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Rambaran TF, Ginigini J, McLenachan PA, Bowen-Forbes CS, Mitchell SA. Morphological Characterisation of Wild Rubus rosifolius (Rosaceae) Plants Growing in Jamaica Prior to Agricultural Pursuits. CARIBB J SCI 2021. [DOI: 10.18475/cjos.v51i1.a1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Theresa F. Rambaran
- Department of Chemistry, Faculty of Science and Technology, The University of the West Indies, Mona, Jamaica
| | - Joape Ginigini
- Institute of Applied Sciences, Faculty of Science and Technology, University of the South Pacific, Suva, Fiji
| | | | - Camille S. Bowen-Forbes
- Department of Chemistry, Faculty of Science and Technology, The University of the West Indies, Mona, Jamaica
| | - Sylvia Adjoa Mitchell
- The Biotechnology Centre, Faculty of Science and Technology, The University of the West Indies, Mona, Jamaica
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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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Lebedev VG, Subbotina NM, Maluchenko OP, Lebedeva TN, Krutovsky KV, Shestibratov KA. Transferability and Polymorphism of SSR Markers Located in Flavonoid Pathway Genes in Fragaria and Rubus Species. Genes (Basel) 2019; 11:E11. [PMID: 31877734 PMCID: PMC7017068 DOI: 10.3390/genes11010011] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 12/14/2019] [Accepted: 12/19/2019] [Indexed: 12/16/2022] Open
Abstract
Strawberry (Fragaria) and raspberry (Rubus) are very popular crops, and improving their nutritional quality and disease resistance are important tasks in their breeding programs that are becoming increasingly based on use of functional DNA markers. We identified 118 microsatellite (simple sequence repeat-SSR) loci in the nucleotide sequences of flavonoid biosynthesis and pathogenesis-related genes and developed 24 SSR markers representing some of these structural and regulatory genes. These markers were used to assess the genetic diversity of 48 Fragaria and Rubus specimens, including wild species and rare cultivars, which differ in berry color, ploidy, and origin. We have demonstrated that a high proportion of the developed markers are transferable within and between Fragaria and Rubus genera and are polymorphic. Transferability and polymorphism of the SSR markers depended on location of their polymerase chain reaction (PCR) primer annealing sites and microsatellite loci in genes, respectively. High polymorphism of the SSR markers in regulatory flavonoid biosynthesis genes suggests their allelic variability that can be potentially associated with differences in flavonoid accumulation and composition. This set of SSR markers may be a useful molecular tool in strawberry and raspberry breeding programs for improvement anthocyanin related traits.
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Affiliation(s)
- Vadim G. Lebedev
- Pushchino State Institute of Natural Sciences, Prospekt Nauki 3, 142290 Pushchino, Russia; (V.G.L.); (N.M.S.)
- Branch of the Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Prospekt Nauki 6, 142290 Pushchino, Russia;
| | - Natalya M. Subbotina
- Pushchino State Institute of Natural Sciences, Prospekt Nauki 3, 142290 Pushchino, Russia; (V.G.L.); (N.M.S.)
- Branch of the Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Prospekt Nauki 6, 142290 Pushchino, Russia;
| | - Oleg P. Maluchenko
- All-Russian Research Institute of Agricultural Biotechnology, Timiriazevskaya Str. 42, 127550 Moscow, Russia;
| | - Tatyana N. Lebedeva
- Institute of Physicochemical and Biological Problems of Soil Science, Russian Academy of Sciences, Institutskaya Str. 2, 142290 Pushchino, Russia;
| | - Konstantin V. Krutovsky
- Department of Forest Genetics and Forest Tree Breeding, Georg-August University of Göttingen, Büsgenweg 2, 37077 Göttingen, Germany
- Center for Integrated Breeding Research, Georg-August University of Göttingen, Albrecht-Thaer-Weg 3, 37075 Göttingen, Germany
- Laboratory of Population Genetics, N. I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkin Str. 3, 119333 Moscow, Russia
- Laboratory of Forest Genomics, Genome Research and Education Center, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, 660036 Krasnoyarsk, Russia
- Department of Ecosystem Science and Management, Texas A&M University, 2138 TAMU, College Station, TX 77843-2138, USA
| | - Konstantin A. Shestibratov
- Branch of the Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Prospekt Nauki 6, 142290 Pushchino, 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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Hu P, Shao Y, Xu J, Wang T, Li Y, Liu H, Rong M, Su W, Chen B, Cui S, Cui X, Yang F, Tamate H, Xing X. Genome-wide study on genetic diversity and phylogeny of five species in the genus Cervus. BMC Genomics 2019; 20:384. [PMID: 31101010 PMCID: PMC6525406 DOI: 10.1186/s12864-019-5785-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 05/08/2019] [Indexed: 01/01/2023] Open
Abstract
Background Previous investigations of phylogeny in Cervus recovered many clades without whole genomic support. Methods In this study, the genetic diversity and phylogeny of 5 species (21 subspecies/populations from C. unicolor, C. albirostris, C. nippon, C. elaphus and C. eldii) in the genus Cervus were analyzed using reduced-representation genome sequencing. Results A total of 197,543 SNPs were identified with an average sequencing depth of 16 x. A total of 21 SNP matrices for each subspecies/population and 1 matrix for individual analysis were constructed, respectively. Nucleotide diversity and heterozygosity analysis showed that all 21 subspecies/populations had different degrees of genetic diversity. C. eldii, C. unicolor and C. albirostris showed relatively high expected and observed heterozygosity, while observed heterozygosity in C. nippon was the lowest, indicating there was a certain degree of inbreeding rate in these subspecies/populations. Phylogenetic ML tree of all Cervus based on the 21 SNP matrices showed 5 robustly supported clades that clearly separate C. eldii, C. unicolor, C. albirostris, C. elaphus and C. nippon. Within C. elaphus clade, 4 subclades were well differentiated and statistically highly supported: C. elaphus (New Zealand), C. e. yarkandensis, C. c. canadensis and the other grouping the rest of C. canadensis from China. In the C. nippon clade, 2 well-distinct subclades corresponding to C. n. aplodontus and other C. nippon populations were separated. Phylogenetic reconstruction indicated that the first evolutionary event of the genus Cervus occurred approximately 7.4 millions of years ago. The split between C. elaphus and C. nippon could be estimated at around 3.6 millions of years ago. Phylogenetic ML tree of all samples based on individual SNP matrices, together with geographic distribution, have shown that there were 3 major subclades of C. elaphus and C. canadensis in China, namely C. e. yarkandensis (distributed in Tarim Basin), C. c. macneilli/C. c. kansuensis/C. c. alashanicus (distributed in middle west of China), and C. c. songaricus/C. c. sibiricus (distributed in northwest of China). Among them, C. e. yarkandensis was molecularly the most primitive subclade, with a differentiation dating back to 0.8–2.2 Myr ago. D statistical analysis showed that there was high probability of interspecific gene exchange between C. albirostris and C. eldii, C. albirostris and C. unicolor, C. nippon and C. unicolor, and there might be 2 migration events among 5 species in the genus Cervus. Conclusions Our results provided new insight to the genetic diversity and phylogeny of Cervus deer. In view of the current status of these populations, their conservation category will need to be reassessed. Electronic supplementary material The online version of this article (10.1186/s12864-019-5785-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Pengfei Hu
- State key laboratory for molecular biology of special economic animals, Key laboratory of genetics, breeding and reproduction of special economic animals, Institute of special animal and plant sciences, Chinese academy of agricultural sciences, Changchun, China
| | - Yuanchen Shao
- State key laboratory for molecular biology of special economic animals, Key laboratory of genetics, breeding and reproduction of special economic animals, Institute of special animal and plant sciences, Chinese academy of agricultural sciences, Changchun, China
| | - Jiaping Xu
- State key laboratory for molecular biology of special economic animals, Key laboratory of genetics, breeding and reproduction of special economic animals, Institute of special animal and plant sciences, Chinese academy of agricultural sciences, Changchun, China
| | - Tianjiao Wang
- State key laboratory for molecular biology of special economic animals, Key laboratory of genetics, breeding and reproduction of special economic animals, Institute of special animal and plant sciences, Chinese academy of agricultural sciences, Changchun, China
| | - Yiqing Li
- State key laboratory for molecular biology of special economic animals, Key laboratory of genetics, breeding and reproduction of special economic animals, Institute of special animal and plant sciences, Chinese academy of agricultural sciences, Changchun, China
| | - Huamiao Liu
- State key laboratory for molecular biology of special economic animals, Key laboratory of genetics, breeding and reproduction of special economic animals, Institute of special animal and plant sciences, Chinese academy of agricultural sciences, Changchun, China
| | - Min Rong
- State key laboratory for molecular biology of special economic animals, Key laboratory of genetics, breeding and reproduction of special economic animals, Institute of special animal and plant sciences, Chinese academy of agricultural sciences, Changchun, China
| | - Weilin Su
- State key laboratory for molecular biology of special economic animals, Key laboratory of genetics, breeding and reproduction of special economic animals, Institute of special animal and plant sciences, Chinese academy of agricultural sciences, Changchun, China
| | - Binxi Chen
- Animal Health Supervision Institute of Hainan Province, Haikou, China
| | - Songhuan Cui
- State key laboratory for molecular biology of special economic animals, Key laboratory of genetics, breeding and reproduction of special economic animals, Institute of special animal and plant sciences, Chinese academy of agricultural sciences, Changchun, China
| | - Xuezhe Cui
- State key laboratory for molecular biology of special economic animals, Key laboratory of genetics, breeding and reproduction of special economic animals, Institute of special animal and plant sciences, Chinese academy of agricultural sciences, Changchun, China
| | - Fuhe Yang
- State key laboratory for molecular biology of special economic animals, Key laboratory of genetics, breeding and reproduction of special economic animals, Institute of special animal and plant sciences, Chinese academy of agricultural sciences, Changchun, China
| | | | - Xiumei Xing
- State key laboratory for molecular biology of special economic animals, Key laboratory of genetics, breeding and reproduction of special economic animals, Institute of special animal and plant sciences, Chinese academy of agricultural sciences, Changchun, China.
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Kallio HP. Historical Review on the Identification of Mesifurane, 2,5-Dimethyl-4-methoxy-3(2 H)-furanone, and Its Occurrence in Berries and Fruits. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:2553-2560. [PMID: 29489353 PMCID: PMC6203179 DOI: 10.1021/acs.jafc.8b00519] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2018] [Revised: 02/28/2018] [Accepted: 02/28/2018] [Indexed: 06/08/2023]
Abstract
Mesifurane, 2,5-dimethyl-4-methoxy-3(2 H)-furanone, is a natural compound used a worldwide as a flavoring for foods, beverages, and cosmetics. Global sales of mesifurane are around $100 million. Its significance as a flavor-impact compound in some Nordic berries was discovered in the early 1970s in Finland. Synthesized mesifurane was used as a key compound in aroma mixes exploited in a Finnish patent. Mesifurane is a significant flavorant in arctic brambles, mangoes, strawberries, and many other fruits and berries and is an enzymatic methylation product of 2,5-dimethyl-4-hydroxy-3(2 H)-furanone. Because of the obscurity of the information on the history of the commonly used trivial name, mesifurane, it is time to lift the veil and reveal the background of the present situation. The key player was a northern berry, arctic bramble ( Rubus arcticus), the Finnish name of which is mesimarja. Forty years ago, aroma research was limited by technical factors, but nowadays there is a surplus of information.
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Wong MML, Gujaria-Verma N, Ramsay L, Yuan HY, Caron C, Diapari M, Vandenberg A, Bett KE. Classification and characterization of species within the genus lens using genotyping-by-sequencing (GBS). PLoS One 2015; 10:e0122025. [PMID: 25815480 PMCID: PMC4376907 DOI: 10.1371/journal.pone.0122025] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 02/08/2015] [Indexed: 11/18/2022] Open
Abstract
Lentil (Lens culinaris ssp. culinaris) is a nutritious and affordable pulse with an ancient crop domestication history. The genus Lens consists of seven taxa, however, there are many discrepancies in the taxon and gene pool classification of lentil and its wild relatives. Due to the narrow genetic basis of cultivated lentil, there is a need towards better understanding of the relationships amongst wild germplasm to assist introgression of favourable genes into lentil breeding programs. Genotyping-by-sequencing (GBS) is an easy and affordable method that allows multiplexing of up to 384 samples or more per library to generate genome-wide single nucleotide Polymorphism (SNP) markers. In this study, we aimed to characterize our lentil germplasm collection using a two-enzyme GBS approach. We constructed two 96-plex GBS libraries with a total of 60 accessions where some accessions had several samples and each sample was sequenced in two technical replicates. We developed an automated GBS pipeline and detected a total of 266,356 genome-wide SNPs. After filtering low quality and redundant SNPs based on haplotype information, we constructed a maximum-likelihood tree using 5,389 SNPs. The phylogenetic tree grouped the germplasm collection into their respective taxa with strong support. Based on phylogenetic tree and STRUCTURE analysis, we identified four gene pools, namely L. culinaris/L. orientalis/L. tomentosus, L. lamottei/L. odemensis, L. ervoides and L. nigricans which form primary, secondary, tertiary and quaternary gene pools, respectively. We discovered sequencing bias problems likely due to DNA quality and observed severe run-to-run variation in the wild lentils. We examined the authenticity of the germplasm collection and identified 17% misclassified samples. Our study demonstrated that GBS is a promising and affordable tool for screening by plant breeders interested in crop wild relatives.
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Affiliation(s)
- Melissa M. L. Wong
- Department of Plant Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK, S7N 5A8, Canada
| | - Neha Gujaria-Verma
- Department of Plant Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK, S7N 5A8, Canada
| | - Larissa Ramsay
- Department of Plant Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK, S7N 5A8, Canada
| | - Hai Ying Yuan
- Department of Plant Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK, S7N 5A8, Canada
| | - Carolyn Caron
- Department of Plant Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK, S7N 5A8, Canada
| | - Marwan Diapari
- Department of Plant Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK, S7N 5A8, Canada
| | - Albert Vandenberg
- Department of Plant Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK, S7N 5A8, Canada
| | - Kirstin E. Bett
- Department of Plant Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK, S7N 5A8, Canada
- * E-mail:
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