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 (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.

Expression analysis,single nucleotide polymorphisms within SIRT4 and SIRT7 genes and their association with body size and meat quality traits in Qinchuan cattle

Silent information regulator 2 （Sir2） proteins, or sirtuins, are nicotine adenine dinucleotide （NAD）-dependent deacetylases that connect metabolism with longevity in lower organisms. In mammals, there are seven Sir2 homologs, namely, silent information regulators （SIRT1-7）. SIRT4 and SIRT7 genes play a crucial role in regulating lipid metabolism, cellular growth and metabolism. This suggests that they are potential candidate genes for affecting body size and meat quality traits in animals. Hence, this study aimed to detect genetic variations of both SIRT4 and SIRT7 bovine genes in Qinchuan cattle, and to evaluate the effect of these variations on economically important body size and meat quality traits. Expression analysis using quantitative real-time PCR （qPCR） indicated that SIRT4 and SIRT7 were broadly expressed in all thirteen studied tissues. The expression of SIRT4 was higher in liver, muscle, and in subcutaneous fat tissue. In the case of SIRT7, the expression was higher in lung, abomasum, and subcutaneous fat. Using DNAsequencing, a total of three single nucleotide polymorphisms （SNPs） were identified within SIRT4 and SIRT7 genes in 468 Qinchuan cattle. These included one novel SNP within 3＇ untranslated regions （UTR） of SIRT4 （SNP1： g. 13915A〉G） and two novel synonymous substitutions in SIRT7 （SNP2： g.3587C〉T and SNP3： g.3793T〉C）. Statistical analyses indicated that all three SNPs could significantly influence some body size and meat quality traits in Qinchuan cattle. These novel findings will provide a background for application of bovine SIRT4 and SIRT7 genes in the selection program of Chinese cattle.

Single Nucleotide Polymorphisms in a Male Infertility-Related Gene CatSper

Objective To identify single nucleotide polymorphisms (SNPs) of human CatSper gene, themouse homologous gene product, which plays a crucial role in mouse male sterility.Methods We demonstrated a systematic screening of SNPs in coding regions and flankingintronic regions of human CatSper gene in a sample subset from a total 210 male individuals byDNA sequencing. Then we used PCR single-strand conformation polymorphism (SSCP) analy-sis to determine the allele frequencies of the possible SNPs among the whole 210 Chinese Hanmale individuals.Results Three SNPs, including two novels, were identified and their allele frequencies weredetermined in the 210 Chinese Han male individuals. These SNPs were assembled into largeSNP database that promises to enable the dissection of the genetic basis of disease.

Association of Single Nucleotide Polymorphisms in IRF6 and TGFA Genes With Nonsyndromic Cleft Lip With Or Without Cleft Palate in Chinese Patients

Objective： Nonsyndromic cleft lip with or without cleft palate（NSCL/P） is a common birth defect with unclear etiology. Both genetic and environmental factors may contribute to NSCL/P. Many genes have been identified as candidate genes associated with this disease. Interferon regulatory factor 6（IRF6） gene and transforming growth factor-a（TGFA） gene seem to be crucial in the predisposition of NSCL/ P. Here we evaluated some single nucleotide polymorphisms（SNPs） loci of TGFA and IRF6 genes in Chinese nuclear families consisting of fathers, mothers and affected offspring with NSCL/P. Methods：Fifty patients of NSCL/P were confirmed by the plastic surgeons. They and their parents were included in the study, all with the informed consents. SNPs loci of TGFA and IRF6 genes were analyzed by microarray technology. Some PCR products were randomly chosen and sequenced to check microarray results. The distribution of gene type and allele frequency between patient group and parents group were compared. Then a Haplotype Relative Risk（HRR） and Transmission Disequilibrium Test（TDT） were performed. Results：The sequences of randomly selected PCR products were all consistent with the microarray results. All loci were in Hardy-Weinberg equilibrium. There were no significant differences in the distribution of genotypes and alleles between patients and their parents. Using HRR and TDT analyses the V274I of IRF6 was associated with NSCL/P, while another SNP locus oflRF6 was not. Strong evidence of linkage disequilibrium was found between the 2 SNP loci of TGFA and disease with the HRR analysis, but not with the TDT analysis. Conclusion：Our study confirms the contribution of IRF6 in the etiology of NSCL/P in populations of Asian ancestry. The association of TGFA with NSCL/P requires further research.

Single nucleotide polymorphisms in intron 1 and intron 2 of Larimichthys crocea growth hormone gene are correlated with growth traits

The growth hormone gene (GH) affects animal growth and is a potential target for genetic studies of variation related to growth traits. In this study, we analyzed single nucleotide polymorphisms (SNPs) in GH intron regions and their associations with growth traits in large yellow croaker, Larimichthys crocea, from Zhejiang and Fujian stocks. The results of PCR-single strand conformation polymorphism showed two haplotypes of intron 1, named AA and AB genotypes, in Zhejiang stock. AB exhibited an SNP at position 196 (G A) that was negatively correlated with body height and positively correlated with standard length/body height (P 0.05). Two different genotypes, CC and CD, were identified in intron 2 in Fujian stock, with CD showing an SNP at position 692 (T C). The CD genotype had a significantly positive correlation with both weight and total length (P 0.01). These basic data highlight the potential for using GH as a genetic marker of fish growth in marker assisted selection.

Association between single nucleotide polymorphisms on chromosome 17q and the risk of prostate cancer in a Chinese population

In European populations,7 single nucleotide polymorphisms(SNPs) on chromosome 17q,3 SNPs on 17q12,and 4 SNPs on 17q24.3 were recently identified to be closely related to the risk of prostate cancer by a genome-wide association study.In Japanese populations,the correlation between 2 SNPs on 17q and the risk of prostate cancer and tumor aggressiveness was also confirmed by a large-scale experiment.However,whether 17q is associated with prostate cancer and its clinical manifestations in Chinese populations is still unknown.Therefore,we conducted a case-control study in a northern Chinese population and tested 2 SNPs,rs4430796 and rs1859962,on 17q in 124 prostate cancer patients and 111 controls using polymerase chain reaction-high resolution melting curve(PCR-HRM) combined with sequencing.We analyzed the association of the 2 SNPs with the risk of prostate cancer as well as patients' lifestyles,onset ages,Gleason scores,PSA levels,and pathologic stages.We found a significant difference in the G allele of SNP rs1859962(P = 0.035,OR = 1.51,95% CI = 1.03-2.21) but not in the rs4430796 genotype frequency or allele frequency distribution between prostate cancer patients and the controls(P > 0.05).Neither of the SNPs was significantly associated with the onset age,Gleason score,PSA level,pathologic stage,or other clinical indicators of patients with prostate cancer(P > 0.05).Our results show that polymorphism of the G allele of SNP rs1859962 is associated with the risk of prostate cancer in a Chinese population.

Single nucleotide polymorphisms of MAGE-A3 gene and its clinical implications in Chinese patients with non-small cell lung cancer(NSCLC)

Background： Available study revealed advanced tumors have a higher expression rate of MAGE-A3 gene which has a lot of single nucleotide polymorphism（SNP） loci with polymorphisms. This study aimed to analyze the allele frequency of SNP loci in MAGE-A3 gene and investigate the relationship between MAGE-A3 gene polymorphisms and clinical factors.Methods： Tumor samples of a cohort of 191 NSCLC patients were collected. EGFR m RNA expression were detected by q RT-PCR. SNPs in whole length of MAGE-A3 gene were detected by direct sequencing. Frequencies of the SNPs were correlated to gene expression, mutation status of EGFR and clinical factors.Results： Sequencing analysis confirmed that allele frequencies of genotypes on SNP loci rs5970360, rs5925210, rs5970361, rs5925211 and rs35123853 were CC（0.681）/CT（0.319）, CC（0.660）/CG（0.340）, CC（0.681）/CA（0.319）, AA（0.984）/AT（0.016） and GG（1.000）/GA（0.000）, respectively, which were different from the frequencies and genotypes of MAGE-A3 in SNP database. Chi-square tests showed the EGFR mR NA expression level had significant correlation with the genotypes of SNP loci rs5970360 and rs5925210. But all frequencies of each MAGE-A3 SNPs were not found significantly different between EGFR mutant and wild type patients. MAGE-A3 gene polymorphisms had no significant effects on survival of NSCLC patients.Conclusions： Chinese patients with NSCLC had different SNP patterns of MAGE-A3 in comparison with those in international SNP database. These MAGE-A3 SNP loci might have not prognostic significance. MAGE-A3 SNP loci rs5970360 and rs5925210 might be predictive for EGFR m RNA expression levels and helpful to the selection of patients for epidermal growth factor receptor（EGFR） targeted immunotherapy.

Corelation Between Single Nucleotide Polymorphisms in Mu Opioid Receptor Exon 2 and Stereotypic Behaviour in Sows

Three breeds of sows were observed to investigate the relationship between Single Nucleotide Polymorphisms（SNPs） in Mu Opioid Receptor（MOR）and stereotypic behaviour,such as,sham-chewing,bar biting and standing still in order to better understand the mechanism of stereotypic development of the animals in restrained conditions.MOR exon 2 partial sequences were amplified to analyze single nucleotide polymorphisms by PCR-SSCP.One SNP,a silence mutant was found.A significant difference （P〈0.01）was found in the frequency of genotypes in these 3 breeds where only the BB genotype,which was identical to that published in GenBank,was found in the Duroc breed,while no AA genotype was found in Landrace,3 genotypes AA,BB and AB were found in Yorkshire.The result also indicated that the individuals with AA and AB genotypes tended to be more active in sham-chewing than those with the BB genotype（P〈0.05）.The overall results of this study suggested that sham-chewing of sows may be subjected to both genetic control and environmental conditions,but activity level was more likely to be affected by their environment.We can putatively draw the conclusion that MOR gene has effect on the sham-chewing behavioral traits of sow.

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.

Sequence Information on Simple Sequence Repeats and Single Nucleotide Polymorphisms through Transcriptome Analysis of Mungbean

Mungbean （Vigna radiata （L.） Wilczek） is a unique species in its ability to fix atmospheric nitrogen, with early maturity, and relatively good drought resistance. We used 454 sequencing technology for transcriptome sequencing. A total of 150 159 and 142 993 reads produced 5 254 and 6 374 large contigs （〉_500 bp） with an average length of 833 and 853 for Sunhwa and Jangan, respectively. Functional annotation to known sequences yielded 41.34% and 41.74% unigenes for Jangan and Sunhwa. A higher number of simple sequence repeat （SSR） motifs was identified in Jangan （1 630） compared with that of Sunhwa （1 334）. A similar SSR distribution pattern was observed in both varieties. A total of 8 249 single nucleotide polymorphisms （SNPs） and indels with 2 098 high-confidence candidates were identified in the two mungbean varieties. The average distance between individual SNPs was -860 bp. Our report demonstrates the utility of transcriptomic data for implementing a functional annotation and development of genetic markers. We also provide large resource sequence data for mungbean improvement programs.

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。

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。

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。

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。

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。

Development of organelle single nucleotide polymorphism (SNP) markers and their application for the identification of cytoplasmic inheritance patterns in Pyropia yezoensis (Bangiales,Rhodophyta)

The genus Pyropia contains several important cultivated species.Genetic research in nori species has mainly focused on the cell nucleus,with few studies on organelles(chloroplast and mitochondria).Due to the high copy numbers of organelles in cells,which influence the development and traits of algae,it is necessary to study their genetic mechanism.In this study,the marine red alga Pyropia yezoensis,an important economic macroalga,was selected as the study object.To investigate organelle(chloroplast and mitochondria)inheritance in P.yezoensis,the wild type RZ(maternal strain)was crossed with the red mutant HT(paternal strain)and 30 color-sectors from 11 F1 gametophytic blades were examined.The complete chloroplast and mitochondrial genomes of the red mutant(HT)were assembled for the first time.One reliable and stable single nucleotide polymorphism(SNP)loci filtrated by bioinformatics analysis was used as a molecular marker for chloroplast and mitochondrial DNA,respectively,in subsequent experiments.PCR amplification and sequence analysis showed that the haplotypes of color-sectors detected were consistent with those of the maternal parent,confirming that both chloroplast and mitochondrial genomes were inherited maternally in P.yezoensis.The inheritance pattern of organelles in P.yezoensis can be used to guide the hybridization and breeding of nori.Additionally,the organelle SNP markers developed in this study can be applied in subsequent genetic research.

植物SNP数据库及转化CAPS的方法

单核苷酸多态性(SNP)在植物基因组中广泛存在,基于SNP的分子标记也正越来越广泛地应用到植物基因定位、图位克隆及分子标记辅助育种等方面。模式植物拟南芥和水稻的全基因组序列测定已经完成,拟南芥有两种生态型完成了全序列测定,水稻有两个品种完成了全序列测定。许多植物有来自不同品种或不同组织器官或生长发育阶段的大量的EST序列。这些序列是植物SNP开发的重要资源。利用生物信息学手段对全基因组序列或EST序列进行分析已经形成了许多SNP位点数据库,这些数据库的建立为基于SNP的基因功能研究及分子标记开发提供了宝贵的资源。本文对植物SNP位点开发涉及的数据库资源及已经形成的SNP位点数据库进行了总结,并讨论了将SNP位点转化成CAPS或dCAPS标记的方法和相应的工具软件。

小麦中基于转录组测序SNP的dCAPS标记的高通量开发及验证

结合六倍体小麦品系P7001与P216杂交F5代群体中1对相对性状池的二代转录组测序的单核苷酸多态性(SNP)分析结果,应用最近开发的CAPS/dCAPS Designer工具进行批量的CAPS/dCAPS(衍生/限制性内切酶多态性)标记开发,最终筛选20个CAPS/dCAPS标记进行亲本间的多态性验证。结果表明,将二代转录组测序的SNP分析结果和高通量的CAPS/dCAPS标记设计软件相结合能高效地进行多态性分子标记的开发。

基于转录组SNP构建油茶主要品种资源的分子身份证

【目的】近年来,油茶(Camellia oleifera)产业发展迅速,已成为中国四大油料之一。油茶良种不断涌现,但品质参差不齐,“同名异物、同物异名”等现象时有发生。建立油茶品种资源的单核苷酸多态性(single-nucleotide polymorphism,SNP)分子标记数据库,筛选重要SNP位点,开发油茶品种资源DNA指纹图谱,构建油茶品种资源的分子身份证,为品种鉴别、品种追溯等提供分子水平鉴别技术支撑。【方法】以221份普通油茶品种资源为材料,提取未成熟种子RNA,进行转录组测序。以二倍体南荣油茶基因组为参考,识别供试油茶品种资源的SNP位点并基因分型,利用SNP数据分析油茶群体及亚群的遗传多样性,分析SNP位点的观测杂合度、期望杂合度、多态信息含量(PIC)等信息,筛选核心SNP位点并采用Sanger测序验证,得到最优SNP位点组合后,结合品种资源基本信息构建油茶品种资源分子身份证。【结果】从油茶转录组中共检测到1 849 953个高质量SNP位点。群体遗传多样性分析发现,油茶群体观测杂合度为0.2966,期望杂合度为0.2462,固定指数为-0.2048,PIC为0.2073,最小等位基因频率为0.1648。参试群体的各亚群间遗传分化较小,存在较高的基因流,主要变异存在于亚群内。根据PIC、连锁不平衡衰退距离(LD)等参数从所有SNP位点中筛选出31个多态性高的核心位点,Sanger测序验证其中8个核心位点基因分型的准确率在91.36%以上。利用核心位点组成DNA指纹图谱,可区分出全部参试油茶品种资源。DNA指纹图谱结合油茶品种资源基本信息,构建成由66位数字组成的油茶品种资源分子身份证。【结论】依据SNP标记的PIC、LD等指标,筛选出31个核心SNP位点,精准区分全部供试油茶品种资源。将31个SNP位点所构建的油茶品种资源DNA指纹图谱与品种资源的起源、资源类型和亚群分布等基本属性信息相结合,构建了每份油茶品种资源唯一的分子身份证,并生成相应的条形码和二维码。