ArticleBMC genomics2015
Construction of a high density SNP linkage map of kelp (Saccharina japonica) by sequencing Taq I site associated DNA and mapping of a sex determining locus.
Article in BMC genomics, 2015. 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.
- Genetic association of toxin production in the dinoflagellateMicrobial genomics · 2022Article
- Single-base methylome profiling of the giant kelp Saccharina japonica reveals significant differences in DNA methylation to microalgae and plants.The New phytologist · 2020Article
- High-Density Linkage Map and Mapping for Sex and Growth-Related Traits of Largemouth Bass (Frontiers in genetics · 2019Article
- Article
- Construction of a highly saturated Genetic Map for Vitis by Next-generation Restriction Site-associated DNA Sequencing.BMC plant biology · 2018Article
- High-density SNP-based QTL mapping and candidate gene screening for yield-related blade length and width in Saccharina japonica (Laminariales, Phaeophyta).Scientific reports · 2018Article
- Low recombination rates in sexual species and sex-asex transitions.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2017Article
- Quantitative trait loci from identification to exploitation for crop improvement.Plant cell reports · 2017Review
- High-density genetic map and identification of QTLs for responses to temperature and salinity stresses in the model brown alga Ectocarpus.Scientific reports · 2017Article
- Algal Cell Factories: Approaches, Applications, and Potentials.Marine drugs · 2016Review
- Improving seedless kelp (Saccharina japonica) during its domestication by hybridizing gametophytes and seedling-raising from sporophytes.Scientific reports · 2016Article
- Development of a universal and simplified ddRAD library preparation approach for SNP discovery and genotyping in angiosperm plants.Plant methods · 2016Article
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12 authors.
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No grant is acknowledged in the PubMed record.
Abstract
backgroundKelp (Saccharina japonica) has been intensively cultured in China for almost a century. Its genetic improvement is comparable with that of rice. However, the development of its molecular tools is extremely limited, thus its genes, genetics and genomics. Kelp performs an alternative life cycle during which sporophyte generation alternates with gametophyte generation. The gametophytes of kelp can be cloned and crossed. Due to these characteristics, kelp may serve as a reference for the biological and genetic studies of Volvox, mosses and ferns.
resultsWe constructed a high density single nucleotide polymorphism (SNP) linkage map for kelp by restriction site associated DNA (RAD) sequencing. In total, 4,994 SNP-containing physical (tag-defined) RAD loci were mapped on 31 linkage groups. The map expanded a total genetic distance of 1,782.75 cM, covering 98.66% of the expected (1,806.94 cM). The length of RAD tags (85 bp) was extended to 400-500 bp with Miseq method, offering us an easiness of developing SNP chips and shifting SNP genotyping to a high throughput track. The number of linkage groups was in accordance with the documented with cytological methods. In addition, we identified a set of microsatellites (99 in total) from the extended RAD tags. A gametophyte sex determining locus was mapped on linkage group 2 in a window about 9.0 cM in width, which was 2.66 cM up to marker_40567 and 6.42 cM down to marker_23595.
conclusionsA high density SNP linkage map was constructed for kelp, an intensively cultured brown alga in China. The RAD tags were also extended so that a SNP chip could be developed. In addition, a set of microsatellites were identified among mapped loci, and a gametophyte sex determining locus was mapped. This map will facilitate the genetic studies of kelp including for example the evaluation of germplasm and the decipherment of the genetic bases of economic traits.
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