorphism of designed primers are comparatively low.
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