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Fang C, Du H, Wang L, Liu B, Kong F. Mechanisms underlying key agronomic traits and implications for molecular breeding in soybean. J Genet Genomics 2024; 51:379-393. [PMID: 37717820 DOI: 10.1016/j.jgg.2023.09.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 09/05/2023] [Accepted: 09/05/2023] [Indexed: 09/19/2023]
Abstract
Soybean (Glycine max [L.] Merr.) is an important crop that provides protein and vegetable oil for human consumption. As soybean is a photoperiod-sensitive crop, its cultivation and yield are limited by the photoperiodic conditions in the field. In contrast to other major crops, soybean has a special plant architecture and a special symbiotic nitrogen fixation system, representing two unique breeding directions. Thus, flowering time, plant architecture, and symbiotic nitrogen fixation are three critical or unique yield-determining factors. This review summarizes the progress made in our understanding of these three critical yield-determining factors in soybean. Meanwhile, we propose potential research directions to increase soybean production, discuss the application of genomics and genomic-assisted breeding, and explore research directions to address future challenges, particularly those posed by global climate changes.
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Affiliation(s)
- Chao Fang
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, Guangdong 510006, China
| | - Haiping Du
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, Guangdong 510006, China
| | - Lingshuang Wang
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, Guangdong 510006, China
| | - Baohui Liu
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, Guangdong 510006, China
| | - Fanjiang Kong
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, Guangdong 510006, China.
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2
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Liang X, Li J, Yang Y, Jiang C, Guo Y. Designing salt stress-resilient crops: Current progress and future challenges. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:303-329. [PMID: 38108117 DOI: 10.1111/jipb.13599] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 12/10/2023] [Accepted: 12/15/2023] [Indexed: 12/19/2023]
Abstract
Excess soil salinity affects large regions of land and is a major hindrance to crop production worldwide. Therefore, understanding the molecular mechanisms of plant salt tolerance has scientific importance and practical significance. In recent decades, studies have characterized hundreds of genes associated with plant responses to salt stress in different plant species. These studies have substantially advanced our molecular and genetic understanding of salt tolerance in plants and have introduced an era of molecular design breeding of salt-tolerant crops. This review summarizes our current knowledge of plant salt tolerance, emphasizing advances in elucidating the molecular mechanisms of osmotic stress tolerance, salt-ion transport and compartmentalization, oxidative stress tolerance, alkaline stress tolerance, and the trade-off between growth and salt tolerance. We also examine recent advances in understanding natural variation in the salt tolerance of crops and discuss possible strategies and challenges for designing salt stress-resilient crops. We focus on the model plant Arabidopsis (Arabidopsis thaliana) and the four most-studied crops: rice (Oryza sativa), wheat (Triticum aestivum), maize (Zea mays), and soybean (Glycine max).
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Affiliation(s)
- Xiaoyan Liang
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, 100094, China
| | - Jianfang Li
- State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100194, China
| | - Yongqing Yang
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, 100094, China
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, 100094, China
| | - Caifu Jiang
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, 100094, China
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, 100094, China
- Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing, 100193, China
| | - Yan Guo
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, 100094, China
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, 100094, China
- Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing, 100193, China
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Phosuwan S, Nounjan N, Theerakulpisut P, Siangliw M, Charoensawan V. Comparative quantitative trait loci analysis framework reveals relationships between salt stress responsive phenotypes and pathways. FRONTIERS IN PLANT SCIENCE 2024; 15:1264909. [PMID: 38463565 PMCID: PMC10920293 DOI: 10.3389/fpls.2024.1264909] [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: 07/21/2023] [Accepted: 02/07/2024] [Indexed: 03/12/2024]
Abstract
Soil salinity is a complex abiotic stress that involves several biological pathways. Hence, focusing on a specific or a few salt-tolerant phenotypes is unlikely to provide comprehensive insights into the intricate and interwinding mechanisms that regulate salt responsiveness. In this study, we develop a heuristic framework for systematically integrating and comprehensively evaluating quantitative trait loci (QTL) analyses from multiple stress-related traits obtained by different studies. Making use of a combined set of 46 salinity-related traits from three independent studies that were based on the same chromosome segment substitution line (CSSL) population of rice (Oryza sativa), we demonstrate how our approach can address technical biases and limitations from different QTL studies and calling methods. This allows us to compile a comprehensive list of trait-specific and multi-trait QTLs, as well as salinity-related candidate genes. In doing so, we discover several novel relationships between traits that demonstrate similar trends of phenotype scores across the CSSLs, as well as the similarities between genomic locations that the traits were mapped to. Finally, we experimentally validate our findings by expression analyses and functional validations of several selected candidate genes from multiple pathways in rice and Arabidopsis orthologous genes, including OsKS7 (ENT-KAURENE SYNTHASE 7), OsNUC1 (NUCLEOLIN 1) and OsFRO1 (FERRIC REDUCTASE OXIDASE 1) to name a few. This work not only introduces a novel approach for conducting comparative analyses of multiple QTLs, but also provides a list of candidate genes and testable hypotheses for salinity-related mechanisms across several biological pathways.
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Affiliation(s)
- Sunadda Phosuwan
- Doctor of Philosophy Program in Biochemistry (International Program), Faculty of Science, Mahidol University, Bangkok, Thailand
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Noppawan Nounjan
- Biodiversity and Environmental Management Division, International College, Khon Kaen University, Khon Kaen, Thailand
| | - Piyada Theerakulpisut
- Salt-tolerant Rice Research Group, Department of Biology, Faculty of Science, Khon Kaen University, Khon Kaen, Thailand
| | - Meechai Siangliw
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Luang, Thailand
| | - Varodom Charoensawan
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand
- Integrative Computational BioScience (ICBS) Center, Mahidol University, Nakhon Pathom, Thailand
- Division of Medical Bioinformatics, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Siriraj Genomics, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- School of Chemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima, Thailand
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4
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Li Y, Ye H, Vuong TD, Zhou L, Do TD, Satish Chhapekar S, Zhao W, Li B, Jin T, Gu J, Li C, Chen Y, Li Y, Wang ZY, Nguyen HT. A novel natural variation in the promoter of GmCHX1 regulates conditional gene expression to improve salt tolerance in soybean. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:1051-1062. [PMID: 37864556 PMCID: PMC10837011 DOI: 10.1093/jxb/erad404] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 10/20/2023] [Indexed: 10/23/2023]
Abstract
Identification and characterization of soybean germplasm and gene(s)/allele(s) for salt tolerance is an effective way to develop improved varieties for saline soils. Previous studies identified GmCHX1 (Glyma03g32900) as a major salt tolerance gene in soybean, and two main functional variations were found in the promoter region (148/150 bp insertion) and the third exon with a retrotransposon insertion (3.78 kb). In the current study, we identified four salt-tolerant soybean lines, including PI 483460B (Glycine soja), carrying the previously identified salt-sensitive variations at GmCHX1, suggesting new gene(s) or new functional allele(s) of GmCHX1 in these soybean lines. Subsequently, we conducted quantitative trait locus (QTL) mapping in a recombinant-inbred line population (Williams 82 (salt-sensitive) × PI 483460B) to identify the new salt tolerance loci/alleles. A new locus, qSalt_Gm18, was mapped on chromosome 18 associated with leaf scorch score. Another major QTL, qSalt_Gm03, was identified to be associated with chlorophyll content ratio and leaf scorch score in the same chromosomal region of GmCHX1 on chromosome 3. Novel variations in a STRE (stress response element) cis-element in the promoter region of GmCHX1 were found to regulate the salt-inducible expression of the gene in these four newly identified salt-tolerant lines including PI 483460B. This new allele of GmCHX1 with salt-inducible expression pattern provides an energy cost efficient (conditional gene expression) strategy to protect soybean yield in saline soils without yield penalty under non-stress conditions. Our results suggest that there might be no other major salt tolerance locus similar to GmCHX1 in soybean germplasm, and further improvement of salt tolerance in soybean may rely on gene-editing techniques instead of looking for natural variations.
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Affiliation(s)
- Yang Li
- Institute of Nanfan & Seed Industry, Guangdong Academy of Science, Guangzhou, 510316, China
- Division of Plant Science and Technology, University of Missouri, Columbia, MO 65211, USA
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Heng Ye
- Division of Plant Science and Technology, University of Missouri, Columbia, MO 65211, USA
| | - Tri D Vuong
- Division of Plant Science and Technology, University of Missouri, Columbia, MO 65211, USA
| | - Lijuan Zhou
- Division of Plant Science and Technology, University of Missouri, Columbia, MO 65211, USA
| | - Tuyen D Do
- Division of Plant Science and Technology, University of Missouri, Columbia, MO 65211, USA
| | | | - Wenqian Zhao
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Bin Li
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ting Jin
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jinbao Gu
- Institute of Nanfan & Seed Industry, Guangdong Academy of Science, Guangzhou, 510316, China
| | - Cong Li
- Institute of Nanfan & Seed Industry, Guangdong Academy of Science, Guangzhou, 510316, China
| | - Yanhang Chen
- Institute of Nanfan & Seed Industry, Guangdong Academy of Science, Guangzhou, 510316, China
| | - Yan Li
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhen-Yu Wang
- Institute of Nanfan & Seed Industry, Guangdong Academy of Science, Guangzhou, 510316, China
| | - Henry T Nguyen
- Division of Plant Science and Technology, University of Missouri, Columbia, MO 65211, USA
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Atta K, Mondal S, Gorai S, Singh AP, Kumari A, Ghosh T, Roy A, Hembram S, Gaikwad DJ, Mondal S, Bhattacharya S, Jha UC, Jespersen D. Impacts of salinity stress on crop plants: improving salt tolerance through genetic and molecular dissection. FRONTIERS IN PLANT SCIENCE 2023; 14:1241736. [PMID: 37780527 PMCID: PMC10540871 DOI: 10.3389/fpls.2023.1241736] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Accepted: 08/14/2023] [Indexed: 10/03/2023]
Abstract
Improper use of water resources in irrigation that contain a significant amount of salts, faulty agronomic practices such as improper fertilization, climate change etc. are gradually increasing soil salinity of arable lands across the globe. It is one of the major abiotic factors that inhibits overall plant growth through ionic imbalance, osmotic stress, oxidative stress, and reduced nutrient uptake. Plants have evolved with several adaptation strategies at morphological and molecular levels to withstand salinity stress. Among various approaches, harnessing the crop genetic variability across different genepools and developing salinity tolerant crop plants offer the most sustainable way of salt stress mitigation. Some important major genetic determinants controlling salinity tolerance have been uncovered using classical genetic approaches. However, its complex inheritance pattern makes breeding for salinity tolerance challenging. Subsequently, advances in sequence based breeding approaches and functional genomics have greatly assisted in underpinning novel genetic variants controlling salinity tolerance in plants at the whole genome level. This current review aims to shed light on physiological, biochemical, and molecular responses under salt stress, defense mechanisms of plants, underlying genetics of salt tolerance through bi-parental QTL mapping and Genome Wide Association Studies, and implication of Genomic Selection to breed salt tolerant lines.
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Affiliation(s)
- Kousik Atta
- ICAR-Indian Agricultural Research Institute, New Delhi, India
- Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, West Bengal, India
| | - Saptarshi Mondal
- Department of Crop and Soil Sciences, University of Georgia, Griffin, GA, United States
| | - Shouvik Gorai
- Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, West Bengal, India
| | - Aditya Pratap Singh
- Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, West Bengal, India
- School of Agriculture, GIET University, Gunupur, Rayagada, Odisha, India
| | - Amrita Kumari
- Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, West Bengal, India
| | - Tuhina Ghosh
- ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Arkaprava Roy
- ICAR-Indian Agricultural Research Institute, New Delhi, India
- ICAR- National Institute of Biotic Stress Management, Raipur, India
| | - Suryakant Hembram
- WBAS (Research), Government of West Bengal, Field Crop Research Station, Burdwan, India
| | | | - Subhasis Mondal
- Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, West Bengal, India
| | | | | | - David Jespersen
- Department of Crop and Soil Sciences, University of Georgia, Griffin, GA, United States
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Haidar S, Lackey S, Charette M, Yoosefzadeh-Najafabadi M, Gahagan AC, Hotte T, Belzile F, Rajcan I, Golshani A, Morrison MJ, Cober ER, Samanfar B. Genome-wide analysis of cold imbibition stress in soybean, Glycine max. FRONTIERS IN PLANT SCIENCE 2023; 14:1221644. [PMID: 37670866 PMCID: PMC10476531 DOI: 10.3389/fpls.2023.1221644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 07/17/2023] [Indexed: 09/07/2023]
Abstract
In Canada, the length of the frost-free season necessitates planting crops as early as possible to ensure that the plants have enough time to reach full maturity before they are harvested. Early planting carries inherent risks of cold water imbibition (specifically less than 4°C) affecting seed germination. A marker dataset developed for a previously identified Canadian soybean GWAS panel was leveraged to investigate the effect of cold water imbibition on germination. Seed from a panel of 137 soybean elite cultivars, grown in the field at Ottawa, ON, over three years, were placed on filter paper in petri dishes and allowed to imbibe water for 16 hours at either 4°C or 20°C prior to being transferred to a constant 20°C. Observations on seed germination, defined as the presence of a 1 cm radicle, were done from day two to seven. A three-parameter exponential rise to a maximum equation (3PERM) was fitted to estimate germination, time to the one-half maximum germination, and germination uniformity for each cultivar. Genotype-by-sequencing was used to identify SNPs in 137 soybean lines, and using genome-wide association studies (GWAS - rMVP R package, with GLM, MLM, and FarmCPU as methods), haplotype block analysis, and assumed linkage blocks of ±100 kbp, a threshold for significance was established using the qvalue package in R, and five significant SNPs were identified on chromosomes 1, 3, 4, 6, and 13 for maximum germination after cold water imbibition. Percent of phenotypic variance explained (PVE) and allele substitution effect (ASE) eliminated two of the five candidate SNPs, leaving three QTL regions on chromosomes 3, 6, and 13 (Chr3-3419152, Chr6-5098454, and Chr13-29649544). Based on the gene ontology (GO) enrichment analysis, 14 candidate genes whose function is predicted to include germination and cold tolerance related pathways were identified as candidate genes. The identified QTLs can be used to select future soybean cultivars tolerant to cold water imbibition and mitigate risks associated with early soybean planting.
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Affiliation(s)
- Siwar Haidar
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, Canada
- Department of Biology, Ottawa Institute of Systems Biology, Carleton University, Ottawa, ON, Canada
| | - Simon Lackey
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, Canada
- Department of Biology, Ottawa Institute of Systems Biology, Carleton University, Ottawa, ON, Canada
| | - Martin Charette
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, Canada
| | | | - A. Claire Gahagan
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, Canada
| | - Thomas Hotte
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, Canada
| | - Francois Belzile
- Department of Phytology, Institut de Biologie Intégrative et des Systèmes (IBIS), Université de Laval, Quebec City, QC, Canada
| | - Istvan Rajcan
- Department of Plant Agriculture, University of Guelph, Guelph, ON, Canada
| | - Ashkan Golshani
- Department of Biology, Ottawa Institute of Systems Biology, Carleton University, Ottawa, ON, Canada
| | - Malcolm J. Morrison
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, Canada
| | - Elroy R. Cober
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, Canada
| | - Bahram Samanfar
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, Canada
- Department of Biology, Ottawa Institute of Systems Biology, Carleton University, Ottawa, ON, Canada
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Susmitha P, Kumar P, Yadav P, Sahoo S, Kaur G, Pandey MK, Singh V, Tseng TM, Gangurde SS. Genome-wide association study as a powerful tool for dissecting competitive traits in legumes. FRONTIERS IN PLANT SCIENCE 2023; 14:1123631. [PMID: 37645459 PMCID: PMC10461012 DOI: 10.3389/fpls.2023.1123631] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 06/08/2023] [Indexed: 08/31/2023]
Abstract
Legumes are extremely valuable because of their high protein content and several other nutritional components. The major challenge lies in maintaining the quantity and quality of protein and other nutritional compounds in view of climate change conditions. The global need for plant-based proteins has increased the demand for seeds with a high protein content that includes essential amino acids. Genome-wide association studies (GWAS) have evolved as a standard approach in agricultural genetics for examining such intricate characters. Recent development in machine learning methods shows promising applications for dimensionality reduction, which is a major challenge in GWAS. With the advancement in biotechnology, sequencing, and bioinformatics tools, estimation of linkage disequilibrium (LD) based associations between a genome-wide collection of single-nucleotide polymorphisms (SNPs) and desired phenotypic traits has become accessible. The markers from GWAS could be utilized for genomic selection (GS) to predict superior lines by calculating genomic estimated breeding values (GEBVs). For prediction accuracy, an assortment of statistical models could be utilized, such as ridge regression best linear unbiased prediction (rrBLUP), genomic best linear unbiased predictor (gBLUP), Bayesian, and random forest (RF). Both naturally diverse germplasm panels and family-based breeding populations can be used for association mapping based on the nature of the breeding system (inbred or outbred) in the plant species. MAGIC, MCILs, RIAILs, NAM, and ROAM are being used for association mapping in several crops. Several modifications of NAM, such as doubled haploid NAM (DH-NAM), backcross NAM (BC-NAM), and advanced backcross NAM (AB-NAM), have also been used in crops like rice, wheat, maize, barley mustard, etc. for reliable marker-trait associations (MTAs), phenotyping accuracy is equally important as genotyping. Highthroughput genotyping, phenomics, and computational techniques have advanced during the past few years, making it possible to explore such enormous datasets. Each population has unique virtues and flaws at the genomics and phenomics levels, which will be covered in more detail in this review study. The current investigation includes utilizing elite breeding lines as association mapping population, optimizing the choice of GWAS selection, population size, and hurdles in phenotyping, and statistical methods which will analyze competitive traits in legume breeding.
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Affiliation(s)
- Pusarla Susmitha
- Regional Agricultural Research Station, Acharya N.G. Ranga Agricultural University, Andhra Pradesh, India
| | - Pawan Kumar
- Department of Genetics and Plant Breeding, College of Agriculture, Chaudhary Charan Singh (CCS) Haryana Agricultural University, Hisar, India
| | - Pankaj Yadav
- Department of Bioscience and Bioengineering, Indian Institute of Technology, Rajasthan, India
| | - Smrutishree Sahoo
- Department of Genetics and Plant Breeding, School of Agriculture, Gandhi Institute of Engineering and Technology (GIET) University, Odisha, India
| | - Gurleen Kaur
- Horticultural Sciences Department, University of Florida, Gainesville, FL, United States
| | - Manish K. Pandey
- Department of Genomics, Prebreeding and Bioinformatics, International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
| | - Varsha Singh
- Department of Plant and Soil Sciences, Mississippi State University, Starkville, MS, United States
| | - Te Ming Tseng
- Department of Plant and Soil Sciences, Mississippi State University, Starkville, MS, United States
| | - Sunil S. Gangurde
- Department of Plant Pathology, University of Georgia, Tifton, GA, United States
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8
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Wang Z, Yu D, Morota G, Dhakal K, Singer W, Lord N, Huang H, Chen P, Mozzoni L, Li S, Zhang B. Genome-wide association analysis of sucrose and alanine contents in edamame beans. FRONTIERS IN PLANT SCIENCE 2023; 13:1086007. [PMID: 36816489 PMCID: PMC9935843 DOI: 10.3389/fpls.2022.1086007] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 12/29/2022] [Indexed: 06/18/2023]
Abstract
The sucrose and Alanine (Ala) content in edamame beans significantly impacts the sweetness flavor of edamame-derived products as an important attribute to consumers' acceptance. Unlike grain-type soybeans, edamame beans are harvested as fresh beans at the R6 to R7 growth stages when beans are filled 80-90% of the pod capacity. The genetic basis of sucrose and Ala contents in fresh edamame beans may differ from those in dry seeds. To date, there is no report on the genetic basis of sucrose and Ala contents in the edamame beans. In this study, a genome-wide association study was conducted to identify single nucleotide polymorphisms (SNPs) related to sucrose and Ala levels in edamame beans using an association mapping panel of 189 edamame accessions genotyped with a SoySNP50K BeadChip. A total of 43 and 25 SNPs was associated with sucrose content and Ala content in the edamame beans, respectively. Four genes (Glyma.10g270800, Glyma.08g137500, Glyma.10g268500, and Glyma.18g193600) with known effects on the process of sucrose biosynthesis and 37 novel sucrose-related genes were characterized. Three genes (Gm17g070500, Glyma.14g201100 and Glyma.18g269600) with likely relevant effects in regulating Ala content and 22 novel Ala-related genes were identified. In addition, by summarizing the phenotypic data of edamame beans from three locations in two years, three PI accessions (PI 532469, PI 243551, and PI 407748) were selected as the high sucrose and high Ala parental lines for the perspective breeding of sweet edamame varieties. Thus, the beneficial alleles, candidate genes, and selected PI accessions identified in this study will be fundamental to develop edamame varieties with improved consumers' acceptance, and eventually promote edamame production as a specialty crop in the United States.
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Affiliation(s)
- Zhibo Wang
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, United States
| | - Dajun Yu
- Department of Food Science and Technology, Virginia Tech, Blacksburg, VA, United States
| | - Gota Morota
- School of Animal Sciences, Virginia Tech, Blacksburg, VA, United States
| | - Kshitiz Dhakal
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, United States
| | - William Singer
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, United States
| | - Nilanka Lord
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, United States
| | - Haibo Huang
- Department of Food Science and Technology, Virginia Tech, Blacksburg, VA, United States
| | - Pengyin Chen
- Fisher Delta Research Center, University of Missouri, Portageville, MO, United States
| | - Leandro Mozzoni
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR, United States
| | - Song Li
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, United States
| | - Bo Zhang
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, United States
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9
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Almira Casellas MJ, Pérez‐Martín L, Busoms S, Boesten R, Llugany M, Aarts MGM, Poschenrieder C. A genome-wide association study identifies novel players in Na and Fe homeostasis in Arabidopsis thaliana under alkaline-salinity stress. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 113:225-245. [PMID: 36433704 PMCID: PMC10108281 DOI: 10.1111/tpj.16042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 11/11/2022] [Accepted: 11/21/2022] [Indexed: 06/16/2023]
Abstract
In nature, multiple stress factors occur simultaneously. The screening of natural diversity panels and subsequent Genome-Wide Association Studies (GWAS) is a powerful approach to identify genetic components of various stress responses. Here, the nutritional status variation of a set of 270 natural accessions of Arabidopsis thaliana grown on a natural saline-carbonated soil is evaluated. We report significant natural variation on leaf Na (LNa) and Fe (LFe) concentrations in the studied accessions. Allelic variation in the NINJA and YUC8 genes is associated with LNa diversity, and variation in the ALA3 is associated with LFe diversity. The allelic variation detected in these three genes leads to changes in their mRNA expression and correlates with plant differential growth performance when plants are exposed to alkaline salinity treatment under hydroponic conditions. We propose that YUC8 and NINJA expression patters regulate auxin and jasmonic signaling pathways affecting plant tolerance to alkaline salinity. Finally, we describe an impairment in growth and leaf Fe acquisition associated with differences in root expression of ALA3, encoding a phospholipid translocase active in plasma membrane and the trans Golgi network which directly interacts with proteins essential for the trafficking of PIN auxin transporters, reinforcing the role of phytohormonal processes in regulating ion homeostasis under alkaline salinity.
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Affiliation(s)
- Maria Jose Almira Casellas
- Plant Physiology Laboratory, Bioscience FacultyUniversitat Autònoma de BarcelonaC/de la Vall Moronta s/nE‐08193BellaterraSpain
| | - Laura Pérez‐Martín
- Plant Physiology Laboratory, Bioscience FacultyUniversitat Autònoma de BarcelonaC/de la Vall Moronta s/nE‐08193BellaterraSpain
- Department of Botany and Plant BiologyUniversity of Geneva1211GenevaSwitzerland
| | - Silvia Busoms
- Plant Physiology Laboratory, Bioscience FacultyUniversitat Autònoma de BarcelonaC/de la Vall Moronta s/nE‐08193BellaterraSpain
| | - René Boesten
- Laboratory of GeneticsWageningen University and ResearchDroevendaalsesteeg 16708 PBWageningenThe Netherlands
| | - Mercè Llugany
- Plant Physiology Laboratory, Bioscience FacultyUniversitat Autònoma de BarcelonaC/de la Vall Moronta s/nE‐08193BellaterraSpain
| | - Mark G. M. Aarts
- Laboratory of GeneticsWageningen University and ResearchDroevendaalsesteeg 16708 PBWageningenThe Netherlands
| | - Charlotte Poschenrieder
- Plant Physiology Laboratory, Bioscience FacultyUniversitat Autònoma de BarcelonaC/de la Vall Moronta s/nE‐08193BellaterraSpain
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10
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Feng C, Gao H, Zhou Y, Jing Y, Li S, Yan Z, Xu K, Zhou F, Zhang W, Yang X, Hussain MA, Li H. Unfolding molecular switches for salt stress resilience in soybean: recent advances and prospects for salt-tolerant smart plant production. FRONTIERS IN PLANT SCIENCE 2023; 14:1162014. [PMID: 37152141 PMCID: PMC10154572 DOI: 10.3389/fpls.2023.1162014] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 03/31/2023] [Indexed: 05/09/2023]
Abstract
The increasing sodium salts (NaCl, NaHCO3, NaSO4 etc.) in agricultural soil is a serious global concern for sustainable agricultural production and food security. Soybean is an important food crop, and their cultivation is severely challenged by high salt concentration in soils. Classical transgenic and innovative breeding technologies are immediately needed to engineer salt tolerant soybean plants. Additionally, unfolding the molecular switches and the key components of the soybean salt tolerance network are crucial for soybean salt tolerance improvement. Here we review our understandings of the core salt stress response mechanism in soybean. Recent findings described that salt stress sensing, signalling, ionic homeostasis (Na+/K+) and osmotic stress adjustment might be important in regulating the soybean salinity stress response. We also evaluated the importance of antiporters and transporters such as Arabidopsis K+ Transporter 1 (AKT1) potassium channel and the impact of epigenetic modification on soybean salt tolerance. We also review key phytohormones, and osmo-protectants and their role in salt tolerance in soybean. In addition, we discuss the progress of omics technologies for identifying salt stress responsive molecular switches and their targeted engineering for salt tolerance in soybean. This review summarizes recent progress in soybean salt stress functional genomics and way forward for molecular breeding for developing salt-tolerant soybean plant.
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Affiliation(s)
- Chen Feng
- College of Life Sciences, Jilin Agricultural University, Changchun, China
| | - Hongtao Gao
- Hainan Yazhou Bay Seed Laboratory, Sanya Nanfan Research Institute of Hainan University, Sanya, China
- College of Tropical Crops, Hainan University, Haikou, China
| | - Yonggang Zhou
- Hainan Yazhou Bay Seed Laboratory, Sanya Nanfan Research Institute of Hainan University, Sanya, China
- College of Tropical Crops, Hainan University, Haikou, China
| | - Yan Jing
- Hainan Yazhou Bay Seed Laboratory, Sanya Nanfan Research Institute of Hainan University, Sanya, China
- College of Tropical Crops, Hainan University, Haikou, China
| | - Senquan Li
- Hainan Yazhou Bay Seed Laboratory, Sanya Nanfan Research Institute of Hainan University, Sanya, China
- College of Tropical Crops, Hainan University, Haikou, China
| | - Zhao Yan
- College of Life Sciences, Jilin Agricultural University, Changchun, China
| | - Keheng Xu
- Hainan Yazhou Bay Seed Laboratory, Sanya Nanfan Research Institute of Hainan University, Sanya, China
- College of Tropical Crops, Hainan University, Haikou, China
| | - Fangxue Zhou
- Hainan Yazhou Bay Seed Laboratory, Sanya Nanfan Research Institute of Hainan University, Sanya, China
- College of Tropical Crops, Hainan University, Haikou, China
| | - Wenping Zhang
- Hainan Yazhou Bay Seed Laboratory, Sanya Nanfan Research Institute of Hainan University, Sanya, China
- College of Tropical Crops, Hainan University, Haikou, China
| | - Xinquan Yang
- School of Chemistry and Chemical Engineering, Guangzhou University, Guangzhou, China
| | - Muhammad Azhar Hussain
- Hainan Yazhou Bay Seed Laboratory, Sanya Nanfan Research Institute of Hainan University, Sanya, China
- College of Tropical Crops, Hainan University, Haikou, China
- *Correspondence: Muhammad Azhar Hussain, ; Haiyan Li,
| | - Haiyan Li
- College of Life Sciences, Jilin Agricultural University, Changchun, China
- Hainan Yazhou Bay Seed Laboratory, Sanya Nanfan Research Institute of Hainan University, Sanya, China
- College of Tropical Crops, Hainan University, Haikou, China
- *Correspondence: Muhammad Azhar Hussain, ; Haiyan Li,
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11
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Rasheed A, Raza A, Jie H, Mahmood A, Ma Y, Zhao L, Xing H, Li L, Hassan MU, Qari SH, Jie Y. Molecular Tools and Their Applications in Developing Salt-Tolerant Soybean (Glycine max L.) Cultivars. Bioengineering (Basel) 2022; 9:bioengineering9100495. [PMID: 36290463 PMCID: PMC9598088 DOI: 10.3390/bioengineering9100495] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 09/09/2022] [Accepted: 09/13/2022] [Indexed: 01/18/2023] Open
Abstract
Abiotic stresses are one of the significant threats to soybean (Glycine max L.) growth and yields worldwide. Soybean has a crucial role in the global food supply chain and food security and contributes the main protein share compared to other crops. Hence, there is a vast scientific saddle on soybean researchers to develop tolerant genotypes to meet the growing need of food for the huge population. A large portion of cultivated land is damaged by salinity stress, and the situation worsens yearly. In past years, many attempts have increased soybean resilience to salinity stress. Different molecular techniques such as quantitative trait loci mapping (QTL), genetic engineering, transcriptome, transcription factor analysis (TFs), CRISPR/Cas9, as well as other conventional methods are used for the breeding of salt-tolerant cultivars of soybean to safeguard its yield under changing environments. These powerful genetic tools ensure sustainable soybean yields, preserving genetic variability for future use. Only a few reports about a detailed overview of soybean salinity tolerance have been published. Therefore, this review focuses on a detailed overview of several molecular techniques for soybean salinity tolerance and draws a future research direction. Thus, the updated review will provide complete guidelines for researchers working on the genetic mechanism of salinity tolerance in soybean.
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Affiliation(s)
- Adnan Rasheed
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Ali Raza
- Center of Legume Crop Genetics and Systems Biology/College of Agriculture, Oil Crops Research Institute, Fujian Agriculture and Forestry University (FAFU), Fuzhou 350002, China
| | - Hongdong Jie
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Athar Mahmood
- Department of Agronomy, University of Agriculture Faisalabad, Faisalabad 38040, Pakistan
| | - Yushen Ma
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Long Zhao
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Hucheng Xing
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Linlin Li
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Muhammad Umair Hassan
- Research Center on Ecological Sciences, Jiangxi Agricultural University, Nanchang 330045, China
| | - Sameer H. Qari
- Department of Biology, Al-Jumum University College, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Yucheng Jie
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
- Correspondence:
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12
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Singh AK, Raina SK, Kumar M, Aher L, Ratnaparkhe MB, Rane J, Kachroo A. Modulation of GmFAD3 expression alters abiotic stress responses in soybean. PLANT MOLECULAR BIOLOGY 2022; 110:199-218. [PMID: 35779188 DOI: 10.1007/s11103-022-01295-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 06/06/2022] [Indexed: 06/15/2023]
Abstract
KEY MESSAGE This study focused on enhancing resilience of soybean crops to drought and salinity stresses by overexpression of GmFAD3A gene, which plays an important role in modulating membrane fluidity and ultimately influence plants response to various abiotic stresses. Fatty acid desaturases (FADs) are a class of enzymes that mediate desaturation of fatty acids by introducing double bonds. They play an important role in modulating membrane fluidity in response to various abiotic stresses. However, a comprehensive analysis of GmFAD3 in drought and salinity stress tolerance in soybean is lacking. We used bean pod mottle virus (BPMV)-based vector for achieving rapid and efficient overexpression as well as silencing of Omega-3 Fatty Acid Desaturase gene from Glycine max (GmFAD3) to assess the functional role of GmFAD3 in abiotic stress responses in soybean. Higher levels of recombinant BPMV-GmFAD3A transcripts were detected in overexpressing soybean plants. Overexpression of GmFAD3A in soybean resulted in increased levels of jasmonic acid and higher expression of GmWRKY54 as compared to mock-inoculated, vector-infected and FAD3-silenced soybean plants under drought and salinity stress conditions. The GmFAD3A-overexpressing plants showed higher levels of chlorophyll content, efficient photosystem-II, relative water content, transpiration rate, stomatal conductance, proline content and also cooler canopy under drought and salinity stress conditions as compared to mock-inoculated, vector-infected and FAD3-silenced soybean plants. Results from the current study revealed that GmFAD3A-overexpressing soybean plants exhibited tolerance to drought and salinity stresses. However, soybean plants silenced for GmFAD3 were vulnerable to drought and salinity stresses.
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Affiliation(s)
- Ajay Kumar Singh
- National Institute of Abiotic Stress Management, Baramati, Pune, Maharashtra, 413115, India.
| | - Susheel Kumar Raina
- National Bureau of Plant Genetic Resources, Regional Station, Srinagar, Jammu & Kashmir, 191132, India
| | - Mahesh Kumar
- National Institute of Abiotic Stress Management, Baramati, Pune, Maharashtra, 413115, India
| | - Lalitkumar Aher
- National Institute of Abiotic Stress Management, Baramati, Pune, Maharashtra, 413115, India
| | | | - Jagadish Rane
- National Institute of Abiotic Stress Management, Baramati, Pune, Maharashtra, 413115, India
| | - Aardra Kachroo
- Department of Plant Pathology, University of Kentucky, Lexington, KY, 40546, USA
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13
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Yin X, Bi Y, Jiang F, Guo R, Zhang Y, Fan J, Kang MS, Fan X. Fine mapping of candidate quantitative trait loci for plant and ear height in a maize nested-association mapping population. FRONTIERS IN PLANT SCIENCE 2022; 13:963985. [PMID: 35991429 PMCID: PMC9386523 DOI: 10.3389/fpls.2022.963985] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 07/05/2022] [Indexed: 05/31/2023]
Abstract
Plant height (PH) and ear height (EH) are two important traits in maize (Zea mays L.), as they are closely related to lodging resistance and planting density. Our objectives were to (1) investigate single-nucleotide polymorphisms (SNPs) that are associated with PH and EH for detecting quantitative trait loci (QTL) and new gene that determines PH and EH, (2) explore the value of the QTL in maize breeding, and (3) investigate whether the "triangle heterotic group" theory is applicable for lowering PH and EH to increase yield. Seven inbred female parents were crossed with a common founder male parent Ye 107 to create a nested association mapping (NAM) population. The analysis of phenotypic data on PH and EH revealed wide variation among the parents of the NAM population. Genome-wide association study (GWAS) and high-resolution linkage mapping were conducted using the NAM population, which generated 264,694 SNPs by genotyping-by-sequencing. A total of 105 SNPs and 22 QTL were identified by GWAS and found to be significantly associated with PH and EH. A high-confidence QTL for PH, Qtl-chr1-EP, was identified on chromosome 1 via GWAS and confirmed by linkage analysis in two recombinant inbred line (RIL) populations. Results revealed that the SNP variation in the promoter region of the candidate gene Zm00001d031938, located at Qtl-chr1-EP, which encoded UDP-N-acetylglucosamine-peptide N-acetyl-glucosaminyl-transferase, might decrease PH and EH. Furthermore, the triangle heterotic pattern adopted in maize breeding programs by our team is practicable in selecting high-yield crosses based on the low ratio of EH/PH (EP).
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Affiliation(s)
- Xingfu Yin
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, China
- Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Yaqi Bi
- Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Fuyan Jiang
- Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Ruijia Guo
- Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Yudong Zhang
- Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Jun Fan
- Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Manjit S. Kang
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States
| | - Xingming Fan
- Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming, China
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14
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A Large-Scale Genomic Association Analysis Identifies the Candidate Genes Regulating Salt Tolerance in Cucumber ( Cucumis sativus L.) Seedlings. Int J Mol Sci 2022; 23:ijms23158260. [PMID: 35897836 PMCID: PMC9332819 DOI: 10.3390/ijms23158260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 07/19/2022] [Accepted: 07/19/2022] [Indexed: 02/04/2023] Open
Abstract
Salt stress seriously restricts plant growth and development, affects yield and quality, and thus becomes an urgent problem to be solved in cucumber stress resistance breeding. Mining salt tolerance genes and exploring the molecular mechanism of salt tolerance could accelerate the breeding of cucumber germplasm with excellent salt stress tolerance. In this study, 220 cucumber core accessions were used for Genome-Wide Association Studies (GWAS) and the identification of salt tolerance genes. The salinity injury index that was collected in two years showed significant differences among the core germplasm. A total of seven loci that were associated with salt tolerance in cucumber seedlings were repeatedly detected, which were located on Chr.2 (gST2.1), Chr.3 (gST3.1 and gST3.2), Chr.4 (gST4.1 and gST4.2), Chr.5 (gST5.1), and Chr.6 (gST6.1). Within these loci, 62 genes were analyzed, and 5 candidate genes (CsaV3_2G035120, CsaV3_3G023710, CsaV3_4G033150, CsaV3_5G023530, and CsaV3_6G009810) were predicted via the functional annotation of Arabidopsis homologous genes, haplotype of extreme salt-tolerant accessions, and qRT-PCR. These results provide a guide for further research on salt tolerance genes and molecular mechanisms of cucumber seedlings.
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15
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Zhang M, Cao J, Zhang T, Xu T, Yang L, Li X, Ji F, Gao Y, Ali S, Zhang Q, Zhu J, Xie L. A Putative Plasma Membrane Na +/H + Antiporter GmSOS1 Is Critical for Salt Stress Tolerance in Glycine max. FRONTIERS IN PLANT SCIENCE 2022; 13:870695. [PMID: 35651772 PMCID: PMC9149370 DOI: 10.3389/fpls.2022.870695] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 03/29/2022] [Indexed: 05/24/2023]
Abstract
Soybean (Glycine max) is a staple crop and a major source of vegetable protein and vegetable oil. The growth of soybean is dramatically inhibited by salt stress, especially by the excessive toxic Na+. Salt Overly Sensitive 1 (SOS1) is the only extensively characterized Na+ efflux transporter in multiple plant species so far. However, the role of GmSOS1 in soybean salt stress responses remains unclear. Herein, we created three gmsos1 mutants using the CRISPR-Cas9 system in soybean. We found a significant accumulation of Na+ in the roots of the gmsos1 mutants, resulting in the imbalance of Na+ and K+, which links to impaired Na+ efflux and increased K+ efflux in the roots of the gmsos1 mutants under salt stress. Compared to the wild type, our RNA-seq analysis revealed that the roots of the gmsos1-1 showed preferential up and downregulation of ion transporters under salt stress, supporting impaired stress detection or an inability to develop a comprehensive response to salinity in the gmsos1 mutants. Our findings indicate that the plasma membrane Na+/H+ exchanger GmSOS1 plays a critical role in soybean salt tolerance by maintaining Na+ homeostasis and provides evidence for molecular breeding to improve salt tolerance in soybean and other crops.
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Affiliation(s)
- Minghui Zhang
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin, China
| | - Junfeng Cao
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin, China
| | - Tianxu Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Tao Xu
- The Editorial Board of Journal of Forestry Research, Northeast Forestry University, Harbin, China
| | - Liyuan Yang
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin, China
- Laboratory Department, Qitaihe Center for Disease Control and Prevention, Qitaihe, China
| | - Xiaoyuan Li
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin, China
| | - Fengdan Ji
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin, China
| | - Yingxue Gao
- Shanghai Center for Plant Stress Biology and Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Shahid Ali
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Qingzhu Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Jianhua Zhu
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, College Park, MD, United States
| | - Linan Xie
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin, China
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16
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Marsh JI, Hu H, Petereit J, Bayer PE, Valliyodan B, Batley J, Nguyen HT, Edwards D. Haplotype mapping uncovers unexplored variation in wild and domesticated soybean at the major protein locus cqProt-003. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:1443-1455. [PMID: 35141762 PMCID: PMC9033719 DOI: 10.1007/s00122-022-04045-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 01/22/2022] [Indexed: 05/04/2023]
Abstract
KEY MESSAGE The major soy protein QTL, cqProt-003, was analysed for haplotype diversity and global distribution, and results indicate 304 bp deletion and variable tandem repeats in protein coding regions are likely causal candidates. Here, we present association and linkage analysis of 985 wild, landrace and cultivar soybean accessions in a pan genomic dataset to characterize the major high-protein/low-oil associated locus cqProt-003 located on chromosome 20. A significant trait-associated region within a 173 kb linkage block was identified, and variants in the region were characterized, identifying 34 high confidence SNPs, 4 insertions, 1 deletion and a larger 304 bp structural variant in the high-protein haplotype. Trinucleotide tandem repeats of variable length present in the second exon of gene Glyma.20G085100 are strongly correlated with the high-protein phenotype and likely represent causal variation. Structural variation has previously been found in the same gene, for which we report the global distribution of the 304 bp deletion and have identified additional nested variation present in high-protein individuals. Mapping variation at the cqProt-003 locus across demographic groups suggests that the high-protein haplotype is common in wild accessions (94.7%), rare in landraces (10.6%) and near absent in cultivated breeding pools (4.1%), suggesting its decrease in frequency primarily correlates with domestication and continued during subsequent improvement. However, the variation that has persisted in under-utilized wild and landrace populations holds high breeding potential for breeders willing to forego seed oil to maximize protein content. The results of this study include the identification of distinct haplotype structures within the high-protein population, and a broad characterization of the genomic context and linkage patterns of cqProt-003 across global populations, supporting future functional characterization and modification.
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Affiliation(s)
- Jacob I Marsh
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, WA, 6009, Australia
| | - Haifei Hu
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, WA, 6009, Australia
| | - Jakob Petereit
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, WA, 6009, Australia
| | - Philipp E Bayer
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, WA, 6009, Australia
| | - Babu Valliyodan
- Department of Agriculture and Environmental Sciences, Lincoln University, Jefferson City, MO, 65101, USA
| | - Jacqueline Batley
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, WA, 6009, Australia
| | - Henry T Nguyen
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO, 65211, USA
| | - David Edwards
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, WA, 6009, Australia.
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17
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Hasseb NM, Sallam A, Karam MA, Gao L, Wang RRC, Moursi YS. High-LD SNP markers exhibiting pleiotropic effects on salt tolerance at germination and seedlings stages in spring wheat. PLANT MOLECULAR BIOLOGY 2022; 108:585-603. [PMID: 35217965 PMCID: PMC8967789 DOI: 10.1007/s11103-022-01248-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Accepted: 01/25/2022] [Indexed: 06/01/2023]
Abstract
Salt tolerance at germination and seedling growth stages was investigated. GWAS revealed nine genomic regions with pleiotropic effects on salt tolerance. Salt tolerant genotypes were identified for future breeding program. With 20% of the irrigated land worldwide affected by it, salinity is a serious threat to plant development and crop production. While wheat is the most stable food source worldwide, it has been classified as moderately tolerant to salinity. In several crop plants; such as barley, maize and rice, it has been shown that salinity tolerance at seed germination and seedling establishment is under polygenic control. As yield was the ultimate goal of breeders and geneticists, less attention has been paid to understanding the genetic architecture of salt tolerance at early stages. Thus, the genetic control of salt tolerance at these stages is poorly understood relative to the late stages. In the current study, 176 genotypes of spring wheat were tested for salinity tolerance at seed germination and seedling establishment. Genome-Wide Association Study (GWAS) has been used to identify the genomic regions/genes conferring salt tolerance at seed germination and seedling establishment. Salinity stress negatively impacted all germination and seedling development parameters. A set of 137 SNPs showed significant association with the traits of interest. Across the whole genome, 33 regions showed high linkage disequilibrium (LD). These high LD regions harbored 15 SNPs with pleiotropic effect (i.e. SNPs that control more than one trait). Nine genes belonging to different functional groups were found to be associated with the pleiotropic SNPs. Noteworthy, chromosome 2B harbored the gene TraesCS2B02G135900 that acts as a potassium transporter. Remarkably, one SNP marker, reported in an early study, associated with salt tolerance was validated in this study. Our findings represent potential targets of genetic manipulation to understand and improve salinity tolerance in wheat.
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Affiliation(s)
- Nouran M Hasseb
- Department of Botany, Faculty of Science, Fayoum University, Fayoum, 63514, Egypt
| | - Ahmed Sallam
- Department of Genetics, Faculty of Agriculture, Assiut University, Assiut, 71526, Egypt.
| | - Mohamed A Karam
- Department of Botany, Faculty of Science, Fayoum University, Fayoum, 63514, Egypt
| | - Liangliang Gao
- Department of Plant Pathology and Wheat Genetics Resource Center, Kansas State Univ, Manhattan, KS, 66502, USA
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Buxin Road 97, Dapeng-District, Shenzhen, 518120, Guangdong, China
| | - Richard R C Wang
- USDA-ARS Forage and Range Research Lab, Utah State University, Logan, UT, 84322-6300, USA
| | - Yasser S Moursi
- Department of Botany, Faculty of Science, Fayoum University, Fayoum, 63514, Egypt
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18
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Li X, Guo D, Xue M, Li G, Yan Q, Jiang H, Liu H, Chen J, Gao Y, Duan L, Xie L. Genome-Wide Association Study of Salt Tolerance at the Seed Germination Stage in Flax (Linum usitatissimum L.). Genes (Basel) 2022; 13:genes13030486. [PMID: 35328040 PMCID: PMC8949523 DOI: 10.3390/genes13030486] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 03/03/2022] [Accepted: 03/05/2022] [Indexed: 02/04/2023] Open
Abstract
Soil salinization seriously affects the growth and distribution of flax. However, there is little information about the salt tolerance of flax. In this study, the salt tolerance of 200 diverse flax accessions during the germination stage was evaluated, and then the Genome-wide Association Study (GWAS) was carried out based on the relative germination rate (RGR), relative shoot length (RSL) and relative root length (RRL), whereby quantitative trait loci (QTLs) related to salt tolerance were identified. The results showed that oil flax had a better salt tolerance than fiber flax. A total of 902 single nucleotide polymorphisms (SNPs) were identified on 15 chromosomes. These SNPs were integrated into 64 QTLs, explaining 14.48 to 29.38% (R2) of the phenotypic variation. In addition, 268 candidate genes were screened by combining previous transcriptome data and homologous gene annotation. Among them, Lus10033213 is a single-point SNP repeat mapping gene, which encodes a Glutathione S-transferase (GST). This study is the first to use GWAS to excavate genes related to salt tolerance during the germination stage of flax. The results of this study provide important information for studying the genetic mechanism of salt tolerance of flax, and also provide the possibility to improve the salt tolerance of flax.
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Genetic Aspects and Molecular Causes of Seed Longevity in Plants—A Review. PLANTS 2022; 11:plants11050598. [PMID: 35270067 PMCID: PMC8912819 DOI: 10.3390/plants11050598] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 02/17/2022] [Accepted: 02/22/2022] [Indexed: 12/19/2022]
Abstract
Seed longevity is the most important trait related to the management of gene banks because it governs the regeneration cycle of seeds. Thus, seed longevity is a quantitative trait. Prior to the discovery of molecular markers, classical genetic studies have been performed to identify the genetic determinants of this trait. Post-2000 saw the use of DNA-based molecular markers and modern biotechnological tools, including RNA sequence (RNA-seq) analysis, to understand the genetic factors determining seed longevity. This review summarizes the most important and relevant genetic studies performed in Arabidopsis (24 reports), rice (25 reports), barley (4 reports), wheat (9 reports), maize (8 reports), soybean (10 reports), tobacco (2 reports), lettuce (1 report) and tomato (3 reports), in chronological order, after discussing some classical studies. The major genes identified and their probable roles, where available, are debated in each case. We conclude by providing information about many different collections of various crops available worldwide for advanced research on seed longevity. Finally, the use of new emerging technologies, including RNA-seq, in seed longevity research is emphasized by providing relevant examples.
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Cho KH, Kim MY, Kwon H, Yang X, Lee SH. Novel QTL identification and candidate gene analysis for enhancing salt tolerance in soybean (Glycine max (L.) Merr.). PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 313:111085. [PMID: 34763870 DOI: 10.1016/j.plantsci.2021.111085] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 10/05/2021] [Accepted: 10/08/2021] [Indexed: 06/13/2023]
Abstract
Soybean, a glycophyte that is sensitive to salt stress, is greatly affected by salinity at all growth stages. A mapping population derived from a cross between a salt-sensitive Korean cultivar, Cheongja 3, and a salt-tolerant landrace, IT162669, was used to identify quantitative trait loci (QTLs) conferring salt tolerance in soybean. Following treatment with 120 mM NaCl for 2 weeks, phenotypic traits representing physiological damage, leaf Na+ content, and K+/Na+ ratio were characterized. Among the QTLs mapped on a high-density genetic map harboring 2,630 single nucleotide polymorphism markers, we found two novel major loci, qST6, on chromosome 6, and qST10, on chromosome 10, which controlled traits related to ion toxicity and physiology in response to salinity, respectively. These loci were distinct from the previously known salt tolerance allele on chromosome 3. Other QTLs associated with abiotic stress overlapped with the genomic regions of qST6 and qST10, or with their paralogous regions. Based on the functional annotation and parental expression differences, we identified eight putative candidate genes, two in qST6 and six in qST10, which included a phosphoenolpyruvate carboxylase and an ethylene response factor. This study provides additional genetic resources to breed soybean cultivars with enhanced salt tolerance.
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Affiliation(s)
- Kang-Heum Cho
- Department of Agriculture, Forestry and Bioresources and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea.
| | - Moon Young Kim
- Department of Agriculture, Forestry and Bioresources and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea; Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826, Republic of Korea.
| | - Hakyung Kwon
- Department of Agriculture, Forestry and Bioresources and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea.
| | - Xuefei Yang
- Key Laboratory of Herbage & Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010000, China.
| | - Suk-Ha Lee
- Department of Agriculture, Forestry and Bioresources and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea; Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826, Republic of Korea.
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21
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Oluwole OO, Aworunse OS, Aina AI, Oyesola OL, Popoola JO, Oyatomi OA, Abberton MT, Obembe OO. A review of biotechnological approaches towards crop improvement in African yam bean ( Sphenostylis stenocarpa Hochst. Ex A. Rich.). Heliyon 2021; 7:e08481. [PMID: 34901510 PMCID: PMC8642607 DOI: 10.1016/j.heliyon.2021.e08481] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 05/11/2021] [Accepted: 11/19/2021] [Indexed: 11/29/2022] Open
Abstract
Globally, climate change is a major factor that contributes significantly to food and nutrition insecurity, limiting crop yield and availability. Although efforts are being made to curb food insecurity, millions of people still suffer from malnutrition. For the United Nations (UN) Sustainable Development Goal of Food Security to be achieved, diverse cropping systems must be developed instead of relying mainly on a few staple crops. Many orphan legumes have untapped potential that can be of significance for developing improved cultivars with enhanced tolerance to changing climatic conditions. One typical example of such an orphan crop is Sphenostylis stenocarpa Hochst. Ex A. Rich. Harms, popularly known as African yam bean (AYB). The crop is an underutilised tropical legume that is climate-resilient and has excellent potential for smallholder agriculture in sub-Saharan Africa (SSA). Studies on AYB have featured morphological characterisation, assessment of genetic diversity using various molecular markers, and the development of tissue culture protocols for rapidly multiplying propagules. However, these have not translated into varietal development, and low yields remain a challenge. The application of suitable biotechnologies to improve AYB is imperative for increased yield, sustainable utilisation and conservation. This review discusses biotechnological strategies with prospective applications for AYB improvement. The potential risks of these strategies are also highlighted.
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Affiliation(s)
- Olubusayo O. Oluwole
- Department of Biological Sciences, Covenant University, Canaan Land, Ota, Nigeria
- Genetic Resources Centre, International Institute of Tropical Agriculture, Ibadan, Nigeria
| | - Oluwadurotimi S. Aworunse
- Department of Biological Sciences, Covenant University, Canaan Land, Ota, Nigeria
- UNESCO Chair on Plant Biotechnology, Plant Science Research Cluster, Covenant University, Canaan Land, Ota, Nigeria
| | - Ademola I. Aina
- Department of Crop Protection and Environmental Biology, University of Ibadan, Oyo State, Nigeria
- Genetic Resources Centre, International Institute of Tropical Agriculture, Ibadan, Nigeria
| | - Olusola L. Oyesola
- Department of Biological Sciences, Covenant University, Canaan Land, Ota, Nigeria
- UNESCO Chair on Plant Biotechnology, Plant Science Research Cluster, Covenant University, Canaan Land, Ota, Nigeria
| | - Jacob O. Popoola
- Department of Biological Sciences, Covenant University, Canaan Land, Ota, Nigeria
- UNESCO Chair on Plant Biotechnology, Plant Science Research Cluster, Covenant University, Canaan Land, Ota, Nigeria
| | - Olaniyi A. Oyatomi
- Genetic Resources Centre, International Institute of Tropical Agriculture, Ibadan, Nigeria
| | - Michael T. Abberton
- Genetic Resources Centre, International Institute of Tropical Agriculture, Ibadan, Nigeria
| | - Olawole O. Obembe
- Department of Biological Sciences, Covenant University, Canaan Land, Ota, Nigeria
- UNESCO Chair on Plant Biotechnology, Plant Science Research Cluster, Covenant University, Canaan Land, Ota, Nigeria
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22
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Sharmin RA, Karikari B, Chang F, Al Amin GM, Bhuiyan MR, Hina A, Lv W, Chunting Z, Begum N, Zhao T. Genome-wide association study uncovers major genetic loci associated with seed flooding tolerance in soybean. BMC PLANT BIOLOGY 2021; 21:497. [PMID: 34715792 PMCID: PMC8555181 DOI: 10.1186/s12870-021-03268-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 09/29/2021] [Indexed: 06/01/2023]
Abstract
BACKGROUND Seed flooding stress is one of the threatening environmental stressors that adversely limits soybean at the germination stage across the globe. The knowledge on the genetic basis underlying seed-flooding tolerance is limited. Therefore, we performed a genome-wide association study (GWAS) using 34,718 single nucleotide polymorphism (SNPs) in a panel of 243 worldwide soybean collections to identify genetic loci linked to soybean seed flooding tolerance at the germination stage. RESULTS In the present study, GWAS was performed with two contrasting models, Mixed Linear Model (MLM) and Multi-Locus Random-SNP-Effect Mixed Linear Model (mrMLM) to identify significant SNPs associated with electrical conductivity (EC), germination rate (GR), shoot length (ShL), and root length (RL) traits at germination stage in soybean. With MLM, a total of 20, 40, 4, and 9 SNPs associated with EC, GR, ShL and RL, respectively, whereas in the same order mrMLM detected 27, 17, 13, and 18 SNPs. Among these SNPs, two major SNPs, Gm_08_11971416, and Gm_08_46239716 were found to be consistently connected with seed-flooding tolerance related traits, namely EC and GR across two environments. We also detected two SNPs, Gm_05_1000479 and Gm_01_53535790 linked to ShL and RL, respectively. Based on Gene Ontology enrichment analysis, gene functional annotations, and protein-protein interaction network analysis, we predicted eight candidate genes and three hub genes within the regions of the four SNPs with Cis-elements in promoter regions which may be involved in seed-flooding tolerance in soybeans and these warrant further screening and functional validation. CONCLUSIONS Our findings demonstrate that GWAS based on high-density SNP markers is an efficient approach to dissect the genetic basis of complex traits and identify candidate genes in soybean. The trait associated SNPs could be used for genetic improvement in soybean breeding programs. The candidate genes could help researchers better understand the molecular mechanisms underlying seed-flooding stress tolerance in soybean.
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Affiliation(s)
- Ripa Akter Sharmin
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
- Jagannath University, Dhaka, 1100, Bangladesh
| | - Benjamin Karikari
- Department of Crop Science, Faculty of Agriculture, Food and Consumer Sciences, University for Development Studies, Tamale, Ghana
| | - Fangguo Chang
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - G M Al Amin
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Mashiur Rahman Bhuiyan
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Aiman Hina
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Wenhuan Lv
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhang Chunting
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Naheeda Begum
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Tuanjie Zhao
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China.
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23
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Sinha P, Singh VK, Bohra A, Kumar A, Reif JC, Varshney RK. Genomics and breeding innovations for enhancing genetic gain for climate resilience and nutrition traits. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:1829-1843. [PMID: 34014373 PMCID: PMC8205890 DOI: 10.1007/s00122-021-03847-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 04/29/2021] [Indexed: 05/03/2023]
Abstract
KEY MESSAGE Integrating genomics technologies and breeding methods to tweak core parameters of the breeder's equation could accelerate delivery of climate-resilient and nutrient rich crops for future food security. Accelerating genetic gain in crop improvement programs with respect to climate resilience and nutrition traits, and the realization of the improved gain in farmers' fields require integration of several approaches. This article focuses on innovative approaches to address core components of the breeder's equation. A prerequisite to enhancing genetic variance (σ2g) is the identification or creation of favorable alleles/haplotypes and their deployment for improving key traits. Novel alleles for new and existing target traits need to be accessed and added to the breeding population while maintaining genetic diversity. Selection intensity (i) in the breeding program can be improved by testing a larger population size, enabled by the statistical designs with minimal replications and high-throughput phenotyping. Selection priorities and criteria to select appropriate portion of the population too assume an important role. The most important component of breeder's equation is heritability (h2). Heritability estimates depend on several factors including the size and the type of population and the statistical methods. The present article starts with a brief discussion on the potential ways to enhance σ2g in the population. We highlight statistical methods and experimental designs that could improve trait heritability estimation. We also offer a perspective on reducing the breeding cycle time (t), which could be achieved through the selection of appropriate parents, optimizing the breeding scheme, rapid fixation of target alleles, and combining speed breeding with breeding programs to optimize trials for release. Finally, we summarize knowledge from multiple disciplines for enhancing genetic gains for climate resilience and nutritional traits.
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Affiliation(s)
- Pallavi Sinha
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- International Rice Research Institute (IRRI), IRRI South Asia Hub, ICRISAT, Hyderabad, India
| | - Vikas K Singh
- International Rice Research Institute (IRRI), IRRI South Asia Hub, ICRISAT, Hyderabad, India
| | - Abhishek Bohra
- ICAR- Indian Institute of Pulses Research (IIPR), Kanpur, India
| | - Arvind Kumar
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Jochen C Reif
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, WA, Australia.
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24
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Jia Q, Li MW, Zheng C, Xu Y, Sun S, Li Z, Wong FL, Song J, Lin WW, Li Q, Zhu Y, Liang K, Lin W, Lam HM. The soybean plasma membrane-localized cation/H + exchanger GmCHX20a plays a negative role under salt stress. PHYSIOLOGIA PLANTARUM 2021; 171:714-727. [PMID: 33094482 DOI: 10.1111/ppl.13250] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Revised: 10/01/2020] [Accepted: 10/20/2020] [Indexed: 06/11/2023]
Abstract
Cation/H+ -exchanger (CHX) perform diverse functions in plants, including being a part of the protective mechanisms to cope with salt stress. GmCHX1 has been previously identified as the causal gene in a major salt-tolerance quantitative trait locus (QTL) in soybean, but little is known about another close paralog, GmCHX20a, found in the same QTL. In this study, GmCHX20a was characterized along with GmCHX1. The expression patterns of the two genes and the direction of Na+ flux directed by overexpression of these two transporters are different, suggesting that they are functionally distinct. The ectopic expression of GmCHX20a led to an increase in salt sensitivity and osmotic tolerance, which was consistent with its role in increasing Na+ uptake into the root. Although this seems counter-intuitive, it may in fact be part of the mechanism by which soybean could counter act the effects of osmotic stress, which is commonly manifested in the initial stage of salinity stress. On the other hand, GmCHX1 from salt-tolerant soybean was shown to protect plants via Na+ exclusion under salt stress. Taken together these results suggest that GmCHX20a and GmCHX1 might work complementally through a concerted effort to address both osmotic stress and ionic stress as a result of elevated salinity.
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Affiliation(s)
- Qi Jia
- Key Laboratory for Genetics Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- School of Life Sciences and Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Man-Wah Li
- School of Life Sciences and Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Chengwen Zheng
- Key Laboratory for Genetics Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yiyue Xu
- School of Life Sciences and Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Song Sun
- Key Laboratory for Genetics Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhong Li
- Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, China
| | - Fuk-Ling Wong
- School of Life Sciences and Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Junliang Song
- Key Laboratory for Genetics Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Wei-Wei Lin
- Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, China
| | - Qinghua Li
- Putian Institute of Agricultural Sciences, Putian, China
| | - Yebao Zhu
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Kangjing Liang
- Key Laboratory for Genetics Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Wenxiong Lin
- Key Laboratory for Genetics Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, China
| | - Hon-Ming Lam
- School of Life Sciences and Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
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25
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Jasmonates and Plant Salt Stress: Molecular Players, Physiological Effects, and Improving Tolerance by Using Genome-Associated Tools. Int J Mol Sci 2021; 22:ijms22063082. [PMID: 33802953 PMCID: PMC8002660 DOI: 10.3390/ijms22063082] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 03/11/2021] [Accepted: 03/15/2021] [Indexed: 12/18/2022] Open
Abstract
Soil salinity is one of the most limiting stresses for crop productivity and quality worldwide. In this sense, jasmonates (JAs) have emerged as phytohormones that play essential roles in mediating plant response to abiotic stresses, including salt stress. Here, we reviewed the mechanisms underlying the activation and response of the JA-biosynthesis and JA-signaling pathways under saline conditions in Arabidopsis and several crops. In this sense, molecular components of JA-signaling such as MYC2 transcription factor and JASMONATE ZIM-DOMAIN (JAZ) repressors are key players for the JA-associated response. Moreover, we review the antagonist and synergistic effects between JA and other hormones such as abscisic acid (ABA). From an applied point of view, several reports have shown that exogenous JA applications increase the antioxidant response in plants to alleviate salt stress. Finally, we discuss the latest advances in genomic techniques for the improvement of crop tolerance to salt stress with a focus on jasmonates.
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26
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Bohra A, Chand Jha U, Godwin ID, Kumar Varshney R. Genomic interventions for sustainable agriculture. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:2388-2405. [PMID: 32875704 PMCID: PMC7680532 DOI: 10.1111/pbi.13472] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Revised: 07/21/2020] [Accepted: 08/16/2020] [Indexed: 05/05/2023]
Abstract
Agricultural production faces a Herculean challenge to feed the increasing global population. Food production systems need to deliver more with finite land and water resources while exerting the least negative influence on the ecosystem. The unpredictability of climate change and consequent changes in pests/pathogens dynamics aggravate the enormity of the challenge. Crop improvement has made significant contributions towards food security, and breeding climate-smart cultivars are considered the most sustainable way to accelerate food production. However, a fundamental change is needed in the conventional breeding framework in order to respond adequately to the growing food demands. Progress in genomics has provided new concepts and tools that hold promise to make plant breeding procedures more precise and efficient. For instance, reference genome assemblies in combination with germplasm sequencing delineate breeding targets that could contribute to securing future food supply. In this review, we highlight key breakthroughs in plant genome sequencing and explain how the presence of these genome resources in combination with gene editing techniques has revolutionized the procedures of trait discovery and manipulation. Adoption of new approaches such as speed breeding, genomic selection and haplotype-based breeding could overcome several limitations of conventional breeding. We advocate that strengthening varietal release and seed distribution systems will play a more determining role in delivering genetic gains at farmer's field. A holistic approach outlined here would be crucial to deliver steady stream of climate-smart crop cultivars for sustainable agriculture.
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Affiliation(s)
- Abhishek Bohra
- ICAR‐Indian Institute of Pulses Research (IIPR)KanpurIndia
| | - Uday Chand Jha
- ICAR‐Indian Institute of Pulses Research (IIPR)KanpurIndia
| | - Ian D. Godwin
- Centre for Crop ScienceQueensland Alliance for Agriculture and Food Innovation (QAAFI)The University of QueenslandBrisbaneQldAustralia
| | - Rajeev Kumar Varshney
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
- The UWA Institute of AgricultureThe University of Western AustraliaPerthAustralia
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27
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Li B. Identification of Genes Conferring Plant Salt Tolerance using GWAS: Current Success and Perspectives. PLANT & CELL PHYSIOLOGY 2020; 61:1419-1426. [PMID: 32484868 DOI: 10.1093/pcp/pcaa073] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 05/25/2020] [Indexed: 06/11/2023]
Abstract
An understanding of the molecular mechanisms that underlie plant salt tolerance is important for both economic and scientific interests. Genome-wide association study (GWAS) is a promising approach to pinpoint genes that confer plant salt tolerance. With the advancement of supporting technology and methodology, GWAS has enabled the discovery of genes that play central roles in regulating plant salt tolerance in the past decade. Here, I highlight recent successful GWAS work in unveiling the molecular factors underlying plant salt tolerance and discuss the concerns and opportunities in conducting such experiments. It is anticipated that GWAS will be increasingly successful in the identification of key genes that are useful for crop improvement.
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Affiliation(s)
- Bo Li
- School of Life Sciences, Lanzhou University, Lanzhou 730000, China
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, Lanzhou 730000, China
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28
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Pawlowski ML, Vuong TD, Valliyodan B, Nguyen HT, Hartman GL. Whole-genome resequencing identifies quantitative trait loci associated with mycorrhizal colonization of soybean. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:409-417. [PMID: 31707439 DOI: 10.1007/s00122-019-03471-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 11/01/2019] [Indexed: 05/15/2023]
Abstract
KEY MESSAGE A whole-genome resequencing-derived SNP dataset identified six quantitative trait loci (QTL) significantly associated with colonization of soybean by an arbuscular mycorrhizal fungus (Rhizophagus intraradices). Candidate genes identified in these QTL regions include homologs to known nodulin protein families and other symbiosis-specific genes. Arbuscular mycorrhizal fungi (AMF) form associations with over 80% of all terrestrial plant species and assist their host plants by increasing their nutrient uptake, drought tolerance, and resilience against pathogens and pests. Genotypic variation of crop plants to AMF colonization has been identified in crops, including soybean; however, the genetics controlling levels of AMF colonization in soybean are unknown. The overall goal of our study was to identify genomic regions associated with mycorrhizal colonization in soybean using genome-wide association analysis. A diverse panel of 350 exotic soybean genotypes inoculated with Rhizophagus intraradices were microscopically evaluated for root colonization using a modified gridline intersect method. Root colonization differed significantly (P < 0.001) among genotypes and ranged from 11 to 70%. A whole-genome resequencing-derived SNP dataset identified six quantitative trait loci (QTL) significantly associated with R. intraradices colonization that explained 24% of the phenotypic variance. Candidate genes identified in these QTL regions include homologs to known nodulin protein families and other symbiosis-specific genes. The results showed there was a significant genetic component to the level of colonization by R. intraradices in soybean. This information may be useful in the development of AMF-sensitive soybean cultivars to enhance nutrient uptake, drought tolerance, and disease resistance in the crop.
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Affiliation(s)
- Michelle L Pawlowski
- Department of Crop Science, University of Illinois, 1101 W. Peabody Drive, Urbana, IL, 61801, USA
| | - Tri D Vuong
- Department of Plant Sciences, University of Missouri, Columbia, MO, USA
| | - Babu Valliyodan
- Department of Plant Sciences, University of Missouri, Columbia, MO, USA
| | - Henry T Nguyen
- Department of Plant Sciences, University of Missouri, Columbia, MO, USA
| | - Glen L Hartman
- Department of Crop Science, University of Illinois, 1101 W. Peabody Drive, Urbana, IL, 61801, USA.
- USDA, Agricultural Research Services, University of Illinois, 1101 W. Peabody Dr., Urbana, IL, USA.
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