Construction of a High-Density Genetic Map and Quantitative Trait Locus Mapping in the Manila clam Ruditapes philippinarum
Tóm tắt
Từ khóa
Tài liệu tham khảo
FAO 2015. Global Production Statistics 1950–2013: Ruditapes philippinarum [Internet] http://www.fao.org/figis/servlet/SQServlet?file=/work/FIGIS/prod/webapps/figis/temp/hqp_6100035986887626905.xml&outtype=html. Accessed 14 December 2015.
Won, E. J., Hong, S., Ra, K., Kim, K. T. & Shin, K. H. Evaluation of the potential impact of polluted sediments using Manila clam Ruditapes philippinarum: bioaccumulation and biomarker responses. Environ Sci Pollut Res Int 19, 2570–80 (2011).
Zhang, G. et al. The oyster genome reveals stress adaption and complexity of shell formation. Nature 490, 49–54 (2012).
Milan, M. et al. Transcriptome sequencing and microarray development for the Manila clam, Ruditapes philippinarum: genomic tools for environmental monitoring. BMC Genomics 12, 234 (2011).
Ghiselli, F. et al. De novo assembly of the Manila clam Ruditapes philippinarum transcriptome provides new insights into expression bias, mitochondrial doubly uniparental inheritance and sex determination. Mol Biol Evol 29, 771–786 (2012).
Moreira, R. et al. Transcriptomics of in vitro immune-stimulated hemocytes from the Manila clam Ruditapes philippinarum using high-throughput sequencing. PLoS ONE 7, e35009 (2012).
Hasanuzzaman, A. F. Md. et al. Transcriptomic profile of Manila clam (Ruditapes philippinarum) haemocytes in response to Perkinsus olseni infection. Aquaculture 467, 170–181 (2016).
Nie, H. T. et al. Transcriptomic responses to low temperature stress in the Manila clam, Ruditapes philippinarum. Fish Shellfish Immun 55, 358–366 (2016).
Knapik, E. W. et al. A microsatellite genetic linkage map for zebrafish (Danio rerio). Nat Genet 18, 338–343 (1998).
Yu, Y. et al. Genome survey and high-density genetic map construction provide genomic and genetic resources for the Pacific White Shrimp Litopenaeus vannamei. Scientific Reports 5, 15612 (2015).
Tian, M. et al. Construction of a High-Density Genetic Map and Quantitative Trait Locus Mapping in the Sea Cucumber Apostichopus japonicas. Scientific Reports 5, 14852 (2015).
Baxter, S. W. et al . Linkage mapping and comparative genomics using next-generation RAD sequencing of a non-model organism. PLoS ONE 6, doi:10.1371/journal.pone.0019315c (2011).
Moen, T. et al. A linkage map of the Atlantic salmon (Salmo salar) based on EST-derived SNP markers. BMC Genomics 9, 223 (2008).
Xia, J. H. et al. A consensus linkage map of the grass carp (Ctenopharyngodon idella) based on microsatellites and SNPs. BMC Genomics 11, 135 (2010).
Kucuktas, H. et al. Construction of genetic linkage maps and comparative genome analysis of catfish using gene-associated markers. Genetics 181, 1649–1660 (2009).
Guyomard, R. et al. A Type I and Type II microsatellite linkage map of Rainbow trout (Oncorhynchus mykiss) with presumptive coverage of all chromosome arms. BMC Genomics 7, 302 (2006).
Baranski, M. et al. The development of a high density linkage map for black tiger shrimp (Penaeus monodon) based on cSNPs. PLoS ONE 9, e85413 (2014).
Jiao, W. et al. High-resolution linkage and quantitative trait locus mapping aided by genome survey sequencing: building up an integrative genomic framework for a bivalve mollusc. DNA Res 21, 85–101 (2014).
Wang, J. et al. A High-Density SNP Genetic Linkage Map and QTL Analysis of Growth-Related Traits in a Hybrid Family of Oysters (Crassostrea gigas × Crassostrea angulata) Using Genotyping-by-Sequencing. G3-Genes Genomes Genetics 6(5), 1417–1426 (2016).
Carlson, B. M. et al. A High-Density Linkage Map for Astyanax mexicanus Using Genotyping-by-Sequencing Technology. G3-Genes Genomes Genetics 5, 241–251 (2015).
Davey, J. W. et al. Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nat Rev Genet 12, 499–510 (2011).
Elshire, R. J. et al. A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS ONE 6, e19379 (2011).
Rowe, H. C., Renaut, S. & Guggisberg, A. RAD in the realm of next generation sequencing technologies. Mol Ecol 20, 3499–3502 (2011).
Everett, M. V., Miller, M. R. & Seeb, J. E. Meiotic maps of sockeye salmon derived from massively parallel DNA sequencing. BMC Genomics 13, 521 (2012).
Li, C. et al. SNP discovery in wild and domesticated populations of blue catfish, Ictalurus furcatus, using genotyping-by-sequencing and subsequent SNP validation. Mol Ecol Resour 14, 1261–1270 (2014).
Hecht, B. C., Campbell, N. R., Holecek, D. E. & Narum, S. R. Genome-wide association reveals genetic basis for the propensity to migrate in wild populations of rainbow and steelhead trout. Mol Ecol 22, 3061–3076 (2013).
Larson, W. A. et al. Genotyping by sequencing resolves shallow population structure to inform conservation of Chinook salmon (Oncorhynchus tshawytscha). Evol Appl 7, 355–369 (2014).
Hess, J. E. et al. Use of genotyping-by-sequencing data to develop a high throughput and multi-functional SNP panel for conservation applications in Pacific lamprey. Mol Ecol Resour 15, 187–202 (2015).
Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754–1760 (2009).
He, J. et al. Genotyping-bysequencing (GBS), an ultimate marker-assisted selection (MAS) tool to accelerate plant breeding. Front Plant Sci 5, 484 (2014).
Poland, J. et al. Genomic selection in wheat breeding using genotyping-by-sequencing. Plant Genome 5, 103–113 (2012).
Ward, J. A. et al. Saturated linkage map construction in Rubus idaeus using genotyping by sequencing and genome-independent imputation. BMC Genomics 14, 2 (2013).
Zhang, G. F. & Yan, X. W. Development of new three-phase culture methods for Manila clam, Ruditapes philippinarum, farming in northern China. Aquaculture 258, 452–261 (2006).
Chiesa, S. et al. The invasive Manila clam Ruditapes philippinarum (Adams and Reeve, 1850) in Northern Adriatic Sea: population genetics assessed by an integrated molecular approach. Fish Res 110, 259–267 (2011).
An, H. S., Park, W. J., Cho, K. C., Han, H. S. & Myeong, J.-I. Genetic structure of Korean populations of the clam Ruditapes philippinarum inferred from microsatellite marker analysis. Biochem Syst Ecol 44, 186–195 (2012).
Mura, L. et al. Genetic variability in the Sardinian population of the manila clam. Ruditapes philippinarum. Biochem Syst Ecol 41, 74–82 (2012).
Yasuda, N., Nagai, S., Yamaguchi, S., Lian, C. L. & Hamaguchi, M. Development of microsatellite markers for the Manila clam Ruditapes philippinarum. Mol Ecol Notes 7, 43–45 (2007).
An, H. S., Kim, E. M. & Park, J. Y. Isolation and characterization of microsatellite markers for the clam Ruditapes philippinarum and cross-species amplification with the clam Ruditapes variegate. Conserv Genet 10, 1821–1823 (2009).
Hurtado, N. S., Pérez-García, C., Morán, P. & Pasantes, J. J. Genetic and cytological evidence of hybridization between native Ruditapes decussatus and introduced Ruditapes philippinarum (Mollusca, Bivalvia, Veneridae) in NW Spain. Aquaculture 311, 123–128 (2011).
Kitada, S. et al. Molecular and morphological evidence ofhybridization between native Ruditapes philippinarum and the introduced Ruditapes form in Japan. Cons Genet 14, 717–733 (2013).
Gaur, R. et al. High-throughput SNP discovery and genotyping for constructing a saturated linkage map of chickpea (Cicer arietinum L.). DNA Res 19, 357–373, doi:10.1093/dnares/dss018 (2012).
Simakov, O. et al. Insights into bilaterian evolution from three spiralian genomes. Nature 493, 526–531 (2013).
Jiao, W. et al. High-resolution linkage and quantitative trait locus mapping aided by genome survey sequencing: building up an integrative genomic framework for a bivalve mollusc. DNA Res 21, 85–101 (2014).
Grattapaglia, D. & Sederoff, R. Genetic linkage maps of Eucalyptus grandis and Eucalyptus urophylla using a pseudo-testcross: mapping strategy and RAPD markers. Genetics 137, 1121–1137 (1994).
Shi, Y. et al. High-density single nucleotide polymorphisms linkage and quantitative trait locus mapping of the pearl oyster, Pinctada fucata martensii Dunker. Aquaculture 434, 376–384 (2014).
Andriantahina, F., Liu, X. & Huang, H. Genetic map construction and quantitative trait locus (QTL) detection of growth-related traits in Litopenaeus vannamei for selective breeding applications. PLoS ONE 8, e75206 (2013).
Kakioka, R. et al. A RAD-based linkage map and comparative genomics in the gudgeons (genus Gnathopogon, Cyprinidae). BMC Genomics 14, 32 (2013).
Palaiokostas, C. et al. Mapping the sex determination locus in the Atlantic halibut (Hippoglossus hippoglossus) using RAD sequencing. BMC Genomics 14, 566 (2013).
Sun, X. W. et al. SLAF-seq: An Efficient Method of Large-Scale De Novo SNP Discovery and Genotyping Using High-Throughput Sequencing. PLoS ONE 8, e58700 (2013).
Wang, C. M. et al. A high-resolution linkage map for comparative genome analysis and QTL fine mapping in Asian seabass, Lates calcarifer. BMC Genomics 12, 174 (2011).
Shao, C. et al. Genome-wide SNP identification for the construction of a high-resolution genetic map of Japanese flounder (Paralichthys olivaceus): applications to QTL mapping of Vibrio anguillarum disease resistance and comparative genomic analysis. DNA Res 22, 161–170 (2015).
Alcivar-Warren, A. et al. ShrimpMap: A low-density, microsatellite-based linkage map of the pacific whiteleg shrimp, Litopenaeus vannamei: Identification of sex-linked markers in linkage group 4. J shellfish Res 26, 1259–1277 (2007).
Lyons, R. E. et al. Identification and characterization of QTL markers for growth traits in Kuruma shrimp P. japonicus. Aquaculture 272, S284–285 (2007).
Van Ooijen, J. W. & Voorrips, R. E. JoinMap® 3.0, Software for the calculation of genetic linkage maps. Wageningen (the Netherlands), Plant Research International (2001).