Development of a 690 K SNP array in catfish and its application for genetic mapping and validation of the reference genome sequence

[1]  Zhanjiang Liu,et al.  A genome-wide association study of heat stress-associated SNPs in catfish. , 2017, Animal genetics.

[2]  Jia-Le Li,et al.  Construction of a high-density genetic map and QTL mapping for pearl quality-related traits in Hyriopsis cumingii , 2016, Scientific Reports.

[3]  Degui Zhi,et al.  A Genome-Wide Association Study Identifies Multiple Regions Associated with Head Size in Catfish , 2016, G3: Genes, Genomes, Genetics.

[4]  B. Fu,et al.  A high-density genetic map and growth related QTL mapping in bighead carp (Hypophthalmichthys nobilis) , 2016, Scientific Reports.

[5]  Zhanjiang Liu,et al.  Transcriptome Display During Testicular Differentiation of Channel Catfish (Ictalurus punctatus) as Revealed by RNA-Seq Analysis1 , 2016, Biology of reproduction.

[6]  S. Koren,et al.  The channel catfish genome sequence provides insights into the evolution of scale formation in teleosts , 2016, Nature Communications.

[7]  Jian Xu,et al.  An ultra-high density linkage map and QTL mapping for sex and growth-related traits of common carp (Cyprinus carpio) , 2016, Scientific Reports.

[8]  K. Gerhardt.  Mother's Gut Arms Offspring , 2016, Biology of reproduction.

[9]  Li Li,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 , 2016, G3: Genes, Genomes, Genetics.

[10]  J. Kong,et al.  High-resolution genetic linkage mapping, high-temperature tolerance and growth-related quantitative trait locus (QTL) identification in Marsupenaeus japonicus , 2016, Molecular Genetics and Genomics.

[11]  H. Kucuktas,et al.  High-density interspecific genetic linkage mapping provides insights into genomic incompatibility between channel catfish and blue catfish. , 2016, Animal genetics.

[12]  Zhi-Yong Wang,et al.  Gene map of large yellow croaker (Larimichthys crocea) provides insights into teleost genome evolution and conserved regions associated with growth , 2015, Scientific Reports.

[13]  Pasi Rastas,et al.  Construction of Ultradense Linkage Maps with Lep-MAP2: Stickleback F2 Recombinant Crosses as an Example , 2015, Genome biology and evolution.

[14]  P. Liu,et al.  Construction of a high-density linkage map and fine mapping of QTL for growth in Asian seabass , 2015, Scientific Reports.

[15]  Chao Bian,et al.  Construction of the High-Density Genetic Linkage Map and Chromosome Map of Large Yellow Croaker (Larimichthys crocea) , 2015, International journal of molecular sciences.

[16]  Hongkun Zheng,et al.  Genome survey and high-density genetic map construction provide genomic and genetic resources for the Pacific White Shrimp Litopenaeus vannamei , 2015, Scientific Reports.

[17]  Shi Wang,et al.  Construction of a High-Density Genetic Map and Quantitative Trait Locus Mapping in the Sea Cucumber Apostichopus japonicus , 2015, Scientific Reports.

[18]  Jingwei Jiang,et al.  High-Density Genetic Mapping with Interspecific Hybrids of Two Sea Urchins, Strongylocentrotus nudus and S. intermedius, by RAD Sequencing , 2015, PloS one.

[19]  M. Bekaert,et al.  A new SNP-based vision of the genetics of sex determination in European sea bass (Dicentrarchus labrax) , 2015, Genetics Selection Evolution.

[20]  M. Samanta,et al.  Second-Generation Linkage Maps for the Pacific Oyster Crassostrea gigas Reveal Errors in Assembly of Genome Scaffolds , 2015, G3: Genes, Genomes, Genetics.

[21]  E. Peatman,et al.  Physiology and immunology of mucosal barriers in catfish (Ictalurus spp.) , 2015, Tissue barriers.

[22]  T. Koyama,et al.  Second generation physical and linkage maps of yellowtail (Seriola quinqueradiata) and comparison of synteny with four model fish , 2015, BMC Genomics.

[23]  Zhanjiang Liu,et al.  A genome-wide association study in catfish reveals the presence of functional hubs of related genes within QTLs for columnaris disease resistance , 2015, BMC Genomics.

[24]  J. Kong,et al.  High-Density Genetic Linkage Mapping in Turbot (Scophthalmus maximus L.) Based on SNP Markers and Major Sex- and Growth-Related Regions Detection , 2015, PloS one.

[25]  Songlin Chen,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 , 2015, DNA research : an international journal for rapid publication of reports on genes and genomes.

[26]  Kateryna D. Makova,et al.  The effects of chromatin organization on variation in mutation rates in the genome , 2015, Nature Reviews Genetics.

[27]  G. Amdam,et al.  Genomic correlates of recombination rate and its variability across eight recombination maps in the western honey bee (Apis mellifera L.) , 2015, BMC Genomics.

[28]  L. Bargelloni,et al.  Second generation genetic linkage map for the gilthead sea bream Sparus aurata L. , 2014, Marine genomics.

[29]  Zhanjiang Liu,et al.  Construction of a high-density, high-resolution genetic map and its integration with BAC-based physical map in channel catfish , 2014, DNA research : an international journal for rapid publication of reports on genes and genomes.

[30]  Maoxian He,et al.  Genetic Mapping and QTL Analysis of Growth-Related Traits in Pinctada fucata Using Restriction-Site Associated DNA Sequencing , 2014, PloS one.

[31]  Zhanjiang Liu,et al.  Identification and Analysis of Genome-Wide SNPs Provide Insight into Signatures of Selection and Domestication in Channel Catfish (Ictalurus punctatus) , 2014, PloS one.

[32]  R. Devlin,et al.  Comparative Mapping Between Coho Salmon (Oncorhynchus kisutch) and Three Other Salmonids Suggests a Role for Chromosomal Rearrangements in the Retention of Duplicated Regions Following a Whole Genome Duplication Event , 2014, G3: Genes, Genomes, Genetics.

[33]  Atushi Fujiwara,et al.  A ddRAD-based genetic map and its integration with the genome assembly of Japanese eel (Anguilla japonica) provides insights into genome evolution after the teleost-specific genome duplication , 2014, BMC Genomics.

[34]  Zhanjiang Liu,et al.  Development of the catfish 250K SNP array for genome-wide association studies , 2014, BMC Research Notes.

[35]  T. Cezard,et al.  Linkage maps of the Atlantic salmon (Salmo salar) genome derived from RAD sequencing , 2014, BMC Genomics.

[36]  M. Kent,et al.  The Development of a High Density Linkage Map for Black Tiger Shrimp (Penaeus monodon) Based on cSNPs , 2014, PloS one.

[37]  Kerry A. Naish,et al.  A Dense Linkage Map for Chinook salmon (Oncorhynchus tshawytscha) Reveals Variable Chromosomal Divergence After an Ancestral Whole Genome Duplication Event , 2013, G3: Genes, Genomes, Genetics.

[38]  Zhanjiang Liu,et al.  Bulk segregant RNA-seq reveals expression and positional candidate genes and allele-specific expression for disease resistance against enteric septicemia of catfish , 2013, BMC Genomics.

[39]  David B. Jones,et al.  A high-density SNP genetic linkage map for the silver-lipped pearl oyster, Pinctada maxima: a valuable resource for gene localisation and marker-assisted selection , 2013, BMC Genomics.

[40]  Xinhua Wang,et al.  A second generation genetic linkage map for silver carp (Hypophthalmichehys molitrix) using microsatellite markers , 2013 .

[41]  Xiaoting Huang,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 , 2013, DNA research : an international journal for rapid publication of reports on genes and genomes.

[42]  M. Bekaert,et al.  Mapping the sex determination locus in the Atlantic halibut (Hippoglossus hippoglossus) using RAD sequencing , 2013, BMC Genomics.

[43]  Zhanjiang Liu,et al.  Male-Biased Genes in Catfish as Revealed by RNA-Seq Analysis of the Testis Transcriptome , 2013, PloS one.

[44]  Zhanjiang Liu,et al.  RNA-Seq reveals expression signatures of genes involved in oxygen transport, protein synthesis, folding, and degradation in response to heat stress in catfish. , 2013, Physiological genomics.

[45]  Katsutoshi Watanabe,et al.  A RAD-based linkage map and comparative genomics in the gudgeons (genus Gnathopogon, Cyprinidae) , 2013, BMC Genomics.

[46]  Zhanjiang Liu,et al.  Efficient assembly and annotation of the transcriptome of catfish by RNA-Seq analysis of a doubled haploid homozygote , 2012, BMC Genomics.

[47]  Z. Sha,et al.  Second-Generation Genetic Linkage Map of Catfish and Its Integration with the BAC-Based Physical Map , 2012, G3: Genes | Genomes | Genetics.

[48]  Zhanjiang Liu,et al.  Transcriptomic signatures of attachment, NF-κB suppression and IFN stimulation in the catfish gill following columnaris bacterial infection. , 2012, Developmental and comparative immunology.

[49]  R. Guyomard,et al.  A synthetic rainbow trout linkage map provides new insights into the salmonid whole genome duplication and the conservation of synteny among teleosts , 2012, BMC Genetics.

[50]  Keith S. Sheppard,et al.  Discovery of novel variants in genotyping arrays improves genotype retention and reduces ascertainment bias , 2012, BMC Genomics.

[51]  Zhanjiang Liu,et al.  RNA-seq analysis of mucosal immune responses reveals signatures of intestinal barrier disruption and pathogen entry following Edwardsiella ictaluri infection in channel catfish, Ictalurus punctatus. , 2012, Fish & shellfish immunology.

[52]  S. Omholt,et al.  A dense SNP-based linkage map for Atlantic salmon (Salmo salar) reveals extended chromosome homeologies and striking differences in sex-specific recombination patterns , 2011, BMC Genomics.

[53]  Chun Ming Wang,et al.  A high-resolution linkage map for comparative genome analysis and QTL fine mapping in Asian seabass, Lates calcarifer , 2011, BMC Genomics.

[54]  Zhanjiang Liu,et al.  Generation of genome-scale gene-associated SNPs in catfish for the construction of a high-density SNP array , 2011, BMC Genomics.

[55]  J. Kawai,et al.  A second generation genetic linkage map of Japanese flounder (Paralichthys olivaceus) , 2010, BMC Genomics.

[56]  M. Rothschild,et al.  A gene-based SNP linkage map for pacific white shrimp, Litopenaeus vannamei. , 2010, Animal genetics.

[57]  R. Breaker,et al.  Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea, and their metagenomes , 2010, Genome Biology.

[58]  Feng Liu,et al.  A consensus linkage map of the grass carp (Ctenopharyngodon idella) based on microsatellites and SNPs , 2010, BMC Genomics.

[59]  S. Omholt,et al.  BAC-based upgrading and physical integration of a genetic SNP map in Atlantic salmon. , 2010, Animal Genetics.

[60]  Z. Sha,et al.  Assembly of 500,000 inter-specific catfish expressed sequence tags and large scale gene-associated marker development for whole genome association studies , 2010, Genome Biology.

[61]  J. Mank.  The evolution of heterochiasmy: the role of sexual selection and sperm competition in determining sex-specific recombination rates in eutherian mammals. , 2009, Genetics research.

[62]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[63]  Z. Sha,et al.  Construction of Genetic Linkage Maps and Comparative Genome Analysis of Catfish Using Gene-Associated Markers , 2009, Genetics.

[64]  Zhanjiang Liu,et al.  A BAC-based physical map of the channel catfish genome. , 2007, Genomics.

[65]  B. Zhu,et al.  Characterization of a BAC Library from Channel Catfish Ictalurus punctatus: Indications of High Levels of Chromosomal Reshuffling Among Teleost Genomes , 2007, Marine Biotechnology.

[66]  Lei Liu,et al.  Towards the ictalurid catfish transcriptome: generation and analysis of 31,215 catfish ESTs , 2007, BMC Genomics.

[67]  M. Duke,et al.  A first generation BAC-based physical map of the channel catfish genome , 2007, BMC Genomics.

[68]  M. Ron,et al.  Amh and Dmrta2 Genes Map to Tilapia (Oreochromis spp.) Linkage Group 23 Within Quantitative Trait Locus Regions for Sex Determination , 2006, Genetics.

[69]  P. Hunt,et al.  Sex, not genotype, determines recombination levels in mice. , 2005, American journal of human genetics.

[70]  Zhanjiang Liu,et al.  Bioinformatic Mining of Type I Microsatellites from Expressed Sequence Tags of Channel Catfish (Ictalurus punctatus) , 2004, Marine Biotechnology.

[71]  Zhanjiang Liu,et al.  An AFLP-based genetic linkage map of channel catfish (Ictalurus punctatus) constructed by using an interspecific hybrid resource family. , 2003, Genetics.

[72]  Zhanjiang Liu,et al.  Expression Profile of the Channel Catfish Spleen: Analysis of Genes Involved in Immune Functions , 2002, Marine Biotechnology.

[73]  Zhanjiang Liu,et al.  Transcriptome analysis of channel catfish (Ictalurus punctatus): initial analysis of gene expression and microsatellite-containing cDNAs in the skin. , 2002, Gene.

[74]  J. Postlethwait,et al.  Sex-specific recombination rates in zebrafish (Danio rerio). , 2002, Genetics.

[75]  A. Karsi,et al.  Transcriptome of channel catfish (Ictalurus punctatus): initial analysis of genes and expression profiles of the head kidney. , 2001, Animal genetics.

[76]  D. Nonneman,et al.  A microsatellite-based genetic linkage map for channel catfish, Ictalurus punctatus. , 2001, Genetics.

[77]  R. Dunham,et al.  Transcriptome analysis of channel catfish (Ictalurus punctatus): genes and expression profile from the brain. , 2000, Gene.

[78]  S. Khoo,et al.  A microsatellite linkage map of rainbow trout (Oncorhynchus mykiss) characterized by large sex-specific differences in recombination rates. , 2000, Genetics.

[79]  M. Kondo,et al.  A detailed linkage map of medaka, Oryzias latipes: comparative genomics and genome evolution. , 2000, Genetics.

[80]  Zhanjiang Liu,et al.  Development of Polymorphic EST Markers Suitable for Genetic Linkage Mapping of Catfish , 1999, Marine Biotechnology.

[81]  R. Dunham,et al.  Transcriptional activities in the pituitaries of channel catfish before and after induced ovulation by injection of carp pituitary extract as revealed by expressed sequence tag analysis. , 1998, Journal of molecular endocrinology.

[82]  R. Dunham,et al.  Inheritance and usefulness of AFLP markers in channel catfish (Ictalurus punctatus), blue catfish (I. furcatus), and their F1, F2, and backcross hybrids , 1998, Molecular and General Genetics MGG.

[83]  A. García-Dorado,et al.  On the use of the classical tests for detecting linkage. , 1992, The Journal of heredity.

[84]  R. Dunham,et al.  Karyology of Three Species of Catfishes (Ictaluridae: Ictalurus) and Four Hybrid Combinations , 1984 .

[85]  J. Ott,et al.  Strategies for multilocus linkage analysis in humans. , 1984, Proceedings of the National Academy of Sciences of the United States of America.