A Single Nucleotide Polymorphism of Chicken Acetyl-CoA Carboxylase A Gene Associated with Fatness Traits

Acetyl-CoA carboxylase α (ACCα) is a major rate-limiting enzyme in the biogenesis of long-chain fatty acids. It can catalyze the carboxylation of acetyl-CoA to form malonyl-CoA that plays a key role in the regulation of fatty acid metabolism. The objective of the present study was to investigate the associations of ACCα gene polymorphisms with chicken growth and body composition traits. The Northeast Agricultural University broiler lines divergently selected for abdominal fat content and the Northeast Agricultural University F₂ Resource Population were used in the current study. Body weight and body composition traits were measured in the aforementioned two populations. A synonymous mutation was detected in the exon 19 region of ACCα gene, then polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method was developed to genotype all the individuals derived from the aforementioned populations. Association analysis revealed that the polymorphism was associated with abdominal fat weight and percentage of abdominal fat in the two populations. The results suggested that ACCα gene could be a candidate locus or linked to a major gene that affects abdominal fat content in the chicken.     

鸡Myostatin基因单核苷酸多态性的群体遗传学分析

肌肉生长抑制素是控制骨骼肌生长发育的重要细胞因子,采用PCR－SSCP和测序的方法发现了5个位于Myostatin基因5′－和3′－调控区的单核苷酸多态性位点,对北京油鸡、白耳鸡、石歧杂、矮小黄鸡、小型黄鸡、惠阳胡须鸡、隐性白羽鸡、海兰、AA鸡等不同鸡种的该单核苷酸多态性分析结果表明：Myostatin基因的5′调控区引物P60／P61扩增片段多态性是由3个核苷酸的改变而产生的[分别是G→A（304位）、A→G（322位）、G→（344位）],引物P93／P94扩增片段的多态性是由G→A（167位）突变造成的,引物P117。P118PC扩增片段多态性是由T→C（177位）造成的。3′调控我引物P80／P81扩增片段多态性是由第7263位A突变为T造成的,引物P76／P77扩增片段多态性是由A→G（6935位）造成的。不同鸡种群体遗传学分析表明,5′－调控区引物60／P61扩增片段多态性片段多态性是由A→G（6935位）造成的。不同鸡种群体遗传学分析表明,5′－调控区引物P60／P61扩增片段多态性位点在北京油鸡的基因型频率分布与其他的品种有很大的差异,其BB型频率为0．700,AA基因型频率仅为0．033,而其他鸡种中以A基因优势;对于引物P93／P94,品种间的基因型频率差异极显著（P＜0．01）,北京油鸡和AA鸡的EE型频率鸡种中以A基因占优势;对于引物P93／P94,品种间的基因型频率差异极显著（P＜0．01）,北京油鸡和AA鸡的EE型频率低于其他品种,白耳鸡和海兰蛋鸡以EE型为主,其频率高于其他品种;3′－调控区引物P80／P81多态怀位点在9个鸡种中都是等位基因C占优势。引物P76／P77,总体上MM型的频率较低,杂合子MN型的频率较高。     

hRFT2基因单核苷酸多态性的生物信息学分析

旨在筛选可能与人类疾病有关的hRFT2基因单核苷酸多态性(single nucleotide polymorphisms,nsSNPs)和突变位点,从SNP数据库中检索并筛选出395个有效的hRFT2基因SNPs,其中包括30个同义SNPs(synonymous SNPs,sSNPs)和31个非同义SNPs(non-synonymous single nucleotide polymorphisms,nsSNPs)。分别采用SIFT、SNPs3D和PolyPhen-2方法分析nsSNPs引起的氨基酸替换是否可能影响hRFT2的功能。结果表明,5个nsSNPs(rs11477762、rs146302587、rs146492942、rs76947760和rs145431028)可能严重影响hRFT2蛋白的功能,其中rs76947760和rs145431028的影响已得到临床证明,另外3个nsSNPs(rs148387972、rs140391358和rs3746802)也可能对hRFT2有较大的影响。     

猪UCP3基因部分编码区序列分析及其单核苷酸多态与胴体、肉质性状的遗传效应

以猪解耦联蛋白基因 3(UCP3)作为控制猪胴体与肉质性状主基因的候选基因。利用直接测序法对 4个品种猪骨骼肌中UCP3基因的部分编码区序列 (第 4外显子部分及第 5、6、7外显子全部片段 )进行比较分析 ,发现3个cSNP位点 ,其中ORF中第 84 2碱基的突变可导致相应编码氨基酸序列的改变 :甲硫氨酸→苏氨酸 ,选取此位点作为猪UCP3基因的多态位点。用PCR SSCP检测方法在 3个品种猪中进行该cSNP位点多态性片段的基因型分型 ,结果显示在 3个猪群中表现出 3种基因型 (AA、AB、BB) ,χ2 独立性检验结果表明 3种基因型在各品种间分布不一致 ,梅山猪同大白、长白猪分别比较差异极显著 (P <0 0 1) ;对大白×梅山资源家系F2 代 139头个体进行了该多态片段的基因型鉴定 ,并对其基因型与所检测个体相应的胴体、肉质性状采用GLM分析进行遗传效应研究 ,结果表明 :该基因对一些胴体、肉质性状有显著性影响 ,并且该基因以加性效应为主 (如 ,眼肌高度、背最长肌色值、系水力的加性效应都达显著水平 )。因此 ,推测UCP3基因可能是影响猪胴体及肉质性状的主效基因或与主效基因紧密连锁的标记基因 ,并且能够在分子标记辅助选择中用于对猪胴体、肉质性状的遗传改良及固定     

Polymorphisms of the Myostatin Gene and Its Relationship with Reproduction Traits in the Bian Chicken

Myostatin, or growth and differentiation factor 8, is a member of the transforming growth factor-β superfamily; it functions as a negative regulator of skeletal muscle development and growth in mammals. In this study, single nucleotide polymorphisms in the 5′ regulatory region and exon 1 of the myostatin gene were detected by PCR–SSCP in the Bian, Jinghai, Youxi, and Arbor Acre chickens, and the associations of the polymorphisms with reproduction traits were analyzed. Seven SNPs (A326G, C334G, C1346T, G1375A, A1473G, G1491A, and G2283A) were found in the myostatin gene. Association analysis showed that the G2283A were significantly associated with reproduction traits. Bian chickens of the GG genotype had a greater age at first egg than those of the GA and AA genotypes (P < 0.01). Correspondingly, Bian chickens of the GA and AA genotypes had larger egg number at 300 days than those of the GG genotype (P < 0.05 and P < 0.01, respectively). Bian chickens of the AA genotype had significantly higher body weight at 300 days than those of the GG genotype (P < 0.05). These results suggested that the myostatin gene may have certain effects on reproduction traits other than merely as a negative regulator of skeletal muscle development and growth in mammals previously reported.     

Genetic Polymorphisms of the CACNA2D1 Gene and Their Association with Carcass and Meat Quality Traits in Cattle

The objective of this study was to identify genetic polymorphisms of the CACNA2D1 gene and to analyze associations between SNPs and carcass and meat quality traits in cattle. Through PCR-RFLP and DNA sequencing methods, a new allelic variant corresponding to the A → G mutation (aspartic to glycine amino acid replacement) of the bovine CACNA2D1 gene was detected. Two alleles and three genotypes (AA, AG, and GG) were defined. Genetic character indicated that the A526745G locus showed moderate polymorphism and was in Hardy–Weinberg equilibrium. Gene-specific SNP marker association analysis showed that the A526745G mutant was significantly associated with carcass weight, dressing percentage, meat percentage, and backfat thickness. The results add new evidence that CACNA2D1 is an important candidate gene for the selection of carcass and meat quality traits in the cattle industry.     

Single Nucleotide Polymorphisms in HSP17.8 and Their Association with Agronomic Traits in Barley

Small heat shock protein 17.8 (HSP17.8) is produced abundantly in plant cells under heat and other stress conditions and may play an important role in plant tolerance to stress environments. However, HSP17.8 may be differentially expressed in different accessions of a crop species exposed to identical stress conditions. The ability of different genotypes to adapt to various stress conditions resides in their genetic diversity. Allelic variations are the most common forms of genetic variation in natural populations. In this study, single nucleotide polymorphisms (SNPs) of the HSP17.8 gene were investigated across 210 barley accessions collected from 30 countries using EcoTILLING technology. Eleven SNPs including 10 from the coding region of HSP17.8 were detected, which form nine distinguishable haplotypes in the barley collection. Among the 10 SNPs in the coding region, six are missense mutations and four are synonymous nucleotide changes. Five of the six missense changes are predicted to be deleterious to HSP17.8 function. The accessions from Middle East Asia showed the higher nucleotide diversity of HSP17.8 than those from other regions and wild barley (H. spontaneum) accessions exhibited greater diversity than the cultivated barley (H. vulgare) accessions. Four SNPs in HSP17.8 were found associated with at least one of the agronomic traits evaluated except for spike length, namely number of grains per spike, thousand kernel weight, plant height, flag leaf area and leaf color. The association between SNP and these agronomic traits may provide new insight for study of the gene''s potential contribution to drought tolerance of barley.     

BRD7单核苷酸多态性及鼻咽癌易感性分析

为了探讨BRD7基因的遗传变异在鼻咽癌发生的作用,采用PCR-SSCP和直接测序方法对BRD7基因的编码区进行单核苷酸多态性（coding-region single nucleotide polymorphism,cSNP）分析,并对两个鼻咽癌家系的高危成员、57个散发性鼻咽癌病人和50个正常人进行了BRD7等位基因分型.在BRD7基因的编码区发现了3个cSNP（C450T、A538C和A737G）,其中A538C颠换导致其编码蛋白的第162个氨基酸由Asp变为Ala;C450T改变与同义的A737C多态性偶联发生在87.7%的鼻咽癌活检组织和配对的外周血、所有的鼻咽癌家系的患者及8个易感成员,但是仅存在于22%的正常人血标本中.C450T多态性变化可以导致其编码蛋白在第133位氨基酸的翻译终止（G133Ter）.以上结果说明,C450T和A737C偶联的多态性改变是鼻咽癌发生和发展的重要遗传易感风险因子之一（P＜0.01）;BRD7基因有两种翻译方式,G133Ter可以导致另一种截断的翻译本（truncated     

白羽王鸽肌生成抑制因子基因的多态性与组织表达

肌生成抑制因子在抑制成肌细胞的增殖与分化中起着重要作用。本文采用PCR-SSCP与实时定量RT-PCR方法分析白羽王鸽肌生成抑制因子(MSTN基因)的多态性和在脑、肝脏、胸肌组织中的mRNA表达水平及其与体重的相关性。结果表明在白羽王鸽MSTN基因的外显子1和外显子3区域分别检测到一个多态位点,且均属于沉默突变;肝脏、肌肉和脑组织中MSTN基因的表达量依次为肝脏脑肌肉,且差异极显著。而对不同发育阶段的乳鸽研究发现,随着乳鸽日龄(1～25d)的增长,MSTN基因在各组织中的表达量无明显的线性变化规律。该结果为进一步确定MSTN基因的作用机理提供了新的实验依据。     

Association Between Single Nucleotide Polymorphisms of DOT1L Gene and Risk of Knee Osteoarthritis in a Chinese Han Population

To investigate associations between single nucleotide polymorphisms rs12982744 and rs12459350 in the DOT1L gene and knee osteoarthritis (OA) susceptibility in a Chinese Han population. DOT1L rs12982744 and rs12459350 polymorphisms were genotyped in patients with knee OA and age- and sex-matched OA-free controls from a Chinese Han population. A total of 605 patients with knee OA and 615 controls were enrolled in the study. GC and CC genotypes of rs12982744, and variant C, were associated with a significantly increased risk of knee OA. On stratification analysis, the association between the risk of OA and rs12982744 GC heterozygotes compared with GG homozygotes was stronger in females and those aged >65 years. In contrast, the GA and AA genotypes of rs12459350 were not significantly associated with the risk of knee OA, even after further stratification analysis according to age or sex. Our results showed that DOT1L rs12982744 G to C change and variant C genotype may contribute to knee OA risk in a Chinese Han population.     

Association between Single Nucleotide Polymorphisms in the ADD3 Gene and Susceptibility to Biliary Atresia

Background and Objectives

Based on the results of previous studies, the ADD3 gene, located in the 10q24.2 region, may be a susceptibility gene of biliary atresia (BA). In this study, two single nucleotide polymorphisms (SNPs) in the ADD3 gene, rs17095355 C/T and rs10509906 G/C, were selected to investigate whether there is an association between these SNPs and susceptibility to BA in a Chinese population.

Methods

A total of 752 Han Chinese (134 BA cases and 618 ethnically matched healthy controls) were included in the present study. The ADD3 gene polymorphisms were genotyped using a TaqMan genotyping assay.

Results

Positive associations were found for the SNP rs17095355 in the codominant model; specifically, the frequencies of the CT and TT genotypes and the T allele were higher in the cases than the controls, demonstrating a significant risk for BA (odds ratio [OR] = 1.62, 95% confidence interval [CI] = 1.02–2.58; OR = 2.89, 95% CI = 1.72–4.86; and OR = 1.75, 95% CI = 1.34–2.29, respectively). Regarding rs10509906, the per-C-allele conferred an OR of 0.70 (95% CI = 0.49–1.00) under the additive model. A greater risk of BA was associated with the T_a-G_b (a for rs17095355 and b for rs10509906) haplotype (OR = 1.82, 95% CI = 1.27–2.61) compared with the C_a-C_b haplotype.

Conclusion

This study suggests that the ADD3 gene plays an important role in BA pathogenesis and reveals a significant association between two SNPs, rs17095355 and rs10509906, and BA.     

Prediction of the Damage-Associated Non-Synonymous Single Nucleotide Polymorphisms in the Human MC1R Gene

The melanocortin 1 receptor (MC1R) is involved in the control of melanogenesis. Polymorphisms in this gene have been associated with variation in skin and hair color and with elevated risk for the development of melanoma. Here we used 11 computational tools based on different approaches to predict the damage-associated non-synonymous single nucleotide polymorphisms (nsSNPs) in the coding region of the human MC1R gene. Among the 92 nsSNPs arranged according to the predictions 62% were classified as damaging in more than five tools. The classification was significantly correlated with the scores of two consensus programs. Alleles associated with the red hair color (RHC) phenotype and with the risk of melanoma were examined. The R variants D84E, R142H, R151C, I155T, R160W and D294H were classified as damaging by the majority of the tools while the r variants V60L, V92M and R163Q have been predicted as neutral in most of the programs The combination of the prediction tools results in 14 nsSNPs indicated as the most damaging mutations in MC1R (L48P, R67W, H70Y, P72L, S83P, R151H, S172I, L206P, T242I, G255R, P256S, C273Y, C289R and R306H); C273Y showed to be highly damaging in SIFT, Polyphen-2, MutPred, PANTHER and PROVEAN scores. The computational analysis proved capable of identifying the potentially damaging nsSNPs in MC1R, which are candidates for further laboratory studies of the functional and pharmacological significance of the alterations in the receptor and the phenotypic outcomes.     

Polymorphisms of Flanking Region of the ASB15 Gene and Their Associations with Performance Traits in Chicken

Research on the identity of genes and their relationship with traits of economic importance in chickens could assist in the selection of poultry. In this study, an F₂ resource population of Gushi chickens crossed with Anka broilers was used to detect single-nucleotide polymorphisms (SNPs) in the flanking region of the ASB15 gene by DNA sequencing and polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). One SNP of ?1271 C>T in 5′ flanking region of the chicken ASB15 gene and two SNPs of the 10618 A>G and 10716 G>A in 3′ flanking region were identified. Furthermore, the 10618 A>G and 10716 G>A in 3′ flanking region were in complete linkage. Association analysis results showed that ?1271 C>T was not associated with performance traits, while the 10618 A>G and 10716 G>A were significantly associated with BW2, 4, 6, 8, 10, 12, SL12, CD8, CW4, 8, 12, BSL4, 8, 12, and SEW, EW, WW, BMW, LW, CW, SFT. Our results suggest that the ASB15 gene profoundly affects chicken performance traits.     

血管内皮细胞生长因子基因-2578C/A多态性与中国北方汉族人群银屑病易感性的相关性研究

目的:探讨血管内皮细胞生长因子(vascular endothelial cell growth factor,VEGF)基因-2578 C/A单核苷酸多态性位点与中国北方地区银屑病易感性的相关性.方法:随机收集2005年10月至2007年5月在哈尔滨医科大学附属一、二院皮肤科门诊就诊的246例寻常型银屑病患者(实验组)和271名正常对照个体(对照组)的外周静脉血,使用聚合酶链反应-限制性片段长度多态性(PCR-RFLP)方法分析VEGF-2578 C/A多态位点基因型,并进行统计学分析.结果:在实验组中,VEGF-2578 C/A等位基因频率分别为74.80％、25.20％;在正常对照组中,VEGF-2578 C/A等位基因频率分别为76,59％、23.41％,两组VEGF-2578 C/A多态位点基因型的分布差异无统计学意义(P＞0.05).结论:VEGF基因-2578 C/A的多态性与中国北方汉族人群银屑病的易感性无明显相关性.     

Association of the FCN2 Gene Single Nucleotide Polymorphisms with Susceptibility to Pulmonary Tuberculosis

Ficolin-2 (FCN2) is an innate immune pattern recognition molecule that can activate the complement pathway, opsonophagocytosis, and elimination of the pathogens. The present study aimed to investigate the association of the FCN2 gene single nucleotide polymorphisms (SNPs) with susceptibility to pulmonary tuberculosis (TB). A total of seven SNPs in exon 8 (+6359 C>T and +6424 G>T) and in the promoter region (-986 G>A, -602 G>A, -557 A>G, -64 A>C and -4 A>G) of the FCN2 gene were genotyped using the PCR amplification and DNA sequencing methods in the healthy controls group (n = 254) and the pulmonary TB group (n = 282). The correlation between SNPs and pulmonary TB was analyzed using the logistic regression method. The results showed that there were no significant differences in the distribution of allelic frequencies of seven SNPs between the pulmonary TB group and the healthy controls group. However, the frequency of the variant homozygous genotype (P = 0.037, -557 A>G; P = 0.038, -64 A>C; P = 0.024, +6424 G>T) in the TB group was significantly lower than the control group. After adjustment for age and gender, these variant homozygous genotypes were found to be recessive models in association with pulmonary TB. In addition, -64 A>C (P = 0.047) and +6424 G>T (P = 0.03) were found to be codominant models in association with pulmonary TB. There was strong linkage disequilibrium (r² > 0.80, P < 0.0001) between 7 SNPs except the -602 G>A site. Therefore, -557 A>G, -64 A>C and +6424 G>T SNPs of the FCN2 gene were correlated with pulmonary TB, and may be protective factors for TB. This study provides a novel idea for the prevention and control of TB transmission from a genetics perspective.     

Role of Single Nucleotide Polymorphisms of KIF1B Gene in HBV-Associated Viral Hepatitis

Background/Aim

Kinesin family member 1B (KIF1B) gene resides in the chromosomal region 1p36.22 and has been reported to have frequent deletions in a variety of human cancers. A recent genome wide association study (GWAS) study conducted on a Chinese population has reported the involvement of a KIF1B genetic variant in Hepatitis B virus (HBV)-related hepatocellular carcinoma (HCC). This study aims to investigate the significance of KIF1B genetic variations in HBV-associated hepatitis in patients of Saudi Arabian ethnicity.

Methods

TaqMan genotyping assay was used to investigate the association of three SNPs (rs17401966, rs12734551, and rs3748578) in 584 normal healthy controls and 660 HBV-infected patients. The patients were categorized into inactive carriers (Case I), active carriers (Case II), Cirrhosis (Case III) and Cirrhosis-HCC (Case IV) sub-groups.

Results

Since SNPs rs12734551 and rs3748578 are in strong linkage disequilibrium (LD) with rs17401966, only results for the latter SNP are reported. Therefore, the allele frequency of rs17401966 among HBV-infected patients and healthy controls were comparable and therefore, no significant association was observed (P = 0.2811, Odds Ratio (OR) 0.897). A similar analysis was performed among the different sub-groups in order to determine whether KIF1B SNPs were associated with the advancement of the disease. No significant differences were observed in any of the comparisons performed.

Conclusion

Polymorphisms at KIF1B gene locus investigated in this study showed no significant association with HBV infection or with HBV-associated diseases such as liver cirrhosis or HCC.     

Computational Analysis of Functional Single Nucleotide Polymorphisms Associated with the CYP11B2 Gene

Single nucleotide polymorphisms (SNPs) are the most common type of genetic variations in humans and play a major role in the genetics of human phenotype variation and the genetic basis of human complex diseases. Recently, there is considerable interest in understanding the possible role of the CYP11B2 gene with corticosterone methyl oxidase deficiency, primary aldosteronism, and cardio-cerebro-vascular diseases. Hence, the elucidation of the function and molecular dynamic behavior of CYP11B2 mutations is crucial in current genomics. In this study, we investigated the pathogenic effect of 51 nsSNPs and 26 UTR SNPs in the CYP11B2 gene through computational platforms. Using a combination of SIFT, PolyPhen, I-Mutant Suite, and ConSurf server, four nsSNPs (F487V, V129M, T498A, and V403E) were identified to potentially affect the structure, function, and activity of the CYP11B2 protein. Furthermore, molecular dynamics simulation and structure analyses also confirmed the impact of these nsSNPs on the stability and secondary properties of the CYP11B2 protein. Additionally, utilizing the UTRscan, MirSNP, PolymiRTS and miRNASNP, three SNPs in the 3′UTR region were predicted to exhibit a pattern change in the upstream open reading frames (uORF), and eight microRNA binding sites were found to be highly affected due to 3′UTR SNPs. This cataloguing of deleterious SNPs is essential for narrowing down the number of CYP11B2 mutations to be screened in genetic association studies and for a better understanding of the functional and structural aspects of the CYP11B2 protein.     

3个鸡种GARS-AIRS-GART基因第21号外显子的SNPs检测

采用PCR-SSCP和DNA测序法对安卡鸡、文昌鸡和如皋鸡中GARS-AIRS-GART基因的第21号外显子进行SNPs检测.结果发现该外显子含4个核苷酸多态位点:G29943A、C29968T、T30011C和C30017T,其中3处为非同义突变,分别为:29 943处天冬氨酸(Asp)→天冬酰胺(Asn)、30 011处色氨酸(Trp)→精氨酸(Arg)、30 017处精氨酸(Arg)→半胱氨酸(Cys);另一处为同义突变.对多态位点进行单倍型分析,发现12种单倍型,其中两种单倍型(5号和6号)的频率超过10%,分别为0.330 0和0.162 8,1号、3号、9号和10号单倍型频率介于1%～10%之间,其余都小于1%.另外共检测到11种基因型,存在5种等位基因,安卡鸡的D和E等位基因的基因频率较高,基因型与其它两个鸡品种之间都存在着极显著的差异(P<0.01),表明我国地方鸡种和外来鸡种在遗传组成上存在着差异.本研究将为鸡肉品质相关研究积累基础数据,为今后深入开展肉品质的开发利用奠定理论基础.