斑点叉尾GHRH基因3个SNPs位点及其单倍型组合与生长性状的关联分析

研究旨在探讨生长激素释放激素基因(Growth hormone-releasing hormone,GHRH)对斑点叉尾(Ictalurus punctatus)生长性状的影响。采用DNA混池测序法筛选GHRH基因的单核苷酸多态性(Single nucleotide polymorphisms,SNPs)位点,使用SNa Pshot法将筛选到的SNPs多态性位点进行分型,并对这些位点进行连锁不平衡和单倍型分析。结果表明,在GHRH基因内含子区域共检测到4个SNPs位点,并成功地对3个位点进行了分型,3个位点间均不存在强连锁不平衡;3个SNPs位点在176尾斑点叉尾中形成了6种有效单倍型。关联分析表明SNP位点g.6301 GA的AA基因型的体质量显著性地高于AG和GG型(P0.05),比群体的平均体质量高14%。单倍型组合H1/H4和H1/H5个体的体质量和体长极显著性地高于其他单倍型组合(P0.01),体质量比群体平均体质量分别高30%和15%,体长比群体平均体长分别高7%和6%。研究为斑点叉尾生长性状分子标记辅助选育和QTL定位提供了参考依据。     

中华绒螯蟹MSTN基因SNPs多态性及与生长性状的关联分析

为研究中华绒螯蟹(Eriocheir sinensis)肌肉生长抑制素基因(myostatin, MSTN)的多态性及其与生长性状的相关性, 对中华绒螯蟹3个群体(育种群体、大赛群体、野生群体)共321个个体MSTN基因的多态性进行筛选, 发现该基因的第1外显子存在3个多态性SNP位点(S1: C714T; S2:G729A; S3:G753T), 均为处于Hardy-Weinberg平衡(P>0.05)的中、高度多态性位点。利用一般线性模型分析3个位点及其基因型组合与生长性状的相关性, 发现S1位点对中华绒螯蟹的体重和壳长等生长性状有显著影响(P≤0.05), 而其余2个位点与生长性状无显著关联性。结果表明S1位点的TT基因型对中华绒螯蟹的生长最为有利, 可作为分子标记辅助育种的候选标记。     

猪Pitx2c基因4个SNPs的鉴定及其与肉质性状的关联分析

为研究猪Pitx2c基因与肉质性状的关系,在猪Pitx2c基因中共发现了8个SNPs位点,对其中的4个SNPs位点在4个商业猪种及8个中国地方猪种进行了等位基因频率检测,并在大白×梅山猪F2资源家系中进行了性状关联分析.结果显示,位点c.474C〉T（P〈0.01）及c.636C〉T（P〈0.05）与肉色（MCV1）存在显著或极显著相关;位点c.＊37G〉A及c.＊47G〉A与滴水损失（DLR）、系水力（WHC）及肉色（MCV1）均存在显著相关（P〈0.05）.连锁不平衡分析表明,临近的位点两两之间存在连锁不平衡（LD）.单倍型分析显示,存在两种主要单倍型,并且两拷贝的单倍型-CCGG-有利于肉质的改善.     

植酸酶对斑点叉尾鲴生长性能及磷当量的研究

试验旨在研究饲料中添加植酸酶对斑点叉尾 [初始平均体重(1.70±0.04) g]生长性能及植酸磷利用的影响, 确定植酸酶的磷当量。试验采用单因素试验设计, 以 Ca(H2PO4)2提供外源无机磷, 同时添加不同浓度植酸酶, 试验设计为 10 个处理组, 分别为 1 个对照试验组、4 个无机磷试验组(0.3%、0.5%、0.8%、1.2%)和 5 个植酸酶试验组(300、500、1000、1500、2000 U/kg), 每个处理 3 个重复, 每个重复 30 尾鱼。通过折线模型确定植酸酶的最佳添加量; 通过回归分析, 建立响应指标(特定生长率、椎骨磷)与外源磷添加量之间的线性关系, 进而确定植酸酶的磷当量值。结果表明: (1)添加植酸酶的处理组与对照组相比, 增重率、特定生长率、蛋白质效率、肥满度均有显著提高(P<0.05), 饲料系数、肝体比、脏体比均有下降(P<0.05), 成活率各处理组没有显著差别(P>0.05); 鱼体粗蛋白、粗灰分、钙、磷及椎骨粗灰分、钙、磷均有显著提高(P<0.05), 鱼体粗脂肪含量有所下降。(2)无机磷添加水平与响应指标之间线性关系如下: Y1=0.2714X+2.294(X-无机磷, Y1-特定生长率, R2=0.9238), 300、500、1000、1500 和 2000 U/kg 植酸酶分别可替代 1 kg 饲料中 0.13%、0.57%、0.76%、1.46% 和 1.35% 的 磷 酸 二 氢 钙 , 等 效 于 添 加 了 0.03% 、 0.14% 、 0.19% 、 0.36% 和 0.33% 的 有 效 磷 ;Y2=0.8737X+5.1028(X-无机磷, Y2-椎骨磷, R2=0.9638), 300、500、1000、1500 和 2000 U/kg 植酸酶分别可替代1 kg 饲料中 0.47%、1.11%、1.18%、1.38%和 1.41%的磷酸二氢钙, 等效于添加了 0.12%、0.27%、0.29%、0.34%和 0.35%的有效磷。在试验条件下, 添加 1000―2000 U/kg 植酸酶能有效改善斑点叉尾 生长性能, 有利于营养物质在鱼体中的沉积, 促进骨骼矿化。以特定生长率为响应指标, 植酸酶最佳添加量为 1435 U/kg等效于添加了 0.37%的有效磷; 以椎骨磷为响应指标, 植酸酶最佳添加量为 1226 U/kg 等效于添加了 0.33%的有效磷。     

口腔扁平苔藓患者的CIITA基因单倍型分析

目的:分析CIITA基因中单核苷酸多态性(Single Nucleotide Polymorphism,SNP)的单倍型与口腔扁平苔藓(Oral Lichen Planus,OLP)之间的关系,并探讨计算单倍型的新方法。方法:在得到42名患者与86名对照的CIITA基因中15个SNP位点的信息后,通过Haploview和SHEsis软件以及本研究组设计的频数计数法进行单倍型分析。组间比较使用χ2检验,并以P=0.05作为统计检验标准。结果:在本研究群体中,CIITA基因上的15个SNP位点能够形成两个单体域(haploblock),其中由位点rs6498124,rs11647384和rs4774所组成的单倍型GAC在三种单倍型分析方法中均显示出显著的统计学差异(Haploview:Chi2=6.127,P=0.013;SHEsis:Chi2=6.469 P=0.011;频数计数法:Chi2=5.460,P=0.019)。结论:在由CIITA基因的SNP位点rs6498124,rs11647384,rs4774组成的单体域中,单倍型GAC对OLP的患病具有潜在的保护性。频数计数法显示,rs4774位点本身的保护性及其与同一单体域内另外两个位点之间的完全连锁不平衡关系是单体型GAC显示出保护性的主要依据。提示单倍型对疾病易感性的解释在于其中的特定SNP位点等位基因型,及其该位点与其它相关位点间的连锁不平衡关系。     

大口黑鲈IGFBP1基因SNPs的筛选及与生长性状的关联分析

本研究使用PCR技术扩增得到2 743 bp长度的大口黑鲈IGFBP1基因序列,序列含4个外显子和3个内含子,编码263个氨基酸。采用直接测序法在IGFBP1基因上筛选到4个SNPs位点,分别位于该基因核苷酸序列中的第147个、第791个、第2 436个和第2 676个碱基,其中2个位点位于外显子上,A-141C位点发生了同义突变,C-791T发生了错义突变,随机检测同批430尾实验个体中4个位点的基因型,均符合Hardy-Weinberg定律。其中A-2436G和C-2676T位点完全连锁,组成单倍型标记H1。分析H1标记中的AB和AA基因型实验群体,显示两者在尾柄长、全长指标上存在显著差异(p0.05)。综合分析表明,H1标记可用于大口黑鲈分子辅助育种研究。     

氧化油脂对斑点叉尾鮰生长、体色和抗氧化能力的影响

为考察正常及氧化鱼油、豆油、混合油脂(鱼油﹕豆油=1﹕1)对斑点叉尾鮰(Ictalurus punctatus)生长性能、体色和肝脏抗氧化能力的影响, 设计6组等氮等脂饲料, 分别添加6%鱼油、6%豆油、3%鱼油+3%豆油、6%氧化鱼油、6%氧化豆油、3%氧化鱼油+3%氧化豆油, 饲喂6组初始体重(150.5±4.2 g)的斑点叉尾鮰8周, 每组3个重复, 每个重复14尾鱼。结果表明, 摄食6%鱼油、6%豆油、3%鱼油+3%豆油饲料的斑点叉尾鮰在增重率、饲料系数、肌肉组成、体色和肝脏抗氧化指标上均无显著差异(P>0.05); 摄食3组氧化油脂饲料后, 鱼体增重率和肌肉粗脂肪含量降低(P<0.05), 饲料系数和背部、尾部皮肤b*(黄度值)增加(P<0.05), 肝脏丙二醛(MDA)和血清谷丙转氨酶(ALT)、谷草转氨酶(AST)、总胆红素(TBIL)和直接胆红素升高(DBIL)(P<0.05), 肝脏超氧化物歧化酶(SOD)、过氧化氢酶(CAT)、还原型谷胱甘肽降低(GSH)(P<0.05), 而肌肉色度值(L*、a* 、b*)和肌肉水分、粗蛋白质、灰分含量无显著差异(P>0.05)。以上结果表明, 6%氧化油脂(鱼油、豆油或混合油脂)导致斑点叉尾鮰生长性能下降、皮肤黄度增加、肝脏抗氧化能力受损; 豆油可替代斑点叉尾鮰饲料中鱼油的使用, 而不会对生长产生负面影响。     

A-FABP基因多态性与肉鸡生长和体组成性状的关联

为探讨A-FABP基因多态性对肉鸡生长和体组成性状的影响,文章选用肉鸡高、低脂双向选择品系第十世代肉仔鸡为实验材料,采用测序、PCR-RFLP、PCR-LP、DHPLC方法进行基因多态性检测和个体基因型分析,通过对8个SNPs进行连锁不平衡分析并选择5个标签SNPs构建单倍型,进而利用单位点和单倍型分别与鸡生长和体组成性状进行关联分析。结果表明,7个SNPs(除SNP 5以外)及单倍型同时对鸡肌胃重、肌胃率有显著影响(P<0.05),而对生长和其他体组成性状无显著影响(P>0.05)。鉴于不同物种A-FABP基因现有的功能研究均没有发现其对消化系统有重要作用,因此该基因是否为影响肉鸡肌胃重和肌胃率的主效基因还有待于进一步研究。     

中华鳖GHSR基因SNPs的筛选及生长性状的关联分析

为探究GHSR基因多态性对中华鳖(Pelodiscus sinensis)生长相关性状的影响,采用直接测序法在GHSR基因5'侧翼和3'侧翼上筛选SNPs位点,共检测到5个单核苷酸多态性位点:A335T、G397T、A527G、A13482C和T13526A。随机选取同批繁殖的1冬龄200只中华鳖用直接测序法进行SNPs位点的分型,并分析与生长性状的相关性。检测结果显示,所有SNP位点均符合Hardy-Weinberg平衡状态(p>0.05)。方差分析显示,A336T位点的AT、TT基因型的体重、背甲长、背甲宽和裙边宽4项生长数据均显著高于AA基因型。A13482C位点的AC基因型的体重、背甲长、背甲宽和裙边宽4项数据均显著高于AA基因型(p<0.05)。研究表明,本实验在GHSR基因上获得的这些SNP位点可能影响着中华鳖的生长性状或与之紧密连锁,可为中华鳖分子辅助育种提供助力与参考。     

中华鳖GHRL基因SNPs的筛选及生长性状的关联分析

为探究GHRL基因多态性对中华鳖(Pelodiscus sinensis)生长性状的影响, 采用直接测序法在GHRL基因上检测到14个单核苷酸多态性位点C289T、G501T、T738C、G776T、A841G、T885C、T2960C、A2987T、G3390A、A3857C、G4718A、T4820C、A4850C、T4979C。随机选取同批繁殖的120只中华鳖用飞行时间质谱法进行SNPs位点的分型, 并分析与生长性状的相关性。检测结果显示, 所有SNP位点均符合Hardy-Weinberg平衡状态(P>0.05)。方差分析结果显示, C289T位点CT、CC基因型的5项生长数据均显著高于TT基因型(P<0.05)。S2位点AB基因型的体重、背甲长、背甲宽和裙边宽4项数据均显著高于AA基因型(P<0.05)。G3390A位点AG基因型的背甲长、背甲宽2项数据显著高于AA基因型(P<0.05)。G4718A位点AG基因型的背甲长、背甲宽、裙边宽3项数据显著高于AA基因型(P<0.05)。在GHRL基因上获得的SNP位点可能影响着中华鳖的生长性状或与之紧密连锁, 可为中华鳖分子辅助育种提供助力与参考。     

Association of the carboxyl-terminal PDZ ligand of neuronal nitric oxide synthase gene with schizophrenia in the Chinese Han population

Several independent linkage studies have demonstrated that the 1q22 region is likely to harbor candidate schizophrenia susceptibility genes. Recently, some genetic variants within CAPON have been reported as exhibiting significant linkage disequilibrium to schizophrenia in Canadian familial-schizophrenia pedigrees. We examined nine single nucleotide polymorphisms (SNPs), which span an approximately 236-kb region of CAPON, in 664 schizophrenia cases and 941 controls in the Chinese Han population. We detected a significant difference in allele distributions of SNP rs348624 (P = 0.000017). Moreover, the overall frequency of haplotypes constructed from three SNPs including rs348624 showed significant difference between cases and controls (P = 0.000025). Our findings indicate that CAPON gene may be a candidate susceptibility gene for schizophrenia in Chinese Han population, and also provide further support for the potential importance of NMDAR-mediated glutamatergic transmission in the etiology of schizophrenia.     

Common variation in KLKB1 and essential hypertension risk: tagging-SNP haplotype analysis in a case-control study

The human plasma kallikrein gene (KLKB1) encodes plasma kallikrein, a serine protease that catalyzes the release of kinins and other vasoactive peptides and may be involved in the pathogenesis of hypertension. In this study, we performed a haplotype-based study to assess the effect of common genetic variation in the KLKB1 gene on the risk of essential hypertension. Eight common single nucleotide polymorphisms (SNPs) were selected from the HapMap database and used to determine the pattern of linkage disequilibrium (LD) and haplotype structure within the KLKB1 gene. Four tag SNPs were then identified with over 85% power to predict both common haplotypes and remaining common SNPs, and genotyped in 1,317 cases with essential hypertension and 1,269 healthy controls. Single SNP analyses indicated that SNPs rs2304595 and rs4253325 were significantly associated with hypertension, adjusted for covariates. Compared with the most common Hap2 CAGC, Hap1 AGAC and Hap3 CGAC, which carry the susceptible rs2304595 G allele and rs4253325 A allele, were found to significantly increase the risk of essential hypertension with adjusted odds ratios equal to 1.37 and 1.17, respectively (P < 0.0001 and 0.028). A strongly significant interaction with gene-drinking was also observed. Among drinkers, the adjusted OR for Hap1 relative to Hap2 was increased to 2.50 (95% CI, 2.40 to 2.61; P < 0.0001). This was the first study to perform association analysis of the KLKB1 gene with essential hypertension. Our findings suggested that common genetic variation in the KLKB1 gene might contribute to the risk of hypertension in the northern Han Chinese population. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. Conflict of interests: None.     

Characterization of growth hormone-releasing hormone (GHRH) binding to cloned porcine GHRH receptor

To study structure-activity relationships of growth hormone-releasing hormone (GHRH), a competitive binding assay was developed using cloned porcine adenopituitary GHRH receptors expressed in human kidney 293 cells. Specific binding of [His¹,¹²⁵I-Tyr¹⁰,Nle²⁷]hGHRH(1–32)-NH₂ increased linearly with protein concentration (10–45 μg protein/tube). Binding reached equilibrium after 90 min at 30°C and remained constant for at least 240 min. Binding was reversible to one class of high-affinity sites (K_d = 1.04 ± 0.19 nM, B_max = 3.9 ± 0.53 pmol/mg protein). Binding was selective with a rank order of affinity (IC₅₀) for porcine GHRH (2.8 ± 0.51 nM), rat GHRH (3.1 ± 0.69 nM), [N-Ac-Tyr¹, -Arg²]hGHRH(3–29)-NH₂ (3.9 ± 0.58 nM), and [ -Thr⁷]GHRH(1–29)-NH₂ (189.7 ± 14.3 nM), consistent with their binding to a GHRH receptor. Nonhydrolyzable guanine nucleotides inhibited binding. These data describe a selective and reliable method for a competitive GHRH binding assay that for the first time utilizes rapid filtration to terminate the binding assay.     

长江中游渔业资源现状研究

研究对前期建立的青鱼(Mylopharyngodon piceus)家系高密度遗传连锁图谱及体长QTL的定位结果进行深入分析, 在10号连锁群上识别到与体长相关的QTL区域, 存在2个与体长强烈相关的紧密连锁SNP位点。研究利用特异性标记判定青鱼遗传性别, 对SNP位点侧翼序列PCR扩增子进行sanger测序。得到准确的SNP位点基因型信息后, 研究对紧密连锁SNP位点不同基因型与邗江青鱼群体生长性状进行了细致的关联分析。结果表明, 在563尾邗江青鱼群体中, 雌鱼290尾, 雄鱼273尾, 雌雄比约为1.06﹕1。遗传分析显示, SNP₇₉₅₇G>C和SNP₉₈₀₂T>A有效等位基因数(N_e)分别为1.754和1.399, 观测杂合度(H_o)分别为0.384和0.266, 期望杂合度(H_e)分别为0.430和0.285, 多态信息含量分别(PIC)为0.508和0.378。相比雄鱼, 雌鱼生长速度更快, 但是变异系数更高, 说明雌鱼生长性状离散程度更大。SNP₇₉₅₇G>C和SNP₉₈₀₂T>A不同基因型在群体体长性状中存在显著差异。SNP₇₉₅₇G>C位点的GG基因型在雄鱼体长性状中具有显著优势(P<0.05), SNP₇₉₅₇G>C和SNP₉₈₀₂T>A单标记其他基因型与生长性状之间存在差异, 但未达到统计学差异。在SNP位点不同基因型构建的二倍型中, 雌雄个体表现出一定的生长差异, D8(GGTA)在生长方面具有显著优势 (P<0.05), 具有一定育种价值。研究结果可为选育快速生长青鱼新品种提供分子标记, 为未来青鱼遗传改良和分子标记辅助育种策略提供科学依据。

     

A novel efficient dynamic programming algorithm for haplotype block partitioning

In this paper, a new efficient algorithm is presented for haplotype block partitioning based on haplotype diversity. In this algorithm, finding the largest meaningful block that satisfies the diversity condition is the main goal as an optimization problem. The algorithm can be performed in polynomial time complexity with regard to the number of haplotypes and SNPs. We apply our algorithm on three biological data sets from chromosome 21 in three different population data sets from HapMap data bulk; the obtained results show the efficiency and better performance of our algorithm in comparison with three other well known methods.     

An economical mtDNA SNP assay detecting different mitochondrial haplogroups in identical HVR 1 samples of Caucasian ancestry

BackgroundWe had sequenced 329 Caucasian samples in Hypervariable Region 1 (HVR 1) and found that they belong to eleven different mitochondrial DNA (mtDNA) haplotypes. The sample set was further analysed by an mtDNA assay examining 32 single nucleotide polymorphisms (SNPs) for haplogroup discrimination.In a validation study on 160 samples of different origin it was shown that these SNPs were able to discriminate between the evolved superhaplogroups worldwide (L, M and N) and between the nine most common Caucasian haplogroups (H, I, J, K, T, U, V, W and X).ResultsThe 32 mtDNA SNPs comprised 42 different SNP haplotypes instead of only eleven haplotypes after HVR 1 sequencing. The assay provided stable results in a range of 5 ng genomic DNA down to virtually no genomic DNA per reaction. It was possible to detect samples of African, Asian and Eurasian ancestry, respectively.DiscussionThe 32 mtDNA SNP assay is a helpful adjunct to further distinguish between identical HVR 1 sequences of Caucasian origin. Our results suggest that haplogroup prediction using HVR 1 sequencing provides instable results. The use of coding region SNPs for haplogroup assignment is more suited than using HVR 1 haplotypes.     

Association of G72/G30 with schizophrenia in the Chinese population

Recently, the G72 gene was reported to be associated with schizophrenia in the French Canadian and Russian populations. Here, we report the results obtained from the study of six single-nucleotide polymorphisms (SNPs: rs3916965, rs3916967, rs2391191, rs1935062, rs778293, and rs3918342), which span an 82-kb region covering the complementary DNA sequences of G72 and G30, in 537 schizophrenia cases and 538 controls of the Han Chinese. In this work, we have identified statistically significant differences in allele distributions of two markers rs3916965 (P = 0.019) and rs2391191 (P = 0.0010), and a highly significant association between haplotype AGAC of the G72/G30 locus (P = 1.7 x 10(-4)) and schizophrenia. Our data provide further evidence that markers of the G72/G30 genes are associated with schizophrenia in a non-Caucasian population.