Phylogenetic relationships among Triticum L. and Aegilops L. species as genome progenitors of bread wheat based on sequence diversity in trnT-F region of chloroplast DNA

Cultivated wheat, (Triticum aestivum L.), is one of the most important food crops in the world. The Aegilops L. genus is frequently utilized by plant breeders for improving the current wheat cultivars due to their close relationships. Therefore, understanding the phylogenetic relationships among the species of these genera is not only valuable for plant taxonomy, but also for plant breeding efforts. The presented phylogenetic analysis was based on the sequences of trnT-F chloroplast DNA containing three non-coding sub-regions. Twelve genotypes belonging to four species of Triticum L. genus and twenty-four genotypes belonging to eight species of Aegilops genus were used in the current study. The results postulated a close genetic relationship between diploid Aegilops species containing the BB genome and polyploid Triticum species. With the exception of Aegilops cylindrica Host (CCDD), all other Aegilops species having the CC genome were alienated from Aegilops speltoides Tausch (BB) and clustered together. These two clusters joined by a third cluster including the AA genome containing diploid Triticum species.     

Comparison of the efficiency of A–PAGE and SDS–PAGE,ISSRs and RAPDs in resolving genetic relationships among <Emphasis Type="Italic">Triticum</Emphasis> and <Emphasis Type="Italic">Aegilops</Emphasis> species

Species that belong to the genus Triticum L. and the genetically related Aegilops L. genus are important genetic and economic resources because they have an evolutionary relationship with the two main agricultural crops T. aestivum (bread wheat) and T. durum (durum wheat). Therefore, it is important to understand the genetic relationships among the cultivated wheat species and their wild relatives. The latter have a great role in the improvement of cultivated wheat. Molecular markers are the best choice and most reliable means to study these relationships accurately. In this study, we compared the efficiency of the biochemical methods A–PAGE and SDS–PAGE on seed storage proteins and the molecular methods RAPDs and ISSRs to explore the genetic relationships among seven species of Triticum and 20 Aegilops species. Three phylogenetic trees obtained in this study were compared with available classifications and phylogenetic trees constructed earlier for these species. It was noted that the tree based on ISSRs data was the most congruent with those classification and trees. This may be attributed to the fact that ISSRs is more specific, and therefore more reliable. This study is the first to study genetic relationships among all species studied here using biochemical and molecular techniques.     

Identification of <Emphasis Type="Italic">Aegilops</Emphasis> L. species and <Emphasis Type="Italic">Triticum aestivum</Emphasis> L. based on chloroplast DNA

The genus Aegilops L. is a very important genetic resource for the breeding of bread wheat Triticum aestivum. Therefore, an accurate and easy identification of Aegilops species is required. Traditionally, identification of Aegilops species has relied heavily on morphological characters. These characters, however, are either not variable enough among Aegilops species or too plastic to be used for identification at the species level. Molecular markers that are more stable within species, therefore, could be the alternative strategy towards an accurate identification. Since the chloroplast DNA has a lower level of evolution compared to the nuclear genome, an attempt was made in this study to investigate polymorphism in the chloroplast DNA among 21 Aegilops species (including Ae. mutica that is now known as Amblyopyrum muticum) and between the latter and T. aestivum to generate markers for the diagnosis of all targeted species. Cleaved amplified polymorphic sequence (CAPS) applied on 22 coding and non-coding chloroplast regions using 80 endonucleases and sequencing of two of those regions revealed little polymorphism between T. aestivum and the various Aegilops species examined and to a less extent was the variation among Aegilops species. Polymorphism observed among species analysed allowed the discrimination of T. aestivum and 12 Aegilops species.     

Morphological and isozyme variation in genebank accessionsof Aegilops umbellulata Zhuk., a wild relative of wheat

Morphological variation and genetic variation at 15 enzyme lociwere studied in genebank accessions of Aegilopsumbellulata Zhuk., the diploid genome donor to all thepolyploid species of the section Aegilops ofAegilops. Accessions from the Greek Islands hadshorter spikes with smaller number of spikelets and smaller number ofawns on the empty glume. The number of alleles per locus (A= 2.01) and the proportion of polymorphic loci (P= 0.627) were similar to those of the other species ofAegilops so far reported. Genetic distancescalculated from isozyme variations among five regions revealed thataccessions from the Greek Islands are more distantly related to theother four continental regions, Iran and Iraq, Southeast Turkey,Central Turkey and South and West Turkey. The present resultsindicated the importance of collection covering the whole range ofgeographical distribution to capture the genetic variation present inAe. umbellulata.     

Phylogenetic relationships of Cajanus cajan (L.) Millsp. (pigeonpea) and its wild relatives based on seed protein profiles

Total seed storage protein of 9 accessions of cultivated C. cajan and 10 wild Cajanus species was reported and compared by sodium dodecyl sulphate polyacrylamide gel electrophoresis. A considerable variation was detected among the protein profiles of different accessions of C. cajan while those of wild species were very specific and distinctly different from each other. Relative similarities between various taxa were estimated by Jaccard's similarity index and cluster analysis was performed to produce a UPGMA dendrogram. The clustering of 10 wild species and C. cajan more or less agrees with their sectional classification and available data based on morphological characteristics, crossability, genome pairing in hybrids and nuclear RFLPs. The species closest to C. cajan is C. cajanifolia although the accessions of C. cajan also share some bands present in the profiles of C. scarabaeoides, C. goensis, C. lineatus, C. acutifolius and C. volubilis. This points towards polyphyletic origin of the cultigen which has been discussed in this paper.     

Genetic diversity and species delimitation in the cultivated and wild Guinea yams (Dioscorea spp.) from Southwest Ethiopia as determined by AFLP (amplified fragment length polymorphism) markers

Yams (Dioscorea spp.) rank as the fourth most important root and tuber crop after potatoes, cassava and sweet potatoes. They are an economic crop in most of the tropics especially in West Africa, which produces over 95 % of the world output. Despite their cultural and economic importance there is taxonomic confusion regarding Guinea yams. The currently used classification scheme, which relies on vegetative and inflorescence characters, does not consistently delimit species boundaries between members of Guinea yams (D. cayenensis Lam.–D. rotundata Poir. complex), their wild relatives (D. abyssinica Kunth and D. praehensilis Benth.,) and D. sagittifolia Pax. Establishing the taxonomic identity of the germplasm and understanding the systematic relationships among crops is vital to the management of genetic resources and the utilization of accessions. In this study, amplified fragment length polymorphism (AFLP) genetic fingerprinting was used to evaluate and characterize 43 individual plants, belonging to different populations of wild and cultivated Guinea yams. The three primer combinations used in the AFLP analyses generated 158 scorable bands, with an overall polymorphism of 78 %. Ordination and cluster analyses of AFLP data failed to produce any clear species boundary between either the Guinea yam accessions or between them and their wild relatives. The average genetic similarity between the study individuals of Guinea yams and their wild relatives ranged from 60 to 100 %. The first, second and third principal coordinates axes cumulatively account for 77.45 % of the total variation. AFLP analyses also revealed a higher genetic divergence among cultivated Guinea yam accessions of the Sheko cultivars. Ordination and cluster analysis using UPGMA revealed no clear species boundaries between members of the complex. Thus, the taxonomy of these “species” needs to be revisited using other markers.     

Diversity analysis of <Emphasis Type="Italic">Aegilops</Emphasis> species from Morocco using RAPD markers

The diversity of 51 representative populations of the 5 Aegilops species from Moroccan collection was analyzed using 22 RAPD primers. We investigated the associations among these 5 Aegilops species (A. geniculata Roth (UUMM), A. triuncialis L. (UUCC), A. ventricosa Tausch (DDNN), A. peregrina (Hackel) Maire et Weiller (UUMM) and A. neglecta Req. ex Bert. subsp. recta (Zhuk.) K. Hammer (UUMMNN)); some diploid species considered as their ancestors; accessions of some neighboring countries and also accessions of Triticums. A total of 650 polymorphic RAPD fragments were amplified. A dendrogram was constructed using the un-weighed pair group method arithmetic average (UPGMA) and Jaccard`s similarity coefficient. The UPGMA clustering showed a regrouping to the level species with high level of the structuration of the diversity at A. geniculata. We confirm as reported by other authors, the proximity of N genome to U genome and C genome to M genome and also the difference between the genomes M and N. Thus, the phylogeny between the species and the different genomes were retracted.     

A chemosystematic study of the flavonoids of Vigna

Summary Flavonoid chemical markers together with other biochemical markers and/or morphological data can provide useful characters for defining species in Vigna genus. In this paper flavonid HPLC fingerprints have been utilized to assess taxonomic relationships amongst species and accessions of Vigna. Within the taxa analysed there is evidence of both infra- and interspecific chemical variations. In some species chromatographic data support evidence for the existence of different flavonoid chemotypes, which may reflect differences in geographic origin. As far as interspecific relationships are concerned, species belonging to sections Vigna, Plectotropis and Ceratotropis do not show flavonoid glycosides in common with cultivated lines of Vigna. By contrast, some relationships have been found between cultivated lines and wild species of section Catiang. Kaempferol-3-rutinoside and an unidentified kaempferol-glycoside were the only flavonoids detected in the three subgenera analysed. Finally, a greater variability in flavonoid aglycone class and glycosylation pattern has been observed in cultivars of V. unguiculata (L.) Walp. compared to the wild species. This observation may confirm that cultivation and/or domestication may cause or increase species diversification.     

Collecting spanish populations of the genusAegilops L.

Summary Several expeditions were made to the greater part of Peninsular Spain and the Balearic Islands, in order to collect samples from populations ofAegilops spp. The result has been the compilation of a collection reflecting both the presence and the distribution of the genus in Spain. The localisation and collection of two populations ofAe. cylindrica is particularly noteworthy.Ae. ovata is found all over the Peninsula except in the north and northwest of the country. It extends also to the Balearic Islands, which lie within the same biogeographical region.Ae. triuncialis also has a widespread distribution though smaller than that ofAe. ovata. In the Balearic Islands it is found only in Mallorca. All other species were found in more localised areas.Ae. neglecta was found in regions of W and SW Spain with the limits of its distribution bordering those ofAe. biuncialis, which is found in central Spain and in the South.     

Single-copy nuclear PolA1 gene sheds light on the origin of S genome with relationships to B and G genomes of polyploid wheat species

PolA1, a single-copy nuclear gene encoding the largest subunit of RNA polymerase I, comprises highly polymorphic intron 19 and nucleotide tag (Ntag) sequences. We analyzed these sequences in 42 accessions, which differed in ploidy, of Triticum–Aegilops and Hordeum species. The lengths of the intron 19 sequences were ca. 110?bp long in Triticum–Aegilops species, except in four Sitopsis species, Ae. longissima, Ae. searsii, Ae. sharonensis, Ae. speltoides, which had introns similar in length to those of Hordeum species, i.e., ca. 240?bp long. Phylogenetic analyses of the Ntag sequences showed that the four Sitopsis and remaining Triticum–Aegilops species were classified into two discrete Hordeum and Triticum clades, respectively. The A and D genome-specific Ntag sequences of polyploid wheats were highly homologous with those of T. urartu and Ae. tauschii, respectively. In Ae. bicornis, another Sitopsis species, two accessions had the short intron 19 and Triticum–type Ntag sequence, which were highly homologous with those of the B genome in polyploid wheats, whereas one accession contained the long intron 19 and Hordeum–type Ntag sequences. In contrast, partial sequence analyses revealed that the three accessions of Ae. bicornis shared highly homology to single-copy DMC1 and EF-G genes. The discrepancy between these results indicates that the Sitopsis species were probably established by hybrid speciation including ancient introgressive hybridization between progenitors of Triticum–Aegilops and Hordeum. Although many researchers have proposed Ae. speltoides as a candidate for the B genome donor, our data suggest the existence of diploid B genome species in the past that were responsible for the origin of both polyploid wheats and Sitopsis species, including Ae. speltoides.     

Size homoplasy and mutational behavior of chloroplast simple sequence repeats (cpSSRs) inferred from intra- and interspecific variations in four chloroplast regions of diploid and polyploid <Emphasis Type="Italic">Triticum</Emphasis> and <Emphasis Type="Italic">Aegilops</Emphasis> species

Chloroplast simple sequence repeats (cpSSRs) are widely distributed in the chloroplast genomes of all plant species, and are frequently employed for genotypic and phylogenetic analysis. However, information on intra- and interspecies variation in cpSSRs is lacking. In this study, we sequenced four intergenic (non-coding) chloroplast DNA regions in 57 accessions of 12 tetraploid, and 16 accessions of 4 hexaploid species of Triticum and Aegilops. These sequence data added to our previous data for diploid species in the same chloroplast regions. Intra- and interspecific genetic variation was analyzed for a total of 189 accessions of 13 diploid, 12 tetraploid, and 4 hexaploid species of Triticum and Aegilops, such that all species were represented by multiple accessions. The data were used to infer phylogenetic relationships within and among Triticum and Aegilops species. Based on this robust phylogenetic tree, seven of eight cpSSR loci clearly exhibited “size homoplasy,” referring to the fact that cpSSRs of identical size and DNA sequence can arise even if the alleles are not descended from a common ancestor. These data indicate that cpSSRs should be used with caution in phylogenetic analyzes. Interestingly, as observed from several previous studies, our data also suggest that observed mutation rates may increase significantly when mononucleotide (homopolymer) repeat numbers reach or exceed 9 bp. In the present report, using this sequence data set involving cpSSRs, 81 unique haplotypes among 189 accessions were detected, and five tetraploid Triticum and Aegilops species were successfully identified and genotyped. Our results indicate that combinations of nucleotide substitutions, indels and SSRs of chloroplast nucleotide sequences are available for genotyping at the species accession level.     

Morphophysiological variation in some Mexican species of vegetable Amaranthus: evolutionary tendencies under domestication

Summary Amaranth (Amaranthus spp.) is an important food resource for indigenous peoples of México. Grain-producing species are mostly cultivated plants, while the species used as vegetables are commonly encouraged in maize plots. Notable biological differences exist between these two types of amaranths. This study analyzes the morphophysiological variation in some Mexican species of Amaranthus and its relationship to the use and management of this taxa. A sample of individuals grown from 14 field collections representing 3 species and putative hybrid derivatives were grown in experimental plots and 18 morphological and physiological characters were measured. A statistical multivariate analysis was performed on these data. The results show that the grain-producing plants tend to allocate a high proportion of energy to the production of inflorescences while the plants used as vegetables allocate a higher proportion of biomass to the foliage. This suggests thatdomestication of Mexican species of Amaranthus have taken two different evolutionary paths depending upon the form of use and management by humans.     

Alien cytoplasm effects on phytosiderophore release in two spring wheats (Triticum aestivum L.)

Iron (Fe) deficiency is a difficult nutrient problem particularly in crop plants grown on calcareous soils. Recently, phytosiderophore (PS) release has been linked to the ability of graminaceous species and genotypes to withstand Fe-deficiency chlorosis. So enhancing PS release is a critical step to improve iron efficiency of plants grown on iron stressed soils. The effects of alien cytoplasm on PS release in spring wheat were studied by analyzing PS release from twenty wheat genotypes, including two spring wheat 881 and 352-35, and their 18 alloplasmic lines with the participation of cytoplasms from the Aegilops and Triticum species. Different genotypes were grown in iron sufficient and deficient nutrient solution under controlled environmental conditions. PS release rates were determined at two or three days intervals after onset of iron deficiency symptoms by the measurement of iron mobilizing capacity of root exudates from freshly precipitated Fe^III hydroxide. High amounts of phytosiderophores were released from roots of all wheat genotypes without iron supplied, and the amount progressively increased with the development of iron deficiency chlorosis. The results revealed that (1) the release rate of phytosiderophores from roots of common wheat could be considerably influenced by alien cytoplasms. Some alien cytoplasms exerted positive effects, some ones did negative effects, and the other ones had no significant effects. (2) the same alien cytoplasm could affect similarly or oppositely the phytosiderophores release from different wheat. (3) some alien cytoplasms, such as Chinese Spring, Ae. speltoides Tausch and Ae. cylindrica Host showed promising and potential in improving the rate of phytosiderophore release in common wheat. These cytoplasms which showed the desired effect should be given priority in interspecific and intergeneric hybridization to develop and reconstruct the needed wheat cultivars.     

The RAPD evidence for the phylogenetic relationship of the closely related species of cultivated apple

The phylogenetic relationship of cultivated apple and its closely related species is still not clear in the taxonomy of genus Malus. To try to find new evidence for the origin and evolution of the cultivated apple, random amplified polymorphic DNA (RAPD) markers of 14 taxa of Malus, among which a reference species (M. toringoides) and six presumably ancestral species of cultivated apple in the genus were investigated. The RAPD data obtained were used to construct both unrooted and rooted trees using TREECON software package. The result showed in our rooted tree that M. sieversii from the Xinjiang Autonomous Region of China is the species which is most closely related to the cultivated apple, M. domesticacv. `Golden Delicious'. The phylogenetic relationships among the species studied are discussed.     

Seed protein diversity in Solanum melongena L. and its wild and weedy relatives

Seed protein profiles by SDS-PAGE were studied in 72 accessions ofSolanum melongena L. and its related taxa in subgenusLeptostemonum (Dunal) Bitter. Comparisons based onJaccard's similarity and UPGMA clustering revealed interrelationships broadly inconformity with the conventional taxonomic treatments. Thus,S. viarum Dunal (sectionAcanthophora Dunal), S.torvum Swartz (section Torva Nees) andS. sisymbriifolium Lam. (sectionCryptocarpum Dunal) were located on separate branches ofthe dendrogram while all taxa of section Melongena Dunal,except S. macrocarpon Dunal, wereclustered closer together. S.melongena, incanum and insanum,all members of the eggplant complex, were revealed to bear very high similaritywith each other. Most of their accessions had identical band patterns supportingthe contention that these represent an interbreeding complex with limitedgenetic differentiation.     

On the Taxonomy of the Members of ‘Saccharum Complex’

The difficulty and problems encountered in the study of cultivated plants, in general and sugarcane, in particular has been indicated. In order to understand these problems, a brief review on the taxonomy of Saccharum and closely related taxa, namely, Erianthus, Sclerostachya, Narenga and Miscanthus (generally known as ‘Saccharum complex’) has been given. A short account on the important morphological features that are specific to sugarcane has also been stated as classification is commonly based on such morphological characters. A note has been added on the chromosome number, origin, and distribution of the species of ‘Saccharum complex’ members. Taxonomic keys have been devised for identification of the genera of Saccharinae and for the species of Saccharum and Erianthus occurring in India. A new combination, Sclerostachya fallax (Balansa) Amalraj et Balasundaram, has also been proposed.     

Divergent evolution of wild and cultivated subspecies of <Emphasis Type="Italic">Triticum timopheevii</Emphasis> as revealed by the study of <Emphasis Type="Italic">PolA1</Emphasis> gene

Triticum timopheevii (genome symbol AAGG) comprises two subspecies, cultivated ssp. timopheevii, and wild ssp. armeniacum. These two subspecies are considered as allotetraploids of AA genome from Triticum diploid species and SS genome from Aegilops species. The difference in genome symbol (G vs. S) is due to wide genetic variations among four SS genome species, Ae. bicornis, Ae. longissima, Ae. searsii, and Ae. speltoides. In order to study the origin of T. timopheevii, we compared 19th intron (PI19) sequence of the PolA1 gene, encoding the largest subunit of RNA polymerase I. Two different sized DNA fragments containing PI19 sequences (PI19A and PI19G) were amplified both in ssp. timopheevii and ssp. armeniacum. Shorter PI19A (112 bp) sequences of both subspecies were identical to PI19 sequences of two AA species, T. monococcum and T. urartu. Interestingly, the longer PI19G (241–243 bp) sequences of ssp. armeniacum showed more similarity to PI19 sequences of Ae. speltoides whereas ssp. timopheevii showed more similarity to PI19 sequences of other three SS genome species. The results indicated that two subspecies of T. timopheevii, ssp. armeniacum or ssp. timopheevii, might have arisen independently by allotetraploidization of AA genome with Ae. speltoides or one of the remaining three Aegilops species, respectively.     

Genetic diversity of the African hexaploid species Solanum scabrum Mill. and Solanum nigrum L. (Solanaceae)

Two hexaploid species of Solanum sect. Solanum are present in Africa: Solanum scabrum and S. nigrum. Solanum scabrum is a widely cultivated species and is used as a leafy vegetable, as a source of medicine and as a source of ink dye. In previous studies a wide range of morphological diversity has been reported in this species and in some studies subspecies have been proposed. Subspecies are also recognized in S. nigrum. However, it has not been established whether or not the morphological differences are reflected at the genomic level. The present study applies AFLPs to study the genetic diversity in S. scabrum and its relationship to geographical provenance, morphological differences and the possible existence of subspecies within S. scabrum and S. nigrum. The data obtained were analyzed with cluster analysis (using UPGMA and NJ). The results indicate that the genetic variation within S. scabrum was higher within accessions than between accessions. Accessions did not cluster according to their geographical provenance, indicating that accessions from different geographical areas were not significantly different genetically. The clustering reflected neither morphological differences nor domestication status (cultivated or wild). The morphological differences exhibited by S. scabrum could be due to selection by farmers for different plant types. The AFLP derived clustering pattern did not segregate the subspecies recognized in S. scabrum and S. nigrum into separate subclusters.     

Brassica sect.Brassica (Brassicaceae)

Summary An extensive crossing program including 10 wild taxa and 23 accessions representing 6 major cultivated forms and landraces of theBrassica oleracea group was carried out. Data for crossability, germination, viability, fertility inF ₁ andF ₂ were studied as well as the meiotic chromosomal pairing inF ₁ hybrids in some combinations. The fertility of hybrids between all cultivated forms and wild populations ofB. oleracea was high and it was concluded that all, including the Chinese endemicalboglabra form, belong to the same biological species. Among the other species,B. macrocarpa, B. montana, andB. rupestris had the lowest andB. cretica the highest fertility values in crosses with cultivated forms. The crossing data do not give any further information as to the genetic differentiation ofB. oleracea during the course of domestication. Introgression between wild and cultivated forms has probably occurred frequently. All members of theB. oleracea cytodeme belong to the primary and secondary gene pools of the 18 chromosomic crops and are as such of great importance for breeding purposes.     

Analysis of Wheat Disease Resistance Data Originating from Screenings of Gatersleben Genebank Accessions during 1933 and 1992

Series of 10,348 accessions belonging to 21 species (hexaploid, tetraploid, diploid) of the genus Triticum and 489 accessions belonging to 20 species of the genus Aegilops were scored for disease resistance during a period of 60 years. Tests were performed at the seedling stage for powdery mildew (Erysiphe graminis DC. f. sp. tritici March.), leaf rust (Puccinia recondita Rob. ex Desm. f. sp. tritici Erikss.), stripe rust (Puccinia striiformis West. f. sp. tritici Erikss.) and eyespot (Pseudocercosporella herpotrichoides (Fron.) Deight.) but also at the adult plant stage considering powdery mildew, leaf rust, stripe rust, eyespot and glume blotch (Septoria nodorum Berk.). About 150,000 disease scores recorded on index cards using different scoring scales were transferred to the computer, converted into a 1–9 scale and used to summarise the results. Within the genus Triticum 20% of the material analysed was classified as heterogeneous. For the accessions without detectable segregation a large variability for resistance/susceptibility was detected. At the adult plant stage resistant accessions without visible infections were identified for all diseases. The percentages of resistant accessions at that growth stage were always higher than the ones found in the material tested at the seedling stage. The probability for finding resistant material was shown to be highest in the diploid species ( > 50%) but decreased with increasing ploidy level to about 10% in the hexaploids. For Aegilops it was shown that most of the accessions were homogeneous and highly resistant against powdery mildew (seedling and adult plant stage), leaf rust (adult plant stage) and eyespot (seedling and adult plant stage/natural infection). The data obtained for the individual accessions are available via Internet (http://www.ipk-gatersleben.de). An erratum to this article is available at .