Genetic diversity of common carp from two largest Chinese lakes and the Yangtze River revealed by microsatellite markers

Six polymorphic microsatellites (eight loci) were used to study the genetic diversity and population structure of common carp from Dongting Lake (DTC), Poyang Lake (PYC), and the Yangtze River (YZC) in China. The gene diversity was high among populations with values close to 1. The number of alleles per locus ranged from 2 to 11, and the average number of alleles among 3 populations ranged from 6.5 to 7.9. The mean observed (H (O)) and expected (H (E)) heterozygosity ranged from 0.4888 to 0.5162 and from 0.7679 to 0.7708, respectively. Significant deviations from Hardy-Weinberg Equilibrium expectation were found at majority of the loci and in all three populations in which heterozygote deficits were apparent. The analysis of molecular variance (AMOVA) indicated that the percent of variance among populations and within populations were 3.03 and 96.97, respectively. The Fst values between populations indicated that there were significant genetic differentiations for the common carp populations from the Yangtze River and two largest Chinese freshwater lakes. The factors that may result in genetic divergence and significant reduction of the observed heterozygosity were discussed.

Macrozoobenthic community of Poyang Lake, the largest freshwater lake of China, in the Yangtze floodplain

Poyang Lake (Poyang Hu) is located at the junction of the middle and lower reaches of the Yangtze (Changjiang) River, covering an area of 3283 km(2). As one of the few lakes that are still freely connected with the river, it plays an important role in the maintenance of the unique biota of the Yangtze floodplain ecosystem. To promote the conservation of Poyang Lake, an investigation of the macrobenthos in the lake itself and adjoining Yangtze mainstream was conducted in 1997-1999. Altogether 58 benthic taxa, including, 22 annelids, 8 mollusks, 26 arthropods, and 2 miscellaneous animals, were identified from quantitative samples. The benthic fauna shows a high diversity and a marine affinity. The standing crops of benthos in the lake were much higher than those in the river, being 659 individuals/m(2) and 187.3g/m(2) (wet mass) in the main lake, and 549 individuals/m(2) and 116.6 g/m(2) in the lake outlet, but only 129 individuals/m(2) and 0.4g/m(2) in the river. The dominant roup in the lake was Mollusca, comprising 63.4% of the total in density and 99.5% in biomass. An analysis of the functional feeding structure indicated that collector-filterers and scrapers were predominant in the lake, up to 42.2% and 24.7% in density and 70.2% and 29.2% in biomass, respectively, while shredders and collector-gatherers were relatively common in the river. The present study was restricted to the northern outlet and the northeast part of Poyang Lake. A scrutiny is required for the remaining areas.

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 ranging 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.

A common SNP of MCPH1 is associated with cranial volume variation in Chinese population

Microcephaly (MCPH) genes are informative in understanding the genetics and evolution of human brain volume. MCPH1 and abnormal spindle-like MCPH associated (ASPM) are the two known MCPH causing genes that were suggested undergone recent positive selectio

The identification and quantification of highly stable 'common hairpin' in the dynamic process of co-transcriptional mRNA folding

In our studies, 88 human mRNA samples were collected from the Integrated Sequence-Structure database and then the dynamic process in co-transcriptional mRNA folding was simulated using the RNAstructure version 4.1 program. Through statistical analyses of the frequencies of occurrence of hairpins, a group of special folding structures-the 'common hairpins'-were identified. These 'common hairpins' have lower energies and occur in all the subsequent folding units that formed in the dynamic folding process. By applying the formulas (1)-(4) of the 'common hairpins' statistical model, 163 'common hairpins' were found, to make up about 7% of the total of 2286 hairpins. Classified studies further show that the 'common hairpins' that were studied may oscillate in the dynamic folding process. However, the hairpin loops of the 'common hairpins' and stems proximal to those 'common hairpins' loops maintain topologically stable structures, while other loops and stems distal to the 'common hairpins' loops are shown to be alterable structures. Strikingly, further studies indicate that the stable structures of these 'common hairpins' may have unbeknown effects on controlling the formation of protein structures in the translation process (unpublished results). (c) 2005 Elsevier B.V. All rights reserved.

A one-year investigation of the relationship between serum GH levels and the growth of F-4 transgenic and non-transgenic common carp Cyprinus carpio

It has been demonstrated that growth hormone (GH) transgenic fish often posses a trait for fast growth. Here, we investigated the growth of F-4 'all-fish' GH transgenic carp Cyprinus carpio and their serum GH levels for a year. The results showed that F-4 all-fish GH transgenic carp were significantly larger in body mass (c. two-fold, P < 0 center dot 001) and body length (c. 1 center dot 3 fold, P < 0 center dot 001), compared with the non-transgenic group. The discrepancy of serum GH levels between the transgenic carp group and control group is 54 fold, when the water temperature was 12-34 degrees C. When the water temperature decreased to 3 center dot 5 degrees C in January, the discrepancy was 256 fold. The serum GH level of the transgenic group was relatively constant, while that of control varied greatly based on month and water temperature. The changes of growth rates between the transgenic group and the control group were similar for a year. Taken together, the results indicated that F-4 all-fish GH transgenic carp had not only higher and constant serum GH levels but also a significant fast-growing effect, compared with the control. To our knowledge, this is the first report on a one-year investigation of growth trait and serum growth hormone level in F-4 all-fish GH transgenic carp.

Elevated ability to compete for limited food resources by 'all-fish' growth hormone transgenic common carp Cyprinus carpio

Food consumption, number of movements and feeding hierarchy of juvenile transgenic common carp Cyprinus carpio and their size-matched non-transgenic conspecifics were measured under conditions of limited food supply. Transgenic fish exhibited 73 center dot 3% more movements as well as a higher feeding order, and consumed 1 center dot 86 times as many food pellets as their non-transgenic counterparts. After the 10 day experiment, transgenic C. carpio had still not realized their higher growth potential, which may be partly explained by the higher frequency of movements of transgenics and the 'sneaky' feeding strategy used by the non-transgenics. The results indicate that these transgenic fish possess an elevated ability to compete for limited food resources, which could be advantageous after an escape into the wild. It may be that other factors in the natural environment (i.e. predation risk and food distribution), however, would offset this advantage. Thus, these results need to be assessed with caution.

Structure, organization and expression of common carp (Cyprinus carpio L.) NKEF-B gene

Natural killer (NK) cell enhancing factor (NKEF) belongs to the newly defined peroxiredoxin (Prx) family. Its functions are to enhance NK cell cytotoxicity and to protect DNA and proteins from oxidative damage. In this study, a partial cDNA sequence of carp NKEF-B was isolated from thymus cDNA library. Subsequently, the full-length cDNA of carp NKEF-B was obtained by means of 3' and 5' RACE, respectively. The full-length cDNA of carp NKEF-B was 1022 bp, consisting of a 73 bp 5'-terminal untranslated region (UTR), a 355 bp T-terminal UTR, and a 594 bp open reading frame coding for a protein of 197 amino acids. Carp NKEF-B contained two consensus Val-Cys-Pro (VCP) motifs and three consensus cysteine (Cys-51, Cys-70 and Cys-172) residues. Sequence comparison showed that the deduced amino acid sequence of carp NKEF-B had an overall similarity of 74-96% to that of other species homologues. Phylogenetic analysis revealed that carp NKEF-B forms a cluster with other known teleost NKEF-Bs. Then, by PCR we obtained a 5.1 -k long genomic DNA of carp NKEF-B containing six exons and five introns. Realtime RT-PCR results showed that carp NKEF-B gene was predominantly detected in kidney and head kidney under un-infected conditions. Whereas under SVCV-infection condition, the expression of NKEF-B gene was significantly increased in blood cells, gill, intestine and spleen, but maintained in liver, and decreased significantly in kidney and head kidney. Finally, the rNKEF-B was constructed and expressed in Escherichia coli. By using an antibody against carp rNKEF-B, immunohistochemical study further indicated that NKEF-B positive cells are mainly some RBCs and a few epithelial cells in gill and intestine, and that under SVCV-infection condition, these positive cells or positive products in their cytoplasm were mainly increased in gill and spleen sections of carp. The results obtained in the present study will help to understand the function of NKEF-B in teleost innate immunity. (C) 2008 Elsevier Ltd. All rights reserved.

Reduced swimming abilities in fast-growing transgenic common carp Cyprinus carpio associated with their morphological variations

Critical swimming speeds (U-crit) and morphological characters were compared between the F-4 generation of GH-transgenic common carp Cyprinus carpio and the non-transgenic controls. Transgenic fish displayed a mean absolute U-crit value 22.3% lower than the controls. Principal component analysis identified variations in body shape, with transgenic fish having significantly deeper head, longer caudal length of the dorsal region, longer standard length (L-S) and shallower body and caudal region, and shorter caudal length of the ventral region. Swimming speeds were related to the combination of deeper body and caudal region, longer caudal length of the ventral region, shallower head depth, shorter caudal length of dorsal region and L-S. These findings suggest that morphological variations which are poorly suited to produce maximum thrust and minimum drag in GH-transgenic C. carpio may be responsible for their lower swimming abilities in comparison with non-transgenic controls.

Metabolism traits of 'all-fish' growth hormone transgenic common carp (Cyprinus carpio L.)

Transgenic animals with improved qualities have the potential to upset the ecological balance of a natural environment. We investigated metabolic rates of 'all-fish' growth hormone (GH) transgenic common carp under routine conditions and during starvation periods to determine whether energy stores in transgenic fish would deplete faster than controls during natural periods of starvation. Before the oxygen uptake was measured, the mean daily feed intake of transgenic carp was 2.12 times greater than control fish during 4 days of feeding. The average oxygen uptake of GH transgenic fish was 1.32 times greater than control fish within 96 h of starvation, but was not significantly different from controls between 96 and 144 h of starvation. At the same time, GH transgenic fish did not deplete energy reserves at a faster rate than did the controls, as the carcass energy contents of the two groups following a 60-d starvation period were not significantly different. Consequently, we suggest that increased routine oxygen uptake in GH transgenic common carp over that of control fish may be mainly due to the effects of feeding, and not to an increase in basal metabolism. GH transgenic fish are similar to controls in the regulation of metabolism to normally distribute energy reserves during starvation. (c) 2008 Published by Elsevier B.V.

Determination of the surface area of common carp, Cyprinus carpio L.

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.