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High-Density Genetic Mapping with Interspecific Hybrids of Two Sea Urchins, Strongylocentrotus nudus and S. intermedius, by RAD Sequencing.

Zhou Z, Liu S, Dong Y, Gao S, Chen Z, Jiang J, Yang A, Sun H, Guan X, Jiang B, Wang B - PLoS ONE (2015)

Bottom Line: A genome-wide scan resulted in the identification of one putative QTL for body size which spanned from 25.3 cM to 30.3 cM.This study showed the efficiency of RAD-Seq based high-density genetic map construction using F1 progenies for species with no prior genomic information.The integration of the genetic map with genome assembly would provide an unprecedented opportunity to conduct QTL analysis, comparative genomics, and population genetics studies.

View Article: PubMed Central - PubMed

Affiliation: Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning, 116023, China.

ABSTRACT
Sea urchins have long been used as research model organisms for developmental biology and evolutionary studies. Some of them are also important aquaculture species in East Asia. In this work, we report the construction of RAD-tag based high-density genetic maps by genotyping F1 interspecific hybrids derived from a crossing between a female sea urchin Strongylocentrotus nudus and a male Strongylocentrotus intermedius. With polymorphisms present in these two wild individuals, we constructed a female meiotic map containing 3,080 markers for S. nudus, and a male meiotic map for S. intermedius which contains 1,577 markers. Using the linkage maps, we were able to anchor a total of 1,591 scaffolds (495.9 Mb) accounting for 60.8% of the genome assembly of Strongylocentrotus purpuratus. A genome-wide scan resulted in the identification of one putative QTL for body size which spanned from 25.3 cM to 30.3 cM. This study showed the efficiency of RAD-Seq based high-density genetic map construction using F1 progenies for species with no prior genomic information. The genetic maps are essential for QTL mapping and are useful as framework to order and orientate contiguous scaffolds from sea urchin genome assembly. The integration of the genetic map with genome assembly would provide an unprecedented opportunity to conduct QTL analysis, comparative genomics, and population genetics studies.

No MeSH data available.


Genetic map of female Strongylocentrotus nudus.
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pone.0138585.g003: Genetic map of female Strongylocentrotus nudus.

Mentions: We constructed the female- and male-specific maps separately due to the large differences between the two species. Both female and male genetic maps were composed of 21 linkage groups (Figs 3 and 4), which is consistent with the chromosome number of haploid genome of S. nudus and S. intermedius [23, 24]. The homology of linkage groups between S. nudus and S. intermedius was determined based on the locations of their markers on the scaffolds of the S. purpuratus genome assembly. The one-to-one homologous relationships were clearly developed as listed in Table 1.


High-Density Genetic Mapping with Interspecific Hybrids of Two Sea Urchins, Strongylocentrotus nudus and S. intermedius, by RAD Sequencing.

Zhou Z, Liu S, Dong Y, Gao S, Chen Z, Jiang J, Yang A, Sun H, Guan X, Jiang B, Wang B - PLoS ONE (2015)

Genetic map of female Strongylocentrotus nudus.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4580576&req=5

pone.0138585.g003: Genetic map of female Strongylocentrotus nudus.
Mentions: We constructed the female- and male-specific maps separately due to the large differences between the two species. Both female and male genetic maps were composed of 21 linkage groups (Figs 3 and 4), which is consistent with the chromosome number of haploid genome of S. nudus and S. intermedius [23, 24]. The homology of linkage groups between S. nudus and S. intermedius was determined based on the locations of their markers on the scaffolds of the S. purpuratus genome assembly. The one-to-one homologous relationships were clearly developed as listed in Table 1.

Bottom Line: A genome-wide scan resulted in the identification of one putative QTL for body size which spanned from 25.3 cM to 30.3 cM.This study showed the efficiency of RAD-Seq based high-density genetic map construction using F1 progenies for species with no prior genomic information.The integration of the genetic map with genome assembly would provide an unprecedented opportunity to conduct QTL analysis, comparative genomics, and population genetics studies.

View Article: PubMed Central - PubMed

Affiliation: Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning, 116023, China.

ABSTRACT
Sea urchins have long been used as research model organisms for developmental biology and evolutionary studies. Some of them are also important aquaculture species in East Asia. In this work, we report the construction of RAD-tag based high-density genetic maps by genotyping F1 interspecific hybrids derived from a crossing between a female sea urchin Strongylocentrotus nudus and a male Strongylocentrotus intermedius. With polymorphisms present in these two wild individuals, we constructed a female meiotic map containing 3,080 markers for S. nudus, and a male meiotic map for S. intermedius which contains 1,577 markers. Using the linkage maps, we were able to anchor a total of 1,591 scaffolds (495.9 Mb) accounting for 60.8% of the genome assembly of Strongylocentrotus purpuratus. A genome-wide scan resulted in the identification of one putative QTL for body size which spanned from 25.3 cM to 30.3 cM. This study showed the efficiency of RAD-Seq based high-density genetic map construction using F1 progenies for species with no prior genomic information. The genetic maps are essential for QTL mapping and are useful as framework to order and orientate contiguous scaffolds from sea urchin genome assembly. The integration of the genetic map with genome assembly would provide an unprecedented opportunity to conduct QTL analysis, comparative genomics, and population genetics studies.

No MeSH data available.