鸡EX-FABP基因遗传变异及与肌内脂肪含量的相关分析

利用PCR-SSCP结合DNA测序方法,对贵妃鸡、怀乡鸡及二者的杂交F1代共计360个个体EX-FABP基因遗传特征及品种差异进行研究,发现2773T>C,2867 C>T和2913 G>A三个位点在贵妃鸡中表现为单态,在怀乡鸡和杂交F1群体中表现为多态,这3个位点有望作为贵妃鸡、怀乡鸡乃致其他品种鸡种质资源鉴定的参考依据。对比分析3个群体胸肌肌内脂肪含量(IMF)表明,怀乡鸡和杂交鸡母鸡的IMF显著高于贵妃鸡;而3个群体公鸡间的IMF差异不显著;除贵妃鸡外,同一品种内公鸡的IMF均小于母鸡(P<0.05)。多态位点与鸡胸肌肌内脂肪含量的相关性分析结果表明,在2773位点,TC基因型个体的IMF值大于TT基因型;在2913位点,AA基因型个体的IMF值大于GG基因型,但没有达到显著水平(P>0.05)。     

Single Nucleotide Polymorphism of FSHβ Gene Associated with Reproductive Traits in Japanese Flounder (Paralichthys olivaceus)

Follicle stimulating hormone β (FSHβ) of Japanese flounder (Paralichthys olivaceus) plays a key role in the regulation of gonadal development.This study aimed to investigate molecular genetic characteristics of the FSHβ gene and elucidate the effects of single nucleotide polymorphisms (SNPs) of FSHβ on reproductive traits in Japanese flounder.We used polymerase chain reaction single-strand conformation polymorphism (PCR-SSCP) and sequencing of the FSHβ gene in 60 individuals.We identified only an SNP (T/C) in the coding region of exon3 of FSHβ.The SNP (T/C) did not lead to amino acid changes at the position 340 bp of FSHβ gene.Statistical analysis showed that the SNP was significantly associated with testosterone (T) level and gonadosomatic index (GSI) (P0.05).Individuals with genotype TC of the SNP had significantly higher serum T levels and GSI (P0.05) than that of genotype CC.Therefore, FSHβ gene could be a useful molecular marker in selection for prominent reproductive trait in Japanese Flounder.     

Mutations in exons of the CYP17-II gene affect sex steroid concentration in male Japanese flounder (Paralichthys olivaceus)

As a specific gene of fish,cytochrome P450c17-Ⅱ(CYP17-Ⅱ) gene plays a key role in the growth,development and reproduction level of fish.In this study,the single-stranded conformational polymorphism(SSCP) technique was used to characterize polymorphisms within the coding region of CYP17-Ⅱ gene in a population of 75 male Japanese flounder(Paralichthys olivaceus).Three single nucleotide polymorphisms(SNPs) were identified in CYP17-Ⅱ gene of Japanese flounder.They were c.G594A(p.G188R),c.G939A and c.G1502A(p.G490D).SNP1(c.G594A),located in exon 4 of CYP17-Ⅱ gene,was significantly associated with gonadosomatic index(GSI).Individuals with genotype GG of SNP1 had significantly lower GSI(P < 0.05) than those with geno-type AA or AG.SNP2(c.G939A) located at the CpG island of CYP17-Ⅱ gene.The mutation changed the methylation of exon 6.Indi-viduals with genotype AA of SNP2 had significantly lower serum testosterone(T) level and hepatosomatic index(HSI) compared to those with genotype GG.The results suggested that SNP2 could influence the reproductive endocrine of male Japanese flounder.How-ever,the SNP3(c.G1502A) located in exon 9 did not affect the four measured reproductive traits.This study showed that CYP17-Ⅱ gene could be a potentially useful candidate gene for the research of genetic breeding and physiological aspects of Japanese flounder.     

Single nucleotide polymorphisms in intron 1 and intron 2 of Larimichthys crocea growth hormone gene are correlated with growth traits

The growth hormone gene (GH) affects animal growth and is a potential target for genetic studies of variation related to growth traits. In this study, we analyzed single nucleotide polymorphisms (SNPs) in GH intron regions and their associations with growth traits in large yellow croaker, Larimichthys crocea, from Zhejiang and Fujian stocks. The results of PCR-single strand conformation polymorphism showed two haplotypes of intron 1, named AA and AB genotypes, in Zhejiang stock. AB exhibited an SNP at position 196 (G A) that was negatively correlated with body height and positively correlated with standard length/body height (P 0.05). Two different genotypes, CC and CD, were identified in intron 2 in Fujian stock, with CD showing an SNP at position 692 (T C). The CD genotype had a significantly positive correlation with both weight and total length (P 0.01). These basic data highlight the potential for using GH as a genetic marker of fish growth in marker assisted selection.     

Development of Genomic Microsatellite Multiplex PCR Using Dye-Labeled Universal Primer and Its Validation in Pedigree Analysis of Pacific Oyster(Crassostrea gigas)

There is an increasing requirement for traceability of aquaculture products, both for consumer protection and for food safety. There are high error rates in the conventional traceability systems depending on physical labels. Genetic traceability technique depending on DNA-based tracking system can overcome this problem. Genealogy information is essential for genetic traceability, and microsatellite DNA marker is a good choice for pedigree analysis. As increasing genotyping throughput of microsatellites, microsatellite multiplex PCR has become a fast and cost-effective technique. As a commercially important cultured aquatic species, Pacific oyster Crassostrea gigas has the highest global production. The objective of this study was to develop microsatellite multiplex PCR panels with dye-labeled universal primer for pedigree analysis in C. gigas, and these multiplex PCRs were validated using 12 full-sib families with known pedigrees. Here we developed six informative multiplex PCRs using 18 genomic microsatellites in C. gigas. Each multiplex panel contained a single universal primer M13(-21) used as a tail on each locus-specific forward primer and a single universal primer M13(-21) labeled with fluorophores. The polymorphisms of the markers were moderate, with an average of 10.3 alleles per locus and average polymorphic information content of 0.740. The observed heterozygosity per locus ranged from 0.492 to 0.822. Cervus simulations revealed that the six panels would still be of great value when massive families were analysed. Pedigree analysis of real offspring demonstrated that 100% of the offspring were unambiguously allocated to their parents when two multiplex PCRs were used. The six sets of multiplex PCRs can be an important tool for tracing cultured individuals, population genetic analysis, and selective breeding program in C. gigas.     

Population dynamics of four dominant copepods in Prydz Bay, Antarctica, during austral summer from 1999 to 2006

Population dynamics of four dominant Antarctic copepods, Calanoides acutus, Calanus propinquus, Metridia gerlachei and Rhincalanus gigas were studied based on zooplankton samples collected in the Prydz Bay during austral summer from 1999 to 2006. We found that C. acutus was the most abundant species among these four copepods, followed by C. propinquus, M. gerlachei and R. gigas. R. gigas occurred mainly in the warmer oceanic regions and showed distribution patterns discrete from the other three species, whose distribution in the whole survey area overlapped. By December 15th (about one month before our sampling) of the years 1999, 2003 and 2006, sea ice retreated earlier and polynyas existed in the neritic region one month before sampling. These periods were characterized by numerical dominance of C. acutus, C. propinquus and M. gerlachei, elevated proportions of Copepodite I and Copepodite II stages especially in the neritic region. While for the years 2000, 2002, and 2005, the ice edge located more northerly and polynyas did not exist in the neritic region, the copepods abundance was lower, indicating poor recruitment. Population structure of R. gigas was mainly composed of advanced stages Copepodite V and female during all cruises. Log10 (x+1) transformed densities of C. acutus, C. propinquus and M. gerlachei showed positive correlation with temperature and chlorophyll a concentration, while mean population stages of these copopods were negatively correlated with these environmental variables. Younger copepodite stages of C. acutus, C. propinquus and M. gerlachei appeared more often in neritic regions. We confirmed that the polynyas had a great contribution to phytoplankton blooms, which promote copepods reproduction and recruitment success. The study suggested that population dynamics of the four copepods have good correspondence with sea ice and polynya variations during all cruises of the Prydz Bay.     

3种柔鱼线粒体基因与核核糖体基因片段序列比较分析

为准确检测柔鱼（Ommαstrephesbartram川、茎柔鱼（ Dosidicus gigas）与阿根廷滑柔鱼（ IIIex argentinus ） 的种间遗传差异,对线粒体16SrRNA、细胞色素b（Cytb）与编码核糖体大亚基的基因（28SrDNA）片段序列进 行测定。经比对获得同源片段序列的长度分别为444、430、464坤,其中16SrRNA与28SrDNA基因片段上分别存在3处和47处碱基插入/缺失。核昔酸组成分析表明;3种柔鱼在3个基因片段上的核音酸组成差异不显著, 在线粒体2个基因片段上的A＋T含量（16SrRNA;69.90%、72.01%、74.66%; Cytb; 63.61%、68.91%、71.65% ） 均明显高于C＋C含量（16SrRNA;30.10%、27.99%、25.34%; Cytb; 36.39%、31.09%、28.35% ）,而在28SrDNA 基因片段上的A＋T含量（37.16%、36.74%、38.29% ）明显低于C＋C含量（62.84%、63.26%、61.71 %）0 3种柔鱼 在28SrDNA基因片段上检测到的核昔酸替代率最低,为6.68%,而蛋白质编码基因Cytb核昔酸替代率最高,为 20.93%,核营酸替代均发生在密码子第3位点上,而且未引起氨基酸替代。基于邻接法、最大简约法与最大似然 法重建的系统树显示,柔鱼与茎柔鱼的亲缘关系较近。根据C严b基因片段序列分析,柔鱼与茎柔鱼和阿根廷滑柔鱼的分歧时间分别为653-790万a和765 - 925万a,种间分化事件发生在中新世至上新世间。     

基于转录组测序的方斑东风螺单核苷酸多态性位点挖掘及功能注释

【目次】了解方斑东风螺中响应LPS刺激的SNP位点及SNP所在基因SNP-Unigenes的功能。【方法】使用SOAPsnp软件分析不同时间条件下转录组数据中的SNP位点,使用GO、COG和KEGG数据库进行功能注释。【结果】转录组数据中共挖掘到673 782个SNP位点,分布在110 869条SNP-unigenes序列上。SNP类型分析表明,转换位点发生的频率远高于颠换位点,且6种单碱基变异类型中以A/G转换发生概率最大。有5866条SNP-unigenes富集到298个KEGG子集中,其中以"内吞作用"子集中富集的SNP-Unigenes最多,共富集182条。     

Development of organelle single nucleotide polymorphism(SNP) markers and their application for the identification of cytoplasmic inheritance patterns in Pyropia yezoensis(Bangiales,Rhodophyta)

The genus Pyropia contains several important cultivated species.Genetic research in nori species has mainly focused on the cell nucleus,with few studies on organelles(chloroplast and mitocho ndria).Due to the high copy numbers of organelles in cells,which influence the development and traits of algae,it is necessary to study their genetic mechanism.In this study,the marine red alga yezoensis,an important economic macroalga,was selected as the study object.To investigate organelle(chloroplast and mitochondria) inheritance in P yezoensis,the wild type RZ(maternal strain) was cro ssed with the red mutant HT(paternal strain) and 30 color-sectors from 11 F1 gametophytic blades were examined.The complete chloroplast and mitochondrial genomes of the red mutant(HT) were assembled for the first time.One reliable and stable single nucleotide polymorphism(SNP) loci filtrated by bioinformatics analysis was used as a molecular marker for chloroplast and mitochondrial DNA,respectively,in subsequent experiments.PCR amplification and sequence analysis showed that the haplotypes of color-sectors detected were consistent with those of the maternal parent,confirming that both chloroplast and mitochondrial genomes were inherited maternally in P.yezoensis.The inheritance pattern of organelles in P.yezoensis can be used to guide the hybridization and breeding of nori.Additionally,the organelle SNP markers developed in this study can be applied in subsequent genetic research.     

Development of 101 novel EST-derived single nucleotide polymorphism markers for Zhikong scallop (Chlamys farreri)

Zhikong scallop(Chlamys farreri) is an important maricultured species in China.Many researches on this species,such as population genetics and QTL fine-mapping,need a large number of molecular markers.In this study,based on the expressed sequence tags(EST),a total of 300 putative single nucleotide polymorphisms(SNPs) were selected and validated using high resolution melting(HRM) technology with unlabeled probe.Of them,101(33.7%) were found to be polymorphic in 48 individuals from 4 populations.Further evaluation with 48 individuals from Qingdao population showed that all the polymorphic loci had two alleles with the minor allele frequency ranged from 0.046 to 0.500.The observed and expected heterozygosities ranged from 0.000 to 0.925 and from 0.089 to 0.505,respectively.Fifteen loci deviated significantly from Hardy-Weinberg equilibrium and significant linkage disequilibrate was detected in one pair of markers.BLASTx gave significant hits for 72 of the 101 polymorphic SNP-containing ESTs.Thirty four polymorphic SNP loci were predicted to be non-synonymous substitutions as they caused either the change of codons(33 SNPs) or pretermination of translation(1 SNP).The markers developed can be used for the population studies and genetic improvement on Zhikong scallop.     

Relationship Between Shell Color and Growth and Survival Traits in the Pacific Oyster Crassostrea gigas

Shell color is regarded as an economic trait in many breeding programs of bivalve mollusks, but the relationship between shell color and production traits remains controversial. In our breeding program of Crassostrea gigas, solid white, black, and orange shell lines were obtained, and second-generation(F2) and testcross families with segregating shell colors were constructed by crossing these three lines. These segregating families provided ideal samples for investigating the relationship between shell color and production traits in C. gigas. The growth and survival of 7-month-old oysters with different shell colors sampled within the same families were compared in seven F2 families and 13 testcrosses. In addition, the growth and survival of oysters from the three shell color lines were compared at 4 and 16 months of age. The growth and survival rates of the orange shell line were significantly lower than those of the white and black shell lines. However, no significant difference in growth between oysters with different shell colors was observed within segregating families, except the testcrosses produced by crossing orange-and white-shelled grandparents, and no significant difference in survival was observed in any family. Overall, no significant correlation was observed between shell color and production traits in C. gigas. These results suggest that shell color cannot be used as a marker to guide the selection of growth and survival traits. Thus shell color and production traits should be selected independently in oyster breeding programs.     

Impacts of El Ni?o on the somatic condition of Humboldt squid based on the beak morphology

The Humboldt squid Dosidicus gigas has a short life span,and environmental variability plays a significant role in regulating its population dynamics and distribution.An analysis of 1 096 samples of D.gigas collected by the Chinese commercial fishing vessels during 2013,2014,and 2016 off the Peruvian Exclusive Economic Zone,was conducted to evaluate the impacts of El Ni?o events on the somatic condition of D.gigas.This study indicates that the slopes of all beak variables in relation to mantle length(ML)for females were greater than those of males during 2013,2014,and 2016,and slopes of the upper crest length and the lower ro strum length significantly differed between females and males in 2013(P0.05).Variation in the slopes for beak variables among years was studied;no significant difference was observed(ANCOVA,P0.05).The Fulton's condition coefficients(K)of females and males in 2013 and 2014 were significantly greater than tho se in 2016(P0.01).01).The K values of females were greater than tho se of males in 201 3,2014,and 2016,and K values significantly differed between females and males in 201 3.In normal years,the chlorophyll a(Chl a)concentration showed an N-shaped variability from January to December.However,in the El Ni?o period,it tended to weaken the upwelling coupled with warm and low Chl a concentration waters.We suggest that the poor somatic condition of D.gigas during the El Ni?o year was resulted from the low Chl a concentration in the waters,and the abundance of D.gigas would decrease due to the unfavourable environment and the lack of prey items in the El Ni?o year.     

Variations in retention efficiency of bivalves to different concentrations and organic content of suspended particles

Retention efficiencies (RE) of scallop (Chlamys farreri),oyster (Crassostrea gigas) and mussel (Mytilus edulis) in a flow-through system were measured to understand the short-term response to various particle and organic matter concentrations.By comparing the RE of C.farreri with that of C.gigas and M.edulis,we gained further knowledge on the feeding physiological characteristics of C.farreri and ascertained the possible cause of high summer mortalities of this species.The experimental feeding conditions in...     

Development of high-resolution chloroplast markers for intraspecific phylogeographic studies of Phaeocystis globosa

Phaeocystis globosa is an important harmful algal bloom causative species distributing widely in temperate and tropical coastal waters in the world.The morphological,physiological,and biochemical characte ristics are different amo ng geographic strains,which can not be distinguished with nuclear ribo somal DNA markers at present.Therefore,the genetic distance and phylogeographic relationships of nuclear 28 S rDNA D1-D2 and ITS regions,and three chloroplast intergenic spacers(petN-trnS1,trnM1-psbA,and rbcS-rpl27) were analyzed and compared among 13 strains of P.globosa isolated from the Pacific Ocean and Atlantic Ocean in this study.In addition,the nucleotide polymorphisms of 28 S rDNA D1-D2,ITS,and rbcS-rpl27 regions were evaluated in two P.globosa strains.The various levels of nucleotide polymorphism were in the nuclear 28 S rDNA D1-D2 region and ITS region,but no polymorphism was in the chloroplast rbcS-rpl27 intergenic spacer.A reasonable intraspecific phylogeographic relationship was presented by rbcS-rpl27 intergenic spacer,which had the strongest distinction to geographic strains compared to those of 28 S rDNA D1-D2 and ITS regions.In the phylogenetic tree of rbcS-rpl27 intergenic spacer,the two strains from the North Sea of the Atlantic Ocean were divided firstly from the species of P.globosa,and then formed an independent clade,while the other Atlantic strains and all of Pacific strains j oined up to build the other clade.It was implied that at least two genetically distant populations of P.globosa existed in the Atlantic coastal regions.This study provided a high-resolution chloroplast marker to analyze intraspecific phylogeographic populations of P.globosa,and preliminarily clarified the genetic relationships of the Pacific and Atlantic strains of P.globosa.     

Seasonal Variation of the Glycogen Enzyme Activity in Diploid and Triploid Pacific Oyster Gonad During Sexual Maturation

The glycogen content and the activities of two key enzymes in glycogen metabolism, glycogen phosphorylase and gly- cogen synthetase, in the gonad of diploid and triploid Pacific oysters (Crassostrea gigas) were compared during maturation. The glycogen content in the gonad of diploids decreased with gametogenesis (by 85.7%), but the glycogen content in the gonad of trip- loids did not vary significantly. Activity of glycogen phosphorylase (GP) in the gonad of diploids decreased with gametogenesis (by 55.5%), while GP activity of triploids did not vary significantly during maturation. Activity of glycogen synthetase (GS) in the gonad of diploids increased slightly with gametogenesis, reaching a peak in June. Activity of GS declined sharply from June to July, which might be due to gonad spawning. GS activity of triploid oysters in spawning time (July and August) was significantly higher than that in other months, which might be explained with a ‘compensating’ mechanism for the higher glycogen content in triploids.     

SIUDIES ON THE BIOCHEMICAL COMPOSITION,ENERGETICS AND ESSENTIAL AMINO ACIDS OF THREE MUDSKIPPERS IN XIAMEN HARBOUR

Measurements were made on the contents of protein,lipid,glycogen(PLG)and water,and on caloric values and amino acids,in muscle of three mudskippers periophthalmus cantonensis,Scarteiaosviridis and Boleophthalmus pectinirostris collected from Haicang,Xiamen.The essential amino acids(EAA)for these fishes were also studied with radioisotopic trace method.The results showed:(1)Thecontent of each component in tested fish muscles differed slightly,and protein was the most importantcomponent making up from 6.685% to 9.891% of the wet weight (about 44.21%-50.45% of dryweight);(2)Energy calculated from the sum of protein, lipid and glycogen in wet muscle was low (<4.3kJ/g) in these Fishes, especially in B. pectinirostris(<3.1 kJ/g), the ratios of energy to protein content (E/P) also were low(<39.873-45.535kJ/g), (3)Seventeen amino acids were determined in thesethree fishes.The content of the same amino acid(among the seventeen) tested in different species andsexes varied slightly.The amounts of methionine, phenyl