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BMC Genomics
2015 Mar 15;161:189. doi: 10.1186/s12864-015-1371-1.
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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.
Zhang N
,
Zhang L
,
Tao Y
,
Guo L
,
Sun J
,
Li X
,
Zhao N
,
Peng J
,
Li X
,
Zeng L
,
Chen J
,
Yang G
.
Abstract
BACKGROUND: Kelp (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.
RESULTS: We 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.
CONCLUSIONS: A 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.
Figure 1.
Microsatellite segregation pattern of mapping panel. Eight randomly selected gametophyte clones from mapping panel were genotyped with D5
(A); H45
(B) and H123
(C). The gametophyte clones of mapping panel segregate as expected.
Figure 2.
The decreasing number of quality tags. These tags were generated for parental female and male gametophyte clones (bar 1 and 2, respectively) and 140 gametophyte clones of mapping panel (bar 3 through 143).
Figure 3.
A brief illustration of the linkage map. The linkage map constructed was briefly shown. The illustrated include 31 linkage groups which are equal to the chromosomes reported early, and the unevenness of marker distribution on these groups. The horizontal bars represent linkage groups while the vertical (red) lines represent SNP markers.
Figure 4.
The number of gametophyte clones with different numbers of mapped RAD loci.
Figure 5.
The number of SNPs found at different nucleotide positions of RAD tags.
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