DNA polymorphisms and genetic relationship among populations of Acacia leucophloea 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.     

Quantitative determination of alpha-tocopherol in Arbutus unedo by TLC-densitometry and colorimetry.

A quantitative determination of alpha-tocopherol in Arbutus unedo leaves was established by TLC-densitometry and colorimetry. Data obtained by TLC-densitometry were compared with those obtained by colorimetry. Also, the alpha-tocopherol content in leaves collected at different times of the year was studied comparatively. The highest amount of alpha-tocopherol was found in the March collection.     

Water relations, gas exchange and growth of dominant and suppressed shoots of Arbutus unedo L

Basal shoots produced by Arbutus unedo L. after cutting at ground level vary in size and growth rate, and are classified accordingly as dominant or suppressed. The suppressed shoots eventually cease growth and die. In this study, we investigated the role of light and water in the competition among shoots of A. unedo. Dominant and suppressed shoots of A. unedo showed similar leaf water potentials and tissue water relations over the year, suggesting that water status is not responsible for the lack of flushing in suppressed shoots. Although suppressed shoots did not flush under low light, they showed many characteristics of shade-tolerant plants. Leaves of suppressed shoots had lower leaf conductance and light-saturated photosynthetic rate, and higher specific leaf area than leaves of dominant shoots. We conclude that light was the main resource determining competition among shoots and the death of suppressed shoots.     

Post-fire selective thinning of Arbutus unedo L. coppices keeps animal diversity unchanged: the case of ants

Context

In the Mediterranean area, different post-fire management strategies are used for coppices of resprouting species to promote a more regular forest structure, enhance plant growth, and reduce fire risk. However, the effects of these management treatments on forest-associated fauna are unknown, which in turn could be limiting their beneficial effects.

Aims

The aim of this work was to determine whether forest management of a recently burned area dominated by a vigorous resprouting tree species (Arbutus unedo L.) affects ant communities.

Methods

Ant communities, sampled using pitfall traps, were examined from unmanaged and selective thinning coppices of A. unedo. Ants are here used as bioindicators of ecosystem health and surrogates for other animal groups.

Results

Very limited effects of these post-fire management strategies on the structure and composition of ant communities were found. The lack of effects could be due to the reported small changes in physical conditions among treatments; or either, the most sensitive ant species to these post-fire management treatments might be the same ones affected by fire and, consequently, the ant species that would potentially be affected most were no longer in the study area.

Conclusion

The lack of any significant effects caused by these post-fire management practices on the associated fauna of A. unedo coppices points out the suitability of these treatments in these circumstances.     

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.

     

Monitoring genetic stability inQuercus serrata Thunb. somatic embryogenesis using RAPD markers

Genetic stability of propagules regeneratedvia somatic embryogenesis is of paramount importance for its application to clonal forestry. Random amplified polymorphic DNA (RAPD) markers were used to determine the genetic stability in somatic embryogenesis ofQuercus serrata Thunb. (Japanese white oak). Forty samples from an embryogenic line, consisting of regenerated plantlets, somatic embryos, and embryogenic calli, were examined using 54 decanucleotide primers. A total of 6520 clear reproducible bands obtained from these studies exhibited no aberration in RAPD banding pattern among the tested samples. Our results show that somaclonal variation is absent in our plant propagation system. The genetic stability is discussed in terms of the origin of somatic embryos.     

Relationships between morphological descriptors and RAPD markers for assessing genetic variability in Hippophae rhamnoides L.

Knowledge of genetic relatedness among accessions of germplasm is necessary for the development of breeding strategies to produce improved cultivars.The present investigation on Hippophae rhamnoides was carried out to assess its genetic variability in Himachal Pradesh,India,by employing morphological and RAPD markers.Different areas of Himachal Pradesh were surveyed and eight sites were finally selected.Twenty four genotypes were selected for further studies,i.e.,three genotypes from each site.On the basis of morphological studies,the genotypes of the Ropa site(Kinnaur)were considered elite genotypes.To assess the variability at the molecular level,RAPD patterns were studied by random primers.The total number of bands amplified was 607,out of which 487 bands were identified as polymorphic,depicting 80.23 per cent variability.Six unique bands were produced from three primers(OPA-05,OPA-10 and OPD-08)specific for five genotypes,including three genotypes of the Ropa site,Kinnaur District.     

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.     

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.

     

Fingerprinting and genetic variability in cork oak (Quercus suber L.) elite trees using ISSR and SSR markers

Quercus suber L., is a socially, economically and ecologically important forest species in rural areas of the Mediterranean basin. Fifty three elite-trees from nine stands of four provenance regions in the Community of Extremadura (Spain) were analysed with the aim to establish their DNA-fingerprinting and the genetic relationships among them. Two types of molecular markers, microsatellites and intermicrosatellites, were used for tree genotyping. Microsatellite markers could distinguish 94% of the trees. Observed and expected heterozygosities, and effective number of alleles were correlated with the polymorphism information content (PIC). Intermicrosatellite patterns were used to construct a dendrogram. They showed high levels of genetic diversity in these elite trees, without any clear relationship with provenance regions. Both types of markers detected a high level of intra-stand variability, which is common in Quercus species, probably due to its mating system, the low distance among stands and the small size of stands. Others factors that could affect this result, such as introgression between Q. suber L. and Q. ilex L., are also commented. The high level of genetic variability detected in these elite trees can be useful for improvement programs. Also the usefulness of SSR and ISSR markers to establish the DNA-fingerprinting of each tree could be focused to select clonal lines of commercial interest.     

天山樱桃野生居群遗传多样性SSR分析

为给天山樱桃种质资源的保护和开发利用提供参考,应用SSR标记技术对新疆天山樱桃4个居群44份种质的遗传多样性进行分析。结果表明:筛选的14对SSR引物共检测到191个位点,包含148个多态性位点。Nei’s基因多样性指数和Shannon信息指数分别为0.239 8和0.367 6,各居群遗传分化系数为0.193 5,基因流为2.084 3。天山樱桃遗传分化水平较低,各居群间基因交流频繁,遗传变异主要存在于居群内。由基于遗传距离的聚类结果可知,裕民县与大西沟居群遗传关系最近,与特克斯居群遗传距离较远,4个天山樱桃居群中大西沟居群遗传多样性最高。     

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.     

Mycorrhizal synthesis between Pisolithus arhizus and adult clones of Arbutus unedo in vitro and in nursery

Arbutoid mycorrhizae were synthesized between adult se-lected clones of Arbutus unedo L. and Pisolithus arhizus. Two micro-propagated clones were tested:AL1, in vitro and C1 (acclimatized plants) in nu...     

新疆野生山楂资源遗传多样性及亲缘关系的ISSR分析

为给新疆野生山楂资源的保护与利用提供理论依据和技术支持,采取新疆3种野生山楂共计63份材料,利用ISSR标记技术,对其遗传多样性和亲缘关系进行分析。结果表明,12条引物共扩增出233条带,其中多态性条带221条,多态性位点率为94.4%,平均每个引物获得19.42个扩增带。POPGENE1.32分析结果表明:3种野生山楂材料的多态性位点率、观测等位基因数、有效等位基因数、Nei’s基因多样性和Shannon信息指数,均为准噶尔山楂最高,阿尔泰山楂次之,红果山楂最低。3种新疆野生山楂进行两两比较,其Nei’s遗传相似度为0.862 2~0.904 4,平均值为0.890 2;遗传距离为0.100 5~0.148 3,平均值为0.1166。3种野生山楂中,准噶尔山楂存在较为丰富的遗传变异,其次是阿尔泰山楂,红果山楂的遗传变异较小。阿尔泰山楂和红果山楂的亲缘关系较近;准噶尔山楂和红果山楂间亲缘关系较远。     

Detection of genetic variation among seed and seedlings ofChamaecyparis obtusa using allozyme markers

The effects of nursery practices on genetic composition and structure were studied inChamaecyparis obtusa by analyzing seeds and one-, two-, and three-year-old seedlings. Enzyme polymorphisms of the6Pgd-2, G6pd, Got, Gk, Shd-2, Pod, Dia-1, andPgm loci were used. OnlyDia-1 indicated significantly different allelic frequencies between seeds and three-year-old seedlings. Most of the genetic diversity of the parental clones in this seed orchard could be transferred to the offsprings. Genetic diversity on the basis of an average expected heterozygosity did not differ between seeds and seedlings. A slight excess of homozygotes in seeds and a significant excess of heterozygotes in seedlings of different ages to the expected panmictic proportions were found. Most of the differences in genotypic distributions among the seed and seedling stages, probably resulted from viability selection favoring outcrosses, and selective removal of inbred offsprings including self-fertilized ones prior to their transplantation in the nursery. A part of this paper was orally presented at the 107th Annual Meeting of the Japanese Forestry Society (1996).     

Detection of genetic variation between Ophiostoma ulmi and the NAN and EAN races of O. novo-ulmi in Switzerland using RAPD markers

The structure of the Ophiostoma ulmi and Ophiostoma novo-ulmi population of Switzerland was analysed. 79 Swiss isolates were compared to reference strains from various countries. A dendrogram from RAPD profiles was produced. O. ulmi and O. novo-ulmi were clearly separated into two major clusters. O. novo-ulmi was further divided into the EAN and NAN races. This classification is consistent with subgroups by taxonomic parameters (growth rate, culture aspect, fertility barriers). The variation detected within the EAN and NAN races indicates a post-epidemic situation in Switzerland. A clonal population is present only in a restricted area in mid-eastern Switzerland, indicating a still active disease front.     

Analysis of genetic relationship in 12 species of Section Strobus with ISSR markers

Genetic relationship of 12 species of Section Strobus was analyzed with ISSR markers. 117 loci were detected with 12 ISSR primers. Percentage of polymorphic bands （PPB） varied from 5.93% to 19.92%. P. pumila had the highest levels of genetic differentiation and P. flexilis had lowest. Total genetic diversity （Hr） of 12 species in Section Strobus was 26.21%, of which intraspecific genetic diversity （Hs） was 7.66%, and interspecific genetic diversity （DST） was 18.55%, and the genetic variation in interspecies accounted for 70.78% of the total genetic diversity. According to the cluster results of genetic distance, the 12 species were classified into two groups. The first group included P. griffithii, P.armandi, P. fenzeliana, P. kwangtungensis, P. strobus, P. monticola and P. wangii. The second group included P. albicaulis, P pumila, P. flexilis, P. sibirica and P koraiensis.     

RAPD analysis of genetic relationships among Sphaeropsis sapinea isolates

Genetic relationships were studied among 23 isolates of Sphaeropsis sapinea collected from China, the United States, England, South Africa and Chile by using a random amplification of a polymorphic DNA (RAPD) analytical method. One hundred and 35 DNA fragments were amplified with 12 random primers by a polymerase chain reaction PCR technique and 96.3% were polymorphic. The genetic dendrogram based on RAPD analysis showed that the S. sapinea isolates could be divided into three types. Isolate CWS41 from Chile was separated genetically as the first type that was different from other isolates and isolates F2 and J2 from China comprised the second group. The third RAPD group accommodated other isolates including the B morphotype isolate CWS43 from the United States. __________ Translated from Journal of Nanjing Forestry University, 2006, 30(1): 13–16 [译自: 南京林业大学学报]     

DNA fingerprinting of Populus trichocarpa clones using RAPD markers

Nine trees from a single, natural population of black cottonwood (Populus trichocarpa Torr. et Gray) in Alaska were screened for randomly amplified polymorphic DNA (RAPD) markers with ten different 10-base random oligonucleotide primers in order to evaluate the use of RAPD analysis for distinguishing black cottonwood clones. Nine primers amplified the genomic DNA targets; two primers were able to differentiate all clones. Eight clones were distinguished among the nine tree samples assayed. Two trees showed identical banding patterns with all primers used; therefore it is suggested that these trees are from the same clone. The RAPD fingerprinting method is simple and powerful-one primer can distinguish different clones, while the use of multiple primers reduces fingerprint similarity and resolves discrepancies.     

A population genetic study in a scattered forest species, wild service tree [Sorbus torminalis (L.) Crantz], using RAPD markers

Wild service tree [Sorbus torminalis (L.) Crantz] is a forest tree widespread in Europe, characterized by a scattered distribution. Its hermaphroditic flowers are pollinated by insects, and outcrossing is the prominent mating system, also due to the presence of gametophytic self-incompatibility. Genetic diversity and differentiation of 22 populations from northwestern Italy were investigated by means of variation scored at 53 polymorphic RAPD (Random Amplified Polymorphic DNA) loci. Populations differed in genetic variation, with Shannon diversity index ranging from 0.166 to 0.469. According to Analysis of Molecular Variance (AMOVA), most of the genetic variation was found within populations (61.78%) with a significant proportion of variance attributable to genetic differences between regions (23.60%) and between populations (14.62%). Evidence for isolation by distance was found in the set of populations sampled. The effect of habitat fragmentation on genetic variation was also evaluated. The efficacy of RAPD markers in analysing genetic variation, and the contribution of the results in terms of the preservation of biodiversity are discussed.