Xingguo Red Carp Research Articles

Genetic variation of common carp Cyprinus carpio L. in China based on mitochondrial COII gene

196 common carp (Cyprinus carpio L.) samples from five wild populations and ten domestic strains (six Chinese and four European) in China were collected and the genetic variation was analyzed using direct DNA sequencing of mitochondrial Cytochrome c oxidase subunit 2 gene (COII). As a result, a total of 22 haplotypes were identified, and one maternal ancestral haplotype (Hap_1) distributed in all populations exclusive of Songpu carp (SPC) and Hainan wild carp (HWC). For the other two major haplotypes, Hap_3 was mainly shared by German mirror carp (GMC) and populations from Amur River Basin, whereas Hap_16 appeared mainly in scatted scaled mirror carp (SSMC), Xingguo red carp (XGR), Songpu carp (SPC), and part of Yangtze River wild carp (YRWC). Although the genetic variance among populations accounted for only 27.79 % of the total variance, significant differentiation between HWC and other populations were spotted. The apparent split between HWC and other Eurasian populations supported the hypothesis that C. carpio emerged in East Asia as a species. Chinese wild populations exhibited highest genetic diversity (Hd = 0.801 ± 0.032; π = 0.0031 ± 0.0003), followed by introduced European strains (Hd = 0.735 ± 0.036; π = 0.0020 ± 0.0002) and Chinese domestic varieties (Hd = 0.657 ± 0.039, π = 0.0016 ± 0.0003). Significant negative Tajima’s D value was only found in SPC, which was probably the consequence of small founder size and subsequent population expansion.

Mitochondrial genome sequences reveal the evolutionary relationship among different common carp varieties (Cyprinus carpino L.)

In China, many common carp varieties have also been developed in the regional distribution and cultivation zones over thousands of years. However, little is known about the evolutionary relationship between these varieties. In the present study, the complete mitochondrial genomes of one wild and three domestic common carp varieties were compared. The results revealed that seven of 63 nucleotide substitutions led to radical amino acid replacements that may alter mitochondrial protein function. Three radical substitutions were found in complex I (ND4 and ND5) of Xingguo red carp. Furthermore, one amino acid substitution (P-S) was detected in the ATPase 6, and the variation within this region may be related to the high growth rate and high oxygen consumption rate of Russian scattered scale mirror carp. Phylogenetic analysis indicated that Xingguo red carp should be originated from Yangtze River wild common carp, while the purse red carp have a closer relationship with Yuanjiang wild common carp. In addition, phylogenetic analysis basing on the D-loop sequences also showed that Russian scattered scaled mirror carp and German mirror carp should be originated from the same ancestry.

Phylogeny and Evolution of Multiple Common Carp (Cyprinus carpio L.) Populations Clarified by Phylogenetic Analysis Based on Complete Mitochondrial Genomes.

Common carp (Cyprinus carpio L.) is one of the oldest, most widely farmed commercially important freshwater fish in the world. However, many undetermined phylogenetic relationships and origins of common carp lineages remain, which are obstacles to conservation and genetic breeding of this species. Phylogenetic analyses based on molecular tools are helpful to distinguish the origin of species, understand and clarify their evolutionary history, and provide a genetic basis for selective breeding. In this study, we demonstrated a method to extract complete mitochondrial genome sequences from whole-genome resequencing data using the Illumina platform. The complete mitochondrial genome sequences of 26 individuals representing nine strains were obtained and subjected to a phylogenetic analysis. We reconstructed the phylogenetic topologies of the nine strains and analyzed the haplotypes. Results from both analyses suggested that the genome sequences belonged to two distinct subspecies from Europe and East Asia. We also estimated the time of divergence of the nine strains, which was up to 100 KYA. The phylogenetic results clarified the breeding history of Songpu mirror carp and suggest that this species may be hybrid of paternal European mirror carp and maternal Xingguo red carp. The results also support a previous hypothesis that koi may have originated from or have close ancestry with Oujiang color carp in China.

Comparative transcriptome analysis reveals the genetic basis of skin color variation in common carp.

BackgroundThe common carp is an important aquaculture species that is widely distributed across the world. During the long history of carp domestication, numerous carp strains with diverse skin colors have been established. Skin color is used as a visual criterion to determine the market value of carp. However, the genetic basis of common carp skin color has not been extensively studied.Methodology/Principal FindingsIn this study, we performed Illumina sequencing on two common carp strains: the reddish Xingguo red carp and the brownish-black Yellow River carp. A total of 435,348,868 reads were generated, resulting in 198,781 assembled contigs that were used as reference sequences. Comparisons of skin transcriptome files revealed 2,012 unigenes with significantly different expression in the two common carp strains, including 874 genes that were up-regulated in Xingguo red carp and 1,138 genes that were up-regulated in Yellow River carp. The expression patterns of 20 randomly selected differentially expressed genes were validated using quantitative RT-PCR. Gene pathway analysis of the differentially expressed genes indicated that melanin biosynthesis, along with the Wnt and MAPK signaling pathways, is highly likely to affect the skin pigmentation process. Several key genes involved in the skin pigmentation process, including TYRP1, SILV, ASIP and xCT, showed significant differences in their expression patterns between the two strains.ConclusionsIn this study, we conducted a comparative transcriptome analysis of Xingguo red carp and Yellow River carp skins, and we detected key genes involved in the common carp skin pigmentation process. We propose that common carp skin pigmentation depends upon at least three pathways. Understanding fish skin color genetics will facilitate future molecular selection of the fish skin colors with high market values.

Complete mitochondrial genome of Xingguo red carp (Cyprinus carpio var. singuonensis) and purse red carp (Cyprinus carpio var. wuyuanensis)

The complete mitochondrial genomes of Xingguo red carp (Cyprinus carpio var. singuonensis) and purse red carp (Cyprinus carpio var. wuyuanensis) were sequenced. Comparison of these two mitochondrial genomes revealed that the mtDNAs of these two common carp varieties were remarkably similar in genome length, gene order and content, and AT content. However, size variation between these two mitochondrial genomes presented here showed 39 site differences in overall length. About 2 site differences were located in rRNAs, 3 in tRNAs, 3 in the control region, 31 in protein-coding genes. Thirty-one variable bases in the protein-coding regions between the two varieties mitochondrial sequences led to three variable amino acids, which were mainly located in the protein ND5 and ND4.

Genome-Wide SNP Discovery from Transcriptome of Four Common Carp Strains

BackgroundSingle nucleotide polymorphisms (SNPs) have been used as genetic marker for genome-wide association studies in many species. Gene-associated SNPs could offer sufficient coverage in trait related research and further more could themselves be causative SNPs for traits. Common carp (Cyprinus carpio) is one of the most important aquaculture species in the world accounting for nearly 14% of freshwater aquaculture production. There are various strains of common carp with different economic traits, however, the genetic mechanism underlying the different traits have not been elucidated yet. In this project, we identified a large number of gene-associated SNPs from four strains of common carp using next-generation sequencing.ResultsTranscriptome sequencing of four strains of common carp (mirror carp, purse red carp, Xingguo red carp, Yellow River carp) was performed with Solexa HiSeq2000 platform. De novo assembled transcriptome was used as reference for alignments, and SNP calling was done through BWA and SAMtools. A total of 712,042 Intra-strain SNPs were discovered in four strains, of which 483,276 SNPs for mirror carp, 486,629 SNPs for purse red carp, 478,028 SNPs for Xingguo red carp and 488,281 SNPs for Yellow River carp were discovered, respectively. Besides, 53,893 inter-SNPs were identified. Strain-specific SNPs of four strains were 53,938, 53,866, 48,701, 40,131 in mirror carp, purse red carp, Xingguo red carp and Yellow River carp, respectively. GO and KEGG pathway analysis were done to reveal strain-specific genes affected by strain-specific non-synonymous SNPs. Validation of selected SNPs revealed that 48% percent of SNPs (12 of 25) were tested to be true SNPs.ConclusionsTranscriptome analysis of common carp using RNA-Seq is a cost-effective way of generating numerous reads for SNP discovery. After validation of identified SNPs, these data will provide a solid base for SNP array designing and genome-wide association studies.

Genetic map construction and quantitative trait locus (QTL) analysis on growth-related traits in common carp (Cyprinus carpio L.)

Common carp (Cyprinus carpio L.) is one of the most widely distributed freshwater species in the world with important values in aquaculture, however, its quantitative trait loci (QTLs) associated to growth-related traits have been rarely identified. In this study, using F2 populations derived from a cross between Purse red common carp (C. carpio var. wuyuanensis) and Xingguo red common carp (C. carpio var.singuonensis), a genetic linkage map of common carp based on amplified fragment length polymorphisms (AFLP) and microsatellite (SSR) markers was constructed, meanwhile QTL analysis were conducted for growth-related traits. A total of 347 AFLP and 22 SSR markers were assembled on the map, which comprised 50 linkage groups and covered 5608.1cM Kosambi. A total of 25 QTLs were identified for growth-related traits, including four QTLs for body weight, one QTL for total length, four QTLs for standard length, six QTLs for body height, eight QTLs for caudal peduncle length and two QTLs for caudal peduncle height, which explained 0.05 to 61.40% of phenotypic variation. Meanwhile, comparison of linkage maps between common carp and zebrafish was also conducted, providing a new insight into the genetic base of the QTL affecting the growth-related traits. This study will be useful for conducting marker-assisted selection (MAS) breeding programs in common carp. Key words: Cyprinus carpio, F2 populations, amplified fragment length polymorphisms, microsatellite, quantitative traits locus.

Determination of the surface area of common carp,Cyprinus carpioL.

A wrap method adaptation combined with AutoCAD2005 and Scion Image for Windows were used to determine the surface area of a fish. Compared with the corresponding r(2) and F of many models, the most accurate formula: S = 752.15W(0.675) (r(2) = 0.999, F = 18362.94, P < 0.0001) for estimating the surface area of common carp was obtained. Similarly, the fin formula: S = 1834.12W(0.708) (r(2) = 0.992, F = 2690.47, P < 0.0001) was also obtained for the same purpose. It was proven that these two formulae gave good estimates of surface and fin areas of four strains of common carp: Yellow-river carp, fancy carp, mirror carp and Xingguo red carp.

Molecular phylogeny of three subspecies of common carp Cyprinus carpio, based on sequence analysis of cytochrome b and control region of mtDNA

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Genetic Variation Analysis within and among Six Varieties of Common Carp (Cyprinus carpio L.) in China Using Microsatellite Markers

Five microsatellites were used to study the genetic diversity and genetic structure of one wild and five domestic varieties of common carp in China (the Yangtze River wild common carp, Xingguo red carp, purse red carp, Qingtian carp, Russian scattered scaled mirror carp and Japanese decorative carp). All loci in this study showed marked polymorphism with the number of alleles from 4 to 13. Domestic varieties (except Xingguo red carp) showed less genetic diversity than the Yangtze River wild common carp in terms of allelic diversity. Population differentiation was assessed and each combination of populations displayed significant differentiation (p < 0.05) with the exception of that between the Yangtze River wild common carp and Xingguo red carp. Genetic distance analysis (Nei's standard genetic distance and pairwise F(st) distance) showed that the largest distance was between Russian scattered scaled mirror carp and the Yangtze River wild common carp and the smallest distance was between the Yangtze River wild common carp and Xingguo red carp. However, among six populations Japanese decorative carp displayed the highest level of variability in terms of heterozygosity.

Studies on fish heterosis with DNA fingerprinting

One Tilapia hybridization, Oreochromis aureus, (Steindachner) ♂ × Oreochromis niloticus, (Linnaeus) ♀, and two common carp, Cyprinus carpio, (Linnaeus) ♂, hybridizations, Russian mirror carp ♂ × Xingguo red carp ♀, and German mirror carp ♂ × Xingguo red carp ♀ were used to study the feasibility of predicting heterosis using genetic distance from DNA fingerprinting. The results indicated that highly polymorphic DNA fingerprints could be obtained with human minisatellite 33.6 as a probe on the studied varieties. The within-population similarity indices of O. aureus, O. niloticus, Russian mirror carp, German mirror carp and Xingguo red carp were 0.785, 0.577, 0.432, 0.348 and 0.339 respectively. The similarity indices between F1 and their parents of three hybridization combinations were not significantly different (P > 0.05). There were larger genetic distances between two hybridization combinations, O. aureus♂ × O. niloticus♀ and Russian mirror carp ♂ × Xingguo red carp ♀, which showed heterosis in production and were extensively used in Chinese aquaculture. The genetic distance between O. aureus♂ and O. niloticus♀ was 0.338, and that between Russian mirror carp and Xingguo red carp was 0.344. However, the genetic distance between German mirror carp and Xingguo red carp was 0.129; this corresponded with the fact that their F1 generation did not show heterosis in the Chinese fish hybridization experiment. The study suggested that genetic distance could be used to predict fish heterosis.

The formation of tetraploid stocks of red crucian carp×common carp hybrids as an effect of interspecific hybridization

F 3–F 8 hybrids of red crucian carp ( Carassius auratus red var.) (♀)×common carp ( Cyprinus carpio L.) (♂) were found to be allotetraploids by examining the numbers and karyotypes of chromosomes, the DNA content of red blood cells, and the mean nuclear erythrocyte volumes. The chromosome numbers of F 3–F 8 were 4 n=200. The chromosome numbers of two types of triploids produced by mating F 3–F 8 (♂), respectively, with diploid Japanese crucian carp ( C. auratus cuvieri T. et S.) (♀) and Xingguo red carp (♀) were 3 n=150. The mean DNA content of F 3 and the triploid are, respectively, two times and 1.5 times of that of diploid Japanese crucian carp. F 3 hybrids had mean erythrocyte nuclear volumes about two times larger than diploid Japanese crucian carp. The hybrids F 3–F 8 were fertile. It is easy for F 3–F 8 to produce their tetraploid offspring. The triploids were sterile. Based on the analysis of karyotype and the intermediate appearance with two pairs of small bases of barbels, F 3–F 8 hybrids were proved to be allotetraploids with two chromosome sets of red crucian carp and two chromosome sets of common carp. It is concluded that the females and males of F 2 hybrids were able to produce, respectively, diploid eggs and diploid spermatozoa and they fertilized to form tetraploid fish.

Application of the random amplified polymorphic DNA technique in a study of heterosis in common carp, Cyprinus carpio L.

Random amplified polymorphic DNA (RAPD) analysis was applied to three varieties of common carp, Cyprinus carpio L.: Xingguo red carp, German mirror carp and Russian mirror carp. Twenty-seven decamer primers pre-screened from 40 random primers were used to assay polymorphisms within and between the populations. One hundred and ninety-nine fragments were generated in the three populations; 155 of these fragments were polymorphic. The similarity indices and genetic distances within and between the three populations of carp were calculated. The results indicated that the highest value of similarity within populations was obtained for German mirror carp, and the genetic distance between Xingguo red carp and Russian mirror carp was the farthest. It can be presumed that the heterosis between Xingguo red carp and Russian mirror carp is the highest within these three populations.

An artificial multiple triploid carp and its biological characteristics

The chromosomes of the artificial triploid carp consist of three complete genomes from Xingguo red carp ( Cyprinus carpio), mirror carp ( Cyprinus carpio) and red crucian carp ( Carassius auratus). Starch and polyacrylamide gel analysis reveals that some SOD and s-MDH alleles of red crucian carp are undetectable in tissues of the artificial multiple triploid carp. It was found that the majority of oocytes of female artificial multiple triploid carp (XXX) developed to maturity, but spermatocytes of the male (XXY) developed abnormally and no spermatozoa were found. The external features of the triploid carp egg are quite different from those of normal diploid eggs. Sections of fertilized eggs reveal that the majority of eggs are polyspermous. Irradiated sperm was used to induce the gynogenesis of the artificial multiple triploid carp eggs. The eggs cleaved and developed normally, but the numbers of chromosomes of gastrular cells were variable, i.e., 50, 75, 100 and 150. This suggests that the behavior of the chromosomes in meiosis is polytypic, and some female nuclei of the eggs remain triploid after activation. All viable offspring of gynogenetic artificial multiple triploid carp are triploid and no segregation was found in their appearances, scale-covering type and body coloration.