共查询到19条相似文献，搜索用时 671 毫秒
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[目的]基于转录组数据开发适用于桤木属树种的SSR标记,揭示其在转录组序列中的分布类型及特征,为桤木属树种分子标记辅助育种提供有利工具。[方法]利用Micro SAtellite(MISA)软件对所有转录组序列进行SSRs搜索,并对SSR位点的数量、分布特征进行统计分析。设计100对SSR引物,采用琼脂糖凝胶电泳和毛细管电泳分离检测方法对3种不同倍性桤木属植物(12份材料)进行遗传多样性检测,确定引物多态性及通用性。[结果]85 769条Unigenes序列中发现8 678个SSR位点,分布在8 298条Unigenes中发生频率为9.67%,转录组序列中平均每14.04 kb长度就有一个SSR位点分布。其中,二核苷酸重复类型数量最多,占65.87%。根据转录组Unigenes序列,利用Primer 3软件共设计出4 531对符合要求的引物,挑选出的100对SSR引物中,获得18对多态性高、稳定性好的SSR引物。[结论]本研究可扩增出多态性位点的引物重复单元以二、三核苷酸重复为主。基于桤木属转录组序列的SSR标记开发是可行的,开发的引物为桤木属遗传多样性分析、分子育种、遗传图谱构建和功能基因的挖掘提供了丰富的候选分子标记。 相似文献
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利用直接测序法开发小叶杨抗逆转录因子基因内一套新的核基因组SSR标记。通过对3个抗逆转录因子共21个成员在36个小叶杨基因型个体中的序列比较分析后共检测到31个SSR多态性位点,SSR出现的频率为1/1916bp。在小叶杨自然群体中,SSR多态性位点的碱基重复呈现出2～5碱基形式,基元重复次数变异范围为3～20次,其中以二碱基重复的位点较多,占总数的51.6%。在此基础上,依据SSR位点两侧的保守序列,设计31对SSR位点PCR扩增引物对。利用设计的引物检测所开发的SSR位点在杨属内22个基因型个体中PCR扩增的有效性及SSR位点的保守性。PCR扩增结果显示,93.5%的SSR位点能够在杨属内至少4个派内有效扩增,每对引物组合可检测到SSR多样性位点数3～12个,平均6个。基于抗逆转录因子基因内开发的SSR标记位点为分子标记辅助小叶杨抗逆性状育种提供工具。 相似文献
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白桦EST-SSR信息分析与标记的开发 总被引：11，自引：0，他引：11
对NCBI(美国国立生物技术信息中心)中2 5 48条欧洲白桦ESTs的序列进行分析,结果表明:其中260条ESTs中含有306个SSRs,为全部 ESTs序列的10.2%,SSR频率为12.01%.其中,二核苷酸重复比例为81.37%,三核苷酸重复比例为16.67%,四核苷酸重复比例为1.96%.不同软件设计引物的效率不同,Pri mer3设计出176对SSR引物,在白桦中扩增成功的引物比例为59.09%,而具有多态性的引物比例仅为25.96%;SSR Primer设计出100对引物,在白桦中扩增成功的引物比例为37%,而具有多态性的引物比例为48.65%. 相似文献
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《中国林副特产》2017,(2)
以我国推广面积较大的9个玉米杂交种为试材,利用盐溶蛋白电泳法与SSR分子标记鉴定法对试验材料进行了杂交种纯度鉴定的比较试验。结果表明:盐溶蛋白电泳法可以很好地鉴定出8个组合,且具有简单、快速、准确、稳定和低成本的特点,可用于大批量检测。但因一些种子蛋白质水平差异较小,有1个组合难以鉴定,具有一定的局限性。而SSR分子标记法经过40对引物的重复筛选,仅用3个多态性好的SSR引物能鉴定出所有的组合,具有更好的精确性。但因实验条件要求高,成本相对较高,不宜用于大批量检测。因此,可将盐溶蛋白电泳法作为首选大批量种子纯度的检测方法,而对难以鉴定的品种可采用SSR分子标记法进行鉴定。 相似文献
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毛白杨木材形成功能基因内SSR标记的开发及评价 总被引：2，自引：0，他引：2
利用直接测序法开发木材形成功能基因内一套新的核基因组SSR标记.通过对参与木材形成的16个基因在40个毛白杨基因型个体中的序列比较分析,共检测剑20个SSR多态性位点.在毛白杨自然群体中,SSR多态性位点的碱基重复呈现出二碱基、三碱基、五碱基、六碱基与七碱基形式,基元霞复次数变异范围为2～34次,其中以二碱基重复的位点较多,占总数的55.0%.在此基础上,依据SSR位点两侧的保守序列,设计20对SSR位点PCR扩增引物对.利用设计的引物检测开发的SSR位点在杨属内15个基因型个体中PCR扩增的有效性及SSR位点的保守性.PCR扩增结果显示,90.0%的SSR位点能够在杨属至少2个派内有效扩增,每对引物组合可检测到SSR多样性位点数为3～9个,平均5.3个.开发的这些SSR位点在功能基因内小同区域的分布频率不同. 相似文献
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对NCBI(美国国立生物技术信息中心)中牡丹的ESTs(expressed sequence tags)的序列进行分析,结果表明:在所分析的2 204条序列中,仅324条分布有SSRs(simple sequence repeats),占全部ESTs序列的14.70%;SSR的出现频率为15.20%,共计335个,其中,二核苷酸重复比例84.18%,三核苷酸重复比例为15.22%,四和六核苷酸重复比例为0.30%。在此基础上,利用软件(serafer 1.3)设计了51对备选SSR引物,以6个滇牡丹不同花色类群DNA为模板对引物进行筛选,其中,10对引物有扩增产物;用这些引物进一步在10个类群50个DNA模板进行多态性测试,结果显示:上述10对SSR引物均有多态性,且同一类群内不同模板DNA间也存在多态性。本研究结果证明:基于牡丹EST信息建立SSR标记是一种有效而可行的方法,有助于滇牡丹遗传多样性分析及基因组学方面的研究。 相似文献
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选用一组高效SSR引物,用于澳洲坚果杂交优株及诱变优株的DNA分子标记数据采集。从早期设计并筛选的SSR标记中挑选多态性高、重复性好、在染色体上分布均匀的9对引物,经PCR扩增,利用毛细管电泳,对1份化学诱变优株、52份杂交优株及13个亲本共66份材料进行电泳检测。1对引物在66份材料中存在较高的数据缺失率,最终选取7对SSR引物用于后续数据的采集。将7个亲本选为参照品种,并设置了7个亲本的两组平行试验,建立了53份优良单株及其亲本的分子标记数据库,可为其新品种登记提供技术支持。 相似文献
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利用磁珠富集高效微卫星分离法,设计生物素标记的寡核苷酸（AG）15与（AC）15作为探针,快速分离油茶微卫星序列并建立其SSR分子标记体系。从获得的52份具微卫星序列的克隆测序结果中,成功开发40对油茶SSR引物,序列开发引物成功率在76.9%;对扩增结果进行比较分析后,共得到14对具有清晰扩增条带的SSR引物,占总引物的35%;进一步利用18个油茶无性系开展引物多态性检测,显示6对SSR引物具良好的多态性。研究结果可为油茶遗传学研究提供新的分子标记工具,同时为山茶属其他重要经济树种的相关研究提供很好的借鉴。 相似文献
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Filomena Gomes Rita Costa Maria M. Ribeiro Elisa Figueiredo Jorge M. Canhoto 《林业研究》2013,24(2):227-236
The strawberry tree (Arbutus unedo L.) is an underutilized, drought tolerant, fire resistant species with a south western distribution in Europe, and with ecological and putative socio-economical impact in Portugal and Mediterranean countries. Our aim was to develop an appropriate set of molecular markers to enable genetic diversity to be assessed and to fingerprint Arbutus unedo genotypes for breeding and conservation purposes in Portugal. Twenty-seven trees from a broad geographic range were screened with 20 random amplified polymorphic DNA (RAPD primers) and 11 microsatellite markers (SSR). The RAPDs generated 124 bands, 57.3% of which were polymorphic, with an expected heterozygosity of 27%. We cross-amplified 11 SSR primers developed for Vaccinium spp., and 5 were found to be polymorphic in A. unedo, with 75% of expected heterozygosity, a number of alleles of 11.6, a null allele frequency of 7.6% and a polymorphic information content of 71%. Although the SSRs were more polymorphic and informative than the RAPDs, both markers displayed high genetic variability with the gathered data. No geographic pattern was observed in the genetic variation distribution based on both marker systems, and the lack of correlation between genetic and geographical matrices was confirmed by Mantel tests. Likely, no correlation was found between pairwise SSR and RAPD band-sharing matrices. These results and their implications on A. unedo breeding and conservation programs are discussed. 相似文献
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Khalid Majourhat Youssef Jabbar Abdellatif Hafidi Pedro Martínez-Gómez 《Annals of Forest Science》2008,65(8):805-805
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Peroxidase plays important roles in many stress-related interactions and catalyzes important reactions in various physiological processes. Since peroxidase played critical roles in the evolution of almond(Prunus dulcis Miller(D.A Webb) syn P. amygdalus Batsch), peroxidase-gene-based analyses may increase the understanding of evolution of this species. Peroxidase gene polymorphism(POGP) markers were used to determine genetic diversity and relationships among 69 Turkish genotypes/cultivars and 27 foreign almond cultivars by using unweighted pair group method with arithmetic mean(UPGMA) analysis. This study is the first evaluation of the use of POGP markers for diversity analysis in almond.Totally, 83 fragments were obtained from eight peroxidase primer pairs, and polymorphism was identified as 94 %.Similarity level among the genotypes ranged between 0.63 and 0.93, and all materials were distinguished. In general,Turkish and foreign genotypes were mixed in clusters since they share a common genetic background and gene migration among the sites. Clusters were not based on geographic regions except for some minor groupings. This study indicated that peroxidase gene markers can be reliably used to determine genetic relationships in almonds. 相似文献
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本文对锥栗SSR富集文库进行Illumina MiSeq高通量测序,利用生物信息学对得到的序列进行SSR特征分析,开发锥栗基因组SSR并对农家品种进行了遗传多样性分析。在2051475条序列中,总共搜索到2117345个SSR,以复合形式存在的SSR数量为640155个。二核苷酸为重复单元的SSR数量最多,占总数的73.22%,之后依次为三核苷酸(12.61%)、单核苷酸(12.56%)、四核苷酸(1.33%),单碱基重复、二碱基重复和三碱基重复的优势重复单元分别为:A/T、AC/GT、AAG/CTT。对SSR的长度多态性进行了评价。以8个农家品种为材料,在100对基因组SSR引物中筛选出多态性和特异性较好的引物10对。对25个锥栗农家品种进行了遗传多样性分析观测等位基因和期望杂合度分别为6.3和0.705,有效等位基因数为3.628,Shannon信息指数为1.441,表明锥栗农家品种具有较高的遗传多样性水平。 相似文献
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Chokri Messaoud Makrem Afif Abdennacer Boulila Mohamed Nejib Rejeb Mohamed Boussaid 《Annals of Forest Science》2007,64(8):845-853
The genetic variation of six Tunisian Myrtus communis L. (Myrtaceae) populations was assessed using nine isozymes coding for 17 putative loci and 79 RAPD markers, amplified by five decamer random primers. The analysed populations belonged to three bioclimatic zones (lower humid, sub-humid and upper semi-arid). A high genetic diversity within populations was detected both by isozymes and RAPDs. The level of variation differed according to bioclimate. Populations collected from sub-humid bioclimate showed more polymorphism than those grown in the upper semi-arid zone. For all populations, the genetic diversity revealed by RAPDs was more pronounced than that detected with isozymes. A high differentiation among populations related to bioclimate and geographic distance was revealed by both methods. Population’s structure based on RAPD markers was more concordant with bioclimatic zones in comparison with isozymes. Differentiation between ecological groups was higher than that revealed within groups. Conservation programs should take into account the level of genetic diversity within population revealed by the two complementary classes of markers according to bioclimate. 相似文献
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A comparison of genetic diversity and differentiation in five Chinese pines using cpSSR and AFLP markers 总被引：1，自引：0，他引：1
Gene diversity and genetic differentiation in five Chinese pines, Pinus henryi, P. tabulaeformis, P. yunnanensis, P. taiwanensis and P. massoniana, were compared using amplified fragment length polymorphism (AFLP) and simple chloroplast sequence repeat (cpSSR). High genetic
differentiation and median gene diversity with cpSSR markers were found both at population and species level, while median
differentiation and higher gene diversity in AFLP data. Measures of subdivision that consider similarity between haplotypes
offered better information on the geographic structure of plants than the standard subdivisions. Among several methods analyzed
in AFLPs, the square root method provided downwardly biased estimates of the genetic parameters, while the Lynch and Milligan
method over-estimated genetic diversity due to a small sample size. The Bayesian statistic was the most accurate and popular
method for these dominant species and its value of species differentiation (θ
B = 0.1035) was close to the parameter given by analysis of molecular variance (AMOVA).
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Translated from Acta Botanica Boreali-Occidentalia Sinica, 2007, 27(12): 2385–2392 [译自: 西北植物学报] 相似文献
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In our previous study, RAPD (Random Amplified Polymorphic DNA) analysis revealed species-specific markers for three medicinal Echinacea species (Asteraceae): E. angustifolia DC., E. pallida (Nutt.) Nutt. and E. purpurea (L.) Moench. In the present work, we have converted a RAPD marker (750 bp) for E. purpurea into a SCAR (Sequence Characterized Amplified Region) marker. SCAR-PCR, in fact, revealed the expected amplicon (330 bp) only in E. purpurea and not in the other two species, giving further evidence for differences in medicinal Echinacea spp. genome and confirming a greater similarity between E. pallida and angustifolia. 相似文献
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对31 308条来自NCBI的芭蕉属(Musa)EST序列进行拼接得到全长为13.51 Mb的21 129条无冗余EST序列(含3 818条contigs及17 311条singletons),其中,4 944条(23.40%)EST序列含有5 416条SSRs,SSR的出现频率为25.63%,平均分布距离2.49 Kb,有234条(1.11%)含有1个以上的SSR。在所检测的SSR中,二、三、四核苷酸重复是主导重复类型,分别占EST-SSR总数的21.80%(1 181条)、52.55%(2 846条)和14.55% (788条)。AG/CT、AAG/CTT与AGG/CCT和AAAG/CTTT与AAAT/ATTT分别是二、三、四核苷酸的优势重复基元。随机设计了238对EST-SSR引物在24个地涌金莲个体中进行筛选,116对有扩增产物,其中,78对EST-SSR引物扩增出清晰稳定的目的片段,49对引物表现出多态性。本研究检测的15对引物扩增等位基因数范围是2~7个,平均3.067个;表观杂合度(Ho)范围是0.042 0.750,平均0.250;期望杂合度(He)范围是0.232~0.823,平均0.522。 相似文献
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C. H. Bock T. T. Endalew B. K. Biswas A. K. Yadav V. Sitther M. W. Hotchkiss K. L. Stevenson B. W. Wood 《Forest Pathology》2014,44(4):266-275
Fusicladium effusum infects pecan causing yield loss, but no information is available on the genetic diversity of F. effusum. Randomly amplified polymorphic DNAs (RAPDs) and universally primed polymerase chain reaction (UP‐PCR) were compared to detect polymorphisms on a group of 20 isolates of F. effusum from 11 geographical locations in the southeastern USA. Two tests (run 1 and 2) of both the RAPD and UP‐PCRs were conducted to assess the repeatability of the methods, and the markers scored on agarose gels. In addition, the UP‐PCR markers from run 1 were scored using an automated capillary system. Both RAPDs and UP‐PCR markers detected a high level of polymorphism among the scored markers (92 and 91% of RAPD markers, and 86 and 87% of manually scored UP‐PCR markers in run 1 and 2 were polymorphic, respectively; 93% of UP‐PCR markers were polymorphic when scored using the automated system). Unweighted paired group method of arithmetic averages (UPGMA) analysis showed both RAPDs and UP‐PCR markers individually identified each isolate, producing three groupings, but only the groupings based on run 1 and 2 of the UP‐PCR contained the same isolates. Bootstrap analysis based on the Dice coefficient produced phenograms from the UP‐PCR data with weak to moderate node support (≥54) for the primary branch, but no support for the RAPDs data (≤34). A Mantel test of runs 1 and 2 using RAPDs or UP‐PCR showed good agreement (r = 0.8761 and 0.8289, p < 0.0001), but poor agreement between RAPDs and UP‐PCR. UP‐PCR results based on the interisolate Dice coefficients showed a weak to strong association with distance. Based on these results, both RAPDs and UP‐PCR markers were capable of demonstrating polymorphisms and identifying relationships among isolates of F. effusum; however, UP‐PCR markers appear to be more reliable. 相似文献