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Fu S, Chen X, Wang K, Chen J, Zhou J, Yi W, Lyu M, Ye Z, Bu W. Shared phylogeographic patterns and environmental responses of co-distributed soybean pests: Insights from comparative phylogeographic studies of Riptortus pedestris and Riptortus linearis in the subtropics of East Asia. Mol Phylogenet Evol 2024; 195:108055. [PMID: 38485106 DOI: 10.1016/j.ympev.2024.108055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 01/31/2024] [Accepted: 03/07/2024] [Indexed: 03/19/2024]
Abstract
Comparative phylogeographic studies of closely related species sharing co-distribution areas can elucidate the role of shared historical factors and environmental changes in shaping their phylogeographic pattern. The bean bugs, Riptortus pedestris and Riptortus linearis, which both inhabit subtropical regions in East Asia, are recognized as highly destructive soybean pests. Many previous studies have investigated the biological characteristics, pheromones, chemicals and control mechanisms of these two pests, but few studies have explored their phylogeographic patterns and underlying factors. In this study, we generated a double-digest restriction site-associated DNA sequencing (ddRAD-seq) dataset to investigate phylogeographic patterns and construct ecological niche models (ENM) for both Riptortus species. Our findings revealed similar niche occupancies and population genetic structures between the two species, with each comprising two phylogeographic lineages (i.e., the mainland China and the Indochina Peninsula clades) that diverged approximately 0.1 and 0.3 million years ago, respectively. This divergence likely resulted from the combined effects of temperatures variation and geographical barriers in the mountainous regions of Southwest China. Further demographic history and ENM analyses suggested that both pests underwent rapid expansion prior to the Last Glacial Maximum (LGM). Furthermore, ENM predicts a northward shift of both pests into new soybean-producing regions due to global warming. Our study indicated that co-distribution soybean pests with overlapping ecological niches and similar life histories in subtropical regions of East Asia exhibit congruent phylogeographic and demographic patterns in response to shared historical biogeographic drivers.
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Affiliation(s)
- Siying Fu
- College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Xin Chen
- College of Life Sciences, Cangzhou Normal University, Cangzhou, China(2)
| | - Kaibin Wang
- College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Juhong Chen
- College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Jiayue Zhou
- College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Wenbo Yi
- Department of Biology, Xinzhou Normal University, Xinzhou, Shanxi, China(2)
| | - Minhua Lyu
- Nanchang University, Affiliated Hospital 1, Jiangxi, China(2)
| | - Zhen Ye
- College of Life Sciences, Nankai University, Tianjin 300071, China.
| | - Wenjun Bu
- College of Life Sciences, Nankai University, Tianjin 300071, China.
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Yu X, Fu X, Yang Q, Jin H, Zhu L, Yuan F. Genetic and Phenotypic Characterization of Soybean Landraces Collected from the Zhejiang Province in China. Plants (Basel) 2024; 13:353. [PMID: 38337886 PMCID: PMC10856940 DOI: 10.3390/plants13030353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 01/12/2024] [Accepted: 01/19/2024] [Indexed: 02/12/2024]
Abstract
The soybean is an important feed, industrial raw material, and food crop in the world due to its rich components. There is a long history of soybean cultivation with different types and rich resources in the Zhejiang province of China. It is important to understand genetic diversity as well as phenotypic variation for soybean breeding. The objective of this study was to analyze both genetic and phenotypic characteristics of the 78 soybean landraces collected, and to explore a potential advantage of germplasm resources for further application. These 78 autumn-type soybean landraces have been propagated, identified, and evaluated in both 2021 and 2022. There were agronomic, quality, and genetic variations according to the comprehensive analyses. There was a good consistency between seed size and seed coat color. There were significant differences of seed protein, fat, and sugar contents based upon the seed coat color. These soybean landraces were genotyped using 42 simple sequence repeat markers and then clustered into two groups. The two groups had a consistency with the seed coat color. This study gave us a combined understanding of both the phenotypic variation and the genetic diversity of the soybean landraces. Therefore, the reasonable crossing between different soybean types is highly recommended.
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Affiliation(s)
- Xiaomin Yu
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (X.F.); (Q.Y.); (H.J.); (L.Z.)
| | - Xujun Fu
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (X.F.); (Q.Y.); (H.J.); (L.Z.)
| | - Qinghua Yang
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (X.F.); (Q.Y.); (H.J.); (L.Z.)
| | - Hangxia Jin
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (X.F.); (Q.Y.); (H.J.); (L.Z.)
| | - Longming Zhu
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (X.F.); (Q.Y.); (H.J.); (L.Z.)
| | - Fengjie Yuan
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (X.F.); (Q.Y.); (H.J.); (L.Z.)
- Xianghu Laboratory, Hangzhou 311231, China
- Key Laboratory of Information Traceability for Agricultural Products, Ministry of Agriculture and Rural Affairs of China, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
- Key Laboratory of Digital Upland Crops of Zhejiang Province, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
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Yang R, Dong Y, Gao F, Li J, Stevanovic ZD, Li H, Shi L. Comprehensive Analysis of Secondary Metabolites of Four Medicinal Thyme Species Used in Folk Medicine and Their Antioxidant Activities In Vitro. Molecules 2023; 28:molecules28062582. [PMID: 36985554 PMCID: PMC10052123 DOI: 10.3390/molecules28062582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/04/2023] [Accepted: 03/08/2023] [Indexed: 03/14/2023] Open
Abstract
Thyme is a colloquial term for number of aromatic species belonging to the genus Thymus L., known for their expressed biological activities and therefore used worldwide for seasoning and in folk medicine. In the present paper, the content of the total polyphenols (TP), total flavonoids (TF), and antioxidant capacity were assessed in the extracts of four traditionally used thyme species. Moreover, a comprehensive metabolomic study of thyme bioactive compounds was performed, and the obtained data were processed using multivariate statistical tests. The results clearly demonstrated the positive correlation between the content of the TP, TF, and antioxidant activity, and TF was more significant than TP. The findings revealed that four selected thyme species contained 528 secondary metabolites, including 289 flavonoids and 146 phenolic acids. Thymus marschallianus had a higher concentration of active ingredients, which improve its antioxidant capacity. Differentially accumulated metabolites were formed by complex pathways such as flavonoid, flavone, flavonol, isoflavonoid, and anthocyanin biosynthesis. Correlation analysis showed that 59 metabolites (including 28 flavonoids, 18 phenolic acids, and 7 terpenoid compounds) were significantly correlated with obtained values of the antioxidant capacity. The results suggested that selected thyme species exhibit a great diversity in antioxidant-related components, whereas flavonoids may be responsible for the high antioxidant capacity of all studied thyme species. The present study greatly expands our understanding of the complex phytochemical profiles and related applications of selected medicinal plants.
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Affiliation(s)
- Rui Yang
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; (R.Y.); (Y.D.); (F.G.); (J.L.)
- China National Botanical Garden, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanmei Dong
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; (R.Y.); (Y.D.); (F.G.); (J.L.)
- China National Botanical Garden, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fei Gao
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; (R.Y.); (Y.D.); (F.G.); (J.L.)
- China National Botanical Garden, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jingyi Li
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; (R.Y.); (Y.D.); (F.G.); (J.L.)
| | - Zora Dajic Stevanovic
- Department of Agrobotany, University of Belgrade Faculty of Agriculture, Nemanjina 6, 11080 Zemun, Serbia;
| | - Hui Li
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; (R.Y.); (Y.D.); (F.G.); (J.L.)
- China National Botanical Garden, Beijing 100093, China
- Correspondence: (H.L.); (L.S.)
| | - Lei Shi
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; (R.Y.); (Y.D.); (F.G.); (J.L.)
- China National Botanical Garden, Beijing 100093, China
- Correspondence: (H.L.); (L.S.)
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Ramlal A, Nautiyal A, Baweja P, Kumar Mahto R, Mehta S, Pujari Mallikarunja B, Vijayan R, Saluja S, Kumar V, Kumar Dhiman S, Lal SK, Raju D, Rajendran A. Harnessing heterosis and male sterility in soybean [ Glycine max (L.) Merrill]: A critical revisit. Front Plant Sci 2022; 13:981768. [PMID: 36299790 PMCID: PMC9589222 DOI: 10.3389/fpls.2022.981768] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 08/29/2022] [Indexed: 06/16/2023]
Abstract
Soybean is a predominantly self-pollinated crop. It is also one of the important oilseed legumes. Soybean is an excellent crop having industrial, traditional, culinary, feeding, and cultural roles. Genetic diversity in breeding programs is of prime importance as it ensures the success of any breeding by enhancing the outcomes and results of the plants. The phenomenon wherein the progeny exhibits greater biomass (yield) and a faster rate of development and fertility than its parents is referred to as heterosis. As of now, heterosis is mainly limited to the trait of seed yield and is considered the basis for the development of better (superior) varieties. Male sterility (MS) is extensively used for the production of seeds and the improvement of crops coupled with the traditional breeding programs and molecular technology. Therefore, deployment of MS and heterosis in breeding soybean could yield better outcomes. This review aims to focus on two aspects, namely, MS and heterosis in soybean with its scope for crop improvement.
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Affiliation(s)
- Ayyagari Ramlal
- Division of Genetics, ICAR-Indian Agricultural Research Institute (IARI), Pusa Campus, New Delhi, India
- Department of Botany, Institute of Science, Banaras Hindu University (BHU), Varanasi, Uttar Pradesh, India
| | - Aparna Nautiyal
- Department of Botany, Deshbandhu College, University of Delhi, New Delhi, India
- DBC i4 Center, Deshbandhu College, New Delhi, India
| | - Pooja Baweja
- Department of Botany, Maitreyi College, University of Delhi, New Delhi, India
| | - Rohit Kumar Mahto
- Division of Genetics, ICAR-Indian Agricultural Research Institute (IARI), Pusa Campus, New Delhi, India
- School of Biotechnology, Institute of Science, Banaras Hindu University (BHU), Varanasi, Uttar Pradesh, India
| | - Sahil Mehta
- School of Agricultural Sciences, K. R. Mangalam University, Gurugram, Haryana, India
| | - Bingi Pujari Mallikarunja
- Division of Genetics, Regional Research Centre, ICAR-Indian Agricultural Research Institute (IARI), Dharwad, Karnataka, India
| | - Roshni Vijayan
- Regional Agricultural Research Station, Kerala Agricultural University, Pattambi, Kerala, India
| | - Shukla Saluja
- Department of Botany, Sri Venkateswara College, University of Delhi, New Delhi, India
| | - Vijay Kumar
- Department of Botany, Shivaji College, University of Delhi, New Delhi, India
| | - Sunil Kumar Dhiman
- Department of Botany, Kirori Mal College, University of Delhi, New Delhi, India
| | - S. K. Lal
- Division of Genetics, ICAR-Indian Agricultural Research Institute (IARI), Pusa Campus, New Delhi, India
| | - Dhandapani Raju
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute (IARI), Pusa Campus, New Delhi, India
| | - Ambika Rajendran
- Division of Genetics, ICAR-Indian Agricultural Research Institute (IARI), Pusa Campus, New Delhi, India
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Liu X, Li C, Cao J, Zhang X, Wang C, He J, Xing G, Wang W, Zhao J, Gai J. Growth period QTL-allele constitution of global soybeans and its differential evolution changes in geographic adaptation versus maturity group extension. Plant J 2021; 108:1624-1643. [PMID: 34618996 DOI: 10.1111/tpj.15531] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 09/27/2021] [Indexed: 06/13/2023]
Abstract
Soybean (Glycine max (L.) Merr.) has been disseminated globally as a photoperiod/temperature-sensitive crop with extremely diverse days to flowering (DTF) and days to maturity (DTM) values. A population with 371 global varieties covering 13 geographic regions and 13 maturity groups (MGs) was analyzed for its DTF and DTM QTL-allele constitution using restricted two-stage multi-locus genome-wide association study (RTM-GWAS). Genotypes with 20 701 genome-wide SNPLDBs (single-nucleotide polymorphism linkage disequilibrium blocks) containing 55 404 haplotypes were observed, and 52 DTF QTLs and 59 DTM QTLs (including 29 and 21 new ones) with 241 and 246 alleles (two to 13 per locus) were detected, explaining 84.8% and 74.4% of the phenotypic variance, respectively. The QTL-allele matrix characterized with all QTL-allele information of each variety in the global population was established and subsequently separated into geographic and MG set submatrices. Direct comparisons among them revealed that the genetic adaptation from the origin to geographic subpopulations was characterized by new allele/new locus emergence (mutation) but little allele exclusion (selection), while that from the primary MG set to emerged early and late MG sets was characterized by allele exclusion without allele emergence. The evolutionary changes involved mainly 72 DTF and 71 DTM alleles on 28 respective loci, 10-12 loci each with three to six alleles being most active. Further recombination potential for faster maturation (12-21 days) or slower maturation (14-56 days) supported allele convergence (recombination) as a constant genetic factor in addition to migration (inheritance). From the QTLs, 44 DTF and 36 DTM candidate genes were annotated and grouped respectively into nine biological processes, indicating multi-functional DTF/DTM genes are involved in a complex gene network. In summary, we identified QTL-alleles relatively thoroughly using RTM-GWAS for direct matrix comparisons and subsequent analysis.
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Affiliation(s)
- Xueqin Liu
- Soybean Research Institute & MOA National Center for Soybean Improvement & MOA Key Laboratory of Biology and Genetic Improvement of Soybean (General) & State Key Laboratory for Crop Genetics and Germplasm Enhancement & Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
- Department of Agronomy and Horticulture, Jiangsu Vocational College of Agriculture and Forestry, Jurong, 212400, China
| | - Chunyan Li
- Soybean Research Institute & MOA National Center for Soybean Improvement & MOA Key Laboratory of Biology and Genetic Improvement of Soybean (General) & State Key Laboratory for Crop Genetics and Germplasm Enhancement & Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
- Shengfeng Experiment station, Shengfeng Seed Company Limited, Jining, 272100, China
| | - Jiqiu Cao
- Shengfeng Experiment station, Shengfeng Seed Company Limited, Jining, 272100, China
| | - Xiaoyan Zhang
- Soybean Research Institute & MOA National Center for Soybean Improvement & MOA Key Laboratory of Biology and Genetic Improvement of Soybean (General) & State Key Laboratory for Crop Genetics and Germplasm Enhancement & Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
- Shengfeng Experiment station, Shengfeng Seed Company Limited, Jining, 272100, China
| | - Can Wang
- Soybean Research Institute & MOA National Center for Soybean Improvement & MOA Key Laboratory of Biology and Genetic Improvement of Soybean (General) & State Key Laboratory for Crop Genetics and Germplasm Enhancement & Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jianbo He
- Soybean Research Institute & MOA National Center for Soybean Improvement & MOA Key Laboratory of Biology and Genetic Improvement of Soybean (General) & State Key Laboratory for Crop Genetics and Germplasm Enhancement & Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Guangnan Xing
- Soybean Research Institute & MOA National Center for Soybean Improvement & MOA Key Laboratory of Biology and Genetic Improvement of Soybean (General) & State Key Laboratory for Crop Genetics and Germplasm Enhancement & Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Wubin Wang
- Soybean Research Institute & MOA National Center for Soybean Improvement & MOA Key Laboratory of Biology and Genetic Improvement of Soybean (General) & State Key Laboratory for Crop Genetics and Germplasm Enhancement & Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jinming Zhao
- Soybean Research Institute & MOA National Center for Soybean Improvement & MOA Key Laboratory of Biology and Genetic Improvement of Soybean (General) & State Key Laboratory for Crop Genetics and Germplasm Enhancement & Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Junyi Gai
- Soybean Research Institute & MOA National Center for Soybean Improvement & MOA Key Laboratory of Biology and Genetic Improvement of Soybean (General) & State Key Laboratory for Crop Genetics and Germplasm Enhancement & Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
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Laggoun F, Ali N, Tourneur S, Prudent G, Gügi B, Kiefer-Meyer MC, Mareck A, Cruz F, Yvin JC, Nguema-Ona E, Mollet JC, Jamois F, Lehner A. Two Carbohydrate-Based Natural Extracts Stimulate in vitro Pollen Germination and Pollen Tube Growth of Tomato Under Cold Temperatures. Front Plant Sci 2021; 12:552515. [PMID: 34691089 PMCID: PMC8529017 DOI: 10.3389/fpls.2021.552515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 09/14/2021] [Indexed: 06/13/2023]
Abstract
To date, it is widely accepted by the scientific community that many agricultural regions will experience more extreme temperature fluctuations. These stresses will undoubtedly impact crop production, particularly fruit and seed yields. In fact, pollination is considered as one of the most temperature-sensitive phases of plant development and until now, except for the time-consuming and costly processes of genetic breeding, there is no immediate alternative to address this issue. In this work, we used a multidisciplinary approach using physiological, biochemical, and molecular techniques for studying the effects of two carbohydrate-based natural activators on in vitro tomato pollen germination and pollen tube growth cultured in vitro under cold conditions. Under mild and strong cold temperatures, these two carbohydrate-based compounds significantly enhanced pollen germination and pollen tube growth. The two biostimulants did not induce significant changes in the classical molecular markers implicated in pollen tube growth. Neither the number of callose plugs nor the CALLOSE SYNTHASE genes expression were significantly different between the control and the biostimulated pollen tubes when pollens were cultivated under cold conditions. PECTIN METHYLESTERASE (PME) activities were also similar but a basic PME isoform was not produced or inactive in pollen grown at 8°C. Nevertheless, NADPH oxidase (RBOH) gene expression was correlated with a higher number of viable pollen tubes in biostimulated pollen tubes compared to the control. Our results showed that the two carbohydrate-based products were able to reduce in vitro the effect of cold temperatures on tomato pollen tube growth and at least for one of them to modulate reactive oxygen species production.
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Affiliation(s)
- Ferdousse Laggoun
- UNIROUEN, Normandie Université, Laboratoire de Glycobiologie et Matrice Extracellulaire Végétale, SFR NORVEGE FED 4277, Carnot I2C, IRIB, Rouen, France
- Sanofi Pasteur, Val-de-Reuil, France
| | - Nusrat Ali
- Centre Mondial de l’Innovation, Laboratoire Nutrition Végétale, Groupe Roullier, Saint-Malo, France
| | - Sabine Tourneur
- UNIROUEN, Normandie Université, Laboratoire de Glycobiologie et Matrice Extracellulaire Végétale, SFR NORVEGE FED 4277, Carnot I2C, IRIB, Rouen, France
- Laboratoire de Biologie et Pathologie Végétales, Université de Nantes, Université Bretagne Loire, Nantes, France
| | - Grégoire Prudent
- UNIROUEN, Normandie Université, Laboratoire de Glycobiologie et Matrice Extracellulaire Végétale, SFR NORVEGE FED 4277, Carnot I2C, IRIB, Rouen, France
| | - Bruno Gügi
- UNIROUEN, Normandie Université, Laboratoire de Glycobiologie et Matrice Extracellulaire Végétale, SFR NORVEGE FED 4277, Carnot I2C, IRIB, Rouen, France
| | - Marie-Christine Kiefer-Meyer
- UNIROUEN, Normandie Université, Laboratoire de Glycobiologie et Matrice Extracellulaire Végétale, SFR NORVEGE FED 4277, Carnot I2C, IRIB, Rouen, France
| | - Alain Mareck
- UNIROUEN, Normandie Université, Laboratoire de Glycobiologie et Matrice Extracellulaire Végétale, SFR NORVEGE FED 4277, Carnot I2C, IRIB, Rouen, France
| | - Florence Cruz
- Centre Mondial de l’Innovation, Laboratoire Nutrition Végétale, Groupe Roullier, Saint-Malo, France
| | - Jean-Claude Yvin
- Centre Mondial de l’Innovation, Laboratoire Nutrition Végétale, Groupe Roullier, Saint-Malo, France
| | - Eric Nguema-Ona
- Centre Mondial de l’Innovation, Laboratoire Nutrition Végétale, Groupe Roullier, Saint-Malo, France
| | - Jean-Claude Mollet
- UNIROUEN, Normandie Université, Laboratoire de Glycobiologie et Matrice Extracellulaire Végétale, SFR NORVEGE FED 4277, Carnot I2C, IRIB, Rouen, France
| | - Frank Jamois
- Centre Mondial de l’Innovation, Laboratoire Nutrition Végétale, Groupe Roullier, Saint-Malo, France
| | - Arnaud Lehner
- UNIROUEN, Normandie Université, Laboratoire de Glycobiologie et Matrice Extracellulaire Végétale, SFR NORVEGE FED 4277, Carnot I2C, IRIB, Rouen, France
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Van Pamel E, Cnops G, Van Droogenbroeck B, Delezie EC, Van Royen G, Vlaemynck GM, Aper J, Muylle H, Bekaert KM, Cooreman K, Robbens J, Delbare D, Roldan-Ruiz I, Crivits M, De Ruyck H, Herman L. Opportunities within the Agri-food System to Encourage a Nutritionally Balanced Diet – Part I. Food Reviews International 2021. [DOI: 10.1080/87559129.2020.1719504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Els Van Pamel
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Technology and Food Science Unit, Melle, Belgium
| | - Gerda Cnops
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Plant Sciences Unit, Melle, Belgium
| | - Bart Van Droogenbroeck
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Technology and Food Science Unit, Melle, Belgium
| | - Evelyne C. Delezie
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Animal Sciences Unit, Melle, Belgium
| | - Geert Van Royen
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Technology and Food Science Unit, Melle, Belgium
| | - Geertrui Mml Vlaemynck
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Technology and Food Science Unit, Melle, Belgium
| | - Jonas Aper
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Plant Sciences Unit, Melle, Belgium
| | - Hilde Muylle
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Plant Sciences Unit, Melle, Belgium
| | - Karen Mm Bekaert
- Flanders Research Institute for Agriculture Fisheries and Food (ILVO), Animal Sciences Unit, Oostende, Belgium
| | - Kris Cooreman
- Flanders Research Institute for Agriculture Fisheries and Food (ILVO), Animal Sciences Unit, Oostende, Belgium
| | - Johan Robbens
- Flanders Research Institute for Agriculture Fisheries and Food (ILVO), Animal Sciences Unit, Oostende, Belgium
| | - Daan Delbare
- Flanders Research Institute for Agriculture Fisheries and Food (ILVO), Animal Sciences Unit, Oostende, Belgium
| | - Isabel Roldan-Ruiz
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Plant Sciences Unit, Melle, Belgium
| | - Maarten Crivits
- Flanders Research Institute for Agriculture Fisheries and Food (ILVO), Social Sciences Unit, Merelbeke, Belgium
| | - Hendrik De Ruyck
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Technology and Food Science Unit, Melle, Belgium
| | - Lieve Herman
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Technology and Food Science Unit, Melle, Belgium
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8
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Zhou Y, Kim SY, Lee JS, Shin BK, Seo JA, Kim YS, Lee DY, Choi HK. Discrimination of the Geographical Origin of Soybeans Using NMR-Based Metabolomics. Foods 2021; 10:435. [PMID: 33671190 DOI: 10.3390/foods10020435] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 02/10/2021] [Accepted: 02/12/2021] [Indexed: 02/01/2023] Open
Abstract
With the increase in soybean trade between countries, the intentional mislabeling of the origin of soybeans has become a serious problem worldwide. In this study, metabolic profiling of soybeans from the Republic of Korea and China was performed by nuclear magnetic resonance (NMR) spectroscopy coupled with multivariate statistical analysis to predict the geographical origin of soybeans. The optimal orthogonal partial least squares-discriminant analysis (OPLS-DA) model was obtained using total area normalization and unit variance (UV) scaling, without applying the variable influences on projection (VIP) cut-off value, resulting in 96.9% sensitivity, 94.4% specificity, and 95.6% accuracy in the leave-one-out cross validation (LOO-CV) test for discriminating between Korean and Chinese soybeans. Soybeans from the northeastern, middle, and southern regions of China were successfully differentiated by standardized area normalization and UV scaling with a VIP cut-off value of 1.0, resulting in 100% sensitivity, 91.7%–100% specificity, and 94.4%–100% accuracy in a LOO-CV test. The methods employed in this study can be used to obtain essential information for the authentication of soybean samples from diverse geographical locations in future studies.
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Kim SY, Kim SY, Lee SM, Lee DY, Shin BK, Kang DJ, Choi HK, Kim YS. Discrimination of Cultivated Regions of Soybeans ( Glycine max) Based on Multivariate Data Analysis of Volatile Metabolite Profiles. Molecules 2020; 25:E763. [PMID: 32050669 PMCID: PMC7036852 DOI: 10.3390/molecules25030763] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 01/31/2020] [Accepted: 02/06/2020] [Indexed: 01/20/2023] Open
Abstract
Soybean (Glycine max) is a major crop cultivated in various regions and consumed globally. The formation of volatile compounds in soybeans is influenced by the cultivar as well as environmental factors, such as the climate and soil in the cultivation areas. This study used gas chromatography-mass spectrometry (GC-MS) combined by headspace solid-phase microextraction (HS-SPME) to analyze the volatile compounds of soybeans cultivated in Korea, China, and North America. The multivariate data analysis of partial least square-discriminant analysis (PLS-DA), and hierarchical clustering analysis (HCA) were then applied to GC-MS data sets. The soybeans could be clearly discriminated according to their geographical origins on the PLS-DA score plot. In particular, 25 volatile compounds, including terpenes (limonene, myrcene), esters (ethyl hexanoate, butyl butanoate, butyl prop-2-enoate, butyl acetate, butyl propanoate), aldehydes (nonanal, heptanal, (E)-hex-2-enal, (E)-hept-2-enal, acetaldehyde) were main contributors to the discrimination of soybeans cultivated in China from those cultivated in other regions in the PLS-DA score plot. On the other hand, 15 volatile compounds, such as 2-ethylhexan-1-ol, 2,5-dimethylhexan-2-ol, octanal, and heptanal, were related to Korean soybeans located on the negative PLS 2 axis, whereas 12 volatile compounds, such as oct-1-en-3-ol, heptan-4-ol, butyl butanoate, and butyl acetate, were responsible for North American soybeans. However, the multivariate statistical analysis (PLS-DA) was not able to clearly distinguish soybeans cultivated in Korea, except for those from the Gyeonggi and Kyeongsangbuk provinces.
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Affiliation(s)
- So-Yeon Kim
- Department of Food Science and Engineering, Ewha Womans University, Seoul 03760, Korea; (S.-Y.K.); (S.Y.K.); (S.M.L.)
| | - So Young Kim
- Department of Food Science and Engineering, Ewha Womans University, Seoul 03760, Korea; (S.-Y.K.); (S.Y.K.); (S.M.L.)
| | - Sang Mi Lee
- Department of Food Science and Engineering, Ewha Womans University, Seoul 03760, Korea; (S.-Y.K.); (S.Y.K.); (S.M.L.)
| | - Do Yup Lee
- Department of Agricultural Biotechnology, Research Institute for Agricultural and Life Sciences, Seoul National University, Seoul 08779, Korea;
| | - Byeung Kon Shin
- National Agricultural Products Quality Management Service, Gimcheon 39660, Korea; (B.K.S.); (D.J.K.)
| | - Dong Jin Kang
- National Agricultural Products Quality Management Service, Gimcheon 39660, Korea; (B.K.S.); (D.J.K.)
| | | | - Young-Suk Kim
- Department of Food Science and Engineering, Ewha Womans University, Seoul 03760, Korea; (S.-Y.K.); (S.Y.K.); (S.M.L.)
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Sedivy EJ, Wu F, Hanzawa Y. Soybean domestication: the origin, genetic architecture and molecular bases. New Phytol 2017; 214:539-553. [PMID: 28134435 DOI: 10.1111/nph.14418] [Citation(s) in RCA: 108] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2016] [Accepted: 11/28/2016] [Indexed: 05/20/2023]
Abstract
Domestication provides an important model for the study of evolution, and information learned from domestication research aids in the continued improvement of crop species. Recent progress in de novo assembly and whole-genome resequencing of wild and cultivated soybean genomes, in addition to new archeological discoveries, sheds light on the origin of this important crop and provides a clearer view on the modes of artificial selection that drove soybean domestication and diversification. This novel genomic information enables the search for polymorphisms that underlie variation in agronomic traits and highlights genes that exhibit a signature of selection, leading to the identification of a number of candidate genes that may have played important roles in soybean domestication, diversification and improvement. These discoveries provide a novel point of comparison on the evolutionary bases of important agronomic traits among different crop species.
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Affiliation(s)
- Eric J Sedivy
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Faqiang Wu
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Yoshie Hanzawa
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
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Li J, Wang X, Song W, Huang X, Zhou J, Zeng H, Sun S, Jia H, Li W, Zhou X, Li S, Chen P, Wu C, Guo Y, Han T, Qiu L. Genetic variation of maturity groups and four E genes in the Chinese soybean mini core collection. PLoS One 2017; 12:e0172106. [PMID: 28207889 PMCID: PMC5312940 DOI: 10.1371/journal.pone.0172106] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 01/31/2017] [Indexed: 11/19/2022] Open
Abstract
The mini core collection (MCC) has been established by streamlining core collection (CC) chosen from China National Genebank including 23,587 soybean (Glycine max) accessions by morphological traits and simple sequence repeat (SSR) markers. Few studies have been focused on the maturity that has been considered as one of the most critical traits for the determination of the adaptation-growing region of the soybean. In the current study, two hundred and ninty-nine accessions of MCC planted for two years at four locations namely in Heihe, Harbin, Jining and Wuhan cities in China were used to assess the variation of maturity in MCC and identify the integrated effect of 4 E loci on flowering and maturity time in soybean. Forty-two North American varieties served as references of maturity groups (MG). Each accession in MCC was classified by comparing with the MG references in the days from VE (emergence) and physiological maturity (R7). The results showed that MCC covered a large range of MGs from MG000 to MGIX/X. Original locations and sowing types were revealed as the major affecting factors for maturity groups of the MCC accessions. The ratio of the reproductive period to the vegetative period (R/V) varied among MCC accessions. Genotyping of 4 maturity genes (i.e. E1, E2, E3 and E4) in 228 accessions indicated that recessive alleles e1, e2, e3 and e4 promoted earlier flowering and shortened the maturity time with different effects, while the dominate alleles were always detected in accessions with longer maturity. The allelic combinations determined the diversification of soybean maturity groups and adaptation to different regions. Our results indicated that the maturity of Chinese soybean MCC showed genetic diversities in phenotype and genotype, which provided information for further MG classification, geographic adaptation analysis of Chinese soybean cultivars, as well as developing new soybean varieties with adaptation to specific regions.
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Affiliation(s)
- Jicun Li
- MOA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
- Jining Academy of Agricultural Sciences, Jining, Shandong, China
| | - Xiaobo Wang
- MOA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
- School of Agronomy, Anhui Agricultural University, Hefei, China
| | - Wenwen Song
- MOA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xinyang Huang
- Jining Academy of Agricultural Sciences, Jining, Shandong, China
| | - Jing Zhou
- Jining Academy of Agricultural Sciences, Jining, Shandong, China
| | - Haiyan Zeng
- MOA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shi Sun
- MOA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hongchang Jia
- Heihe Branch of Heilongjiang Academy of Agricultural Sciences, Heihe, China
| | - Wenbin Li
- College of Agronomy, Northeast Agricultural University, Harbin, China
| | - Xinan Zhou
- Oil Crops Research Institute, Chinese Academy of Agricultural Science, Wuhan, China
| | - Suzhen Li
- Jining Academy of Agricultural Sciences, Jining, Shandong, China
| | - Pengyin Chen
- Department of Crop, Soil and Environmental Sciences, University of Arkansas, Fayetteville, Arkansas, United States of America
| | - Cunxiang Wu
- MOA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yong Guo
- MOA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Tianfu Han
- MOA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lijuan Qiu
- MOA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
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Htwe NMPS, Luo ZQ, Jin LG, Nadon B, Wang KJ, Qiu LJ. Functional marker development of miR1511-InDel and allelic diversity within the genus Glycine. BMC Genomics 2015; 16:467. [PMID: 26084707 PMCID: PMC4470002 DOI: 10.1186/s12864-015-1665-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 05/29/2015] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Single-stranded non-protein coding small RNAs, 18-25 nucleotides in length, are ubiquitous throughout plants genomes and are involved in post-transcriptional gene regulation. Several types of DNA markers have been reported for the detection of genetic diversity or sequence variation in soybean, one of the most important legume crops in worldwide for seed protein and oil content. Recently, with the available of public genomic databases, there has been a shift from the labor-intensive development of PCR-based markers to sequence-based genotyping and the development of functional markers within genes, often coupled with the use of RNA information. But thus far miRNA-based markers have been only developed in rice and tobacco. Here we report the first functional molecular miRNA marker, miR1511-InDel, in soybean for a specific single copy locus used to assess genetic variation in domesticated soybean (Glycine max [L.] Merr) and its wild progenitor (Glycine soja Sieb. & Zucc.). RESULTS We genotyped a total of 1,669 accessions of domesticated soybean (G. max) and its wild progenitor G. soja which are native throughout the China and parts of Korea, Japan and Russia. The results indicate that the miR1511 locus is distributed in cultivated soybean and has three alleles in annual wild soybean. Based on this result, we proposed that miR-InDel marker technology can be used to assess genetic variation. The inclusion of geo-reference data with miR1511-InDel marker data corroborated that accessions from the Yellow River basin (Huanghuai) exhibited high genetic diversity which provides more molecular evidence for gene diversity in annual wild soybean and domestication of soybean. CONCLUSIONS These results provide evidence for the use of RNA marker, miRNA1511-InDel, as a soybean-specific functional maker for the study of genetic diversity, genotyping of germplasm and evolution studies. This is also the first report of functional marker developed from soybean miRNA located within the functional region of pre-miRNA1511.
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Affiliation(s)
- Nang Myint Phyu Sin Htwe
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, 100081, Beijing, China.
| | - Zhong-Qin Luo
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, 100081, Beijing, China.
| | - Long-Guo Jin
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, 100081, Beijing, China.
| | - Brian Nadon
- Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, Athens, GA, USA.
| | - Ke-Jing Wang
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, 100081, Beijing, China.
| | - Li-Juan Qiu
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, 100081, Beijing, China.
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Wang F, Wang H, Wang D, Fang F, Lai J, Wu T, Tsao R. Isoflavone, γ-aminobutyric acid contents and antioxidant activities are significantly increased during germination of three Chinese soybean cultivars. J Funct Foods 2015. [DOI: 10.1016/j.jff.2015.02.016] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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Lanes ÉCM, Motoike SY, Kuki KN, Nick C, Freitas RD. Molecular characterization and population structure of the macaw palm, Acrocomia aculeata (Arecaceae), ex situ germplasm collection using microsatellites markers. J Hered 2014; 106:102-12. [PMID: 25425677 DOI: 10.1093/jhered/esu073] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The Acrocomia aculeata is one of the most promising plants for sustainable production of renewable energy. In order to understand patterns of the distribution of the allelic diversity of A. aculeata ex situ germplasm collection, the present study investigated the hypothesis that the genetic variability of the accessions may match their geographical origin. A genotypic analysis of 77 A. aculeata accessions was conducted with 6 simple sequence repeat markers. A high degree of molecular diversity among the accessions was found, with an average of 9 alleles per locus and a polymorphic information content with a mean of 0.76. A total of 4 clusters was identified by the Bayesian analysis of population structure. The highest subpopulation diversity was identified in Pop1, mainly formed by accessions from State of Mato Grosso do Sul. The populations Pop2A, Pop2B, and Pop2C, all from the State of Minas Gerais, showed high genetic variability as determined by a higher F st, and a wide genetic variance, which were identified within and among the population by analysis of molecular variance. Based on our results and on Vavilov's theory on crop origins, one possible diversity center for A. aculeata is proposed to be in a region in southeast Brazil.
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Affiliation(s)
- Éder C M Lanes
- From the Laboratory of Biotechnology and Plant Breeding, Federal University of Viçosa, Viçosa MG 36570-000, Brazil (Lanes, Motoike, and Freitas); and Department of Plant Science, Federal University of Viçosa, Viçosa MG 36570-000, Brazil (Motoike, Kuki, and Nick).
| | - Sérgio Y Motoike
- From the Laboratory of Biotechnology and Plant Breeding, Federal University of Viçosa, Viçosa MG 36570-000, Brazil (Lanes, Motoike, and Freitas); and Department of Plant Science, Federal University of Viçosa, Viçosa MG 36570-000, Brazil (Motoike, Kuki, and Nick)
| | - Kacilda N Kuki
- From the Laboratory of Biotechnology and Plant Breeding, Federal University of Viçosa, Viçosa MG 36570-000, Brazil (Lanes, Motoike, and Freitas); and Department of Plant Science, Federal University of Viçosa, Viçosa MG 36570-000, Brazil (Motoike, Kuki, and Nick)
| | - Carlos Nick
- From the Laboratory of Biotechnology and Plant Breeding, Federal University of Viçosa, Viçosa MG 36570-000, Brazil (Lanes, Motoike, and Freitas); and Department of Plant Science, Federal University of Viçosa, Viçosa MG 36570-000, Brazil (Motoike, Kuki, and Nick)
| | - Renata D Freitas
- From the Laboratory of Biotechnology and Plant Breeding, Federal University of Viçosa, Viçosa MG 36570-000, Brazil (Lanes, Motoike, and Freitas); and Department of Plant Science, Federal University of Viçosa, Viçosa MG 36570-000, Brazil (Motoike, Kuki, and Nick)
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15
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Korir PC, Zhang J, Wu K, Zhao T, Gai J. Association mapping combined with linkage analysis for aluminum tolerance among soybean cultivars released in Yellow and Changjiang River Valleys in China. Theor Appl Genet 2013; 126:1659-75. [PMID: 23515677 DOI: 10.1007/s00122-013-2082-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2012] [Accepted: 03/01/2013] [Indexed: 05/03/2023]
Abstract
Association mapping (AM) combined with linkage mapping (LM) was executed to identify molecular markers and QTL regions associated with aluminum (Al) tolerance using relative root elongation (RRE) in hydroponics as an indicator. A set of 188 soybean cultivars released in Yellow and Changjiang River Valleys and 184 recombinant inbred lines (RIL) derived from a cross KF No. 1 (tolerant) × NN1138-2 (susceptible) was used in the study. Inheritance analysis of the RIL population suggested four major genes and polygenes controlled Al-tolerance. Further, LM indicated four additive and four epistatic QTL pairs plus a collective unmapped minor QTL were responsible for Al-tolerance and explained 29.39, 18.75 and 43.07 % of the phenotypic variation (PV), respectively. In the set of released cultivars, AM identified 11 markers significant at P < 0.03 that explained 85.2 % of PV with six of which at P < 0.01 accounted for 57.9 % of PV. Ten of these eleven AM marker-QTL were mapped within range of ~2.0 cM to ~43.0 cM outside confidence interval of respective Al-tolerance QTL in previous studies. Five markers, Satt209, Sat_364, Sat_240, Sct_190 and Satt284, were located near Al-tolerance QTL regions in this and previous LM studies. Thus, the two methods confirmed these markers as being the most likely candidate regions for Al-tolerance. Allele effects relative to the population mean for the 11 QTL were estimated, and the allele A210 of Satt209 showed greatest phenotypic effect on Al-tolerance. The two most favorable alleles from each of the 11 marker loci and their carriers were identified, and accordingly the genetic constitution of Al-tolerance for the 188 cultivars was dissected as a QTL-allele matrix. Therefore, marker-assisted pairing of crosses and marker-assisted selection of progenies can be carried out to pyramid favorable alleles of all the 11 loci. This marker-assisted breeding procedure was designated as breeding by design using a QTL-allele matrix.
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Affiliation(s)
- Paul C Korir
- Soybean Research Institute, Nanjing Agricultural University, Nanjing 210095, China
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Wang C, Jia G, Zhi H, Niu Z, Chai Y, Li W, Wang Y, Li H, Lu P, Zhao B, Diao X. Genetic diversity and population structure of Chinese foxtail millet [Setaria italica (L.) Beauv.] landraces. G3 (Bethesda) 2012; 2:769-77. [PMID: 22870400 DOI: 10.1534/g3.112.002907] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2011] [Accepted: 05/03/2012] [Indexed: 01/07/2023]
Abstract
As an ancient cereal of great importance for dryland agriculture even today, foxtail millet (Setaria italica) is fast becoming a new plant genomic model crop. A genotypic analysis of 250 foxtail millet landraces, which represent 1% of foxtail millet germplasm kept in the Chinese National Gene Bank (CNGB), was conducted with 77 SSRs covering the foxtail millet genome. A high degree of molecular diversity among the landraces was found, with an average of 20.9 alleles per locus detected. STRUCTURE, neighbor-jointing, and principal components analyses classify the accessions into three clusters (topmost hierarchy) and, ultimately, four conservative subgroups (substructuring within the topmost clusters) in total, which are in good accordance with eco-geographical distribution in China. The highest subpopulation diversity was identified in the accessions of Pop3 from the middle regions of the Yellow River, followed by accessions in Pop1 from the downstream regions of the Yellow River, suggesting that foxtail millet was domesticated in the Yellow River drainage area first and then spread to other parts of the country. Linkage disequilibrium (LD) decay of less than 20 cM of genetic distance in the foxtail millet landrace genome was observed, which suggests that it could be possible to achieve resolution down to the 20 cM level for association mapping.
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Kaga A, Shimizu T, Watanabe S, Tsubokura Y, Katayose Y, Harada K, Vaughan DA, Tomooka N. Evaluation of soybean germplasm conserved in NIAS genebank and development of mini core collections. Breed Sci 2012; 61:566-92. [PMID: 23136496 PMCID: PMC3406788 DOI: 10.1270/jsbbs.61.566] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2011] [Accepted: 11/24/2011] [Indexed: 05/09/2023]
Abstract
Genetic variation and population structure among 1603 soybean accessions, consisted of 832 Japanese landraces, 109 old and 57 recent Japanese varieties, 341 landrace from 16 Asian countries and 264 wild soybean accessions, were characterized using 191 SNP markers. Although gene diversity of Japanese soybean germplasm was slight lower than that of exotic soybean germplasm, population differentiation and clustering analyses indicated clear genetic differentiation among Japanese cultivated soybeans, exotic cultivated soybeans and wild soybeans. Nine hundred ninety eight Japanese accessions were separated to a certain extent into groups corresponding to their agro-morphologic characteristics such as photosensitivity and seed characteristics rather than their geographical origin. Based on the assessment of the SNP markers and several agro-morphologic traits, accessions that retain gene diversity of the whole collection were selected to develop several soybean sets of different sizes using an heuristic approach; a minimum of 12 accessions can represent the observed gene diversity; a mini-core collection of 96 accession can represent a major proportion of both geographic origin and agro-morphologic trait variation. These selected sets of germplasm will provide an effective platform for enhancing soybean diversity studies and assist in finding novel traits for crop improvement.
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Affiliation(s)
- Akito Kaga
- National Institute of Agrobiological Sciences, Kannondai 2-1-2, Tsukuba, Ibaraki 305-8602, Japan
| | - Takehiko Shimizu
- National Institute of Agrobiological Sciences, Kannondai 2-1-2, Tsukuba, Ibaraki 305-8602, Japan
- Institute of Society for Techno-Innovation of Agriculture, Forestry and Fisheries, Kamiyokoba Ippaizuka 446-1, Tsukuba, Ibaraki 305-0854, Japan
| | - Satoshi Watanabe
- National Institute of Agrobiological Sciences, Kannondai 2-1-2, Tsukuba, Ibaraki 305-8602, Japan
| | - Yasutaka Tsubokura
- National Institute of Agrobiological Sciences, Kannondai 2-1-2, Tsukuba, Ibaraki 305-8602, Japan
| | - Yuichi Katayose
- National Institute of Agrobiological Sciences, Kannondai 2-1-2, Tsukuba, Ibaraki 305-8602, Japan
| | - Kyuya Harada
- National Institute of Agrobiological Sciences, Kannondai 2-1-2, Tsukuba, Ibaraki 305-8602, Japan
| | - Duncan A. Vaughan
- National Institute of Agrobiological Sciences, Kannondai 2-1-2, Tsukuba, Ibaraki 305-8602, Japan
| | - Norihiko Tomooka
- National Institute of Agrobiological Sciences, Kannondai 2-1-2, Tsukuba, Ibaraki 305-8602, Japan
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Abstract
The recently acquired archaeological record for soybean from Japan, China and Korea is shedding light on the context in which this important economic plant became associated with people and was domesticated. This paper examines archaeological (charred) soybean seed size variation to determine what insight can be gained from a comprehensive comparison of 949 specimens from 22 sites. Seed length alone appears to represent seed size change through time, although the length × width × thickness product has the potential to provide better size change resolution. A widespread early association of small seeded soybean is as old as 9000-8600 cal BP in northern China and 7000 cal BP in Japan. Direct AMS radiocarbon dates on charred soybean seeds indicate selection resulted in large seed sizes in Japan by 5000 cal BP (Middle Jomon) and in Korea by 3000 cal BP (Early Mumun). Soybean seeds recovered in China from the Shang through Han periods are similar in length to the large Korean and Japanese specimens, but the overall size of the large Middle and Late Jomon, Early Mumun through Three Kingdom seeds is significantly larger than any of the Chinese specimens. The archaeological record appears to disconfirm the hypothesis of a single domestication of soybean and supports the view informed by recent phyologenetic research that soybean was domesticated in several locations in East Asia.
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Affiliation(s)
- Gyoung-Ah Lee
- Department of Anthropology, University of Oregon, Eugene, Oregon, United States of America.
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Li YH, Li W, Zhang C, Yang L, Chang RZ, Gaut BS, Qiu LJ. Genetic diversity in domesticated soybean (Glycine max) and its wild progenitor (Glycine soja) for simple sequence repeat and single-nucleotide polymorphism loci. New Phytol 2010; 188:242-53. [PMID: 20618914 DOI: 10.1111/j.1469-8137.2010.03344.x] [Citation(s) in RCA: 100] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
• The study of genetic diversity between a crop and its wild relatives may yield fundamental insights into evolutionary history and the process of domestication. • In this study, we genotyped a sample of 303 accessions of domesticated soybean (Glycine max) and its wild progenitor Glycine soja with 99 microsatellite markers and 554 single-nucleotide polymorphism (SNP) markers. • The simple sequence repeat (SSR) loci averaged 21.5 alleles per locus and overall Nei's gene diversity of 0.77. The SNPs had substantially lower genetic diversity (0.35) than SSRs. A SSR analyses indicated that G. soja exhibited higher diversity than G. max, but SNPs provided a slightly different snapshot of diversity between the two taxa. For both marker types, the primary division of genetic diversity was between the wild and domesticated accessions. Within taxa, G. max consisted of four geographic regions in China. G. soja formed six subgroups. Genealogical analyses indicated that cultivated soybean tended to form a monophyletic clade with respect to G. soja. • G. soja and G. max represent distinct germplasm pools. Limited evidence of admixture was discovered between these two species. Overall, our analyses are consistent with the origin of G. max from regions along the Yellow River of China.
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Affiliation(s)
- Ying-Hui Li
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Lab of Germplasm Utilization (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, 100081 Beijing, China
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20
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Guo J, Wang Y, Song C, Zhou J, Qiu L, Huang H, Wang Y. A single origin and moderate bottleneck during domestication of soybean (Glycine max): implications from microsatellites and nucleotide sequences. Ann Bot 2010; 106:505-14. [PMID: 20566681 PMCID: PMC2924825 DOI: 10.1093/aob/mcq125] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2010] [Revised: 04/19/2010] [Accepted: 05/13/2010] [Indexed: 05/03/2023]
Abstract
Background and Aims It is essential to illuminate the evolutionary history of crop domestication in order to understand further the origin and development of modern cultivation and agronomy; however, despite being one of the most important crops, the domestication origin and bottleneck of soybean (Glycine max) are poorly understood. In the present study, microsatellites and nucleotide sequences were employed to elucidate the domestication genetics of soybean. Methods The genomes of 79 landrace soybeans (endemic cultivated soybeans) and 231 wild soybeans (G. soja) that represented the species-wide distribution of wild soybean in East Asia were scanned with 56 microsatellites to identify the genetic structure and domestication origin of soybean. To understand better the domestication bottleneck, four nucleotide sequences were selected to simulate the domestication bottleneck. Key Results Model-based analysis revealed that most of the landrace genotypes were assigned to the inferred wild soybean cluster of south China, South Korea and Japan. Phylogeny for wild and landrace soybeans showed that all landrace soybeans formed a single cluster supporting a monophyletic origin of all the cultivars. The populations of the nearest branches which were basal to the cultivar lineage were wild soybeans from south China. The coalescent simulation detected a bottleneck severity of K' = 2 during soybean domestication, which could be explained by a foundation population of 6000 individuals if domestication duration lasted 3000 years. Conclusions As a result of integrating geographic distribution with microsatellite genotype assignment and phylogeny between landrace and wild soybeans, a single origin of soybean in south China is proposed. The coalescent simulation revealed a moderate genetic bottleneck with an effective wild soybean population used for domestication estimated to be approximately 2 % of the total number of ancestral wild soybeans. Wild soybeans in Asia, especially in south China, contain tremendous genetic resources for cultivar improvement.
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Affiliation(s)
- Juan Guo
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, the Chinese Academy of Sciences, Wuhan, Hubei 430074, China
| | - Yunsheng Wang
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, the Chinese Academy of Sciences, Wuhan, Hubei 430074, China
| | - Chi Song
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, the Chinese Academy of Sciences, Wuhan, Hubei 430074, China
| | - Jianfeng Zhou
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, the Chinese Academy of Sciences, Wuhan, Hubei 430074, China
| | - Lijuan Qiu
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Lab of Germplasm & Biotechnology (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 10081, China
| | - Hongwen Huang
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, the Chinese Academy of Sciences, Wuhan, Hubei 430074, China
| | - Ying Wang
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, the Chinese Academy of Sciences, Wuhan, Hubei 430074, China
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Zinn KE, Tunc-Ozdemir M, Harper JF. Temperature stress and plant sexual reproduction: uncovering the weakest links. J Exp Bot 2010; 61:1959-68. [PMID: 20351019 PMCID: PMC2917059 DOI: 10.1093/jxb/erq053] [Citation(s) in RCA: 316] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2009] [Revised: 02/11/2010] [Accepted: 02/15/2010] [Indexed: 05/18/2023]
Abstract
The reproductive (gametophytic) phase in flowering plants is often highly sensitive to hot or cold temperature stresses, with even a single hot day or cold night sometimes being fatal to reproductive success. This review describes studies of temperature stress on several crop plants, which suggest that pollen development and fertilization may often be the most sensitive reproductive stage. Transcriptome and proteomic studies on several plant species are beginning to identify stress response pathways that function during pollen development. An example is provided here of genotypic differences in the reproductive stress tolerance between two ecotypes of Arabidopsis thaliana Columbia (Col) and Hilversum (Hi-0), when reproducing under conditions of hot days and cold nights. Hi-0 exhibited a more severe reduction in seed set, correlated with a reduction in pollen tube growth potential and tropism defects. Hi-0 thus provides an Arabidopsis model to investigate strategies for improved stress tolerance in pollen. Understanding how different plants cope with stress during reproductive development offers the potential to identify genetic traits that could be manipulated to improve temperature tolerance in selected crop species being cultivated in marginal climates.
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Affiliation(s)
| | | | - Jeffrey F. Harper
- Biochemistry Department MS200, University of Nevada, Reno, NV 89557, USA
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Li Y, Guan R, Liu Z, Ma Y, Wang L, Li L, Lin F, Luan W, Chen P, Yan Z, Guan Y, Zhu L, Ning X, Smulders MJM, Li W, Piao R, Cui Y, Yu Z, Guan M, Chang R, Hou A, Shi A, Zhang B, Zhu S, Qiu L. Genetic structure and diversity of cultivated soybean (Glycine max (L.) Merr.) landraces in China. Theor Appl Genet 2008; 117:857-71. [PMID: 18587557 DOI: 10.1007/s00122-008-0825-0] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2007] [Accepted: 06/08/2008] [Indexed: 05/10/2023]
Abstract
The Chinese genebank contains 23,587 soybean landraces collected from 29 provinces. In this study, a representative collection of 1,863 landraces were assessed for genetic diversity and genetic differentiation in order to provide useful information for effective management and utilization. A total of 1,160 SSR alleles at 59 SSR loci were detected including 97 unique and 485 low-frequency alleles, which indicated great richness and uniqueness of genetic variation in this core collection. Seven clusters were inferred by STRUCTURE analysis, which is in good agreement with a neighbor-joining tree. The cluster subdivision was also supported by highly significant pairwise Fst values and was generally in accordance with differences in planting area and sowing season. The cluster HSuM, which contains accessions collected from the region between 32.0 and 40.5 degrees N, 105.4 and 122.2 degrees E along the central and downstream parts of the Yellow River, was the most genetically diverse of the seven clusters. This provides the first molecular evidence for the hypotheses that the origin of cultivated soybean is the Yellow River region. A high proportion (95.1%) of pairs of alleles from different loci was in LD in the complete dataset. This was mostly due to overall population structure, since the number of locus pairs in LD was reduced sharply within each of the clusters compared to the complete dataset. This shows that population structure needs to be accounted for in association studies conducted within this collection. The low value of LD within the clusters can be seen as evidence that much of the recombination events in the past have been maintained in soybean, fixed in homozygous self-fertilizing landraces.
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Affiliation(s)
- Yinghui Li
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Lab of Germplasm and Biotechnology (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, 100081 Beijing, People's Republic of China
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Kassem MA, Shultz J, Meksem K, Cho Y, Wood AJ, Iqbal MJ, Lightfoot DA. An updated 'Essex' by 'Forrest' linkage map and first composite interval map of QTL underlying six soybean traits. Theor Appl Genet 2006; 113:1015-26. [PMID: 16953420 DOI: 10.1007/s00122-006-0361-8] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2006] [Accepted: 06/26/2006] [Indexed: 05/11/2023]
Abstract
DNA marker maps based on single populations are the basis for gene, loci and genomic analyses. Individual maps can be integrated to produce composite maps with higher marker densities if shared marker orders are consistent. However, estimates of marker order in composite maps must include sets of markers that were not polymorphic in multiple populations. Often some of the pooled markers were not codominant, or were not correctly scored. The soybean composite map was composed of data from five separate populations based on northern US germplasm but does not yet include 'Essex' by 'Forrest' recombinant inbred line (RIL) population (E x F) or any southern US soybean cultivars. The objectives were, to update the E x F map with codominant markers, to compare marker orders among this map, the Forrest physical map and the composite soybean map and to compare QTL identified by composite interval maps to the earlier interval maps. Two hundred and thirty seven markers were used to construct the core of the E x F map. The majority of marker orders were consistent between the maps. However, 19 putative marker inversions were detected on 12 of 20 linkage groups (LG). Eleven marker distance compressions were also found. The number of inverted markers ranged from 1 to 2 per LG. Thus, marker order inversions may be common in southern compared to northern US germplasm. A total of 61 QTL among 37 measures of six traits were detected by composite interval maps, interval maps and single point analysis. Seventeen of the QTL found in composite intervals had previously been detected among the 29 QTL found in simple interval maps. The genomic locations of the known QTL were more closely delimited. A genome sequencing project to compare Southern and Northern US soybean cultivars would catalog and delimit inverted regions and the associated QTL. Gene introgression in cultivar development programs would be accelerated.
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Affiliation(s)
- M A Kassem
- Plant Biotechnology and Genomics Core-Facility, Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA
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