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.     

Molecular phylogenetics and systematics of Trigonella L. (Fabaceae) based on nuclear ribosomal ITS and chloroplast trnL intron sequences

The genus Trigonella includes the widely cultivated T. foenum-graecum and a number of other medicinal and aromatic plant species distributed around the Mediterranean region. Sectional delimitation of Trigonella species is still based on morphology and interspecific relationships within the genus are not yet sufficiently resolved. Phylogenetic relationships in 22 species representing 11 of the 12 sections recognized within the genus Trigonella were analyzed using nuclear ITS and plastid trnL-F DNA sequences. Within nuclear ITS region, ITS-II was found to evolve faster compared to ITS-I. Maximal phylogenetic resolution and support was obtained in the combined analysis of the two selected regions. Trees resulting from maximum parsimony as well as Bayesian inference of combined data provided evidence for Trigonella being monophyletic with high support but did not agree with the traditional subgeneric division. Phylogenetic reconstructions indicated three major lineages supported by apomorphies in inflorescence and stipule. The phylogram supported the sectional delimitation of sections Cylindricae, Vérae, Samaroideae, Pectinatae, Erosae and Callicerates. There is strong support to combine monotypic sections Pectinatae and Erosae into one. However, species belonging to section Foenum-graecum and Falcatulae clustered in different subclades, contrary to their current classification. Inflorescence type appears to be a useful character with taxonomic potential for phenetic implications at subgeneric and sectional level within the genus. Moreover, some legume and seed characteristics, considered important in existing taxonomy, appear to have arisen more than once in Trigonella and are homoplastic.     

Actinomycetal complex of light sierozem on the Kopet-Dag piedmont plain

The population density of actinomycetes in the samples of light sierozem from the Kopet Dag piedmont plain (75 km from Ashkhabad, Turkmenistan) reaches hundreds of thousand CFU/g soil. The actinomycetal complex is represented by two genera: Streptomyces and Micromonospora. Representatives of the Streptomyces genus predominate and comprise 73 to 87% of the actinomycetal complex. In one sample, representatives of the Micromonospora genus predominated in the complex (75%). The Streptomyces genus in the studied soil samples is represented by the species from several sections and series: the species of section Helvolo-Flavus series Helvolus represent the dominant component of the streptomycetal complex; their portion is up to 77% of all isolated actinomycetes. The species of other sections and series are much less abundant. Thus, the percentage of the Cinereus Achromogenes section in the actinomycetal complex does not exceed 28%; representatives of the Albus section Albus series, Roseus section Lavendulae-Roseus series, and Imperfectus section belong to rare species; they have been isolated not from all the studied samples of light sierozem, and their portion does not exceed 10% of the actinomycetal complex.     

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.     

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.     

A review of genetic resources of almonds and stone fruits (<Emphasis Type="Italic">Prunus</Emphasis> spp.) in Iran

Iran is amongst the countries in the world widely known for cultivation of Prunus spp. (or stone fruits). It is both a centre of origin and diversity of the stone fruits. Numerous wild species as well as many cultivars and landraces of these fruit crops are important genetic resources today in Iran and can be used for improvement and breeding of scion and rootstock cultivars which are resistant to many biotic and abiotic stresses through modern genomics and genetic technologies. This paper discusses the distribution, ethno-botany, diversity and utilization of wild and domesticated genetic resources of stone fruits including almond (Prunus dulcis (Miller) D. A. Webb.), peach and nectarine (P. persica Batsch), European and Japanese plum (P. × domestica L., and P. salicina L., respectively), sweet and sour cherry (P. avium L., and P. cerasus L., respectively), and apricot (P. armeniaca L.), all of which are members of the Rosaceae family. The goal of this paper is to highlight the importance of Iran as a main contributor to the diversity of Prunus genetic resources in the world, as well as, present major achievements regarding identification, collection, evaluation, conservation and utilization of this valuable genetic resource in Iran.     

Biodiversity in Ethiopian linseed (<Emphasis Type="Italic">Linum usitatissimum</Emphasis> L.): molecular characterization of landraces and some wild species

Molecular characterization of germplasm is important for sustainable exploitation of crops. DNA diversity was measured using inter-retrotransposon-amplified-polymorphism and inter-simple-sequence-repeat markers in 203 Ethiopian landraces and reference varieties of linseed (flax, Linum usitatissimum) and wild Linum species. Molecular diversity was high (PIC, 0.16; GD, 0.19) compared to other reports from the species. Genotyping separated reference from landrace accessions, and clustered landrace accessions from different altitudes and geographical regions. Collections showed evidence for recent introduction of varieties in some regions. The phylogeny supported L. bienne Mill. as the progenitor of domesticated L. usitatissimum. Markers developed here will be useful for genetic mapping and selection of breeding lines. The results show the range of characters that can be exploited in breeding lines appropriate for smallholder and commercial farmers in Ethiopia, producing a sustainable, secure, high-value crop meeting agricultural, economic and cultural needs.     

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.     

Farmers perception of pesticide use and genetic erosion of landraces of tetraploid wheat (<Emphasis Type="Italic">Triticum</Emphasis> spp.) in Ethiopia

Perception of farmers’ about the use of pesticides and genetic erosion of tetraploid wheat landraces of Ethiopia was assessed through focus group discussions with farmers, on-farm observations, personal interviews with farmers, by using structured questionnaires of temporal and spatial methods. A total of 1496 farmers from seven provinces in the country were interviewed. Farmers’ knowledge about pesticide increases suggests that they are not happy on using chemicals because of their negative impact on farm land. About 75 % of the farmers believe that, although the use of pesticides may increase the production of wheat, it has a negative impact on (human) health and environment. Women showed a higher concern for pesticides’ harmfulness than men. Farmers’ valuation of genetic erosion was estimated as reduced importance of landraces, as shown by a the lower proportion of landraces either grown or sold on the market. The four most important factors cited for loss of landraces were reduction in land area per capita, displacement by released/modern varieties of hexaploid wheat and teff, reduced benefit from landraces, and displacement by other crops and chat. Genetic erosion of 100 % was observed for Triticum dicoccon in the provinces of Gojam and Gonder and for T. polonicum in Tigray and Gojam. Overall, genetic erosion in the country was 32.0, 35.3, 55.9, 84.4 and 84.4 % for T. durum Desf., T. turgidum L., T. aethiopicum Jakubz., T. polonicum L. and T. dicoccon Schrank, respectively.     

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.     

The influence of <Emphasis Type="Italic">Aster x salignus</Emphasis> Willd. Invasion on the diversity of soil yeast communities

The annual dynamics of yeast communities were studied in the soddy-podzolic soil under the thickets of Aster x salignus Willd., one of the widespread invasive plant species in central Russia. Yeast groups in the soils under continuous aster thickets were found to differ greatly from the yeast communities in the soils under the adjacent indigenous meadow vegetation. In both biotopes the same species (Candida vartiovaarae, Candida sake, and Cryptococcus terreus) are dominants. However, in the soils under indigenous grasses, eurybiontic yeasts Rhodotorula mucilaginosa, which almost never occur in the soil under aster, are widespread. In the soil under aster, the shares of other typical epiphytic and pedobiontic yeast fungi (ascomycetic species Wickerhamomyces aniomalus, Barnettozyma californica and basidiomycetic species Cystofilobasidium macerans, Guehomyces pullulans) significantly increase. Thus, the invasion of Aster x salignus has a clear effect on soil yeast complexes reducing their taxonomic and ecological diversity.     

Population genetics of traditional landraces of <Emphasis Type="Italic">Cucurbita pepo</Emphasis> L., 1753 in the cloud forest in Baja Verapaz,Guatemala

Little is known regarding the effect of fragmentation and human agricultural management on the genetic variation and gene flow of Cucurbita pepo L., 1753 in moderate fragmented areas in central Guatemala. We hypothesize that the genetic variation of C. pepo is affected by forest fragmentation and by traditional agricultural management. Therefore, we aim to determine: (1) the genetic diversity and genetic structure of C. pepo in the Cloud Forest Corridor (CFC) (2) the extent of genetic admixture between commercial variety (CV) and traditional landraces (TL) of C. pepo, (3) the effect of habitat fragmentation in the population genetics of C. pepo with a landscape approach, and (4) the potential relationship between traditional management practices and genetic diversity of C. pepo in the CFC. We detected the existence of high level of genetic diversity (AR = 3.43; He = 0.50), inbreeding (Fis = 0.25) and moderate population structure of C. pepo in the CFC (Fst = 0.16). No correlation between landscape and genetics was found. Also, we found high genetic admixture between CV and TL. It seems that human practices, mainly related with seed exchange patterns, could affect genetic diversity of C. pepo in the CFC. C. pepo populations in the CFC are structured, with inbreeding, and show admixture with the CV, an aspect that could affect its genetic diversity. The agricultural management influenced the population genetics of C. pepo in the CFC, but the landscape did not. We suggest that special efforts should be made to preserve the diversity of this important indigenous food source for Guatemalan people as well as their management practices.     

Genetic diversity and relationships of wild and cultivated <Emphasis Type="Italic">Zanthoxylum</Emphasis> germplasms based on sequence-related amplified polymorphism (SRAP) markers

The genus Zanthoxylum, belonging to Rutaceae, has a long history of cultivation both for economic and chemical values in China. To effectively conserve and sustainably utilize this genus resource, a study on genetic diversity and relationships of Zanthoxylum germplasms was carried out by employing SRAP markers. We used 16 primer combinations to assess genetic variations and relationships among 175 accessions from eight cultivated provenances, including Shandong, Henan, Shanxi, Shaanxi, Gansu, Sichuan, Guizhou and Yunnan. A total of 145 clear repetitive and intense bands were yielded, and the percentage of polymorphic bands was 100 % for per primer combination, indicating a relatively high diversity among Zanthoxylum germplasms. From a geographic perspective, the highest genetic diversity level was observed within Guizhou provenance (N _a  = 1.97, Ne = 1.52, H = 0.31, I = 0.46) while Henan provenance had the lowest genetic diversity (N _a  = 1.68, Ne = 1.45, H = 0.25, I = 0.37). Based on AMOVA results, the abundant genetic variation was mainly caused by variation of intra-provenances (84.96 %), rather than among provenances (15.038 %). The results indicated low genetic differentiation (G _st  = 0.133) and high gene flow (N _m  = 3.2605) among provenances. The neighbor-joining tree revealed that the 175 accessions could be divided into four groups, and groupings indicated a divergence between the cultivated accessions of Zanthoxylum bungeanum Maxim. and Z. armatum DC. Moreover, three accessions of Z. piperitum DC. var. inerme without prickles introduced from Japan gathered one cluster. Cluster IV is composed of accessions of different geographical origin, including 11 wild species and 10 cultivated accessions of Z. bungeanum. The cluster analysis also reflected a relatively close relationship between the geographical origins and the classification of accessions in cluster I. Structure analysis indicated that collected Zanthoxylum accessions could be divided into two major groups. The information obtained from our research would benefit to make use of Zanthoxylum germplasms and assist the management of a Zanthoxylum germplasms collection.     

Discriminating power of microsatellites in cranberry organelles for taxonomic studies in <Emphasis Type="Italic">Vaccinium</Emphasis> and Ericaceae

Simple sequence repeats (SSRs) in chloroplast and mitochondrial DNA, which have not been previously developed in the Ericaceae or, more specifically, in the genus Vaccinium, can be powerful tools for determining evolutionary relationships among taxa. In this study, 30 chloroplast, 23 mitochondrial, and 1 mitochondrion-like SSRs were identified in cranberry (V. macrocarpon), and primer-pairs were developed and tested for each locus. Although no polymorphisms were detected for any of the 54 SSR loci in nine diverse cranberry genotypes, all primers were cross-transferable to some extent to a panel of 12 additional Vaccinium taxa and four non-Vaccinium Ericaceae species. A Neighbor-Joining tree of the estimated average squared distances resolved the species by genus and by section within Vaccinium. Similar topologies with increased branch support were observed in Bayesian inference trees constructed from the DNA sequences of six plastid and two mitochondrial SSR loci. Two multiplexing/poolplexing panels of M13 fluorescently labeled primers, which amplify 24 of the 54 markers, were developed and can serve as an efficient, cost-effective means for characterizing the basic molecular phylogeny of Vaccinium. Increased understanding of evolutionary relationships among Vaccinium species should facilitate interspecific hybridization and introgression efforts to improve economically important traits of commercial berry crops.     

Mesophilic and thermotolerant actinomycetes in strongly heated soils

Mesophilic and thermotolerant actinomycetes were identified in strongly heated desert-steppe soils of Mongolia, mountainous meadow soils of the Central Caucasus, and cyanobacterial films on volcanic ash near hot springs of Kamchatka. Thermotolerant actinomycetes in these soil objects were more abundant and had a greater taxonomic diversity in comparison with mesophilic actinomycetes. Thermotolerant Streptomyces were present in all the objects, except for sample 117 from the desert-steppe soil and the cyanobacterial film on volcanic ash. Thermotolerant actinomycetes from the Micromonospora and Actinomadura genera predominated in the desert-steppe soil; representatives of the Micromonospora genus predominated in the cyanobacterial film on volcanic ash, and representatives of the Microtetraspora genus predominated in the samples of geyserite near hot springs of Kamchatka.     

Genetic relationship of diploid wheat (<Emphasis Type="Italic">Triticum</Emphasis> spp.) species assessed by SSR markers

Genetic diversity of 139 accessions of diploid Triticum species including Triticum urartu, Triticum boeoticum and Triticum monococcum was studied using 11 SSR (simple sequence repeats) markers. A total of 111 alleles with an average of 10 alleles per locus were detected. The polymorphism information content (PIC) of each SSR marker ranged from 0.30 to 0.90 with an average value of 0.62. Among the three Triticum species T. urartu had the highest number of total alleles (Na?=?81), private alleles (Npa?=?15) and showed higher genetic diversity (Hex?=?0.58; PIC?=?0.54). The genotypes from Turkey exhibited the highest genetic diversity (PIC?=?0.6), while the least diversity was observed among 4 Georgian accessions (PIC?=?0.11). Cluster analysis was able to distinguish 139 wheat accessions at the species level. The highest genetic similarity (GS) was noted between T. boeticum and T. monococcum (GS?=?0.84), and the lowest between T. urartu and T. monococcum (GS?=?0.46). The grouping pattern of the PCoA analysis corresponded with cluster analysis. No significant differences were found in clustering of T. urartu and T. monococcum accessions with respect to their geographic regions, while within T. boeoticum species, accessions from Iran were somewhat associated with their geographical origin and clustered as a close and separate group. The results from our study demonstrated that SSR markers were good enough for further genetic diversity analysis in einkorn wheat species.     

Relationship between spike morphology and habitat of four <Emphasis Type="Italic">Aegilops</Emphasis> species of section Sitopsis

This study examines the relationship between spike morphology and natural habitat for 84 accessions of four Aegilops species, belongs to section Sitopsis, Ae. bicornis, Ae. longissima, Ae. searsii, and Ae. sharonensis in genus Aegilops, section Sitopsis, wild relatives of Triticum aestivum L. These species are considered valuable genetic resources for future cultivation and breeding of domesticated wheat. The goals of the study were to: (1) document variation in spike morphology among these four species; (2) examine the relationship between spike morphology and native habitat; (3) document geographical distribution of distinct spike morphology; and (4) examine the relationship between spike morphology and heading time and value for these four species. The results reveal significant differences in spike morphology among species of section Sitopsis. The most noteworthy variation involved the absence/presence of lateral awn, such that species with lateral awn were restricted in coastal, though species without lateral awn were mainly distributed in inland. This suggests that local climate may be a determinant of variation in lateral awn, and that this trait may be subject to convergent evolution. Differences in heading time in sympatric area were also observed. The differences may enhance species divergence and could represent a lead speciation event. The results of this study will facilitate identification of populations or accessions of wild wheat with favorable traits and/or novel adaptive genes.     

Maize diversity in southern Brazil: indication of a microcenter of <Emphasis Type="Italic">Zea mays</Emphasis> L.

‘Microcenters of diversity’ are restricted geographical areas within which a significant diversity of genetic resources is accumulated. Maize genetic variability, one of the largest among cultivated species, particularly in far western Santa Catarina, southern Brazil, has shown a rich store of landraces, conserved on farm by small-scale farmers. Thus, this study aimed to characterize the diversity of Zea mays L. landraces in two municipalities of this micro-region in Santa Catarina, as well as its geographic distribution, developing the census of diversity as a methodological proposal. Diagnosis was made according to the farmers’ knowledge. The field survey was conducted in 70 rural communities involving 2049 farms. The methodology allowed identifying 136 populations of wild relatives, of which some belong to the species Zea luxurians (Durieu and Ascherson) Bird, and 1513 populations of maize landraces, comprising 1078 of popcorn, 337 of common maize, 61 of sweet maize and 37 of flour maize. The identification of 59 morphological groups, the high use, adaptive and agronomic values, and the Shannon index (H′), estimated according to the grain shape (0.79), endosperm type (0.73), size (0.87), color (1.40), and morphological group (3.16), showed at set a considerable diversity distribution conserved on farm in this micro-region. Landrace richness and the presence of wild relative species, associated with the local human activity and sociocultural aspects, allowed to characterize the far western Santa Catarina as a ‘microcenter of diversity’ of Zea mays L.