Study On Genetic Diversity Of Red Common Carps In China

Red common carps are very important genetics breeding materials in China, but the study about genetics diversity is scare, quantitative genetics have been hardly evaluated by now. In China, there is a special common carp, Oujiang color common carp, which has a variety of body color with very great value, however, any study have not been done for exploitation and utilization. Base on these current status, genetic diversity, genetics effect and breeding value of red common carps were systematically studied in this paper, the aims were made to broadly and deeply understand the genetic diversity of red common carps in China, and to replenish the study blank about fisheries quantitative genetics in China. Meanwhile, the study on exploitation and utilization of Oujiang color common carp (focused on genetic relationship analysis between body color and relative economic traits) was undertaken to make theoretical and technical foundation in breeding of ornament carp with beautiful colors and table color carp with fast growth. The content of the paper includes three parts as following: Part ⅠGenetic Difference and Relationship of Red Common Carps in China 1 Morphological Difference The traditional biostatistics analysis and modern cluster analysis, discriminant analysis, principle component analysis were combined to conduct a multivariation analysis about 8 countable characters,10 traditional meristic characters and 20 truss network meristic characters of Glass red common carp (Cyprinus carpio var.wananensis), Xingguo red common carp (Cyprinus carpio var. xinguonensis), Purse red common carp (Cyprinus carpi var. wuyuanensi) and Oujiang color common carp (Cyprinus carpio .var. color), the results indicated that : (1) There were no significant differences among these four kinds of red common carps in countable characters (P>0.05); (2) In meristic characters , the cluster analysis indicated that Oujiang color common carp, Xingguo red common carp and Glass red common carp were close to each other , and Purse red common carp was far from the above three carps; The discriminant analysis indicated that there were extremely significant differences among these four kinds of red common carps (P<0.01), the discriminant accuracy was 98.06%, and the synthetic discriminant accuracy from constructed discriminant function of four kinds of red common carp was 92.13%, discriminant result showed highly significant difference(P<0.01); The principle component analysis indicated that the morphological differences among four kinds of red common carps mostly caused by variations in front part of body shape. The results from cluster analysis, discriminant analysis and principle component analysis all showed that the morphology of purse red common carp differentiated from the other three red common carps, and the morphological difference of these four red common carps can be well differentiated by these three analysis methods. 2 Biochemical Genetic Difference 10 kinds of isoenzymes (proteins) of Xingguo red common carp, glass red common carp, purse red common carp and Oujiang color common carp were analyzed by polyacrylamide gel electrophoresis. The percentage of polymorphic loci was : purse red common carp (21.05%) > Oujiang color common carp (15.79%)= glass red common carp (15.79%) > Xingguo red common carp (10.53%); Average heterozygosity (expected value) was: Oujiang color common carp (0.0742) > purse red common carp (0.0721) > glass red common carp (0.0653) > Xingguo red common carp (0.0458); the genetic diversity of Oujiang color common carp was the richest and Xingguo red common carp was the poorest; the phylogenetics relationship tree established based on biochemical genetics distance indicated Xingguo red common carp,glass red common carp,Oujiang color common carp were close to each other, but purse red common carp was far from above three carp.3 RAPD Analysis of Genomic Genetic Difference Genetic diversity of Xingguo red common carp, glass red common carp, purse red common carp and Oujiang color common carp was studied by Random Amplified Polymorphic DNA (RAPD) analysis with 40 arbitrary primers. The results indicated 3 rows of distinctive bands could be observed, the 570bp band amplified by primer S11 was only observed in glass red common carp, the 660bp band amplified by primer S50 in purse red common carp, and the 510bp band amplified by primer S52 in Oujiang color common carp; The genetic similarity index of four red common carp was: Oujiang color common carp (0.2074) > purse red common carp (0.1706) > Xingguo red common carp (0.1516) > glass red common carp (0.1342); The average genetic similarity index within each population ranked as: Oujiang color common carp (0.771)< purse red common carp 0.786 glass red common carp(0.0491) > Oujiang color common carp (0.0102) > purse red common carp (0.0000), the nucleotide diversity among populations indicated that purse red common carp had obviously difference from the other three red common carps; (2) The polymorphism of α3 gene was very lower than that ofα2 gene sequence, there were only 8 nucleotide variable loci in 135bp studied sequence, the percentage of polymorphic nucleotide lociwas 5.93%; the nucleotide diversity within population was glass red common carp (0.0241) > Xingguo red common carp(0.0164) > purse red common carp (0.0101) > Oujiang color common carp(0.0075); the nucleotide diversity among populations indicated that there were the highest variability between Xingguo red common carp and purse red common carp and the least variability between glass red common carp and purse red common carp. (3) The phylogenetic tree constructed by nucleotide sequences of α2 gene was consistent with that of deduced amino acid sequences of α2 gene, Xingguo red common carp was close to Oujiang color common carp, purse red common carp was far away from other three red common carps. (4) The phylogenetic trees constructed by nucleotide sequences of α3 gene showed that Xingguo red common carp was close to purse red common carp, but the phylogenetic trees by deduced amino acid sequence showed Xingguo red common carp was close to Oujiang color common carp; (5) Xingguo red common carp and glass red common carp had been undertaken more selective stress than purse red common carp and Oujinag color common carp, and genetic bottleneck would had been happened in purse red common carp. (5) Combined α2 with α3 gene and their amino acid sequences, the results indicated that the relationship between Xingguo red common carp and Oujiang color common carp was the closest, and they came from the common evolutionary branch, whereas glass red common carp and Purse red common carp came from another 2 different evolutionary branch. (5) α2 gene had higher polymorphism than α3 gene, so it suitable to be used as molecular genetic marker for identification of these populations. 5 The Evolutionary Relationship (1) RFLP Analysis of Mitochondrial DNA RFLP analysis of mtDNA from Xingguo red common carp, glass red common carp, purse red common carp and Oujiang color common carp was conducted by 13 restriction endonucleases. The results indicated that: (1) There were 17 restriction morphs in all red carps and 5 of which were polymorphic and could be sorted into 5 haplotypes; (2) The average nucleotide diversity was ranked as: Oujiang color common carp(2.86%) > purse red common carp (1.47%) > Xingguo red common carp (1.18%) > glass red common carp (0.86%), the genetic diversity of Oujiang color common carp was the richest; (3) Oujiang color common carp living in Zhejiang province and glassred common carp, purse red common carp living in Jiangxi province originated from two different maternal ancestors, Oujiang color common carp and Xingguo red common carp originated early, about 90,000~115,000(9~11.5 ten thousands) years, and purse red common carp and glass red common carp originated lately, about 25,000~60,000(2.5~6 ten thousands) years. (2) Analysis of Mitochondria COⅡGene Sequence Mitochondrial COⅡgene sequences about 607bp fragment length of Xingguo red common carp, glass red common carp, purse red common carp, Oujiang color common carp, Guangxi long-fin red common carp, Oujiang wild common carp and Japanese Koi carp were analyzed by combined PCR with DNA sequencing technique to take insight of phylogenetic relationship of red carps, the results indicated that: (1)there were all 23 nucleotide variable loci among 7 common carps and 2 of which were insert/lack loci, the percentage of nucleotide polymorohic loci was 3.79%, the ratio of average transition numbers and transversion numbers of nucleotides was 2.3; (2) the obvious nucleotide diversity was observed between the group of wild common carp, glass red common carp , purse red common carp and the group of Xingguo red common carp , Oujiang color red common carp , Guangxi long-fin red common carp and Japanese Koi carp, but obvious nucleotide diversity was not observed among Oujiang color common carp, Guangxi long-fin red common carp, Xingguo red common carp and Japanese Koi common carp, the lowest nucleotide diversity (0.0000-0.0001) existed among Oujiang color common carp, Guangxi long-fin red common carp and Japanese Koi common carp. (3) The low genetic distance among 7 common carps indicated there were the short originated history among them, the originated history of red common carps in China ranked as Oujiang color common carp> Xingguo red common carp > purse red common carp > glass common carp > Guangxi long-fin common carp. (4)The molecular phylogenetic trees showed that the group of glass red common carp and purse red common carp and the group of Xingguo red common carp, Oujiang color common carp, Guangxi long-fin red common carp, Japanese Koi common carp originated from two different ancestors. Japanese Koi carp may originated from China and shared the common ancestor with the Oujiang color common carp. (5) The gene flow between Guangxi long-fin carp and Japanese Koi carp may resulted in high degree of relationship among Oujiang color carp, Guangxi long-fin carp and Japanese Koi carp.(3) The Genetic Relationship of Oujiang Color Common Carp, Guangxi Long-fin Carp and Japanese Koi Carp (RAPD Analysis) Genetic relationship of 3 kinds of color common carps of Oujiang color common carp, Guangxi long-fin common carp and Japanese Koi carp was studied by RAPD analysis with 40 arbitrary primers of 10 base pairs. (1) The genetic diversity index ranked as Oujiang color common carp(0.2229) > Guangxi long-fin common carp (0.2164) > Japanese Koi carp(0.1165) , the genetic similarity indexes within populations was Japanese Koi carp(0.8974) > Guangxi long-fin common carp(0.6936) > Oujiang color common carp(0.6888). (2) The total genetic divergence index (Gst) among 3 populations was 0.5819, and the high genetic divergence index was showed between Japanese Koi carp and another two populations in China. (3) The relationship tree constructed by NJ method showed that Oujiang color common carp was the closest to Japanese Koi carp, Japanese Koi carp would originated from China and shared the common ancestor with the Oujiang color common carp or directly originated from Oujiang color common carp . Part ⅡQuantitative Genetics Analysis of Red Common Carps in China 6 Genetic Analysis of Genotype --Environment Interaction Effect in Bodyweight and Morphological Traits Genetic effects for 11 traits, such as body-weight and standard length were analyzed by using genotype –environment interaction genetic model, the results indicated that: The bodyweight ,total length, standard length ,head length ,snout length ,distance between eyes and caudal peduncle length were controlled by dominant effect and also affected by genotype --environment interaction effect, the dominance variance of these 7 traits accounted for over 50% of total genetic variance, which showed that these 7 traits are controlled by the main genetic effect. The dominant variance (accounted for over 80% of total genetic variance) for bodyweight was extremely significant different,the genotype --environment interaction variance of body weight was very low, which showed heterosis would be easily gained in practice. The genotype --environment interaction variance for body depth, body width, eye diameter and caudal peduncle depth were significant different, which showed that these 4 traits were controlled by genotype --environment interaction effect. The heritabilities in the broad sense for these 11 traits were very high, but the heritabilities in the narrow sense were very low, which showed selection and breeding in red carps would be difficult in practice. but the heterosis would be easily to be got. Additive effects of parents and dominance effects of F1 hybrids were also predicated and the results showed the heterosis from the hybrids of Xingguo red carp ×Oujiang color carp would been significant. 7 Genetic Analysis of Paternal Effect and Maternal Effect for Body-weight and Morphological Traits The paternal effect and maternal effect were analyzed by using diallel crossing biology model. the paternal effect of 11 traits were not observed, the significant maternal effect in only 3 traits of full length, body width and body height were examined as well as the significant paternal --environment interaction were examined in 4 traits of the standard length ,eye diameter, distance between eyes and caudal peduncle length. The significant mater --environment interaction of 10 traits (except for eye diameter) were observed, In conclusion, maternal effect would be higher than paternal effect and the body shape of hybrids would close to their mother. 8 Development Genetics Analysis of the Body-weight and Morphological Traits in Different Months of One-year Old An additive –dominance mixed genetic model with genotype –environment interaction was employed to analyze the genetic behavior and gene expression difference of the traits of bodyweight ,standard length, body depth. The results indicated that the unconditional variance and conditional variance in each month were not significant. but according to the variance components in each month, a useful information was presented that body weight were controlled by additive variance before July and was controlled by the dominance –environment interaction variance after Aug. During August and September of red carps with fast growth, additive gene and dominance gene expressed more actively than before, especially additive gene, meanwhile, environmental effect was low at the same time. the expression of additiveeffect gene and dominant effect gene drop after October. According to developmental genetic analysis information, selection made during the 1-2 month (June-July) after hatched of fry and during 6-7 month (November-December) would be effective. 9 Preliminary Study on Molecular Genetics Basis of Heterosis RAPD analysis from genomic DNA of Xingguo red common carp, purse red common carp, Oujiang color common carp and their hybrids was employed in this paper. The results showed that the more the genetics difference between parents, the higher significance of heterozygosity in hybrids. The hybrids share the more genetic similarity with maternal individuals than paternal individuals because of hybrids gained mitochondrial DNA from maternal individuals. It was very limited to predicate the heterosis by RAPD analysis and it was difficult to explain heterosis mechanism and predict heterosis through simple molecular marker (especially RAPD maker)by now. Part ⅢGenetic Relationship between Body Color and Major Economic Traits in Oujiang Color Common Carp 10 Preliminary Study on Body Color Genetic Capability The experiment of self-mating and cross-mating from Oujiang color common carp with different pigmentation types were conducted to study the genetic characters of body color, the results indicated that: (1). The body color has been steadily presented when the fry growed about three months. (2). The experiment of self-mating of the parents with the same pigmentation types showed the frequency of body color of offspring with the same body color with their parents was rather high, more than 70% individuals of generation F1 shared the same pigmentation types with their parent's, the frequency in generation F2 was higher than that in generation F1 , which indicated that the frequency of body color gene can be added in filial generations and it is very possible to select a series of stead strain of color common carp with different pigmentation types. (3). The experiment of cross-mating of the parents with different types showed that the body color of "whole red" was dominant to "red color with bigblack spots", and " black spots" was dominant to "non-black spots". gene R and r control the appearance of red and white body colors, gene B and b control the appearance of black spots. The speculating genes controlling the Five kinds of body color were R_bb ("whole red"), R_B_ ("red color with big black spots"), R_B'_ ("red color with small big spots"), rrbb ("whole white") and rrB_ ("white color with big black spots"). But in some hybridization combinations, body color segregation in filial generation did not consistent with Mendel`s Segregation Principle , which showed body color inheritance mechanism of color common carp was complex and next study need to be conducted. 11 Correlation between Body Color and Growth Performance In 2000 , the growth experiments on Oujiang color common carp with five pigmentation types of one-year old (reared in concrete tank) and two-year old(reared in net case in reservoir) were conducted. In 2001, the growth experiment on Oujiang color common carp with five pigmentation types reared in different environments ( concrete tank, paddy field and net cage in reservoir) were also conducted. the results indicated that: (1) the experiment of one-year old in 2000, AGRW and IGRW of body weight among these pigmentation types ranked as "red color with big black spots">" red color with small black spots"> "white color with big black spots"> "whole red "> "whole white"(P<0.01); the experiment of two-year old in 2000, AGRW and IGRW of "red color with big black spots"and "whole white"were significantly higher than those of other three kinds of pigmentation types. (2) At paddy field environment in 2001, AGRW and IGRW of "whole white"and "red color with small black spots"extremely significant higher than those of the other three kinds pigmentation types (P<0.01); At net cage environment in 2001, AGRW and IGRW of "red color with big black spots", "whole white"and "whole color with big black spots "were extremely significant higher than those of "whole red"and "red color with small black spots"(P<0.01); At concrete tank environment in 2001, AGRW and IGRW of "red color with big black spots"were extremely significant higher than those of other four kinds of pigmentation types (P<0.01), but the other four kinds of pigmentation types had no significant difference in growth rate (P>0.05). (3) There was a linkage between body color and growth character ; "whole red"and "red color with small black spots"are more suitable to be reared in paddy field than to be reared in concrete tank and net cage with broadand deep water body , "red color with big black spots", "whole white"and "white color with big black spots"were more suitable to be reared in concrete tank and net cages than to be reared paddy field; (4) "white color with big black spots"showed the most obvious genotype -environment interaction, it is need to pay attention to its rearing management, and to create more suitable environment to develop its growth superiority. 12 Correlation between Body Color and Reproduction Characters The reproduction character of color male and female carp with five different pigmentation types at two and three years old were studied, the result indicated that : There were no significant difference in gonadosomatic index, egg gravity, absolute fecundity and Relative fecundity among female color carps with five different pigmentation types(P<0.05). and no significant difference in gonadosomatic index among male color carps with five different pigmentation types (P<0.05).