Association mapping and candidate gene identification for yield traits in European hazelnut (Corylus avellana L.)
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ABSTRACT:
SUBMITTER: Baytar A
PROVIDER: S-EPMC11336203 | biostudies-literature | 2024 Aug
REPOSITORIES: biostudies-literature
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Project description:European hazelnut (Corylus avellana) is a diploid (2n = 22), monecious and wind-pollinated species, extensively cultivated for its nuts. Turkey is the world-leading producer of hazelnut, supplying 70-80% of the world's export capacity. Hazelnut is mostly grown in the Black Sea Region, and maintained largely through clonal propagation. Understanding the genetic variation between hazelnut varieties, and defining variety-specific and disease resistance-associated alleles, would facilitate hazelnut breeding in Turkey. Widely grown varieties 'Karafındık' (2), 'Sarıfındık' (5), and 'Yomra' (2) were collected from Akçakoca in the west, while 'Tombul' (8), 'Çakıldak' (3), 'Mincane' (2), 'Allahverdi' (2), 'Sivri' (4), and 'Palaz' (5) were collected from Ordu and Giresun provinces in the east (numbers in parentheses indicate sample sizes for each variety). Powdery mildew resistant and susceptible hazelnut genotypes were collected from the field gene bank and heavily infected orchards in Giresun. Every individual was subjected to double digest restriction enzyme-associated DNA sequencing (ddRAD-seq) and a RADtag library was created. RADtags were aligned to the 'Tombul' reference genome, and Stacks software used to identify polymorphisms. 101 private and six common alleles from nine hazelnut varieties, four private from resistants and only one from susceptible were identified for diagnosis of either a certain hazelnut variety or powdery mildew resistance. Phylogenetic analysis and population structure calculations indicated that 'Mincane', 'Sarıfındık', 'Tombul', 'Çakıldak', and 'Palaz' were genetically close to each other; however, individuals within every varietal group were found in different sub-populations. Our findings indicated that years of clonal propagation of some preferred varieties across the Black Sea Region has resulted in admixed sub-populations and great genetic diversity within each variety. This impedes the development of a true breeding variety. For example, 'Tombul' is the most favored Turkish variety because of its high quality nuts, but an elite 'Tombul' line does not yet exist. This situation continues due to the lack of a breed protection program for commercially valuable hazelnut varieties. This study provides molecular markers suitable for establishing such a program.
| S-EPMC8282208 | biostudies-literature
Project description:The control of bud burst process depending on temperature is crucial factor in woody perennial plants to survive in unfavorable ecological conditions. Although it has important economic and agronomic values, little information is available on the molecular mechanism of the bud burst process in Corylus avellana. Here for the first time, we conducted a de novo transcriptome-based experiment using eco-dormant leaf bud tissues. Four transcriptome libraries were constructed from the leaf bud tissues and sequenced via Illumina platform. Transcriptome analysis revealed 86,394 unigenes with a mean length of 1189 nt and an N50 of 1916 nt. Among these unigenes, 63,854 (73.78%) of them were annotated by at least one database. De novo assembled transcripts were enriched in phenylpropanoid metabolism, phytohormone biosynthesis and signal transduction pathways. Analyses of phytohormone-associated genes revealed important changes during bud burst, in response to gibberellic acid, auxin, and brassinosteroids. Approximately 2163 putative transcription factors were predicted, of which the largest number of unique transcripts belonged to the MYB transcription factor family. These results contribute to a better understanding of the regulation of bud burst genes in perennial plants.
| S-EPMC6352538 | biostudies-literature
Project description:The characterization of plant genetic resources is a precondition for genetic improvement and germplasm management. The increasing use of molecular markers for DNA-based genotype signature is crucial for variety identification and traceability in the food supply chain. We collected 75 Sicilian hazelnut accessions from private and public field collections, including widely grown varieties from the Nebrodi Mountains in north east Sicily (Italy). The germplasm was fingerprinted through nine standardized microsatellites (SSR) for hazelnut identification to evaluate the genetic diversity of the collected accessions, validating SSR discrimination power. We identified cases of homonymy and synonymy among acquisitions and the unique profiles. The genetic relationships illustrated by hierarchical clustering, structure, and discriminant analyses revealed a clear distinction between local and commercial varieties. The comparative genetic analysis also showed that the Nebrodi genotypes are significantly different from the Northern Italian, Iberian, and Turkish genotypes. These results highlight the need and urgency to preserve Nebrodi germplasm as a useful and valuable source for traits of interest employable for breeding. Our study demonstrates the usefulness of molecular marker analysis to select a reference germplasm collection of Sicilian hazelnut varieties and to implement certified plants' production in the supply chain.
| S-EPMC8912283 | biostudies-literature
Project description:To explore the flavor related regulatory mechanisms of fresh Corylus heterophylla × Corylus avellana, a joint analysis of metabolome and transcriptome were utilized to compare the two typical C. heterophylla × C. avellana varieties with different flavors ('yuzhui' and 'pingou21') in this paper. The results showed that the genes including E2.4.1.67-1, E2.4.1.67-2, SUS-1, SUS-2, SUS-4, SUS-5, SUS-7, SUS-8, SUS-9, UGP2-2 were identified as responsible for regulating the levels of stachyose, manninotriose and raffinose in hazelnuts. CS and OGDH were deemed as the genes involved in the citric acid cycle, which was a central metabolic pathway that generated energy through the oxidation of carbohydrates, fats and proteins in hazelnuts. The genes trpD, ALDO, PK-1, PK-2, ilvH, argE-1, argE-4, argE-5, argD, PDAH, GLTI were regarded as involved in the biosynthesis of various amino acids like tryptophan, valine, alanine, and arginine. These amino acids determined the taste of C. heterophylla × C. avellana and were important precursors of other flavor-related compounds. The genes LOX2S-2, LOX2S-3, LOX2S-4 and LCAT3 were viewed as involved in the regulation of lipid biosynthesis, specifically involving 13(S)-HPODE, 9,10,13-trihome and 13(S)-HOTrE in C. heterophylla × C. avellana. These findings highlight the significance of genes and metabolites and internal regulatory mechanisms in shaping the flavor of fresh C. heterophylla × C. avellana cultivated in temperate continents. This study provides the theoretical basis for breeding excellent food functional hazelnut varieties.
| S-EPMC11821611 | biostudies-literature
Project description:In Europe, hazelnuts (Corylus avellana) are a frequent cause of food allergies. Several important hazelnut allergens have been previously identified and characterized. Specific N-glycans are known to induce strong IgE responses of uncertain clinical relevance, but so far the allergenic potential of glycoproteins from hazelnut has not been investigated. The aim of the study was the molecular characterization of the glycosylated vicilin Cor a 11 from hazelnut and the analysis of its allergenic activity. Although MALDI-TOF (matrix-assisted laser-desorption ionization-time-of-flight) MS showed that one of two potential glycosylation sites of Cor a 11 was glycosylated, CD spectroscopy indicated that recombinant and natural Cor a 11 share similar secondary structures. Thus to analyse the impact of the glycan residues of Cor a 11 on IgE binding, the allergenic activity of natural glycosylated Cor a 11 and recombinant Cor a 11 was compared. In addition, the IgE sensitization pattern to recombinant Cor a 11, Cor a 1, Cor a 2 and Cor a 8 of 65 hazelnut allergic patients was determined in vitro. The prevalence of IgE reactivity to hazelnut vicilin Cor a 11 was below 50%. Basophil histamine-release assays were used to determine the allergenic activity of both natural and recombinant Cor a 11 in comparison with Cor a 1, a birch (Betula verrucosa) pollen-related major hazelnut allergen. Both forms of Cor a 11 induced mediator release from basophils to a similar extent, indicating that the hazelnut allergic patients had cross-linking IgE antibodies binding to the protein backbone and not to carbohydrate structures. In comparison to Cor a 1, a 10000-fold higher concentration of Cor a 11 was required to induce similar basophil mediator release. In conclusion, the hazelnut vicilin Cor a 11 is a minor allergen both in regard to prevalence and allergenic potency, whereas its glycan does not contribute to its allergenic activity.
| S-EPMC1134074 | biostudies-literature
Project description:Four fungi isolated from trunks and branches of European hazelnut (Corylus avellana L.) from commercial orchards in the Willamette Valley, Oregon were characterized and pathogenicity was tested on potted hazelnut trees. The acreage of hazelnuts in Oregon has expanded greatly in recent years in response to the availability of Eastern filbert blight resistant cultivars. Fungi were characterized using the BLASTn algorithm and the GenBank database with multiple partial gene sequence(s). If BLASTn and GenBank were not sufficient for species-level identification, then a multilocus sequence analysis (MLSA) was performed. The four pathogens were identified as Diplodia mutilla (Fr.) Mont., Dothiorella omnivora B.T. Linaldeddu, A. Deidda & B. Scanu, Valsa cf. eucalypti Cooke & Harkn., and Diaporthe eres Nitschke. All pathogens but D. omnivora have not been previously reported from European hazelnut in the literature. All four pathogens caused lesions on trunks bare root hazelnut trees cv. 'Jefferson' planted in pots in the greenhouse and fungi were re-isolated from inoculated trees. D. mutilla appeared particularly aggressive in repeated inoculation experiments.
| S-EPMC6786572 | biostudies-literature
Project description:Plant genomes are now sequenced rapidly and inexpensively. In silico approaches allow efficient development of simple sequence repeat markers, also known as microsatellite markers, from these sequences. A search of the genome sequence of 'Jefferson' hazelnut (Corylus avellana L.) identified 8,708 tri-nucleotide simple sequence repeats with at least five repeat units, and stepwise removal of the less promising sequences led to the development of 150 polymorphic markers. Fragments in the 'Jefferson' sequence containing tri-nucleotide repeats were used as references and aligned with genomic sequences from seven other cultivars. Following in silico alignment, sequences that showed variation in number of repeat units were selected and primer pairs were designed for 243 of them. Screening on agarose gels identified 173 as polymorphic. Removal of duplicate and previously published sequences reduced the number to 150, for which fluorescent primers and capillary electrophoresis were used for amplicon sizing. These were characterized using 50 diverse hazelnut accessions. Of the 150, 132 generated the expected one or two alleles per accession while 18 amplified more than two amplicons in at least one accession. Diversity parameters of the 132 marker loci averaged 4.73 for number of alleles, 0.51 for expected heterozygosity (He), 0.49 for observed heterozygosity (Ho), 0.46 for polymorphism information content (PIC), and 0.04 for frequency of null alleles. The clustering of the 50 accessions in a dendrogram constructed from the 150 markers confirmed the wide genetic diversity and presence of three of the four major geographic groups: Central European, Black Sea, and Spanish-Italian. In the mapping population, 105 loci segregated, of which 101 were assigned to a linkage group (LG), with positions well-dispersed across all 11 LGs. These new markers will be useful for cultivar fingerprinting, diversity studies, genome comparisons, mapping, and alignment of the linkage map with the genome sequence and physical map.
| S-EPMC5439716 | biostudies-literature
Project description:Climate change and population increase are two challenges for crop production in the world. Hazelnut (Corylus avellana L.) is considered an important nut regarding its nutritional and economic values. As a fact, the application of supporting materials as foliage sprays on plants will decrease biotic and abiotic stresses. In this study, the effects of salicylic acid (0, 1 mM and 2.5 mM) and kaolin (0, 3% and 6%) sprays were investigated on morphological, physiological, pomological, and biochemical characteristics of hazelnut. The results showed that 1 mM salicylic acid and 6% kaolin had the best effects on nut and kernel weight compared to control. Biochemical parameters such as chlorophyll a, b, a + b, and carotenoid contents showed that salicylic acid and kaolin improved pigment concentration. Proline and antioxidant contents such as phenolic acids, SOD, APX, and CAT enzyme activities increased by these applications. On the other hand, lipid peroxidation, protein content, and H2O2 content were decreased. Based on the tolerance index result, Merveille de Bollwiller cultivar showed the highest tolerance while 'Fertile de Coutard' had the lowest value. Therefore, hazelnut performance may be improved through exogenous application of the signaling (salicylic acid) and particle film (Kaolin) compounds in warmer climates.
| S-EPMC7907359 | biostudies-literature
Project description:The choice of plant species is crucial, as different plants provide unique biomolecules that influence nanoparticle characteristics. Biomolecules in plant extracts, such as proteins, amino acids, enzymes, polysaccharides, alkaloids, tannins, phenolics, saponins, terpenoids, and vitamins, act as stabilizing and reducing agents. This study explores the synthesis of silver nanoparticles (AgNPs) using leaf extracts from collard greens (Brassica oleracea var. acephala), hazelnut (Corylus avellana var. avellana), and green tea (Camellia sinensis). NPs were synthesized using silver nitrate (AgNO3) solution at two different molarities (1 mM and 5 mM) and characterized by UV-Vis spectroscopy, XRD, TEM, and FTIR. The Surface Plasmon Resonance (SPR) peaks appeared rapidly for hazelnut and green tea extracts, within 30 and 15 min, respectively, while collard greens extract failed to produce a distinct SPR peak. X-Ray Diffraction confirmed the formation of face-centered cubic silver. TEM analysis revealed high polydispersity and agglomeration in all samples, with particle size generally decreasing at higher AgNO3 concentrations. However, hazelnut extract showed a slight increase in size at higher molarity. Among all samples, green tea-derived AgNPs synthesized with 5 mM AgNO3 were the smallest and least polydisperse, highlighting the significant role of plant type in optimizing nanoparticle synthesis.
| S-EPMC11643465 | biostudies-literature
Project description:The present study evaluates natural composition of Serbian roasted hazelnut skins (HS) with potential role in application as functional nutrient of various food products. Total phenols (TPC) and flavonoids contents (TFC) in HS extracts obtained with different ethanol concentrations (10%-I, 50%-II and 96%-III) and their antioxidant activities were investigated. The highest total phenols content (706.0 ± 9.7 mgGAE/gextract) was observed in 96% ethanol HS extract. Ethanol HS extracts showed very high antioxidant activity with effective concentrations (EC50) ranged between 0.052 and 0.066 mg/mL. The phenol and flavonoid content of roasted HS extracts I-III was determined by HPLC-ESI-MS/MS analyses. Contents of lipids, proteins, carbohydrates, metals, and C, H, N, S elements in roasted HS were also determined. Relatively high C/N, C/P and C/N/P ratios, rich metal contents and fatty acids composition indicated that hazelnut skin might be a good candidate for use as either human or fungal functional nutrient. In addition, possible application of phenolic HS extracts as UV booster was studied by recording UV spectra (220-440 nm) of 10 mg/L of HS extracts I-III combined with 10 mg/L of chemical sunscreen agent benzophenone-3 and in vitro sun protection factor (SPF) was calculated.
| S-EPMC7230596 | biostudies-literature