Characterization of American hazelnut (Corylus americana) accessions and Corylus americana?×?Corylus avellana hybrids using microsatellite markers

The American hazelnut (Corylus americana Marshall) is native to the eastern United States and Southern Canada. In the early decades of the last century, breeding work by several individuals attempted to combine the cold hardiness and disease resistance of the American hazelnut with the larger nut size of the European hazelnut (C. avellana L.). Many hybrid selections grown today trace back to these early efforts. Over the past three decades, representatives of C. americana were collected and are preserved in Corvallis, Oregon. Seeds were collected along roadsides, in hedgerows, in woodland clearings, and in gardens. The seeds were germinated and the best of the resulting seedlings were preserved for later use. In this study, genetic diversity was studied in 87 American and 67 hybrid hazelnut selections using 21 microsatellite loci. The total number of alleles was 266 in the 162 accessions examined, of which 229 were present in C. americana accessions, but only 168 in the Arbor Day Farm hybrids, and 116 in the hybrids of C. americana ‘Rush’. In the American accessions, a high level of genetic diversity was observed (H _e ?=?0.74, H _o ?=?0.68). A genetic similarity matrix of the American and hybrid accessions, and a few European cultivars, was constructed and the resulting dendrogram revealed seven major groups: European cultivars and ‘Rush’ hybrids, two groups of Arbor Day Farm hybrids, three groups of C. americana accessions, and a mixed group of hybrid and American accessions. Analysis confirmed the reported parentage of 10 hybrids. The genetic diversity among the American hazelnut accessions, untapped to date, will be useful in breeding hybrids that will allow expansion of hazelnut production into eastern North America.     

Comparative analysis of genetic diversity using molecular and morphometric markers in Andrographis paniculata (Burm. f.) Nees

Andrographis paniculata is a medicinal plant of immense therapeutic value. The present study was aimed to elucidate its genetic diversity based on morphochemical and RAPD markers from 53 accessions belonging to 5 eco-geographic regions. Analysis of variance and D ² statistics revealed significant differences in all the metric traits and sufficient inter-cluster distances indicating considerable diversity among the accessions. The complementary approach of RAPD was used to evaluate the genetic dissimilarities among all the accessions using 6 highly polymorphic primers. The average proportion of polymorphic loci across primers was 96.28%. The molecular genetic diversity based on Shannon index per primer averaged 5.585 with values ranging from 3.08 to 8.70 indicating towards wide genetic base. RAPD based UPGMA and D ² cluster analysis also revealed that various accessions available in different eco-geographic regions might have originated from native places of wild abundance. Similarity matrices were generated for molecular markers and morphometric data to determine the degree of congruence between the two. A highly significant but low correlation (r = 0.547, P < 0.001) was obtained thus implying the correspondence between the two. The species is hermaphroditic and a habitual inbreeder. The present study yielded a typical triangular congruence between its breeding system, morphometric traits and RAPD markers thus elucidating the usefulness of complementary approaches to make diversity analysis more explanatory and purposeful for optimum genetic amelioration and effective conservation of its genotypic variability.     

Intra-varietal genetic diversity of the grapevine (<Emphasis Type="Italic">Vitis vinifera</Emphasis> L.) cultivar ‘Nero d’Avola’ as revealed by microsatellite markers

The Sicilian grape cultivar ‘Nero d’Avola’ is among the oldest and most cultivated in the island, taking part in the production of several red wines exported worldwide, including DOC wines (Etna Rosso and Cerasuolo di Vittoria). Due to the ancient origin and repeated clonally propagation of the cultivar, phenotypic variability has been observed. Clone identification in this important cultivar has so far relied on phenotypic and chemical traits analyses, often affected by environmental conditions. Genetic markers, such as microsatellites, are particularly useful for cultivar identification, parentage testing, pedigree reconstruction and population structure studies. In the present paper, microsatellites were used to analyze the intra-varietal genetic diversity among 118 plants of ‘Nero d’Avola’, collected in 30 vineyards displaced in different areas of Sicily. Out of 22 microsatellites, 11 showed polymorphism among samples and 15 different phylogenetic groups were identified. Results show that ‘Nero d’Avola’ actually comprises different genetic profiles, although most of clones share a common origin.     

Genetic diversity in local cultivars of garden pea (Pisum sativum L.) conserved ‘on farm’ and in historical collections

During a national Swedish collection mission of vegetable varieties conserved ‘on farm’ more than 70 pea accessions were obtained, many of which had been grown locally for more than 100 years. In spite of a likely origin in the multitude of obsolete commercial pea varieties available on the Swedish seed market in the nineteenth century, the rediscovered local cultivars have lost their original names and cultivar identity while being maintained ‘on farm’. To analyze genetic diversity in the repatriated material, 20 accessions were genotyped with twelve SSR markers and compared with 15 obsolete cultivars kept in genebanks and 13 cultivars preserved as non-viable seeds collected in 1877–1918. Most of the local cultivars were genetically distinct from each other, and in only a few cases could a possible origin in a tested obsolete cultivar be suggested. These results reflect the wide diversity of pea cultivars present in Sweden during the nineteenth century. Both between and within accession genetic diversity was larger among the historical samples of obsolete cultivars compared to local cultivars and cultivars preserved in genebanks, indicating genetic erosion over time both in genebanks and during conservation ‘on farm’. The constraints on identifying and verifying historical cultivars using genetic markers are discussed.     

Assessment of molecular diversity and population structure of the Ethiopian sorghum [Sorghum bicolor (L.) Moench] germplasm collection maintained by the USDA–ARS National Plant Germplasm System using SSR markers

The molecular diversity and population structure present in the Ethiopian sorghum collection maintained at the USDA–ARS National Plant Germplasm System (NPGS) has not been studied. In addition, 83 % of the accessions in the Ethiopian collection lack passport information which has constrained their evaluation and utility. Therefore, 137 Ethiopian accessions from NPGS were randomly selected and characterized with 20 strategically selected simple sequence repeat markers. These markers indentified 289 alleles with average polymorphic information content of 0.78. The allele frequency distribution reflects that 62 % of the alleles were rare (<0.05), 17 % range from 0.05 to 0.10, and 22 % were higher than 0.10. Expected and observed heterozygosity were estimated at 0.78 and 0.23, respectively, demonstrating Ethiopia has high sorghum genetic diversity germplasm. Population structure analysis indentified two subpopulations of 77 and 41 accessions, respectively, while a third group was constituted by 19 accessions whose classifications were not defined (i.e. hybrids). Analysis of molecular variances determined variation within subpopulations as the major source of variation. Likewise, genetic differentiation between subpopulations was moderate (F_st = 0.10). These results indicated that a continuous exchange of genes between subpopulations of sorghum exists in Ethiopia. The absence of a well defined population structure positioned this germplasm as an important resource for the study and dissection of agricultural traits by association mapping. However, genetic redundancy analysis indicated the presence of highly related accessions, therefore, strategic selected accessions must be consider prior to phenotype evaluation of larger number of accessions. The Ethiopian collection is composed of highly genetically diverse germplasm, and the genetic information presented herein is valuable to ex situ and in situ conservation programs to promote the use of this germplasm for breeding programs.     

Trace metal pollution in freshwater sediments of the world’s largest mercury mining district: sources,spatial distribution,and environmental implications

Purpose

The Almadén mining district has suffered long-term extraction activity, and this has left significant areas of decommissioned mining liabilities. Nowadays, the uncontrolled runoff and related erosion and transport of trace metal-enriched soils and sediments affect the whole freshwater ecosystem. The goal of this study was to distinguish geogenic from mining-related sources of trace metals in freshwater sediments, to understand their dispersion in the watershed, and, finally, to evaluate the potential environmental implications for future corrective plans.

Materials and methods

Freshwater surface sediment samples were collected from ten points along the main streams of the watershed (nine inside the mining district and one control point outside the district). Sediments were air dried and analyzed by different standard methods for pH, total major and trace element concentrations, total organic carbon, and grain size. In addition to the determination of the enrichment factor, a multi-statistical approach was applied involving discriminant analysis, Student’s t test, and Mann-Whitney U analysis.

Results and discussion

Sediments inside the district contained high levels of major and trace elements with respect to the control point. The predominance of fine fractions in these sediment samples appears to be one of the most important factors that affects trace metal concentrations. Among the trace elements, not only Hg but also As, Pb, and Zn are discriminative geochemical markers, thus allowing the identification of the different mining sources and their individual or combined impact throughout the district. Furthermore, the high enrichment factors obtained for As, Hg, Pb, and Zn with respect to the local background values highlight the persistent and severe impact from the decommissioned mines on the freshwater surficial sediments and their potential geoavailable risk for aquatic organisms.

Conclusions

The geochemistry of freshwater sediments alone demonstrates that different contamination sources are recognizable within the mining district and these can be related to the specific decommissioned mines. In addition, the discrete sources can be clearly distinguished on the basis of the statistical analysis of the geochemical data. Despite the closure of the mines, stream sediments are still the main repository of trace metals within the district, and they are therefore a potential threat to the freshwater ecosystem.

     

Trait phenotyping and SSR markers characterization of wheat (Triticum aestivum L.) germplasm for breeding early maturing wheat’s for Western-Himalayas

Genetic Resources and Crop Evolution - The study involved evaluation of 96 wheat genotypes for early maturity and related traits and molecular characterization of trait specific candidate genotypes...     

Genetic diversity and population structure in a regional collection of Kersting’s groundnut (Macrotyloma geocarpum (Harms) Maréchal & Baudet)

Genetic Resources and Crop Evolution - Kersting’s groundnut (Macrotyloma geocarpum (Harms) Maréchal &amp; Baudet) is an important source of protein and essential nutrients that...     

Molecular distinction among mulberry (Morus spp.) species and varieties cultivated in the Democratic People’s Republic of Korea

Mulberry (Morus spp.) is a cross-pollinating and highly hybridized plant of which productivity are greatly varied in different varieties. Accurate distinction among mulberry varieties and understanding of phylogenetic relationship among them would be crucial for the development of sericulture. We have analysed molecular distinction among four mulberry species and varieties cultivated in DPR Korea by using nuclear ribosomal internal transcribed spacer (ITS) sequences and inter simple sequence repeat (ISSR) markers. ITS sequences doesn’t represent a remarkable interspecific distinction among four mulberry species used in our study, suggesting that it could not be employed to identify them. ISSR analysis using 16 random primers generated 158 different markers ranging from 100 to 4000 bp in size. The results showed the inter-specific genetic variation (55.34%) was slightly higher than intra-specific genetic variation (44.66%), with comparatively low average number of migrants per generation (Nm) among populations (0.3886). Using ISSR primers selected in this study, in the future, the suitable breeding strategy might be established in raising of elite mulberry varieties on the basis of interspecific hybridization.

     

Genetic diversity and relationship of Guinea yam (<Emphasis Type="Italic">Dioscorea cayenensis</Emphasis> Lam.–<Emphasis Type="Italic">D. rotundata</Emphasis> Poir. complex) germplasm in Benin (West Africa) using microsatellite markers

Guinea yam (Dioscorea cayenensis–D. rotundata complex) is an important tuber crop that highly contributes to food security and poverty alleviation in Benin. The knowledge and understanding of the extent of genetic variation of Guinea yam germplasm is important for planning of the genetic conservation, and the utilisation of this resource. The objective of this study was to assess the genetic diversity and relationships of 64 yam landraces whose dried chips are considered as resistant to insect attacks using 41 simple sequence repeat. Among these primers, 13 were found to be polymorphic, giving 113 polymorphic alleles. The number of alleles per locus ranged from 4 (Ym50) to 13 (Ym29), with an average of 8.69. Unique allele was observed with some landraces (Singou and Tchakatchaka) and can be considered as unique gene and use in yam breeding program. The mean polymorphic information content values for all markers used was 0.76 and ranged between 0.58 and 0.91 in loci YM3 and YM32 respectively. The genetic distance of yam landraces ranged from 0.45 (Yasoubagarou) to 0.04 (Assinapeira and Alahina), indicating that the yam germplasm has a high degree of genetic diversity supported by an averagely observed heterozygosity of 0.78. Cluster analysis using unweighted pair group method with arithmetic average grouped the 64 yam landraces into two distinct clusters. This tendency was also observed in the principal coordinate analysis. The analysis of molecular variance revealed that 96 % of the variation was found within the population and only 4 % between the populations. Genetic diversity and relationship assessments among the 64 yam landraces of Benin could provide useful information for efficient use of these materials, especially for genetic improvement.     

Maize (<Emphasis Type=Italic>Zea mays</Emphasis> L.) management in Yaxcaba,Yucatan, during the twentyfirst century’s first decade is consistent with an overall loss of landrace diversity in southeast Mexico

The status of genetic resource conservation in centers of crop diversity remains disputed. Recent case-study findings of persistent maize diversity in Yaxcaba, Yucatan, a municipality in southeast Mexico, have raised questions on earlier reports of widespread losses across the crop’s center of diversity in Mexico. We break down patterns in maize varietal richness in southeast Mexico to show that temporal trends in Yaxcaba are subsumed under spatial variation in this broader region and consistent with an overall loss of diversity. Persistence of diversity in Yaxcaba can be explained by conditions that allowed subsistence farmers to continue sowing land even as maize prices dropped, but these conditions may be rare in Mexico and likely to change. Yaxcaba emerges as a rare community of exceptional diversity from which valuable policy lessons can be drawn. We find that gaps and omissions in the Mexican Government’s strategy for maize conservation have excluded Yaxcaba and likely resulted in an ineffective intervention elsewhere in the Peninsula. An integrated-systems perspective should help us develop a coherent strategy for resource conservation and climate adaptation based on more efficient and equitable instruments.     

Genetic relationships among improved varieties of rice (<Emphasis Type="Italic">Oryza sativa</Emphasis> L.) in Indonesia over the last 60 years as revealed by morphological traits and DNA markers

Morphological traits and two kinds of molecular markers were employed to study the genetic relationships among improved rice (Oryza sativa ) varieties of Indonesia since 1943. Dendrograms based on morphological traits and both molecular markers (simple sequence repeats, SSR and single nucleotide polymorphism, SNP) agreed in separating the varieties into two primary groups. Based on the morphological traits, a larger group (>60 %) contains varieties with smaller sizes compared with those in the smaller group (<40 %). SSR and SNP markers revealed that most of the varieties belonged to indica (88; 89 %) and japonica (9; 8 %) subspecies, and 3 % of varieties were not involved in two subspecies. The molecular markers revealed that the genetic diversity (H) stagnated between stage II (1967–1985) and stage III (1986–2003). However, during stage I (1943–1966), H was higher than in the other stages as revealed by SNP markers, while H in stage I was lower than in the other stages as revealed by SSR markers. In this study, the two molecular data sets were positively correlated and positive correlations between the phenotypic and molecular data depended on the kind of molecular marker: SNP had higher Mantel r values than SSRs. Besides, SSR markers seem to be appropriate for pedigree studies, while SNP markers could be used to reveal genomic relationships. These findings were attributable to the different properties of these two different markers. These results suggested that the diversity and differentiation of both the phenotypic and molecular marker variations were probably resulted from the crossing and selection in rice breeding in Indonesia. We suggest that Indonesia needs another strategy to improve new varieties to avoid a reduction in genetic diversity and similarity.     

Microsatellite analysis of Alpine grape cultivars (<Emphasis Type="Italic">Vitis vinifera</Emphasis> L.): alleged descendants of Pliny the Elder’s <Emphasis Type="Italic">Raetica</Emphasis> are genetically related

According to Pliny the Elder and other Greco-Roman geoponics, Raetica was a famous white grape as well as a white wine produced in Raetia, a Province of the Roman Empire. Does Raetica grape have modern descendants? Etymologically and geographically, the white ‘Rèze’ from Valais (Switzerland) would be the best candidate. Using available microsatellite data, we searched for relatives of ‘Rèze’ in our database containing over 1,700 genotypes of grape cultivars from all over the world. Twelve cultivars showing putative first-degree (parent–offspring or full-siblings) or second-degree (grandparent–grandoffspring, uncle–nephew or half-siblings) relationships with ‘Rèze’ were then analysed at 60 microsatellite markers. Calculation of allele sharing and likelihood ratios between competing relationship categories revealed that four cultivars had parent–offspring relationship with ‘Rèze’: ‘Cascarolo Bianco’ (Piedmont, Italy), ‘Arvine Grande’ (Valais, Switzerland), ‘Groppello di Revò’ and ‘Nosiola’ (Trentino, Italy). Given that some of these are also said to be Raetica descendants, we may well be on the tracks of Pliny the Elder’s Raetica grape. However, there is no evidence about the identity of Raetica. Analysis of ancient DNA of grape pips excavated from archaeological sites of the Roman times might provide key information. Our first attempts were unsuccessful, but analysis of additional samples and optimisation of the method could provide groundbreaking results about the identity of the grapes cultivated in classical antiquity.