Genetic differentiation in the olive complex (Olea europaea) revealed by RAPDs and RFLPs in the rRNA genes

We assessed the genetic differentiation of the Mediterranean olive from its wild relatives found in different geographic areas (Mediterranean, Asia, Africa) using eighty RAPDs revealed with eight primers. Variance analysis (AMOVA) enabled us to estimate the overall genetic differentiation parameters between wild populations. Oleasters from the Near East and Turkey were discriminated from the other Mediterranean populations. Olea laperrinei, O. maroccana and O. cerasiformis were the taxa the most related to the Mediterranean olive. In contrast, O. africana was shown to be the most genetically distant taxa from the Mediterranean olive. However, we characterised hybrid trees between these two taxa. Significant trends between genetic and geographic distances were met within the subspecies cuspidata and within the Mediterranean olive. A genetic diversity gradient was observed in both subspecies europaea and cuspidata. These results are in agreement with a mechanism of differentiation by distance in the O. europaea complex, but another non-exclusive mechanism could also be gene flow between differentiated taxa. Furthermore, we characterised the discriminating power of each RAPD to recognise the different taxa using intraclass correlation coefficients. Lastly, IGS-RFLPs enabled us to assess rDNA polymorphisms on a sub-sample of individuals. On the basis of these data, a low interspecifc differentiation was found. This suggests a recent genetic divergence between the different taxa of the O. europaea complex or the occurrence of gene flow during favourable periods or because human displacements. All the olive cultivars were genetically related to the oleaster populations supporting that Mediterranean is the olive domestication area.     

Analysis of Genetic Relationships among Turkish Cultivars and Breeding Lines of Lens culinatis Mestile Using RAPD Markers

Randomly Amplified Polymorphic DNA markers were used to determine the genetic relationships among Turkish lentil cultivars and breeding lines. Fourteen cultivars and thirteen breeding lines were evaluated to determine genetic variability using nine random 10-mer primers (among 45 primers). Forty-one reproducible bands were obtained, 54% of which were polymorphic. Genetic distances among cultivars and breeding lines were obtained from the simple matching coefficients (SM). The lowest genetic distance was observed between the cultivars of Ali Dayi and Kafkas with 5.0%, while ‘Seyran-96’ and ‘Ozbek’ had the highest genetic distance with 58.3%. An unweighted pair-group method with arithmetic averages (UPGMA) cluster analysis was performed on the distance matrix using Phylip software. The dendrogram clearly showed two distinct groups. The first group is composed of Akm 565 and Akm 563. The second group contains all the cultivars and remaining eleven breeding lines.     

Determination of F1 hybrid seed purity in pepper using PCR-based markers

We present the potential use of two kinds of PCR-based markers, RAPDs (Random Amplified Polymorphic DNA) and SPARs (Single Primer Amplification Reactions), as tools for hybrid seed purity determination. Five F₁ pepper hybrids (Capsicum annuum L.) and their parents were analyzed with 100 10-mer primers and 10 nucleotide repeat primers. We found at least one useful marker for testing the purity of all hybrids studied. Despite their dominant inheritance these markers could be an efficient implement in the process of quality testing of hybrid seeds. This revised version was published online in August 2006 with corrections to the Cover Date.     

Are the duplicates of perennial kale (Brassica oleracea L. var. ramosa DC.) true duplicates as determined by RAPD analysis?

A collection of vegetatively propagated perennial kales (Brassica oleracea L. var. ramosa DC., 64 accessions in total), predominantly from the Netherlands, was subjected to RAPD analysis in order to confirm or reject the presence of possible duplicates as indicated by isozyme and cytological data, as well as by morphological data described here. By employing 9 decamer primers, seven RAPD patterns could be attributed to almost all of the respective accessions, with up to 22 clones exhibiting identical features for the parameters examined. By these results, a high percentage of duplication is very strongly indicated in the collection, offering possibilities for a reduction in the number of clones to be propagated. The highest level of genetic variation was found in two kales from Portugal, which differed significantly from the other accessions.     

Genetic variation in radish (Raphanus sativus L.) germplasm from Pakistan using morphological traits and RAPDs

Genetic diversity of 30 radish (Raphanus sativus L.) accessions was investigated at the phenotypic level with morphological characters and at the DNA level using the random amplified polymorphic DNA (RAPD) technique. Thirty-six morpho-physiological traits were recorded from seedling stage to harvest. The 31 primers used generated 202 RAPD bands, of which 158 (78.2%) were polymorphic. Multivariate procedures were used to classify the germplasm on the basis of phenotypic traits and RAPD fragments. Dendrograms were generated for the Euclidean distance from the morphological data and the Nei's genetic distance from the RAPD markers. Phenotypically, all the accessions were classified into four major groups corresponding to the different forms of cultivated radish. The morphological diversity existing within each of these groups suggested that they should be discriminated into the three botanical convarieties, sativusT (large-rooted), caudatus (pod-type) and oleifer (oilseed-type). Clustering of the accessions did not show any pattern of association between the morphological characters and the collection sites. Instead, landrace groups were associated with their morphological similarities and horticultural uses. On the other hand, the intra-specific genetic relationships of several accessions based on RAPD analysis were related primarily to their collection sites rather than to their phenotypic affinities. The level of polymorphism exhibited by the various convarieties could be exploited in genetic mapping populations to tag economically important traits. These genotypes also could serve as a useful germplasm source for root, leaf, pod and seed. This preliminary study of traditional radish landraces from Pakistan provides useful information regarding their horticultural potential.     

青藏高原东缘中国沙棘的克隆多样性及克隆结构

应用随机扩增多态性DNA标记(RAPD markers)对青藏高原东缘中国沙棘的克隆结构、克隆多样性进行了初步的探讨。结果表明,1) 14条RAPD引物在8个中国沙棘居群共184个样本中平均形成55.75种条带,平均有15.13种条带在居群内表现出多态性,平均多态条带百分率为27.64%;鉴别出26种基因型,平均每基株形成3.4个分株;2)与应用DNA分子标记研究的其他克隆繁殖能力较强的植物相比,中国沙棘的克隆多样性水平偏低,Simpson’s多样性指数(D)平均值为0.85;Fager’s均匀度指数(E)平均值为0.87;3)克隆结构分析表明,中国沙棘每克隆内分株间的平均距离为1.75 m,克隆繁殖的生长型主要为游击型,并且在居群内存在以某一优势基株为主的克隆分布方式;4) 居群的定居时间、生境及群落结构等对中国沙棘的克隆多样性有一定影响。     

PCR detection of Fusarium oxysporum f.sp. gladioli race 1, causal agent of Gladiolus yellows disease, from infected corms

Fusarium oxysporum f.sp. gladioli (FOG) race 1 infects both large- and small-flowered Gladiolus cultivars. Race 2 isolates infect only small-flowered cultivars but can be present as epiphytes on large-flowered plants. When 160 arbitrary 10-mer oligonucleotide primers were tested on FOG by PCR to find RAPD markers specific for race 1, the RAPD primer G12 amplified two discriminating DNA fragments, AB (609 bp) and EF (1196 bp), in race 1 isolates only. Both fragments were cloned and sequenced. Two pairs of race 1-specific primers for multiplex PCR were designed. Tests of 112 F. oxysporum isolates by PCR showed that, in almost all cases, race 1 isolates of vegetative compatibility group 0340 could be distinguished with these primers. Seven putative race 1 isolates did not react in multiplex PCR; hybridization studies with labelled AB and EF DNA fragments showed that these isolates belong to separate groups. A bioassay was developed to detect corms that were latently infected with FOG race 1. Gladiolus corms were homogenized and incubated for 5 days at 28°C in a semiselective medium to induce growth of Fusarium . Cultivated mycelium was isolated and subjected to the developed multiplex PCR after standard DNA isolation or disruption by microwave treatment.     

Levels and distribution of allozyme and RAPD variation in populations of Elymus fibrosus (Schrenk) Tzvel. (Poaceae)

To study the magnitude and nature of genetic variation in E. fibrosus, the levels and distribution of allozyme and RAPD variations were investigated in populations collected from Finland and Russia. The results obtained from the allozyme and RAPD studies were compared to each other in 10 of the populations. The allozyme analysis showed that 6 of 12 presumed loci (50%) were polymorphic within the species, while the mean number of polymorphic loci within populations was 4.8%. The mean number of allele per locus for the species was 1.5 and 1.05 across the populations. Genetic diversity at the species level was low (H _es = 0.025), and the mean population genetic diversity was even lower (H _ep = 0.007). Both these values were much lower than the average for other Elymus and self-fertilising species. The largest proportion of the total allozyme diversity was found among, rather than within the populations (G _ST = 0.70). The allozyme genetic distances between the populations did not reflect geographic distances. Cluster and principal coordinates analyses revealed the same allozyme relationship patterns among the populations. A comparison of allozyme and RAPD variation in 10 of the populations showed differences in the amount of genetic variation. The RAPD analysis revealed higher levels of variation (A _p = 1.19, P _p = 20.3 and H _ep = 0.09) than the allozyme one) A _p = 1.06, P _p = 5.8 and H _ep = 0.008). For both markers, the largest proportion of the total gene diversity was found among the populations studied (G _st = 0.63 for RAPDs and G _st = 0.65 for allozyme). In contrast to the allozyme analysis, the RAPD based genetic distances did reflect geographic distances. The cluster and principal coordinates analyses showed different grouping of populations for each data set. There was a positive, but not significant, correlation (r = 0.41) between the genetic distance matrices resulting from these markers. Regional comparison revealed that the Finnish populations had a higher diversity than the Russian ones. Generally, this study indicates that E. fibrosus contains low genetic variation in its populations. The results are discussed in the context of conservation of the species.     

利用RAPD进行玉米自交系种质类群划分的研究

对31个玉米自交系进行了RAPDs分析，结果表明：31个玉米自交系可分为5大群，即旅群（IV－1组），La ,II群（IV－2A亚组），Reid群（IV－2B亚组），Lan,I群（IV－1组）和黄改群（IV－5和IV－6两组）和4个小群：I组的P138，II组的郑22，III组的综31和IV－4组的郑32和U8112，依据RAPDS的划分结果同依据系谱关系，配合力和杂种优势的划分结果基本吻合。     

Analysis of genes controlling photoperiod sensitivity in common bean using DNA markers

The genetic basis of the photoperiod response in common bean (Phaseolus vulgaris L.) was investigated using DNA markers and recombinant inbred populations. Two loci affecting photoperiod response were resolved, the previously defined primary locus (Ppd), at which the dominant allele confers sensitivity to photoperiod, and a second locus (herein defined as Hr), which influences the degree to which a plant responds to photoperiod. The DNA marker P5₁₆₀₀ cosegregated with the recessive allele, ppd, displaying a recombination frequency with the photoperiod locus of about 3%. A second marker, B303₆₀₀, was linked to the recessive allele at Hr and mapped approximately 13 cM from this locus. The markers demonstrated that in crosses involving Redkloud and several photoperiod sensitive lines, insensitivity to photoperiod is primarily controlled by ppd and that Hr does not significantly affect flowering time in ppd/ppd plants under the environmental conditions used. This revised version was published online in July 2006 with corrections to the Cover Date.