Yongxin Liu

Genetic analysis for main length ratio associated with morphological traits in Japanese flounder Paralichthys olivaceus

The objective of this study was to estimate genetic parameters of main length ratios associated with morphological traits in Paralichthys olivaceus. At 180, 240 and 360 days of age, body length (L1 ), head length (L2 ), body depth (L3 ), caudal peduncle depth (L4 ) and caudal-peduncle length (L5 ) were observed in 4757-5224 individuals from 52 full-sib families. Based on these observed traits, the main length-ratio traits including L3 :L1 , L2 :L1 , L5 :L1 and L4 :L3 were constructed. Three single-trait animal models were used to examine the phenotypic variation of length-ratio traits and were compared using the likelihood ratio test. As a result, the optimal model for all the analysed traits was determined as the model with the fixed, additive genetic and full-sib family effects. Using the optimal model, animal model analysis for single trait showed that heritabilities were estimated to be low, ranging from 0·122 to 0·276. The estimates for all length-ratio traits decreased while the days of age increased except for L3 :L1 . Multivariate animal model analysis indicated that within and among days of age, genetic correlations between length-ratio traits were different in the direction and magnitude. Genetic parameter estimation of main length ratios would be helpful for genetic improvement of body shape in P. olivaceus.

Constructing a genetic linkage map and mapping quantitative trait loci for skeletal traits in Japanese flounder

A genetic linkage map of Japanese flounder was constructed using 165 doubled haploids (DHs) derived from a single female. A total of 574 genomic microsatellites (type II SSRs) and expressed sequence tag (EST)-derived markers (EST-SSRs) were mapped to 24 linkage groups. The length of linkage map was estimated as 1270.9 centiMorgans (cM), with an average distance between markers of 2.2 cM. The EST-SSRs were used together with type II SSR markers to construct the Japanese flounder genetic linkage map which will facilitate identify quantitative trait locus (QTL) controlling important economic traits in Japanese flounder. Thus, twelve skeletal traits at 2 years of age were measured for all DHs. Forty-one QTLs were detected on 14 linkage groups and totally account for a small proportion of phenotypic variation (4.5 to 17.3%). Most of QTLs detected distribute on linkage groups 5 (9 QTLs), 8 (9 QTLs), 9 (5 QTLs) and 20 (4 QTLs), in which, some QTLs perform the pleiotropy.

Choice of microsatellite markers for identifying homozygosity of mitotic gynogenetic diploids in Japanese flounder Paralichthys olivaceus.

A set of 72 microsatellite markers distributed evenly among 24 linkage groups were selected from the published genetic linkage maps of Japanese flounder Paralichthys olivaceus. In two normal diploid full-sib families, the test for Mendelian inheritance showed that genotypic segregation deviations were not significant at all analysed loci. To estimate microsatellite-centromere map distances, four meiotic gynogenetic diploid lines were produced by the activation of eggs using UV irradiated sperm of red seabream Pagrus major and cold-shock treatment to block the extrusion of the second polar body. Under the assumption of complete interference, 21 markers were located in the centromeric region, 39 in the telomeric region and the rest in the intermediate region of linkage groups. A total of 192 mitotic gynogenetic diploids from one spawn were identified by these markers. Genotype analysis showed that the number of homozygous individuals decreased as microsatellite-centromere map distance increased on each linkage group.

China is initiating the Aquatic 10-100-1,000 Genomics Program

1Chinese Academy of Fishery Sciences, Beijing 100141, China; 2BGI Research Center for Aquatic Genomics, Chinese Academy of Fishery Sciences, Shenzhen 518083, China; 3Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China; 4BGI Shenzhen Academy of Marine Sciences, BGI Fisheries, BGI, Shenzhen 518083, China; 5Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China; 6Marine Research Center, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China

Analysis of genetic diversity in Bohai natural population of Paralichthys olivaceus

To analyze the genetic diversity of natural population and select the specific microsatellite markers for identifying effectively genetic characteristics of population in Japanese flounder( Paralichthys olivaceus)in this study,seventy-four w ild individuals captured from the Bohai Sea w ere used to form the experimental population. A set of 72 microsatellite markers located on different regions in linkage group w ere chosen to carry out the genetic analysis. In these markers,17 w ere located in the centromeric region,36 in the distant region from the centromere and 19 in the intermediate region of linkage groups. Analysis show ed that the number of alleles( A) ranged from 6. 400 to 7. 389,number of effective alleles( N e) ranged from 4. 469 to5. 129 and Shannons information index( I) ranged from 1. 565 to 1. 683 in different regions of linkage group. The observed heterozygosity( H o),unbiased expected heterozygosity( H e) and polymorphism information content( PIC) w as from 0. 568 to 0. 593,from 0. 738 to 0. 753 and from 0. 707 to 0. 746,respectively. The Hardy-Weinberg departure value( d) w as low er than- 0. 200,w hile,genetic distance( G D)among individuals in population w as above than 0. 620. Each genetic parameter demonstrated that there w as richer genetic diversity in experimental population and relatively farther genetic distance among individuals.This population w as suitable for conducting selective breeding as founder population. Significant difference did not exist in the genetic parameters obtained by microsatellite markers located on different regions in linkage group,w hich verified that there w as no necessary correlation betw een the positions of marker located and the degree of genetic diversity of markers. How ever,these polymorphic markers could be used as marker candidates to analyze the genetic structure in population of Japanese flounder.

Identifying genetic characteristics of different diploids in Japanese flounder based on M-C mapping

To analyze the effects of microsatellite markers located in different positions in linkage group on identifying genetic characteristics of different diploids in Japanese flounder in this study,the mature spawners selected from Japanese flounder selection and breeding flounder were used to produce the normal diploids(ND),meiotic gynogenetic diploids(MGD-1),successive two generation meiotic gynogenetic diploids(MGD-2)and inbred diploid(MGD1H)by crossing mature female from MGD-1 with induced sex reversed male.A set of 72 microsatellite markers distributed evenly in 24 linkage groups were selected from the published genetic linkage maps of Japanese flounder.To estimate microsatellite-centromere map distances,four MGD-1 lines were produced.Under the assumption of complete interference,17 markers were located in the centromeric region,36 in the distant region from the centromere and 19 in the intermediate region of linkage groups.The genetic characteristics of four types of diploid in Japanese flounder were identified by these markers.Analysis showed that the number of allele(A)and polymorphism information content(PIC)have limited variation range,in which the A and PIC of ND were the highest while those of MGD1H were the lowest.In four types of diploid,the observed heterozygosity decreased and homozygosity increased as microsatellite-centromere map distance increased.The highest and lowest percentages of homozygous individuals were found in centromeric region from 8.8% to 29.1% and in telomeric region from 2.4% to 23.2%,respectively.The variation ranges of MGD-1and MGD-2 were significantly higher than that of the other diploids.The results demonstrated that choice of microsatellite markers located in different positions in linkage group has great impact on identifying genetic characteristics of different diploids in Japanese flounder.

Correlation analysis of microsatelIite DNA markers with skeletal growth traits of Japanese flounder (Paralichthys olivaceus)

In this article,106 microsatellite markers were used to analyze the genotype of sixty-two mitotic gynogenetic doubled haploids of Japanese flounder,Paralichthys olivaceus.Measurement results of body length and height were got by directly measuring skeleton during the process of X-ray imaging.Correlation and regression analysis of the body weight,length and height were conducted by utilizing SPSS 13.0 soft-ware.Least square method was used to analyze the effects of these 106 microsatellites on body weight,length and height of these 62 doubled haploids.Results revealed that 17 microsatellites were discovered to be very significantly related to body weight,length and height.During these 17 markers,Poli2042TUF,Poli1980TUF,Poli2045TUF,Poli2039TUF,Poli34TUF,PoGT17,HLJYP45,HLJYP81 had a significant impact on body length(P0.05),Poli102TUF,Poli136TUF,Poli62MHFS,6-G3 had a significant impact on body height(P0.05),Poli72HFSM、Poli106TUF had a significant impact on body weight and height(P0.05),Poli2023TUF,Poli1013TUF had a significant impact on body length and height(P0.05),Po-li162TUF had a significant impact on body weight,length and height(P0.05).These microsatellite markers had an advantageous effect on growth traits and these loci could be used as the reference markers for marker-assisted breeding of Japanese flounder.