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.

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.

Isolation,expression and single nucleotide polymorphisms(SNPs) analysis of LACCASE gene(LkLAC8) from Japanese larch(Larix kaempferi)

Nucleotide diversity (pi) and linkage disequilibrium (LD) analysis based on SNP marker could provide a sound basis for choosing an association analysis method. Japanese larch (Larix kaempferi) is an important timber coniferous tree species for pulping and papermaking, but its high lignin content has significantly restricted it application potential. In this study, the LACCASE gene, that plays an important regulatory role for lignin biosynthesis, was selected as research target. The full-length cDNA and genomic sequences of the encoding LkLAC8 gene were isolated from the LACCASE expressed sequence tags of the Japanese larch transcriptome database using the rapid amplification of cDNA ends-polymerase chain reaction (RACE-PCR). The cDNA was determined to be 1940 bp, with an open reading frame (ORF, 1734 bp) that encoded a protein of 577 AA. This protein contains four highly specific Cu2+ binding sites and 11 glycosylation sites, thus belonging to the LACCASE family. The deduced protein sequence shared an 89% identity with the PtaLAC from Pinus taeda. A real-time PCR analysis showed that the LkLAC8 transcript was expressed predominantly in mature xylem, with moderate levels in the immature xylem, cambium and mature leaves, the lowest in the roots. Lastly, the genomic sequences of LkLAC8 in 40 individuals from six naturally distributed populations of Japanese larch were amplified, and a total of 201 SNPs (103 and 98 mutation types of transition and transversion, respectively) were detected; the frequency of the SNPs was 1/19 bp. Nucleotide diversity among the six populations ranged from 0.0034 to 0.0053, which suggested that there were no significant differences among the populations. The LD analysis showed that the LD level decayed rapidly within the increasing length of the LkLAC8 gene. These results implied that LD mapping and association analysis based on candidate gene may be feasible for the marker-assisted breeding of new germplasms with low lignin in Japanese larch.

Mathematical Modeling the Biology of Single Nucleotide Polymorphisms (SNPs) in Whole Genome Adaptation

As a living information and communications system, the genome encodes patterns in single nucleotide polymorphisms (SNPs) reflecting human adaptation that optimizes population survival in differing environments. This paper mathematically models environmentally induced adaptive forces that quantify changes in the distribution of SNP frequencies between populations. We make direct connections between biophysical methods (e.g. minimizing genomic free energy) and concepts in population genetics. Our unbiased computer program scanned a large set of SNPs in the major histocompatibility complex region and flagged an altitude dependency on a SNP associated with response to oxygen deprivation. The statistical power of our double-blind approach is demonstrated in the flagging of mathematical functional correlations of SNP information-based potentials in multiple populations with specific environmental parameters. Furthermore, our approach provides insights for new discoveries on the biology of common variants. This paper demonstrates the power of biophysical modeling of population diversity for better understanding genome-environment interactions in biological phenomenon.

Association between Polymorphisms of SNPs Located at the 3’-Untranslated Region of SET8 and Codon 72 of the TP53 with Breast Cancer among Cameroonian Women

In sub-Saharan Africa, breast cancer (BC) constitutes a serious public health problem and the genetic basis of its development is remaining poorly understood. Although the SNPs at codon 72 of TP53 (rs1042522) and at the UTR of SET8 (rs16917496) have both been associated with BC development among Asian and European women, no published data has been reported within African population. We herein report on the impact of these polymorphisms on the risk of BC among Cameroonian women. Blood samples were collected from 111 breast cancer patients and 224 controls. DNA was extracted from each sample and PCR-RFLP was used to investigate the polymorphisms at SNPs rs1042522 of TP53 and rs16917496 of SET8. Association studies were performed according to ethno-linguistic groups and menopausal status. The minor allele “T” of SET8 gene revealed a protective effect in premenopausal women (OR, 0.327;95% CI 0.125 - 0.852) while the CT genotype of SET8 was associated with increased risk of BC (OR, 2.93;95% CI, 1.1 - 7.8). The minor “G” allele of TP53 gene was significantly associated (OR, 2.533;95% CI, 1.455 - 4.408) with increased disease risk in premenopausal women while the CG genotype was significantly associated (OR, 0.39;95% CI, 0.23 - 0.69) with decreased risk of BC. A synergistic genetic interaction at both loci for CC genotype of SET8 and CG genotype of TP53 was associated (OR, 0.46;95% CI, 0.24 - 0.91) with reduced disease risk. No significant association between polymorphisms at the SET8 and TP53 loci and clinical pathologic features of BC was observed. This study suggests significant associations between the SNPs located at the 3’-UTR of SET8 and codon 72 of the TP53 with the risk of breast cancer development among premenopausal women. There is an interaction between TP53 and SET8 genes.

POU1F1基因SNP位点与尼罗罗非鱼体质量和形态性状的相关性

【目的】研究POU1F1基因的单核苷酸多态性(SNP),评估多态性与尼罗罗非鱼(Oreochromis niloticus)的体质量和形态性状的相关性,为罗非鱼以生长性状为目的的选育提供参考。【方法】利用PCR产物测序方法,从POU1F1中共筛查到28个多态性较高的位点,分析尼罗罗非鱼高要亲代群体的这些位点与其体质量及全长、体长、头长、体高、体宽等6个形态性状的相关性,并在尼罗罗非鱼高要子代群体和番禺群体中验证,将获得的体质量和形态相关位点进一步在尼罗罗非鱼海南群体中验证。【结果与结论】高要亲代群体和子代群体中,分别有6个位点[S3(A-400G)、S4(A-469T)、S5(I-539D)、S6(A-881G)、S7(A-888G)和S12(C-1365T)]和5个位点[S3、S5、S11(I-1358D)、S13(C-1511T)、S14(A-1539T)]与体质量、形态性状相关。POU1F1基因11个SNP位点中,未发现与番禺群体体质量和形态性状相关联的位点。POU1F1基因6个SNP位点与海南雌雄群体关联分析表明,S4位点与海南雌性群体体质量相关,S3和S5位点与雄性群体体质量相关。双倍型与各群体体质量、各形态性状关联分析表明,在高要亲代群体中获得体宽相关双倍型2个;在高要子代群体、番禺群体及海南雄性群体中未获得与生长性状相关双倍型;在海南雌性群体中获得与体质量相关的双倍型1个。

基于SNP标记的小麦品种遗传相似度及其检测准确度分析

遗传相似度检测的准确度估计是对SNP标记法在农作物品种检测体系中应用的必要补充和完善。本研究基于2021年小麦品种SNP标记法跨实验室协同验证实验数据,分析了该方法的检测准确度及在品种间的遗传相似度。分析结果表明:(1)10个实验室对55组小麦品种组合的标记位点相似度检测的总体准确度约为98%。(2)GGE双标图的品种遗传关系功能图显示,7组小麦品种的组内遗传相似度在95%以上,其余组合的遗传相似度较低。(3)依据GGE双标图的“正确度-精确度”功能图和“准确度排序”功能图,发现洛旱7号/洛旱11等品种组合的相似度检测准确度较高,晋麦47/临抗11的检测准确度一般,而济麦22/婴泊700的检测准确度较差。(4)10个实验室的检测准确度存在显著差异,其中2个实验室检测的正确度、精确度和准确度表现显著差于其余实验室。(5)各实验室检测正确度的容许误差分布于1.3%~1.9%之间,平均为1.5%;准确度的容许误差分布于1.5%~2.0%之间,平均为1.7%。其中,Lab2和Lab3的检测正确度和准确度的容许误差显著差于其余实验室。本研究构建了SNP标记法对品种相似性检测的准确度统计模型,分析了品种组合和实验室的检测准确度及其容许误差,采用GGE双标图方法对检测正确度、精确度和准确度进行可视化分析,验证了各实验室对品种位点相似性检测的准确度和可靠性,为SNP标记法在农作物品种遗传相似性检测中的准确度评价提供了理论支持和应用范例。

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。

中国荷斯坦牛3个SNP位点与乳房炎、产奶性状的关联分析

试验旨在开展奶牛群体高乳房炎抗性功能基因的筛选与验证,通过分析SNP位点多态性及其与体细胞数和产奶性状的相关性,探讨其对乳房炎的抗病情况。本研究对北京地区568头中国荷斯坦牛DCK、HIST1H2BK基因的多态性进行了检测,并对3个多态位点不同基因型与体细胞数、产奶性状进行了关联分析。结果表明,DCK基因的SNP位点6:g.86337334 A>G与体细胞数极显著相关(P<0.01),SNP位点6:g.86322040 C>T [rs43472176]与体细胞数也呈现极显著相关(P<0.01);HIST1H2BK基因的SNP位点23:g.31354269 T>G[rs41654340],与体细胞数呈显著关联(P<0.05),与乳脂率和乳蛋白率呈极显著关联(P<0.01)。本研究结果表明DCK、HIST1H2BK基因位点与体细胞数性状显著相关,其可能通过直接或间接的途径影响奶牛的乳脂率或乳蛋白率性状。本研究为荷斯坦牛后续的标记辅助选择奠定了良好的基础。

基于RNA-seq对复合益生菌作用于肉鸡回肠中新转录本预测及可变剪接、SNP分析

为分析复合益生菌饲喂肉鸡回肠转录组中的新转录本预测、可变剪接事件和SNP,选择200只1日龄黄麻肉鸡随机分为2组,每组5个重复,每个重复20只。对照组正常饮水,益生菌组饮用水中补充1%复合菌制剂,试验分为生长前期(1~21 d)、后期(22~42 d)两个阶段。42日龄时进行肉鸡屠宰试验,取对照组和益生菌组回肠各3个样本进行转录组测序。对测序数据进行分析,共发现1047个新基因,20176个新转录本,276个新基因在GO数据库中得到归类注释。对转录组数据进行可变剪接分析,外显子跳跃(SE)占可变剪接类型的比例最高,共筛选到1131个显著的差异剪接基因,在外显子跳跃(SE)、第一个外显子可变剪接(A5SS)、最后一个外显子可变剪接(A3SS)、外显子选择性跳跃(MXE)、内含子滞留(RI)事件中鉴定到的差异剪接基因数分别为588、139、176、136、92。对获得的差异剪接基因进行GO富集分析,主要富集在代谢和免疫GO term。KEGG富集到了胞吞作用、MAPK信号通路等。在各样品中大多数碱基取代均为转换大于颠换,其中转换单核苷酸多态性(SNP)所占百分比为73.53%~73.94%;颠换型SNP所占百分比为26.05%~26.47%。试验对对照组、益生菌组肉鸡的回肠进行了RNA-seq测序分析,为发掘复合益生菌作用于肉鸡回肠中的可变剪接事件提供基础,为进一步了解复合益生菌作用于肉鸡回肠中新转录本的发现和SNP位点提供了数据支撑。

SNP分子标记及其在作物品种鉴定中的应用

作物品种鉴定是优良品种选育和推广的重要保障,而合适的检测方法是对品种进行准确鉴定的关键。随着分子标记技术的发展,第3代分子标记SNP逐渐应用到品种鉴定领域。本研究概述了SNP分子标记的特点,分析了高分辨率熔解曲线、竞争性等位基因特异性PCR、基因芯片、测序法、靶向测序基因型检测等5种作物研究中常用的高通量检测方法的特点及适用性,梳理总结了SNP标记在品种真实性鉴定、纯度检测和亲缘关系分析与分类等方面的研究与应用情况,以期为后续利用SNP分子标记进行品种鉴定提供技术参考。

奶山羊低密度液相SNP芯片开发及有效性验证

为更好地了解奶山羊在世代更替中的遗传谱系,避免因错误谱系记录造成群体近交程度过高,本研究利用液相SNP芯片标记技术确立羊群遗传谱系及其亲缘关系。通过简化基因组测序,对25个不同种群的崂山奶山羊基因组DNA样本进行分析,挑选出1 792个SNP多态性位点,再通过靶向测序基因型分型,合成低通量的探针,最后对探针进行相应的捕获测试,开发出检测崂山奶山羊遗传基因的低密度液相SNP芯片。将该液相芯片应用于300只崂山奶山羊群体的血缘关系鉴定,与已知300只奶山羊系谱记录的亲缘关系进行对比,发现结果高度吻合,证明此芯片具有很高的准确性。本实验开发出均一性高、位点多态性好的低密度液相芯片技术,可专门用于崂山奶山羊亲缘关系鉴定,从而更好地指导奶山羊的选种选配。

基于多重长PCR靶向捕获测序技术的高同源SNP鉴定

为建立一种高同源区段的单核苷酸多态性(SNP)基因分型技术,通过构建本地Blast对SNP所在的200和400 bp区段进行同源性评估,并筛选出高同源区段的SNP。利用第一轮多重长PCR(polymerase chain reaction)捕获329个样本的9个高同源区段SNP所在的长片段,使用纯化后的第一轮PCR产物作为模板进行扩增子建库测序,检测样本共得2 928个SNP位点信息,测序成功率高达98.885 6%。利用Hardy-Weinberg(HWE)法则计算试验研究的9个高同源区段SNP位点的基因频率(p值均大于0.05,符合HWE法则),并与NCBI(national center for biotechnology information)中千人基因组数据库中获取的基因频率相比对,发现二者单碱基基因频率一致(误差限<0.15)。研究表明,利用多重长PCR靶向捕获技术结合二代测序技术为高同源区段的SNP分型提供一个准确、快速、大样本检测方案。

吉林省玉米种质资源SSR和SNP分子身份证的构建及应用

【目的】农作物种质资源具有重要的战略地位。吉林省玉米种质资源库主要存储具有北方春玉米区特色的种质资源。鉴于在传统农作物种质资源管理过程中难以获取真实身份信息的现状,利用分子标记技术构建种质资源分子身份证可以有效鉴定种质资源真实身份,强化种质资源的分类管理。通过深度发掘吉林省玉米种质资源库的优异资源,推动共享利用。【方法】以吉林省玉米种质资源库中的2918份玉米种质资源为研究对象,采用玉米品种鉴定检测标准中推荐的40对SSR标记,以及61214个SNP标记来构建其分子身份证。根据获得的分子身份证信息将种质资源划分为核心、同近源、异质和群体等类进行管理,并进一步针对核心种质进行遗传多样性分析。【结果】为2918份种质资源构建了SSR分子身份证,为除异质性种质外的2502份种质资源构建了SNP分子身份证。分别制定了玉米种质资源SSR和SNP分子身份证的建设规范。其中,SSR分子身份证由40个SSR位点指纹转化为三位数字和一位字母的编码组合构成,并以二维码形式存储;SNP分子身份证由61214个SNP位点指纹转化为可视化的条形码。根据样品纯合度和指纹特异性等特征,将样品划分为1561份核心类、705份同近源类、416份异质类及236份群体类种质资源。遗传多样性分析表明,以旅大红骨群、黄改群为代表的国内种质资源是该库的主要种质资源,占全部核心种质资源的64.38%。【结论】提出了玉米种质资源分子身份证构建流程,为吉林省玉米种质资源库2918份种质资源构建了全部的SSR分子身份证和2502份SNP分子身份证;建立了核心、同近源、异质、群体四类种质资源筛选方案,实现了种质资源的分类管理。

用于玉米品种真实性鉴定的最优核心SNP位点集的研发

品种真实性是种子质量监测的一个重要指标。为建立准确可靠、快速简便、高通量、低成本的玉米品种真实性鉴定技术,本文利用200个核心SNP位点构建的5816个玉米杂交品种,3274个自交系的指纹数据,基于遗传算法、品种识别率评估确定了一套高鉴别力的核心SNP位点集,包含96个SNP位点。这96个SNPs全部位于基因内区域,相对均匀分布在10对染色体上。采用上述杂交品种和自交系的指纹数据评估显示这96个位点具有较高多态性和品种区分能力,PIC、MAF、DP平均值分别为0.36、0.40、0.60和0.36、0.39、0.48,对杂交品种、自交系的品种识别率达到99.14%和99.24%。两两样品成对比较结果显示,99.99%的品种间差异位点数目≥3个,杂交品种和自交系中96.74%和95.67%的成对比较差异位点数目集中在30~65个和30~60个。基于221个主推杂交品种的40个SSR位点、96个SNP位点的基因型数据分析结果显示,这2组标记集的鉴定结果具有较高的一致性。综上所述,本研究报道了一套具有位点数量最少、区分能力最强,兼容多平台、适于自动化分型等优点的最优核心SNP集。期望位点集将在玉米品种真实性监测、种子质量控制中得到广泛应用,进而维护玉米种子市场秩序、保障育种者权利以及保护农民利益。

基于转录组测序的花斑裸鲤SSR、SNP和InDel位点特征分析

为利用分子标记规模化开发与辅助花斑裸鲤(Gymnocypris eckloni)良种选育,以花斑裸鲤(2+龄)的鳃、肾脏和肝脏组织为材料,经总RNA提取和cDNA文库构建后采用Illumina Novaseq 2000平台进行转录组测序,并采用MISA和GATK3软件分析转录组的SSR、SNP和插入缺失标记(InDel)位点特征。结果表明:在486221条Unigenes序列中共发现了128727个SSR,出现频率为26.47%,平均每3.76 kb出现1个SSR;花斑裸鲤SSR包括6个重复类型,以单碱基和二碱基重复基元类型为主,分别占总SSR位点数的46.53%和42.45%,重复基元类型共77种,其中,A/T和AC/GT两种基元的出现频率最高,是花斑裸鲤SSR的优势重复基元;所有重复次数中出现次数最多的为5~15次,占所有SSR位点的87.52%;通过GATK3软件搜索得到399080个SNP位点,转换类型多于颠换类型,分别占总SNP的56.29%和43.71%,转换类型中A/G发生频率略高于C/T,而颠换类型中A/T发生频率最高,C/G发生频率最低;InDel分析显示,从花斑裸鲤转录组Unigenes中共筛选出254065个InDel位点,平均每1903 bp出现1个InDel位点,且SNP位点和InDel位点均以含1个位点的Unigenes数最多。研究表明,花斑裸鲤转录组中SSR、SNP和InDel位点非常丰富,这些位点对花斑裸鲤种质资源鉴定、种群遗传学研究及保护管理具有重要价值。

燕麦SNP高密度遗传图谱构建及β-葡聚糖含量QTL定位

β-葡聚糖是燕麦发挥保健作用的主要功能因子,提高其含量对优质燕麦生产有着重要意义。为促进高β-葡聚糖燕麦种质资源的有效利用和相关基因发掘,本研究以高β-葡聚糖品种夏莜麦和低β-葡聚糖品种赤38组配衍生的219个家系RIL8群体为材料,利用重测序技术构建了包含21个连锁群,5032个bin标记的遗传连锁图谱,图谱总长2045.09 cM,平均图距0.42 cM。利用标准酶法和近红外法对4个环境的RIL群体家系β-葡聚糖含量进行测定,结合测定结果,利用完备区间作图法对β-葡聚糖含量进行QTL定位分析,结果显示不同环境条件下RIL群体β-葡聚糖含量呈正态分布,并出现超亲后代家系,4个环境下群体β-葡聚糖含量变异系数介于9.06%~16.63%之间。QTL定位检测到7个与燕麦β-葡聚糖含量相关的QTL,分布于2D、3D、4C和4D染色体上,其中贡献率最高为14.73%,在2个环境中检测到同一个QTL,其标记区间为Chr4C_mark8361257–Chr4C_mark8384831。研究结果将为燕麦β-葡聚糖分子标记辅助育种提供重要的理论依据。

利用SNP标记鉴定青稞种质资源

近年来,青稞(Hordeum vulgare var.nudum Hook.f.)育种速度逐步加快,青稞品种的类别和数量日渐增多,形成了丰富的青稞品种资源。然而,在青稞资源的大量引种和品种资源交换过程中,造成了同名异物、同物异名的现象,因而建立高效、准确的青稞品种鉴定技术体系和数据系统迫在眉睫。为基于青稞品种基本信息实现青稞品种的快速和准确鉴定,本研究利用简化基因组(GBS)测序获得的青稞基因组高通量SNP基因分型数据,对314份青稞种质资源进行群体结构分析;根据SNP注释结果,筛选获得位于外显子区的SNP并计算其杂合率和遗传多态性指数;用Genstat的去冗余(IRREDUNDANT)指令通过顺序算法(sequential algorithm)获得能够区分参试青稞种质资源的核心SNP位点组合,并构建DNA指纹图谱,结合参试材料地理来源等基本信息构建青稞品种的分子身份证。结果表明,群体遗传结构分析可将314份参试青稞材料划分为3个类群,类群划分与其材料类型密切相关。从4954个位于外显子区域的高质量SNP位点中筛选出14个多态性高且能完全区分青稞种质资源的SNP位点,称其为核心SNP;由14个核心SNP组成青稞种质资源DNA指纹图谱,同时结合种质资源地理来源等的基本信息进行数字编码,最终构建了每份青稞品种资源由17位数字组成的具有唯一标识的分子身份证,并生成相应的条形码和二维码。本研究构建的青稞种质资源DNA指纹图谱和分子身份证,可为青稞品种真实性和纯度鉴定、种质管理及知识产权保护等提供参考。

猪卵泡液外泌体处理卵巢颗粒细胞的SNP/Indel筛选分析

旨在分析卵泡液外泌体对卵巢颗粒细胞基因的影响,了解卵泡液外泌体在卵泡发育过程中的调控机理,为母猪繁殖研究提供理论依据。本研究选取6月龄、健康状态良好且体重相近的二元母猪为材料,屠宰后收集卵巢150枚,利用梯度离心法获取卵泡液外泌体与猪卵巢颗粒细胞(porcine ovarian granulosa cells,POGCs),并在体外将卵泡液外泌体与猪卵巢颗粒细胞共培养。通过RNA-seq技术对猪卵巢颗粒细胞(granulosa cell samples,GC,n=3)和与外泌体共培养的猪卵巢颗粒细胞(granulosa-exosome co-culture samples,GCE,n=3)进行测序。结果显示,在GC和GCE组中平均每个样品获得5.54×10^(7)条clean reads,Q20和Q30质量得分均在92%以上。在GC和GCE组的6个样品中共获得1310979个SNPs突变和104498个InDel突变,其中纯合型SNP/Indel突变数量为170426个,杂合型SNP/Indel突变数量为1245052个,突变杂合子数目明显高于纯合子且SNP的发生率较高。另外,在突变类型中,转换类型共计973003个,颠换类型339974个,转换的类型显著高于颠换类型。经基因注释,突变主要发生在基因3′UTR、5′UTR、内含子区域,其次为外显子和基因间隔区。另外,通过与差异基因对比后,够筛选出1583个候选基因,经GO和KEGG功能富集发现,候选基因主要与细胞周期以及细胞增殖/凋亡过程相关。此外,共发现14个与细胞周期、增殖/凋亡通路相关的关键候选基因,其中11个基因存在互作关系。本研究获得的这些SNP/Indel信息可为后续研究外泌体在母猪生殖上的调控奠定科学基础。