Molecular characterization and genetic relationships among most common identified morphotypes of critically endangered rare Moroccan species Argania spinosa (Sapotaceae) using RAPD and SSR markers

? The objective of this work is the molecular characterization of most common identified morphotypes of critically endangered rare Moroccan species Argania spinosa.

? Eighteen RAPD markers and twenty SSR markers have been assayed in 38 argan tree accessions from the three most commonly identified morphotypes: oval, spherical and spindle fruit types.

? A total of 140 polymorphic RAPD bands were detected out of 146 bands. The number of presumed alleles revealed by the SSR analysis ranged from 1 to 5 alleles per locus with a total number of 32 alleles identified. Results demonstrated an extensive genetic variability within the tested argan accessions. RAPDs presented a high level of polymorphism and greater information content than SSRs.

? Our results could indicate that Vitellaria paradoxa is genetically closer to argan than Manilkara huberi. In addition, the correlation between the clustering based on RAPD and SSR markers were in general low. The observed clustering could be better explained according to geographic proximity than morphotype. For this reason the traditional morphological characterization of the argan accessions in morphotypes (according to fruit phenotype) seem not to be in correlation to the real genetic background (genotype) of this specie. The implications of these results in the creation of effective germplasm core collection in argan have been also discussed.

     

分子标记法和形态学特征对杏仁栽培种及野生种基因型的遗传关系构建的辨别

应用23个形态学特征,19个扩增片段长度多态性(AFLP)引物组合,80个随机扩增多态DNA(RAPD)引物和32个简单序列重复(SSR)引物对,比较三种分子标记法在29个杏仁栽培种和3个野生种遗传关系构建中的信息景和效率.根据预期杂合度的评价,与AFLPs和RAPDs相比,SSRs具有较高水平的多态性和较大的信息量.AFLPs预期朵合度值最低,但其辨别效率值最高,因为AFLPs能揭示每个反应中的大量条带,导致各种类型的多样性指数均较高.三种分子标记法对杏仁基因型的辨别效率均较高,只是SSRs无法辨别‘Monagha'和‘Sefied'杏仁基因型.三种分子标记法基因型相似性相关系数统计上显著,但SSR数据要低于RAPDs和AFLPs的值.尽管三种分子标记法树形图拓扑结构存在一些差异,但相似性水平均较高.SSRs、RAPDs和AFLPs的系统树图及其综合数据都能依据地理散布反映大多数栽培种的关系.AMOVA检测到每个地理组中栽培种和野生种的变异.辅助程序分析表明,实验所应用的标记物数量足以保证基因相似性估计的可靠性和标记法间的比较是有意义的.     

Genetic variation of Tunisian Myrtus communis L. (Myrtaceae) populations assessed by isozymes and RAPDs

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.     

A comparison of UP‐PCR and RAPD markers to study genetic diversity of Fusicladium effusum (G. Winter), cause of pecan scab

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.     

基于桤木属转录组测序的SSR分子标记的开发

[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。     

Genetic diversity in Tunisian Crataegus azarolus L. var. aronia L. populations assessed using RAPD markers

? The genetic diversity of nine wild Tunisian Crataegus azarolus var. aronia L. populations from different bioclimates was assessed using RAPD markers.

? Eight selected primers generated a total of 105 bands, 81 of which were polymorphic. Shannon’s index (H′) ranged from 0.222 to 0.278 according to a population with an average of 0.245. The genetic variation within the species (H _SP = 0.423) was relatively low. A high differentiation (G _ST = 0.421) among populations coupled with a low level of gene flow (N _m = 0.472) were observed. The analysis of molecular variance (AMOVA) revealed also significant differentiation among populations (Φ_ST = 0.371), even at a low scale space. The majority of variation occurred within populations (63.31%). The Mantel test performed on genetic (Φ_ST) and geographic distance matrices among population pairs did not reveal an isolation by distance.

? Interpretation of Neighbour-joining tree based on Nei’s and Li’s genetic distance among individuals showed distinct population groupings. The UPGMA dendrogram based on Φ_ST values revealed two population sub-clusters, each including populations from different bioclimates and/or geographic regions.

? The low level of genetic diversity and the high genetic structure of populations resulted from genetic drift caused both by habitat fragmentation and the low size of populations.

? The high differentiation among populations and the similar low level of diversity within populations suggest that in situ conservation should interest all populations. The ex situ conservation should be based on the collection of seeds rather within than among populations because of the maximum of variation was revealed within populations.

     

An analysis of the pattern of genetic variation in Vitellaria paradoxa using RAPD markers

Vitellaria paradoxa C.F.Gaertn. is one of the most economically and socially important tree species in the Sudano-Sahelian region. Little is known of the pattern of variation within its natural range. Eight populations covering most of the natural range from Senegal to Uganda were sampled and leaves of 118 individual trees were collected. An analysis of molecular diversity was carried out using random amplified polymorphic DNA (RAPD) markers. Fifteen random primers generated 67 polymorphic and 15 monomorphic RAPD loci ranging from size 1670 bp to 280 bp. Shannon's diversity index varied from Central Africa/Ndele (0.374) to Uganda/Amoya (0.350) but the differences between populations were smaller than the population standard errors. Correspondence analysis of unrooted neighbour-joining trees suggested that genetic distances between populations were correlated with geographic distances. This trend was confirmed by a Mantel test giving a coefficient of correlation between genetic and geographic distances of R = 0.88 (P = 0.0001). Result of AMOVA (analyses of molecular variance) showed that 14.8% (P = 0.002) of the RAPD variation was distributed among populations. Nested analysis of variance indicated that variance between the western and eastern groups of population represented 8.7% (P = 0.001) of the total variation and the variation amongst populations within group was 9.5% (P = 0.001). Eighty two percent of the variation was explained by variation amongst individuals within populations. The origin of genetic structure and level of diversity may be explained by the glacial refugia, the biological traits of Vitellaria paradoxa and by the impact of semi-domestication. Based on these results, sampling options of the natural populations are suggested for in or ex situ conservation. For the development of Vitellaria paradoxa breeding population, the sampling should consist of many individual trees selected within a few populations to capture a large proportion of variation.This revised version was published online in November 2005 with corrections to the Cover Date.     

木荷1代育种群体遗传多样性分析

木荷为我国亚热带地区主要的珍贵优质阔叶用材树种和生态防护树种.利用筛选的14对多态性强的SSR引物,对木荷1代育种群体中来自15个产地133个亲本进行遗传多样性分析,为其优异种质资源保存、杂交亲本选配及新种质创制提供科学依据.结果表明:14对引物共扩增86个位点,每对引物检测到的等位基因数(Na)变异范围为2～11个,平均等位基因数(Na)为6.14个,平均有效等位基因数(Ne)为3.23个,平均观察杂合度(Ho)为0.572 0,平均Shannon信息指数(I)和平均Nei's基因多样性指数(Nei)分别为1.224 7和0.599 0,说明木荷1代育种群体具有丰富的遗传多样性,其中,福建建瓯产地遗传多样性最高,浙江遂昌产地遗传多样性最低.木荷1代育种群体中成对亲本间遗传距离为0.023 3～1.633 8,平均为0.6067.不同产地遗传多样性与纬度呈显著的负相关关系(r=-0.5162,p=0.048 9).通过UPGMA聚类,可将133个育种亲本分成3个类群,其中,类群3又分为4个亚类群.木荷亲本选配时,应充分考虑优树的产地来源.     

Genetic variation of isolated Picea balfouriana populations from the southeast of the Qinghai-Tibet Plateau

? The objective of this work is to estimate the level of genetic variation and pattern of genetic structure of isolated Picea balfouriana populations.

? Nine SSR markers and six STS markers were assayed in ten natural populations of P. balfouriana, which is a regionally distributed conifer species in the southeast of the Qinghai-Tibet Plateau.

? Expected heterozygosity ranged from 0.592 to 0.710 based on SSRs, and from 0.489 to 0.635 based on STS markers. The SSR and STS markers revealed that 11% and 12% of variation, respectively, was present among populations. However, the SSRs showed no deviation from the Hardy-Weinberg equilibrium (F _IS = ?0.030), unlike the STS markers (F _IS = 0.249). In addition, assignment methods showed that individuals from the same sampling site usually cluster together.

? Our results indicated that the distribution of genetic variation and population genetic structure of P. balfouriana may be attributed to habitat fragmentation and heterogeneous environments caused by the complex topographic environment in the Qinghai-Tibet Plateau. The population genetic information obtained in our study will benefit the development and utilization of appropriate conservation and breeding strategies for P. balfouriana.

     

杜仲基因组微卫星特征及SSR标记开发

为全面解读杜仲的遗传背景,本研究在基因组测序(数据未公布)的基础上,通过MISA软件搜索杜仲基因组(26 947/854 758 160 bp)中的完整型(1～7核苷酸重复)及复合型SSR序列,共查找出25 694个Scaffolds含有488592个SSR位点,占总Scaffolds的95.3％.从SSR位点分布密度上讲,平均每1 749 bp出现1个微卫星,其中单核苷酸重复单元的SSR含量最多,约占总数的54.34％,其次为二核苷酸(20.47％),而复合模式、三核苷酸、四核苷酸、五核苷酸、六核苷酸和七核苷酸重复分别占20.29％、23.89％、0.77％、0.13％、0.10％和0.01％,并发现SSR中均以含A、T的重复类型占主导地位.根据SSR位点设计并合成引物290对,162对SSR引物扩增出清晰的目的条带,其中16对引物多态性高、稳定性好,在8份杜仲资源中共检测到84个等位基因,平均每个SSR位点检测到5.25个等位基因.本研究对于进一步利用SSR分子标记分析杜仲遗传多样性、遗传图谱构建、杜仲雌雄株早期鉴定等具有较高的应用价值.     

Isozyme and RAPD polymorphisms in Heterobasidion annosum in Italy

Isozyme and random amplified polymorphic DNA (RAPD) polymorphisms were used to study variability in a group of 41 isolates from the Italian population of Heterobasidion annosum. The isolates belonged to the intersterility groups P and S, and particularly to the group that is most widely distributed in Italy, group F. Isozyme analysis was effective in identifying the three intersterility groups and revealed a high degree of genetic divergence within the P group isolates; the mannose phosphate isomerase (MPI-2) locus was diagnostic in the attribution of isolates to the more correlated F and S groups. RAPDs were detected following amplification by the polymerase chain reaction (PCR). 74 RAPD fragments, obtained through amplifications with eight primers, were scored. Isolates from the 3 intersterility groups were clearly divergent based on analysis of RAPD markers. However, a similarity index calculated for the isolates within the F population indicated a high uniformity of the isolates collected throughout the Italian peninsula.     

Genetic analysis and conservation of endangered medicinal tree species <Emphasis Type="Italic">Taxus wallichiana</Emphasis> in the Himalayan region

Taxus wallichiana is one of the most important medicinal tree species of the Himalayan region. Leaf and bark of the species yield an important drug called taxol, which is used for treatment of many types of cancer. There is a serious threat to the existence of the species due to over exploitation in its native habitat. Adequate information on the nature and the extent of genetic diversity in this important species is required for developing suitable strategy for its conservation. Random amplified polymorphic DNA (RAPD) and amplified fragment length polymorphism (AFLP) were used to assess genetic variation in nine natural populations of T. wallichiana from western part of the Himalayan ranges. Both the markers revealed low genetic diversity in these populations. Average heterozygosity for AFLP and RAPD were 0.3715 and 0.3072, respectively. Φ_ST values derived from molecular variance were 0.0855 and 0.1005 for AFLP and RAPD, respectively, whereas the corresponding G_ST values were 0.1796 and 0.2140. Most part of the genetic variation was present within the populations. However, between population variation was low but statistically significant, which suggested that the sampled populations might not constitute a single panmictic population. Cluster analysis and Mantel’s correlation revealed that genetic differentiation broadly followed geographic distribution of the populations. T. wallichiana thus urgently needs to be conserved using both in situ and ex situ conservation approaches.     

板栗主要栽培品种的分子鉴别

应用ＲＡＰＤ分子标记手段，研究板栗品种的遗传多样性，建立了板栗品种ＲＡＰＤ标记的标准程度，以及板栗品种种的ＤＮＡ指纹数据库，并为板栗品种鉴别提供了准确、可靠的标准方法，４６个板栗品种的样品的ＤＮＡ，用１６个引物进行扩增反应的位点总数为１１９个，产生６９个多态位点，建立了４６个板栗品种的ＤＮＡ指纹数据库，并分析出这些板栗品种分子鉴别的最优化引物组合。对特定的引物组合，计算品种间的遗传距离矩阵，从而确定引物组合对这些品种鉴别的特异性。     

Assessment of genetic diversity in <Emphasis Type="Italic">Dalbergia sissoo</Emphasis> clones through RAPD profiling

We studied the genetic polymorphism among 29 clones of shisham (Dalbergia sissoo Roxb) belonging to different geographic regions using random amplified polymorphic DNA (RAPD) markers. Out of 30 primers used, only 20 primers generated polymorphism in amplified product. In total 232 bands were amplified with 20 primers, of which 192 (82%) were polymorphic with an average of 9.6 bands/primer. The resolving power (Rp) ranged from 2.14 (Primer 5) to 11.93 (Primer 4). Primer 4 and Primer 3 possessed high Rp value. Polymorphism information content (PIC) ranged from 0.15 (Primer 5) to 0.37 (Primer 4). Primer 4 amplified total 18 bands in 29 genotypes with PIC value of 0.37 hence; this set of primer was most informative. The similarity coefficient analysis revealed two clusters. The first cluster comprised of only 10 clones and the second major cluster comprised of 19 clones. The genetic similarity among 29 clones ranged from 25.86% (clone 10 and 235) to 100% (clone 19 and 59), suggesting a wide genetic base in shisham clones.     

Assessment of diversity among populations of Rauvolfia serpentina Benth. Ex. Kurtz. from Southern Western Ghats of India,based on chemical profiling,horticultural traits and RAPD analysis

Genetic, morphological and chemical variations of ten natural populations of Rauvolfia serpentina Benth. Ex. Kurtz. from Southern Western Ghats of India were assessed using RAPD markers reserpine content and morphological traits. An estimate of genetic diversity and differentiation between genotypes of breeding germplasm is of key importance for its improvement. Populations were collected from different geographical regions. Data obtained through three different methods were compared and the correlation among them was estimated. Statistical analysis showed significant differences for all horticultural characteristics among the accessions suggesting that selection for relevant characteristics could be possible. Variation in the content of Reserpine ranges from 0.192 g/100 g (population from Tusharagiri) to 1.312 g/100 g (population from Aryankavu). A high diversity within population and high genetic differentiation among them based on RAPDs were revealed caused both by habitat fragmentation of the low size of most populations and the low level of gene flow among them. The UPGMA dendrogram and PCA analysis based on reserpine content yielded higher separation among populations indicated specific adaptation of populations into clusters each of them including populations closed to their geographical origin. Genetic, chemical and morphological data were correlated based on Mantel test. Given the high differentiation among populations conservation strategies should take into account genetic diversity and chemical variation levels in relation to bioclimatic and geographic location of populations. Our results also indicate that RAPD approach along with horticultural analysis seemed to be best suited for assessing with high accuracy the genetic relationships among distinct R. serpentina accessions.     

湿加松亲本间遗传距离与杂种优势的相关性分析

利用SSR标记对17个湿加松亲本无性系进行遗传多样性分析,进而分析亲本遗传距离与子代杂种优势的相关性。结果表明:14个微卫星标记在湿加松亲本群体中均呈现高度多态,共检测到57个等位基因,多态位点百分率为87.72%,平均杂合度为0.144 4 0.884 1,以SSR标记遗传距离聚类,将参试亲本材料划分为2大类群,可以用于湿加松亲本遗传多样性的评价。树高、胸径、材积的杂种优势与亲本遗传距离相关性达显著或极显著水平,相关系数分别为0.542 0、0.641 2、0.639 3,决定系数分别为0.293 8、0.411 0、0.408 7。分子标记遗传距离与树高、胸径、材积的杂种优势相关程度较高,利用SSR标记预测湿加松杂种优势是可行的,为湿加松良种选育及亲本选配提供参考。     

Adaptive genetic diversity and population structure of the “algarrobo” [<Emphasis Type="Italic">Prosopis chilensis</Emphasis> (Molina) Stuntz] analysed by RAPD and isozyme markers

The “algarrobo” [Prosopis chilensis (Molina) Stuntz] is a tree species that represents an important natural resource in arid and semi-arid regions of Argentina. In this paper, we analysed and compared the variability of 46 RAPD (Random Amplified Polymorphic DNA) loci with previous estimates obtained from 12 isozyme markers in nine Argentinean populations of P. chilensis representative of the whole range of this species in Argentina. We evaluated the population structure and the existence of genetic variants associated with environmental variables. Expected heterozygosity (H _e) estimated from RAPD varied significantly among populations and regions. Hierarchical analysis of genetic variability (AMOVA) showed that most (88.1%) of the total diversity occurs within populations, the component among populations within regions (9.3%) was intermediate, while the between-region component was the lowest (2.6%). All three variance components were highly significant. The MDS plot from pair-wise Φ _ST matrix was consistent with the highly significant among-region differentiation indicated by the AMOVA. All 12 variable isozyme loci and 26 out of 46 RAPD loci showed significant or highly significant association with at least one geographic/climatic variable according to the stepwise multiple regression analysis. These results imply that the genetic differentiation among populations is better explained by environmental or biogeographical grounds than by geographical distances, suggesting gametic disequilibrium with loci responsible for the adaptation to particular environmental conditions. The information from RAPD markers would provide a relevant criterion to preserve genetic diversity in programmes for conservation and rationale use of this species.     

RAPD标记在桉属种间杂交一代的分离方式研究

以 1个尾叶桉×细叶桉全同胞家系的 2个亲本和 2 12个子代为材料 ,利用 RAPD分子标记技术进行了 RAPD标记在桉树中的分离方式研究。结果表明 :7个随机引物共扩增出 4 0个标记 ,标记在 F1代的分离方式可以分为两类 :符合孟德尔方式和偏离孟德尔方式。符合孟德尔方式的标记包括 :亲本均有而在子代中不分离的 9个 (在这类位点上代表的杂交组合为 AA× AA、AA× Aa或 Aa× AA) ,亲本间呈多态性而在子代中不分离的 7个 (aa× AA或 AA× aa) ,亲本间均有而在子代中 3∶ 1分离的 2个 (Aa× Aa) ,亲本间呈多态性且在子代中 1∶ 1分离的 9个 (Aa× aa或 aa×Aa)。偏分离的标记包括 :亲本间呈多态性而在子代中偏离 1∶ 1分离的 12个 ,两亲本均有而在子代中偏离 3∶ 1分离的 1个。亲本间呈多态性且在子代中 1∶ 1分离的位点在拟测交策略中可以用于遗传连锁图谱构建 ,这为利用 RAPD标记构建桉树遗传连锁图谱提供了理论支持。     

Genetic diversity in natural populations of Gmelina arborea: implications for breeding and conservation

Gmelina arborea is a valuable plantation tree species that is native to South and Southeast Asia. In this study, 534 samples representing 19 natural populations in India, China, Thailand and Myanmar were analyzed with 10 polymorphic microsatellite markers. The genetic diversity analysis revealed highly polymorphic loci (N_a?=?16.4), a good level of genetic diversity (H_o?=?0.56; H_e?=?0.83) and the deficiency of heterozygotes in G. arborea populations evidenced by positive fixation index and deviation from Hardy?CWeinberg Equilibrium in all loci and most populations. The Analysis of Molecular Variance attributed 21, 10 and 69% of total genetic diversity to among-region, among-population (within region) and within-population variation. Unweighted Pair Group Method with Arithmetic Mean dendrogram and Principle Coordinate Analysis revealed three separate clusters composed of China, India and Thailand/Myanmar that were consistent with geographical distance and the presence of natural barriers to gene flow. Populations from within India grouped together genetically consistent with geographical locations, with the exception of the Nowgong population (eastern India), that might have originated from the Kasa area (western India) with which it has high genetic similarity. Understanding genetic diversity and structure of G. arborea populations serve as an important reference for tree breeding programs and conservation strategy. Breeding populations of G. arborea should include selections from each of the major geographic regions to maximize genetic diversity and heterosis. Vegetative propagated clones of elite trees can be used for plantation to address the issue of high level of segregation among seed derived plants.     

DNA polymorphisms and genetic relationship among populations of <Emphasis Type="Italic">Acacia leucophloea</Emphasis> using RAPD markers

RAPD (randomly amplified polymorphic DNA) markers were employed to characterize polymorphisms among 5 provenances of Acacia leucophloea and to detect genetic relatedness of the species with 6 other acacias (A. holosericea, A. auriculiformis, A. mangium, A. dealbata, A. ferruginea, and A. nilotica) widely grown in India. Of 194 markers scored for the provenances, 29.38% exhibited polymorphism. Also, 326 markers were generated among 7 species of Acacia, accounting for 55.82% of the polymorphisms. The fifteen 10-mer primers employed were capable of producing 1–8 polymorphic bands for the provenances, and 6–17 for all seven species of Acacia. The genetic similarity coefficient based on Jaccard’s coefficient revealed that provenances Thirumangalam and Dharmapuri were closely related. The dendrogram based on a sequential agglomerative hierarchical non-overlapping (SAHN) clustering analysis grouped 4 provenances of A. leucophloea (Dharapuram, Thirumangalam, Pudukottai and Dharmapuri) into one cluster and the other provenance, Sendurai, into a separate cluster. The genetic similarity matrix for 7 Acacia species showed that A. nilotica and A. dealbata were distantly related, while A. holosericea and A. ferruginea were very closely related. Cluster analysis grouped the species of Acacias into 3 major groups of which A. dealbata alone formed a separate group. The RAPD markers generated 36 provenance-specific markers and 162 species-specific markers that could have strong applications for species identification and tree breeding programs for A. leucophloea and for other Acacia species included in this study.