CELⅠ酶在水稻基因多态性检测中的应用

CELⅠ酶是定向诱导基因组局部突变TILLING(Targeting Induced Local Lesions In Genomes)技术中的关键酶，能够特异识别并切割单碱基错配和扭曲的DNA异源双链。实验从芹菜（Apium graveolens）中提取了CELⅠ酶，采用SDS-PAGE检测在43kD处有主带。以杂合双链作为底物，检测了CELⅠ酶的错配切割活性，结果表明CELⅠ酶可在不同材料的DNA所形成的异源双链的错配处准确切割。通过CELⅠ酶的提取、活性分析以及在水稻基因多态性检测中的应用，为基因多态性检测提供一种简单易行的方法。     

早籼稻Wx基因多态性与直链淀粉含量及RVA谱的关系

为明确直链淀粉含量(AC)主要控制基因Wx在浙江早籼稻中的多态性分布及其对稻米AC、RVA谱的影响,本试验以37份早籼稻品种(系)为材料,进行Wx基因型检测,以及AC及RVA谱特征值测定,分析不同Wx基因型对稻米AC、RVA谱的影响及AC、RVA间的相关性。结果表明,Wxa基因型品种(系)AC表现为中、高水平(23.38%~28.93%),Wxb基因型品种AC表现为低水平(11.61%~17.77%),37份材料中未检出Wxin基因型;RVA谱特征值与Wx基因型高度相关,不同Wx基因型背景下各品种(系)RVA谱特征值差异明显,且Wxa基因型消减值为正值,Wxb基因型消减值为负值。Wx基因型不同的各品种(系)的冷胶粘度(CPV)和崩解值(BDV)分布在不重叠的区间。Wxa基因型表现出崩解值小、回复值大的特性,Wxb基因型表现出崩解值大、回复值小的特性。在不区分Wx基因型的条件下,AC与RVA谱特征值极显著相关,在相同Wx基因型内,品种(系)间AC的变化与RVA谱特征值的相关性并不明显。本研究结果为利用Wx等位基因调控早籼稻AC含量,并根据RVA谱特征值筛选优质食用早籼稻提供了一定的理论参考。     

基于173份小麦评价糯蛋白亚基基因(Wx)的分子标记和构建其多重PCR体系

糯蛋白亚基基因(Wx)组成与小麦淀粉品质特性密切相关,筛选和建立其高效的鉴定方法和体系,对小麦品质育种改良和种质资源快速评价具有重要意义。本研究基于SDS-PAGE方法检测173份小麦(Triticum aestivum L.)品种(系)糯蛋白亚基组成的结果,评价序列标签位点(sequence tagged sites,STS)标记的有效性,利用有效的STS标记构建Wx基因分子检测的多重PCR体系。SDS-PAGE方法检测结果表明,20份小麦品种(系)缺失Wx-B1蛋白亚基,1份3个Wx蛋白亚基全部缺失,依次占11.6%和0.6%。4个共显性和2个显性Wx基因STS标记检测供试小麦的结果,与SDS-PAGE结果完全一致。构建了两套分子标记检测的多重PCR体系,其中多重PCR体系Ⅰ能够同时检测Wx-A1和Wx-B1位点的4种等位变异,体系Ⅱ可同时检测Wx-B1和Wx-D1位点的4种等位变异,两套多重PCR体系检测的结果与SDS-PAGE和单一PCR的检测结果也完全一致。筛选的6个STS标记和构建的两套PCR检测体系,用于小麦Wx基因的分子标记辅助选择,将有助于提高小麦品种淀粉品质评价和选育的效率。     

CELⅠ酶的粗纯化及活性分析

TILLING（Targeting-induced local lesions in genomes）技术作为反向遗传学的一个重要研究工具，目前在众多的模式生物分子生物中得到广泛应用，其中CELⅠ酶是TILLING技术的核心。本实验通过硫酸铵沉淀、亲合层析、阴阳离子交换柱层析等常规的蛋白质纯化过程，从芹菜中粗纯化了具有较高活性的稳定的CELⅠ酶。并以杂合双链DNA为底物，对不同纯化程度的CELⅠ酶以及在不同温度、处理时间、有无Taq DNA多聚合酶的条件下进行了CELⅠ酶的错配切割活性分析。结果发现，所获得的CELⅠ酶得到了一定的纯化；CELⅠ酶的反应最适温度范围为40℃～50℃；长时间酶切特异性好；在含有Taq酶的酶切体系中，CELⅠ酶错配切割效果更佳，这与已报道的实验结果基本一致。与其他单位提供的CELⅠ酶活性相比，本实验分离纯化的CELⅠ酶活性值略高。通过对CELⅠ酶的提取及活性分析，为TILLING技术大规模和低成本的应用于家蚕功能基因组研究提供了保障。     

大白菜抽薹相关基因BrFLC1的KASP标记开发

为了提高大白菜耐抽薹品种的分子育种效率,本研究针对大白菜抽薹相关基因BrFLC1第6个内含子的第一个碱基(Pi6+1)G-A的SNP变异开发进行高通量检测的竞争性等位基因特异性PCR(KASP)标记。结果表明,开发的KASP标记BrFLC1-KASP1可有效将晚抽薹类型材料Y177-12(G)和早抽薹类型材料Y195-93(A)分为2组。利用BrFLC1-KASP1标记可以对57份大白菜材料的基因型进行有效鉴别,且鉴定结果与酶切扩增多态性标记(CAPS)G-MvaI以及直接测序法的鉴定结果完全一致。综上所述, BrFLC1-KASP1标记在大白菜材料中具有通用性,且具有准确率高、成本低、效率高的特点。本研究结果对大白菜耐抽薹性的分子标记辅助选择具有重要的育种实践价值。     

水稻不同Wx等位基因对籽粒直链淀粉积累特性的影响

为了解水稻Wx等位变异对籽粒直链淀粉积累特性的影响,本研究选用携带有5种不同Wx等位基因的水稻单片段代换系(Single-segment substitution line,SSSL)为材料,在同一遗传背景下对水稻籽粒灌浆过程中表观直链淀粉含量(Apparent amylose content,AAC)的动态变化及其与颗粒结合性淀粉合成酶(Granule-bound starch synthase,GBSS)酶活的关系进行了研究。结果表明,不同Wx等位基因水稻材料籽粒灌浆过程中的AAC差异在灌浆早期(花后6d)已较明显,随着籽粒发育,非糯水稻花后6~11d是直链淀粉的快速增长期。籽粒灌浆过程中,不同Wx等位基因间籽粒AAC存在显著性差异,并且在直链淀粉积累特性上存在明显不同。较高和高AAC品系(携Wxg2和Wxg3基因)直链淀粉积累速率快,在灌浆初期(花后11d)便达到与籽粒成熟期一致的水平,之后变化不大;低、中等AAC材料(携Wxt和Wxg1基因)直链淀粉积累速率相对中等,灌浆初期(花后11d)AAC并不高,其直链淀粉的积累是个渐近的过程,直至灌浆后期(花后26d)才达到最大含量;糯稻(携wx基因)则在整个籽粒发育过程中AAC变化不大,始终保持着极低的含量水平。在整个灌浆期间,籽粒GBSS酶活与AAC均呈正相关,其中灌浆早期(花后6d)相关度最高,随后相关度逐渐降低,但始终维持在较高的水平(r0.820)。本研究结果可为进一步深入研究Wx座位等位变异机制奠定基础。     

小麦粒重相关基因TaCYP78A16的克隆和CAPS标记开发

粒重是小麦(Triticum aestivum)产量的重要构成要素,为了开发小麦粒重性状相关的功能标记,本研究通过小麦全基因组预测并克隆得到1个潜在粒重相关基因:小麦细胞色素P450单加氧酶基因(Triticum aestivum cytochrome P450 78A16, TaCYP78A16; GenBank No. MH572527),并对其进行基因结构、表达模式、等位变异分析和粒重性状相关功能标记开发。结果表明,TaCYP78A16基因在小麦幼穗和籽粒发育初期高表达,可能参与籽粒发育、影响粒重;对30个小麦品种中TaCYP78A16基因编码区和启动子等位变异进行分析,发现仅TaCYP78A16-A启动子16Ap检测到7个位点的等位变异;根据7个等位变异中的2个SNP位点(SNP2, SNP3)开发了单核苷酸多态性-酶切扩增多态性序列(single nucleotide polymorphisms-cleaved amplified polymorphic sequences, SNP-CAPS)分子标记CAPS-16Ap,该分子标记可将30个小麦品种16Ap序列分成3种基因型:16Ap-Hap1、16Ap-Hap2和16Ap-Hap3;进一步在323个小麦品种中进行验证,结果显示,CAPS-16Ap标记可用于小麦16Ap序列3种基因型的鉴定。本研究将有助于小麦分子标记辅助选择育种。     

苏太猪SLA-DQB和SLA-DRB基因第2外显子多态性及其与繁殖性能的关联分析

采用PCR-RFLP技术对苏太猪SLA-DQB及SLA-DRB基因第2外显子PCR产物进行分析。结果表明,苏太猪SLA-DQB基因经RsaⅠ酶切后共产生3种等位基因,5种基因型;SLA-DRB基因经RsaⅠ酶切后共产生3种等位基因,4种基因型。χ2适合性检验表明,苏太猪SLA-DQB及SLA-DRB基因外显子2的RsaⅠ酶切位点均达到了Hardy-Weinberg平衡状态。将SLA-DQB和SLA-DRB基因的基因型进行组合,共产生12种组合基因型,BBDF的第3胎繁殖性能总产仔数、产活仔数、初生窝重和断奶仔猪数显著高于组合基因型AADD、AADF、ABDD和CCDF(P<0.05)。从繁殖性能看,BBDF在群体中为最优秀的组合基因型。     

基于简化基因组测序技术的甘薯HRM分子标记开发及其应用

目前甘薯中针对SNP位点的分子标记开发及应用的报道较少。为开发甘薯特异SNP分子标记,本研究利用简化基因组测序技术对甘薯种质材料进行测序,筛选稳定的SNP位点,将其开发为基于HRM技术的分子标记,并在甘薯种质材料中进行验证。通过对23个甘薯种质材料简化基因组测序数据的分析,共发现835 756个SNP多态性位点,筛选其中的3 650个含有SNP多态性位点的高质量测序片段,成功设计了134对引物;初步验证发现,22对(16.42%)引物没有扩增产物,15对(11.19%)引物扩增产物2个以上,36对(26.87%)引物的扩增产物没有差异。61对(45.52%)引物在8个样本中的扩增特异性好,而且样本之间有差异。最后筛选34对扩增多态性丰富的引物对52份甘薯种质材料进行扫描,发现材料间多态性介于27.27%~90.91%之间,平均多态性达到59.35%。聚类分析表明,参试52份甘薯种质材料之间的差异较小,多数材料与骨干亲本南瑞苕、徐薯18之间关系较近,国外引进甘薯材料和地方品种差异较大。建议在今后甘薯育种中尽量选用地方品种和国外甘薯品种,从而更好地拓宽甘薯遗传背景。本研究初步建立了基于简化基因组技术和HRM技术开发甘薯SNP分子标记的新思路,为今后甘薯SNP分子标记开发提供了参考。同时本研究开发的甘薯分子标记,丰富了甘薯分子标记类型,为甘薯研究者开展快速的分子标记研究提供了支持。     

猪骨形成蛋白15基因编码区序列的克隆及测序研究

基于比较基因组学方法,选择大白猪和梅山猪作为试验材料,根据人、小鼠和猪的BM P 15基因设计并合成4对引物,进行基因组DNA的PCR扩增、克隆、测序,用BLA ST软件进行DNA序列排列,获得包含猪BM P 15基因外显子1(exon1)和外显子2(exon2)的全部编码区序列。用Pa irw ise BLA ST软件,将大白猪、梅山猪BM P 1 5基因编码区序列进行比较,在外显子2区域发现了一个SNP位点,位于编码区第390个核苷酸处,大白猪为T,梅山猪为A,且该位点导致了限制性内切酶Sp eⅠ酶切位点发生了改变。建立了猪BM P 15基因基于内切酶Sp eⅠ的PCR-RFLP多态性检测技术,发现猪BM P 15基因有3种基因型(BM P 15AA、BM P 15AB、BM P 15BB)。     

Starch physicochemical properties and their associations with microsatellite alleles of starch-synthesizing genes in a rice RIL population

The physicochemical properties of starch, such as apparent amylose content, gelatinization temperature, and pasting viscosities, determine the eating, cooking, and processing qualities of various products of rice. A recombinant inbred line (RIL) population derived from the reciprocal cross of Lemont (a premium high-quality tropical japonica rice) and Jiayu 293 (a high-yield but low-quality indica rice) was used to test the association of microsatellite markers of starch-synthesizing genes with starch quality parameters. The results confirmed the association of Wx and starch synthase I (SSI) alleles with various starch properties measured in rice flour. However, the starch properties were not associated with the starch branching enzyme 1 (SBE 1) gene alleles.     

Analysis of Genetic Diversity and Relationships in Waxy Rice (Oryza sativa L.) using AFLP and ISSR Markers

Opaque endosperm is the main phenotypic indicator for waxy rice, but other phenotypic and genotypic variation among waxy rice accessions has largely been ignored. Previous studies showed that wide diversity in starch physiochemical properties exists in both indica and japonica waxy rices, especially for starch gelatinization temperature (GT) which could be divided into a high- and a low-GT group. In the present study, amplified fragment length polymorphism (AFLP) and inter-simple sequence repeat (ISSR) molecular markers were employed to examine genetic diversity and relationships of 56 waxy rice accessions. A total of 358 AFLP fragments were amplified with five primer combinations, showing a high level of polymorphism (78.3%). A total of 190 ISSR bands were generated with a single primer and a primer pair, showing a very high level of polymorphism (92.2%). The genetic distance matrices obtained from the two sets of markers were significantly correlated (r = 0.731, P = 0.004). The dendrogram generated with combined AFLP and ISSR markers could clearly differentiate the indica and japonica groups. Newly released varieties and breeding lines within each subspecies tended to be clustered together, whereas landraces were more distantly placed in the dendrogram. Only one AFLP band was found specific to the indica type, while no specific bands were found for starch GT. The implications for the conservation and breeding of waxy rice are discussed.     

Genetic diversity and relationships among safflower (<Emphasis Type="Italic">Carthamus tinctorius</Emphasis> L.) analyzed by inter-simple sequence repeats (ISSRs)

Genetic diversity and relationships among 48 safflower accessions were evaluated using 22 inter-simple sequence repeats (ISSR) primers. A total of 429 bands were amplified, and 355 bands (about 82.7%) were polymorphic. Five to forty-one polymorphic bands could be amplified by each primer, with an average of 16.1 polymorphic bands per primer. The results showed that the polymorphism of the safflower germplasm was higher at the DNA level. All the 48 accessions could be distinguished by ISSR markers and were divided into 9 groups based on ISSR GS by using UPGMA method. The genetic relationships among the accessions from different continents were closer. Comparatively, the genetic diversity of the accessions originated from Asia was higher, from Europe assembled. The results also showed that the genetic variation of accessions from Indian and Middle Eastern safflower diversity centers were relatively higher. ISSR is an effective and promising marker system for detecting genetic diversity among safflower and give some useful information on its phylogenic relationships.     

利用MSAP分析18个芥蓝齐口期的表观遗传多样性

本研究利用MSAP检测18个芥蓝齐口期DNA甲基化水平,分析了表观遗传多样性,探讨DNA甲基化模式对齐口期的影响。结果表明,18个芥蓝齐口期平均为50d,叶片数平均为10片,齐口期和叶片数不相关（相关系数为0.296）;变异系数分别为21%和18%;遗传距离分布在0~40,平均值为12.2276,在10.62处分为3类。MSAP分析表明,5对引物组合扩增得到432条多态性条带,201条片段表现出多态性,多态性比率为47%;Nei遗传距离分布在0.004~0.467,平均值为0.0958,表明遗传多样性水平较低;在0.04处分为3类。Mantel测验表明两种分析的遗传距离相关系数为-0.1366,显示齐口期、叶片数与DNA甲基化多态性没有相关性。DNA甲基化模式分析表明,非甲基化片段为110条,甲基化多态性片段为322条,分为3种带型,类型一为非甲基化带型（110条）,类型二为甲基化带型（110条）,类型三为半甲基化带型（152条）,非甲基化片段和半甲基化片段在不同品种之间呈现多态性,甲基化片段在不同品种之间呈现多态性与单态性相差不大,显示MSAP多态性主要来源于非甲基化和半甲基化片段,芥蓝甲基化模式以半甲基化为主。本文推测DNA甲基化水平降低参与芥蓝齐口期调控,MSAP分析既可用于基因组结构研究,又可用于基因组水平上性状的功能研究。     

A single nucleotide polymorphism (SNP839) in the adh1 reference gene affects the quantitation of genetically modified maize (Zea mays L.)

The real-time PCR methods recommended in the European Union for the quantitation of genetically modified (GM) maize events NK603, GA21, and MON 863 measure the number of copies of the GM event in relation to those of the maize-specific adh1 reference gene. The study reported here revealed that the targeted 70 base pair adh1 region exhibits a single nucleotide polymorphism (SNP839) that hampers the binding of the reverse primer used in the adh1 detection method. Partial fragments of the adh1-A and adh1-F allele were cloned. By allele-specific real-time PCR, it was shown that SNP839 corresponds to a common allelic polymorphism in maize. As a result, the quantitation of the GM maize events mentioned is positively or negatively biased, depending on the adh1 genotype of sample and calibrant. Therefore, it is proposed to revise the quantitative detection methods for NK603, GA21, and MON 863 maize.     

Characterization of Seashore Paspalum (Paspalum vaginatum Swartz) Germplasm by Transferred SSRs from Wheat, Maize and Sorghum

One hundred and thirty SSR markers from wheat, maize and sorghum were screened for the transferability to Paspalum. The transfer rate was 67.5, 49.0 and 66.8% respectively. This would be a very efficient approach for DNA marker development for species which are not well studied molecularly. The polymorphism level for transferred SSR markers was 51.5% within species (Paspalum vaginatum) and 87.1% among Paspalum species. The high level of polymorphism is directly related to the high degree of heterozygosity maintained by its way of reproduction, i.e. self-incompatibility. Forty transferred polymorphic SSR markers were selected and used for characterization and evaluation of seventy-three Paspalum accessions. In total, 209 polymorphic bands were detected from these 40 SSR markers, with an average of five polymorphic bands per marker. The Paspalum accessions clustered into three major groups. Two very similar dendrograms can be generated from either 109 or 209 polymorphic bands. This led us to determine that 18 of the transferred SSR markers were sufficient for genetically differentiating the investigated germplasm accessions. The number of SSR markers required for germplasm characterization and evaluation is discussed. This is the first report of the transfer of SSR markers from major field crops to newly emerged environmental turfgrasses.     

AFLP-based genetic diversity assessment among Chinese vegetable mustards (<Emphasis Type="Italic">Brassica juncea</Emphasis> (L.) Czern.)

Amplified fragment length polymorphism (AFLP) analysis was used to evaluate the genetic relationships and diversities of Chinese vegetable mustards. Fourteen pairs of primers generated a total of 366 scorable fragments among 16 accessions of Brassica juncea studied, of which 296 bands were polymorphic with an average of 21.1% polymorphic bands per primer combination. Genetic similarities were obtained using Nei and Li similarity coefficients, and a dendrogram of the 16 accessions was made by UPGMA clustering method. The Nei and Li Similarity coefficient value ranged from 0.63 to 0.88. This result indicated that the 16 accessions of B. juncea possessed high level genetic variations. The cluster analysis showed that the vegetable mustards could be grouped into two main groups and some minor rami, which was partially in accordance with the traditional classification that based on different edible organs of vegetable mustards. The incongruity between morphological and molecular classification might be attributed to the high selection pressure during domestication of Chinese vegetable mustards, producing some accessions with similar genetic backgrounds evolving into abundant morphological variations. The great diversification among Chinese vegetable mustards not only provides an excellent object for molecular evolution research of B. juncea but also is of great value for widening the genetic basis of breeding programs and breeding materials selection. Besides, our study also indicates that AFLP are informative and can provide significant insights for genetic diversity research in B. juncea.