马氏珠母贝(Pinctada fucata martensii)Pm-CTSL基因的克隆及表达分析

组织蛋白酶L (cathepsin L, CTSL)是无脊椎动物体内非特异性免疫的重要组成部分。为了研究马氏珠母贝CTSL (Pm-CTSL)的功能,本实验利用RACE技术克隆获得了Pm-CTSL基因,并对其结构和组织表达模式进行了分析。结果表明,Pm-CTSL基因c DNA序列全长为1 237 bp,其中开放式阅读框957 bp,5'UTR69 bp,3'UTR 211 bp,共编码氨基酸318个。结构域分析发现Pm-CTSL具有CTSL两个典型的结构域Inhibitor_I29和Pept_C1。Pm-CTSL也具有信号肽、保守序列ERFNVN和GNFD、两个潜在的N-糖基化位点和催化活性位点三联体残基(Cys, His和Asn)。多序列比对结果表明Pm-CTSL与太平洋牡蛎的同源性最高,为42%;系统进化分析发现,Pm-CTSL与虾夷扇贝等贝类聚为一支。实时荧光定量分析发现,Pm-CTSL在肝胰腺中显著高表达(p<0.05),表明Pm-CTSL可能参与马氏珠母贝的免疫应答。本研究为进一步探讨CTSL在马氏珠母贝非特异性免疫应答中的作用提供了基础资料。     

Identification of EGFR in pearl oyster (Pinctada fucata martensii) and correlation analysis of its expression and growth traits

Marine pearl production is directly influenced by the growth speed of Pinctada fucata martensii. However, the slow growth rate of this organism remains the main challenge in aquaculture production. Epidermal growth factor receptor (EGFR), an important receptor of tyrosine kinases in animals, plays versatile functions in development, growth and tissue regeneration. In this study, we described the characteristic and function of an EGFR gene identified from P. f. martensii (PmEGFR). PmEGFR possesses a typical EGFR structure and is expressed in all studied tissues, with the highest expression level in adductor muscle. PmEGFR expression level is significantly higher in the fast-growing group than that in the slow-growing one. Correlation analysis represents that shell height and shell weight show positive correlation with PmEGFR expression (p < 0.05), and total weight and tissue weight exhibit positive correlation with it (p < 0.01). This study indicates that PmEGFR is a valuable functional gene associated with growth traits.     

马氏珠母贝(Pinctada fucata martensii)Pm-HSP70基因的克隆及其对温度胁迫的响应

本实验利用RACE技术克隆获得了马氏珠母贝HSP70 (Pm-HSP70)基因,并对其基因和氨基酸序列结构特征进行了生物信息学分析,同时采用荧光定量PCR技术分析了该基因在不同组织的表达模式及不同温度下的时序表达模式。序列分析表明,Pm-HSP70 cDNA序列全长为2 215 bp,其中开放式阅读框1 899 bp,5'UTR 107 bp,3'UTR 209 bp,编码632个氨基酸,理论蛋白分子量为69.44 kD,理论等电点为5.61。该蛋白具有HSP70家族典型的结构域HSP70,以及ATP结合位点、细胞质特征性保守序列和3个HSP70家族标签。多序列比对结果表明Pm-HSP70与菲律宾蛤仔HSP70同源性最高,为80%;系统进化分析发现,Pm-HSP70与菲律宾蛤仔等贝类HSP70聚为一支。组织表达定量分析结果显示,Pm-HSP70在马氏珠母贝多个组织中均有表达,在肝胰腺中表达量最高,其次是性腺;对不同温度下鳃组织中Pm-HSP70的时序表达分析发现,在处理后各时间点高温组(32℃)基因表达水平最高,且均显著高于对照组(22℃)和低温组(17℃)。以上结果表明Pm-HSP70可能参与马氏珠母贝的高温胁迫响应。该研究为进一步探索Pm-HSP70在马氏珠母贝温度适应性中的作用提供了基础资料。     

Chromosome-level wild Hevea brasiliensis genome provides new tools for genomic-assisted breeding and valuable loci to elevate rubber yield

The rubber tree (Hevea brasiliensis) is grown in tropical regions and is the major source of natural rubber. Using traditional breeding approaches, the latex yield has increased by sixfold in the last century. However, the underlying genetic basis of rubber yield improvement is largely unknown. Here, we present a high-quality, chromosome-level genome sequence of the wild rubber tree, the first report on selection signatures and a genome-wide association study (GWAS) of its yield traits. Population genomic analysis revealed a moderate population divergence between the Wickham clones and wild accessions. Interestingly, it is suggestive that H. brasiliensis and six relatives of the Hevea genus might belong to the same species. The selective sweep analysis found 361 obvious signatures in the domesticated clones associated with 245 genes. In a 15-year field trial, GWAS identified 155 marker–trait associations with latex yield, in which 326 candidate genes were found. Notably, six genes related to sugar transport and metabolism, and four genes related to ethylene biosynthesis and signalling are associated with latex yield. The homozygote frequencies of the causal nonsynonymous SNPs have been greatly increased under selection, which may have contributed to the fast latex yield improvement during the short domestication history. Our study provides insights into the genetic basis of the latex yield trait and has implications for genomic-assisted breeding by offering valuable resources in this new domesticated crop.     

Characterization of 31 EST-derived microsatellite markers for the pearl oyster Pinctada martensii (Dunker)

We developed and characterized 31 microsatellite markers from expressed sequence tags of Pinctada martensii (Dunker). The number of alleles per locus ranged from 4 to 18 as determined in 44 individuals from a wild population. The expected heterozygosity ranged from 0.4121 to 0.9436, while the observed heterozygosity ranged from 0.4054 to 0.7273. Most of the loci are in Hardy-Weinberg equilibrium. These markers should be useful for population genetics studies, parentage and genome mapping in this species.     

The influence of cooling rate,developmental stage,and the addition of sugar on the cryopreservation of larvae of the pearl oyster Pinctada fucata martensii

This paper examines the effects of cooling rate, developmental stage, and the addition of sugar on the cryopreservation of the larvae of the pearl oyster, Pinctada fucata martensii. The survival rates of frozen-thawed trochophores was 43.1% at a cooling rate of 1.0 degrees C/min. The survival rate of frozen-thawed larvae increased with developmental stage, except for umbo stage larvae, and the late D-shaped larvae showed a survival rate as high as 91%. The addition of sugar (0.2M glucose or sucrose) improved the survival rate of larvae. These results indicate that the preferred cooling rate, developmental stage, and sugar for the cryopreservation of pearl oyster larvae are 1 degrees C/min, late D-shaped larvae and 0.2M glucose or sucrose.     

奶牛重要经济性状全基因组关联分析研究进展

产奶性状是奶牛最重要的生产性状,随着平衡育种理念的提出和发展,繁殖性状、体型性状、健康性状和长寿性等功能性状也逐渐被重视并纳入育种规划中。鉴定产奶性状和功能性状主效基因或遗传标记并将之应用于奶牛标记辅助选择可望加快遗传进展。随着高密度SNP标记的高通量检测技术的发展,全基因组关联分析已成为鉴定畜禽重要经济性状基因的重要途径。文章对奶牛产奶性状和功能性状全基因组关联分析研究进展进行综述。     

茄子果实相关农艺性状全基因组关联分析研究进展与展望

茄子是重要的园艺作物,也是茄科植物中种植最广泛的蔬菜之一。茄子果实相关农艺性状是一种复杂的数量性状,传统育种选育效率低、周期长。高通量测序技术与生物信息学技术的快速发展,使得全基因组关联分析(genome-wide association study, GWAS)在解析茄子果实相关复杂农艺性状的遗传规律方面展现出巨大的应用前景。本文对全基因组关联分析在茄子的果形、果色等果实相关农艺性状中的研究进展进行了综述;针对茄子数量性状遗传研究中普遍存在的“丢失遗传力”(missing heritability)问题,从4个GWAS策略在茄子果实相关农艺性状研究中的应用热点出发,提出了未来茄子GWAS的发展对策;并结合当前茄子遗传改良的实践需求,展望了GWAS策略在茄子分子育种领域的广阔应用前景。本文为今后利用GWAS解析各种茄子果实相关性状的遗传基础以及选育符合消费者需求的果实材料提供了理论依据和参考。     

奶牛重要经济性状全基因组关联分析研究进展

产奶性状是奶牛最重要的生产性状, 随着平衡育种理念的提出和发展, 繁殖性状、体型性状、健康性状和长寿性等功能性状也逐渐被重视并纳入育种规划中。鉴定产奶性状和功能性状主效基因或遗传标记并将之应用于奶牛标记辅助选择可望加快遗传进展。随着高密度SNP标记的高通量检测技术的发展, 全基因组关联分析已成为鉴定畜禽重要经济性状基因的重要途径。文章对奶牛产奶性状和功能性状全基因组关联分析研究进展进行综述。     

中国人群肝功能检测指标全基因组关联分析研究

肝功能检测(liver function test, LFTs)指标是受遗传和环境影响的复杂性状,具有个体差异性。为系统性研究中国人群全基因组范围内单核苷酸多态性(single nucleotide polymorphism, SNP)与肝功能指标之间的联系,本研究利用英国生物银行(UK Biobank)中1653名中国人的基因分型数据和表型数据为研究对象,利用PLINK软件进行全关联分析研究(genome-wide association study, GWAS),发现229个SNP与中国人群血液中的总胆红素(total bilirubin, TB)相关,27个SNP与中国人群血液中碱性磷酸酶(alkaline phosphatase, ALP)相关,36个SNP与中国人群血液中的γ-谷氨酰转肽酶(γ-glutamyl transpeptidase, GGT)相关,1个SNP与中国人群血液中的门冬氨酸氨基转移酶(aspartate transaminase, AST)相关,最显著的位点中有11个位点是新的LFTs关联位点。通过功能基因组分析,发现这些位点的临床意义(如吉尔伯特综合征)...     

A genome-wide association study identified new variants associated with mathematical abilities in Chinese children

Mathematical ability is moderately heritable, and it is a complex trait which can be evaluated in several different categories. A few genetic studies have been published on general mathematical ability. However, no genetic study focused on specific mathematical ability categories. In this study, we separately performed genome-wide association studies on 11 mathematical ability categories in 1146 students from Chinese elementary schools. We identified seven genome-wide significant single nucleotide polymorphisms (SNPs) with strong linkage disequilibrium among each other (all r² > 0.8) associated with mathematical reasoning ability (top SNP: rs34034296, p = 2.01 × 10⁻⁸, nearest gene: CUB and Sushi multiple domains 3, CSMD3). We replicated one SNP (rs133885) from 585 SNPs previously reported to be associated with general mathematical ability associated with division ability in our data (p = 1.053 × 10⁻⁵). In the gene- and gene-set enrichment analysis by MAGMA, we found three significant enrichments of associations with three mathematical ability categories for three genes (LINGO2, OAS1 and HECTD1). We also observed four significant enrichments of associations with four mathematical ability categories for three gene sets. Our results suggest new candidate genetic loci for the genetics of mathematical ability.     

A genome wide association analysis in the GENDER study

Percutaneous coronary intervention (PCI) has become an effective therapy to treat coronary artery diseases. However, one of the major drawbacks of PCI is the occurrence of restenosis in 8 to 40% of all treated patients. The GENetic Determinants of Restenosis (GENDER) project was designed to study the association between genetic polymorphisims and clinical restenosis. The discovery of genetic variants associated to the occurrence of restenosis after PCI may provide a more tailored therapy and may serve as rationale for new antirestenotic therapies. So far, several candidate gene approaches had already been performed in the GENDER samples but a Genome Wide Association Scan (GWAS) was still lacking. Here, we present preliminary results from the GWAS we are currently carrying out in the GENDER population. (Neth Heart J 2009;17:262–4.)     

Genome-wide association study reveals five nucleotide sequence variants for carcass traits in beef cattle

Genetic associations of nucleotide sequence variants with carcass traits in beef cattle were investigated using a genome-wide single nucleotide polymorphism (SNP) assay. Three hundred and thirteen Korean cattle were genotyped with the Illumina BovineSNP50 BeadChip, and 39,129 SNPs from 311 animals were analysed for each carcass phenotype after filtering by quality assurance. Five sequence markers were associated with one of the meat quantity or quality traits; rs109593638 on chromosome 3 with marbling score, rs109821175 on chromosome 11 and rs110862496 on chromosome 13 with backfat thickness (BFT), and rs110228023 on chromosome 6 and rs110201414 on chromosome 16 with eye muscle area (EMA) (P < 1.27 × 10(-6) , Bonferonni P < 0.05). The ss96319521 SNP, located within a gene with functions of muscle development, dishevelled homolog 1 (DVL1), would be a desirable candidate marker. Individuals with genotype CC at this gene appeared to have increased both EMA and carcass weight. Fine-mapping would be required to refine each of the five association signals shown in the current study for future application in marker-assisted selection for genetic improvement of beef quality and quantity.     

全基因组关联研究通路分析方法现状

全基因组关联研究(genome-wide association study, GWAS)自2005年首次发表以来已不断增进人们对疾病遗传机制的认识,结合系统生物学并改进统计分析方法是对GWAS数据进行深度挖掘的重要途径。通路分析(pathway analysis)将GWAS所检测的遗传变异根据一定的生物学含义组合为集合进行分析,有利于发现对疾病单独效应小却在通路中相互关联的遗传变异,更有利于进行生物学解释。当前通路分析在GWAS数据上已有较为广泛的应用并取得初步成果。与此同时,通路分析的统计方法仍在不断发展。本文旨在介绍现有直接以SNP为对象的GWAS通路分析算法,根据方法中是否采用核函数分为非核算法和核算法两大类,其中非核算法主要包括基因功能富集分析(gene set enrichment analysis, GSEA)和分层贝叶斯优取(hierarchical Bayes prioritization, HBP),核算法包括线性核(linear kernel, LIN)、状态认证核(identity-by-status kernel, IBS)和尺度不变核(powered exponential kernel)。通过介绍这些方法的计算原理和优缺点,以期为新算法的构建提供更好的思路,为GWAS领域研究方法的选择提供参考。     

Genome-wide association study for feed efficiency in collective cage-raised rabbits under full and restricted feeding

Feed efficiency (FE) is one of the most economically and environmentally relevant traits in the animal production sector. The objective of this study was to gain knowledge about the genetic control of FE in rabbits. To this end, GWASs were conducted for individual growth under two feeding regimes (full feeding and restricted) and FE traits collected from cage groups, using 114 604 autosome SNPs segregating in 438 rabbits. Two different models were implemented: (1) an animal model with a linear regression on each SNP allele for growth trait; and (2) a two-trait animal model, jointly fitting the performance trait and each SNP allele content, for FE traits. This last modeling strategy is a new tool applied to GWAS and allows information to be considered from non-genotyped individuals whose contribution is relevant in the group average traits. A total of 189 SNPs in 17 chromosomal regions were declared to be significantly associated with any of the five analyzed traits at a chromosome-wide level. In 12 of these regions, 20 candidate genes were proposed to explain the variation of the analyzed traits, including genes such as FTO, NDUFAF6 and CEBPA previously associated with growth and FE traits in monogastric species. Candidate genes associated with behavioral patterns were also identified. Overall, our results can be considered as the foundation for future functional research to unravel the actual causal mutations regulating growth and FE in rabbits.     

Genome-wide association study on bipolar disorder in the Bulgarian population

Bipolar disorder is a severe psychiatric disorder influenced by environmental and genetic factors. Genetic studies have implicated many variants in the disease's etiology but only few have been successfully replicated. We conducted a genome-wide association study (GWAS) on bipolar disorder in the Bulgarian population followed by a replication study of the top 100 single nucleotide polymorphisms (SNPs) showing the smallest P values. The GWAS was performed on 188 bipolar disorder patients and 376 control subjects genotyped on the Illumina 550 platform. The replication study was conducted on 122 patients and 328 controls. Although our study did not show any association P value that achieved genome-wide significance, and none of the top 100 SNPs reached the Bonferroni-corrected P value in the replication study, the plausible involvement of some variants cannot be entirely discarded. Three polymorphisms, rs8099939 [P = 2.12 × 10(-6), odds ratio (OR) = 1.95, 95% confidence interval (CI) = 1.43-2.67] in GRIK5, rs6122972 (P = 3.11 × 10(-6), OR = 2.02, 95% CI = 1.46-2.80) in PARD6B and rs2289700 (P = 9.14 × 10(-6), OR = 2.13, 95% CI = 1.53-2.95) in CTSH remained associated at a similar level after Mantel-Haenszel test for combining the results from the genome-wide and replication studies. A modest association was also detected for SNP rs1012053 (GWAS P = 4.50 × 10(-2)) in DGKH, which has already been reported as the most significant variant in a previous genome-wide scan on bipolar disorder. However, further studies using larger datasets are needed to identify variants with smaller effects that contribute to the risk of bipolar disorder.     

高原肺水肿易感基因多态性的全基因组关联分析

目的：高原肺水肿严重影响高原人群的健康。筛选高原肺水肿易感基因以用于高原肺水肿易感者的评估及防护。方法：利用Affymetrix SNP Array6．0芯片对23例高原肺水肿患者和17个健康对照进行全基因组SNP分型,利用PLINK软件进行了全基因组关联分析,利用Go和Pathway软件进行分析及作图。结果：全基因组关联分析获得39个相对显著的SNPs位点（P〈10^-4）。通过对这些SNP位点附近27个基因的c0和Pathway富集分析,发现这些基因主要参与细胞增殖调控过程、氮代谢过程和G蛋白耦联受体蛋白信号转导通路等。结论：本文发现的多态性位点及相关基因可能与高原肺水肿易感性相关。     

Genome-wide association study of milk production traits in a crossbred dairy sheep population using three statistical models

Milk production is one of the most important characteristics of dairy sheep, and the identification of genes affecting milk production traits is critical to understanding the genetics and improve milk production in future generations. Three statistical techniques, namely GWAS, ridge-regression BLUP and BayesC , were used to identify SNPs in significant association with three milk production traits (milk yield, fat yield and protein yield) in a crossbred dairy sheep population. The results suggested that chromosomes 1, 3, 4, 5, 7 and 11 were likely to harbor genes important to milk production because these chromosomes had the greatest top-100-SNP variance contributions on the three milk production traits. The GWAS analysis identified between 74 and 288 genome-wide significant SNP (P < 0.05) whereas the BayesCπ model revealed between six and 63 SNPs, each with >95% posterior probability of inclusion as having a non-zero association effect on at least one of the three milk production traits. Positional candidate genes for milk production in sheep were searched, based on the sheep genomic assembly OAR version 3.1, such as those which map position coincided with or was located within 0.1 Mbp of a genome-wide suggestive or significant SNP. These identified SNPs and candidate genes supported some previous findings and also added new information about genetic markers for genetic improvement of lactation in dairy sheep, but keeping in mind that the majority of these positional candidate genes are not necessarily true causative loci for these traits and future validations are thus necessary.