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Construction of a high-density genetic map and mapping of a sex-linked locus for the brown alga Undaria pinnatifida (Phaeophyceae) based on large scale marker development by specific length amplified fragment (SLAF) sequencing.

Shan T, Pang S, Li J, Li X, Su L - BMC Genomics (2015)

Bottom Line: A major sex associated QTL was mapped to LG22 within a window starting at 29.01 cM and ending at 68.81 cM with a total of 68 SLAF markers.For the first time, a major sex associated QTL suggesting a sex determining region was mapped to a single LG.This map will facilitate the further fundamental and applied research such as QTL mapping and map-based gene clone in U. pinnatifida and provide a reference for studies in other kelp species.

View Article: PubMed Central - PubMed

Affiliation: Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, PR China. shantifeng@qdio.ac.cn.

ABSTRACT

Background: Undaria pinnatifida is an important economic brown alga in East Asian countries. However, its genetic and genomic information is very scarce, which hinders further research in this species. A high-density genetic map is a basic tool for fundamental and applied research such as discovery of functional genes and mapping of quantitative trait loci (QTL). In this study the recently developed specific length amplified fragment sequencing (SLAF-seq) technology was employed to construct a high-density genetic linkage map and locate a sex determining locus for U. pinnatifida.

Results: A total of 28.06 Gb data including 140.31 M pair-end reads was obtained. After linkage analysis 4626 SLAF markers were mapped onto the genetic map. After adding the sex linked simple sequence repeat (SSR) marker [GenBank:AY738602.1], the final genetic map was 1816.28 cM long, consisting of 30 linkage groups with an average distance of 0.39 cM between adjacent markers. The length of LGs ranged from 20.12 to 106.95 cM. A major sex associated QTL was mapped to LG22 within a window starting at 29.01 cM and ending at 68.81 cM with a total of 68 SLAF markers. The SSR marker and five SLAF markers (Marker6556, 19020, 43089, 60771 and 26359) were identified as tightly sex-linked markers, as indicated by the absence of recombination between them and the sex phenotype. These markers were located at the position of 59.50 cM, which was supposed to be the sex determining region.

Conclusions: A high-density genetic linkage map was constructed using SLAF-seq technique and F1 gametophyte population for the first time in the economically important brown alga U. pinnatifida. For the first time, a major sex associated QTL suggesting a sex determining region was mapped to a single LG. This map will facilitate the further fundamental and applied research such as QTL mapping and map-based gene clone in U. pinnatifida and provide a reference for studies in other kelp species.

No MeSH data available.


Related in: MedlinePlus

The number of markers in each of eight segregation patterns
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Fig1: The number of markers in each of eight segregation patterns

Mentions: The SLAFs number of maternal and paternal parent was 134,975 and 139,873, with an average coverage of 50.88 and 54.39 fold, respectively. The SLAFs number in the offspring was 104,831, with an average coverage of 8.16 fold (Table 1). In total, 202,572 high-quality SLAFs were developed and 33,093 of them were polymorphic, with a polymorphism percentage of 16.34 % (Table 2). Among the polymorphic SLAFs, 26,887 were classified into eight segregation patterns. Because the mapping population was the F1 haploid population, only SLAFs with the aa × bb segregation pattern was used for genetic map construction. A total of 24,320 SLAFs fell into this class (Fig. 1). After filtering out the SLAFs with the sequencing coverage less than 10 fold in parents, or integrity less than 70 %, or that showing significant segregation distortion (P < 0.05), 4821 SLAFs were obtained and used for construction of the linkage map.Table 1


Construction of a high-density genetic map and mapping of a sex-linked locus for the brown alga Undaria pinnatifida (Phaeophyceae) based on large scale marker development by specific length amplified fragment (SLAF) sequencing.

Shan T, Pang S, Li J, Li X, Su L - BMC Genomics (2015)

The number of markers in each of eight segregation patterns
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4635539&req=5

Fig1: The number of markers in each of eight segregation patterns
Mentions: The SLAFs number of maternal and paternal parent was 134,975 and 139,873, with an average coverage of 50.88 and 54.39 fold, respectively. The SLAFs number in the offspring was 104,831, with an average coverage of 8.16 fold (Table 1). In total, 202,572 high-quality SLAFs were developed and 33,093 of them were polymorphic, with a polymorphism percentage of 16.34 % (Table 2). Among the polymorphic SLAFs, 26,887 were classified into eight segregation patterns. Because the mapping population was the F1 haploid population, only SLAFs with the aa × bb segregation pattern was used for genetic map construction. A total of 24,320 SLAFs fell into this class (Fig. 1). After filtering out the SLAFs with the sequencing coverage less than 10 fold in parents, or integrity less than 70 %, or that showing significant segregation distortion (P < 0.05), 4821 SLAFs were obtained and used for construction of the linkage map.Table 1

Bottom Line: A major sex associated QTL was mapped to LG22 within a window starting at 29.01 cM and ending at 68.81 cM with a total of 68 SLAF markers.For the first time, a major sex associated QTL suggesting a sex determining region was mapped to a single LG.This map will facilitate the further fundamental and applied research such as QTL mapping and map-based gene clone in U. pinnatifida and provide a reference for studies in other kelp species.

View Article: PubMed Central - PubMed

Affiliation: Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, PR China. shantifeng@qdio.ac.cn.

ABSTRACT

Background: Undaria pinnatifida is an important economic brown alga in East Asian countries. However, its genetic and genomic information is very scarce, which hinders further research in this species. A high-density genetic map is a basic tool for fundamental and applied research such as discovery of functional genes and mapping of quantitative trait loci (QTL). In this study the recently developed specific length amplified fragment sequencing (SLAF-seq) technology was employed to construct a high-density genetic linkage map and locate a sex determining locus for U. pinnatifida.

Results: A total of 28.06 Gb data including 140.31 M pair-end reads was obtained. After linkage analysis 4626 SLAF markers were mapped onto the genetic map. After adding the sex linked simple sequence repeat (SSR) marker [GenBank:AY738602.1], the final genetic map was 1816.28 cM long, consisting of 30 linkage groups with an average distance of 0.39 cM between adjacent markers. The length of LGs ranged from 20.12 to 106.95 cM. A major sex associated QTL was mapped to LG22 within a window starting at 29.01 cM and ending at 68.81 cM with a total of 68 SLAF markers. The SSR marker and five SLAF markers (Marker6556, 19020, 43089, 60771 and 26359) were identified as tightly sex-linked markers, as indicated by the absence of recombination between them and the sex phenotype. These markers were located at the position of 59.50 cM, which was supposed to be the sex determining region.

Conclusions: A high-density genetic linkage map was constructed using SLAF-seq technique and F1 gametophyte population for the first time in the economically important brown alga U. pinnatifida. For the first time, a major sex associated QTL suggesting a sex determining region was mapped to a single LG. This map will facilitate the further fundamental and applied research such as QTL mapping and map-based gene clone in U. pinnatifida and provide a reference for studies in other kelp species.

No MeSH data available.


Related in: MedlinePlus