Association between Gene Polymorphisms and SNP-SNP Interactions of the Matrix Metalloproteinase 2 Signaling Pathway and the Risk of Vascular Senescence

Objective This study aimed to explore the association of single nucleotide polymorphisms(SNP)in the matrix metalloproteinase 2(MMP-2)signaling pathway and the risk of vascular senescence(VS).Methods In this cross-sectional study,between May and November 2022,peripheral venous blood of151 VS patients(case group)and 233 volunteers(control group)were collected.Fourteen SNPs were identified in five genes encoding the components of the MMP-2 signaling pathway,assessed through carotid-femoral pulse wave velocity(cf PWV),and analyzed using multivariate logistic regression.The multigene influence on the risk of VS was assessed using multifactor dimensionality reduction(MDR)and generalized multifactor dimensionality regression(GMDR)modeling.Results Within the multivariate logistic regression models,four SNPs were screened to have significant associations with VS:chemokine(C-C motif)ligand 2(CCL2)rs4586,MMP2 rs14070,MMP2rs7201,and MMP2 rs1053605.Carriers of the T/C genotype of MMP2 rs14070 had a 2.17-fold increased risk of developing VS compared with those of the C/C genotype,and those of the T/T genotype had a19.375-fold increased risk.CCL2 rs4586 and MMP-2 rs14070 exhibited the most significant interactions.Conclusion CCL2 rs4586,MMP-2 rs14070,MMP-2 rs7201,and MMP-2 rs1053605 polymorphisms were significantly associated with the risk of VS.

基于全基因组SNPs标记对河南斗鸡遗传多样性及选择信号分析

【目的】对河南斗鸡品种的遗传多样性与全基因组选择信号进行分析,挖掘河南斗鸡品种重要的种质特性基因。【方法】使用AffymetrixAxiom 600K高密度鸡基因分型芯片对来自9个品种的173只鸡的群体(包括20只河南斗鸡及153只商品鸡)进行基因分型;计算各个品种的期望杂合度、观测杂合度、次等位基因频率及核苷酸多样性评估地方鸡群体的遗传多样性;通过构建系统发育树、主成分分析、祖先成分分析方法研究品种的群体结构;利用斗鸡与商品鸡的成对遗传分化指数值进行选择信号分析。【结果】河南斗鸡及各商品鸡群体的观测杂合度为0.153~0.311,期望杂合度为0.158~0.315,次等位基因频率为0.111~0.234,核苷酸多样性为9.77×10^(-5)~1.56×10^(-4),且斗鸡的遗传多样性低于商品肉鸡品种,高于商品蛋鸡品种。系统发育树、主成分分析及祖先成分分析表明品种间有明显的群体分化。河南斗鸡与商品鸡群的主成分分析发现,河南斗鸡与商品肉鸡品种的遗传距离相对较近;将河南斗鸡和商品鸡群进行遗传选择信号后分析发现,河南斗鸡在神经,骨骼肌肉发育,免疫等性状经过高度选择。【结论】本研究从全基因组水平探究了河南斗鸡的遗传多样性和群体结构,筛选出候选基因,为河南斗鸡遗传资源保护和利用提供参考。

欧拉羊角性状相关RXFP2基因SNPs检测及分析

旨在分析有角和无角欧拉羊群体RXFP2基因对犄角表型的调控作用及相关SNP分子标记,以期为欧拉羊的遗传改良、品种培育提供技术支持。通过采集青海省河南县健康成年欧拉羊母羊血液样品100份,其中有角、无角各50份,提取DNA,随机选取有角、无角样品各15份开展全基因组测序,随后采用多重PCR扩增全部血样验证RXFP2基因SNP。全基因组检测结果表明,包含RXFP2基因在内的欧拉羊10号染色体存在强选择信号,最强选择信号出现在RXFP2基因区段;多重PCR检测验证了全基因组重测序筛查到的4个编码区SNP的准确性,并检测到7个欧拉羊RXFP2基因内含子区域高频SNPs(29508704G>A、29509428A>C、29509766G>A、29512170G>A、29512176G>A、29514968T>A、29521377C>A);经统计检验,该7个SNP位点的基因型在犄角有无表型上表现出分离,纯合子基因型均100%表现为无角或有角,杂合子基因型89.66%表现为无角,10.34%表现为有角;突变等位基因频率小于野生等位基因频率,群体表现为哈代温伯格不平衡状态,受到人工选择强度大,但多态信息含量中等,选育改良潜力仍较大。综上,确认了RXFP2基因在欧拉羊群体中对犄角有无的强调控作用,并筛选出了欧拉羊RXFP2基因的7个犄角有无表型的分子标记,相关结果可作为欧拉羊无角性状群体的遗传改良的分子标记。

Single Nucleotide Polymorphisms (SNPs) Discovery and Linkage Disequilib-rium (LD) in Forest Trees

With completion of the Populus genome sequencing project and the availability of many expressed sequence tags （ESTs） databases in forest trees, attention is now rapidly shifting towards the study of individual genetic variation in natural populations. The most abundant form of genetic variation in many eukaryotic species is represented by single nucleotide polymorphisms （SNPs）, which can account for heritable inter-individual differences in complex phenotypes. Unlike humans, the linkage disequilibrium （LD） rapidly decays within candidate genes in forest trees. Thus, SNPs-based candidate gene association studies are considered to be a most effective approach to dissect the complex quantitative traits in forest trees. The present study demonstrates that LD mapping can be used to identify alleles associated with quantitative traits and suggests that this new approach could be particularly useful for performing breeding programs in forest trees. In this review, we will describe the fundamentals, patterns of SNPs distribution and frequency, summarize recent advances in SNPs discovery and LD and comment on the application of LD in the dissection of complex quantitative traits in forest tress. We also put forward the outlook for future SNPs-based association analysis of quantitative traits in forest trees.

Single-nucleotide polymorphisms of HLA and Polygonum multiflorum-induced liver injury in the Han Chinese population

BACKGROUND Polygonum multiflorum is one of the leading causes of herb-induced liver injury in China.HLA-B*35:01 is reported to be a potential biomarker of Polygonum multiflorum-induced liver injury(PM-DILI).However,little is known about the relationship between single-nucleotide polymorphisms(SNPs) and PM-DILI.AIM To identify SNPs that indicate susceptibility to PM-DILI METHODS We conducted a systematic study enrolling 382 participants from four independent hospitals,including 73 PM-DILI patients,118 patients with other drug-induced liver injury(other-DILI) and 191 healthy controls.Whole-exome sequencing was performed for 8 PM-DILI patients and 8 healthy controls who were randomly selected from the above subjects.Nineteen SNPs that showed high frequencies in the 8 PM-DILI patients were selected as candidate SNPs and then screened in 65 PM-DILI patients,118 other-DILI patients and 183 healthy controls using the MassARRAY system.HLA-B high-resolution genotyping was performed for the 73 PM-DILI and 118 other-DILI patients.The Han-MHC database was selected as a population control for HLA-B analysis.P <6.25 x 103 after Bolferroni correction was considered significant.RESULTS The frequencies of rslll686806 in the HLA-A gene,rs1055348 in the HLA-B gene,and rs202047044 in the HLA-DRB1 gene were significantly higher in the PM-DILI group than in the control group [27.2% vs 11.6%,P=1.72×105,odds ratio(OR)=3.96,95% confidence interval(Cl):2.21-7.14;42.5% vs 8.6%,P=1.72×10-19 OR=13.62,95% CI:7.16-25.9;22.9% vs 8.1%,P=4.64×106,OR=4.1,95% CI:2.25-7.47].Only rs1055348 showed a significantly higher frequency in the PM-DILI group than in the other-DILI group(42.5% vs 13.6%,P=1.84×10-10,OR=10.06,95% Cl:5.06-20.0),which suggested that it is a specific risk factor for PM-DILI.rs1055348 may become a tag for HLA-B*35:01 with 100% sensitivity and 97.7% specificity in the PM-DILI group and 100% sensitivity and 98.1% specificity in the other-DILI group.Furthermore,HLA-B*35:01 was confirmed to be associated with PM-DILI with a frequency of 41.1% in the PM-DILI group compared with 11.9%(P=4.30×10-11,OR=11.11,95% CI:5.57-22.19) in the other-DILI group and 2.7%(P=6.22×10-166,OR=62.62,95% Cl:35.91-109.20) in the Han-MHC database.CONCLUSION rslll686806,rs1055348,and rs202047044 are associated with PM-DILI,of which,rs1055348 is specific to PM-DILI.As a tag for HLA-B*35:01,rs1055348 may become an alternative predictive biomarker of PM-DILI.

PLASMA RESISTIN LEVELS AND SINGLE-NUCLEOTIDE POLYMORPHISMS IN RESISTIN GENE 5 FLANKING REGION IN PATIENTS WITH STROKE

Objective To analyze the role of resistin in insulin resistance (IR) through investigating the variation of plasma resistin levels and single-nucleotide polymorphisms (SNPs) in resistin gene 5’ flanking region in stroke patients.Methods In 103 atherothrombotic cerebral infarction (ACI) patients, 85 lacunar infarction (LI) patients, 70 intracerebral hemorrhage (ICH) patients, and 86 healthy controls, plasma resistin and insulin levels were measured by ELISA , SNPs in resistin gene 5’ flanking region were detected by PCR and direct DNA sequencing. The subjects’ body height and weight, the body mass index, quantitative insulin sensitivity check index (QUICKI), blood pressure, and the concentration of fasting plasma glucose, triglyceride, total cholesterol, creatinine, low-density lipoprotein, and high-density lipoprotein were also determined. Results QUICKI was significantly lower in the ACI and ICH patients (0.316±0.037 and 0.309±0.032, respectively) than that in the controls (0.342±0.043, P<0.001), while plasma resistin level was significantly higher in the ACI and ICH patients (6.36±3.79 and 7.15±4.27 ng/mL, respectively) than that in the controls (5.28±2.56 ng/mL, P<0.05), but such difference was not observed in the LI patients compared with controls. There was a statistically negative correlation between plasma resistin level with QUICKI (r=-0.228, P<0.001). The distributions of allele and genotype frequencies of resistin gene -420C>G and -537A>C SNPs were not significantly different among the different groups, and those SNPs were not correlated with other clinical and biochemical parameters.Conclusions Plasma resistin is associated with stroke by participating in the development of IR. The SNPs in resistin gene 5’ flanking region has no impact on the plasma resistin level.

Single Nucleotide Polymorphisms (SNPs) of URAT1 (rs7932775) and ABCG2 (rs3825016) on Chronic Kidney Disease Patients with Hyperuricemia

Background: More and more chronic kidney disease (CKD) patients are accompanied with hyperuricaemia. As is known, hyperuricaemia is an independent hazard of both cardiovascular diseases (CVD) and chronic kidney diseases. We aim at identifying Single Nucleotide Polymorphism (SNP) difference of hURAT1 (rs7932775) and ABCG2 (rs3825016) on CKD patient with hyperuricemia and/or gout. Methods: All forty-two CKD patients were divided into two groups: hyperuricemia, and control group. 24 hours urine sample and serum were prepared for testing biochemistry parameters. The polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method is used to analyze hURAT1 and ABCG2 single nucleotide polymorphisms in different groups. Results: 17 patients have CT SNP of hURAT1 (rs7932775) and 13 patients have CT SNP of ABCG2 (rs3825016) in hyperuricemia group, while only 5 persons and 6 persons have the same mutations in control group respectively. 7 patients have CT SNP of both hURAT1 (rs7932775) and ABCG2 (rs3825016) in hyperuricemia group, while only 2 persons have the same mutations in control group. CT mutation rates of hURAT1 (rs7932775) and ABCG2 (rs3825016) in hyperuricemia group were 60.7% (17/28) and 50% (13/28) respectively, higher than that of control group (35.7% (5/14) and 42.8% (6/14)). What is more, Double SNP mutations in both hURAT1 (rs7932775) and ABCG2 (rs3825016) in hyperuricemia group were 25% (7/28), higher than that of control group (14.2%, 2/14). Conclusion: There are higher mutation rates of CT SNP in hURAT1 (rs7932775) and/or ABCG2 (rs3825016) in hyperuricemia group. We can conclude that hyperuricemia is a high risk factor in progress of CKD, which is necessary to take measures of decreasing serum uric acid to delay CKD progress.

Association of Bovine Fatty Acid Desaturase 2 Gene Single-Nucleotide Polymorphisms with Intramuscular Fatty Acid Composition in Japanese Black Steers

Beef from Japanese Black cattle (JBK), is popular in Japan and valued for its highly marbled fat content. In JBK, genes affecting oleic acid content in meat have been studied mainly to lower the fat melting point and improve tenderness;however, there has been no direct correlation demonstrated between beef taste and oleic acid. To investigate genes affecting other fatty acids other than oleic acid, polymorphisms of the fatty acid desaturase 2 (FADS2) gene were genotyped and associations with fatty acid profile in JBK beef were investigated. Amplifications of 5’-flanking regions, 12 exons, and 3’-untranslated regions of the FADS2 gene in three Japanese and five Western cattle breeds via PCR, were amplified, sequenced and SNPs were identified using specific TaqMan genotyping assay. Fatty acid composition of intramuscular adipose tissue of the Trapezius muscle was analyzed in JBK steers. Six of the 15 identified SNPs are novel and have never been registered in any public bovine SNP database. A non-synonymous SNP (rs211580559;C > T;294 Ala > Val) in exon 7 was examined in order to evaluate its association with fatty acid profiles. The data showed that highly significant association existed between rs211580559 and C18:2 (n-6) composition, and accounted for 22.3% of the variation. There were no significant relationships between rs2115-80559 and the other fatty acids. It was concluded that rs211580559 of the FADS2 gene may be a useful selection marker for reducing unfavorable volatiles generated from linoleic acid in JBK beef during the cooking process.

Haplotype analysis of long-chain non-coding RNA NONHSAT102891 promoter polymorphisms and depression in Chinese individuals: A case-control association study

BACKGROUND Our previous study reported that the single-nucleotide polymorphism(SNP)rs155979 GC in the promoter region of long-chain non-coding RNA(lncRNA)NONHSAT102891 affects depression susceptibility in a Chinese population.AIM To explored associations of two SNPs and haplotypes in the lncRNA NONHSAT102891 promoter region with depression susceptibility in Chinese population.METHODS This this case-control association study was approved by the Ethics Committee of Chengdu Medical College(approval number:201815).Patient diagnosis was based on DSM-IV criteria.We selected a total of 480 patients with depression and 329 healthy controls with no history of psychopathology,and performed genotyping of two SNPs by extracting peripheral venous blood samples from the subjects.The function of the two lncRNA NONHSAT102891 promoter G/C and A/T haplotypes was detected by dual-luciferase reporter assays of human embryonic kidney 293T transfected cells.RESULTS Stratified analysis of clinical and genotypic characteristics of our cohort showed that the degree of mild depressive episodes associated with the rs6230 TC/CC genotype increased by 1.59 times[TC/CC vs TT:odds ratio(OR)=1.59,95%confidence interval(CI):1.08-2.35,P=0.019].The haploid analysis revealed linkage disequilibrium between rs3792747 and rs6230,and the double SNP CG haplotype was more common in the control group compared to case group,indicating that this haplotype significantly reduced the risk of depression(C/G vs T/A:OR=0.42,95%CI:0.21-0.83,P=0.01).There was no significant difference in the dual-luciferase reporter activity of the G/C and A/T haplotypes compared with the control group(P>0.05),indicating that the double SNP haplotype has no transcrip-tional activity.CONCLUSION The rs3792747 and rs6230 CG haplotypes of the lncRNA NONHSA T102891 promoter may be related to a reduced risk of depression in the Han Chinese population.

SNP分型检测技术及其在大鼠遗传检测中的应用

单核苷酸多态性(SNP)是第三代分子遗传标记,由于其广泛性、遗传稳定性、二态性及易于自动化分型的特点,成为当前实验动物遗传检测领域中重要研究的遗传标记。本文概述了SNP概念及特点,重点阐述不同种类SNP分型技术,并对该技术在大鼠遗传检测研究中的应用进行回顾和展望。

Prevalent false positives of azoospermia factor a （AZFa） microdeletions caused by single-nucleotide polymorphism rs72609647 in the sY84 screening of male infertility

Multiplex polymerase chain reaction （PCR） has been widely used to detect Y-chromosome micredeletions, which is one of the major causes of male infertility. Both the European Academy of Andrology （EAA） and the European Molecular Genetics Quality Network （EMQN） have recommended the use of sY84 and sY86 markers for the detection of azoospermia factor a （AZFa） microdeletion during DNA testing for male infertility. In this study, a large-scale analysis of AZF microdeletion in a total of 630 Chinese males, including healthy semen donors （n=200）, infertile males with normal sperm count （n=226） and patients with either nonobstructive azoospermia or severe oligozoospermia （n=204）, was performed. A series of nine sequence-tagged site （STS） markers from the AZF region of the Y chromosome was used to detect microdeletions. All primers were designed based on the recommendations of the National Center for Biotechnology Information. An unusually high incidence （73/630, 11.6%） of sY84-absent but sY86-present genotypes was observed in the AZFa microdeletion screening. Sequencing the sY84-flanking region revealed a total of 73 patients with sY84-absent but sY86-present genotypes have a T-to-G transversion at the fifth base from the 5＇ end of the reverse sY84 primer. These prevalent false positives, which were not only observed in infertile men, but also observed in donors, resulted from a single-nucleotide polymorphism （SNP） named rs72609647 in the targeting sequence of the reverse sY84 primer. Our study suggests that a pre-screening of existence of rs72609647 polymorphism can prevent the frequent false positive results of AZFa microdeletions detection in the infertile Chinese males. Given the SNP rs72609647 was recently found in a deep sequencing of a Chinese individual, the current EAA and EMQN standards may need to be scrutinized among different populations to avoid the potential genetic variations in the primer binding sequences.

中华绒螯蟹MIH基因SNP位点筛选及其与生长性状的关联分析

为明确蜕皮抑制激素基因(MIH)对中华绒螯蟹的生长调控机制,本研究选取100只中华绒螯蟹幼蟹个体,分析幼蟹MIH基因的单核苷酸多态性(SNP)位点及基因型,并对与生长指标相关的多态性位点进行连锁不平衡和单倍型分析,进一步明确多态性位点单倍型与生长性状之间的相关性。结果显示,在中华绒螯蟹幼蟹MIH基因中共筛选鉴定出5个SNP位点,其中3个位点(C640G、C2529T和G2595T)与中华绒螯蟹生长性状具有相关性;3个相关位点中共检测到5种单倍型,其中H1单倍型(GCG)的占比最高(68.8%),为优势单倍型;H3单倍型(GTT)个体的生长性状指标最高,显著高于H2单倍型(CCG)。本研究得到的中华绒螯蟹MIH基因上3个与生长性状相关的SNP位点,可作为候选分子标记用于中华绒螯蟹优质品种选育。

Maternal TMPRSS6 Gene Polymorphism rs855791SNP in Women with Preeclampsia

Introduction: Preeclampsia can lead to several maternal and perinatal adverse effects. There are few published data on the association between transmembrane serine protease 6 (TMPRSS6) gene polymorphism and preeclampsia. Objective: To assess the association between TMPRSS6 gene polymorphism rs855791SNP in women with preeclampsia compared with healthy pregnant women. Method: A case-control study (60 women in each arm) was conducted at Saad Abuaela Maternity Hospital in Khartoum, Sudan. Sociodemographic and clinical data were gathered through a questionnaire. The participant was genotype for TMPRSS6 gene rs855791SNP using Polymerase Chain Reaction and Restriction Fragment Length Polymorphism (PCR-RFLP). The results were confirmed by DNA sequencing. Result: There was no significant difference in the median of age, parity, and body mass index. The distribution of the genotypes and alleles of TMPRSS6 rs855791 was consistent with the HWE. The overall TMPRSS6 rs855791 polymorphism was not significantly associated with preeclampsia. However, the proportion of heterozygotes (TC) was considerably higher in the women with preeclampsia (46.7%) than in the control group (23.3%) (p = 0.001;OR = 2.71;95% CI = 1.21 - 6.07). The proportion of homozygotes (TT) and T alleles was not significantly different between women with preeclampsia and the control group. Conclusion: The overall TMPRSS6 rs855791 polymorphism was not significantly associated with preeclampsia and healthy control.

鸡PLIN1基因的生物信息学分析及其SNP与F2代鸡经济性状的关联分析

为了探究围脂滴蛋白1(perilipin 1,PLIN1)的生物学特性及其基因启动子区的单核苷酸多态性(single nucleotide polymorphism,SNP)与杏花鸡×白洛克鸡杂交二代(F2代)鸡经济性状之间的关联性,试验以清远麻鸡各器官/组织c DNA为模板,克隆PLIN1基因的编码区(coding sequence,CDS)序列,然后对PLIN1基因进行生物信息学分析;随后利用实时荧光定量PCR方法检测各器官/组织中PLIN1基因的相对表达量,并利用PCR-RFLP方法对PLIN1基因进行分型,最后利用SPSS 22.0软件对基因启动子区域的SNP位点与F2代鸡的经济性状进行关联分析。结果表明:鸡PLIN1基因CDS序列全长为1554 bp,共编码518个氨基酸;PLIN1蛋白分子量为125.14 ku,等电点为4.70;二级结构中,α-螺旋占比为53.19%,延伸链占比为2.71%;三级结构预测模型主要为α-螺旋、无规则卷曲等;PLIN1基因编码蛋白与过氧化物酶体增殖物激活受体γ(PPARG)和脂肪酸结合蛋白4(FABP4)等蛋白质具有互作关系;红原鸡和日本鹌鹑的PLIN1基因进化关系较近;除斑马鱼外,PLIN1基因在各物种中呈现保守性。PLIN1基因启动子区域的SNP位点与F2代鸡的胸肌剪切力、63 d胫长和肤色性状显著关联(P<0.05);TT基因型是肤色和胸肌剪切力的优势基因型,而CC基因型是63 d胫长的优势基因型;PLIN1基因在腹部脂肪组织中的相对表达量最高,腹部脂肪组织与其他组织的相对表达量均具有显著差异(P<0.05)。说明PLIN1基因可能与鸡的经济性状有关,并在鸡的脂肪生成中扮演重要角色。

Genome-wide SNP markers provided insights into the reproductive strategy and genetic diversity of the green tide causative species Ulva prolifera in China

Ulva prolifera is the causative species of the annually occurring large-scale green tides in China since 2007.Its specific biological features on reproductivity strategies,as well as intra-species genetic diversity,are still largely unknown,especially at the genome level,despite their importance in understanding the formation and outbreak of massive green tides.In the present study,the restriction site-associated DNA genotyping approach(2b-RAD)was adopted to identify the genome-wide single-nucleotide polymorphisms(SNPs)of 54 individual thalli including samples collected from Subei Shoal in 2019 and Qingdao coast from 2019 to 2021.SNPs genotype results revealed that most of the thalli in 2019 and 2020 were haploid gametophytes,while only half of the thalli were gametophytes in 2021,indicating flexibility in the reproductive strategies for the formation of the green tides among different years and the dominance of asexual and vegetative reproductive mode for the floating period.Besides,population analysis was conducted,and it revealed a very low genetic diversity among samples from Subei Shoal and the Qingdao coast in the same year and a higher divergence among samples in different years.The results showed the efficiency of 2b-RAD in the exploration of SNPs in U.prolifera and provided the first genome-wide scale evidence for the origin of the large-scale green tides on the Qingdao coast.This study improved our understanding of the reproductive strategy and genetic diversity of the green tide causative species and will help further reveal the biological causes of the green tide in China.

Early prediction of growth patterns after pediatric kidney transplantation based on height-related single-nucleotide polymorphisms

Background:Growth retardation is a common complication of chronic kidney disease in children,which can be partially relieved after renal transplantation.This study aimed to develop and validate a predictive model for growth patterns of children with end-stage renal disease(ESRD)after kidney transplantation using machine learning algorithms based on genomic and clinical variables.Methods:A retrospective cohort of 110 children who received kidney transplants between May 2013 and September 2021 at the First Affiliated Hospital of Zhengzhou University were recruited for whole-exome sequencing(WES),and another 39 children who underwent transplant from October 2021 to March 2022 were enrolled for external validation.Based on previous studies,we comprehensively collected 729 height-related single-nucleotide polymorphisms(SNPs)in exon regions.Seven machine learning algorithms and 10-fold cross-validation analysis were employed for model construction.Results:The 110 children were divided into two groups according to change in height-for-age Z-score.After univariate analysis,age and 19 SNPs were incorporated into the model and validated.The random forest model showed the best prediction efficacy with an accuracy of 0.8125 and an area under curve(AUC)of 0.924,and also performed well in the external validation cohort(accuracy,0.7949;AUC,0.796).Conclusions:A model with good performance for predicting post-transplant growth patterns in children based on SNPs and clinical variables was constructed and validated using machine learning algorithms.The model is expected to guide clinicians in the management of children after renal transplantation,including the use of growth hormone,glucocorticoid withdrawal,and nutritional supplementation,to alleviate growth retardation in children with ESRD.

利用55K SNP芯片研究小麦新品种信麦163的遗传构成

为明确国审小麦新品种信麦163的分子遗传基础,利用小麦55K SNP育种芯片对信麦163及其母本信阳234和父本丰抗38进行分析。结果表明,信阳234和丰抗38对信麦163的遗传贡献率分别为49.60%和50.40%。在基因组和染色体水平上,双亲对信麦163的遗传贡献率差异较大:母本信阳234对信麦163 A、B、D三个基因组的贡献率分别为49.34%、52.52%和45.61%,贡献率超过50%的染色体有4A、5A、7A、4B、5B、6B、7B、1D、5D、6D和7D,其中在7A、7B、7D上遗传贡献率超过60%;父本丰抗38对信麦163 A、B、D三个基因组的贡献率分别为50.66%、47.48%和54.39%,贡献率超过50%的染色体有1A、2A、3A、6A、1B、2B、3B、2D、3D和4D,其中在4D染色体上遗传贡献率超过80%。在3A、4D、6B等染色体上的遗传形式主要表现为亲本遗传信息以染色体大片段形式传递到子代。SNP(单核苷酸多态性)基因型图谱、SNP位点分析与遗传贡献率分析结果具有较好的一致性。本研究结果展示了杂交育种对后代基因组造成的影响,可为信麦163在遗传改良和生产中的应用提供科学依据。

利用DNA池和测序技术快速筛查SNPs及估算基因频率

选取产蛋性能具有明显差异的 4个鸡品种(莱航鸡、阳山鸡、丝羽乌骨鸡和隐性白洛克鸡 )构建品种DNA池,采用测序的方法研究鸡催乳素基因 5′侧翼调控区远端序列 (1 028bp)的多态性,快速筛查到 8个可能与产蛋性能相关的SNPs(C 2402T、T 2192C、C 2161G、C 2134G、C 2062G、G 2040A、A 1944G和C 1884A)。进一步利用测序图中SNP等位基因峰高的比值估算各鸡品种等位基因的频率,其中C 2402T、C 2161G、C 1884A和C 2062G、G 2040A位点等位基因频率的估算结果分别被PCR RFLP、PCR SSCP所验证,说明测序峰高比值估算等位基因频率的方法具有一定的可行性。

日本沼虾ITS1序列分析及SNPs位点的筛选

研究采用直接测序法,分析日本沼虾(Macrobrachium nipponense)rDNA基因内转录间隔区ITS1的DNA序列,以筛选日本沼虾SNPs位点。共分析了32个太湖水域野生日本沼虾样本,结果表明,日本沼虾ITS1序列平均长度为1749.8bp,是迄今已报道的最长的ITS1序列,A、G、T和C的平均含量分别为29.9%、28.3%、27.7%、14.0%,G+C的含量平均为42.3%。通过序列比对,共筛选出22个SNPs位点,SNPs位点出现频率为0.0126,其中9个为C/T转换(占40.91%),4个为A/G转换(占18.18%),2个为A/T颠换(占9.09%),5个为T/G颠换(占22.73%),1个为A/C颠换(占4.55%),1个A/T或C颠换(占4.55%)。日本沼虾ITS1序列的22个SNP位点中,21个位点为2个等位基因,1个位点出现了3个等位基因,为复等位基因位点。日本沼虾ITS1序列中还发现3个具有多态性的微卫星位点、1个高度变异区以及大量的缺失、插入。研究首次对日本沼虾ITS1序列进行了分析,并发现了大量的SNP位点,为日本沼虾遗传育种研究提供了新的分子标记。

多倍体植物中单核苷酸多态性(SNPs)的开发

单核苷酸多态性(SNP)是指在基因组水平上由单核苷酸的变异所引起的一种DNA序列多态性.在人、拟南芥、水稻等二倍体生物中,已经开发出大量的SNP标记并被用于群体结构分析、关联作图等研究,而在棉花、油菜、小麦等多倍体植物中,SNP的开发与应用却进展迟缓.为促进多倍体植物中SNP的开发,本文对多倍体植物中SNP标记开发所遇到的难题进行了阐述,并对多倍体中SNP标记开发方法进行了梳理,包括位点特异性引物的PCR片段直接测序,利用多倍体的近缘二倍体区分SNPs和部分同源序列间的差异(homoeologous sequence variants,HSVs),利用2代测序技术大规模发掘SNPs,基于公共数据库的序列通过生物信息学分析获取候选SNPs,通过遗传(分离)模式的研究验证SNPs等.利用上述方法可实现多倍体植物中SNP标记的大规模开发.