中国部分板栗品种的SSR标记

从板栗(Castanea mollissima)燕红中分离到25个SSR标记。为了鉴定这些SSR位点,在重复序列的两侧侧翼序列设计引物,并通过化学荧光检测法对6个板栗样品进行检测,共检测到20个多态性位点,每个位点的等位基因数为2~6个。挑选12个位点,通过半自动系统ABI PRISM377对中国北方24个板栗品种进行分析,这12个标记显示了高达75个等位基因的遗传多态性,每个位点的等位基因为4~10个,平均为6.3个,预期的平均杂合性为0.743(介于0.680~0.845),观察值为0.829(介于0.730~0.930)。无效等位基因估算频率显示为3个位点的正向价值,除了一个位点外,这些价值都很低,鉴定几率为7.01×10-11,亲缘关系鉴定几率非常高,为0.999,足够用于花粉流的研究。     

山西芝麻种质资源SSR遗传多样性及群体结构分析

为探明山西芝麻种质资源的遗传特性,本研究利用30对简单重复序列标记(SSR)对71份山西芝麻种质资源进行遗传多样性分析及群体结构分析。结果表明,30对SSR标记共检测到144个等位基因位点,平均每个SSR标记4.800个等位基因;有效等位基因数在1.058~5.149之间,平均2.805个;Shannon指数变幅为0.128~1.813,平均为1.096;Nei's遗传多样性指数变幅为0.055~0.806,平均为0.558;多态性信息含量变幅为0.053~0.783,平均为0.515。基于SSR标记对参试材料进行聚类分析,遗传相似系数为0.21~0.67,在遗传相似系数0.27处将参试材料分为6个类群;基于SSR标记对参试材料进行群体结构分析,将参试材料划分为5个组群。综上所述,山西芝麻种质资源间遗传差异相对较高,具有丰富的遗传多样性,在今后芝麻种质资源创制利用中,加大山西芝麻种质资源的开发与利用,可为芝麻品种遗传改良和优异基因发掘奠定良好的基础。     

江西野生毛花猕猴桃群体SSR遗传多样性研究

为分析江西野生毛花猕猴桃群体遗传多样性,以江西省境内的5个野生毛花猕猴桃雄性群体(72个个体)为试验材料,采用SSR分子标记技术,选取15对多态性引物,利用聚丙烯酰胺电泳对PCR产物进行检测。结果表明,15对SSR引物共检测到86个位点,多态性位点百分率为100.0%;观察到的平均等位基因数为5.733,有效等位基因数为3.002,Shannon信息指数为1.046。表观杂合度介于0.111~0.819之间,预期杂合度介于0.041~0.876之间,遗传分化系数为2.01,野生毛花猕猴桃雄性群体间存在较大的遗传分化。5个毛花猕猴桃雄性群体遗传距离范围为0.102~0.409,遗传相似度范围为0.665~0.903,群体间遗传距离与地理距离无相关性。群体的遗传多样性丰富度依次为庐山>井冈山>南源山>武功山>麻姑山,江西地区供试的野生毛花猕猴桃雄性群体在分子水平上具有丰富的多态性。本研究结果为毛花猕猴桃雄性品种选育、种质创新与利用提供了一定的理论基础。     

节水抗旱稻品种DNA指纹图谱的构建

为了解节水抗旱稻品种的多样性,利用SSR分子标记技术对24份节水抗旱稻和2份普通水稻品种进行DNA指纹图谱构建和遗传多样性分析。结果表明,24对引物共扩增出96个多态性片段,平均每对引物可检测到4个等位基因,每个SSR位点可以检测到2~6个等位基因。引物多态信息含量(PIC)的变化范围为0.36~0.75,平均值为0.58。指纹图谱显示至少可以利用RM71、RM72、RM336、RM337、RM1195和RM5414这6个核心标记的不同组合鉴别区分26份供试材料。聚类分析结果表明,26份材料间遗传相似系数为0.54~0.98,在遗传相似系数0.65处可以将供试材料分为籼、粳两类,较好地反映了供试材料的亲缘关系。本研究结果为节水抗旱稻新品种保护、真伪鉴定及亲本选配提供了参考。     

基于SSR标记的梨资源遗传多样性分析

本研究利用SSR标记技术对56份梨资源进行了遗传多样性分析。利用筛选出的6对SSR引物共扩增40条谱带,其中多态性位点38个,多态性位点比例为95%,每对引物产生有效等位基因6.3个。各位点期望杂合度H值在0.0354～0.491,平均为0.1964;有效等位基因Ne值在1.0367～1.9648,平均值为1.2958;香农指数I值平均值为0.3256,说明了供试梨材料的遗传多样性较低。利用SSR标记可将44个栽培品种区分开,但无法区分芽变和原种。根据SSR标记揭示的多态性,采用NTSYS-pc软件,以UPGMA法进行聚类分析,结果显示所检测的56份梨材料在相似系数0.71处可分为4组,其中中国的白梨、秋子梨和砂梨相互交错在一起,没有独自各自成组。     

利用复合杂交群体定位陆地棉产量性状QTL

以共同亲本渝棉1号分别与中棉所35和贝尔斯诺杂交F1代,再次杂交得到复合杂交群体.利用6 565对SSR引物对3亲本进行多态性引物筛选,获得92对多态性引物.以多态性引物检测复合杂交群体172个单株的标记基因型,共获得96个标记位点,其中4对引物产生两个位点.构建的遗传连锁图谱包括63个标记、19个连锁群,总长656.0 cM,标记问平均距离10.4 cM,覆盖棉花基因组14.8%.利用多QTL作图方法,以复合杂交群体F2株系的产量性状鉴定结果,检测到7个产量性状QTL,即1个单株铃数(BN)、2个单铃重(BW)、1个衣分(LP)、1个单株籽棉(SC)和2个单株皮棉(LC).7个QTL分布于4条D基因组染色体,其中第19染色体分布4个QTL.同时,不同亲本之间存在产量性状QTL等位基因的差异.     

玉米诱变系的SSR遗传变异分析

从97对SSR引物中筛选出52对扩增产物具有稳定多态性的引物,对基础材料玉米自交系"082"及其48个诱变系进行检测,共检测到170个等位基因变异,每对引物检测出2~6个等位基因,平均为3.27个;每个位点的多态性信息量(PIC)变化于0.039~0.715之间,平均为0.327;49个材料之间的遗传相似系数变化范围在0.377~1.000,平均为0.823。UPGMA聚类分析将49个材料分成6类,表明材料间存在着广泛的遗传差异。这些遗传变异与材料的品质性状、农艺性状相关。     

利用简单重复序列(SSR)标记分析太湖稻区现代粳稻品种的遗传多样性

太湖地区有丰富的粳稻(Oryza satiua ssp.japonica)种植资源,随着品种大面积推广应用,育种材料的遗传基础趋窄,相似性增高,使粳稻育种突破困难。本研究利用分布于水稻(Oryza satiua L.)12条染色体上的24对简单重复序列(simple sequence repeat,SSR)引物对太湖地区的42份粳稻品种进行遗传多样性分析。结果表明,有23对SSR引物在42份粳稻材料间表现出多态性;23对引物共检测到105个等位基因,每对SSR引物检测到等位基因为2~8个,平均为4.57个,有效等位基因共有56.43个,平均每个位点为2.45个。每个多态位点的多态信息含量(polymorphism information content,PIC)变幅为0.083 0~0.8079,平均为0.496 6;每个粳稻材料多态性位点数的变幅为6~19,等位基因总数的变幅为27~55;42份粳稻品种间的遗传相似系数变幅为0.391~0.990,平均为0.610,遗传相似系数在0.50~0.80之间的材料占全部的74.45%,供试材料相似度高;非加权配对算术平均法(unweighed pair group method with arithmetic mean;UPGMA)聚类结果显示,遗传相似系数为0.50,42份粳稻材料可以分为两个类群,一个类群包含19份常规粳稻,另一个类群包括其他23份杂交粳稻。结果显示,太湖地区的粳稻品种总体上遗传背景相似度高,遗传多样性不够丰富,育种工作有待进一步加强新的基因资源引进和利用,创新水稻育种材料。本研究结果为新品种选育提供技术支持和理论根据。     

基于石蒜属转录组序列的SSR分子标记开发应用

为开发石蒜属简单重复序列(SSR)分子标记,并研究SSR引物在石蒜属内的通用性,本研究对石蒜属石蒜、忽地笑、中国石蒜、长筒石蒜、换锦花、香石蒜6个种质转录组测序,检测SSR位点并设计引物,通过PCR扩增和毛细管电泳判断引物的有效性和多态性,绘制石蒜属17个种质资源的指纹图谱并对杂交后代的真实性进行早期检测。结果表明,共获得404 481条Unigenes,利用数据库进行同源比对和功能注释,并对Unigene进行SSR位点挖掘和分析,共检测到59 612个SSR位点。其中,单核苷酸重复>二核苷酸重复>三核苷酸重复,分别占SSR总数的62.88%、20.06%和14.66%,四核苷酸及以上重复单元相对较少。选取并合成8对荧光引物进行PCR扩增,通过毛细管电泳检测发现,8对荧光引物共检测到60个多态位点,多态位点数平均为7.50,多态性信息含量(PIC)值变化范围为0.148 0~0.940 8,平均值为0.593 0。利用引物扩增带型组合法构建了石蒜属17个种资源的指纹图谱,其中引物QZ209可区分所有供试材料,并可用于杂交后代鉴定。本研究开发的SSR标记具有丰富的多态性,在石蒜属植物的资源多样性分析、杂交种鉴定及遗传图谱的构建应用中具有重要意义。     

绵羊皮肤源EST-SSR标记与羊毛性状的关联性分析

为了筛选与绵羊(Ovis aries)毛性状基因座连锁更强的分子标记,本研究选择9个多态性丰富的绵羊皮肤源EST-SSR位点,检测了德国美利奴羊与中国美利奴羊级进杂交F2代群体的遗传多态性,并分析了标记与毛性状间的关联性.分析结果显示,所选的9个EST-SSR位点在供试群体中共检测到39个等位基因,多态性丰富,其中的6个位点基因型间存在显著差异;其中,与自然长度关联的位点有5个,与伸直长度关联的位点有4个,与纤维直径关联的位点有3个.6个EST-SSR位点基因型间存在显著差异;关联性标记对羊毛性状相关效应的F检验结果表明:33176918位点和33176988位点分别对羊毛自然长度、纤维平均直径具有显著的遗传效应(P＜0.05).研究结果提示,与羊毛性状相关的6个位点中,33176918号位点对羊毛的自然长度有较大的标记效应,该位点的CD基因型是羊毛自然长度的有利基因型;33176988号位点对羊毛的纤维直径有显著地标记效应,该位点的BC基因型是纤维直径的有利基因型.这两个位点可能与控制毛形状的基因座紧密连锁.     

利用SSR对60个玉米自交系进行杂种优势群划分初探

用SSR对60个玉米自交系的DNA进行分子标记和杂种优势群划分研究。利用14对SSR引物在供试材料中检测出57个等位基因变异,每对引物检测等位基因2～7个,平均为4．07个,多态信息量变化范围为0．389～0．832,平均为0．692。自交系间遗传相似系数变幅为0．058～0．756,UPGMA聚类分析表明,供试自交系可分为五个类群。利用这14对具有较高多态性信息量的引物,可以对供试材料进行初步鉴定。     

Simple sequence repeats marker polymorphism in emmer wheat (<Emphasis Type="Italic">Triticum dicoccon</Emphasis> Schrank): Analysis of genetic diversity and differentiation

Genetic diversity was investigated in 73 accessions of emmer wheat (Triticum dicoccon Schrank) from 11 geographical regions using a set of 29 simple-sequence repeat (SSR or microsatellite) markers, representing at least two markers for each chromosome. The SSR primers amplified a total of 357 different alleles with an average of 12.31 alleles per locus. The number of fragments detected by each primer ranged between 6 (Xgwm1066) and 21 (Xgwm268). Null alleles were detected in nine of the 29 primers used. A high level of gene diversity index was observed. Across the 29 primers, gene diversity ranged from 0.60 (Xgwm46) to 0.94 (Xgwm655), with a mean of 0.82. There was a highly significant correlation (r=0.882; p<0.01) between gene diversity index and the number of loci, showing the number of loci per se is a strong indicator of diversity. Analysis of genetic diversity within and among eleven geographical regions revealed most of the genetic diversity of the total sample resided within regions. The coefficient of gene differentiation (Gst = 0.27) showed that the genetic variation within and among the 11 geographical regions was 73 and 27%, respectively. High value of mean number of alleles per locus was found in Iran (4.86) followed by Morocco (4.10) and Armenia (4.03). On the contrary, lower mean number of alleles per locus was detected in Yemen (2.83). The average gene diversity index across regions ranged from 0.52 (Slovakia) to 0.67 (Morocco) with an average of 0.60. Multivariate techniques of principal component analysis and clustering were employed to examine genetic relationship among the 73 emmer wheat accessions vis-à-vis geographical regions of collections. The genetic distance coefficients for all possible 55 pairs of regional comparisons ranged from 0.63 (between Iran and Armenia, Georgia and Azerbaijan, Georgia and Slovakia) to 0.97 (between Morocco and Yemen, Spain and Georgia, and Turkey and Iran) with a mean of 0.82. From the PCA results, a two dimensional plot of PC1 versus PC2 was constructed. The scatter plot of the first two principal components which explained altogether 27% of the total variation depicted the presence of a clear pattern of geographical differentiation except in few cases like accessions from Caucasian region. Similar pattern of genetic relationships among accessions was observed in cluster analysis. The study provided genetic information of emmer wheat in relation to geographical regions of origin. The information could be utilized in crop improvement, germplasm conservation programs, and in further investigation.     

Exploitation of <Emphasis Type="Italic">Malus</Emphasis> EST-SSRs and the utility in evaluation of genetic diversity in <Emphasis Type="Italic">Malus</Emphasis> and <Emphasis Type="Italic">Pyrus</Emphasis>

A total of 8117 suitable SSR-contaning ESTs were acquired by screening from a Malus EST database, among which dinudeotide SSRs were the most abundant repeat motif, within which, CT/TC followed by AG/GA were predominant. Based on the suitable sequences, we developed 147 SSR primer pairs, of which 94 pairs gave amplifications within the expected size range while 65 pairs were found to be polymorphic after a preliminary test. Eighteen primer pairs selected randomly were further used to assess genetic relationship among 20 Malus species or cultivars. As a result, these primers displayed high level of polymorphism with a mean of 6.94 alleles per locus and UPGMA cluster analysis grouped twenty Malus accessions into five groups at the similarity level of 0.6800 that were largely congruent to the traditional taxonomy. Subsequently, all of the 94 primer pairs were tested on four accessions of Pyrus to evaluate the transferability of the markers, and 40 of 72 functional SSRs produced polymorphic amplicons from which 8 SSR loci selected randomly were employed to analyze genetic diversity and relationship among a collection of Pyrus. The 8 primer pairs produced expected bands with the similar size in apples with an average of 7.375 alleles per locus. The observed heterozygosity of different loci ranged from 0.29 (MES₉₆) to 0.83 (MES₁₃₈), with a mean of 0.55 which is lower than 0.63 reported in genome-derived SSR marker analysis in Pyrus. The UPGMA dendrogram was similar to the previous results obtained by using RAPD and AFLP markers. Our results showed that these EST-SSR markers displayed reliable amplification and considerable polymorphism in both Malus and Pyrus, and will contribute to the knowledge of genetic study of Malus and genetically closed genera.     

Molecular genetic diversity analysis in emmer wheat (Triticum dicoccon Schrank) from India

Emmer wheat (Triticum dicoccon Schrank) is still largely cultivated in India, and highly appreciated for the preparation of traditional dishes. Moreover, its nutritional characteristics could justify a development of its cultivation. The perspective of genetic improvement however requires a good knowledge of the genetic diversity existing within the eco-geographic group of Indian emmer wheats. A set of 48 emmer wheat accessions from India including 28 from a local collection and 20 Indian accessions obtained from CIMMYT, Mexico, was assessed for genetic variability using 47 microsatellite (SSR) markers, distributed over all the 14 chromosomes. The number of alleles per locus ranged from 2 to 9, with an average of 3.87 alleles per locus. A total of 201 alleles were detected at 52 loci with average polymorphic information content of 0.35 per locus and a mean resolving power of 1. The pair-wise similarity coefficients calculated from binary data matrix based on presence or absence of alleles varied from 0.15 to 0.98, but was greater than 0.5 for most accessions, indicating a high level of similarity. A cluster analysis based on the similarity matrix identified nine distinct accessions and three clusters. All the recently developed commercial varieties were distinctly different from the clusters. Based on the analysis, it appears that Indian emmer wheats are not very diverse. Consequently, there is a need to increase the diversity within the Indian emmer wheat eco-geographic group, by introducing diversity from other eco-geographic groups, or even from other wheat species.     

Molecular diversity of Omani wheat revealed by microsatellites: I. Tetraploid landraces

Results of archaeological studies indicate a millennia-old cultivation history for wheat (Triticum spp.) in Oman. However, in spite of numerous collection surveys and efforts for phenotypic characterization of Omani wheat landraces, no attempts have been made using molecular tools to characterize this germplasm. To fill this gap, 29 microsatellite markers revealing 30 loci were used to study the genetic diversity of 38 tetraploid wheat landrace accessions comprising the species T. dicoccon, T. durum and T. aethiopicum. A total of 219 alleles were detected whereby the number of alleles per locus ranged from 2 to 16 with an average number of 7.1 alleles per locus. The highest number of alleles occurred in the B genome with on average 7.9 alleles per locus as compared to the A genome with 6.5 alleles per locus. Heterogeneity was detected for all microsatellites except for GWM 312, GWM 601 and GWM 192B with an average heterogeneity over all primers and lines of 14.4%. Approximately 10% of the accessions contained rare alleles with an average allele frequency <4%. Gene diversity across microsatellite loci ranged from 0.26 to 0.85. The pairwise comparison of genetic similarity ranged from 0.03 to 0.91 with an average of 0.2. Cluster analysis revealed a clear separation of the two species groups T. dicoccon versus T. durum and T. aethiopicum. Within the species clusters regional patterns of subclustering were observed. Overall, this study confirmed the existence of a surprisingly high amount of genetic diversity in Omani wheat landraces as already concluded from previous morphological analyses and showed that SSR markers can be used for landraces’ analysis and a more detailed diversity evaluation.     

Genetic variability in wild populations of <Emphasis Type="Italic">Prunus divaricata</Emphasis> Ledeb. in northern Iran evaluated by EST-SSR and genomic SSR marker analysis

A population genetic analysis based on eight genomic SSR markers and three EST-SSR (expressed sequence tags) markers developed in peach (Prunus persica (L.) Batsch) and Japanese plum (Prunus salicina Lindl.) was carried out in 12 wild populations of cherry plum (Prunus divaricata Ledeb.) sampled along the Iranian coast of the Caspian Sea. A total of 184 alleles (3–31 per locus) were detected with a mean value of 16.7 alleles per locus. None of the loci or populations showed deviation from Hardy–Weinberg equilibrium, and all markers proved to be unlinked. The mean values for the observed and the expected heterozygosity were 0.66 and 0.73, respectively. There was very little genetic differentiation among populations, as was indicated by low overall values of Wright’s F_ST (0.03) and Nei’s G_ST (0.08). An analysis of molecular variance (AMOVA) showed that 96.8% of the total variance was attributable to differences between individuals within populations. Genetic and geographic distances were nevertheless positively correlated, as evidenced by a Mantel test. The high level of genetic diversity and the apparent lack of genetic structure in wild P. divaricata may be attributed to frequent long distance gene flow through frugivorous birds and possibly humans, as has been documented for other Prunus species.     

Identification of 12 EST-derived SSR markers in Lumbricus rubellus

While many species of earthworms are globally distributed, very little is known about the genetic population dynamics of this diverse group. We present the characterization of novel simple sequence repeat (SSR) markers, including primer information, number of alleles, repeat motif, and approximate size ranges, to be used in population genetic analyses of the earthworm Lumbricus rubellus Hoffmeister 1843. Specifically, we designed and characterized 12 novel, polymorphic markers derived from published expressed sequence tags (EST) for amplification in L. rubellus. The mean number of alleles per locus was 6.25 ± 1.91, indicating these markers will be sufficiently polymorphic for population genetic studies of this species.     

大蒜种质遗传多样性的SSR分析

为了探索中国大蒜种质个体的SSR位点的分布情况,为品种鉴定、保存及遗传改良提供分子生物学依据,利用6对SSR引物对40个大蒜(Allium sativumL.)品种进行聚类分析、主成分分析及遗传多样性评价。共检测到21个多态性位点,平均每对引物可扩增出约3.5条多态性片段,多态性百分率为56.76%;SSR引物组合平均有效等位基因数、Nei基因多样度和Shannon信息指数分别为1.5551、0.3414和0.5188。聚类分析显示,6对SSR引物可把40份大蒜种质资源从0.59相似系数水平上3个类群。第一类群包含28份种质,在相似系数为0.73的水平上进一步又被分成了3个亚类;第二亚类仅包含2份种质;第三亚类包含10份种质,在0.68的相似系数水平上分成了2个亚类。主成分分析和UPGMA的结果基本一致。不同地理来源的大蒜种质的Shannon-Weaver多样性指数的变幅为0.0576~0.4179,说明大蒜种质遗传多样性丰富。本研究利用SSR分子标记技术较准确地解析大蒜不同材料间的亲缘关系及遗传多样性,为中国大蒜SSR分子标记提供基础资料。