Chromosome number of theOxalis tuberosa alliance (Oxalidaceae)

Twelve taxa of theOxalis tuberosa alliance were analysed and found to share the same basic chromosome number x = 8. The karyotypes are composed by small metacentric and submetacentric chromosomes. Different ploidy levels were found among the taxa: there were 9 diploids, 1 tetraploid, 1 hexaploid and 1 octoploid. The last ploidy level corresponds toO. tuberosa, the only tuber bearing taxon found so far in the alliance. Cytotaxonomic evidence and evolutionary considerations suggest to classify theO. tuberosa alliance in sect.Herrerea.     

Congruence between morphological and molecular markers inferred from the analysis of the intra-morphotype genetic diversity and the spatial structure of Oxalis tuberosa Mol.

Oxalis tuberosa is an important crop cultivated in the highest Andean zones. A germplasm collection is maintained ex situ by CIP, which has developed a morphological markers system to classify the accessions into morphotypes, i.e. groups of morphologically identical accessions. However, their genetic uniformity is currently unknown. The ISSR technique was used in two experiments to determine the relationships between both morphological and molecular markers systems. The intra-morphotype genetic diversity, the spatial structures of the diversity and the congruence between both markers systems were determined. In the first experience, 44 accessions representing five morphotypes, clearly distinct from each other, were analyzed. At the molecular level, the accessions exactly clustered according to their morphotypes. However, a genetic variability was observed inside each morphotype. In the second experiment, 34 accessions gradually differing from each other on morphological base were analyzed. The morphological clustering showed no geographical structure. On the opposite, the molecular analysis showed that the genetic structure was slightly related to the collection site. The correlation between both markers systems was weak but significant. The lack of perfect congruence between morphological and molecular data suggests that the morphological system may be useful for the morphotypes management but is not appropriate to study the genetic structure of the oca. The spatial structure of the genetic diversity can be related to the evolution of the species and the discordance between the morphological and molecular structures may result from similar selection pressures at different places leading to similar forms with a different genetic background.     

Genetic relationships among Mediterranean Pistacia species evaluated by RAPD and AFLP markers

Polymorphisms among Mediterranean basin Pistacia species and accessions within species were assessed by random amplified polymorphic DNA (RAPD) and amplified fragment length polymorphism (AFLP) analyses. Twenty-eight Pistacia accessions representing six species from geographically diverse locations in the Mediterranean area were analyzed. With RAPD, a total of 259 DNA fragments were amplified by 27 pre-selected primers, 254 were polymorphic fragments. AFLP analysis with 15 primer sets, produced 954 (93%) polymorphic bands out of a total of 1026. A Mantel test revealed an extremely high correlation (r=0.99) between similarity matrices generated from RAPD and AFLP data sets, indicating that similar results were obtained by the two techniques. Dendrograms constructed from the similarity matrices showed that Pistacia species could be clustered into two groups, one group containing all the #E5/E5#. lentiscus and the second group containing all other accessions. The latter group was divided into two subgroups, one consisting of #E5/E5#. palaestina and #E5/E5#. terebinthus; the other consisting of #E5/E5#. atlantica, #E5/E5#. khinjuk and #E5/E5#. vera. P. vera and P. khinjuk were highly similar, as were P. palaestina and P. terebinthus.     

Plant regeneration from oca (Oxalis tuberosa M.): the effect of explant type and culture media

Shoot regeneration has been obtained from internode and petiole sections of oca on a number of culture media supplemented with 3 mgl^-1 naphthaleneacetic acid and 3 mgl^-1 of either benzylaminopurine or zeatin, the latter being more effective. A greater percentage of sections from the 4th, 5th and 6th internodes (numbered from the apex) produced shoots than sections from older or younger internodes. Of five locally available genotypes based on tuber colour, a weak-growing type white showed the greatest morphogenetic potential. Out of eight nutrient media tested, a modified B₅ medium containing casein hydrolysate and L-glutamate supported the most consistent shoot regeneration. Shoot regeneration was preceded by the formation of a dark red smooth-surfaced callus. This was usually followed by the formation of a short tapering root. Swellings arose at the base of the root and developed into single or multiple shoots. These shoots were excised, rooted in basal Murashige & Skoog medium and transferred to the field.Abbreviations BA 6-benzylaminopurine - 2,4-D 2,4-dichlorophenoxyacetic acid - IAA indole-3-acetic acid - IBA indole-3-butyric acid - 2-iP (2-isopentenyl) adenine - Kn kinetin - NAA -naphthaleneacetic acid - Zn zeatin (mixed isomers)     

Phylogenetic analysis of the genus Pistacia by AFLP markers

This study addresses the phylogenetic relationships among Pistacia species by amplified fragment length polymorphisms (AFLPs). A total of 31 wild Pistacia accessions belonging to P. eurycarpa, P. khinjuk, P. atlantica, P. mutica, P. integerrima, P. terebinthus, P. palaestina, P. mexicana, P. lentiscus species and to a hybrid between P. atlantica and P. integerrima and four P. vera cultivars were the plant materials of this study. Six AFLP primer combinations generated a total of 275 fragments, an average of 45.8 bands per primer pair, of which 254 (92.4) were polymorphic. Unweighted pair group method based on arithmetic average (UPGMA) and principle coordinates (PCo) analysis were performed using both mean character difference and Jaccard similarity matrices. According to the results, P. vera, P. khinjuk, P. eurycarpa, P. atlantica, P. mutica, P. integerrima and P. atlantica x P. integerrima hybrids were in the first cluster. UPGMA analysis using mean character difference clustered P. palaestina, P. terebinthus, P. mexicana and P. lentiscus in the second cluster, whereas UPGMA analysis using Jaccard coefficient separated P. palaestina and P. terebinthus from P. lentiscus and P. mexicana. The P. khinjuk accessions had closer relationships to P. eurycarpa and P. atlantica than to P. vera which led to mis-identification of P. khinjuk samples as P. eurycarpa in this tudy. P. atlantica – P. mutica and P. terebinthus – P. palaestina pairs were the closest species, and therefore P. mutica were classified as P. atlantica, and P. palaestina were as P. terebinthus. The resulted dendrograms and the PCo plots in this study did not support evergreen versus deciduous sectional division of Pistacia species and suggested classifying P. terebinthus in a separate group rather than being in the first cluster. Further study is inevitable including more evergreen species and accessions to clarify the position of P. terebinthus and the evergreen species.     

Utility of AFLP markers for the assessment of molecular relationships in Ceratozamia Brongn. (Zamiaceae)

Abstract

The genus Ceratozamia has a distribution from Mexico to Central America. Molecular relationships were explored among Mexican Ceratozamia species using variable molecular markers, namely Amplified Fragment Length Polymorphisms (AFLP). Three AFLP primer-combinations generated 77 loci for a total of 1,684 fragments. Molecular variation was 75.72% among species and 24.28% within species, and a low correlation was present between genetic and geographical distances. Cluster analysis produced a phenogram in which two distinct clusters are clearly recognizable, one including C. alvarezii, C. sabatoi, C. zaragozae, C. kuesteriana, C. mexicana and C. robusta, and another one with C. zoquorum, C. miqueliana, C. latifolia, C. microstrobila, C. hildae and C. morettii. The AFLP proved to be suitable to study the relationships among species of Ceratozamia, and the results corroborated those from previous morphology-based studies.     

A high-resolution map of the vicinity of the R1 locus on chromosome V of potato based on RFLP and AFLP markers

The R1 allele confers on potato a race-specific resistance to Phytophthora infestans. The corresponding genetic locus maps on chromosome V in a region in which several other resistance genes are also located. As part of a strategy for cloning R1, a high-resolution genetic map was constructed for the segment of chromosome V that is bordered by the RFLP loci GP21 and GP179 and includes the R1 locus. Bulked segregant analysis and markers based on amplified fragment length polymorphisms (AFLP markers) were used to select molecular markers closely linked to R1. Twenty-nine of approximately 3200 informative AFLP loci displayed linkage to the R1 locus. Based on the genotypic analysis of 461 gametes, eight loci mapped within the GP21–GP179 interval. Two of those could not be seperated from R1 by recombination. For genotyping large numbers of plants with respect to the flanking markers GP21 and GP179 PCR based assays were also developed which allowed marker-assisted selection of plants with genotypes Rr and rr and of recombinant plants.     

Identification of AFLP markers in soybean linked to resistance to Meloidogyne javanica and conversion to Sequence Characterized Amplified Regions (SCARs)

Meloidogynejavanica is the most widely spread nematode pest on soybean in SouthAfrica. Only a few registered commercial South African cultivars are poor hostsof this nematode species and there is an urgent need for an efficient breedingprogramme for resistant cultivars of all maturity groups. However, breeding ishampered by laborious screening procedures for selection of poor host cultivarsand/or lines. The objective of this study was to develop an economically viablemolecular marker system for application in selection procedures. BothRestriction Fragment Length Polymorphism (RFLP) and Amplified Fragment LengthPolymorphism (AFLP) screening techniques identified markers linked togall-indexvariation in a segregating population of 60 F₂ progeny from a crossbetween a resistant cultivar (Gazelle) and a highly susceptible variety(Prima).A codominant RFLP marker( B212) was linked significantly to M.javanica resistance and explained 62% of the variation ingall-index.Seven AFLP markers were linked significantly to the resistance trait, of whichfour were linked in repulsion phase and three in coupling phase. All seven AFLPmarkers mapped to LG-F (Linkage Group F) on the public soybean molecular map.The major quantitative trait locus (QTL) for resistance mapped between markersE-ACC/M-CTC2(SOJA6) (linked in coupling phase), B212 and E-AAC/M-CAT1(SOJA7)(linked in repulsion phase). These two AFLP markers bracketing the majorresistance QTL were successfully converted to SCARs (Sequence CharacterizedAmplified Regions). Marker E-ACC/M-CTC2 was converted to a codominant SCARmarker SOJA6, which accounted for 41% of variation in gall-index in the mappingpopulation. Marker E-AAC/M-CAT1 was converted to a dominant SCAR marker (SOJA7)and explained 42% of gall-index variation in the mapping population. These twomarkers mapped approximately 3.8 cM and 2.4 cMrespectively from the resistance QTL. This study represents the first report ofthe development of PCR-based sequence specific markers linked to M.javanica resistance in soybean.     

AFLP analysis of phylogenetic relationships among myrmecophytic species of Macaranga (Euphorbiaceae) and their allies

The palaeotropic pioneer tree genus Macaranga Thouars (Euphorbiaceae) is characterized by various types of mutualistic interactions with specific ant partners (mainly Crematogaster spp.). About 30 species are obligate ant-plants (myrmecophytes). We used amplified fragment length polymorphism (AFLP) markers to assess phylogenetic relationships among 108 Macaranga specimens from 43 species, including all available taxa from the three sections known to contain myrmecophytes. Eight primer combinations produced 426 bands that were scored as presence/absence characters. Banding patterns were analyzed phenetically, cladistically and by principal coordinates analysis. Monophyly of section Pruinosae is clearly supported. There is also good evidence for a monophyletic section Pachystemon that includes the puncticulata group. The monophyly of section Winklerianae and relationships between the three sections remain ambiguous. Section Pachystemon is subdivided into four well-supported monophyletic subclades that presumably correspond to taxonomic entities.We acknowledge the support by the Deutsche Forschungsgemeinschaft (DFG Fi606/4-1, DFG We1830/2-1, 4-1 and 4-2), which in part was granted in the frame of the DFG-SPP 1127 Radiations: origins of biological diversity. Part of the plant material was kindly supplied by Dr. H. Feldhaar (University of Würzburg), Dr. U. Moog (University of Kassel) and Dr. F. Slik (Leiden University Branch, Nationaal Herbarium Nederland). We thank the University of Malaysia (Dr. Rosli b. Hashim) and Taman Taman Sabah (Datuk Lamri Ali; Dr. J. Nais) for permits and logistic support, and EPU for permission to conduct research in Malaysia.     

Genetic relationships of Aglaonema species and cultivars inferred from AFLP markers

BACKGROUND AND AIMS: Aglaonema is an important ornamental foliage plant genus, but genetic relationships among its species and cultivars have not been reported. This study analysed genetic relatedness of 54 cultivars derived from nine species using amplified fragment length polymorphism (AFLP) markers. METHODS: Initially, 48 EcoRI + 2/MseI + 3 primer set combinations were screened, from which six primer sets that showed clear scoreable and highly polymorphic fragments were selected and used for AFLP reactions. AFLP fragments were scored and entered into a binary data matrix as discrete variables. Jaccard's coefficient of similarity was calculated for all pair-wise comparisons among the 54 cultivars, and a dendrogram was constructed by the unweighted pair-group method using the arithmetic average (UPGMA). KEY RESULTS: The number of AFLP fragments generated per primer set ranged from 59 to 112 with fragment sizes varying from 50 to 565 bp. A total of 449 AFLP fragments was detected, of which 314 were polymorphic (70 %). All cultivars were clearly differentiated by their AFLP fingerprints. The 54 cultivars were divided into seven clusters; cultivars within each cluster generally share similar morphological characteristics. Cluster I contains 35 cultivars, most of them are interspecific hybrids developed mainly from A. commutatum, A. crispum or A. nitidum. However, Jaccard's similarity coefficients among these hybrids are 0.84 or higher, suggesting that these popular hybrid cultivars are genetically much closer than previously thought. This genetic similarity may imply that A. nitidum and A. crispum are likely progenitors of A. commutatum. CONCLUSIONS: Results of this study demonstrate the efficiency and ease of using AFLP markers for investigating genetic relationships of ornamental foliage plants, a group usually propagated vegetatively. The AFLP markers developed will help future Aglaonema cultivar identification, germplasm conservation and new cultivar development.     

Genetic characterization of Paspalum notatum accessions by AFLP markers

Paspalum notatum Flügge is a warm-season forage grass with sexual diploid and apomictic tetraploid races. Genetic improvement was achieved in out-breeding diploids. The acquisition of artificial sexual tetraploids has raised the possibility of performing crosses and plant improvement at the tetraploid level. The objective of our study was to obtain a genetic and cytoembryological characterization of a germplasm collection of P. notatum, including 31 accessions from seven countries of America and 11 experimentally obtained genotypes. Morphology of mature gametophytes was observed to assess the mode of reproduction of the accessions. A total of 1342 AFLP fragments were generated across the 42 genotypes and from two reference taxa: P. urvillei and P. procurrens. AFLP data were converted into a binary matrix and similarity relationships were established. The genetic distance among all the accessions showed a maximum value of 0.36. In addition, eleven AFLP fragments were observed exclusively in apomictic plants, which could be linked to genomic regions implicated in the control of apospory.     

琴叶风吹楠资源遗传多样性的AFLP分析

为研究濒危植物琴叶风吹楠(Horsfieldia pandurifolia)的遗传多样性,利用AFLP分子标记技术,对采自云南省西双版纳州、临沧市的8个居群共56份琴叶风吹楠样品进行了分析。结果表明,琴叶风吹楠在物种水平的多态性较高,多态性百分率为75.16%;在居群水平,平均多态性百分率为36.20%;AMOVA分析表明,琴叶风吹楠的遗传变异主要存在于居群内(75.45%),而居群间的变异仅为24.55%;mantel检验结果表明,地理距离和遗传距离存在不显著的正相关(r=0.119 7, P=0.321 0);基于遗传相似性系数,对8个居群进行了UPGMA聚类分析,在遗传相似性系数0.951处可将8个居群聚为3组。这些为琴叶风吹楠的保护和开发利用提供了理论依据,并提出了保护建议。     

Phylogenetic relationships in <Emphasis Type="Italic">Betula</Emphasis> (Betulaceae) based on AFLP markers

The genus Betula comprises various species in boreal and temperate climate zones of the Northern Hemisphere. The taxonomy of Betula is controversial and complicated by parallel evolution of morphological traits, polyploidization events, and extensive hybridization and introgression among species. Multilocus molecular data from AFLPs were used to provide phylogenetic information. A large number of polymorphic markers (321 variable bands) were produced in 107 Betula accessions from 23 species and 11 hybrids. The AFLP results were largely congruent with the results from previously examined nuclear DNA markers. Four distinct subgenera were identified within the genus Betula. These subgenera were partly in disagreement with the traditional (but disputed) division of the genus. In addition, the results indicated several groups of conspecific taxa. The majority of the species fell within subgenus Betula and shared a high degree of similarity with B. pendula. All hybrids were associated with this group, and the AFLP data contained signals on putative parents for some of the interspecific hybrids. Subgenus Chamaebetula and part of the Neurobetula species should be merged with Betula. The subgenera Betulenta, Betulaster, and the remaining part of Neurobetula are distinct and well supported. Although our results indicate that four major taxonomic groups can be recognized within the genus Betula, the relationship between them remains unclear. This may be due to the occurrence of hybridization and introgression, which would have a homogenizing effect on the relationships between species. Naturally occurring Betula species of hybrid origin may explain the low bootstrap values within the Betula clade. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Comparative study of the discriminating capacity of AFLP and ISTR markers for genetic analysis of<Emphasis Type="Italic">Agave fourcroydes</Emphasis>

Two DNA-based marker systems, amplified fragment legnth polymorphism (AFLP) and inverse sequence-tagged repeat (ISTR), were evaluated with respect to their discriminating capacity and efficiency in genetically analyzing henequen (Agave fourcroydes). Samples were taken from a mother plant, sucker-derived daughter plants, and bulbils. ISTR analysis produced more polymorphic markers than AFLP and had a better capacity for quantifying genetic diversity through an average number of alleles per locus, expected heterozygosis of polymorphic loci, expected heterozygosity, effective number of alleles per locus, and total number of effective alleles. ISTR also showed superior discriminatory capacity.     

Geographical diversity and genetic relationships among Cedrus species estimated by AFLP

Genetic diversity was described in 17 cedar populations covering the geographical range of the four species of the genus Cedrus. The study was conducted using amplified fragment length polymorphism (AFLP) on haploid tissues (megagametophytes). Eleven selective AFLP primer pairs generated a total of 107 polymorphic amplification products. Correspondence and genetic distance analyses indicated that Cedrus deodara constitutes a separate gene pool from the Mediterranean cedars. Within Mediterranean cedars, we distinguished two groups: the first one is made of Cedrus atlantica, while the second one is made of Cedrus libani and Cedrus brevifolia, these latter two species being genetically similar despite important divergence previously observed for morphological and physiological traits. The lowest intrapopulation variability was found in the two C. deodara populations analyzed. Surprisingly, C. brevifolia, the endemic taxon from the island of Cyprus that is found in small and fragmented populations, showed one of the highest levels of diversity. This unexpected pattern of diversity and differentiation observed for C. brevifolia suggests a recent divergence rather than a relictual, declining population. Patterns of diversity within- and among-populations were used to test divergence and fragmentation hypotheses and to draw conclusions for the conservation of Cedrus gene pools.     

Genetic diversity and phylogenetic relationships in alder,Alnus firma, revealed by AFLP

Molecular markers for alder,Alnus firma Sieb. et Zucc, have not been studied extensively. Here, we used amplified fragment length polymorphism (AFLP) to investigate genetic relationships among 15 natural populations. EcoRI-ACG + Msel-CTG combinations revealed the highest polymorphism (62.2%). A total of 171 DNA fragments were identified. On average, 58.1% of the AFLP markers that were generated using four primer pairs were polymorphic. Diversity was insignificant among the populations. The combination of a wind-pollinated, outcrossing breeding system along with large population sizes, and the ability to regenerate by stump sprouting may explain the high level of genetic diversity within this species. The majority (98%) of the genetic variance resided within populations. The average number of individuals that were exchanged between populations per generation was very high (N _em = 12.3). Gene dispersal in alder is apparently by seed dispersalvia water and human activity as well as through pollen. Five individuals per population were claded in the same cluster.     

Genetic diversity in recent elite faba bean lines using AFLP markers

Amplified fragment length polymorphism (AFLP) markers were used to study the genetic diversity among a large set (n = 79) of inbred lines of recent elite faba bean (Vicia faba L.) cultivars with Asian, European (Northern and Southern) and North African origin. The inbred lines were analyzed using eight selected AFLP primer combinations that produced 477 polymorphic fragments. Errors when scoring repeated lanes of one pre-amplification reaction on one gel were negligible, whereas errors when scoring lanes of two individuals of the same inbred line run on different gels were markedly higher. Scoring across gels should be backed by replicates and several appropriate check entries. Based on clustering with Jaccard's similarity coefficient and Principal Coordinate Analysis, only the Asian lines were distinct as a group, the other lines showed no marked further grouping. Nevertheless, several known pedigree relationships were verified. A priori grouping of inbred lines (geographic origin and seed size) and AFLP data corroborate available information on the history of spread and cultivation of faba bean in the studied regions. Based on the diversity observed, studies especially concerning the relationship between genetic similarity based on AFLP markers and hybrid performance within the European elite germplasm have been launched.Communicated by H.F. Linskens     

Analysis of genetic diversity in Glyptosternum maculatum (Sisoridae, Siluriformes) populations with AFLP markers

We determined the genetic diversity of geographic populations from three spawning grounds (Nyang River, Lhasa River, Shetongmon Reach of Yarlung Zangbo River) of Glyptosternum maculatum with amplified fragment length polymorphism (AFLP) markers. Five primer combinations detected 332 products, 51 of them (15.4%) were polymorphic in at least one population. The Shetongmon population was found to be the richest in genetic diversity as was indicated by the percentage of polymorphic loci and heterozygosity, followed by the Nyang population and the Lhasa population. The pair-wise genetic distance between populations were all very close, ranging from 0.0015 to 0.0042 with an average of 0.0024. The genetic distance was not proportional to the geographic distance. The analysis of molecular variance demonstrated that all variation occurred within populations. The average estimated fixation index (F _st) of three populations across all polymorphic loci was −0.0184, indicating the absence of genetic differences among the three sampled populations. The differentiation among populations was not significant, and population structure was weak. Our observations will help identify the genetic relationship among populations as the first approach to understand the genetic diversity of Glyptosternum maculatum.