RESUMO
A high-density linkage map of goldfish (Carassius auratus) was constructed using RNA-sequencing. This map consists of 50 linkage groups with 8,521 SNP markers and an average resolution of 0.62 cM. Approximately 84% of markers are in protein-coding genes orthologous to zebrafish proteins. We performed comparative genome analysis between zebrafish and medaka, common carp, grass carp, and goldfish to study the genome evolution events in the Cyprinidae family. The comparison revealed large synteny blocks among Cyprinidae fish and we hypothesized that the Cyprinidae ancestor undergone many inter-chromosome rearrangements after speciation from teleost ancestor. The study also showed that goldfish genome had one more round of whole genome duplication (WGD) than zebrafish. Our results illustrated that most goldfish markers were orthologous to genes in common carp, which had four rounds of WGD. Growth-related regions and genes were identified by QTL analysis and association study. Function annotations of the associated genes suggested that they might regulate development and growth in goldfish. This first genetic map enables us to study the goldfish genome evolution and provides an important resource for selective breeding of goldfish.
Assuntos
Evolução Biológica , Genoma , Carpa Dourada/genética , Animais , Mapeamento Cromossômico , Cyprinidae/genética , Cyprinidae/fisiologia , Carpa Dourada/crescimento & desenvolvimento , Carpa Dourada/fisiologia , Oryzias/genética , Polimorfismo de Nucleotídeo Único , Locos de Características Quantitativas , SinteniaRESUMO
The complete mitochondrial genome of Gnathopogon argentatus was determined to be 16,607 bp long circular molecule with a typical gene arrangement of vertebrate mitochondrial DNA. The complete mitochondrial genome of G. argentatus is 16,607 bp in length with 56.02% AT content, including 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and 1 control region. The complete mitochondrial genome of G. argentatus was obtained for the first time and would play an important role in population structure and conservation genetic studies.
Assuntos
Cyprinidae/genética , Genoma Mitocondrial , Animais , Pareamento de Bases/genética , Sequência de Bases , Códon/genética , DNA Mitocondrial/genética , Fases de Leitura Aberta/genética , RNA de Transferência/genéticaRESUMO
The complete mitochondrial genome of Hemiculter leucisculus was determined to be 16,617 bp. It contains the structure of 22 transfer RNA genes, 13 protein-coding genes, 2 ribosomal RNA genes, and non-coding control region (D-loop). The critical central conserved sequences (CSB-D, CSB-E, and CSB-F) were also detected. The determination of H. leucisculus mitogenome would play an important role in genetic diversity and population vitality in Cyprinidae.
Assuntos
Peixes/genética , Genoma Mitocondrial , Análise de Sequência de DNA , Animais , Fases de Leitura AbertaRESUMO
The complete mitochondrial genome of Saurogobio dabryi is 16,604 bp in length with 55.88% AT content, including 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and 1 control region. The termination-associated sequence and six conserved sequence blocks were also identified. Compared all protein-coding genes and whole genome sequence with four species, Saurogobio dabryi has higher similarity with Gobio gobio than others. The mitogenome sequence of Saurogobio dabryi would play an important role in population structure and conservation genetic studies.
Assuntos
Genoma Mitocondrial , Lagartos/genética , Mitocôndrias/genética , Animais , Composição de Bases , Tamanho do Genoma , Filogenia , Análise de Sequência de DNARESUMO
The complete mitochondrial genome of Amur sturgeon (Acipenser schrenckii) was determined in this study. The mitogenome is 16,684 bp in length and contains 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and 2 non-coding regions (the control region and the putative origin of the light strand replication) with a typical vertebrate mitochondrial gene arrangement. The overall base composition of the heavy strand is 30.07% for A, 29.36% for C, 16.44% for G and 24.13% for T, with a slight AT bias of 54.20%.
Assuntos
Peixes/genética , Genoma Mitocondrial , Animais , Dados de Sequência Molecular , Proteínas/genética , RNA Ribossômico/genética , RNA de Transferência/genéticaRESUMO
In this study, 149 polymorphic markers were screened from 200 microsatellite markers. From a family of mirror carp, which included 107 individuals. All samples were analyzed for body correlation, and intermuscular bone number was tested using the General Linear Model (GLM) single marker regression. Determination of the threshold values by 10,000 permutation tests showed that eight markers had significant correlation (P<0.05), in which HLJ3086, HLJ3642 and HLJ3515 had very significant correlation with intermuscular bone number (P<0.01). In addition, the genotypes of the captured correlative loci were determined by Duncan's test using SPSS17.0 software. Markers were used to screen the protein and nucleotide database in the National Center for Biotechnology Information (NCBI). Blasting results showed that HLJ2891 was highly correlated (92%) with latrophilin-2-like and HLJ3515 was highly correlated (81%) with serine/threonine-protein kinase 32B-like of zebrafish. These functional markers and genotypes may provide an efficient basis for marker-assisted selection of intermuscular bone number in mirror carp.
Assuntos
Tamanho Corporal , Osso e Ossos/química , Carpas/crescimento & desenvolvimento , Carpas/genética , Repetições de Microssatélites , Animais , Feminino , Genótipo , MasculinoRESUMO
Chinese sleeper (Perccottus glenii) belongs to the largest vertebrate order, Perciformes. In this study, the complete mitochondrial genome of P. glenii was determined to be 16,487 bp in length, including 13 protein-coding genes, 22 transfer RNA genes and 2 ribosomal RNA genes. We also analysed the sequence structure of non-coding control region. Comparing the mitochondrial genome of P. glenii with its congener Rhyacichthys aspro showed sequence similarity and the identical gene arrangement. The complete mitochondrial genome of Chinese sleeper provides the basis for the studies in Perciformes evolution and conservation.
Assuntos
DNA Mitocondrial/genética , Genes Mitocondriais/genética , Genoma Mitocondrial/genética , Perciformes/genética , Animais , Composição de Bases , Sequência de Bases , China , Ordem dos Genes/genética , Tamanho do Genoma/genética , Região de Controle de Locus Gênico/genética , Dados de Sequência Molecular , Análise de Sequência de DNA , Especificidade da EspécieRESUMO
Using 16 microsatellite loci we estimated the parentage of 647 progeny in 10 Jian Carp full-sib families. Cervus 3.0 analysis showed that mean PIC value of 16 microsatellites, mean number of allele, and mean expected heterozygosity were 0.7025, 6.63, and 0.7405, respectively. The combined probability of exclusion was 0.99922456 when both parents were unknown and the combined probability of exclusion was 0.99999557 when only one of the parental genotype was known, with the confidence level of 95%. Further simulations based on allele frequencies suggested that to achieve the requirements of paternity test usually took 8 to 12 microsatellite loci when both parents were unknown and 5 to 8 microsatellite loci when one parent was known. Out of 647 progenies, 94.6% were assigned to their parental pairs without the information of both parents in parentage analysis, which were lower than the theoretical assignment rates predicted by the Cervus simulations. This could be explained by the relationship between the candidate parents or existence of null and by typing errors. The identification of 9 families was useful for linkage analysis of Jian Carp and QTL location, also for marker assisted selection for economical traits.
Assuntos
Carpas/genética , Repetições de Microssatélites , Animais , Feminino , Ligação Genética , MasculinoRESUMO
Based on a full-sib family, the genetic linkage map was constructed with 246 microsatellite and 306 SNP markers, which was used to detect the QTLs for standard length (SL), body depth (H), body thickness (BT), and the ratio of standard length and body depth (SLH) in mirror carp by GridQTL software. The results indicated that a total of 14 related QTLs distributed on the 7 linkage groups were obtained. Seven QTLs were related to standard length, of which the linkage groups of LG6, LG17, LG21, LG23, and LG35 were at 5% significant level, and linkage group LG1 and LG28 were at 1% significant level, which explained 6.6%-12.6% of the phenotypic variance. Three QTLs were identified for body depth on the linkage groups of LG17, LG23 and LG28 (P amp; 0.01), accounting for 11.6%, 12.7%, and 15.6% of the phenotypic variance, respectively. Two QTLs were associated with body thickness on the linkage of LG23 and LG28 (P amp; 0.05), which explained 8.6% and 7.2% of the phenotypic variation, respectively. Two QTLs were responsible for the ratio of standard length and body depth on the linkage of LG21 and LG35 (P amp; 0.05), both of which explained 8.2% of the phenotypic variance. The results provide a useful reference for further candidate gene research and molecular marker assisted selection in mirror carp.
