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Martina M, De Rosa V, Magon G, Acquadro A, Barchi L, Barcaccia G, De Paoli E, Vannozzi A, Portis E. Revitalizing agriculture: next-generation genotyping and -omics technologies enabling molecular prediction of resilient traits in the Solanaceae family. FRONTIERS IN PLANT SCIENCE 2024; 15:1278760. [PMID: 38375087 PMCID: PMC10875072 DOI: 10.3389/fpls.2024.1278760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 01/22/2024] [Indexed: 02/21/2024]
Abstract
This review highlights -omics research in Solanaceae family, with a particular focus on resilient traits. Extensive research has enriched our understanding of Solanaceae genomics and genetics, with historical varietal development mainly focusing on disease resistance and cultivar improvement but shifting the emphasis towards unveiling resilience mechanisms in genebank-preserved germplasm is nowadays crucial. Collecting such information, might help researchers and breeders developing new experimental design, providing an overview of the state of the art of the most advanced approaches for the identification of the genetic elements laying behind resilience. Building this starting point, we aim at providing a useful tool for tackling the global agricultural resilience goals in these crops.
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Affiliation(s)
- Matteo Martina
- Department of Agricultural, Forest and Food Sciences (DISAFA), Plant Genetics, University of Torino, Grugliasco, Italy
| | - Valeria De Rosa
- Department of Agricultural, Food, Environmental and Animal Sciences (DI4A), University of Udine, Udine, Italy
| | - Gabriele Magon
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), Laboratory of Plant Genetics and Breeding, University of Padua, Legnaro, Italy
| | - Alberto Acquadro
- Department of Agricultural, Forest and Food Sciences (DISAFA), Plant Genetics, University of Torino, Grugliasco, Italy
| | - Lorenzo Barchi
- Department of Agricultural, Forest and Food Sciences (DISAFA), Plant Genetics, University of Torino, Grugliasco, Italy
| | - Gianni Barcaccia
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), Laboratory of Plant Genetics and Breeding, University of Padua, Legnaro, Italy
| | - Emanuele De Paoli
- Department of Agricultural, Food, Environmental and Animal Sciences (DI4A), University of Udine, Udine, Italy
| | - Alessandro Vannozzi
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), Laboratory of Plant Genetics and Breeding, University of Padua, Legnaro, Italy
| | - Ezio Portis
- Department of Agricultural, Forest and Food Sciences (DISAFA), Plant Genetics, University of Torino, Grugliasco, Italy
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Gramazio P, Alonso D, Arrones A, Villanueva G, Plazas M, Toppino L, Barchi L, Portis E, Ferrante P, Lanteri S, Rotino GL, Giuliano G, Vilanova S, Prohens J. Conventional and new genetic resources for an eggplant breeding revolution. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:6285-6305. [PMID: 37419672 DOI: 10.1093/jxb/erad260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 07/05/2023] [Indexed: 07/09/2023]
Abstract
Eggplant (Solanum melongena) is a major vegetable crop with great potential for genetic improvement owing to its large and mostly untapped genetic diversity. It is closely related to over 500 species of Solanum subgenus Leptostemonum that belong to its primary, secondary, and tertiary genepools and exhibit a wide range of characteristics useful for eggplant breeding, including traits adaptive to climate change. Germplasm banks worldwide hold more than 19 000 accessions of eggplant and related species, most of which have yet to be evaluated. Nonetheless, eggplant breeding using the cultivated S. melongena genepool has yielded significantly improved varieties. To overcome current breeding challenges and for adaptation to climate change, a qualitative leap forward in eggplant breeding is necessary. The initial findings from introgression breeding in eggplant indicate that unleashing the diversity present in its relatives can greatly contribute to eggplant breeding. The recent creation of new genetic resources such as mutant libraries, core collections, recombinant inbred lines, and sets of introgression lines will be another crucial element and will require the support of new genomics tools and biotechnological developments. The systematic utilization of eggplant genetic resources supported by international initiatives will be critical for a much-needed eggplant breeding revolution to address the challenges posed by climate change.
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Affiliation(s)
- Pietro Gramazio
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022 Valencia, Spain
| | - David Alonso
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022 Valencia, Spain
| | - Andrea Arrones
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022 Valencia, Spain
| | - Gloria Villanueva
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022 Valencia, Spain
| | - Mariola Plazas
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022 Valencia, Spain
| | - Laura Toppino
- CREA Research Centre for Genomics and Bioinformatics, Via Paullese 28, 26836 Montanaso Lombardo, LO, Italy
| | - Lorenzo Barchi
- Dipartimento di Scienze Agrarie, Forestali e Alimentari (DISAFA), Plant Genetics, University of Turin, Largo P. Braccini 2, 10095 Grugliasco, TO, Italy
| | - Ezio Portis
- Dipartimento di Scienze Agrarie, Forestali e Alimentari (DISAFA), Plant Genetics, University of Turin, Largo P. Braccini 2, 10095 Grugliasco, TO, Italy
| | - Paola Ferrante
- Agenzia Nazionale Per Le Nuove Tecnologie, L'energia e Lo Sviluppo Economico Sostenibile (ENEA), Casaccia Research Centre, Rome, Italy
| | - Sergio Lanteri
- Dipartimento di Scienze Agrarie, Forestali e Alimentari (DISAFA), Plant Genetics, University of Turin, Largo P. Braccini 2, 10095 Grugliasco, TO, Italy
| | - Giuseppe Leonardo Rotino
- CREA Research Centre for Genomics and Bioinformatics, Via Paullese 28, 26836 Montanaso Lombardo, LO, Italy
| | - Giovanni Giuliano
- Agenzia Nazionale Per Le Nuove Tecnologie, L'energia e Lo Sviluppo Economico Sostenibile (ENEA), Casaccia Research Centre, Rome, Italy
| | - Santiago Vilanova
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022 Valencia, Spain
| | - Jaime Prohens
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022 Valencia, Spain
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Shigita G, Dung TP, Pervin MN, Duong TT, Imoh ON, Monden Y, Nishida H, Tanaka K, Sugiyama M, Kawazu Y, Tomooka N, Kato K. Elucidation of genetic variation and population structure of melon genetic resources in the NARO Genebank, and construction of the World Melon Core Collection. BREEDING SCIENCE 2023; 73:269-277. [PMID: 37840980 PMCID: PMC10570884 DOI: 10.1270/jsbbs.22071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 02/25/2023] [Indexed: 10/17/2023]
Abstract
Numerous genetic resources of major crops have been introduced from around the world and deposited in Japanese National Agriculture and Food Research Organization (NARO) Genebank. Understanding their genetic variation and selecting a representative subset ("core collection") are essential for optimal management and efficient use of genetic resources. In this study, we conducted genotyping-by-sequencing (GBS) to characterize the genetic relationships and population structure in 755 accessions of melon genetic resources. The GBS identified 39,324 single-nucleotide polymorphisms (SNPs) that are distributed throughout the melon genome with high density (one SNP/10.6 kb). The phylogenetic relationships and population structure inferred using this SNP dataset are highly associated with the cytoplasm type and geographical origin. Our results strongly support the recent hypothesis that cultivated melon was established in Africa and India through multiple independent domestication events. Finally, we constructed a World Melon Core Collection that covers at least 82% of the genetic diversity and has a wide range of geographical origins and fruit morphology. The genome-wide SNP dataset, phylogenetic relationships, population structure, and the core collection provided in this study should largely contribute to genetic research, breeding, and genetic resource preservation in melon.
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Affiliation(s)
- Gentaro Shigita
- Graduate School of Environmental and Life Science, Okayama University, 1-1-1 Tsushima-Naka, Kita-ku, Okayama 700-8530, Japan
- Department of Life Science Systems, Technical University of Munich, Emil-Ramann Strasse 2, Freising 85354, Germany
| | - Tran Phuong Dung
- Graduate School of Environmental and Life Science, Okayama University, 1-1-1 Tsushima-Naka, Kita-ku, Okayama 700-8530, Japan
| | - Mst. Naznin Pervin
- Graduate School of Environmental and Life Science, Okayama University, 1-1-1 Tsushima-Naka, Kita-ku, Okayama 700-8530, Japan
| | - Thanh-Thuy Duong
- Graduate School of Environmental and Life Science, Okayama University, 1-1-1 Tsushima-Naka, Kita-ku, Okayama 700-8530, Japan
- Faculty of Agronomy, University of Agriculture and Forestry, Hue University, 102 Phung Hung Street, Hue City, Vietnam
| | - Odirich Nnennaya Imoh
- Graduate School of Environmental and Life Science, Okayama University, 1-1-1 Tsushima-Naka, Kita-ku, Okayama 700-8530, Japan
| | - Yuki Monden
- Graduate School of Environmental and Life Science, Okayama University, 1-1-1 Tsushima-Naka, Kita-ku, Okayama 700-8530, Japan
| | - Hidetaka Nishida
- Graduate School of Environmental and Life Science, Okayama University, 1-1-1 Tsushima-Naka, Kita-ku, Okayama 700-8530, Japan
| | - Katsunori Tanaka
- Faculty of Agriculture and Life Science, Hirosaki University, 3 Bunkyo, Hirosaki, Aomori 036-8561, Japan
| | - Mitsuhiro Sugiyama
- Institute of Vegetable and Floriculture Science, National Agriculture and Food Research Organization (NARO), 360 Kusawa, Ano, Tsu, Mie 514-2392, Japan
| | - Yoichi Kawazu
- Institute of Vegetable and Floriculture Science, National Agriculture and Food Research Organization (NARO), 360 Kusawa, Ano, Tsu, Mie 514-2392, Japan
| | - Norihiko Tomooka
- Research Center of Genetic Resources, National Agriculture and Food Research Organization (NARO), 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Kenji Kato
- Graduate School of Environmental and Life Science, Okayama University, 1-1-1 Tsushima-Naka, Kita-ku, Okayama 700-8530, Japan
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Acetylcholine Content in 100 Accessions from the Worldwide Eggplant (Solanum melongena L.) Core Collection. J Food Compost Anal 2023. [DOI: 10.1016/j.jfca.2023.105233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
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Liao J, Xue H, Li J. Extraction of phenolics and anthocyanins from purple eggplant peels by multi-frequency ultrasound: Effects of different extraction factors and optimization using uniform design. ULTRASONICS SONOCHEMISTRY 2022; 90:106174. [PMID: 36170772 PMCID: PMC9513698 DOI: 10.1016/j.ultsonch.2022.106174] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 09/17/2022] [Accepted: 09/22/2022] [Indexed: 06/16/2023]
Abstract
In this work, multi-frequency ultrasound (working modes for the single-, dual- and tri-frequency in simultaneous ways) was applied to extract bioactive compounds from purple eggplant peels. The single-factor experiments were performed by varying six independent variables. A six-level-five-factor uniform design (UD) was further employed to evaluate the interaction effects between different factors. It was found that extraction temperature and extraction time significantly affected the total phenolic content (TPC), whereas the total monomeric anthocyanins (TMA) was mainly influenced by ethanol concentration, extraction temperature and solid-liquid ratio. Based on partial least-squares (PLS) regression analysis, the optimal conditions for TPC extraction were: 53.6 % ethanol concentration, 0.336 mm particle size, 44.5 °C extraction temperature, 35.2 min extraction time, 1:43 g/mL solid-liquid ratio, and similar optimal conditions were also obtained for TMA. Furthermore, the TPC and TMA extraction were investigated by ultrasound in different frequencies and power levels. Compared with single-frequency (40 kHz) and dual-frequency ultrasound (25 + 40 kHz), the extraction yield of TPC and TMA with tri-frequency ultrasound (25 + 40 + 70 kHz) increased by 23.65 % and 18.76 % respectively, which suggested the use of multi-frequency ultrasound, especially tri-frequency ultrasound, is an efficient strategy to improve the TPC and TMA extracts in purple eggplant peels.
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Affiliation(s)
- Jianqing Liao
- College of Physical Science and Engineering, Yichun University, 576 Xuefu Road, Yichun, Jiangxi 336000, China.
| | - Hongkun Xue
- College of Traditional Chinese Medicine, Hebei University, No. 342 Yuhua East Road, Lianchi District, Baoding 071002, China.
| | - Junling Li
- College of Chemistry and Bioengineering, Yichun University, 576 Xuefu Road, Yichun, Jiangxi 336000, China
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Zhang Q, Qin B, Wang GD, Zhang WJ, Li M, Yin ZG, Yuan X, Sun HY, Du JD, Du YL, Jia P. Exogenous melatonin enhances cell wall response to salt stress in common bean ( Phaseolus vulgaris) and the development of the associated predictive molecular markers. FRONTIERS IN PLANT SCIENCE 2022; 13:1012186. [PMID: 36325547 PMCID: PMC9619082 DOI: 10.3389/fpls.2022.1012186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 09/22/2022] [Indexed: 06/16/2023]
Abstract
Common bean (Phaseolus vulgaris) is an important food crop; however, its production is affected by salt stress. Salt stress can inhibit seed germination, promote senescence, and modify cell wall biosynthesis, assembly, and architecture. Melatonin, an indole heterocycle, has been demonstrated to greatly impact cell wall structure, composition, and regulation in plants under stress. However, the molecular basis for such assumptions is still unclear. In this study, a common bean variety, "Naihua" was treated with water (W), 70 mmol/L NaCl solution (S), and 100 μmol/L melatonin supplemented with salt solution (M+S) to determine the response of common bean to exogenous melatonin and explore regulatory mechanism of melatonin against salt stress. The results showed that exogenous melatonin treatment alleviated salt stress-induced growth inhibition of the common bean by increasing the length, surface area, volume, and diameter of common bean sprouts. Moreover, RNA sequencing (RNA-seq) and real-time quantitative PCR (qRT-PCR) indicated that the cell wall regulation pathway was involved in the salt stress tolerance of the common bean enhanced by melatonin. Screening of 120 germplasm resources revealed that melatonin treatment improved the salt tolerance of more than 65% of the common bean germplasm materials. Melatonin also up-regulated cell wall pathway genes by at least 46%. Furthermore, we analyzed the response of the common bean germplasm materials to melatonin treatment under salt stress using the key genes associated with the synthesis of the common bean cell wall as the molecular markers. The results showed that two pairs of markers were significantly associated with melatonin, and these could be used as candidate markers to predict whether common bean respond to exogenous melatonin and then enhance salt tolerance at the sprouting stage. This study shows that cell wall can respond to exogenous melatonin and enhance the salt tolerance of common bean. The makers identified in this study can be used to select common bean varieties that can respond to melatonin under stress. Overall, the study found that cell wall could response melatonin and enhance the salt tolerance and developed the makers for predicting varieties fit for melatonin under stress in common bean, which may be applied in the selection or development of common bean varieties with abiotic stress tolerance.
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Affiliation(s)
- Qi Zhang
- College of Agriculture, Herlongjiang Bayi Agricultural University, Daqing, China
| | - Bin Qin
- College of Agriculture, Herlongjiang Bayi Agricultural University, Daqing, China
| | - Guang-da Wang
- College of Agriculture, Herlongjiang Bayi Agricultural University, Daqing, China
| | - Wen-jing Zhang
- College of Agriculture, Herlongjiang Bayi Agricultural University, Daqing, China
| | - Ming Li
- College of Agriculture, Herlongjiang Bayi Agricultural University, Daqing, China
| | - Zhen-gong Yin
- Crop Resources Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Xiankai Yuan
- College of Agriculture, Herlongjiang Bayi Agricultural University, Daqing, China
| | - Hao-yue Sun
- Qiqihar Branch, Heilongjiang Academy of Agricultural Sciences, Qiqihaer, China
| | - Ji-dao Du
- College of Agriculture, Herlongjiang Bayi Agricultural University, Daqing, China
- National Coarse Cereals Engineering Research Center, Herlongjiang Bayi Agricultural University, Daqing, China
| | - Yan-li Du
- College of Agriculture, Herlongjiang Bayi Agricultural University, Daqing, China
- National Coarse Cereals Engineering Research Center, Herlongjiang Bayi Agricultural University, Daqing, China
| | - Pengyu Jia
- College of Agriculture, Herlongjiang Bayi Agricultural University, Daqing, China
- National Coarse Cereals Engineering Research Center, Herlongjiang Bayi Agricultural University, Daqing, China
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Öztürk Hİ, Dönderalp V, Bulut H, Korkut R. Morphological and molecular characterization of some pumpkin (Cucurbita pepo L.) genotypes collected from Erzincan province of Turkey. Sci Rep 2022; 12:6814. [PMID: 35474245 PMCID: PMC9042938 DOI: 10.1038/s41598-022-11005-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 04/07/2022] [Indexed: 11/09/2022] Open
Abstract
Plant genetic resources constitute the most valuable assets of countries. It is of great importance to determine the genetic variation among these resources and to use the data in breeding studies. To determine the genetic diversity among genotypes of Cucurbita pepo L. species of pumpkin, which is widely grown in Erzincan, 29 different pumpkin genotypes collected were examined based on the morphological parameters and molecular characteristics. SSR (Simple Sequence Repeat) markers were used to determine genetic diversity at the molecular level. The analysis of morphological characterization within genotypes showed a wide variability in morphological traits of plant, flower, fruit, and leaf. In the evaluation performed using SSR markers, all primers exhibited polymorphism rate of %100. Seven SSR markers yielded a total of 15 polymorphic bands, the number of alleles per marker ranged from 2 to 3, and the mean number of alleles was 2.14. Polymorphic information content (PIC) ranged from 0.06 (GMT-M61) to 0.247 (GMT-P41), and the mean PIC value per marker was 0.152. Cluster analysis using Nei's genetic distance determined that 29 genotypes were divided into 4 major groups. The present findings have revealed the genetic diversity among pumpkin genotypes collected from Erzincan province and may form the basis for further breeding studies in pumpkin.
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Affiliation(s)
- Halil İbrahim Öztürk
- Vocational School of Health Services, Erzincan Binali Yıldırım University, Erzincan, Turkey.
| | | | - Hüseyin Bulut
- Vocational School of Health Services, Erzincan Binali Yıldırım University, Erzincan, Turkey
| | - Recep Korkut
- Erzincan Horticultural Research Institute, Erzincan, Turkey
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Egan LM, Conaty WC, Stiller WN. Core Collections: Is There Any Value for Cotton Breeding? FRONTIERS IN PLANT SCIENCE 2022; 13:895155. [PMID: 35574064 PMCID: PMC9096653 DOI: 10.3389/fpls.2022.895155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Accepted: 04/06/2022] [Indexed: 05/08/2023]
Abstract
Global plant breeding activities are reliant on the available genetic variation held in extant varieties and germplasm collections. Throughout the mid- to late 1900s, germplasm collecting efforts were prioritized for breeding programs to archive precious material before it disappeared and led to the development of the numerous large germplasm resources now available in different countries. In recent decades, however, the maintenance and particularly the expansion of these germplasm resources have come under threat, and there has been a significant decline in investment in further collecting expeditions, an increase in global biosecurity restrictions, and restrictions placed on the open exchange of some commercial germplasm between breeders. The large size of most genebank collections, as well as constraints surrounding the availability and reliability of accurate germplasm passport data and physical or genetic characterization of the accessions in collections, limits germplasm utilization by plant breeders. To overcome these constraints, core collections, defined as a representative subset of the total germplasm collection, have gained popularity. Core collections aim to increase germplasm utilization by containing highly characterized germplasm that attempts to capture the majority of the variation in a whole collection. With the recent availability of many new genetic tools, the potential to unlock the value of these resources can now be realized. The Commonwealth Scientific and Industrial Research Organisation (CSIRO) cotton breeding program supplies 100% of the cotton cultivars grown in Australia. The program is reliant on the use of plant genetic resources for the development of improved cotton varieties to address emerging challenges in pest and disease resistance as well as the global changes occurring in the climate. Currently, the CSIRO germplasm collection is actively maintained but underutilized by plant breeders. This review presents an overview of the Australian cotton germplasm resources and discusses the appropriateness of a core collection for cotton breeding programs.
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Alekseeva M, Zagorcheva T, Rusanova M, Rusanov K, Atanassov I. Genetic and Flower Volatile Diversity in Natural Populations of Origanum vulgare subsp. hirtum (Link) Ietsw. in Bulgaria: Toward the Development of a Core Collection. FRONTIERS IN PLANT SCIENCE 2021; 12:679063. [PMID: 34335650 PMCID: PMC8320660 DOI: 10.3389/fpls.2021.679063] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 06/17/2021] [Indexed: 05/27/2023]
Abstract
We studied the genetic and flower volatile diversity in natural populations of Origanum vulgare subsp. hirtum (Link) Ietsw. in Bulgaria using simple sequence repeat (SSR) and sequence-related amplified polymorphism (SRAP) markers and gas chromatography/mass spectrometry (GC/MS) analysis of flower volatiles from individual plants. Two regions, including the Kresna Gorge and Eastern Rhodopes, typical for the species comprising eight populations and 239 individual plants were included in this study. An analysis with 11 SSR markers and eight SRAP primer combinations showed that SRAP markers were substantially more informative than the SSR markers and were further used for genetic diversity analysis. The results showed low-range to mid-range genetic differentiation between the populations with pairwise fixation index (Fst) values ranging between 0.0047 and 0.11. A total of 10 genetic clusters were identified. An analysis of the flower volatile diversity identified a total of 63 compounds with the vast majority of plants belonging to the carvacrol chemotype and just a single plant to the thymol chemotype. Large deviations were observed for individual compounds within each region as well as within the populations. Hierarchical clustering showed a clear sample grouping based on the two different regions. In addition, an in-depth analysis identified six major and 23 minor metabolite clusters. The overall data set and cluster analysis were further used for the development and testing of a simple and straightforward strategy for the selection of individual plants for the development of a core collection representing the sampled natural populations for this species in Bulgaria. The proposed strategy involves precise genetic clustering of the tested plants followed by the selection of a minimal set from each genetic cluster representing the different metabolite clusters. The selected core set was further compared with a core set extracted by the PowerCore software. A comparison of the genetic and metabolic affiliation of the members of both sets showed that the reported approach selected representatives from each genetic cluster and minor metabolic cluster, whereas some metabolic clusters were unrepresented in the PowerCore set. The feasibility and efficiency of applying the pointed strategy for the development of a core collection representing both the genetic and metabolite diversity of natural populations in aromatic and medicinal plants toward subsequent steps of selection and breeding are discussed.
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10
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Biswas MK, Darbar JN, Borrell JS, Bagchi M, Biswas D, Nuraga GW, Demissew S, Wilkin P, Schwarzacher T, Heslop-Harrison JS. The landscape of microsatellites in the enset (Ensete ventricosum) genome and web-based marker resource development. Sci Rep 2020; 10:15312. [PMID: 32943659 PMCID: PMC7498607 DOI: 10.1038/s41598-020-71984-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 08/24/2020] [Indexed: 12/25/2022] Open
Abstract
Ensete ventricosum (Musaceae, enset) is an Ethiopian food security crop. To realize the potential of enset for rural livelihoods, further knowledge of enset diversity, genetics and genomics is required to support breeding programs and conservation. This study was conducted to explore the enset genome to develop molecular markers, genomics resources, and characterize enset landraces while giving insight into the organization of the genome. We identified 233 microsatellites (simple sequence repeats, SSRs) per Mbp in the enset genome, representing 0.28% of the genome. Mono- and di-nucleotide repeats motifs were found in a higher proportion than other classes of SSR-motifs. In total, 154,586 non-redundant enset microsatellite markers (EMM) were identified and 40 selected for primer development. Marker validation by PCR and low-cost agarose gel electrophoresis revealed that 92.5% were polymorphic, showing a high PIC (Polymorphism Information Content; 0.87) and expected heterozygosity (He = 0.79-0.82). In silico analysis of genomes of closely related species showed 46.86% of the markers were transferable among enset species and 1.90% were transferable to Musa. The SSRs are robust (with basic PCR methods and agarose gel electrophoresis), informative, and applicable in measuring enset diversity, genotyping, selection and potentially breeding. Enset SSRs are available in a web-based database at https://enset-project.org/EnMom@base.html (or https://enset.aau.edu.et/index.html , downloadable from Figshare).
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Affiliation(s)
- Manosh Kumar Biswas
- Department of Genetics and Genome Biology, University of Leicester, Leicester, LE1 7RH, UK.
| | - Jaypal N Darbar
- Department of Genetics and Genome Biology, University of Leicester, Leicester, LE1 7RH, UK
| | | | - Mita Bagchi
- Department of Genetics and Genome Biology, University of Leicester, Leicester, LE1 7RH, UK
| | - Dhiman Biswas
- Department of Computer Science and Engineering, Maulana Abul Kalam Azad University of Technology, Kolkata, West Bengal, India
| | - Gizachew Woldesenbet Nuraga
- Department of Genetics and Genome Biology, University of Leicester, Leicester, LE1 7RH, UK.,Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Sebsebe Demissew
- Department of Plant Biology and Biodiversity Management, Addis Ababa University, Addis Ababa, Ethiopia
| | - Paul Wilkin
- Royal Botanic Gardens, Kew, Richmond, TW9 3AE, Surrey, UK
| | - Trude Schwarzacher
- Department of Genetics and Genome Biology, University of Leicester, Leicester, LE1 7RH, UK.,South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, People's Republic of China
| | - J S Heslop-Harrison
- Department of Genetics and Genome Biology, University of Leicester, Leicester, LE1 7RH, UK. .,South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, People's Republic of China.
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Miyatake K, Saito T, Nunome T, Yamaguchi H, Negoro S, Ohyama A, Wu J, Katayose Y, Fukuoka H. Fine mapping of a major locus representing the lack of prickles in eggplant revealed the availability of a 0.5-kb insertion/deletion for marker-assisted selection. BREEDING SCIENCE 2020; 70:438-448. [PMID: 32968346 PMCID: PMC7495204 DOI: 10.1270/jsbbs.20004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 04/02/2020] [Indexed: 05/29/2023]
Abstract
As prickles cause labour inefficiency during cultivation and scratches on the skin of fruits during transportation, they are considered undesirable traits of eggplant (Solanum melongena L.). Because the molecular basis of prickle emergence has not been entirely revealed in plants, we mapped an eggplant semi-dominant Prickle (Pl) gene locus, which causes the absence of prickles, on chromosome 6 of a linkage map of the F2 population derived from crossing the no-prickly cultivar 'Togenashi-senryo-nigo' and the prickly line LS1934. By performing synteny mapping with tomato, the genomic region corresponding to the eggplant Pl locus was identified. Through bacterial artificial chromosome (BAC) screening, positive BAC clones and the contig sequence that harbour the Pl locus in the prickly eggplant genome were revealed. The BAC contig length was 133 kb, and it contained 16 predicted genes. Among them, a characteristic 0.5-kb insertion/deletion was detected. As the 0.5-kb insertion was commonly identified with the prickly phenotype worldwide, a primer pair that amplifies the insertion/deletion could be used for marker-assisted selection of the no-prickly phenotype. Such findings contribute to map-based-cloning of the Pl gene and the understanding of gene function, ultimately providing new insights into the regulatory molecular mechanisms underlying prickle emergence in plants.
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Affiliation(s)
- Koji Miyatake
- Institute of Vegetable and Floriculture Science (NIVFS), National Agriculture and Food Research Organization (NARO), 360 Kusawa, Ano, Tsu, Mie 514-2392, Japan
| | - Takeo Saito
- Institute of Vegetable and Floriculture Science (NIVFS), National Agriculture and Food Research Organization (NARO), 360 Kusawa, Ano, Tsu, Mie 514-2392, Japan
| | - Tsukasa Nunome
- Institute of Vegetable and Floriculture Science (NIVFS), National Agriculture and Food Research Organization (NARO), 360 Kusawa, Ano, Tsu, Mie 514-2392, Japan
| | - Hirotaka Yamaguchi
- Institute of Vegetable and Floriculture Science (NIVFS), National Agriculture and Food Research Organization (NARO), 360 Kusawa, Ano, Tsu, Mie 514-2392, Japan
| | - Satomi Negoro
- Institute of Vegetable and Floriculture Science (NIVFS), National Agriculture and Food Research Organization (NARO), 360 Kusawa, Ano, Tsu, Mie 514-2392, Japan
| | - Akio Ohyama
- Institute of Vegetable and Floriculture Science (NIVFS), National Agriculture and Food Research Organization (NARO), 360 Kusawa, Ano, Tsu, Mie 514-2392, Japan
| | - Jianzhong Wu
- Institute of Crop Science (NICS), National Agriculture and Food Research Organization (NARO), 1-2 Owashi, Tsukuba, Ibaraki 305-8634, Japan
| | - Yuichi Katayose
- Institute of Crop Science (NICS), National Agriculture and Food Research Organization (NARO), 1-2 Owashi, Tsukuba, Ibaraki 305-8634, Japan
| | - Hiroyuki Fukuoka
- Institute of Vegetable and Floriculture Science (NIVFS), National Agriculture and Food Research Organization (NARO), 360 Kusawa, Ano, Tsu, Mie 514-2392, Japan
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Liu M, Hu X, Wang X, Zhang J, Peng X, Hu Z, Liu Y. Constructing a Core Collection of the Medicinal Plant Angelica biserrata Using Genetic and Metabolic Data. FRONTIERS IN PLANT SCIENCE 2020; 11:600249. [PMID: 33424898 PMCID: PMC7785966 DOI: 10.3389/fpls.2020.600249] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Accepted: 12/02/2020] [Indexed: 05/16/2023]
Abstract
Angelica biserrata is an important medicinal plant in Chinese traditional medicine. Its roots, which are known as Duhuo in Chinese, are broadly applied to treat inflammation, arthritis, and headache. With increasing market demand, the wild resources of A. biserrata have been overexploited, and conservation, assessment of genetic resources and breeding for this species is needed. Here, we sequenced the transcriptome of A. biserrata and developed simple sequence repeat (SSR) markers from it to construct a core collection based on 208 samples collected from Changyang-related regions. A total of 132 alleles were obtained for 17 SSR loci used with the polymorphic information content (PIC) ranging from 0.44 to 0.83. Abundant genetic diversity was inferred by Shannon's information index (1.51), observed (0.57) and expected heterozygosity (0.72). The clustering analysis resulted into two sample groups and analysis of molecular variance (AMOVA) showed only 6% genetic variation existed among populations. A further metabolic analysis of these samples revealed the main coumarin contents, such as osthole and columbianadin. According to the genetic and metabolic data, we adopted the least distance stepwise sampling strategy to construct seven preliminary core collections, of which the 20CC collection, which possessed 42 A. biserrata individuals accounting for 90.20% of the genetic diversity of the original germplasm, represented the best core collection. This study will contribute to the conservation and management of A. biserrata wild germplasm resources and provide a material basis for future selection and breeding of this medicinal plant.
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Affiliation(s)
- Man Liu
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China
| | - Xin Hu
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China
| | - Xu Wang
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China
| | - Jingjing Zhang
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China
| | - Xubing Peng
- Hubei Kangnong Seed Co., Ltd., Yichang, China
| | - Zhigang Hu
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China
- *Correspondence: Zhigang Hu,
| | - Yifei Liu
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China
- Yifei Liu,
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