ArticleBMC genomics2017
Uncovering SNP and indel variations of tetraploid cottons by SLAF-seq.
Article in BMC genomics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- Screening of a core SNP set for the seedling identification of Saccharina japonica cultivars in northern China.PloS one · 2025Article
- Genetic linkage analysis of stable QTLs in Gossypium hirsutum RIL population revealed function of GhCesA4 in fiber development.Journal of advanced research · 2024Article
- Population structure and genetic diversity of mango (Frontiers in plant science · 2024Article
- Identification of molecular markers and candidate regions associated with grain number per spike in Pubing3228 using SLAF-BSA.Frontiers in plant science · 2024Article
- Discovery of DNA polymorphisms via genome-resequencing and development of molecular markers between two barley cultivars.Plant cell reports · 2022Article
- Genome-wide identification and development of InDel markers in tobacco (Physiology and molecular biology of plants : an international journal of functional plant biology · 2022Article
- SNP detection and population structure evaluation ofPhysiology and molecular biology of plants : an international journal of functional plant biology · 2021Article
- Genetic Divergence and Population Structure in Weedy and Cultivated Broomcorn Millets (Frontiers in plant science · 2021Article
- QTL Mapping for Leaf Area of Tea Plants (Frontiers in plant science · 2021Article
- Population Evolution, Genetic Diversity and Structure of the Medicinal Legume,Frontiers in plant science · 2021Article
- The Pivotal Role of Major Chromosomes of Sub-Genomes A and D in Fiber Quality Traits of Cotton.Frontiers in genetics · 2021Review
- Genome-wide dissection of hybridization for fiber quality- and yield-related traits in upland cotton.The Plant journal : for cell and molecular biology · 2020Article
- Identification of candidate genes for key fibre-related QTLs and derivation of favourable alleles in Gossypium hirsutum recombinant inbred lines with G. barbadense introgressions.Plant biotechnology journal · 2020Article
- Revealing Distinctions in Genetic Diversity and Adaptive Evolution Between Two Varieties ofFrontiers in plant science · 2020Article
- A high density SLAF-seq SNP genetic map and QTL for seed size, oil and protein content in upland cotton.BMC genomics · 2019Article
- Genome-wide analysis of genetic variations between dominant and recessive NILs of glanded and glandless cottons.Scientific reports · 2019Article
- Origin and parental genome characterization of the allotetraploid Stylosanthes scabra Vogel (Papilionoideae, Leguminosae), an important legume pasture crop.Annals of botany · 2018Article
- A high density SLAF-SNP genetic map and QTL detection for fibre quality traits in Gossypium hirsutum.BMC genomics · 2018Article
- Linkage and association mapping reveals the genetic basis of brown fibre (Gossypium hirsutum).Plant biotechnology journal · 2018Article
- QTL Mapping for Fiber Quality and Yield Traits Based on Introgression Lines Derived from Gossypium hirsutum × G. tomentosum.International journal of molecular sciences · 2018Article
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4 authors.
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Abstract
backgroundCotton (Gossypium spp.), as the world's most utilized textile fibre source, is an important, economically valuable crop worldwide. Understanding the genomic variation of tetraploid cotton species is important for exploitation of the excellent characteristics of wild cotton and for improving the diversity of cotton in breeding. However, the discovery of DNA polymorphisms in tetraploid cotton genomes has lagged behind other important crops.
resultsA total of 111,795,823 reads, 467,735 specific length amplified fragment (SLAF) tags and 139,176 high-quality DNA polymorphisms were identified using specific length amplified fragment sequencing (SLAF-seq), including 132,880 SNPs and 6,296 InDels between the reference genome (TM-1) and the five tetraploid cotton species. Intriguingly, gene ontology (GO) enrichment analysis revealed that a number of significant terms were related to reproduction in G. barbadense acc. 3-79. Based on the new data sets, we reconstructed phylogenetic trees that showed a high concordance to the phylogeny of diploid and polyploid cottons. A large amount of interspecific genetic variations were identified, and some of them were validated by the single-strand conformation polymorphism (SSCP) method, which will be applied in introgression genetics and breeding with G. hirsutum cv. Emian22 as the receptor and the other species as donors.
conclusionsUsing SLAF-seq, a large number of DNA polymorphisms were identified. The comprehensive analysis of DNA polymorphisms provided invaluable insights into the different tetraploid cotton species. More importantly, the identification of numerous interspecific genetic variations provides the basis and is very practical for future introgression breeding. The results presented herein provide a valuable genomic resource for new insights into the genetics and breeding of cotton.
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