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Mariotti R, Belaj A, de la Rosa R, Muleo R, Cirilli M, Forgione I, Valeri MC, Mousavi S. Genealogical tracing of Olea europaea species and pedigree relationships of var. europaea using chloroplast and nuclear markers. BMC PLANT BIOLOGY 2023; 23:452. [PMID: 37749509 PMCID: PMC10521521 DOI: 10.1186/s12870-023-04440-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 09/04/2023] [Indexed: 09/27/2023]
Abstract
BACKGROUND Olive is one of the most cultivated species in the Mediterranean Basin and beyond. Despite being extensively studied for its commercial relevance, the origin of cultivated olive and the history of its domestication remain open questions. Here, we present a genealogical and kinship relationships analysis by mean of chloroplast and nuclear markers of different genera, subgenus, species, subspecies, ecotypes, cultivated, ancient and wild types, which constitutes one of the most inclusive research to date on the diversity within Olea europaea species. A complete survey of the variability across the nuclear and plastid genomes of different genotypes was studied through single nucleotide polymorphisms, indels (insertions and deletions), and length variation. RESULTS Fifty-six different chlorotypes were identified among the Oleaceae family including Olea europaea, other species and genera. The chloroplast genome evolution, within Olea europaea subspecies, probably started from subsp. cuspidata, which likely represents the ancestor of all the other subspecies and therefore of wild types and cultivars. Our study allows us to hypothesize that, inside the subspecies europaea containing cultivars and the wild types, the ancestral selection from var. sylvestris occurred both in the eastern side of the Mediterranean and in the central-western part of Basin. Moreover, it was elucidated the origin of several cultivars, which depends on the introduction of eastern cultivars, belonging to the lineage E1, followed by crossing and replacement of the autochthonous olive germplasm of central-western Mediterranean Basin. In fact, our study highlighted that two main 'founders' gave the origin to more than 60% of analyzed olive cultivars. Other secondary founders, which strongly contributed to give origin to the actual olive cultivar diversity, were already detected. CONCLUSIONS The application of comparative genomics not only paves the way for a better understanding of the phylogenetic relationships within the Olea europaea species but also provides original insights into other elusive evolutionary processes, such as chloroplast inheritance and parentage inside olive cultivars, opening new scenarios for further research such as the association studies and breeding programs.
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Affiliation(s)
- Roberto Mariotti
- Institute of Biosciences and Bioresources, National Research Council, Perugia, 06128, Italy.
| | | | | | - Rosario Muleo
- Department of Agricultural and Forestry Sciences (DAFNE), University of Tuscia, Viterbo, 01100, Italy
| | - Marco Cirilli
- Department of Agricultural and Environmental Sciences (DiSAA), University of Milan, Milan, Italy
| | - Ivano Forgione
- Department of Agricultural and Forestry Sciences (DAFNE), University of Tuscia, Viterbo, 01100, Italy
| | - Maria Cristina Valeri
- Institute of Biosciences and Bioresources, National Research Council, Perugia, 06128, Italy
| | - Soraya Mousavi
- Institute of Biosciences and Bioresources, National Research Council, Perugia, 06128, Italy.
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Kaur S, Pennington T, Conley EJ, Green A, Kolmer J, Anderson J, Gupta R, Gill U. High-Resolution Melting-Based Marker Development for Wheat Leaf Rust Resistance Gene Lr34. PHYTOPATHOLOGY 2023; 113:508-515. [PMID: 36346374 DOI: 10.1094/phyto-08-22-0313-r] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Deploying adult plant resistance (APR) against rust diseases is an important breeding objective of most wheat-breeding programs. The gene Lr34 is an effective and widely deployed broad-spectrum APR gene in wheat against leaf rust fungus Puccinia triticina. Various molecular markers have been developed for Lr34, but they either require post-PCR handling processes or are not economical. Herein, we developed a high-resolution melting (HRM)-based diagnostic assay for Lr34 based on a 3-bp 'TTC' deletion in exon 11 of the resistant allele. The susceptible cultivar Thatcher (Tc) and the near-isogenic Thatcher line (RL6058) with Lr34 yielded distinct melting profiles and were differentiated with high reproducibility. For further validation, all three copies of Lr34 were cloned in plasmid vectors, and HRM analysis using individual and combination (equimolar mixture of three copies) homoeologs yielded distinct melting profiles. An additional layer of genotyping was provided by a LunaProbe assay. The allele-specific probes successfully distinguished the homoeologs but not Tc and RL6058. Furthermore, the practical deployment of the HRM assay was tested by running the marker on a set of breeding lines. When compared with a kompetitive allele-specific PCR (KASP) Lr34 assay, the HRM assay had similar genotyping results and was able to accurately differentiate the resistant and susceptible breeding lines. However, our HRM assay was unable to detect the heterozygote. To our knowledge, this is the first report of an HRM assay for genotyping a wheat rust resistance gene.
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Affiliation(s)
- Shivreet Kaur
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58108
| | - Taylor Pennington
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58108
| | - Emily J Conley
- Department of Agronomy & Plant Genetics, University of Minnesota, St. Paul, MN 55108
| | - Andrew Green
- Department of Plant Sciences, North Dakota State University, Fargo, ND 58108
| | - James Kolmer
- U.S. Department of Agriculture-Agricultural Research Service, Cereal Disease Laboratory, St. Paul, MN 55108
| | - James Anderson
- Department of Agronomy & Plant Genetics, University of Minnesota, St. Paul, MN 55108
| | - Rajeev Gupta
- U.S. Department of Agriculture-Agricultural Research Service, Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Fargo, ND 58102
| | - Upinder Gill
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58108
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Orlando Marchesano BM, Chiozzotto R, Baccichet I, Bassi D, Cirilli M. Development of an HRMA-Based Marker Assisted Selection (MAS) Approach for Cost-Effective Genotyping of S and M Loci Controlling Self-Compatibility in Apricot (Prunus armeniaca L.). Genes (Basel) 2022; 13:genes13030548. [PMID: 35328101 PMCID: PMC8954599 DOI: 10.3390/genes13030548] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 03/13/2022] [Accepted: 03/15/2022] [Indexed: 12/04/2022] Open
Abstract
The apricot species is characterized by a gametophytic self-incompatibility (GSI) system. While GSI is one of the most efficient mechanisms to prevent self-fertilization and increase genetic variability, it represents a limiting factor for fruit production in the orchards. Compatibility among apricot cultivars was usually assessed by either field pollination experiments or by histochemical evaluation of in vitro pollen tube growth. In apricots, self-compatibility is controlled by two unlinked loci, S and M, and associated to transposable element insertion within the coding sequence of SFB and ParM-7 genes, respectively. Self-compatibility has become a primary breeding goal in apricot breeding programmes, stimulating the development of a rapid and cost-effective marker assisted selection (MAS) approach to accelerate screening of self-compatible genotypes. In this work, we demonstrated the feasibility of a novel High Resolution Melting Analysis (HRMA) approach for the massive screening of self-compatible and self-incompatible genotypes for both S and M loci. The different genotypes were unambiguously recognized by HRMA, showing clearly distinguishable melting profiles. The assay was developed and tested in a panel of accessions and breeding selections with known self-compatibility reaction, demonstrating the potential usefulness of this approach to optimize and accelerate apricot breeding programmes.
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Machado JC, Faria MA, Barata AM, da Silva IG, Cerenak A, Ferreira IMPLVO. Portuguese wild hop diversity assessment by fast SNP genotyping using high-resolution melting. J Appl Genet 2021; 63:103-114. [PMID: 34719770 DOI: 10.1007/s13353-021-00668-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 10/13/2021] [Accepted: 10/19/2021] [Indexed: 11/24/2022]
Abstract
A set of seven SNP markers was used to evaluate the genetic diversity of wild Portuguese hops in comparison with commercial cultivars. A collection of 110 wild genotypes and 33 cultivars was characterized by a high-resolution melting analysis of short amplicons targeting SNP loci. Most of the 143 genotypes (75%) could be differentiated. Phylogenetic analysis showed three main clusters, one included almost exclusively (98%) wild accessions, being the others constituted of both wild and commercial genotypes. The study of population genetic structure placed the accessions into three genetic units, being one exclusively of Portuguese genotypes. The study showed the great biodiversity of the Portuguese hop germplasm and the notable differences (FST = 0.163, p<0.00001) from commercial hops. Results support the usefulness of the use of these seven markers for hop discrimination, with the fast and high-throughput HRMA technique for allele calling and contribute to the affirmation of the high richness breeding potential of Portuguese wild hops.
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Affiliation(s)
- Julio C Machado
- LAQV/REQUIMTE, Laboratório de Bromatologia e Hidrologia, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto, 4050-313, Porto, Portugal
| | - Miguel A Faria
- LAQV/REQUIMTE, Laboratório de Bromatologia e Hidrologia, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto, 4050-313, Porto, Portugal.
| | - Ana Maria Barata
- Banco Português de Germoplasma Vegetal, Instituto Nacional de Investigação Agrária e Veterinária, Quinta de S. José, S. Pedro de Merelim, 4700-859, Braga, Portugal
| | - Isabel Gomes da Silva
- Banco Português de Germoplasma Vegetal, Instituto Nacional de Investigação Agrária e Veterinária, Quinta de S. José, S. Pedro de Merelim, 4700-859, Braga, Portugal
| | - Andreja Cerenak
- Slovenian Institute of Hop Research and Brewing, Cesta Zalskega Tabora 2, 3310, Zalec, Slovenia
| | - Isabel M P L V O Ferreira
- LAQV/REQUIMTE, Laboratório de Bromatologia e Hidrologia, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto, 4050-313, Porto, Portugal
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Galuszynski NC, Potts AJ. Applied phylogeography of Cyclopia intermedia (Fabaceae) highlights the need for 'duty of care' when cultivating honeybush. PeerJ 2020; 8:e9818. [PMID: 32953270 PMCID: PMC7474521 DOI: 10.7717/peerj.9818] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 08/05/2020] [Indexed: 12/26/2022] Open
Abstract
Background The current cultivation and plant breeding of Honeybush tea (produced from members of Cyclopia Vent.) do not consider the genetic diversity nor structuring of wild populations. Thus, wild populations may be at risk of genetic contamination if cultivated plants are grown in the same landscape. Here, we investigate the spatial distribution of genetic diversity within Cyclopia intermedia E. Mey.-this species is widespread and endemic in the Cape Floristic Region (CFR) and used in the production of Honeybush tea. Methods We applied High Resolution Melt analysis (HRM), with confirmation Sanger sequencing, to screen two non-coding chloroplast DNA regions (two fragments from the atpI-aptH intergenic spacer and one from the ndhA intron) in wild C. intermedia populations. A total of 156 individuals from 17 populations were analyzed for phylogeographic structuring. Statistical tests included analyses of molecular variance and isolation-by-distance, while relationships among haplotypes were ascertained using a statistical parsimony network. Results Populations were found to exhibit high levels of genetic structuring, with 62.8% of genetic variation partitioned within mountain ranges. An additional 9% of genetic variation was located amongst populations within mountains, suggesting limited seed exchange among neighboring populations. Despite this phylogeographic structuring, no isolation-by-distance was detected (p > 0.05) as nucleotide variation among haplotypes did not increase linearly with geographic distance; this is not surprising given that the configuration of mountain ranges dictates available habitats and, we assume, seed dispersal kernels. Conclusions Our findings support concerns that the unmonitored redistribution of Cyclopia genetic material may pose a threat to the genetic diversity of wild populations, and ultimately the genetic resources within the species. We argue that 'duty of care' principles be used when cultivating Honeybush and that seed should not be translocated outside of the mountain range of origin. Secondarily, given the genetic uniqueness of wild populations, cultivated populations should occur at distance from wild populations that is sufficient to prevent unintended gene flow; however, further research is needed to assess gene flow within mountain ranges.
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Affiliation(s)
- Nicholas C Galuszynski
- Department of Botany, Nelson Mandela University, Port Elizabeth, Eastern Cape, South Africa
| | - Alastair J Potts
- Department of Botany, Nelson Mandela University, Port Elizabeth, Eastern Cape, South Africa
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Batrinou A, Strati IF, Houhoula D, Tsaknis J, Sinanoglou VJ. Authentication of olive oil based on DNA analysis. GRASAS Y ACEITES 2020. [DOI: 10.3989/gya.0682191] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Olive oil, which has been produced mainly in the Mediterranean area since the ancient times, has a high nutritional value linked to many health benefits. Extra virgin, which is the purest form of olive oil, has excellent quality and premium prices. Many cases of adulteration and fraud necessitate the development of reliable and accurate methods for olive oil authentication. DNA-based methods analyze the residual DNA extracted from olive oil and use molecular markers for genetic identification of different species, subspecies or cultivars because these markers act as signs which reflect distinct genetic profiles. This study reviews the process by which DNA from olive oil is extracted and analyzed by the most recently used markers in the authentication of olive oil, such as Simple Sequence Repeats (SSR) or microsatellites and the single nucleotide polymorphisms (SNPs). Methods of analysis such as qPCR and digital PCR are also discussed with a special emphasis placed on the method of High-Resolution Melting (HRM), a post-polymerase chain reaction method, which enables rapid, high performing identification of genetic variants in the DNA regions of interest without sequencing, and may differentiate very similar cultivars which differ in only one nucleotide in a specific locus.
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Avramidou EV, Doulis AG, Petrakis PV. Chemometrical and molecular methods in olive oil analysis: A review. J FOOD PROCESS PRES 2018. [DOI: 10.1111/jfpp.13770] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
| | - Andreas G. Doulis
- Laboratory of Plant Biotechnology & Genomic Resources, Hellenic Agricultural Organisation “DEMETER"; Institute of Olive Tree, Subtropical Crops and Viticulture; Heraklion Greece
| | - Panos V. Petrakis
- Laboratory of Entomology; Institute of Mediterranean Forest Ecosystems; Athens Greece
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Emenyeonu LC, Croxford AE, Wilkinson MJ. The potential of aerosol eDNA sampling for the characterisation of commercial seed lots. PLoS One 2018; 13:e0201617. [PMID: 30067814 PMCID: PMC6070268 DOI: 10.1371/journal.pone.0201617] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2018] [Accepted: 07/18/2018] [Indexed: 11/28/2022] Open
Abstract
Seed shipments, silos and storage houses often contain weed seeds or seeds of restricted crops such as undeclared genetically modified (GM) varieties. Random sub-sampling is the favoured approach to detect unwanted biological materials in seed lots but is prohibitively expensive or else ineffective for the huge volumes of seeds moved in commercial operations. This study uses maize and cowpea seed admixtures as an exemplar to evaluate the feasibility of using aerosol sampling of "seed dust" as an alternative to seed sub-sampling. In an initial calibration phase, qPCR of the rbcL barcode followed by high-resolution melting (HRM) of a DNA titration series revealed a strong linear relationship between mix composition and HRM profiles. However, the relationship became skewed when flour mixes were used to build the titration, implying a DNA extraction bias favouring cowpea. Aerosol samples of seed dust above a titration of mixed seed samples were then collected along vertical and lateral axes. Aerosols were characterised by light microscopy, qPCR-HRM and next-generation DNA sequencing (Illumina MiSeq). Both molecular approaches again showed bias but this time in a reverse direction to flour samples. Microscopic examination of the aerosol sample suggested this divergence could be attributed to differences in abundance of airborne starch particles. Despite the bias, it was nevertheless possible to estimate relative abundance of each species using the abundance of minibarcodes. In light of these results we explore the feasibility of aerosol sampling for commercial seed lot characterisation.
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Affiliation(s)
- Lorretha C. Emenyeonu
- School of Agriculture, Food and Wine, Waite Campus, Urrbrae, The University of Adelaide, Adelaide, SA, Australia
| | - Adam E. Croxford
- School of Agriculture, Food and Wine, Waite Campus, Urrbrae, The University of Adelaide, Adelaide, SA, Australia
| | - Mike J. Wilkinson
- Pwllpeiran Upland Research Centre, Institute of Biological, Environmental & Rural Sciences, Aberystwyth University, Penglais, Aberystwyth, Ceredigion, United Kingdom
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Ahn YK, Manivannan A, Karna S, Jun TH, Yang EY, Choi S, Kim JH, Kim DS, Lee ES. Whole Genome Resequencing of Capsicum baccatum and Capsicum annuum to Discover Single Nucleotide Polymorphism Related to Powdery Mildew Resistance. Sci Rep 2018; 8:5188. [PMID: 29581444 PMCID: PMC5980001 DOI: 10.1038/s41598-018-23279-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 03/06/2018] [Indexed: 11/08/2022] Open
Abstract
The present study deals with genome wide identification of single-nucleotide polymorphism (SNP) markers related to powdery mildew (PM) resistance in two pepper varieties. Capsicum baccatum (PRH1- a PM resistant line) and Capsicum annuum (Saengryeg- a PM susceptible line), were resequenced to develop SNP markers. A total of 6,213,009 and 6,840,889 SNPs for PRH1 and Saengryeg respectively have been discovered. Among the SNPs, majority were classified as homozygous type SNPs, particularly in the resistant line. Moreover, the SNPs were differentially distributed among the chromosomes in both the resistant and susceptible lines. In total, 4,887,031 polymorphic SNP loci were identified between the two lines and 306,871 high-resolution melting (HRM) marker primer sets were designed. In order to understand the SNPs associated with the vital genes involved in diseases resistance and stress associated processes, chromosome-wise gene ontology analysis was performed. The results revealed the occurrence that SNPs related to diseases resistance genes were predominantly distributed in chromosome 4. In addition, 6281 SNPs associated with 46 resistance genes were identified. Among the lines, PRH1 consisted of maximum number of polymorphic SNPs related to NBS-LRR genes. The SNP markers were validated using HRM assay in 45 F4 populations and correlated with the phenotypic disease index.
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Affiliation(s)
- Yul-Kyun Ahn
- Department of Vegetable Crops, Korea National College of Agriculture and Fisheries, Jeonju, 54874, Republic of Korea.
| | - Abinaya Manivannan
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Jeonju, 55365, Republic of Korea
| | - Sandeep Karna
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Jeonju, 55365, Republic of Korea
| | - Tae-Hwan Jun
- Department of Plant Bioscience, Pusan National University, Busan, 46241, Republic of Korea
| | - Eun-Young Yang
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Jeonju, 55365, Republic of Korea
| | - Sena Choi
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Jeonju, 55365, Republic of Korea
| | - Jin-Hee Kim
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Jeonju, 55365, Republic of Korea
| | - Do-Sun Kim
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Jeonju, 55365, Republic of Korea
| | - Eun-Su Lee
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Jeonju, 55365, Republic of Korea
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Pereira L, Gomes S, Barrias S, Fernandes JR, Martins-Lopes P. Applying high-resolution melting (HRM) technology to olive oil and wine authenticity. Food Res Int 2018; 103:170-181. [DOI: 10.1016/j.foodres.2017.10.026] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 10/11/2017] [Accepted: 10/12/2017] [Indexed: 12/21/2022]
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Belaj A, de la Rosa R, Lorite IJ, Mariotti R, Cultrera NGM, Beuzón CR, González-Plaza JJ, Muñoz-Mérida A, Trelles O, Baldoni L. Usefulness of a New Large Set of High Throughput EST-SNP Markers as a Tool for Olive Germplasm Collection Management. FRONTIERS IN PLANT SCIENCE 2018; 9:1320. [PMID: 30298075 PMCID: PMC6160578 DOI: 10.3389/fpls.2018.01320] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 08/22/2018] [Indexed: 05/08/2023]
Abstract
Germplasm collections are basic tools for conservation, characterization, and efficient use of olive genetic resources. The identification of the olive cultivars maintained in the collections is an important ongoing task which has been performed by both, morphological and molecular markers. In the present study, based on the sequencing results of previous genomic projects, a new set of 1,043 EST-SNP markers has been identified. In order to evaluate its discrimination capacity and utility in diversity studies, this set of markers was used in a representative number of accessions from 20 different olive growing countries and maintained at the World Olive Germplasm Collection of IFAPA Centre 'Alameda del Obispo' (Córdoba, Spain), one of the world's largest olive germplasm bank. Thus, the cultivated material included: cultivars belonging to previously defined core collections by means of SSR markers and agronomical traits, well known homonymy cases, possible redundancies previously identified in the collection, and recently introduced accessions. Marker stability was tested in repeated analyses of a selected number of accessions, as well as in different trees and accessions belonging to the same cultivar. In addition, 15 genotypes from a cross 'Picual' × 'Arbequina' cultivars from the IFAPA olive breeding program and a set of 89 wild genotypes were also included in the study. Our results indicate that, despite their relatively wide variability, the new set of EST-SNPs displayed lower levels of genetic diversity than SSRs in the set of olive core collections tested. However, the EST-SNP markers displayed consistent and reliable results from different plant material sources and plant propagation events. The EST-SNPs revealed a clear cut off between inter- and intra-cultivar variation in olive. Besides, they were able to reliably discriminate among different accessions, to detect possible homonymy cases as well as efficiently ascertain the presence of redundant germplasm in the collection. Additionally, these markers were highly transferable to the wild genotypes. These results, together with the low genotyping error rates and the easy and fully automated procedure used to get the genotyping data, validate the new set of EST-SNPs as possible markers of choice for olive cultivar identification.
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Affiliation(s)
- Angjelina Belaj
- IFAPA Centro Alameda del Obispo, Córdoba, Spain
- *Correspondence: Angjelina Belaj,
| | | | | | | | | | - Carmen R. Beuzón
- Instituto de Hortofruticultura Subtropical y Mediterranea, Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Málaga, Spain
| | - J. J. González-Plaza
- Instituto de Hortofruticultura Subtropical y Mediterranea, Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Málaga, Spain
- Present address: J. J. González-Plaza, Faculty of Forestry and Wood Sciences, Czech University of Life Sciences, Prague, Czechia
| | - A. Muñoz-Mérida
- CIBIO, InBIO – Research Network in Biodiversity and Evolutionary Biology, University of Porto, Porto, Portugal
| | - O. Trelles
- Department of Integrated Bioinformatics, National Institute for Bioinformatics, Universidad de Málaga, Málaga, Spain
| | - Luciana Baldoni
- CNR – Institute of Biosciences and Bioresources, Perugia, Italy
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Haplotype analysis of the germacrene A synthase gene and association with cynaropicrin content and biological activities in Cynara cardunculus. Mol Genet Genomics 2017; 293:417-433. [PMID: 29143866 DOI: 10.1007/s00438-017-1388-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 10/27/2017] [Indexed: 12/13/2022]
Abstract
Cynara cardunculus: L. represents a natural source of terpenic compounds, with the predominant molecule being cynaropicrin. Cynaropicrin is gaining interest since it has been correlated to anti-hyperlipidaemia, antispasmodic and cytotoxicity activity against leukocyte cancer cells. The objective of this work was to screen a collection of C. cardunculus, from different origins, for new allelic variants in germacrene A synthase (GAS) gene involved in the cynaropicrin biosynthesis and correlate them with improved cynaropicrin content and biological activities. Using high-resolution melting, nine haplotypes were identified. The putative impact of the identified allelic variants in GAS protein was evaluated by bioinformatic tools and polymorphisms that putatively lead to protein conformational changes were described. Additionally, cynaropicrin and main pentacyclic triterpenes contents, and antithrombin, antimicrobial and antiproliferative activities were also determined in C. cardunculus leaf lipophilic-derived extracts. In this work we identified allelic variants with putative impact on GAS protein, which are significantly associated with cynaropicrin content and antiproliferative activity. The results obtained suggest that the identified polymorphisms should be explored as putative genetic markers correlated with biological properties in Cynara cardunculus.
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Ferro AM, Ramos P, Guerreiro O, Jerónimo E, Pires I, Capel C, Capel J, Lozano R, Duarte MF, Oliveira MM, Gonçalves S. Impact of novel SNPs identified in Cynara cardunculus genes on functionality of proteins regulating phenylpropanoid pathway and their association with biological activities. BMC Genomics 2017; 18:183. [PMID: 28212611 PMCID: PMC5314637 DOI: 10.1186/s12864-017-3534-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 02/02/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cynara cardunculus L. offers a natural source of phenolic compounds with the predominant molecule being chlorogenic acid. Chlorogenic acid is gaining interest due to its involvement in various biological properties such as, antibacterial, antifungal, antioxidant, hepatoprotective, and anticarcinogenic activities. RESULTS In this work we screened a Cynara cardunculus collection for new allelic variants in key genes involved in the chlorogenic acid biosynthesis pathway. The target genes encode p-coumaroyl ester 3'-hydroxylase (C3'H) and hydroxycinnamoyl-CoA: quinate hydroxycinnamoyl transferase (HQT), both participating in the synthesis of chlorogenic acid. Using high-resolution melting, the C3'H gene proved to be highly conserved with only 4 haplotypes while, for HQT, 17 haplotypes were identified de novo. The putative influence of the identified polymorphisms in C3'H and HQT proteins was further evaluated using bioinformatics tools. We could identify some polymorphisms that may lead to protein conformational changes. Chlorogenic acid content, antioxidant and antithrombin activities were also evaluated in Cc leaf extracts and an association analysis was performed to assess a putative correlation between these traits and the identified polymorphisms. CONCLUSION In this work we identified allelic variants with putative impact on C3'H and HQT proteins which are significantly associated with chlorogenic acid content and antioxidant activity. Further study of these alleles should be explored to assess putative relevance as genetic markers correlating with Cynara cardunculus biological properties with further confirmation by functional analysis.
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Affiliation(s)
- Ana Margarida Ferro
- Centro de Biotecnologia Agrícola e Agro-Alimentar do Alentejo (CEBAL), Instituto Politécnico de Beja (IPBeja), Rua Pedro Soares, 7801-908 Beja, Portugal
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Av. da República, 2781-901 Oeiras, Portugal
| | - Patrícia Ramos
- Centro de Biotecnologia Agrícola e Agro-Alimentar do Alentejo (CEBAL), Instituto Politécnico de Beja (IPBeja), Rua Pedro Soares, 7801-908 Beja, Portugal
- Centre for Research in Ceramics and Composite Materials (CICECO) and Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Olinda Guerreiro
- Centro de Biotecnologia Agrícola e Agro-Alimentar do Alentejo (CEBAL), Instituto Politécnico de Beja (IPBeja), Rua Pedro Soares, 7801-908 Beja, Portugal
- Centro de Investigação Interdisciplinar em Sanidade Animal (CIISA), Faculdade de Medicina Veterinária, University of Lisbon, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
| | - Eliana Jerónimo
- Centro de Biotecnologia Agrícola e Agro-Alimentar do Alentejo (CEBAL), Instituto Politécnico de Beja (IPBeja), Rua Pedro Soares, 7801-908 Beja, Portugal
| | - Inês Pires
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Av. da República, 2781-901 Oeiras, Portugal
| | - Carmen Capel
- Centro de Investigación en Biotecnología Agroalimentaria (BITAL), Universidad de Almería, 04120 Almeria, Spain
| | - Juan Capel
- Centro de Investigación en Biotecnología Agroalimentaria (BITAL), Universidad de Almería, 04120 Almeria, Spain
| | - Rafael Lozano
- Centro de Investigación en Biotecnología Agroalimentaria (BITAL), Universidad de Almería, 04120 Almeria, Spain
| | - Maria F. Duarte
- Centro de Biotecnologia Agrícola e Agro-Alimentar do Alentejo (CEBAL), Instituto Politécnico de Beja (IPBeja), Rua Pedro Soares, 7801-908 Beja, Portugal
| | - M. Margarida Oliveira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Av. da República, 2781-901 Oeiras, Portugal
| | - Sónia Gonçalves
- Centro de Biotecnologia Agrícola e Agro-Alimentar do Alentejo (CEBAL), Instituto Politécnico de Beja (IPBeja), Rua Pedro Soares, 7801-908 Beja, Portugal
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB101SA Cambridge, UK
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Cirilli M, Delfino I, Caboni E, Muleo R. EpiHRMAssay, in tube and in silico combined approach for the scanning and epityping of heterogeneous DNA methylation. Biol Methods Protoc 2017; 2:bpw008. [PMID: 32161783 PMCID: PMC6994072 DOI: 10.1093/biomethods/bpw008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Revised: 11/12/2016] [Accepted: 12/16/2016] [Indexed: 11/18/2022] Open
Abstract
Reliable and cost-effective assays with adequate sensitivity are required to detect the DNA methylation profile in plants for scientific and industrial purposes. The proposed novel assay, named EpiHRMAssay, allows to quantify the overall methylation status at target loci and to enable high-throughput analyses. It combines in tube High Resolution Melting Analysis on bisulphite-treated templates with the in silico prediction of the melting profile of virtual epialleles using uMELTSM software. The predicted melting temperatures (Tm-s) of a set of epialleles characterized by different numbers of methylated cytosines (#mC) or different mC configurations were obtained and used to build calibration models, enabling the quantification of methylation in unknown samples using only the in tube observed melting temperature (Tm-o). EpiHRMAssay was validated by analysing the promoter region of CMT3, DDM1, and ROS1 genes involved in the regulation of methylation/demethylation processes and chromatin remodelling within a population of peach plants. Results demonstrate that EpiHRMAssay is a sensitive and reliable tool for locus-specific large-scale research and diagnostic contexts of the regulative regions of genes, in a broad range of organisms, including mammals. EpiHRMAssay also provides complementary information for the assessment of heterogeneous methylation and can address an array of biological questions on epigenetic regulation for diversity studies and for large-scale functional genomics.
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Affiliation(s)
- Marco Cirilli
- Department of Agricultural and Forestry Sciences, University of Tuscia, Via S. Camillo de Lellis snc, Viterbo 01100, Italy
| | - Ines Delfino
- Department of Ecological and Biological Sciences, University of Tuscia, L.go dell'Università snc, Viterbo 01100, Italy
| | - Emilia Caboni
- Council for Agricultural Research and Analysis of Agricultural Economics (CREA), Fruit Tree Research Center, Via di Fioranello, 52, 00134 Rome, Italy
| | - Rosario Muleo
- Department of Agricultural and Forestry Sciences, University of Tuscia, Via S. Camillo de Lellis snc, Viterbo 01100, Italy
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15
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Pasqualone A, Montemurro C, di Rienzo V, Summo C, Paradiso VM, Caponio F. Evolution and perspectives of cultivar identification and traceability from tree to oil and table olives by means of DNA markers. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2016; 96:3642-3657. [PMID: 26991131 DOI: 10.1002/jsfa.7711] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Revised: 02/21/2016] [Accepted: 03/08/2016] [Indexed: 06/05/2023]
Abstract
In recent years, an increasing number of typicality marks has been awarded to high-quality olive oils produced from local cultivars. In this case, quality control requires effective varietal checks of the starting materials. Moreover, accurate cultivar identification is essential in vegetative-propagated plants distributed by nurseries and is a pre-requisite to register new cultivars. Food genomics provides many tools for cultivar identification and traceability from tree to oil and table olives. The results of the application of different classes of DNA markers to olive with the purpose of checking cultivar identity and variability of plant material are extensively discussed in this review, with special regard to repeatability issues and polymorphism degree. The characterization of olive germplasm from all countries of the Mediterranean basin and from less studied geographical areas is described and innovative high-throughput molecular tools to manage reference collections are reviewed. Then the transferability of DNA markers to processed products - virgin olive oils and table olives - is overviewed to point out strengths and weaknesses, with special regard to (i) the influence of processing steps and storage time on the quantity and quality of residual DNA, (ii) recent advances to overcome the bottleneck of DNA extraction from processed products, (iii) factors affecting whole comparability of DNA profiles between fresh plant materials and end-products, (iv) drawbacks in the analysis of multi-cultivar versus single-cultivar end-products and (v) the potential of quantitative polymerase chain reaction (PCR)-based techniques. © 2016 Society of Chemical Industry.
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Affiliation(s)
- Antonella Pasqualone
- Department of Soil, Plant, and Food Sciences, University of Bari 'Aldo Moro', Via Amendola 165/A, I-70126, Bari, Italy
| | - Cinzia Montemurro
- Department of Soil, Plant, and Food Sciences, University of Bari 'Aldo Moro', Via Amendola 165/A, I-70126, Bari, Italy
| | - Valentina di Rienzo
- Department of Soil, Plant, and Food Sciences, University of Bari 'Aldo Moro', Via Amendola 165/A, I-70126, Bari, Italy
| | - Carmine Summo
- Department of Soil, Plant, and Food Sciences, University of Bari 'Aldo Moro', Via Amendola 165/A, I-70126, Bari, Italy
| | - Vito Michele Paradiso
- Department of Soil, Plant, and Food Sciences, University of Bari 'Aldo Moro', Via Amendola 165/A, I-70126, Bari, Italy
| | - Francesco Caponio
- Department of Soil, Plant, and Food Sciences, University of Bari 'Aldo Moro', Via Amendola 165/A, I-70126, Bari, Italy
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16
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Simko I. High-Resolution DNA Melting Analysis in Plant Research. TRENDS IN PLANT SCIENCE 2016; 21:528-537. [PMID: 26827247 DOI: 10.1016/j.tplants.2016.01.004] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Revised: 12/05/2015] [Accepted: 01/05/2016] [Indexed: 05/22/2023]
Abstract
Genetic and genomic studies provide valuable insight into the inheritance, structure, organization, and function of genes. The knowledge gained from the analysis of plant genes is beneficial to all aspects of plant research, including crop improvement. New methods and tools are continually being developed to facilitate rapid and accurate mapping, sequencing, and analyzing of genes. Here, I review the recent progress in the application of high-resolution melting (HRM) analysis of DNA, a method that allows detecting polymorphism in double-stranded DNA by comparing profiles of melting curves. Use of HRM has expanded considerably in the past few years as the method was successfully applied for high-throughput genotyping, mapping genes, testing food products and seeds, and other areas of plant research.
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Affiliation(s)
- Ivan Simko
- United States Department of Agriculture, Agricultural Research Service, U.S. Agricultural Research Station, 1636 E. Alisal St, Salinas, CA 93905, USA.
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17
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Development of molecular markers, based on chloroplast and ribosomal DNA regions, to discriminate three popular medicinal plant species, Cynanchum wilfordii, Cynanchum auriculatum, and Polygonum multiflorum. Mol Biol Rep 2016; 43:323-32. [DOI: 10.1007/s11033-016-3959-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 02/16/2016] [Indexed: 10/22/2022]
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18
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Lombal AJ, Wenner TJ, Burridge CP. Assessment of high-resolution melting (HRM) profiles as predictors of microsatellite variation: an example in Providence Petrel (Pterodroma solandri). Genes Genomics 2015. [DOI: 10.1007/s13258-015-0327-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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19
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Las Casas G, Scollo F, Distefano G, Continella A, Gentile A, La Malfa S. Molecular characterization of olive (Olea europaea L.) Sicilian cultivars using SSR markers. BIOCHEM SYST ECOL 2014. [DOI: 10.1016/j.bse.2014.07.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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20
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Besnard G, El Bakkali A. Sequence analysis of single-copy genes in two wild olive subspecies: nucleotide diversity and potential use for testing admixture. Genome 2014; 57:145-53. [PMID: 24884690 DOI: 10.1139/gen-2014-0001] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The wild olive distribution extends from the Mediterranean region to south Asia and Austral Africa. The species is also invasive, particularly in Australia. Here, we investigated the sequence variation at five nuclear single-copy genes in 41 native and invasive accessions of the Mediterranean and African olive subspecies. The nucleotide diversity was assessed and the phylogenetic relationships between alleles were depicted with haplotype networks. A Bayesian clustering method (STRUCTURE) was applied to identify the main gene pools. We found an average of 18.4 alleles per locus. Native Mediterranean and African olives only share one allele, which testifies for ancient admixture on the Red Sea hills. The presence of divergent alleles in the Mediterranean olive, as well as the identification of two main genetic clusters, suggests a complex origin with two highly differentiated gene pools from the eastern and western Mediterranean that recently admixed. In the invasive range, relatively high nucleotide diversity is observed as a consequence of the introduction of alleles from two subspecies. Our data confirm that four invasive individuals are early-generation hybrids. Finally, the utility of single-copy gene sequences in olive population genomic and phylogenetic studies is briefly discussed.
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Affiliation(s)
- G Besnard
- a CNRS-UPS-ENFA, EDB, UMR 5174, Bât. 4R1, 31062 Toulouse cedex 9, France
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21
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Ben-Ayed R, Kamoun-Grati N, Rebai A. An Overview of the Authentication of Olive Tree and Oil. Compr Rev Food Sci Food Saf 2013. [DOI: 10.1111/1541-4337.12003] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
| | | | - Ahmed Rebai
- Centre of Biotechnology of Sfax; P.O.Box 1177; 3018 Sfax; Tunisia
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22
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Yan GX, Wu XM, Li D, Zeng CL, Lv PJ, Gao GZ, Chen BY, Xu K, Lv XD. Assessing high-resolution melt curve analysis for accurate detection of DNA polymorphisms in the chloroplast gene accD of Crucifer species. BIOCHEM SYST ECOL 2012. [DOI: 10.1016/j.bse.2012.06.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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23
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Distefano G, Caruso M, La Malfa S, Gentile A, Wu SB. High resolution melting analysis is a more sensitive and effective alternative to gel-based platforms in analysis of SSR--an example in citrus. PLoS One 2012; 7:e44202. [PMID: 22957003 PMCID: PMC3431301 DOI: 10.1371/journal.pone.0044202] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2012] [Accepted: 07/30/2012] [Indexed: 01/15/2023] Open
Abstract
High resolution melting curve analysis (HRM) has been used as an efficient, accurate and cost-effective tool to detect single nucleotide polymorphisms (SNPs) or insertions or deletions (INDELs). However, its efficiency, accuracy and applicability to discriminate microsatellite polymorphism have not been extensively assessed. The traditional protocols used for SSR genotyping include PCR amplification of the DNA fragment and the separation of the fragments on electrophoresis-based platform. However, post-PCR handling processes are laborious and costly. Furthermore, SNPs present in the sequences flanking repeat motif cannot be detected by polyacrylamide-gel-electrophoresis based methods. In the present study, we compared the discriminating power of HRM with the traditional electrophoresis-based methods and provided a panel of primers for HRM genotyping in Citrus. The results showed that sixteen SSR markers produced distinct polymorphic melting curves among the Citrus spp investigated through HRM analysis. Among those, 10 showed more genotypes by HRM analysis than capillary electrophoresis owing to the presence of SNPs in the amplicons. For the SSR markers without SNPs present in the flanking region, HRM also gave distinct melting curves which detected same genotypes as were shown in capillary electrophoresis (CE) analysis. Moreover, HRM analysis allowed the discrimination of most of the 15 citrus genotypes and the resulting genetic distance analysis clustered them into three main branches. In conclusion, it has been approved that HRM is not only an efficient and cost-effective alternative of electrophoresis-based method for SSR markers, but also a method to uncover more polymorphisms contributed by SNPs present in SSRs. It was therefore suggested that the panel of SSR markers could be used in a variety of applications in the citrus biodiversity and breeding programs using HRM analysis. Furthermore, we speculate that the HRM analysis can be employed to analyse SSR markers in a wide range of applications in all other species.
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Affiliation(s)
- Gaetano Distefano
- Dipartimento di Scienze delle Produzioni Agrarie e Alimentari, University of Catania, Catania, Italy
- School of Environmental and Rural Science, University of New England, Armidale, Australia
| | - Marco Caruso
- Dipartimento di Scienze delle Produzioni Agrarie e Alimentari, University of Catania, Catania, Italy
| | - Stefano La Malfa
- Dipartimento di Scienze delle Produzioni Agrarie e Alimentari, University of Catania, Catania, Italy
| | - Alessandra Gentile
- Dipartimento di Scienze delle Produzioni Agrarie e Alimentari, University of Catania, Catania, Italy
- * E-mail: (S-BW); (AG)
| | - Shu-Biao Wu
- School of Environmental and Rural Science, University of New England, Armidale, Australia
- * E-mail: (S-BW); (AG)
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24
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Pasqualone A, Di Rienzo V, Blanco A, Summo C, Caponio F, Montemurro C. Characterization of virgin olive oil from Leucocarpa cultivar by chemical and DNA analysis. Food Res Int 2012. [DOI: 10.1016/j.foodres.2011.05.008] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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25
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Pistelli L, Iacona C, Miano D, Cirilli M, Colao MC, Mensuali-Sodi A, Muleo R. Novel Prunus rootstock somaclonal variants with divergent ability to tolerate waterlogging. TREE PHYSIOLOGY 2012; 32:355-368. [PMID: 22391010 DOI: 10.1093/treephys/tpr135] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Plants require access to free water for nutrient uptake, but excess water surrounding the roots can be injurious or even lethal because it blocks the transfer of free oxygen between the soil and the atmosphere. Genetic improvement efforts in this study were focused on the increased tolerance in roots to waterlogging. Among a pool of clones generated in vitro from leaf explants of rootstock Mr.S.2/5 of Prunus cerasifera L., the S.4 clone was flood tolerant whereas the S.1 clone was sensitive. The S.4 clone formed adventitious roots on exposure to flooding. Moreover, the chlorophyll content and mitochondrial activity in the leaf and root, soluble sugar content, alcohol dehydrogenase activity and ethylene content were different between the clones. The sorbitol transporter gene (SOT1) was up-regulated during hypoxia, the alcohol dehydrogenase genes (ADH1 and ADH3) were up-regulated in the leaves and down-regulated in the roots of the S.4 clone during hypoxia, and the 1-aminocyclopropane-1-oxidase gene (ACO1) was up-regulated in the leaves and roots of the S.4 clone during hypoxia and down-regulated in the wild-type roots. In addition, in the S.4 root, hypoxia induced significant down-regulation of a glycosyltransferase-like gene (GTL), which has a yet-undefined role. Although the relevant variation in the S.4 genome has yet to be determined, genetic alteration clearly conferred a flooding-tolerant phenotype. The isolation of novel somaclonals with the same genomic background but with divergent tolerance to flooding may offer new insights in the elucidation of the genetic machinery of resistance to flooding and aid in the selection of new Prunus rootstocks to be used in various adverse environments.
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Affiliation(s)
- Laura Pistelli
- Dipartimento di Biologia, Università di Pisa, I-56124 Pisa, Italy
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26
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Li F, Niu B, Huang Y, Meng Z. Application of high-resolution DNA melting for genotyping in lepidopteran non-model species: Ostrinia furnacalis (Crambidae). PLoS One 2012; 7:e29664. [PMID: 22253755 PMCID: PMC3256165 DOI: 10.1371/journal.pone.0029664] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2011] [Accepted: 12/02/2011] [Indexed: 11/19/2022] Open
Abstract
Development of an ideal marker system facilitates a better understanding of the genetic diversity in lepidopteran non-model organisms, which have abundant species, but relatively limited genomic resources. Single nucleotide polymorphisms (SNPs) discovered within single-copy genes have proved to be desired markers, but SNP genotyping by current techniques remain laborious and expensive. High resolution melting (HRM) curve analysis represents a simple, rapid and inexpensive genotyping method that is primarily confined to clinical and diagnostic studies. In this study, we evaluated the potential of HRM analysis for SNP genotyping in the lepidopteran non-model species Ostrinia furnacalis (Crambidae). Small amplicon and unlabeled probe assays were developed for the SNPs, which were identified in 30 females of O. furnacalis from 3 different populations by our direct sequencing. Both assays were then applied to genotype 90 unknown female DNA by prior mixing with known wild-type DNA. The genotyping results were compared with those that were obtained using bi-directional sequencing analysis. Our results demonstrated the efficiency and reliability of the HRM assays. HRM has the potential to provide simple, cost-effective genotyping assays and facilitates genotyping studies in any non-model lepidopteran species of interest.
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Affiliation(s)
- FengBo Li
- State Key Laboratory Breeding Base for Zhejiang Sustainable Plant Pest and Disease Control, Laboratory of Entomo-molecular Biology, Sericulture Research Institute, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - BaoLong Niu
- State Key Laboratory Breeding Base for Zhejiang Sustainable Plant Pest and Disease Control, Laboratory of Entomo-molecular Biology, Sericulture Research Institute, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - YongPing Huang
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- * E-mail: (YPH); (ZQM)
| | - ZhiQi Meng
- State Key Laboratory Breeding Base for Zhejiang Sustainable Plant Pest and Disease Control, Laboratory of Entomo-molecular Biology, Sericulture Research Institute, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- * E-mail: (YPH); (ZQM)
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27
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Cirilli M, Bellincontro A, De Santis D, Botondi R, Colao MC, Muleo R, Mencarelli F. Temperature and water loss affect ADH activity and gene expression in grape berry during postharvest dehydration. Food Chem 2011; 132:447-54. [PMID: 26434314 DOI: 10.1016/j.foodchem.2011.11.020] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2011] [Revised: 09/30/2011] [Accepted: 11/02/2011] [Indexed: 01/20/2023]
Abstract
Clusters of Aleatico wine grape were picked at 18°Brix and placed at 10, 20, or 30°C, 45% relative humidity (RH) and 1.5m/s of air flow to dehydrate the berries up to 40% of loss of initial fresh weight. Sampling was done at 0%, 10%, 20%, 30%, and 40% weight loss (wl). ADH (alcohol dehydrogenase) gene expression, enzyme activity, and related metabolites were analysed. At 10°C, acetaldehyde increased rapidly and then declined, while ethanol continued to rise. At 20°C, acetaldehyde and ethanol increased significantly with the same pattern and declined at 40%wl. At 30°C, acetaldehyde did not increase but ethanol increased rapidly already at 10%wl. At the latter temperature, a significant increase in acetic acid and ethyl acetate occurred, while at 10°C their values were low. At 30°C, the ADH activity (ethanol to acetaldehyde direction), increased rapidly but acetaldehyde did not rise because of its oxidation to acetic acid, which increased together with ethyl acetate. At 10°C, the ADH activity increased at 20%wl and continued to rise even at 40%wl, meaning that ethanol oxidation was delayed. At 20°C, the behaviour was intermediate to the other temperatures. The relative expression of the VvAdh2 gene was the highest at 10°C already at 10%wl in a synchrony with the ADH activity, indicating a rapid response likely due to low temperature. The expression subsequently declined. At 20 and 30°C, the expression was lower and increased slightly during dehydration in combination with the ADH activity. This imbalance between gene expression and ADH activity at 10°C, as well as the unexpected expression of the carotenoid cleavage dioxygenase 1 (CCD1) gene, opens the discussion on the stress sensitivity and transcription event during postharvest dehydration, and the importance of carefully monitoring temperature during dehydration.
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Affiliation(s)
- Marco Cirilli
- Department of Agriculture, Forestry, Nature and Energy, University of Tuscia, Viterbo, Italy
| | - Andrea Bellincontro
- Department of Environment, Food, and Forestry Innovative Systems, Postharvest Lab, University of Tuscia, Viterbo, Italy
| | - Diana De Santis
- Department of Environment, Food, and Forestry Innovative Systems, Postharvest Lab, University of Tuscia, Viterbo, Italy
| | - Rinaldo Botondi
- Department of Environment, Food, and Forestry Innovative Systems, Postharvest Lab, University of Tuscia, Viterbo, Italy
| | - Maria Chiara Colao
- Department of Agriculture, Forestry, Nature and Energy, University of Tuscia, Viterbo, Italy
| | - Rosario Muleo
- Department of Agriculture, Forestry, Nature and Energy, University of Tuscia, Viterbo, Italy
| | - Fabio Mencarelli
- Department of Environment, Food, and Forestry Innovative Systems, Postharvest Lab, University of Tuscia, Viterbo, Italy.
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28
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Luchi N, Pratesi N, Simi L, Pazzagli M, Capretti P, Scala A, Slippers B, Pinzani P. High-resolution melting analysis: a new molecular approach for the early detection of Diplodia pinea in Austrian pine. Fungal Biol 2011; 115:715-23. [PMID: 21802051 DOI: 10.1016/j.funbio.2011.05.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2011] [Revised: 05/06/2011] [Accepted: 05/13/2011] [Indexed: 01/31/2023]
Abstract
The differentiation of Diplodia pinea from closely related species, such as Diplodia scrobiculata and Diplodia seriata, and its detection in plant tissue, represented a critical issue for a long time. Molecular screening tools have recently been developed to address this topic. In this study we applied one of the most sensitive and rapid diagnostic screening method so far developed, called High-Resolution Melting Analysis (HRMA), to detect D. pinea in Austrian pine (Pinus nigra). HRMA exploits differences in the melting behaviour of PCR products to rapidly identify DNA sequence variants without the need for cumbersome post-PCR methods. We developed a HRMA method to detect specific fungal sequences in the mitochondrial small subunit ribosome gene (mt SSU rDNA). The reliability of this technique was firstly assessed on DNA extracted from pure cultures of D. pinea and closely related species. Amplicon differences were screened by HRMA and the results confirmed by direct DNA sequencing. Subsequently, HRMA was tested on DNA from symptomatic and symptomless pine shoots, and the presence of the fungus was also confirmed by both conventional and molecular quantitative approaches. The HRMA allowed the distinction of D. pinea from closely related species, showing specific melting profiles for the each pathogen. This new molecular technique, here tested in a plant-fungus pathosystem for the first time, was very reliable in both symptomatic and symptomless shoots. HRMA is therefore a highly effective and accurate technique that permits the rapid screening of pathogens in the host.
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Affiliation(s)
- Nicola Luchi
- Department of Agricultural Biotechnology, Section of Plant Protection, University of Florence, Piazzale delle Cascine 28, I-50144 Florence, Italy.
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29
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Chen Y, Wilde HD. Mutation scanning of peach floral genes. BMC PLANT BIOLOGY 2011; 11:96. [PMID: 21605436 PMCID: PMC3120741 DOI: 10.1186/1471-2229-11-96] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2011] [Accepted: 05/23/2011] [Indexed: 05/30/2023]
Abstract
BACKGROUND Mutation scanning technology has been used to develop crop species with improved traits. Modifications that improve screening throughput and sensitivity would facilitate the targeted mutation breeding of crops. Technical innovations for high-resolution melting (HRM) analysis are enabling the clinic-based screening for human disease gene polymorphism. We examined the application of two HRM modifications, COLD-PCR and QMC-PCR, to the mutation scanning of genes in peach, Prunus persica. The targeted genes were the putative floral regulators PpAGAMOUS and PpTERMINAL FLOWER I. RESULTS HRM analysis of PpAG and PpTFL1 coding regions in 36 peach cultivars found one polymorphic site in each gene. PpTFL1 and PpAG SNPs were used to examine approaches to increase HRM throughput. Cultivars with SNPs could be reliably detected in pools of twelve genotypes. COLD-PCR was found to increase the sensitivity of HRM analysis of pooled samples, but worked best with small amplicons. Examination of QMC-PCR demonstrated that primary PCR products for further analysis could be produced from variable levels of genomic DNA. CONCLUSIONS Natural SNPs in exons of target peach genes were discovered by HRM analysis of cultivars from a southeastern US breeding program. For detecting natural or induced SNPs in larger populations, HRM efficiency can be improved by increasing sample pooling and template production through approaches such as COLD-PCR and QMC-PCR. Technical advances developed to improve clinical diagnostics can play a role in the targeted mutation breeding of crops.
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Affiliation(s)
- Yihua Chen
- Horticulture Department, University of Georgia, Athens, GA 30602, USA
| | - H Dayton Wilde
- Horticulture Department, University of Georgia, Athens, GA 30602, USA
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Bracci T, Busconi M, Fogher C, Sebastiani L. Molecular studies in olive (Olea europaea L.): overview on DNA markers applications and recent advances in genome analysis. PLANT CELL REPORTS 2011; 30:449-62. [PMID: 21212959 DOI: 10.1007/s00299-010-0991-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2010] [Accepted: 12/21/2010] [Indexed: 05/10/2023]
Abstract
Olive (Olea europaea L.) is one of the oldest agricultural tree crops worldwide and is an important source of oil with beneficial properties for human health. This emblematic tree crop of the Mediterranean Basin, which has conserved a very wide germplasm estimated in more than 1,200 cultivars, is a diploid species (2n = 2x = 46) that is present in two forms, namely wild (Olea europaea subsp. europaea var. sylvestris) and cultivated (Olea europaea subsp. europaea var. europaea). In spite of its economic and nutritional importance, there are few data about the genetic of olive if compared with other fruit crops. Available molecular data are especially related to the application of molecular markers to the analysis of genetic variability in Olea europaea complex and to develop efficient molecular tools for the olive oil origin traceability. With regard to genomic research, in the last years efforts are made for the identification of expressed sequence tag, with particular interest in those sequences expressed during fruit development and in pollen allergens. Very recently the sequencing of chloroplast genome provided new information on the olive nucleotide sequence, opening the olive genomic era. In this article, we provide an overview of the most relevant results in olive molecular studies. A particular attention was given to DNA markers and their application that constitute the most part of published researches. The first important results in genome analysis were reported.
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Affiliation(s)
- T Bracci
- Biolabs, Scuola Superiore Sant'Anna, Piazza Martiri della Libertà 33, 56127 Pisa, Italy
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Jeong HJ, Jo YD, Park SW, Kang BC. Identification of Capsicum species using SNP markers based on high resolution melting analysis. Genome 2010; 53:1029-40. [DOI: 10.1139/g10-094] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Single nucleotide polymorphisms (SNPs) derived from both nuclear and cytoplasmic DNA sequences were developed to identify distinct species of Capsicum . Species identification was achieved by detecting allelic variations of these type of markers via high resolution melting analysis (HRM). We used the HRM polymorphisms of COSII markers and the Waxy gene from the nuclear sequence, in addition to the intergenic spacer between trnL and trnF from cytoplasmic DNA as our SNP markers. A total of 31 accessions of Capsicum, representing six species, were analyzed using this method. As single markers were insufficient for identifying Capsicum species, combinations of all markers unambiguously identified all six. A phylogeny based on the SNP markers was consistent with the current taxonomy of Capsicum species. These observations demonstrate that the markers developed in this study are useful for rapid identification of new germplasm for management of Capsicum species.
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Affiliation(s)
- Hee-Jin Jeong
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agricultural Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
| | - Yeong Deuk Jo
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agricultural Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
| | - Soung-Woo Park
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agricultural Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
| | - Byoung-Cheorl Kang
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agricultural Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
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Mencarelli F, Bellincontro A, Nicoletti I, Cirilli M, Muleo R, Corradini D. Chemical and biochemical change of healthy phenolic fractions in winegrape by means of postharvest dehydration. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2010; 58:7557-7564. [PMID: 20521817 DOI: 10.1021/jf100331z] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Clusters of Aleatico winegrape were picked at 18 degrees Brix and placed at 10, 20, or 30 degrees C, 45% relative humidity (RH) and 1.5 m/s of air flow to dehydrate the berries up to 40% of loss of initial fresh weight. Sampling was done at 0, 10, 20, 30, and 40% weight loss (wl). Selected polyphenols and sugar content (expressed as SSC = soluble solids content) both measured on dry weight basis, polyphenol oxidase (PPO), and phenylpropanoid pathway gene expression were analyzed. Phenolic acids increased significantly at 20% wl at 20 degrees C, while at 10 degrees C the increase was lower. Stilbenes (trans-resveratrol and trans-piceid) and catechins rose more than double to 100 mg/kg and more than 3-fold to 135 mg/kg at 20 degrees C and 10% wl. At 10 degrees C the increase of these compounds was less, but higher than initial values. At 30 degrees C, except for a significant rise at 10% wl for catechins and stilbenes, all the rest of the compounds diminished. Anthocyanins increased at 10 and 20 degrees C, but decreased at 30 degrees C. PPO rapidly increased at 20 and 30 degrees C at 10% wl and then declined, while at 10 degrees C the activity lasted longer. Relative gene expression of phenylalanine ammonia lyase (PAL), stilbene synthase (STS), chalcone isomerase (CHI), dihydroflavonol reductase (DFR) were upregulated at 10 degrees C more than at 20 degrees C, at 20% wl, while at 30 degrees C the gene expression was downregulated.
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Affiliation(s)
- Fabio Mencarelli
- Department of Food Science and Technology, University of Tuscia, Viterbo, Italy.
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Population structures of genebank accessions of Salvia officinalis L. (Lamiaceae) revealed by high resolution melting analysis. BIOCHEM SYST ECOL 2010. [DOI: 10.1016/j.bse.2010.01.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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