Phylogenetic implications of the internal transcribed spacers of nrDNA and chloroplast DNA fragments of <Emphasis Type="Italic">Musa</Emphasis> in deciphering the ambiguities related to the sectional classification of the genus

The genus Musa L. comprises of economically important bananas and has been divided into five sections based on their chromosome number and morphological characteristics viz., Australimusa, Callimusa, Eumusa, Rhodochlamys and Ingentimusa. However, this sectional classification has long been disputed. In this study, we present data on sequenced multiple DNA fragments from the maternally inherited chloroplast genome (atpB-rbcL spacer, trnK-matK intron and psbK-psbI spacer) and the biparentally inherited internal transcribed spacers of nuclear ribosomal DNA of three species of Musa along with data available in GenBank database to understand their implications on the sectional relationship and phylogeny of the genus Musa. In our findings, none of the five sections of Musa previously defined based on morphology was recovered in the molecular phylogeny analysis using cpDNA and nrDNA. Instead, the results corroborate with the suggestion that sectional classification in the genus Musa should be reviewed by combining together the section Eumusa and Rhodochlamys as one and section Australimusa and Callimusa as a single different section, along with that of Ingentimusa.     

Phylogenetic relationships within <Emphasis Type="Italic">Lactuca</Emphasis> L. (Asteraceae), including African species,based on chloroplast DNA sequence comparisons

Lettuce (Lactuca sativa L.) belongs to the genus Lactuca L. and is an important vegetable worldwide. Over the past decades, there have been many controversies about the phylogeny of Lactuca species due to their complex and diverse morphological characters and insufficient molecular sampling. In this study we provide the most extensive molecular phylogenetic reconstruction of Lactuca, including African wild species, using two chloroplast genes (ndhF and trnL-F). The sampling covers nearly 40 % of the total endemic African Lactuca species and 34 % of the total Lactuca species. DNA sequences from all the subfamilies of Asteraceae in Genebank and those generated from Lactuca herbarium samples were used to establish the affiliation of Lactuca within Asteracaeae. Based on the subfamily tree, we selected 33 ndhF sequences from 30 species and 79 trnL-F sequences from 48 species to infer relationships within the genus Lactuca using randomized axelerated maximum likelihood and Bayesian inference analyses. Biogeographical, chromosomal and morphological character states were reconstructed over the Bayesian tree topology. We conclude that Lactuca contains two distinct phylogenetic clades—the crop clade and the Pterocypsela clade. Other North American, Asian and widespread species either form smaller clades or mix with the Melanoseris species. The newly sampled African endemic species probably should be treated as a new genus.     

Diversity of <Emphasis Type="Italic">Citrus</Emphasis><Emphasis Type="Italic">depressa</Emphasis> Hayata (Shiikuwasha) revealed by DNA analysis

Citrus depressa Hayata is an indigenous mandarin species on the Ryukyu Islands located in the subtropical region of Japan. We deduced its phylogenetic relationships by evaluating accessions grown on various Ryukyu Islands via cleaved amplified polymorphic sequence analysis of cpDNA and sequence-related amplified polymorphism (SRAP). The cpDNA results indicated that C. depressa could be classified into two types. SRAP revealed patterns of diversity within C. depressa consistent with our cpDNA results. These results indicate that maternal origin may influence or is correlated with the constitution of the nuclear genome of C. depressa. Another Japanese mandarin species, Citrus tachibana (Makino) Tanaka was distinguished from C. depressa by SRAP markers. Moreover, both C. depressa and C. tachibana could be distinguished from other Citrus species. Our results suggest that Japanese mandarin possesses a characteristic genome with the genus Citrus.     

Investigation and evaluation of wild <Emphasis Type="Italic">Iris</Emphasis> resources in Liaoning Province,China

There were 15 species and two variants of wild Iris recorded in Liaoning Province, where is a primary distribution area of Iris in China. According to the division of distribution area for wild plants in Liaoning, twenty-eight sites were selected for investigating wild Iris resources in Liaoning. Distribution, habitat and main accompanying plants of each Iris species were recorded. Fifty-three accessions were collected during the investigation and introduced to suitable environment. Morphological characteristics of each accession were observed. According to previous literatures and specimens, all accessions were identified and classified into 12 species and two variants. The analytic hierarchy process (AHP) was used to perform a comprehensive assessment on the ornamental value of 11 Iris species. The results showed that Iris tigridia Bunge and Iris ensata Thunb. had better ornamental value than the other species. Some suggestions for revision and classification were discussed on several Iris species.     

Combining conservative and variable markers to infer the evolutionary history of Prunus subgen. Amygdalus s.l. under domestication

The genus Prunus L. is large and economically important. However, phylogenetic relationships within Prunus at low taxonomic level, particularly in the subgenus Amygdalus L. s.l., remain poorly investigated. This paper attempts to document the evolutionary history of Amygdalus s.l. and establishes a temporal framework, by assembling molecular data from conservative and variable molecular markers. The nuclear s6pdh gene in combination with the plastid trnSG spacer are analyzed with bayesian and maximum likelihood methods. Since previous phylogenetic analysis with these markers lacked resolution, we additionally analyzed 13 nuclear SSR loci with the δµ² distance, followed by an unweighted pair group method using arithmetic averages algorithm. Our phylogenetic analysis with both sequence and SSR loci confirms the split between sections Amygdalus and Persica, comprising almonds and peaches, respectively. This result is in agreement with biogeographic data showing that each of the two sections is naturally distributed on each side of the Central Asian Massif chain. Using coalescent based estimations, divergence times between the two sections strongly varied when considering sequence data only or combined with SSR. The sequence-only based estimate (5 million years ago) was congruent with the Central Asian Massif orogeny and subsequent climate change. Given the low level of differentiation within the two sections using both marker types, the utility of combining microsatellites and data sequences to address phylogenetic relationships at low taxonomic level within Amygdalus is discussed. The recent evolutionary histories of almond and peach are discussed in view of the domestication processes that arose in these two phenotypically-diverging gene pools: almonds and peaches were domesticated from the Amygdalus s.s. and Persica sections, respectively. Such economically important crops may serve as good model to study divergent domestication process in close genetic pool.     

Collection and evaluation of wild tulip (<Emphasis Type="Italic">Tulipa</Emphasis> spp.) resources in China

China is known throughout the world as one of the most diverse centres of wild Tulipa L. resources. There are 17 wild Tulipa species distributed in China, and 12 species are only distributed in Xinjiang Province. In this paper, total 83 accessions were collected from Xinjiang, Liaoning and several other provinces. Their distribution, collection, classification and evaluation were described. According to morphological characteristics, they were classified into eight species, which included T. sinkiangensis Z. M. Mao, T. altaica Pall. ex Spreng., T. iliensis Regel, T. heterophylla Baker, T. buhseana Boiss., T. thianschanica Regel, T. schrenkii Regel and T. edulis (Miq.) Baker. Their phenotypic genetic relationships were analysed and showed that the eight Tulipa species were divided into two groups: Group I included one species T. edulis, and Group II included the other seven species. Bulb renewal was observed in eight wild Tulipa species; T. iliensis and T. edulis showed that one or more long fleshy stolons formed horizontally or vertically at the basal plate of the mother bulbs, new bulblets (dropper) appeared at the top of each fleshy stolon, and the mother bulbs eventually disappeared. The analytic hierarchy process was used to evaluate the ornamental value, utilization potential and ecological adaptability of the eight identified species. The results showed that T. iliensis, T. buhseana and T. thianschanica had better ornamental value and utilization potential than any other species. The distribution, collection, classification, and evaluation of wild Tulipa species could be helpful in creating novel tulip germplasms in China.     

Analysis of genetic diversity and evolutionary relationships among hexaploid wheats <Emphasis Type="Italic">Triticum</Emphasis> L. using LTR-retrotransposon-based molecular markers

The origin, diversity and distribution of hexaploid wheat still remain somewhat unclear. In this study we examined the patterns of genetic diversity and phylogenetic relationships of seven hexaploid wheat species using integration site polymorphism of the LTR retrotransposons. Forty-eight accessions (most of them aboriginal) of seven wheat species from different geographical regions were studied using sequence-specific amplification polymorphisms. Phylogenetic relationships among species were constructed with SplitsTree 4.10 based on Dice’s matrices. Genetic distances between the accessions clustered with PAST software were estimated by principal component analysis. All the accessions differentiated into two main groups, one including European spelt and the other combining common, club and Indian dwarf (shot) wheat with the Asian spelt. The spelt species T. macha, T. vavilovii and spelt spike (speltoid) free-threshing T. petropavlovskyi were intermediate between the two groups. The separation of these spelt species from all other accessions was determined by differences in the A genome. European spelt was subdivided into Central European and Spanish branches. As different genetic pools were characteristic of European and Asian spelt, European spelt could not originate directly from the Asian one. Supposedly, the A genome mostly harbors the species-forming or taxonomically important genes that distinguish spelt species from free-threshing ones, which group together with Asian spelt. Grouping of Asian spelt with free-threshing wheat suggests their close relatedness and confirms the hypothesis that free-threshing hexaploid wheats originated from the Asian spelt ancestor.     

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.     

Phylogenetic relationship of 40 species of genus Aloe L. and the origin of an allodiploid species revealed by nucleotide sequence variation in chloroplast intergenic space and cytogenetic insitu hybridization

Aloe species, which have been used as medicinal plants, belong to the Asphodelaceae family consisting of 530 species. In this study, genetic diversity and phylogenetic relationships among 40 Aloe species including a putative interspecies hybrid were analyzed using PCR band profiles from eight chloroplast intergenic space markers and nucleotide sequence diversity in the psbK–psbI intergenic region. A phylogenetic tree based on psbK–psbI sequences supported the revised classification of the genus Aloe as polyphyletic with several species be re-allocated into three genera Kumara, Aloidendron, and Aloiampelos. Further, the origin of the putative interspecies Aloe hybrid was characterized through molecular cytogenetics. Fluorescence and genomic insitu hybridization illustrated that the hybrid has a bimodal karyotype with a chromosome complement of 2n = 14, of which complementary halves were derived from two parental species, A. vera and A. arborescens. These findings revealed that the hybrid species was allodiploid. The phylogenetic analysis showed that A. arborescens was the maternal genome donor of the hybrid, as both have identical chloroplast genome sequences. We thus conclude that the allodiploid hybrid should be called A. arborescens × A.vera.     

Investigation and taxonomy of wild <Emphasis Type="Italic">Fragaria</Emphasis> resources in Tibet,China

Tibet is one of the main distribution centers of wild Fragaria species in China. There are abundant, precious and rare wild strawberry resources. This paper focused on the classification, distribution and evaluation of the 65 wild strawberry accessions collected from 17 counties in Tibet. The main taxonomical characters, such as stolon branching, leaflet type, flower sex, fruit shape, status of achene and sepal, and chromosome number were observed for each accession. All accessions were identified and classified into seven Fragaria species and two forms, including F. daltoniana J. Gay (2x), F. nilgerrensis Schlecht. (2x), F. nubicola Lindl. (2x), F. pentaphylla Losinsk. (2x), F. gracilis A. Los. (4x), F. moupinensis (French.) Card. (4x) and F. tibetica Staudt et Dickoré. (4x). The two white-fruited forms were F. nubicola f. alba (2x) and F. moupinensis f. alba (4x). The analytic hierarchy process (AHP) method was used to perform a comprehensive assessment on the value of seven Fragaria species and two forms. The results showed that F. nilgerrensis had better fruit quality, disease resistance and waterlogging tolerance than any other species in Tibet. The collection and identification of wild strawberry resources in Tibet would be helpful to improve the fruit quality and stress resistance of modern strawberry cultivars.     

Electrophoretic variation in seed proteins and interrelationships of species in the genus <Emphasis Type="Italic">Oryza</Emphasis>

Comparative studies of two cultivated and sixteen wild species of the genus Oryza were carried out using one- and two-dimensional gel electrophoresis for variation in their seed proteins for interrelationships of these species. A number of polypeptides in the range of molecular weight 13–110 kDa were seen to vary. Under reducing conditions, polypeptides spread over the regions of mol. wt. 33–40.5, 25–27 and 19–21.5 kDa exhibited maximum variation in their patterns. Two-dimensional gel electrophoresis revealed the occurrence of disulphide-linked glutelin polypeptide pairs of mol. wt. 60, 58, 52 and 25 kDa breaking into a large and a small subunit each in the range of mol. wt. 18–40.5 and 16–25 kDa respectively in Oryza sativa. The number of such polypeptide pairs varied from 2 to 6 in different species and also in O. sativa showed variation in mol. wts. of their constituent subunits. The UPGMA dendrogram revealed that most of the Oryza species occurred in different clusters and subclusters and thus did not share very close relationships. The undisputed and closest relationship observed was that of cultivated rice O. sativa with the O. rufipogon followed by that with O. nivara. The African cultivated O. glaberrima occurring on the nearest branch of the same subcluster, thereby, supporting the phylogenetic of these species suggested in earlier studies. Eight diploid species and seven tetraploid species were included in one part of the dendrogram while the remaining two species with AA genome i.e. O. glumaepatula and O. meridionalis and one with FF i.e. O. brachyantha stood separately from these as scattered in the group of seven tetraploid species with BBCC, CCDD and HHJJ genomes. The tetraploids O. alta, O. latifolia and O. grandiglumis with CCDD genomes which occurred on the farthest part were distantly related with O. sativa. The cyanogen bromide peptide maps and two dimensional gel electrophoresis also supported the closest relationship between O. sativa and O. rufipogon.     

Polymorphism of <Emphasis Type="Italic">Got2</Emphasis> DNA sequences sheds light on <Emphasis Type="Italic">Aegilops tauschii</Emphasis> Coss. intraspecies divergence and origin of <Emphasis Type="Italic">Triticum aestivum</Emphasis> L.

DNA sequences of nuclear gene Got2 was studied in 60 accessions of Aegilops tauschii, 29 of subsp. tauschii and 31 of subsp. strangulata. It was found that Got2 allozyme polymorphism in Ae. tauschii is due to a single, unique, mutation which led to replacement of glutamic acid by isoleucine in residue 256 of the enzyme molecule, encoded by Got2. As revealed by Got2 DNA sequences variation, initially in its history Ae. tauschii was presented by subsp. strangulata, and among phylogenetic lineages of subsp. strangulata, the lineage “t-9¹s” (TauL3) is the most ancient, a relict one. Subspecies tauschii is relatively “young”. Initially it was presented by the lineage marked by combination of allozyme alleles Got2 ¹⁰⁵ and Acph1 ¹⁰⁰. In the past it inhabited the Continental area from Caucasia to Pakistan, but later on it was forced out by newly originated, now—a major lineage of subsp. tauschii, marked by Got2 ¹⁰⁰. This lineage extended the Continental area of the species up to Kirgizstan, but actually failed to penetrate into pre-Caspian area, occupied by subsp. strangulata. These results essentially differ from those obtained previously, using chloroplast DNA (cpDNA) sequences polymorphism. As revealed by cpDNA, the major, “usual”, subsp. strangulata (TauL2) is “younger” than subsp. tauschii, which resided on phylogenetic tree between relict lineage “t-9¹s”of subsp. strangulata—and major subsp. strangulata. But both cpDNA and Got2 DNA sequences indicate that the level of genetic variation in subsp. tauschii is much lower than in subsp. strangulata. According to Got2 DNA sequences variation, it was Ae. tauschii subsp. strangulata lineage “k-109″ which donated genome D to Triticum aestivum L. This lineage includes accessions: k-109 from South-Eastern Precaspian Azerbaijan; KU-2105, KU-2159 from Western Precaspian Iran; KU-2080 from Eastern Precaspian Iran.     

Genetic differentiation,races and interracial admixture in avocado (<Emphasis Type="Italic">Persea americana</Emphasis> Mill.), and <Emphasis Type="Italic">Persea</Emphasis> spp. evaluated using SSR markers

Avocado (Persea americana Mill.) is a subtropical domesticated fruit tree indigenous to Mesoamerica. It is a member of the Lauraceae family and is separated into three horticultural races (Guatemalan, Mexican, and West Indian) mainly corresponding to their ecological adaptation, botanical, and physiological traits. Main objectives of this study were to characterize the population structure, genetic diversity, and horticultural race of a total of 354 Persea spp. trees whose origin is as follow: 221 trees [P. americana, (218), P. nubigena (2) and P. krugii (1)] from the USDA-ARS-Subtropical Horticultural Research Station, Miami; 105 trees from the Fairchild Farm [P. americana (104) and P. schiedeana (1)], and 28 trees collected in Mexico [P. schiedeana (23) and P. americana (5)]. The complexity of their interracial admixture; as well as mislabeling frequency was also evaluated. Molecular marker analysis utilizing a set of 55 simple sequence repeat (SSR) markers amplified a total of 869 alleles with a mean number of alleles per locus of 15.8 and average polymorphism information content value of 0.71, indicating a high variability in the allele frequency for the collection. Significant deviations from Hardy–Weinberg equilibrium were identified after Bonferroni correction for a large number of loci (48; 87%) due to the presence of null alleles. The main source of variation for this population was found to be within individuals (66.84%), with 19.30% variation among populations, and 13.86% variation among individuals within populations. Moreover, population specific inbreeding indices (F _IS ) were calculated for West Indian, Guatemalan, and Mexican [(0.1918; p value 0.0000), (0.1879; p-value 0.0000), (0.0925; p-value 0.0022)], respectively. Bayesian analysis divided the individual genotypes into groups associated with the Guatemalan, Mexican, West Indian races; interracial admixture; complex hybrids and P. schiedeana species. Also, results of the multivariate clustering method (PCA) and genetic distance analyses calculated among all possible individual combinations within the SSR diversity data agreed with Bayesian or Structure analyses results. The 55 SSRs provided complete resolution of all individuals and the estimated mislabeling error was approximately 0.28%.     

Morphological variation related with environmental factors in endemic and threatened <Emphasis Type="Italic">Jatropha</Emphasis> species of Tehuacan-Cuicatlan,Mexico

Jatropha spp. from Mexico includes high species richness and endemism; five species inhabit in the Tehuacan-Cuicatlan Biosphere Reserve (TCBR), and they are important resources as food, medicine and biofuel. The assessment of morphological and agronomic characteristics is essential to identify, use and maintain plant genetic resources. Given the lack of information on the morphological variability of Jatropha species in relation to environment, the objective was to analyze the influence of physiographic, climatic, and anthropogenic factors in the morphological variability of the species: Jatropha neopauciflora and J. rzedowskii, both not-endangered; J. oaxacana, special protection; J. ciliata and J. rufescens, both endangered in the Reserve. Twelve quantitative morphological variables were measured in 24 populations of these species; 14 environmental variables were registered, and the disturbance index in the sites was estimated. The information was analyzed with Principal Components Analysis (PCA), Cluster Analysis and Canonical Correspondence Analysis (CCA). PCA detected interspecific variation: J. ciliata and J. rufescens have longer and broader leaves and longer flowers, while the other three species have smaller leaves and flowers. J. oaxacana population has intermediate size of leaves, fruits and seeds, compared with those of J. neopauciflora and J. rzedowskii. CCA detected intra-specific variation among the populations of J. neopauciflora and J. rzedowskii, which were separated in two groups due to fruit and seed size. Axis 1 of CCA correlated positively with altitude and annual temperature range, and negatively with mean annual temperature; at the intra-specific level, both species are adapted to variations of temperature and altitude.     

Diversity and differentiation of <Emphasis Type="Italic">Oryza sativa</Emphasis> and <Emphasis Type="Italic">O. rufipogon</Emphasis> in Indonesia

Analysis of the genetic structure of Indonesian Oryza sativa and O. rufipogon using neighbour-joining trees based on single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) markers revealed that O. sativa in Indonesia is separated from O. rufipogon. Accessions of O. sativa in this study were differentiated into two major groups, indica and tropical japonica, excluding some varieties. SSR and SNP markers revealed the high value of differentiation (F _ST) and genetic distance (D) between indica and tropical japonica and we discovered four loci by SNP markers and one locus by SSR markers that play a role in differentiation between indica and tropical japonica. Interestingly, genetic diversity (H) in O. rufipogon was lower than that in O. sativa, however H in O. rufipogon was the highest and H in tropical japonica was the lowest when O. sativa was divided into two groups. Inbreeding coefficient (Fst) showed evidences that gene flow (Nm) between species and within species might be one of the mechanisms related to the diversification and differentiation of Indonesian rice germplasm by asymmetric pattern between species and within O. sativa as revealed by SSR and SNP markers. In addition, we found evidences on stabilizing selection in Indonesian rice germplasm and they might be the reasons why Indonesian rice germplasm did not differentiate due to source location of landrace. However, we found a weak relation between SSR and SNP markers probably due to highly polymorphic in SSR and the different properties of both markers.     

Assessment of artificial selection in maize (<Emphasis Type="Italic">Zea mays</Emphasis> L.) and Asian rice (<Emphasis Type="Italic">Oryza sativa</Emphasis> L.) using QTL data

Maize (Zea mays L.) and Asian rice (Oryza sativa L.), two most important cereals for human nutrition, have undergone strong artificial selection during a long period of time. Currently, a number of genes with stronger signals of selection have been identified through combining genomic and population genetic approach, but research on artificial selection of maize and Asian rice is scarcely done from the perspective of phenotypic difference of a number of agronomic traits. In this study, such an investigation was carried out on the basis of 179 published studies about phenotypic quantitative trait locus (QTL) mapping of Zea and Oryza species via QTL sign test. At the overall level, the proportions of antagonistic QTLs of Zea and Oryza species were 0.2446 and 0.2382 respectively, deviating significantly from neutrality. It indicated that these two genera have undergone similar selection strength during their evolutionary process. A previous study showed that 4 traits undergoing the directional selection during domestication were identified in Asian rice via QTL sign test, and 16 individual traits in Asian rice and 38 ones in maize that newly detected in this study deviated significantly from neutrality as well, demonstrating the dominant influence of artificial selection on them. Moreover, analysis of different categories of cross type including O. sativa × Oryza rufipogon (perennial and annual forms) crosses, maize × teosinte (Zea mays subsp. parviglumis) crosses, O. sativa × O. sativa crosses, and maize × maize crosses showed that their proportions of antagonistic QTLs were 0.1869, 0.1467, 0.2649, and 0.2618 respectively. These results revealed that selection strength of domestication is significantly stronger than that of modern genetic improvement. However, interestingly, the proportion of antagonistic QTLs (0.1591) in maize × maize with long-term selection was very similar to that (0.1467) in the maize × teosinte (Zea mays subsp. parviglumis) crosses. It suggested that some favorable traits could be cultivated within a few decades if we carry out strong selection. In addition, the proportions of antagonistic QTLs of the widely cultivated hybrids of rice (Minghui 63 × Zhenshan 97) and maize (Zheng 58 × Chang 7-2) in China were 0.309 and 0.3472 respectively. It suggested that selection during modern genetic improvement has significantly acted on them.     

Genetic diversity of cultivated rice (<Emphasis Type="Italic">Oryza sativa</Emphasis> L.) and wild rice (<Emphasis Type="Italic">Oryza rufipogon</Emphasis> Griff.) in Asia,especially in Myanmar,as revealed by organelle markers

Asian rice (Oryza sativa L.) is widely cultivated in Asia, where it has been classified into Indica and Japonica Group, the latter is further classified into Tropical and Temperate Japonica Subgroup. O. rufipogon is believed to be the closest ancestor to O. sativa, but it remains unclear whether the two groups arose from a single ancestor or different ancestors. Therefore, here, we investigated the matrilineal ancestors of O. sativa using markers for organelle (chloroplast and mitochondrial) genomes, and 119 O. sativa landraces, 10 O. glaberrima Steud., 115 O. rufipogon Griff. from Asia, and 39 accessions from other wild rice species with AA genomes. We screened 18 organelle markers developed based on polymorphic loci in the organelle genomes. In addition, we used the open reading frame 100 of a chloroplast marker. The results indicated that O. rufipogon first differentiated into two lineages and then further differentiated into Indica and Japonica Group, respectively. Accessions of O. rufipogon (R-1f and R-2d types) from Myanmar appear to be the closest ancestors of Tropical Japonica Subgroup and Indica Group, respectively. Therefore, these wild strains may have made a strong contribution to the domestication of rice landraces in Myanmar.     

Remarks on genetic diversity and relationship of <Emphasis Type="Italic">Punica protopunica</Emphasis> and <Emphasis Type="Italic">P. granatum</Emphasis> assessed by molecular analyses

Here, two Punica species, viz., P. protopunica Balf. fil., reported as native to Socotra, and P. granatum L., were compared for the first time. Analysis of one P. protopunica and eleven P. granatum accessions was performed using three molecular markers, i.e., sequence related amplified polymorphism (SRAP), target region amplification polymorphism (TRAP), and intron targeted amplified polymorphism (ITAP), along with analysis of pgWD40 sequences, a gene involved in anthocyanin biosynthesis. All markers revealed the relationship between the two species and placed them at 33% similarity. SRAP, TRAP, and ITAP generated a total of 299, 260, and 160 bands, respectively. Of these, 78, 74, and 41 bands were specific for P. protopunica, and 92, 85, and 57 bands, respectively, were shared between both species. Sequence analysis of pgWD40~870 bp amplicons exhibited 100% identity among P. granatum accessions and 98% identity to that of P. protopunica. Phylogenetic analysis of WD40 sequences from monocot and dicot species, including both Punica species confirmed the relation between P. protopunica and P. granatum, supporting earlier reports that P. protopunica could be an ancestral species of P. granatum. Furthermore, the genetic diversity among and within P. granatum accessions from Egypt (3), Mexico (5), and Yemen (3) was assessed. Molecular marker-based relationships among region-bulked accessions was approximately the same (~90% similarity), whereas the degree of genetic variation was altered within each region. Specific bands (alleles) for accessions of each region along with those shared among them were identified. Thus, these bands could be used for pomegranate genotyping and breeding programs.     

Polymorphism of gliadins in <Emphasis Type="Italic">Aegilops tauschii</Emphasis> Coss. local populations in two primary habitats in Dagestan

Polymorphism of gliadins was investigated in Aegilops tauschii from primary habitats “4”, near Hily, and “6”, near Rukel, in Dagestan, Russia 205 individual plants were analysed (53/50 and 54/48 plants of subsp. tauschii/subsp. strangulata from the habitats “4” and “6”, respectively) and 1/7 and 18/14 different haplotypes were found among the plants of subsp. tauschii/subsp. strangulata from the habitats “4” and “6”, respectively. No direct evidences of cross-pollination were pointed out, although gliadins electrophoretic phenotypes obtained allowed to suggest that it occur in Ae. tauschii with very low frequency. The data obtained revealed that during Ae. tauschii evolutionary history a local habitat could be populated many times by different phylogenetic lineages of the species. It was found that in Dagestan, at the very edge of the species area, several different lineages belonging to different subspecies could for a long time co-exist together in a local habit, and in such case a very high level of genetic variation in Ae. tauschii could be accumulated on a square of less than one hectare. The further studies of genetic variation in Ae. tauschii local populations, based on molecular genetic methods seems to be very prospective for understanding of peculiarities of the species evolution.