Simple Sequence Repeat Profiles Research Articles

Assessing the Genetic Diversity of Daylily Germplasm Using SSR Markers: Implications for Daylily Breeding.

This work aims to characterize the genetic diversity of species, early hybrids, and cultivars using microsatellite simple sequence repeat (SSR) markers, as well as analyze and identify the origin of Hemerocallis spp. early hybrids. For this research, samples were collected from different types of daylily species, early hybrids (known or hypothetically first-generation hybrids from Hemerocallis species), foreign, and Lithuanian varieties. An initial screening of SSR primers developed for Hemerocallis citrina was performed, and their suitability for testing other daylily species and hybrids was evaluated. The genetic diversity was assessed with the selected eight-primer set, and molecular SSR profiles were created. Primer SAU00097 is the most informative according to heterozygosity (0.95) and polymorphism information content (PIC) (0.17). The highest heterozygosity was observed in Lithuanian cultivars (0.713), the lowest in species (0.583). Genetic relationships between species show that only fulvous daylilies are separated into a different cluster. The highest variation among genotypes was observed in the species group (18%), while modern cultivars had the slightest variation among genotypes (1%). The putative origin of early hybrids was analyzed using a likelihood heatmap of all genotypes. Results show what species might be used in breeding for early hybrids. Several modern diploid and tetraploid daylily cultivars have triploid species as ancestors.

Metabolite Profiling of Gardenia jasminoides Ellis In Vitro Cultures with Different Levels of Differentiation.

Gardenia jasminoides Ellis is an aromatic and medicinal plant of high economic value. Much research has focused on the phytochemistry and biological activities of Gardenia fruit extracts; however, the potential of the Gardenia plant in vitro cultures used as mass production systems of valuable secondary metabolites has been understudied. This paper presents data on metabolite profiling (GC/MS and HPLC), antioxidant activities (DPPH, TEAC, FRAP, and CUPRAC), and SSR profiles of G. jasminoides plant leaves and in vitro cultures with different levels of differentiation (shoots, callus, and cell suspension). The data show strong correlations (r = 0.9777 to r = 0.9908) between antioxidant activity and the concentrations of chlorogenic acid, salicylic acid, rutin, and hesperidin. Eleven co-dominant microsatellite simple sequence repeats (SSRs) markers were used to evaluate genetic variations (average PIC = 0.738 ± 0.153). All of the investigated Gardenia in vitro cultures showed high genetic variabilities (average Na = 5.636 ± 2.157, average Ne = 3.0 ± 1.095). This is the first report on a study on metabolite profiles, antioxidant activities, and genetic variations of G. jasminoides in vitro cultures with different levels of differentiation.

Genetic characterization of cultivated apple (Malus x domestica Borkh.) in Morocco using microsatellite (SSR) markers

Genetic diversity of 27 apple genotypes from four geographical regions of Morocco was analyzed using 26 simple sequence repeat (SSR) primers. In total, 195 polymorphic SSR alleles were detected, with sizes ranging from 78 to 209 bp. The results obtained for the average number of alleles per locus (7.5), effective number of alleles (4.62), Shannon information index (1.66), expected heterozygosity (0.76), observed heterozygosity (0.74) and polymorphism information content (0.76) showed a moderate level of polymorphism, which suggests that Moroccan apple cultivars exhibit significant genetic diversity. Over the 26 SSR loci used, the probability of identity P (ID) was 4.62 10 −29 indicating that most markers were highly discriminating and powerful for cultivars characterization. The principal coordinate analysis and hierarchical classification suggested the presence of four well defined groups, which was confirmed later by model based population structure. Furthermore, strong genetic differentiation between these four groups was also detected (FST = 0.28) . Most of the individuals segregated into the four groups showing a membership coefficient greater than 0.80, which indicates their better genetic integrity. A parentage analysis, however, shows that cultivars from the four regions are minimally hybridized. After comparing SSR profiles and genotypes names, we conclude that the problem of homonyms and/or labeling errors appear in the studied cultivars.Thus, based on genetic profiles, two individuals (Beldi 1/Beldi 2 and Laakri 5/Laakri 6) found to be duplicated. Additionally, some cultivars with the same name are grouped in different clusters suggesting the existence of possible homonymy. Lastly, the present work confirms the usefulness of SSR markers for the elimination of duplications and characterization of diversity and hybrid characters of apple genotypes in Morocco.

Microsatellite markers as a tool for active germplasm management and bridging the gap between national and local collections of apple

Simple sequence repeat (SSR) microsatellite markers have been extensively used to identify duplication and analyse genetic diversity in germplasm collections of apple. Here, we present findings from the use of a standard set of SSR loci in the managed repropagation of a significant international germplasm collection: the UK National Fruit Collection (NFC). A subset of eight SSR loci was deemed sufficient to distinguish all apart from the clonal relatives across a sample of 1995 accessions, with a single exception being one pair of full siblings. In total, 99% of accessions were able to be confirmed present and correct after the replacement of trees initially identified to be incorrectly propagated. In parallel to the curation of the collection itself, through an initiative led by the UK local apple enthusiast community, 3373 SSR profiles for apples held in local collections were compared to the NFC holdings. Overall, in both sets of material, diversity remained high with average gene diversity values of 0.800 and 0.812 in the NFC holdings and local collections, respectively. Accessions in local collections were not found to differ in their overall coverage of genetic diversity to that of the NFC collection (FST = 0.0035) although significant numbers of locally valued, and genetically distinguishable individuals were identified, some of which may represent ‘lost’ cultivars.

Towards a Joint International Database: Alignment of SSR Marker Data for European Collections of Cherry Germplasm.

The objective of our study was the alignment of microsatellite or simple sequence repeat (SSR) marker data across germplasm collections of cherry within Europe. Through the European Cooperative program for Plant Genetic Resources ECPGR, a number of European germplasm collections had previously been analysed using standard sets of SSR loci. However, until now these datasets remained unaligned. We used a combination of standard reference genotypes and ad-hoc selections to compile a central dataset representing as many alleles as possible from national datasets produced in France, Great Britain, Germany, Italy, Sweden and Switzerland. Through the comparison of alleles called in data from replicated samples we were able to create a series of alignment factors, supported across 448 different allele calls, that allowed us to align a dataset of 2241 SSR profiles from six countries. The proportion of allele comparisons that were either in agreement with the alignment factor or confounded by null alleles ranged from 67% to 100% and this was further improved by the inclusion of a series of allele-specific adjustments. The aligned dataset allowed us to identify groups of previously unknown matching accessions and to identify and resolve a number of errors in the prior datasets. The combined and aligned dataset represents a significant step forward in the co-ordinated management of field collections of cherry in Europe.

Microsatellite fingerprinting and metabolite profiling for the geographical authentication of commercial green teas

The authentication of geographical provenance is an important issue with respect to commercial tea products. Here, simple sequence repeat (SSR) fingerprinting and metabolite profiling were implemented to differentiate between 37 commercial green teas, produced in China, Japan and Korea. A set of 21 SSR assays detected 175 alleles, and a multiplex of three of these assays was sufficient to distinguish each of the samples. Metabolite profiling based on ultra-high performance liquid chromatography coupled with high resolution mass spectrometry detected features which proved to be correlated with a specific provenance. There was only a moderate level of correlation between the SSR and metabolite profiles. Such a level of correlation suggests that genotype, environment and post-harvest processing are all determinants of end-use quality. The two analytical approaches are complementary to one another, and are recommended to be used in conjunction.

Black rice cultivar from Java Island of Indonesia revealed genomic, proteomic, and anthocyanin nutritional value.

Black rice is considered to be functional food containing anthocyanins as bioactive compounds. This study examined the genomic and proteomic patterns in local black rice from Java Island, Indonesia, with attention to the mechanism of anthocyanin synthesis. Three kinds of black rice from Java Island, including black rice from East Java (BREJ), black rice from Central Java (BRCJ), and black rice from West Java (BRWJ), were studied in comparison to white rice (WREJ) and red rice (RREJ). Genomic profiling was done by simple sequence repeat (SSR) analysis, and sequencing of red coleoptile (Rc) and glycosyltransferase (GT) genes, followed by in silico analysis. Total anthocyanin was investigated by ultra-high performance liquid chromatography- diode array detector (UHPLC-DAD). The proteomic profiles were determined by liquid-chromatography and mass spectrometry of tryptic peptides. The SSR profiles showed a specific band in each black rice variant. The Rc gene exon-2 sequences were similar in the three black rice cultivars. The GT gene sequence was identified as a new variant that correlates with the purple stem, leaf, bran, and whole grain morphology seen exclusively in the BRWJ cultivar. The anthocyanin composition in Java black rice is diverse. The highest cyanidin level was seen in BRWJ and the highest level of peonidin-3-O-glucoside in BREJ. Proteomic profiling of the black rice cultivars demonstrated that the expression of proteins that might be related to the levels of anthocyanin synthesis varied. These studies conclude that the genomic, proteomic and anthocyanins composition of Java black rice cultivars may be used the improvement of their functional nutrition values.

SSR Markers in Genetic Diversity Assessment of Fig Ficus carica L. Populations in Kurdistan Region – Iraq

In the current study, simple sequence repeats (SSR) markers were used to assess the phylogenetic relationships and to investigate genetic polymorphism among 28 fig landraces in Kurdistan Region-Iraq. Fifteen SSR loci produced 73 alleles were produced across all studied genotypes. The observed heterozygosity (Ho) was (0.000) detected with all primers. The expected heterozygosity (He) was ranged from 0.000 to 0.875. The Polymorphic information content PIC was ranged from 0.000 to 0.843, and Fixation index values were ranged from +0.999 to +1.000. The SSR profiles produced were further used for assessing similarities (genetic distance) between the cultivars studied. Genetic distance calculation was achieved using computer software (NTSYS-PC). The genetic distances among the studied genotypes were ranged between (0.1029-0.9485). Genetic distances were supported by the developed dendrogram using UPGMA method. This dendrogram was split into two major groups, and each group was further divided into subgroups. The product of the general data and study of the clusters suggested that almost all the fig cultivars revealed significant genetic diversities. The microsatellite markers allowed clearly the differentiation between studied fig landraces and gave the reliability of these markers in fingerprinting of fig genotypes. It is worth to mention that the study findings will help the management of fig genotypes and might help the selection of landraces for future breeding program in this region.

Unraveling the genetics of calcium content in finger millet grains through association mapping

Combating mineral deficiencies has been a major challenge for agricultural scientists world over. Lack of calcium in diets could be overcome through biofortifying food crops especially cereals. Finger millet (Eleusine coracana) grains are highly rich in calcium, therefore in the present study this phenotypic trait was explored using association study on a natural population of finger millet. A total of 238 accessions of finger millet were analysed using 85 simple sequence repeats (SSR) markers. SSR profiles generated 160 alleles and 20 primer pairs which were polymorphic across the population with 0.14 to 0.78 polymorphic information content. Grain Calcium content (GCC) varied from 72 to 452 mg/100g seed. Two accessions, GPHCPB45 (452.8 mg) and GPHCPB 439.8 mg) each from Northern India and exotic areas were found with highest GCC. Association analysis through the general linear model in TASSEL software detected two markers UGEP78 and UGEP60 in significant association (P less than 0.001) to calcium content. The molecular marks, UGEP60 can be a potential marker with phenotypic variance amounting to 13.8%. However, the mixed linear model did not detect any significant associations probably because of low polymorphism within the finger millet collection considered in this study. Identification of two accessions with higher calcium content may be useful in finger millet improvement.

Simple Sequence Repeat Characterisation of Traditional Apple Cultivars (Malus domestica Borkh.) Grown in the Region of Madrid (Central Spain)

The genetic diversity of many Spanish apple collections has been evaluated, but some areas from Central Spain have not been included. In the present work, a set of 41 accessions (33 diploids and 8 triploids) of 23 traditional apple cultivars collected in the region of Madrid and maintained at the IMIDRA collection was analysed with 13 simple sequence repeats (SSRs) to evaluate its diversity. Three reference cultivars (‘Fuji’, ‘Granny Smith’ and ‘Reineta Gris’) were included as reference to align the SSR profiles. The average number of alleles per locus was 7.66, which increased to 8.75 with triploids, and the number of rare alleles was 36. Moreover, the observed heterozygosity (Ho) was 0.74 and the expected heterozygosity (He) was 0.66, indicating disequilibrium. The probability to find two identical individuals was very low (PID = 3.60 × 10−12). After the cluster analysis, 29% of the accessions were found to have redundant profiles. Principal coordinate analysis, clustering and Bayesian model suggested the presence of four well-defined subgroups in the diploid of traditional apple. In clustering, diploid reference cultivars were nested with triploids independently from diploid traditional cultivars. Finally, after comparing profiles and names with other traditional Spanish cultivars, we conclude that the following studied collection shares the ubiquitous accessions from cultivar groups, such as «camuesas», «peros» and ‘Reineta’ but contains novel and uncharacterised cultivars with potential opportunities in breeding programmes and rural development: ‘Agridulce’, ‘Amarillo de El Paular’, ‘Hojancas’, ‘Mailla blanca’, ‘Pepita de melon’ and ‘Rabudas’. As these cultivars were collected in such a small area with environmental distinctiveness, they constitute a singular germplasm reservoir, which deserves to be preserved and more deeply studied.

The hyperdominant tropical tree Eschweilera coriacea (Lecythidaceae) shows higher genetic heterogeneity than sympatric Eschweilera species in French Guiana

Background and aims – The evolutionary history of Amazonia’s hyperabundant tropical tree species, also known as “hyperdominant” species, remains poorly investigated. We assessed whether the hyperdominant Eschweilera coriacea (DC.) S.A.Mori (Lecythidaceae) represents a single genetically cohesive species, and how its genetic constitution relates to other species from the same clade with which it occurs sympatrically in French Guiana.Methods – We sampled 152 individuals in nine forest sites in French Guiana, representing 11 species of the genus Eschweilera all belonging to the Parvifolia clade, with emphasis on E. coriacea. Samples were genotyped at four simple sequence repeat (SSR) markers. We delimited gene pools, i.e., genetically coherent putative taxa, using STRUCTURE software and principal component analysis. We compared the genetic assignment of individuals with their morphological species determination and estimated genetic diversity and differentiation for gene pools and species. We also estimated genome size using flow cytometry.Key results – SSR profiles commonly displayed up to four alleles per genotype, suggesting that the investigated Eschweilera species bear a paleopolyploid signature. Flow cytometry suggested that the studied species are diploid with haploid genome sizes of 871–1046 Mbp. We detected five gene pools and observed a good correspondence between morphological and genetic delimitation for Eschweilera sagotiana Miers and the undescribed morphospecies E. sp. 3 (which resembles E. grandiflora (Aubl.) Sandwith), and to a lesser extent for E. decolorans Sandwith and E. micrantha (O.Berg) Miers. Eschweilera coriacea was the most genetically diverse species and included individuals assigned to each gene pool. Conclusions – We found no conclusive evidence for cryptic species within E. coriacea in French Guiana. SSRs detected fewer gene pools than expected based on morphology in the Parvifolia clade but discriminated evolutionary relationships better than available plastid markers. A positive trend between demographic abundance of species and allelic richness illustrates that hyperdominants may have a high evolutionary potential. This hypothesis can be tested using more powerful genomic data in combination with tree phenotypic trait variation and characterization of niche breadth, to enhance our understanding of the causes of hyperdominance in Amazonian trees.

Identification of rare traditional grapevine cultivars using SSR markers and their geographical location within the Czech Republic

The designation of traditional varieties of grapevine is usually based on verbal information or very dated records. Old rare cultivars found in the Czech Republic were identified by Simple Sequence Repeat (SSR) analysis, a generally accepted method for cultivar identification. These cultivars are primarily maintained in a national collection of genetic resources. Finally a total of 102 candidate genotypes was selected where 49 traditional varieties were identified on the base of nine SSR loci compared with the European Vitis Database. Thirty-six items were registered under the correct designation. The remaining genotypes included four clones, and two genotypes could be described as synonyms. Seven genotypes were found to be incorrectly marked. For three of them, the correct name was found in the database under their SSR profile and four items were considered to be unique as no identical profile was found.

Identifying evolutionary lineages in the Elaeocarpus obovatus complex: population genetics and morphometric analyses support a new subspecies, Elaeocarpus obovatus subsp. umbratilis, from northern Queensland, Australia

With the aim to solve long-standing problems of taxonomic delimitation within the E. obovatus species complex (E. obovatus G.Don, E. arnhemicus F.Muell., E. sp. Mt Bellenden Ker (L.J.Brass 18336) Qld Herbarium and E. coorangooloo J.F.Bailey & C.T.White), diversity and relatedness were assessed using a combined population genetics and morphometric approach among 181 and 102 individuals respectively. Simple sequence-repeat (SSR) markers were analysed with clustering methods, analysis of molecular variance (AMOVA) and STRUCTURE. The morphometric data were analysed using cluster and classification and regression tree (CART) methods. The morphometric and genetic analyses together resolve discrete groups corresponding to E. arnhemicus, E. coorangooloo, E. obovatus and E. sp. Mt Bellenden Ker. Elaeocarpus arnhemicus is clearly distinct from all other entities on most of the morphometric and genetic analyses. By contrast, E. sp. Mt Bellenden Ker and E. obovatus were not clearly separated from each other in many morphometric analyses, but can be distinguished clearly by the strongly curved pedicels in early bud and hairy ovary, and, to a lesser extent, by the frequent occurrence of two racemes per axil and cuneate leaf bases, and on the results of the genetic analyses. Elaeocarpus coorangooloo exhibits considerable genetic admixture with the other entities, but it is morphologically distinct. SSR profiles suggested that E. arnhemicus and E. obovatus may be tetraploid, whereas the other entities are diploid. This study has clarified the taxonomic limits of the currently recognised species E. arnhemicus, E. obovatus and E. coorangooloo and supports recognition of E. sp. Mt Bellenden Ker at subspecies rank, described herein as E. obovatus subsp. umbratilis Y.Baba & Crayn. A key to all taxa and revised accounts of E. arnhemicus, E. obovatus subsp. obovatus and E. coorangooloo are provided.

Studies on single and double layered biocompatible encapsulation of somatic embryos in Albizia lebbeck and genetic homogeneity appraisal among synseed derived lines through ISSR markers

Embryogenic synseeds were prepared in Albizia lebbeck by encapsulating cotyledon stage somatic embryos derived from in vitro maintained embryogenic cultures in different types of Ca-alginate beads. The germination rate of somatic embryos was affected significantly by the bead type, matrix composition and germination substrate. A matrix made of 3% Na2-alginate complexed with 100 mM CaCl2·2H2O for a hardening period of 20 min provided uniform encapsulation of somatic embryo. Among different types of synseeds, type IIA, wherein somatic embryos encapsulated in a single layer of Ca-alginate matrix composed of MS medium supplemented with 2 g L−1 activated charcoal and 1.0 µM gibberellic acid (GA3) as reconstituted endosperm, was found to be the most efficient type having maximum germination rates (88.6 ± 0.51%). Incorporation of GA3 in the alginate beads stimulated greater germination of somatic embryos as against GA3 supplementation in the germination substrate. Further, viability studies on short term cold (4 °C) storage of different types of embryogenic synseeds revealed that double layered synseeds (DLS) were found comparatively more robust to withstand longer storage durations than single layered synseeds as evident by greater germination rates of the former after 4–8 weeks of refrigerated storage. Also, the elevated levels of antioxidative enzymes (superoxide dismutase, catalase, ascorbate peroxidase and glutathione reductase) and leaf proline content in the plantlets derived from DLS reveals the possible role of alginate coatings in conferring alleviation to low temperature stress generated during different storage durations. Similar Inter simple sequence repeat profiles of embryogenic synseeds derived plantlets and mother tree nullifies the possible occurrence of somaclones, thereby establishing the efficacy of synseed technology for clonal propagation of A. lebbeck germplasm. Encapsulation of cotyledonary stage somatic embryos combined with high in vitro germination rates provides a feasible tool for interim storage and exchange of A. lebbeck germplasm.

True-to-type confirmation of 20 unknown grapevine accessions at a grape germplasm collection in Split, Croatia

Twenty unknown accessions maintained in the field collection of the Institute for Adriatic Crops and Karst Reclamation (IAC), Split, Croatia, were identified. Morphological validation was done using standard OIV descriptors encompassing shoot, leaf and cluster characteristics. A standard set of nine simple sequence repeats (SSRs) were amplified and genetic diversity indices were calculated. The allelic data of the 20 unknown genotypes were compared with reference SSR profiles from the European database Vitis International Variety Catalogue (VIVC; http://www.vivc.de/) and grape germplasm collection of the UK. Three accessions proved to be mislabelled and were identified as known European grapevine cultivars (‘Blaufraenkisch’, ‘Chardonnay’ and ‘Merlot’), two unknown accessions showed identical genotypes matching ‘Chasselas blanc’ and ‘Chasselas rose’, while 12 unknown genotypes confirmed their declared status. Finally, three unknown genotypes of interspecific crosses (‘Ljana’, ‘Original’, ‘Nero’) were not found in VIVC database or in published literature, revealing SSR profiles that are novel to the best of our knowledge. This study presents necessary information to establish cultivar status (true to type) of 20 unknown accessions from the IAC Split grape collection.

Extensive genotyping of a large collection of rootstocks, population structure analysis and core collection extrapolation for new breeding programs

A large repository of 441 rootstocks and other non-vinifera grape cultivars was established, beginning in 2013, by the University of Milan with the aim of collecting most of the genetic variability of Vitis species useful for rootstock genetic improvement. This kind of collection is the largest in Italy, with accessions from different donor institutes in California, Spain and Italy, and also encompassing progenies obtained by University of Milan breeding programs. A preliminary genetic characterization was performed, as is usually done for better management of grape germplasm. Eighty-six per cent of the accessions were evaluated by genotyping with simple sequence repeat (SSR) markers and also by phenotyping the sex of flowers. Twenty-two carefully selected and highly polymorphic SSR markers were used, out of 41 taken into consideration, which encompassed the nine markers applied internationally for V. vinifera genotyping and 26 VChr SSRs having a longer core tandem repeat. However, five of the 22 markers were shown to be critical when applied on a large scale for genotyping of non-vinifera plants and were subsequently discarded. SSR profile comparisons showed that more than a third of the accessions were redundant. Fewer than half were identified as true-to-type, and more than a third remained anonymous. These anonymous, as-yet uncharacterized genotypes represent a precious reservoir of genetic diversity. Analysis of the genetic structure revealed four main groups, with more than a third of genotypes classified as admixed. A genetic core collection able to capture the whole allelic variation was set up as a valuable starting point for both rootstock breeding and genome-wide association studies.

Microsatellites as a tool for identifying successful pollinators of the pear cultivar ‘Ingeborg’ in Ullensvang, Norway

Due to their Mendelian inheritance, microsatellites or SSRs (simple sequence repeats) can readily be used for parentage analyses of pear seedlings, thus revealing the female and male parents of the plant. However, in cases where obtained pear seeds display low viability, conducting a parentage analyses on the pear seeds themselves could be used in order to identify the male parent (successful pollinator). In this study, batches of seeds were extracted from fruits of the triploid ‘Ingeborg’ pear (‘Conference’ × ‘Bonne Louise’), the main commercial pear cultivar in Norway. Mature pears were collected from eight commercial pear orchards located in Ullensvang, at 60° North and seeds were collected. Genomic DNA was subsequently isolated from the obtained seed batches and genotyped using 12 microsatellite markers. The same markers were also used for the genetic characterization of ‘Ingeborg’ and five pear genotypes used as pollinators in the sampled orchards (‘Clara Frijs’, ‘Herzogine Elsa’, ‘Anna’, ‘Coloree de Juillet’ and ‘Belle lucrative’). The obtained SSR profiles were used in paternity analyses, as well as for gene assignment analyses. Both approaches identified pear ‘Clara Frijs’ to be the most successful pollinator in most of the sampled orchards. Subsequent S allele genotyping of ‘Ingeborg’ and five pear genotypes used as pollinators in the sampled orchards revealed that the preferential pollination by individual genotypes was not caused by gametophytic incompatibility or semi-compatibility.

Soybean-Macrophomina phaseolina-Specific Interactions and Identification of a Novel Source of Resistance.

Charcoal rot, caused by the fungus Macrophomina phaseolina, is an economically important disease of soybean (Glycine max) worldwide. Objectives of the present research were to (i) study the genetic and pathogenic diversity in a collection of M. phaseolina isolates from Argentina and Paraguay and (ii) develop an improved in vitro phenotyping method to evaluate disease response of soybean genotypes to M. phaseolina isolates. Cluster analysis showed no clear association among simple sequence repeat profiles, year of collection, pathogenicity, and geographical origin of the isolates from Argentina and Paraguay. Subsequently, the response of four soybean genotypes against seven M. phaseolina isolates was evaluated in the field and the results were confirmed using the in vitro assay developed. This assay, which is based on root disease development on soybean seedlings, allowed the detection of a differential level of aggressiveness among the isolates on four soybean genotypes. The results suggest the existence of specific interactions among soybean genotypes and M. phaseolina isolates. In addition, cultivar Munasqa RR showed a superior response against M. phaseolina compared with DT 97-4290 (moderately resistant), thus becoming a novel source of resistance to charcoal rot.

Genetic, Phenotypic, and Commercial Characterization of an Almond Collection from Sardinia.

Background: Recent nutritional and medical studies have associated the regular consumption of almonds with a wide range of health benefits. As a consequence, kernel quality has become an important goal for breeding, considering not only the chemical composition conferring a specific organoleptic quality but also physical traits related to industrial processing. Methods: We characterized an almond collection from Sardinia through analysis of 13 morpho-physiological traits and eight essential oil profiles. The genetic structure of the collection was studied by analyzing the polymorphism of 11 simple sequence repeats (SSR). Results: Both commercial and phenotypic traits showed wide ranges of variation. Most genotypes were early flowering with low yield potential. Several genotypes showed moderate to high yield and very interesting oil compositions of kernels. Based on 11 SSR profiles and Bayesian clustering, the Sardinian cultivars were assigned to groups which were differentiated for several agronomic and commercial traits. Conclusions: Several cultivars showed a high kernel oil content and high oleic to linoleic content ratio. Based on morphological traits, we propose that some of the analyzed cultivars could be interesting for industrial applications. Finally, we highlight the importance of characterizing early blooming cultivars for sites which are experiencing a rise in mean temperatures due to the effects of global climate changes.

The Landscape of Repetitive Elements in the Refined Genome of Chilli Anthracnose Fungus Colletotrichum truncatum.

The ascomycete fungus Colletotrichum truncatum is a major phytopathogen with a broad host range which causes anthracnose disease of chilli. The genome sequencing of this fungus led to the discovery of functional categories of genes that may play important roles in fungal pathogenicity. However, the presence of gaps in C. truncatum draft assembly prevented the accurate prediction of repetitive elements, which are the key players to determine the genome architecture and drive evolution and host adaptation. We re-sequenced its genome using single-molecule real-time (SMRT) sequencing technology to obtain a refined assembly with lesser and smaller gaps and ambiguities. This enabled us to study its genome architecture by characterising the repetitive sequences like transposable elements (TEs) and simple sequence repeats (SSRs), which constituted 4.9 and 0.38% of the assembled genome, respectively. The comparative analysis among different Colletotrichum species revealed the extensive repeat rich regions, dominated by Gypsy superfamily of long terminal repeats (LTRs), and the differential composition of SSRs in their genomes. Our study revealed a recent burst of LTR amplification in C. truncatum, C. higginsianum, and C. scovillei. TEs in C. truncatum were significantly associated with secretome, effectors and genes in secondary metabolism clusters. Some of the TE families in C. truncatum showed cytosine to thymine transitions indicative of repeat-induced point mutation (RIP). C. orbiculare and C. graminicola showed strong signatures of RIP across their genomes and “two-speed” genomes with extensive AT-rich and gene-sparse regions. Comparative genomic analyses of Colletotrichum species provided an insight into the species-specific SSR profiles. The SSRs in the coding and non-coding regions of the genome revealed the composition of trinucleotide repeat motifs in exons with potential to alter the translated protein structure through amino acid repeats. This is the first genome-wide study of TEs and SSRs in C. truncatum and their comparative analysis with six other Colletotrichum species, which would serve as a useful resource for future research to get insights into the potential role of TEs in genome expansion and evolution of Colletotrichum fungi and for development of SSR-based molecular markers for population genomic studies.