猪13号染色体q41区的3个功能基因STS多态性与产肠毒素大肠杆菌F4ab／ac易感性相关

由产肠毒素大肠杆菌（Escherichia coli）F4（ETECF4）引起的断奶前仔猪腹泻病是一种常见细菌感染病,对养猪业造成了巨大经济损失．编码ETECF4ab／ac受体的位点已被定位于猪（Susscrofa）13号染色体（SSC13）q41区域,S0075为最紧密连锁的标记之一．本研究从S0075侧翼染色体区域选择了SLC12A8,MYLK和KPNAI3个基因,建立猪特异性序列标签位点（STS）．利用白色杜洛克×二花脸资源家系群体中的ETECF4ab／ac侵染抗性和易感个体,通过比较测序法,建立了这3个基因的STS,并鉴别到7个单核苷酸多态位点．进一步检测了白色杜洛克×二花脸资源家系群体祖代、亲本代和755头F2个体在SLC12A8g．159A〉G,MYLKg．1673A〉G和KPNA1g．306A〉G多态位点的基因型．传递不平衡检测（TDT）分析表明：这些多态位点和相应的单倍型与ETECF4ab／ac（特别是F4ac）刷状缘黏附表型存在显著相关,表明这些多态位点和单倍型与ETECF4ab／ac受体的编码基因因果突变存在连锁不平衡．本研究进一步证实了SSC13q41存在ETECF4ab/ac侵染易感性的遗传位点,为ETECF4ab／ac受体基因的精细定位提供了新型多态标记．     

甘南牦牛(Bos grunniens)FBXO32基因突变及其与胴体和肉质性状关联分析

为了分析甘南牦牛(Bos grunniens)肌肉萎缩盒蛋白32(F-box protein 32,FBXO32)基因的单核苷酸多态性(single nucleotide polymorphism, SNP)位点,以及基因型与胴体和肉质性状间的相关性,本研究以593头甘南牦牛为研究对象,采用混池测序和竞争性等位基因特异性PCR(kompetitive allele specific PCR, KASP)技术,检测了甘南牦牛FBXO32基因突变位点及基因型,分析了基因型与甘南牦牛胴体及肉质性状的相关性。结果表明,从甘南牦牛FBXO32基因检测到7个SNP位点,分别是位于5′UTR区的SNP1(g.267A>C)、外显子1区的SNP2(g.326G>T)、外显子8区的SNP3(g.31231G>C),以及3′UTR区的SNP4(g.31352G>A)、 SNP5(g.31424C>T)、 SNP6(g.31503A>C)和SNP7(g.31504A>G)。其中,SNP1、 SNP4、 SNP5、 SNP6与肌肉嫩度显著相关(P<0.05), ...     

前列腺素F2α受体(PTGFR)基因在白色杜洛克×二花脸资源群体中的遗传变异及其与母猪母性行为的关联性

母猪分娩期间的母性行为对新生仔猪的成活致关重要,失败的母性行为如杀婴行为和压仔行为等经常在一些母猪中发生,给养猪业造成巨大的经济损失,给仔猪福利带来严重影响。前列腺素F2α不但可促发母猪产前的做窝行为,而且通过其受体基因(PTGFR)编码的蛋白FP在母猪繁殖过程和母性行为中发挥重要作用。文章以白色杜洛克×二花脸资源群体为材料,对PTGFR基因进行了SNP搜寻并分析其与母猪产前做窝行为、产后杀婴行为和压仔行为的关联性。结果:在PTGFR基因的两个外显子中共搜寻到5个同义突变SNP。选择Exon1g.250AG、Exon1g.619GA和Exon2g.483TC3个SNP在F0、F1个体和289头F2母猪中进行了基因型判定。基于家系基础上的传递不平衡(TDT)分析结果显示,PTGFR基因的3个SNP及单倍型与母猪做窝行为、杀婴行为和压仔行为均未达到显著相关(P0.05)。所以PTGFR基因可能并不是影响母猪母性行为的主效候选基因。     

猪前列腺素内过氧化物酶2(PTGS2)基因的遗传变异及其与繁殖性状相关性研究

前列腺素内过氧化物酶2是花生四烯酸合成前列腺素的限速酶,在包括排卵、受精、着床、分娩等一系列生殖过程中起着重要作用,因而编码该酶的基因是影响繁殖性状的重要候选基因。通过PCR—RFLP分析前列腺索内过氧化物酶2基因在15个中外不同繁殖性能猪种中的遗传变异,结果表明,不同类型中国地方猪种和外来商业猪种往此摹因位点上存在丰富的多态性,繁殖性能相埘较好的江海型、华北型和华中型猪种中A等位基因表现为优势等位基因,卡方检验显示其基因频率分布与西方商业猪种及繁殖性能较低的高原型藏猪和华南型猪种差异均极为显著（P〈0．001）。利用二花脸x杜洛克资源家系F2群体分析该基因与繁殖性状的相关性,在180头F2代母猪群体中,未能进一步证实该基凶位点对总产仔数、产活仔数和死胎数3个繁殖性状存在显著影响（P〉0．05）,但携带优势等位基因4的个体趋向于拥有较高的总产仔数、产活仔数和偏低的死胎数,鉴于该基因的重要作用,基于全基因序列的SNP扫描和大样本群体的相关性分析仍很有必要。     

水牛ApoB基因多态性与泌乳性状关联分析

本研究旨在探究水牛(Bubalus bubalis)载脂蛋白B基因(ApoB)在地中海水牛群体中的遗传多态性,并与地中海水牛泌乳性状进行关联分析,筛选水牛产奶性状分子标记。本研究以350头地中海纯种奶水牛为研究对象,利用直接测序法和基质辅助激光解吸电离飞行时间质谱(MALDI-TOF-MS)法筛选基因多态性(single nucleotide polymorphisms, SNPs)与基因分型,并进一步分析单倍型与泌乳性状的相关性。结果显示,在地中海水牛群体ApoB基因中筛选到10个SNPs,分别位于启动子(g.-1718A>G、g.-1823G>C和g.-2063A>C)、第7内含子(g.8105G>A)、第26内含子(g.30643G>A)、第5外显子(g.5903G>A)、第26外显子(g.30879T>C、g.33638A>C和g.37375G>A)和第29外显子(g.40787A>G)区域。10个SNPs位点多态信息含量均大于0.25且小于0.5,属于中度多态。其中g.-1718A>G、g.-1823G>...     

一个鼻咽癌家系中存在COX7B2基因的低频变异

在中国南方鼻咽癌(nasopharyngeal carcinoma, NPC)高发地区, 遗传易感性在鼻咽癌发病中起重要作用, 在4p11-4p14区域存在一个鼻咽癌易感位点. 采用PCR-直接测序法对位于该区域内的细胞色素C氧化酶亚单位Ⅶb2 (COX7B2)基因进行单核苷酸多态性(single nucleotide polymorphism, SNP)筛查, 对发现的变异在家系患者、散发病例和正常人群中进行分型分析, 探讨COX7B2基因变异是否与鼻咽癌有关. 在COX7B2基因中共发现5个新的SNP位点, 分别位于上游启动子区(&#8722;158101G>T和&#8722;157322G>A)、第2内含子区域(&#8722;109602A>G)、第3外显子区(78T>A)和3′-非翻译区(354T>A). 位于第3外显子编码区的78T>A变异导致CAT26CAA (His26Gln)改变, 在31号鼻咽癌家系中与患者易感单体连锁, 但不存在于其他家系患者和散发病人中. 在广东地区和华东地区对照个体中78T>A变异的频率分别为0.45%(2/448)和0.26%(1/384), 在白人、黑人样本中没有发现该变异. 蛋白质序列比对显示COX7B2亚基26His位点在人、大猩猩、黑猩猩、长臂猿、大鼠和小鼠中十分保守. 上述结果提示COX7B2基因26His是一个保守的位点, 低频的His26Gln变异可能与31号家系的鼻咽癌高发有关.     

鸡Apo-AI基因g.-163 A>T单核苷酸多态性的功能性分析

鸡Apo-AI基因g.-163 A>T单核苷酸多态性(SNP)与鸡腹脂重和腹脂率显著相关. 生物信息分析显示,该SNP位于鸡Apo AI基因转录起始位点,提示它可能是一个功能性SNP. 为确定该SNP的功能性, 本研究分别构建了含该SNP位点A和T等位基因的启动子报告基因载体,分别在DF1细胞和HepG2细胞中比较这2个等位基因对鸡Apo AI基因启动子活性的影响. 研究发现,T等位基因的启动子报告基因活性及报告基因mRNA表达水平均显著高于A等位基因（P<0.05）,表明该SNP影响基因表达,是1个功能性SNP. 本研究结果提示,鸡Apo-AI基因g.-163 A>T有望作为优质鸡育种的功能性分子标记.     

不同品种猪肌肉生长抑制素基因单核苷酸多态性分析

用PCR-RFLPs和PCR-SSCP分析方法,对"双肌臀”大白猪、大白猪、长白猪、杜洛克、汉普夏、皮特兰、二花脸、东北民猪、湖北白猪和部分杂交猪等不同品种猪肌肉生长抑制素基因3＇编码区、5＇调控区及内含子1区3个单核苷酸多态性位点(SNPs)进行了分析.结果表明,3＇编码区的SNP发生的频率较低,在274头猪中未检出突变纯合体.对5＇调控区的SNP,引进猪种(大白猪、长白猪、杜洛克、汉普夏和皮特兰)及其杂交猪以等位基因T为主,二花脸和湖北白猪则以等位基因A为主,均偏离Hardy-Weinberg平衡状态(P＜0.01).东北民猪的3种基因型近乎相等,处于Hardy-Weinberg衡状态.对内含子1区的SNP,大白猪及其与长白猪的杂交猪等位基因G占优势,二花脸和湖北白猪则以等位基因A为主,均偏离Hardy-Weinberg平衡状态(P＜0.01);东北民猪和大二猪的等位基因G和A近乎相等,处于Hardy-Weinberg平衡状态."双肌臀”大白猪在5＇调控区和内含子1区这两个位点的A等位基因稍高于普通大白猪.5＇调控区和内含子1区SNPs所产生的等位基因表现出连锁遗传现象.     

复杂疾病的遗传易感基因区域的精细定位

以单核苷酸多态性(Single-nucleotide polymorphism, SNP)为遗传标记, 采用全基因组关联研究(Genome-wide association studies, GWAS)的策略, 已经在660多种疾病(或性状)中发现了3800多个遗传易感基因区域。但是, 其中最显著关联的遗传变异或致病性的遗传变异位点及其生物学功能并不完全清楚。这些位点的鉴定有助于阐明复杂疾病的生物学机制, 以及发现新的疾病标记物。后GWAS时代的主要任务之一就是通过精细定位研究找到复杂疾病易感基因区域内最显著关联的易感位点或致病性的易感位点并阐明其生物学功能。针对常见变异, 可通过推断或重测序增加SNP密度, 寻找最显著关联的SNP位点, 并通过功能元件分析、表达数量性状位点(Expression quantitative trait locus, eQTL)分析和单体型分析等方法寻找功能性的SNP位点和易感基因。针对罕见变异, 则可采用重测序、罕见单体型分析、家系分析和负荷检验等方法进行精细定位。文章对这些策略和所面临的问题进行了综述。     

广西巴马小型猪MCP-1、MMP-9基因启动子区SNP位点与动脉粥样硬化相关血清指标的关联分析

本研究目的是分析广西巴马小型猪MCP-1和MMP-9基因启动子区SNP位点与血清指标的关联性,筛选可能与动脉粥样硬化相关的高风险分子标记,为后续培育广西巴马小型猪动脉粥样硬化疾病模型易感家系打下基础。采用PCR-RFLP对90头正常饲喂的广西巴马小型猪的MCP-1和MMP-9基因启动子区SNP位点进行分型,统计该位点的基因型频率和等位基因频率,比较分析基因型频率与动脉粥样硬化相关血清指标的关联性。结果显示,广西巴马小型猪MMP-9基因-1267位点、-1287位点和MCP-1基因-1782位点均存在3种基因型:AA型、AG型和GG型。MCP-1基因-1782位点和MMP-9基因-1267位点以GG型为优势基因型,MMP-9基因-1287位点以AG型为优势基因型。MMP-9基因两个突变位点的各基因型个体的血清指标及其分析值之间差异均不显著。MCP-1基因-1782位点AG型个体血清LDL平均值和LDL/HDL比值均显著高于GG型个体(p0.05),AG型个体HDL和TC浓度均值、AI值稍高于GG型个体,但差异均不显著。MCP-1基因AG型个体患动脉粥样硬化疾病的风险高,可作为培育建模易感家系的分子标记。     

Polymorphisms of the TIM-1 gene are associated with rheumatoid arthritis in the Chinese Hui minority ethnic population

The T-cell immunoglobulin and mucin domain 1 (TIM-1) is known to be associated with susceptibility to rheumatoid arthritis (RA). We investigated the association of four single-nucleotide polymorphisms (SNPs) in the promoter region of the TIM-1 gene with susceptibility to RA in a Chinese Hui ethnic minority group. Using RFLP or sequence specific primer-PCR, 118 RA patients and 118 non-arthritis control individuals were analyzed for the -1637A>G, -1454G>A, -416G>C, and -232A>G SNPs in the TIM-1 gene. The polymorphisms -232A>G and -1637A>G in the promoter region of TIM-1 were found to be associated with susceptibility to the RA gene in the Hui population, while -416G>C and -1454G>A SNPs were not. Of these, the polymorphism of -232A>G is inconsistent with that found in a Korean population, suggesting that genetic variations of the TIM-1 gene contribute to RA susceptibility in different ways among different populations. Based on haplotype analysis, individuals with haplotypes AGCA (Χ(2) = 22.0, P < 0.01, OR (95%CI) >1), AGCG (Χ(2) = 18.16, P < 0.01, OR (95%CI) >1) and AGGA (Χ(2) = 5.58, P < 0.05, OR (95%CI) >1) are at risk to develop RA in the Chinese Hui population; those with the GAGA (Χ(2) = 7.44, P < 0.01, OR (95%CI) <1) haplotype may have a decreased likelihood of RA. GGCA and GGCG are more common in both RA and non-RA subjects. We conclude that -1637A>G and -232A>G polymorphisms of TIM-1 are associated with susceptibility to RA in the Chinese Hui population.     

Polymorphisms of three gene-derived STS on pig chromosome 13q41 are associated with susceptibility to enterotoxigenic Escherichia coli F4ab/ac in pigs

Neonatal diarrhea caused by enterotoxigenic Escherichia coli(ETEC)F4 is a common and serious disease,resulting in significant economical loss in the pig industry.The locus encoding ETEC F4 receptor has been mapped to pig chromosome(SSC)13q41,and one of the most significantly linked markers is S0075.In this study,we selected three genes including SLC12A8,MYLK and KPNA1 from a chromosomal region flanking S0075 on SSC13 to develop pig specific sequence tagged sites(STS). Seven single nucleotide polymorphisms were identified in the three pig STS using DNA of four full-sib susceptible and resistant animals in a White Duroc×Erhualian intercross.All grandparents,parents and 755 offspring in the intercross were genotyped for three polymorphisms,including SLC12A8 g.159A>G,MYLK g.1673A>G and KPNA1 g.306A>G.Family-based transmission disequilibrium test(TDT) revealed that all polymorphisms and the corresponding haplotypes are significantly associated with ETEC F4ab/ac(especially F4ac)brush border adhesion phenotypes,indicating that these polymor- phism are in linkage disequlibrium with causal mutation(s)of the gene encoding ETEC F4ab/ac receptor. Our results strengthen the evidence for the involvement of SSC13q41 in high acquiring risk of ETEC F4ab/ac infection,and provide novel polymorphic markers for fine mapping of the ETEC F4ab/ac receptor locus.     

Genetic variation and association of prostaglandin F2alpha receptor (PTGFR) gene with sow maternal behaviors in a White Duroc x Erhualian resource population

Maternal behaviors of sows around parturition are important for survival of newborn offspring. Failure to establish normal maternal bonds such as maternal infanticide and crushing often occurs in some individuals. It causes both significant economic losses to the pig industry and severe problems of piglet welfare. Prostaglandin F2-alpha not only can stimulate the nest-building behavior of sows before parturition but also plays an important role in reproductive process and maternal behavior through protein FP encoded by the prostaglandin F receptor gene (PTGFR) as its receptor. In this study, genetic variation and association study of PTGFR gene with nest-building behavior, maternal infanticide, and crushing behavior was carried out in a White Duroc x Erhualian resource population. As a result, five synonymous mutations were identified on exon 1 and exon 2. Exon 1 g .250 A>G, Exon 1 g.619 G>A and Exon 2 g.483 T>C were chosen for genotyping in individuals of F0, F1 and 289 F2 sows. Family-based transmission disequilibrium test (TDT) demonstrated that there were no significant associations of 3 SNPs and haplotypes of PTGFR gene with sow nest-building, maternal infanticide and crushing behavior (P > 0.05). Therefore, it can be concluded that PTGFR gene is not the causative candidate gene for sow maternal behaviors.     

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.     

Three novel SNPs of the bovine Tf gene in Chinese native cattle and their associations with milk production traits

Transferrin (Tf) is a β-globulin protein that transports iron ions in mammalian cells. It contributes to innate immunity to microbial pathogens, primarily by limiting microbial access to iron. Thus, polymorphisms present in bovine Tf could potentially underlie inherited differences in mastitis resistance and milk production traits. We detected three novel single-nucleotide polymorphisms of the Tf gene in Chinese native cattle by screening for genetic variation of Tf in 751 individuals of three Chinese cattle breeds, namely China Holstein, Luxi Yellow and Bohai Black, using PCR-RFLP and DNA sequencing techniques. The three new SNPs, g.-1748G>A ss250608649, g.13942T>C ss250608650, and g.14037A>G ss250608651, had allele frequencies of 85.9, 86.3 and 92.5%, 64.5, 73.3 and 65.0%, and 67.6, 73.7 and 60.0%, respectively. SNP g.-1748G>A was located in the 5' flanking region of Tf. SNP g.14037A>G was located in intron 8 of Tf. SNP g.13942T>C, located in exon 8 of Tf, was a synonymous mutation (TTA > CTA), encoding a leucine (326 aa) in the Tf protein. Associations of the Tf SNPs with milk traits were also analyzed. Significant (P < 0.05) relationships among the Tf polymorphisms, somatic cell scores (SCS), and milk productive traits were observed. Cows with genotypes TT (g.13942T>C), GG (g.-1748G>A) and AG (g.14037A>G) had a lower SCS and higher protein levels and 305-day milk yield. Nineteen combinations of different haplotypes from the three SNPs were identified in Chinese Holstein cattle. The haplotype combination ATA/GCA, GCA/GCA and GCG/ GTA was dominant in cows with a lower SCS, a higher protein level and a higher 305-day milk yield, respectively. Moreover, the gene expression level of Tf was higher in mastitis-affected mammary tissues than in normal mammary tissues. These results suggest that the Tf gene affects milk production, as well as mastitis-resistance traits, in Chinese Holsteins.     

Identification of TDRP1 gene and its association with pig reproduction traits

This study was performed to identify and characterize the pig TDRP1 gene and to investigate its association with reproduction traits. The obtained pig TDRP1 cDNA (713 base pair [bp]) comprises a 561-bp open reading frame, which encodes a peptide of 187 amino acids. The identities of pig TDRP1 cDNA were 84.6%, 75.7%, and 77.4% with its counterparts in human, rat, and mice, respectively. Real-time polymerase chain reaction indicated that pig TDRP1 gene was highly expressed in pituitary of male and uterus of female animals. The pig TDRP1 gene contains three exons and two introns. A total of 13 single-nucleotide polymorphisms (SNPs) and 1 indel were identified in the screened partial genomic sequence, with most polymorphisms in introns. Allelic frequencies of five SNPs among eight pig breeds were further investigated, and it indicated that Landrace had the lowest genetic diversity. In Yorkshire, three SNPs (c.215+144T>C, c.215+249A>G, and c.215+672T>C) exhibited complete linkage disequilibrium in one haplotype block, and association analyses showed that all of them were significantly associated with number born alive of first parity (NBA1) (p<0.05). c.215+672T>C was also significantly associated with NBA6 (p<0.05). In addition, these three SNPs and two other ones (c.215+1001G>A and c.215+1026C>T) were associated with total born alive of second parity (TBA2) and TBA6 at the suggestive level (0.05相似文献