Start Codon Targeted (SCoT) markers provide new insights into the genetic diversity analysis and characterization of Tunisian Citrus species

Start Codon Targeted markers were used to establish phylogenetic relationship among seven species from Citrus L. genus. Twelve SCoT primers were used for their ability to reveal polymorphism of the targeted codon of initiation. A total of 132 amplicons were generated and 93.9% of them were polymorphic. The polymorphism information content of 0.884 and the resolving power of 75.22 illustrate the efficiency of the tested SCoT primers in highlighting polymorphism. The average Nei's (1973) gene diversity (0.376), the Schannon's index (0.548) and the Gst parameter (0.346) describe an important polymorphism at the interspecies level in Citrus genus. Analysis of molecular variance suggested significant genetic differences within species. In fact, 84% of variance occurs within the species, whereas 16% of the variation was recorded among the species of Citrus. The limited gene flow (Nm = 0.941) was recognized as a major factor to explain the partition of the observed diversity. The principal coordinates analyses, Neighbor Joining and the Bayesian clustering approach based on the SCoT markers also confirm the discrimination of the species of Citrus. Our results confirm the relevance and suggest the effectiveness of the SCoT markers for assessing genetic diversity, characterization and identification of the species of Citrus.     

地黄SCoT分子标记体系的建立和指纹图谱的构建

该研究采用L_(25)(5~6)正交设计和单因素两种方法,对影响地黄SCoT-PCR反应的5个因素(模板DNA浓度,引物浓度,ddH_2O和Mix的用量以及退火温度)进行了优化。结果表明:优化后的反应体系总体积为25μL,含有8μL ddH_2O,1μL模板DNA(80 ng·μL~(-1)),1μL引物(8μmol·L~(-1))和15μL Mix,退火温度为45℃。运用30份地黄种质材料,对优化的SCoT-PCR正交体系进行多次重复验证,获得了多态性丰富、条带清晰的扩增图谱,证明该反应体系稳定可靠。利用该体系对32条SCoT引物进行两次筛选,得到14个扩增产物清晰、重复性好且多态性条带相对较高的引物。利用SCoT_4等5条引物构建了上述地黄2个种共30份种质的SCoT指纹图谱。利用这5个SCoT引物指纹图谱可将7个地黄常用栽培品种区分开。这表明SCoT分子标记体系适用于地黄主要品种亲缘关系及遗传多样性的研究,所构建的指纹图谱也为地黄常见的7个栽培品种的区分提供参考依据。     

SCoT分子标记在植物研究中的应用进展

SCo T是一种新型的目的基因分子标记,该标记不仅能获得与性状联系紧密的目的基因,而且能对性状进行跟踪,已被广泛应用于多种植物的研究。本文概述了SCo T标记的原理、引物设计方法及特点,并从PCR反应体系建立与优化、种质资源遗传多样性与亲缘关系分析、种质鉴定与指纹图谱构建、基因差异表达与分子遗传连锁图谱构建等方面总结了SCo T标记的应用进展。同时,对其存在的问题进行了讨论,并展望了该标记的发展应用前景。     

Characterization of genetic diversity in chickpea using SSR markers,Start Codon Targeted Polymorphism (SCoT) and Conserved DNA-Derived Polymorphism (CDDP)

Physiology and Molecular Biology of Plants - To evaluate the genetic diversity among 48 genotypes of chickpea comprising cultivars, landraces and internationally developed improved lines genetic...     

棉花遗传多样性SCoT和SRAP标记的研究及比较分析

利用SCoT和SRAP两种分子标记技术对30份彩色棉与白色棉种质资源,进行遗传多样性研究。用29对SRAP引物组合和26个SCoT引物分别对供试棉花的基因组DNA进行扩增。SCoT引物共扩增出163条带,多态性比率为61.96%,遗传相似系数GS值变化范围为0.5405～0.9972。SRAP引物组合共扩增条带1067条,多态性比率仅为14.1%,遗传相似系数GS值变化范围为0.5415～0.9109。两种标记系统得到了相似但并不完全相同的聚类图,2种标记方法间存在显著相关性(r=0.5518,P<0.05)。结果表明,SRAP与SCoT标记均适用于棉花种质的遗传多样性分析,且SCoT的标记指数MI高于SRAP标记,为SCoT这种新兴的标记技术在棉花育种中的应用提供了重要的依据。     

濒危植物秦岭石蝴蝶的SCoT遗传多样性分析

利用筛选到的24条SCoT引物,分析秦岭石蝴蝶人工繁育和野生种群60份材料的遗传多样性和遗传结构,为秦岭石蝴蝶的濒危机制和制定种群保护与修复策略提供理论依据。结果显示:(1)60份秦岭石蝴蝶供试样品的观察等位基因数平均为1.51,有效等位基因数平均为1.31,Nei's基因多样性平均为0.2305,Shannon指数平均为0.3703,表明供试材料种群的遗传多样性较低。(2)种群间的遗传距离与遗传相似系数分析结果表明,3个种群60份供试材料间的遗传相似系数为0.9551~0.9705,平均相似系数0.9634,进一步表明供试材料之间的遗传相似性极高,遗传背景较为狭窄。(3)秦岭石蝴蝶种群分子方差分析结果显示15%的变异来自于种群间,而85%的变异来自于种群内部。综合分析表明,秦岭石蝴蝶各种群内和种群之间的遗传多样性较低,遗传背景狭窄,这可能是秦岭石蝴蝶适应环境能力差,从而导致其濒危的重要原因之一。     

Conservation Strategy for African Medicinal Species: <i>In Vitro</i> Biotechnological Approach

The use of medicinal plants for different therapeutic values is well documented in African continent. African diverse biodiversity hotspots provide a wide range of endemic species, which ensures a potential medicinal value. The feasible conservation approach and sustainable harvesting for the medicinal species remains a huge challenge. However, conservation approach through different biotechnological tools such as micropropagation, somatic embryogenesis, synthetic seed production, hairy root culture, molecular markers based study and cryopreservation of endemic African medicinal species is much crucial. In this review, an attempt has been made to provide different in vitro biotechnological approaches for the conservation of African medicinal species. The present review will be helpful in further technology development and deciding the priorities at decision-making levels for in vitro conservation and sustainable use of African medicinal species.     

Molecular characterization and expression analysis of a GTP-binding protein (MiRab5) in Mangifera indica

The Rab family, the largest branch of Ras small GTPases, plays a crucial role in the vesicular transport in plants. The members of Rab family act as molecular switches that regulate the fusion of vesicles with target membranes through conformational changes. However, little is known about the Rab5 gene involved in fruit ripening and stress response. In this study, the MiRab5 gene was isolated from stress-induced Mangifera indica. The full-length cDNA sequence was 984 bp and contained an open reading frame of 600 bp, which encoded a 200 amino acid protein with a molecular weight of 21.83 kDa and a theoretical isoelectric point of 6.99. The deduced amino acid sequence exhibited high homology with tomato (91% similarity) and contains all five characteristic Rab motifs. Real-time quantitative RT-PCR analysis demonstrated that MiRab5 was ubiquitously expressed in various mango tree tissues at different levels. The expression of MiRab5 was up-regulated during later stages of fruit ripening. Moreover, MiRab5 was generally up-regulated in response to various abiotic stresses (cold, salinity, and PEG treatments). Recombinant MiRab5 protein was successfully expressed and purified. SDS-PAGE and western blot analysis indicated that the expressed protein was recognized by the anti-6-His antibody. These results provide insights into the role of the MiRab5 gene family in fruit ripening and stress responses in the mango plant.     

中国鸭茅主栽品种DNA指纹图谱构建

利用SSR标记和SCoT标记构建了我国主栽的21个鸭茅品种的DNA指纹图谱。从180对SSR引物和80个SCoT引物中,筛选出多态性高、谱带清晰的SSR引物和SCoT引物各24个。24对SSR引物在供试材料中共检测到186个条带,其中多态性条带为175个,品种特异条带6个,平均多态性比率94.03%,多态性信息量均值0.845,Shannon指数变幅0.4479~0.6549,基因多样性指数变幅0.2946~0.4633,可鉴别的品种数2~21个;利用24个SCoT引物在供试材料中共检测到321个条带,其中多态性条带为249个,品种特异条带6个,平均多态性比率76.33%,多态性信息量均值0.907,Shannon指数变幅0.2588~0.6329,基因多样性指数变幅0.1695~0.4451,可鉴别的品种数1~21个;5对SSR引物和5个SCoT引物在10个品种上具有唯一特征谱带,最终综合各项指标筛选出5个引物(A01E14、A01K14、B03E14、D02K13和SCoT23)上的37个条带用于鸭茅品种DNA指纹图谱构建,数据库中每个品种均具有唯一DNA指纹编码,构建的DNA指纹数据可用于鸭茅品种真伪鉴定,为品种权保护提供了科学依据。     

利用SCoT分析柳枝稷遗传资源的多样性

本研究利用SCoT标记对96份柳枝稷种质的亲缘关系和遗传变异进行了研究。筛选出20条引物对96份供试材料进行PCR扩增,共获得445条带,其中多态性条带402条,平均多态性条带比率(PPB)达90.31%,多态性信息含量(PIC)为0.166~0.410,平均值为0.332,标记指数(MI)为10.20。遗传相似系数(GS)为0.498~0.912,平均值为0.688。表明SCoT标记能够揭示柳枝稷种质间的遗传变异。通过UPGMA分析表明,96份种质资源聚为高地型和低地型两大类。经POPGENE1.32软件分析结果显示:96份柳枝稷基因多样性指数(H)为0.285,Shannon指数(I)为0.431,表明供试的种质间遗传多样性丰富,遗传多样性水平高。经AMOVA 1.55方差分析揭示:96份柳枝稷生态型内的遗传变异占总变异的72.85%,生态型间遗传变异占总变异的27.15%,结果表明ScoT可用于柳枝稷遗传多样性研究,该研究结果可为柳枝稷种质资源的进一步开发利用提供重要信息。