Chemical Diversity in Lippia alba (Mill.) N. E. Brown Germplasm.
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ABSTRACT:
SUBMITTER: Blank AF
PROVIDER: S-EPMC4446488 | biostudies-other | 2015
REPOSITORIES: biostudies-other
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Project description:The present study aimed to chemically characterize 31 accessions and seven cultivars of basil. The percentage composition of the essential oils of the accessions and cultivars was based on the 14 most abundant constituents: 1,8-cineole, linalool, methyl chavicol, neral, nerol, geraniol, geranial, methyl cinnamate, β-bourbonene, methyl eugenol, α-trans-bergamotene, germacrene-D, epi-α-cadinol, and δ-cadinene. The genetic materials were classified into eight clusters according to the chemical composition of the essential oils: Cluster 1--mostly linalool and 1,8-cineole; Cluster 2--mostly linalool, geraniol, and α-trans-bergamotene; Cluster 3--mostly linalool, methyl chavicol, methyl cinnamate, and β-bourbonene; Cluster 4--mostly linalool, methyl chavicol, epi-α-cadinol, and α-trans-bergamotene; Cluster 5--mainly linalool, methyl eugenol, α-trans-bergamotene, and epi-α-cadinol; Cluster 6--mainly linalool, geraniol, and epi-α-cadinol; Cluster 7--mostly linalool and methyl chavicol; Cluster 8--mainly geranial and neral.
| S-EPMC4299303 | biostudies-other
Project description:BackgroundDiscovering a genome-wide set of avocado (Persea americana Mill.) single nucleotide polymorphisms and characterizing the diversity of germplasm collection is a powerful tool for breeding. However, discovery is a costly process, due to loss of loci that are proven to be non-informative when genotyping the germplasm.ResultsOur study on a collection of 100 accessions comprised the three race types, Guatemalan, Mexican, and West Indian. To increase the chances of discovering polymorphic loci, three pools of genomic DNA, one from each race, were sequenced and the reads were aligned to a reference transcriptome. In total, 507,917 polymorphic loci were identified in the entire collection. Of these, 345,617 were observed in all three pools, 117,692 in two pools, 44,552 in one of the pools, and only 56 (0.0001%) were homozygous in the three pools but for different alleles. The polymorphic loci were validated using 192 randomly selected SNPs by genotyping the accessions within each pool. The sensitivity of polymorphic locus prediction ranged from 0.77 to 0.94. The correlation between the allele frequency estimated from the pooled sequences and actual allele frequency from genotype calling of individual accessions was r = 0.8. A subset of 109 SNPs were then used to evaluate the genetic relationships among avocado accessions and the genetic diversity of the collection. The three races were distinctly clustered by projecting the genetic variation on a PCA plot. As expected, by estimating the kinship coefficient for all the accessions, many of the cultivars from the California breeding program were closely related to each other, especially, the Hass-like ones. The green-skin avocados, e.g., 'Bacon', 'Zutano', 'Ettinger' and 'Fuerte' were also closely related to each other.ConclusionsA framework for SNP discovery and genetically characterizing of a breeder's accessions was described. Sequencing pools of gDNA is a cost-effective approach to create a genome-wide stock of polymorphic loci for a breeding program. Reassessing the botanical and the genetic knowledge about the germplasm accessions is valuable for future breeding. Kinship analysis may be used as a first step in finding a parental candidates in a parentage analyses.
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Project description:Abies alba (Mill.) is an important forest tree species, native to the mountainous regions of Europe but has been also widely introduced in the lowlands outside its native range. Like most forest tree species, A. alba forms obligate mutualisms with ectomycorrhizal (ECM) fungi. This investigation sought to examine ECM fungal communities of A. alba when the species grows 400 km north of its native range in the region of Pomerania in Poland. We surveyed for ECM fungi by sampling live roots from four mature forest stands where the A. alba component ranged from 20 to 100%. Ectomycorrhizal fungal symbionts were identified based on morphotyping and sequencing of the internal transcribed spacer (ITS) of nuclear ribosomal DNA (rDNA). Thirty-five ECM fungal taxa were distinguished on root tips of A. alba from all tested stands with 22 to 27 ECM fungal taxa in the individual stand. The diversity and similarity metrics revealed a lack of statistical differences in the structure of the ECM fungal community between stands varying in overstory tree composition. Cenococcum geophilum was the most common fungal species at all investigated A. alba stands, with an abundance of 50 to 70%. The ECM community was characterized by the lack of Abies-specific fungal symbionts and a rich and diverse suite of host-generalist mycobionts that seem to be sufficient for successful growth and development of A. alba outside of its native range.
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Project description:BackgroundRosa damascena Mill is a well-known species of the rose family. It is famous for its essential oil content. The aim of the present study was to assess the genetic diversity and population structure of a mini core collection of the Iranian Damask rose germplasm. This involved the use of universal rice primers (URP) and start codon targeted (SCoT) molecular markers.ResultsFourteen URP and twelve SCoT primers amplified 268 and 216 loci, with an average of 19.21 and 18.18 polymorphic fragments per primer, respectively. The polymorphic information content for URR and SCoT primers ranged from 0.38 to 0.48 and 0.11 to 0.45, with the resolving power ranging from 8.75 to 13.05 and 9.9 to 14.59, respectively. Clustering was based on neighbor-joining (NJ). The mini core collection contained 40 accessions and was divided into three distinct clusters, centered on both markers and on the combination of data.ConclusionCluster analysis and principal coordinate analysis were consistent with genetic relationships derived by STRUCTURE analysis. The findings showed that patterns of grouping did not correlate with geographical origin. Both molecular markers demonstrated that the accessions were not genetically diverse as expected, thereby highlighting the possibility that gene flow occurred between populations.
| S-EPMC8484433 | biostudies-literature
Project description:A world collection of 132 yellow mustard (Sinapis alba L.) accessions was characterized in a greenhouse to identify germplasm with polycotyledony and to assess the genetic segregation of tricot and tetracot seedlings in selfed S1 and S2 generations. The effort identified a set of 46 yellow mustard accessions with frequent occurrences of polycotyledony. The revealed genetic segregations seemed to suggest the development of tricot and tetracot seedlings in yellow mustard was largely controlled by a combination of genes at multiple diallelic loci. The identified tricot germplasm can be used to facilitate the genetic and/or genomic analysis of polycotyledonous germplasm for a better understanding of genetic and developmental mechanisms conditioning polycotyledony and the development of yellow mustard lines for explorable tricot breeding.
| S-EPMC10707805 | biostudies-literature
Project description:Background Morinda officinalis How (MO) is a perennial herb distributed in tropical and subtropical regions, which known as one of the “Four Southern Herbal Medicines”. The extent of genetic variability and the population structure of MO are presently little understood. Here, nine morphological traits, six chemical components and Single nucleotide polymorphism (SNP) markers were used in integrative research of MO germplasm variation among 88 individuals collected from ten populations across four geographical provinces of China. Results Both phenotype and chemical composition have significant genetic variation, and there is a certain correlation between them such as root diameter and the nystose content, as well as geographical distribution. The principal component analysis (PCA) showed the leaf length, leaf width, nystose, 1F-furanosaccharide nystose, and the section color were the major contributors to diversity. The cluster analysis based on phenotypic and oligosaccharide data distinguished three significant groups, which was consistent with the result of a corresponding analysis with 228,615 SNP markers, and importantly, they all showed a significant correlation with geographical origin. However, there was little similarity between two cluster results. The Shannon’s information index (I) varied from 0.17 to 0.53 with a mean of 0.37, suggesting a high level of genetic diversity in MO populations, which mainly existed among individuals within populations, accounting for 99.66% of the total according to the analysis of molecular variance (AMOVA) results. Each population also maintains the connection because of certain gene communication, so that the genetic differentiation between populations was not very significant. The STRUCTURE software was used to analyse the population structure and the result showed that 88 accessions were clustered into three groups, and 67% of them were pure type, which was also confirmed through PCA. Conclusions The comprehensive study of phenotypic, chemical and molecular markers will provide valuable information for future breeding plans and understanding the phylogenetic relationship of MO population. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08817-w.
| S-EPMC9392303 | biostudies-literature
Project description:BackgroundPlant mitogenomes vary widely in size and genomic architecture. Although hundreds of plant mitogenomes of angiosperm species have already been sequence-characterized, only a few mitogenomes are available from gymnosperms. Silver fir (Abies alba) is an economically important gymnosperm species that is widely distributed in Europe and occupies a large range of environmental conditions. Reference sequences of the nuclear and chloroplast genome of A. alba are available, however, the mitogenome has not yet been assembled and studied.ResultsHere, we used paired-end Illumina short reads generated from a single haploid megagametophyte in combination with PacBio long reads from high molecular weight DNA of needles to assemble the first mitogenome sequence of A. alba. Assembly and scaffolding resulted in 11 mitogenome scaffolds, with the largest scaffold being 0.25 Mbp long. Two of the scaffolds displayed a potential circular structure supported by PCR. The total size of the A. alba mitogenome was estimated at 1.43 Mbp, similar to the size (1.33 Mbp) of a draft assembly of the Abies firma mitogenome. In total, 53 distinct genes of known function were annotated in the A. alba mitogenome, comprising 41 protein-coding genes, nine tRNA, and three rRNA genes. The proportion of highly repetitive elements (REs) was 0.168. The mitogenome seems to have a complex and dynamic structure featured by high combinatorial variation, which was specifically confirmed by PCR for the contig with the highest mapping coverage. Comparative analysis of all sequenced mitogenomes of gymnosperms revealed a moderate, but significant positive correlation between mitogenome size and proportion of REs.ConclusionsThe A. alba mitogenome provides a basis for new comparative studies and will allow to answer important structural, phylogenetic and other evolutionary questions. Future long-read sequencing with higher coverage of the A. alba mitogenome will be the key to further resolve its physical structure. The observed positive correlation between mitogenome size and proportion of REs will be further validated once available mitogenomes of gymnosperms would become more numerous. To test whether a higher proportion of REs in a mitogenome leads to an increased recombination and higher structural complexity and variability is a prospective avenue for future research.
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Project description:Root-associated fungal communities are important components in ecosystem processes, impacting plant growth and vigor by influencing the quality, direction, and flow of nutrients and water between plants and fungi. Linkages of plant phenological characteristics with belowground root-associated fungal communities have rarely been investigated, and thus our aim was to search for an interplay between contrasting phenology of host ectomycorrhizal trees from the same location and root-associated fungal communities (ectomycorrhizal, endophytic, saprotrophic and pathogenic root-associated fungi) in young and in adult silver fir trees. The study was performed in a managed silver fir forest site. Twenty-four soil samples collected under two phenologically contrasting silver fir groups were analyzed for differences in root-associated fungal communities using Illumina sequencing of a total root-associated fungal community. Significant differences in beta diversity and in mean alpha diversity were confirmed for overall community of ectomycorrhizal root-associated fungi, whereas for ecologically different non-ectomycorrhizal root-associated fungal communities the differences were significant only for beta diversity and not for mean alpha diversity. At genus level root-associated fungal communities differed significantly between early and late flushing young and adult silver fir trees. We discuss the interactions through which the phenology of host plants either drives or is driven by the root-associated fungal communities in conditions of a sustainably co-naturally managed silver fir forest.
| S-EPMC6413537 | biostudies-literature
Project description:This paper describes the antigerminant capacity of water extracts of silver fir needles created by means of hydrodynamic cavitation processes. Fir needles (2 kg fresh weight) collected in the winter were blended and crushed in ice, poured in water only (120 L) and processed in a controlled hydrodynamic cavitation device based on a fixed Venturi-shaped reactor. The A. alba water extract (AWE), comprising an oil-in-water emulsion of silver fir needles' essential oil (100% AWE), was diluted in distilled water to 75% and 50% AWE, and all aqueous solutions were tested as antigerminant against four weeds and four horticultural species and compared to control (distilled water). This study shows the effective inhibitory effect of pure AWE on germination, which mainly contains limonene (15.99 ng/mL) and α-pinene (11.87 ng/mL). Seeds showed delayed germination and inhibition but also a reduction in radicle elongation in AWE treatments as compared to control. This combined effect was particularly evident in three weeds (C. canadensis, C. album and A. retrofllexus) while horticultural species showed mainly effects on the radicle elongation as found in L. sativa, P. crispum and S. lycospermum, which showed on average 58%, 32% and 28%, respectively, shorter radicles than in the control. P. sativum was not affected by AWE, thus raising the hypothesis that seed characteristics and nutrition reserve might play a role in the resistance to terpenes inhibitory effect.
| S-EPMC8309281 | biostudies-literature
Project description:While the functionality and healthy food value of red rice have increased its popularity, such that market demand for it is expected to rise, most strains suffer from low grain yield. To perform diversity and population structure analyses of red rice germplasm, therefore, becomes essential for improving yields for commercial production. In this study, fifty red rice germplasm from the Bangladesh Rice Research Institute (BRRI) genebank were characterized both morphologically and genetically using fifty simple sequence repeat (SSR) markers. Overall, 162 alleles were detected by the markers with the detected allele number varying from two to seven. Additionally, 22 unique alleles were identified for use as a germplasm diagnostic tool. The highest and lowest polymorphic information content (PIC) indices were 0.75 and 0.04 found in markers RM282 and RM304, respectively, and genetic diversity was moderate, varying from 0.05 to 0.78 (average: 0.35). While phylogenetic cluster analysis of the fifteen distance-based agro-morphological traits divided the germplasm into five clusters (I, II, III, IV and V), a similar SSR analysis yielded only three major groups (I, II, and III), and a model-based population structure analysis yielded four (A, B, C and D). Both principal component and neighbors joining tree analysis from the population structure method showed the tested germplasm as highly diverse in structure. Moreover, an analysis of molecular variance (AMOVA), as well as a pairwise FST analysis, both indicated significant differentiation (ranging from 0.108 to 0.207) among all pairs of populations, suggesting that all four population structure groups differed significantly. Populations A and D were the most differentiated from each other by FST. Findings from this study suggest that the diverse germplasm and polymorphic trait-linked SSR markers of red rice are suitable for the detection of economically desirable trait loci/genes for use in future molecular breeding programs.
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