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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

Linkage group 22 and the location of cosegregating markers with the sex phenotype
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Fig4: Linkage group 22 and the location of cosegregating markers with the sex phenotype

Mentions: In the QTL linkage analysis of sex phenotype, the threshold of LOD was determined to be 4.1 (P = 0.01). A major sex associated locus 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 (Figs. 3, 4 and Additional file 5). The SSR marker (UP-AC-2A8) and five SLAF markers (Marker 6556, 19020, 43089, 60771 and 26359) were identified as tightly sex-linked markers, as indicated by the zero recombination rate between them and sex phenotype. These markers were located at the position of 59.50 cM (Fig. 4). In blast search against unigene database of U. pinnatifida, Marker 60771 showed significant similarity to the unigene CL11961Contig1, which was annotated as an unnamed protein product of Chondrus crispus (Additional files 6 and 7). Marker 43089 had significant similarities to CL134Contig1 and CL1827Contig1, with the former being annotated as a hypothetical protein of E.siliculosus and the latter unannotated.Fig. 3


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)

Linkage group 22 and the location of cosegregating markers with the sex phenotype
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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

Fig4: Linkage group 22 and the location of cosegregating markers with the sex phenotype
Mentions: In the QTL linkage analysis of sex phenotype, the threshold of LOD was determined to be 4.1 (P = 0.01). A major sex associated locus 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 (Figs. 3, 4 and Additional file 5). The SSR marker (UP-AC-2A8) and five SLAF markers (Marker 6556, 19020, 43089, 60771 and 26359) were identified as tightly sex-linked markers, as indicated by the zero recombination rate between them and sex phenotype. These markers were located at the position of 59.50 cM (Fig. 4). In blast search against unigene database of U. pinnatifida, Marker 60771 showed significant similarity to the unigene CL11961Contig1, which was annotated as an unnamed protein product of Chondrus crispus (Additional files 6 and 7). Marker 43089 had significant similarities to CL134Contig1 and CL1827Contig1, with the former being annotated as a hypothetical protein of E.siliculosus and the latter unannotated.Fig. 3

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