Assessment of phenotypic variation of Malus orientalis in the North Caucasus region

Malus orientalis Uglitzk. is the predominant Malus species of the Caucasian forests distributed in the north of Anatolia, Armenia, Russia as well as in Iran. It is considered as one of the probable minor ancestors of domestic apples. Although M. orientalis has a lower diversity of fruit quality, other valuable traits such as later blooming, adaptation to a wider array of habitats, and capacity for longer storage of the apples should be taken into account for improving the genetic makeup of the domestic apple. A joint expedition of scientists of the Julius Kühn-Institute from Germany and the Nikolaj I. Vavilov Research Institute of Plant Industry from Russia was performed into the North Caucasus region during August/September 2011. Altogether 101 M. orientalis accessions were collected from eight sites at the North Caucasus. Twenty-six traits such as size, color, shape, flavor and firmness of fruit and tree habit were used for phenotypic evaluation of the accessions. A high phenotypic diversity within the collected material of M. orientalis was indicated. Accessions characterized by suitable fruit traits like bigger size, larger cover color, less bitterness and better firmness as well as more sweetness and better flavor were found. However, small-sized flavorless fruits were also detected. Tree habit varied widely from upright to weeping. Subsequently, a comprehensive phenotypic and genetic evaluation of M. orientalis increases the knowledge of diversity, may provide new resources of agronomically important traits for breeding purposes, and gives support to determine accessions for a core collection.     

Diversity of the European indigenous wild apple Malus sylvestris (L.) Mill. in the East Ore Mountains (Osterzgebirge), Germany: I. Morphological characterization

Malus sylvestris (L.) Mill. is the only indigenous wild apple species in Europe and recognized as rare and endangered species. An important prerequisite for the preservation of M. sylvestris is the identification of ‘true type’ M. sylvestris individuals because hybrids with cultivated apple could be also occurred. In this study variations among 625 putative M. sylvestris trees originated in the East Ore Mountains were evaluated with 20 selected morphological traits. The importance of these traits concerning the differentiation of ‘true type’ and hybrids of M. sylvestris were determined by statistical analysis. The results demonstrated a strong correlation of individual traits and those contributing mostly to variation of M. sylvestris were detected by the Principal Component Analysis. The relationship of 284 M. sylvestris, 18 M.?×?domestica, M. floribunda 821 and M. robusta 5 individuals were calculated based on the morphological data and presented in a dendrogram. The individuals grouped in two main clusters and 68 hybrids of M. sylvestris were identified. The main result of the morphological data of these hybrids indicates that the grouping is mainly based on the flower and leaf pubescence and less on the fruit size.     

Genetic diversity of dihydrochalcone content in <Emphasis Type="Italic">Malus</Emphasis> germplasm

Dihydrochalcones, beneficial phenolic compounds, are abundant in Malus Mill. species, particularly in vegetative tissues and seeds. Phloridzin (phloretin 2′-O-glucoside) is the primary dihydrochalcone in most Malus species including cultivated apple, Malus?×?domestica Borkh. A few species contain sieboldin (3-hydroxyphloretin 4′-O-glucoside) or trilobatin (phloretin 4′-O-glucoside) in place of phloridzin, and interspecific hybrids may contain combinations of phloridzin, sieboldin, and trilobatin. Proposed health benefits of phloridzin include anti-cancer, antioxidant, and anti-diabetic properties, suggesting the potential to breed apples for nutritional improvement. Sieboldin and trilobatin are being investigated for nutritional value and unique chemical properties. Although some of the biosynthetic steps of dihydrochalcones are known, little is known about the extent of variation within Malus germplasm. This research explores the genetic diversity of leaf dihydrochalcone content and composition in Malus germplasm. Dihydrochalcone content was measured using high performance liquid chromatography (HPLC) from leaf samples of 377 accessions, representing 50 species and interspecific hybrids from the USDA-Agricultural Research Service (ARS) National Plant Germplasm System Malus collection. Within the accessions sampled, 284 accessions contained phloridzin as the primary dihydrochalcone, one had only trilobatin, two had phloridzin and trilobatin, 36 had sieboldin and trilobatin, and 54 had all three. Leaf phloridzin content ranged from 17.3 to 113.7 mg/g with a heritability of 0.76 across all accessions. Beyond the potential of dihydrochalcones for breeding purposes, dihydrochalcone composition may be indicative of hybridization or species misclassification.     

Genetic variation in Tunisian melon (Cucumis melo L.) germplasm as assessed by morphological traits

The morphological variation and the systematical status of 28 traditional melon including two ancient varieties collected from different geographical and bioclimatic areas of Tunisia were assessed based on 34 qualitative and quantitative traits. Yellow Canary was used as a reference variety. Significant differences among accessions within and among sites of collection were revealed for the majority of traits. The accessions from the Sahel were more polymorphic than those from Tozeur’s oasis. However, the classification of the local accessions according to Munger and Robinson’s varietal groups did not allow clear segregation of several of them because of their high heterogeneity. The principal component analysis (PCA) performed on all measured traits, allowed a distinction among the introduced varieties clustered according to their varietal group, and the local accessions grouped separately according to their geographical origin and bioclimatic zone. Mahalanobis distances among PCA’s groups were significant. The correlation found between Mahalanobis distance matrix and geographical distance matrix among origins corroborated isolation per distance. Conservation strategies should be made appropriately according to origins. Accessions from the Sahel showing the highest polymorphism within and among sites of collection should be firstly preserved.     

Patterns of morphological diversity in relation to geographical origins of wild Lupinus angustifolius from the Aegean region

Summary Patterns of morphological diversity were examined in relation to geographical origins of 157 accessions of wild Lupinus angustifolius from the Aegean region using multivariate techniques. Genetic diversity was extremely large for most morphological traits, with significant variation detected among localities in Greece and within and between collection sites for some traits. Canonical variates and correlation analysis showed that early flowering, tall and large-seeded accessions were associated with warm winters and drier climates in southern Greece. Thirteen groups of accessions were identified by hierarchical cluster analysis of 19 morphological traits, accounting for 81 % of genotype and 41 % of genotype x trait sums of squares. The distinguishing features of these groups were clarified by principal coordinates analysis. Two groups, with very desirable agronomic characteristics, originated from the Dhodhekanisos Islands (Kos, Leros, Patmos) in the south-eastern Aegean: these had rapid and tall growth, prolific podding on the main stem, pods high off the ground, many upper lateral branches, large leaves, pods and seeds, and high seed yield. Accessions from the Kikladhes Islands of the central Aegean were extremely variable and those from Naxos Island were represented in 9 of the 13 groups. Accessions from northern Greece grouped together as later flowering, shorter, and smaller-seeded types, but some accessions from the southern Greek Islands were grouped with the northern mainland types. This study identified regions in Greece, such as the south-eastern islands, where further collection may be warranted for traits of obvious agronomic value for domesticated L. angustifolius. Extreme morphological variability occurs within and between collection sites, and between localities in Greece.     

Phenotypic biodiversity of an endemic wild pear, Pyrus mamorensis Trab., in North-Western Morocco using morphological descriptors

In this paper, we report on morphological diversity, ecology and flowering phenological records of an endangered and an endemic species of Morocco Pyrus mamorensis Trab. For this study, a survey was undertaken in North-Western Morocco (Mamora forest and Zaër region) whereby 67 accessions of P. mamorensis were sampled. A set of 33 genotypes of Pyrus spp. from the international collection INRA-Angers (France) of the genus Pyrus were also analyzed. The variability of the total of 100 accessions was assessed by twenty-six characters including fourteen qualitative and twelve quantitative traits. The results demonstrated high levels of morphological variation in the sampled accessions of P. mamorensis and established the relationships among the local germplasm using the UPGMA cluster analysis and the factorial discriminant analysis. Furthermore, we were able to distinguish three types of flowering in the Mamora forest: early, intermediate and late flowering type. Otherwise, the UPGMA classification comparing local accessions of P. mamorensis to the international collection led to the formation of four major groups showing the closest correspondence to their geographical origins: (1) The North African species represented by P. mamorensis, (2) The East Asian pea species, (3) The West Asian species and (4) The European species. These findings suggest the importance of implementing a conservation strategy preserving the genetic resources of wild pear in North-Western Morocco.     

Retrotransposon-based sequence-specific amplified polymorphism markers for the analysis of genetic diversity and phylogeny in <Emphasis Type="Italic">Malus</Emphasis> Mill. (Rosaceae)

Sequence-Specific Amplified Polymorphism (S-SAP)-analysis of 131 accessions of different species from five sections of the genus Malus was carried out to study genetic diversity, and to clarify phylogenetic and taxonomic issues. S-SAP-markers, based on long terminal repeat (LTR)-retrotransposons TRIM2 and dem1, were developed, which identified 679 polymorphic fragments in the studied Malus species. S-SAP technique proved to be effective for taxonomic studies in Malus. The obtained results generally support the existing sectional taxonomy in the genus Malus and allowed to determine the taxonomic status of some Russian landraces. The genetic diversity and taxonomic status of the Russian apple Antonovka landraces, widely used in breeding programs for their increased adaptation to abiotic stress and scab resistance, were clarified. All of them belong to M. domestica, section Malus. However, Antonovka Olginskaya might have a hybrid origin with some contribution from Gymnomeles species according to PCO analysis data. The taxonomic status was resolved for another Russian landrace, Yakutskaya, which exhibits increased winter hardiness and drought resistance; it belongs to section Gymnomeles, with a high resemblance to M. baccata.     

Agro-morphological and molecular variability in <Emphasis Type="Italic">Triticum boeoticum</Emphasis> accessions from Zagros Mountains,Iran

Genetic erosion in cultivated wheat provides a good reason for studying genetic diversity in crop wild relatives. In the present study, genetic diversity of 32 accessions belonging to T. boeoticum species collected from different parts of Iran were evaluated using 13 morphological traits as well as ten inter-simple sequence repeat primers. Statistical analysis for morphological traits showed significant differences among accessions (except number of fertile tillers and total tillers per plant). In principal component analysis, the first three PCA showed 82.65 % of the total morphological variation. Based on the morphological traits, accessions were separated into two main groups by cluster analysis. In molecular analysis, polymerase chain reactions amplified 105 DNA fragments, out of which, 95 (90.47 %) were polymorphic. From geographic perspective, the accessions sampled from western and southwestern of Iran showed the highest and lowest polymorphism, respectively. However, the maximum values of effective number of alleles (Ne), Nei’s gene diversity (He) and Shannon’s information index (I) was related to accessions collected from NW regions. Also, according to cluster analysis and PCoA plot genetic diversity was not related to geographical distribution. Overall, our results revealed a remarkable level of genetic diversity among studied Iranian T. boeoticum accessions; especially accessions collected from Kermanshah and Lorestan provinces, which can be of interest for future breeding programs. So, conservation of germplasm of these areas is recommended.     

Genetic identity and relationships of Iranian apple (Malus?×?domestica Borkh.) cultivars and landraces, wild Malus species and representative old apple cultivars based on simple sequence repeat (SSR) marker analysis

In order to shed light on the role of Iran in apple evolution and domestication, we chose to investigate the relationships of a collection of 159 accessions of wild and domesticated apples including Iranian indigenous apple cultivars and landraces, selected wild species, and old apple scion and rootstock cultivars from different parts of the world. The majority of the wild species belonged to M. sieversii, which is widely believed to be the main maternal wild ancestor of domestic apples, from Kazakhstan and M. orientalis, which is one of the probable minor ancestors of domestic apples, from Turkey and Russia located on the east and west of Iran, respectively. The accessions were assigned into six arbitrary populations for the purpose of generating information on genetic parameters. Nine simple sequence repeat (SSR) loci selected from previous studies in apple were screened over DNA extracted from all the accessions. Results showed that all SSR loci displayed a very high degree of polymorphism with 11–25 alleles per locus. In total, there were 153 alleles across all loci with an average of 17 alleles per locus. The SSR allelic data were then used for estimation of population genetic parameters, including genetic variation statistics, F-statistics, gene flow, genetic identity, genetic distance and then cluster analysis using POPGENE 1.32 software. The F-statistics and gene flow in particular, showed that there was more intra-population than between population variation. The genetic identity and genetic distance estimates, and the dendrogram generated from the un-weighted pair group arithmetic average (UPGMA) method of cluster analysis showed that the Iranian cultivars and landraces were more closely related to M. sieversii from Central Asia (east of Iran) and M. orientalis native to Turkey and Russia than to other accessions of Malus species. Also, the old apple cultivars from different parts of the world have a closer genetic relationship to M. sieversii, M. orientalis and the Iranian apples, than to other wild species. Based on these results, we suggest that the Iranian apples may occupy an intermediate position between the domesticated varieties and wild species. We propose that Iran could be one of the major players in apples’ domestication and transfer from Central Asia to the western countries.     

Collection of Lupinus angustifolius L. Germplasm and Characterisation of Morphological and Molecular Diversity

Lupinus angustifolius L. is a Mediterranean species, domesticated in the 20th century, representing an important grain legume crop in Australia and other countries. This work is focused on the collection of wild germplasm and on the characterisation of morphological and molecular diversity of germplasm accessions. It reports the collection of 81 wild L. angustifolius accessions from the South and Centre of Portugal, available at the ‘Instituto Superior de Agronomia Gene Bank’, with subsequent morphological and molecular characterisation of a selection of these and other accessions. A multivariate analysis of morphological traits on 88 L. angustifolius accessions (including 59 wild Portuguese accessions, 15 cultivars and 14 breeding lines) showed a cline of variation on wild germplasm, with plants from Southern Portugal characterised by earlier flowering, higher vegetative development and larger seeds. AFLP and ISSR molecular markers grouped modern cultivars as sub-clusters within the wider diversity of wild germplasm, revealing the narrow pool of genetic diversity on which domesticated accessions are based. The importance of preserving, characterising and using wild genetic resources for L. angustifolius crop improvement is outlined by the results obtained.     

Socio-economic and horticultural potential of Khirni [Manilkara hexandra (Roxb.) Dubard]: a promising underutilized fruit species of India

Manilkara hexandra (Roxb.) Dubard (Khirni) is a socio-economically important fruit and nut species of tribal population of tropical deciduous forests of western and central India. Survey and collection missions were undertaken to study the extent of variability and socio-economic importance of Khirni germplasm in diversity rich areas of Rajasthan, Gujarat, Madhya Pradesh and Maharashtra. A total of 99 accessions of this important tree species were collected from surveyed regions, of which 47 diverse accessions were selected for morphological characterization showing wide range of variation in agro-morphological traits. During the survey, sizable variability in morphological characters and high socio-economic potential of Khirni was recorded. Bark, fresh fruits and extracted seeds have high nutritional and medicinal value. Tree provides substantial livelihood support to local inhabitants as collected fresh fruits from natural populations fetch good price in local markets. Besides livelihood support species, M. hexandra contributes in the nutritional security of the women and children of this area by fulfilling the need of micronutrients and vitamin A. Due to the high market demand of fresh fruits and seeds and without any organized cultivation, pressure on natural wild populations is severely building up since last several decades and therefore, the genetic variability of this species is now facing a great threat and need immediate complementary conservation efforts. Based on higher diversity index and natural population size of this species six in situ conservation sites have been suggested for dynamic conservation in western and central Indian states and 60 accessions have been successfully cryostored.     

Genetic diversity analysis in Phaseolus vulgaris L. using morphological traits

Common bean (Phaseolus vulgaris) is an important export crop in Kyrgyzstan since the end of the twentieth century. Genetic diversity analysis of common bean populations is useful for breeding programs, as it helps to select genetic material to be used for further crossing. Twenty-seven common bean accessions were analyzed using 13 qualitative morphological traits. In some cases, obtained morphological data were combined with previously published results based on microsatellite markers. The similarity matrices generated from the molecular and morphological data were significantly correlated (r = 0.49, P < 0.01). Cluster analyses based on Dice’s similarity coefficient were constructed based on morphological data and the combined data set of morphology and microsatellite, and both grouped the 27 accessions according to their origin: 15 belonged to the Andean and 12 to the Mesoamerican gene pool. On average, the Andean accessions were less diverse than the Mesoamerican accessions. The average diversity based on the Shannon diversity index for the 13 qualitative morphological traits was 0.05. Overall, this study revealed that qualitative morphological markers are efficient in assigning modern cultivars to their gene pools of origin.     

Biodiversity in the barnyard millet (<Emphasis Type="Italic">Echinochloa frumentacea</Emphasis> Link,Poaceae) germplasm in India

One hundred ninety four accessions of barnyard millet collected from different eco-geographical regions of India were evaluated for 14 quantitative traits during kharif 2003 and 2005. These accessions were grouped into 5 groups on the basis of place of collection. These groups differed significantly in their mean values for quantitative traits and magnitude of correlation among traits indicates origin based association. The group ‘C’ (source of origin is unknown) was found most diverse group (mean coefficient of variation 17.67%), while rest of the groups recorded mean coefficient of variation between 12 and 13%. Correlation studies indicate that flag leaf width, number of racemes along with internode length should be considered while performing selection in segregating generations. The plotting of first and second principal component axes scores suggests that presence of three distinct morphotypes in the present study. These morphotypes are quite similar to three botanical varieties viz., var. robusta, var. intermedia and var. stolonifera in their morphological traits, while botanical variety laxa (endemic to Sikkim area of India) was completely absent from the present study.     

Characterization of sesame (<Emphasis Type="Italic">Sesamum indicum</Emphasis> L.) germplasm regenerated in Georgia,USA

Sesame, Sesamum indicum L. is used worldwide for cooking oil and food. The United States Department of Agriculture, Agricultural Research Service, Plant Genetic Resources Conservation Unit (USDA, ARS, PGRCU) conserves 1,226 accessions originating from Europe, Africa, Asia, North America, and South America. Sesame accessions were directly seeded to the field in Griffin, GA between 15 May and 01 June 2003–2007. At 50% maturity, 192 accessions were characterized for morphological, phenological, and reproductive traits during the regeneration cycles. High quality plants regenerated from all accessions produced 131 to more than 80,000 seeds per accession. Sesame can be successfully grown and regenerated in Griffin, GA. Coefficients of variation and principal component analysis revealed considerable variability among accessions for phenological, morphological and reproductive traits. Assuming appropriate levels of heritability, sufficient variation among sesame accessions exists for days to maturity, plant height, and reproductive traits among these sesame accessions to warrant breeding programs for new sesame cultivar development.     

Collection and morphological characterization of Panicum coloratum L. in Argentina

Panicum coloratum (Poaceae) is a perennial grass native to South Africa, distributed all over the world, but poorly adopted by ranchers in Argentina. Adapted to a wide range of soil and climatic conditions, it constitutes a good forage resource for zones with edaphic and climatic restrictions, where cattle rising activities are here displaced. The high polymorphism in the species has made it difficult to delineate sub specific taxonomic categories. It has been classified in botanical varieties, types and/or cultivars. In order to document the morphological variability in P. coloratum and to investigate the differences between var. makarikariense and var. coloratum, a collection was gathered in INTA Rafaela composed by fourteen accessions from different provinces of Argentina: six accessions of var. makarikariense and eight from var. coloratum. The evaluation of 152 individuals gives evidence of a wide morphological variation in the collection in traits related to forage and caryopses production; seven out of nine traits showed significant differences between var. makarikariense and var. coloratum. Based on the study of local type specimens, a morphological key to distinguish between P. coloratum varieties is provided. These results report new information about the diversity in P. coloratum in Argentina and provide valuable insights for future use of the collection as the base material of a breeding program.     

Morphological and genetic diversity of Momordica cochinchinenesis (Cucurbitaceae) in Vietnam and Thailand

Momordica cochinchinensis (Cucurbitaceae) is native to South East Asia and is important for its nutritional and medicinal properties. There is little information available on morphological and genetic diversity, crop selection and strategic germplasm collection for M. cochinchinensis. In this study, 42 accessions of M. cochinchinensis collected from Vietnam, Thailand and Australia were analysed for diversity study both at a morphological and molecular level. Both morphological and molecular analyses were in agreement and clustered the accessions based on the country of origin. The markers investigated in this study could be used for future applications with samples from unknown origins or for gene tracking for important cultivars. The Momordica accessions were highly polymorphic based on the markers suggesting high genetic diversity. Therefore the results from this study will be important in future strategic germplasm collection, conservation, horticultural development and commercial propagation of M. cochinchinensis.     

Exploitation of <Emphasis Type="Italic">Malus</Emphasis> EST-SSRs and the utility in evaluation of genetic diversity in <Emphasis Type="Italic">Malus</Emphasis> and <Emphasis Type="Italic">Pyrus</Emphasis>

A total of 8117 suitable SSR-contaning ESTs were acquired by screening from a Malus EST database, among which dinudeotide SSRs were the most abundant repeat motif, within which, CT/TC followed by AG/GA were predominant. Based on the suitable sequences, we developed 147 SSR primer pairs, of which 94 pairs gave amplifications within the expected size range while 65 pairs were found to be polymorphic after a preliminary test. Eighteen primer pairs selected randomly were further used to assess genetic relationship among 20 Malus species or cultivars. As a result, these primers displayed high level of polymorphism with a mean of 6.94 alleles per locus and UPGMA cluster analysis grouped twenty Malus accessions into five groups at the similarity level of 0.6800 that were largely congruent to the traditional taxonomy. Subsequently, all of the 94 primer pairs were tested on four accessions of Pyrus to evaluate the transferability of the markers, and 40 of 72 functional SSRs produced polymorphic amplicons from which 8 SSR loci selected randomly were employed to analyze genetic diversity and relationship among a collection of Pyrus. The 8 primer pairs produced expected bands with the similar size in apples with an average of 7.375 alleles per locus. The observed heterozygosity of different loci ranged from 0.29 (MES₉₆) to 0.83 (MES₁₃₈), with a mean of 0.55 which is lower than 0.63 reported in genome-derived SSR marker analysis in Pyrus. The UPGMA dendrogram was similar to the previous results obtained by using RAPD and AFLP markers. Our results showed that these EST-SSR markers displayed reliable amplification and considerable polymorphism in both Malus and Pyrus, and will contribute to the knowledge of genetic study of Malus and genetically closed genera.