Seed Paternity Analysis Using SSR Markers to Assess Successful Pollen Donors in Mixed Olive Orchards.
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ABSTRACT:
SUBMITTER: Vuletin Selak G
PROVIDER: S-EPMC8624852 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Premise:Pollen dispersal plays a critical role in gene flow of seed plants. Most often, pollen dispersal is measured using paternity assignment. However, this approach can be time-consuming because it typically entails genotyping all pollen donors, receptors, and offspring at several molecular markers. Methods:We developed a faster, simpler protocol to track paternity, using pollen receptors and grouped pollen donors that possess rare alleles. We tested this approach using wind-pollinated Amaranthus tuberculatus and insect-pollinated Solanum lycopersicum. After screening potential markers for rare alleles, we grew both species in experimental arrays under field conditions. Results:All tested A. tuberculatus seeds and 97% of S. lycopersicum fruits could be assigned to the grouped pollen donors using each of two markers. From these results, we could infer paternity of untested offspring and assess pollen dispersal patterns in each array. Discussion:By combining rare alleles and grouped pollen donors, we could assess pollen dispersal for both species and across all arrays after genotyping a small number of pollen donors and a representative subset of offspring. While directly applicable to A. tuberculatus and S. lycopersicum, this approach could be used in other species to assess pollen dispersal under field conditions.
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Project description:Cross-pollination can improve fruit yield, fruit size and nutritional quality of many food crops. However, we rarely understand what proportions of the crop result from self- or cross-pollination, how cross-pollination affects crop quality, and how far pollen is transported by pollinators. Management strategies to improve pollination services are consequently not optimal for many crops. We utilised a series of SNP markers, unique for each cultivar of avocado, to quantify proportions of self- and cross-paternity in fruit of Hass avocado at increasing distances from cross-pollen sources. We assessed whether distance from a cross-pollen source determined the proportions of self-pollinated and cross-pollinated fruit, and evaluated how self- and cross-paternity affected fruit size and nutritional quality. Avocado fruit production resulted from both self- and cross-pollination in cultivar Hass in Queensland, Australia. Cross-pollination levels decreased with increasing distance from a cross-pollen source, from 63% in the row adjacent to another cultivar to 25% in the middle of a single-cultivar block, suggesting that pollen transport was limited across orchard rows. Limited pollen transport did not affect fruit size or quality in Hass avocados as xenia effects of a Shepard polliniser on size and nutritional quality were minor.
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Project description:Artificial pollination of black walnut (Juglans nigra L.) is not practical and timber breeders have historically utilized only open-pollinated half-sib families. An alternate approach called "breeding without breeding," consists of genotyping open-pollinated progeny using DNA markers to identify paternal parents and then constructing full-sib families. In 2014, we used 12 SSR markers to genotype 884 open-pollinated half-sib progeny harvested from two clonal orchards containing 206 trees, comprised of 52 elite timber selections. Seed was harvested in 2011 from each of two ramets of 23 clones, one upwind and one downwind, based on prevailing wind direction from the west-southwest. One orchard was isolated from wild black walnut and composed of forward selections while the other orchard was adjacent to a natural forest containing mature black walnut composed of backward selections. Isolation significantly increased within-orchard pollination (85%) of the progeny from the isolated orchard compared to 42% from the non-isolated orchard. Neither prevailing wind direction nor seed tree position in the orchard affected paternity patterns or wild pollen contamination. Genetic diversity indices revealed that progeny from both orchards were in Hardy-Weinberg equilibrium with very little inbreeding and no selfing. A significant level of inbreeding was present among the forward selected parents, but not the first generation (backward selected) parents. Some orchard clones failed to sire any progeny while other clones pollinated upwards of 20% of progeny.
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Project description:Fungal endophytes have been increasingly recognized to promote host plant protection to pathogens, but knowledge of the multiple effects that they could have in crop diseases is still scarce. This work attempts to understand the role of fungal endophytes in crop diseases, specifically in reducing disease development and interfering on lifestyle transition of the pathogen. To accomplish this, the endophytic fungal community of reproductive organs of olive tree from two orchards showing different levels of anthracnose incidence, a major disease of olive fruits, was characterized and compared between them. The two orchards showed distinct endophytic communities, differing in species richness, abundance and composition, with highest isolation rates and richness of endophytes in the orchard with low anthracnose incidence. These differences among orchards were greater on fruits than on flowers, suggesting that these changes in endophytic fungal composition may influence the lifestyle shifts in pathogen (from latent to pathogen). A number of fungal taxa were found to be positively associated to one of the two orchards. The fungal endophytes best correlated with high incidence of anthracnose are pathogens, while endophytes-associated to low anthracnose incidence are described to protect plants. Altogether, the results suggest varying pathogen-endophyte interactions among the two orchards.
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Project description:Analysis of gene-expression profiles by microarrays can be very useful to characterize new potential candidate genes, key regulatory networks, and to define phenotypes or molecular signatures to improve the diagnosis or classification of the disease. We have used this approach in the study of one of the major causes of allergic diseases in Mediterranean countries, the olive pollen response, in order to find differential molecular markers among five clinical groups, Non-allergic, Asymptomatic, Allergic but not to olive pollen, Non-treated, olive pollen allergic patients and Olive pollen allergic patients (under specific-immunotherapy). The results of gene-expression by principal components analysis (PCA) clearly showed five clusters of samples that correlated with the five clinical groups. Analysis of differential gene-expression by multiple testing, and functional analysis by KEGG and Gene-Ontology revealed differential genes and pathways among the 5 clinical groups.
2013-02-28 | GSE37157 | GEO
Project description:BACKGROUND:Olive production is the main agricultural activity in Tunisia. The diversity of fungi was explored in two different olive groves located in two distant geographical zones in Sfax (Tunisia) with different management practices. RESULTS:Fungal isolation was made from soil and the major olive tree pests, namely the Olive fly, Bactrocera oleae Gmelin (Diptera: Tephritidae), and the Olive psyllid, Euphyllura olivina Costa (Homoptera: Psyllidae). A total of 34 fungal isolates were identified according to their phenotypic, genotypic, biochemical and biological activities. Twenty fungal species were identified belonging to six different genera (Alternaria, Aspergillus, Cladosporium, Fusarium, Lecanicillium and Penicillium) by the analysis of their ITS1-5.8S-ITS2 ribosomal DNA region. Different bioassays performed in this work revealed that 25/34 (73.5%) of the identified fungal isolates showed an entomopathogenic and/or antagonistic activity, 9/34 (26.5%) of them displayed phytopathogenic features. CONCLUSIONS:Fungal species that showed entomopathogenic and/or antagonistic potentialities and that are non-phytopathogenic, (17/34; 50%) of our fungal isolates, could be explored for olive protection against fungal diseases and pests, and might have a future application as biocontrol agents.
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Project description:Several simulation models of the olive crop have been formulated so far, but none of them is capable of analyzing the impact of environmental conditions and management practices on water relations, growth and productivity under both well-irrigated and water-limiting irrigation strategies. This paper presents and tests OliveCan, a process-oriented model conceived for those purposes. In short, OliveCan is composed of three main model components simulating the principal elements of the water and carbon balances of olive orchards and the impacts of some management operations. To assess its predictive power, OliveCan was tested against independent data collected in two 3-year field experiments conducted in Córdoba, Spain, each of them applying different irrigation treatments. An acceptable level of agreement was found between measured and simulated values of seasonal evapotranspiration (ET, range 393 to 1016 mm year-1; RMSE of 89 mm year-1), daily transpiration (Ep, range 0.14-3.63 mm d-1; RMSE of 0.32 mm d-1) and oil yield (Yoil, range 13-357 g m-2; RMSE of 63 g m-2). Finally, knowledge gaps identified during the formulation of the model and further testing needs are discussed, highlighting that there is additional room for improving its robustness. It is concluded that OliveCan has a strong potential as a simulation platform for a variety of research applications.
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Project description:Self-incompatibility (SI) in flowering plants potentially represents a major obstacle for sexual reproduction, especially when the number of S-alleles is low. The situation is extreme in the commercially important olive tree, where in vitro pollination assays suggested the existence of a diallelic SI (DSI) system involving only two groups (G1 and G2). Varieties belonging to the same SI group cannot fertilize each other, such that successful fruit production is predicted to require pollination between varieties of different groups. To test this prediction, we explored the extent to which the DSI system determines fertilization patterns under field conditions. One hundred and seventeen olive cultivars were first genotyped using 10 highly polymorphic dinucleotide Simple Sequence Repeat (SSR) markers to ascertain varietal identity. Cultivars were then phenotyped through controlled pollination tests to assign each of them to one of the two SI groups. We then collected and genotyped 1440 open pollinated embryos from five different orchards constituted of seven local cultivars with known group of incompatibility groups. Embryos genotype information were used: (i) to assign embryos to the most likely pollen donor genotype in the neighbourhood using paternity analysis, and (ii) to compare the composition of the pollen cloud genetic among recipient trees in the five sites. The paternity analysis showed that the DSI system is the main determinant of fertilization success under field open pollination conditions: G1 cultivars sired seeds exclusively on G2 cultivars, and reciprocally. No self-fertilization events were observed. Our results demonstrate that DSI is a potent force determining pollination success among varieties within olive orchards used for production. They have the potential to improve management practices by guiding the selection of compatible varieties to avoid planting orchards containing sets of varieties with strongly unbalanced SI groups, as these would lead to suboptimal olive production.
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Project description:Field surveys were conducted in Greek olive orchards from 2017 to 2020 to collect information on the sanitary status of the trees. Using a high-throughput sequencing approach, viral sequences were identified in total RNA extracts from several trees and assembled to reconstruct the complete genomes of two isolates of a new viral species of the genus Tepovirus (Betaflexiviridae), for which the name olive virus T (OlVT) is proposed. A reverse transcription-polymerase chain reaction assay was developed which detected OlVT in samples collected in olive growing regions in Central and Northern Greece, showing a virus prevalence of 4.4% in the olive trees screened. Sequences of amplified fragments from the movement-coat protein region of OlVT isolates varied from 75.64% to 99.35%. Three olive varieties (Koroneiki, Arbequina and Frantoio) were infected with OlVT via grafting to confirm a graft-transmissible agent, but virus infections remained latent. In addition, cucumber mosaic virus, olive leaf yellowing-associated virus and cherry leaf roll virus were identified.
| S-EPMC8150953 | biostudies-literature
Project description:Analysis of gene-expression profiles by microarrays can be very useful to characterize new potential candidate genes, key regulatory networks, and to define phenotypes or molecular signatures to improve the diagnosis or classification of the disease. We have used this approach in the study of one of the major causes of allergic diseases in Mediterranean countries, the olive pollen response, in order to find differential molecular markers among five clinical groups, Non-allergic, Asymptomatic, Allergic but not to olive pollen, Non-treated, olive pollen allergic patients and Olive pollen allergic patients (under specific-immunotherapy). The results of gene-expression by principal components analysis (PCA) clearly showed five clusters of samples that correlated with the five clinical groups. Analysis of differential gene-expression by multiple testing, and functional analysis by KEGG and Gene-Ontology revealed differential genes and pathways among the 5 clinical groups. The study population comprised 28 subjects, selected from a previous immunological study (Aguerri et al. Eur. J. Inflammation 2012, in press), from Andalusia, who were recruited in 2 olive pollen exposure situations: during (April-June) and outside the pollen season (October-December). We established 5 groups, and 6 subjects from each group were selected for gene-expression analysis: Group 1, non-allergic subjects; Group 2, asymptomatic subjects (diagnosed with olive pollen allergy by skin testing, with no seasonal respiratory symptoms [rhinitis and/or asthma], and who consulted for adverse reaction to drugs); Group 3, patients who were allergic, but not to olive pollen; Group 4, non-treated olive pollenM-bM-^@M-^Sallergic; and Group 5, olive pollenM-bM-^@M-^Sallergic patients (receiving olive pollenM-bM-^@M-^Sspecific immunotherapy).The subjects were unrelated and recruited at the Allergy Service of 4 hospitals in Andalusia (Granada, JaM-CM-)n, Sevilla, and MM-CM-!laga). Olive pollenM-bM-^@M-^Sallergic patients fulfilled the following criteria: seasonal rhinitis and/or asthma from April to June, a positive skin prick test result for O. europaea pollen extract (ALK AbellM-CM-3, Madrid, Spain), and no previous immunotherapy. Informed consent was obtained from each subject. Ethical approval for the study was obtained from the Ethical and Research Committee of the participating hospitals. PBMCs were isolated from heparin-containing peripheral blood samples taken during and outside pollen season, by gradient centrifugation on Lymphoprep (Comercial Rafer, Zaragoza, Spain) following the manufacturerM-bM-^@M-^Ys instructions.
2013-02-28 | E-GEOD-37157 | biostudies-arrayexpress