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McDougall GJ, Allwood JW, Dobson G, Austin C, Verrall S, Alexander CJ, Hancock RD, Graham J, Hackett CA. Quantitative trait loci mapping of polyphenol metabolites from a 'Latham' x 'Glen Moy' red raspberry (Rubus idaeus L) cross. Metabolomics 2023; 19:71. [PMID: 37552331 PMCID: PMC10409862 DOI: 10.1007/s11306-023-02033-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 07/13/2023] [Indexed: 08/09/2023]
Abstract
OBJECTIVE The objective of this study was to investigate the genetic control of polyphenol accumulation in red raspberry (Rubus idaeus L). METHODS The levels of total anthocyanins and 37 individual polyphenol metabolites were measured over three years in a raspberry biparental mapping population. Quantitative trait loci (QTLs) for these traits were mapped onto a high-density SNP linkage map. RESULTS At least one QTL was detected for each trait, with good consistency among the years. On four linkage groups (LG), there were major QTLs affecting several metabolites. On LG1, a QTL had large effects on anthocyanins and flavonols containing a rutinoside or rhamnose group. On LG4, a QTL had large effects on several flavonols and on LG5 and LG6 QTLs had large effects on ellagic acid derivatives. Smaller QTLs were found on LG2 and LG3. CONCLUSION The identification of robust QTLs for key polyphenols in raspberry provides great potential for marker-assisted breeding for improved levels of potentially health beneficial components.
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Affiliation(s)
- G J McDougall
- Plant Biochemistry and Food Quality Group, Environmental and Biochemical Sciences Department, The James Hutton Institute, Dundee, DD2 5DA, Scotland, UK.
| | - J W Allwood
- Plant Biochemistry and Food Quality Group, Environmental and Biochemical Sciences Department, The James Hutton Institute, Dundee, DD2 5DA, Scotland, UK
| | - G Dobson
- Plant Biochemistry and Food Quality Group, Environmental and Biochemical Sciences Department, The James Hutton Institute, Dundee, DD2 5DA, Scotland, UK
| | - C Austin
- Plant Biochemistry and Food Quality Group, Environmental and Biochemical Sciences Department, The James Hutton Institute, Dundee, DD2 5DA, Scotland, UK
| | - S Verrall
- Ecological Sciences Department, The James Hutton Institute, Dundee, DD2 5DA, Scotland, UK
| | - C J Alexander
- Biomathematics and Statistics Scotland (BioSS), The James Hutton Institute, Dundee, DD2 5DA, Scotland, UK
| | - R D Hancock
- Cell and Molecular Sciences Department, The James Hutton Institute, Dundee, DD2 5DA, Scotland, UK
| | - J Graham
- Cell and Molecular Sciences Department, The James Hutton Institute, Dundee, DD2 5DA, Scotland, UK
| | - C A Hackett
- Biomathematics and Statistics Scotland (BioSS), The James Hutton Institute, Dundee, DD2 5DA, Scotland, UK
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Burns C, Villalobos S, Vamosi JC. When less is more: Visitation by generalist pollinators can have neutral or negative effects on plant reproduction. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.1012809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Selection for specialized coevolutionary relationships can arise if generalized opportunistic pollinators, while still delivering some pollen, operate as less effective pollen delivery agents. Nevertheless, generalization could buffer high-latitude communities from loss of specialist pollinator species by providing some pollination service. Currently, there is limited understanding of the ecosystem services provided by generalized pollinators and whether they increase the fitness of the plants they visit. Network data and thorough observations of floral visitors, paired with estimates of seed set, offer some insight into the role of generalists, which in turn can inform us about how plants are likely to respond to ecosystem disturbances, such as losses of some pollinators, or changes in land cover. Here, we report on plant-pollinator visitation networks in Canada with high levels of generalization and examine the effects of generalization on seed set under different disturbance histories. We also then take a case study of one crop wild relative, Rubus arcticus or Arctic raspberry, and report on a near-complete characterization of pollinator interactions in different environmental conditions. Our findings indicate that generalized pollinators, though frequent and robust to variable temperatures and moisture conditions, do not appear to play a strong role in increasing the reproductive output of many plant species, and may provide only a weak buffer against the stronger effects of disturbance.
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Kamnev АМ, Antonova OY, Dunaeva SЕ, Gavrilenko TA, Chukhina IG. [Molecular markers in the genetic diversity studies of representatives of the genus Rubus L. and prospects of their application in breeding]. Vavilovskii Zhurnal Genet Selektsii 2020; 24:20-30. [PMID: 33659777 PMCID: PMC7893148 DOI: 10.18699/vj20.591] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Род Rubus L. (семейство Rosaceae Juss.), по оценкам разных систематиков, состоит из 12–16 подродов, объединяющих ~750 видов. Самые крупные по числу видов подроды – Idaeobatus (Focke) Focke, к которому относятся малины, и типовой подрод Rubus (=Eubatus Focke), включающий виды ежевик. Представители рода Rubus обладают высокой пищевой и хозяйственной ценностью, а также лекарственными свойствами. Селекционные исследования направлены на расширение генетического разнообразия и создание новых сортов малин и ежевик, устойчивых к биотическим и абиотическим стрессорам и отличающихся высоким качеством плодов. Современные селекционно-генетические программы все шире включают достижения молекулярной генетики и геномики. В данной статье представлен обзор фундаментальных и прикладных исследований генетического разнообразия культивируемых и дикорастущих видов рода Rubus, выполненных на основе методов молекулярного маркирования. Рассмотрены основные типы молекулярных маркеров (RFLP, RAPD, SSR, ISSR, AFLP, SCAR, SSCP, ретротранспозонные маркеры и т. д.) и области их применения в изучении представителей рода Rubus. Приведены результаты работ по использованию методов ДНК-маркирования для решения самых разных задач, включая: исследование межвидового и внутривидового генетического разнообразия, филогенетических связей видов и надвидовых таксонов, выяснение спорных вопросов систематики, генотипирование и уточнение родословных сортов малин и ежевик, изучение сомаклональной изменчивости и др. Наиболее важным результатом в практическом плане является создание насыщенных молекулярно-генетических карт для разных видов малин и ежевик, на которых локализованы многочисленные гены и QTL, детерминирующие различные хозяйственно ценные признаки. В то же время необходимо отметить, что число маркеров, перспективных для проведения эффективного молекулярного скрининга, пока еще недостаточно.
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Affiliation(s)
- А М Kamnev
- Federal Research Center the N.I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR), St. Petersburg, Russia Altai State University, Barnaul, Russia
| | - O Yu Antonova
- Federal Research Center the N.I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR), St. Petersburg, Russia
| | - S Е Dunaeva
- Federal Research Center the N.I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR), St. Petersburg, Russia
| | - T A Gavrilenko
- Federal Research Center the N.I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR), St. Petersburg, Russia
| | - I G Chukhina
- Federal Research Center the N.I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR), St. Petersburg, Russia
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Foster TM, Bassil NV, Dossett M, Leigh Worthington M, Graham J. Genetic and genomic resources for Rubus breeding: a roadmap for the future. HORTICULTURE RESEARCH 2019; 6:116. [PMID: 31645970 PMCID: PMC6804857 DOI: 10.1038/s41438-019-0199-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 08/17/2019] [Accepted: 08/27/2019] [Indexed: 05/09/2023]
Abstract
Rubus fruits are high-value crops that are sought after by consumers for their flavor, visual appeal, and health benefits. To meet this demand, production of red and black raspberries (R. idaeus L. and R. occidentalis L.), blackberries (R. subgenus Rubus), and hybrids, such as Boysenberry and marionberry, is growing worldwide. Rubus breeding programmes are continually striving to improve flavor, texture, machine harvestability, and yield, provide pest and disease resistance, improve storage and processing properties, and optimize fruits and plants for different production and harvest systems. Breeders face numerous challenges, such as polyploidy, the lack of genetic diversity in many of the elite cultivars, and until recently, the relative shortage of genetic and genomic resources available for Rubus. This review will highlight the development of continually improving genetic maps, the identification of Quantitative Trait Loci (QTL)s controlling key traits, draft genomes for red and black raspberry, and efforts to improve gene models. The development of genetic maps and markers, the molecular characterization of wild species and germplasm, and high-throughput genotyping platforms will expedite breeding of improved cultivars. Fully sequenced genomes and accurate gene models facilitate identification of genes underlying traits of interest and enable gene editing technologies such as CRISPR/Cas9.
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Affiliation(s)
- Toshi M. Foster
- The New Zealand Institute for Plant and Food Research (PFR) Ltd, 55 Old Mill Road, Motueka, New Zealand
| | - Nahla V. Bassil
- USDA ARS National Clonal Germplasm Repository (NCGR), 33447 Peoria Rd., Corvallis, OR USA
| | - Michael Dossett
- Blueberry Council (in Partnership with Agriculture and Agri-Food Canada) Agassiz Food Research Centre, Columbia, BC V0M 1A0 Canada
| | - Margaret Leigh Worthington
- Department of Horticulture, University of Arkansas, 316 Plant Science Building, Fayetteville, AR 72701 USA
| | - Julie Graham
- The James Hutton Institute, Errol Road, Invergowrie, Dundee, DD2 5DA Scotland
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Raspberry as a Source for the Development of Drosophila suzukii Attractants: Laboratory and Commercial Polytunnel Trials. INSECTS 2019; 10:insects10050137. [PMID: 31083484 PMCID: PMC6572601 DOI: 10.3390/insects10050137] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 05/04/2019] [Accepted: 05/08/2019] [Indexed: 11/17/2022]
Abstract
Several commercial products and home-made attractants have been developed for monitoring and mass-trapping of the spotted wing drosophila, Drosophila suzukii. Growers in Mexico have adopted an attractant based on a fermenting mixture of raspberry pulp and sucrose, with anecdotally promising results. We compared the capture rates of traps baited with raspberry pulp + sucrose with captures from a range of alternative attractants. Raspberry pulp alone or with sucrose was more attractive than apple cider vinegar (ACV) or SuzukiiTrap and similar to baker's yeast + sucrose in laboratory cage studies. Synthetic raspberry aroma (0.1-10% concentration), in water or mixed with ACV, did not improve capture rates in the laboratory. Traps baited with raspberry + sucrose or ACV had similar captures of D. suzukii in raspberry or blackberry polytunnels in Michoacán, Mexico. Raspberry + sucrose baited traps captured significantly higher numbers of other drosophilid species, leading to higher total numbers of captured flies (all species), which may explain why Mexican growers favor the raspberry-based attractant. The commercial products SuzukiiTrap and Z-Kinol had lower captures than ACV in polytunnels, although SuzukiiTrap had the highest selectivity in captures of D. suzukii (81% of flies captured). A two-component trap (2C trap) baited with ACV + ethanol as the drowning solution and raspberry pulp + sucrose or baker's yeast + sucrose in a ventilated tube device was markedly more effective than the trap currently used by growers. We conclude that raspberry pulp + sucrose is as effective for the attraction of D. suzukii as ACV under commercial polytunnel conditions. The 2C trap performed better than the transparent cup trap currently used by berry producers in Mexico.
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Hackett CA, Milne L, Smith K, Hedley P, Morris J, Simpson CG, Preedy K, Graham J. Enhancement of Glen Moy x Latham raspberry linkage map using GbS to further understand control of developmental processes leading to fruit ripening. BMC Genet 2018; 19:59. [PMID: 30111279 PMCID: PMC6094467 DOI: 10.1186/s12863-018-0666-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 08/08/2018] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND The changing climate is altering timing of key fruit ripening processes and increasing the occurrence of fruit defects. To improve our understanding of the genetic control of raspberry fruit development an enhanced genetic linkage map was developed and used to examine ripening phenotypic data. RESULTS In this study we developed an enhanced genetic linkage map for the raspberry cvs. Glen Moy x Latham reference mapping population using genotyping by sequencing (GbS). Alignment to a newly sequenced draft reference genome of red raspberry, cultivar (cv.) Glen Moy, identified 8019 single nucleotide polymorphisms (SNPs). After stringent filtering to take account of read coverage over all the progeny individuals, association with a single chromosome, heterozygosity and marker regression mapping, 2348 high confidence SNPs were retained and integrated with an existing raspberry genetic map. The linkage map contained many more SNPs segregating in Latham than in Glen Moy. This caused difficulties in quantitative trait loci (QTL) mapping with standard software and a novel analysis based on a hidden Markov model was used to improve the mapping. QTL mapping using the newly generated dense genetic map not only corroborated previously identified genetic locations but also provided additional genetic elements controlling fruit ripening in raspberry. CONCLUSION The high-density GbS map located the QTL peaks more precisely than in earlier studies, aligned the QTLs with Glen Moy genome scaffolds, narrowed the range of potential candidate genes to these regions that can be utilised in other populations or in gene expression studies to confirm their role and increased the repertoire of markers available to understand the genetic control of fruit ripening traits.
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Affiliation(s)
| | - Linda Milne
- The James Hutton Institute, Invergowrie, Dundee, DD25DA Scotland
| | - Kay Smith
- The James Hutton Institute, Invergowrie, Dundee, DD25DA Scotland
| | - Pete Hedley
- The James Hutton Institute, Invergowrie, Dundee, DD25DA Scotland
| | - Jenny Morris
- The James Hutton Institute, Invergowrie, Dundee, DD25DA Scotland
| | - Craig G. Simpson
- The James Hutton Institute, Invergowrie, Dundee, DD25DA Scotland
| | - Katharine Preedy
- Biomathematics and Statistics Scotland, Invergowrie, Dundee, DD25DA Scotland
| | - Julie Graham
- The James Hutton Institute, Invergowrie, Dundee, DD25DA Scotland
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Williams D, Britten A, McCallum S, Jones H, Aitkenhead M, Karley A, Loades K, Prashar A, Graham J. A method for automatic segmentation and splitting of hyperspectral images of raspberry plants collected in field conditions. PLANT METHODS 2017; 13:74. [PMID: 29118819 PMCID: PMC5664591 DOI: 10.1186/s13007-017-0226-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 09/11/2017] [Indexed: 05/12/2023]
Abstract
Hyperspectral imaging is a technology that can be used to monitor plant responses to stress. Hyperspectral images have a full spectrum for each pixel in the image, 400-2500 nm in this case, giving detailed information about the spectral reflectance of the plant. Although this technology has been used in laboratory-based controlled lighting conditions for early detection of plant disease, the transfer of such technology to imaging plants in field conditions presents a number of challenges. These include problems caused by varying light levels and difficulties of separating the target plant from its background. Here we present an automated method that has been developed to segment raspberry plants from the background using a selected spectral ratio combined with edge detection. Graph theory was used to minimise a cost function to detect the continuous boundary between uninteresting plants and the area of interest. The method includes automatic detection of a known reflectance tile which was kept constantly within the field of view for all image scans. A method to split images containing rows of multiple raspberry plants into individual plants was also developed. Validation was carried out by comparison of plant height and density measurements with manually scored values. A reasonable correlation was found between these manual scores and measurements taken from the images (r2 = 0.75 for plant height). These preliminary steps are an essential requirement before detailed spectral analysis of the plants can be achieved.
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Affiliation(s)
| | - Avril Britten
- James Hutton Limited, Invergowrie, Dundee, DD2 5DA UK
| | | | - Hamlyn Jones
- Division of Plant Sciences, University of Dundee at the James Hutton Institute, Dundee, UK
- School of Agriculture and Environment, University of Western Australia, Perth, Australia
| | | | - Alison Karley
- James Hutton Institute, Invergowrie, Dundee, DD2 5DA UK
| | - Ken Loades
- James Hutton Institute, Invergowrie, Dundee, DD2 5DA UK
| | - Ankush Prashar
- School of Agriculture, Food and Rural Development, Newcastle University, Newcastle upon Tyne, NE1 7RU UK
| | - Julie Graham
- James Hutton Institute, Invergowrie, Dundee, DD2 5DA UK
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Simpson CG, Cullen DW, Hackett CA, Smith K, Hallett PD, McNicol J, Woodhead M, Graham J. Mapping and expression of genes associated with raspberry fruit ripening and softening. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:557-572. [PMID: 27942774 DOI: 10.1007/s00122-016-2835-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 11/26/2016] [Indexed: 05/24/2023]
Abstract
QTL mapping identifies a range of underlying and unrelated genes with apparent roles in raspberry fruit ripening and softening that show characteristic developing fruit expression profiles. Fruit softening is an important agronomical trait that involves a complex interaction of plant cell processes. We have used both qualitative and quantitative scoring of fruit firmness, length, mass, and resistance to applied force to identify QTL in a raspberry mapping population. QTLs were located primarily on linkage group (LG) 3 with other significant loci on LG 1 and LG 5 and showed mostly additive effects between the two parents. The expression of key genes that underlie these QTLs with roles in cell-wall solubility, water uptake, polyamine synthesis, transcription, and cell respiration was tested across five stages of fruit development, from immature green to red ripe fruit, using real-time RT-qPCR. Gene expression patterns showed variable expression patterns across fruit development with a highly significant positive and negative correlation between genes, supporting precise regulation of expression of different cell processes throughout raspberry fruit development. Variable timing in expression was also found in some genes at different fruit development stages between soft and firm cultivars. Multiple processes have a role to play in fruit softening and this will require development of multiple marker combinations to genes that characterise raspberry fruit softening.
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Affiliation(s)
- Craig G Simpson
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK.
| | - Danny W Cullen
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | | | - Kay Smith
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Paul D Hallett
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, AB24 3UU, UK
| | - Jim McNicol
- Biomathematics and Statistics Scotland, Invergowrie, Dundee, DD2 5DA, UK
| | - Mary Woodhead
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Julie Graham
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
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