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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1371-1) contains supplementary material, which is available to authorized users.
Highlights
Kelp (Saccharina japonica) has been intensively cultured in China for almost a century
The quality tags of a gametophyte clone were aligned into restriction site associated DNA (RAD)-tag piles with those covering only one tag discarded in order to ensure sequencing reliability
We identified a set of microsatellites, 99 in total, from the mapped and extended RAD tags following relatively strict standards, which distributed on all single nucleotide polymorphism (SNP) linkage groups (Additional files 2 and 4 in red color)
Summary
Kelp (Saccharina japonica) has been intensively cultured in China for almost a century. 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. In Chinese aquaculture community, Saccharina japonica is referred to as kelp [1,2] other species, e.g., giant kelp (Macrocystis pyrifera), have been tentatively cultured in recent years. Chinese kelp breeders and farmers call the cultured kelp either Japanese kelp or true kelp as its scientific name S. japonica indicated; the cultured kelp of China may have been contaminated genetically by S. longissima as two interspecific hybrids [3,4] and a hybrid-derived variety [5] at least have been developed and commercially cultured recently. Kelp has been integrated into environmental remediation and healthy animal culture systems in China
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