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Zhang Y, Guo Z, Chen X, Li X, Shi Y, Xu L, Yu C, Jing B, Li W, Xu A, Shi X, Li K, Huang Z. Identification candidate genes for salt resistance through quantitative trait loci-sequencing in Brassica napus L. JOURNAL OF PLANT PHYSIOLOGY 2024; 294:154187. [PMID: 38422630 DOI: 10.1016/j.jplph.2024.154187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 01/22/2024] [Accepted: 01/22/2024] [Indexed: 03/02/2024]
Abstract
Rapeseed (Brassica napus L.) is one of the most important oil crops worldwide. However, its yield is greatly limited by salt stress, one of the primary abiotic stresses. Identification of salt-tolerance genes and breeding salt-tolerant varieties is an effective approach to address this issue. Unfortunately, little is known about the salt-tolerance quantitative trait locus (QTL) and the identification of salt tolerance genes in rapeseed. In this study, high-throughput quantitative trait locus sequencing (QTL-seq) was applied to identifying salt-tolerant major QTLs based on two DNA pools from an F2:3 population of a cross between rapeseed line 2205 (salt tolerant) and 1423 (salt sensitive). A total of twelve major QTLs related to the salt tolerance rating (STR) were detected on chromosomes A03, A08, C02, C03, C04, C06, C07 and C09. To further enhance our understanding, we integrated QTL-seq data with transcriptome analysis of the two parental rapeseed plants subjected to salt stress, through which ten candidate genes for salt tolerance were identified within the major QTLs by gene differential expression, variation and annotated functions analysis. The marker SNP820 linked to salt tolerance was successfully validated and would be useful as a diagnostic marker in marker-assisted breeding. These findings provide valuable insights for future breeding programs aimed at developing rapeseed cultivars resistant to salt stresses.
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Affiliation(s)
- Yan Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas/College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Zhiting Guo
- State Key Laboratory of Crop Stress Biology for Arid Areas/College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xiaoqin Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas/College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xinru Li
- State Key Laboratory of Crop Stress Biology for Arid Areas/College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yiji Shi
- State Key Laboratory of Crop Stress Biology for Arid Areas/College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Liang Xu
- Academy of Agricultural and Forestry Sciences of Qinghai University, Key Laboratory of Spring Rape Genetic Improvement of Qinghai Province, Rapeseed Research and Development Center of Qinghai Province, Xining, 810016, Qinghai, China
| | - Chengyu Yu
- State Key Laboratory of Crop Stress Biology for Arid Areas/College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Bing Jing
- State Key Laboratory of Crop Stress Biology for Arid Areas/College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Weiwei Li
- State Key Laboratory of Crop Stress Biology for Arid Areas/College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Aixia Xu
- State Key Laboratory of Crop Stress Biology for Arid Areas/College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xue Shi
- State Key Laboratory of Crop Stress Biology for Arid Areas/College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Keqi Li
- State Key Laboratory of Crop Stress Biology for Arid Areas/College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Zhen Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas/College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China.
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Zhou T, Wu PJ, Chen JF, Du XQ, Feng YN, Hua YP. Pectin demethylation-mediated cell wall Na + retention positively regulates salt stress tolerance in oilseed rape. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:54. [PMID: 38381205 DOI: 10.1007/s00122-024-04560-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 01/20/2024] [Indexed: 02/22/2024]
Abstract
KEY MESSAGE Integrated phenomics, ionomics, genomics, transcriptomics, and functional analyses present novel insights into the role of pectin demethylation-mediated cell wall Na+ retention in positively regulating salt tolerance in oilseed rape. Genetic variations in salt stress tolerance identified in rapeseed genotypes highlight the complicated regulatory mechanisms. Westar is ubiquitously used as a transgenic receptor cultivar, while ZS11 is widely grown as a high-production and good-quality cultivar. In this study, Westar was found to outperform ZS11 under salt stress. Through cell component isolation, non-invasive micro-test, X-ray energy spectrum analysis, and ionomic profile characterization, pectin demethylation-mediated cell wall Na+ retention was proposed to be a major regulator responsible for differential salt tolerance between Westar and ZS11. Integrated analyses of genome-wide DNA variations, differential expression profiling, and gene co-expression networks identified BnaC9.PME47, encoding a pectin methylesterase, as a positive regulator conferring salt tolerance in rapeseed. BnaC9.PME47, located in two reported QTL regions for salt tolerance, was strongly induced by salt stress and localized on the cell wall. Natural variation of the promoter regions conferred higher expression of BnaC9.PME47 in Westar than in several salt-sensitive rapeseed genotypes. Loss of function of AtPME47 resulted in the hypersensitivity of Arabidopsis plants to salt stress. The integrated multiomics analyses revealed novel insights into pectin demethylation-mediated cell wall Na+ retention in regulating differential salt tolerance in allotetraploid rapeseed genotypes. Furthermore, these analyses have provided key information regarding the rapid dissection of quantitative trait genes responsible for nutrient stress tolerance in plant species with complex genomes.
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Affiliation(s)
- Ting Zhou
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, China
- Zhengzhou Key Laboratory of Quality Improvement and Efficient Nutrient Use for Main Economic Crops, Zhengzhou, 450001, China
| | - Peng-Jia Wu
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, China
- Zhengzhou Key Laboratory of Quality Improvement and Efficient Nutrient Use for Main Economic Crops, Zhengzhou, 450001, China
| | - Jun-Fan Chen
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, China
- Zhengzhou Key Laboratory of Quality Improvement and Efficient Nutrient Use for Main Economic Crops, Zhengzhou, 450001, China
| | - Xiao-Qian Du
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, China
- Zhengzhou Key Laboratory of Quality Improvement and Efficient Nutrient Use for Main Economic Crops, Zhengzhou, 450001, China
| | - Ying-Na Feng
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, China
- Zhengzhou Key Laboratory of Quality Improvement and Efficient Nutrient Use for Main Economic Crops, Zhengzhou, 450001, China
| | - Ying-Peng Hua
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, China.
- Zhengzhou Key Laboratory of Quality Improvement and Efficient Nutrient Use for Main Economic Crops, Zhengzhou, 450001, China.
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Knoch D, Meyer RC, Heuermann MC, Riewe D, Peleke FF, Szymański J, Abbadi A, Snowdon RJ, Altmann T. Integrated multi-omics analyses and genome-wide association studies reveal prime candidate genes of metabolic and vegetative growth variation in canola. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:713-728. [PMID: 37964699 DOI: 10.1111/tpj.16524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 10/17/2023] [Accepted: 10/23/2023] [Indexed: 11/16/2023]
Abstract
Genome-wide association studies (GWAS) identified thousands of genetic loci associated with complex plant traits, including many traits of agronomical importance. However, functional interpretation of GWAS results remains challenging because of large candidate regions due to linkage disequilibrium. High-throughput omics technologies, such as genomics, transcriptomics, proteomics and metabolomics open new avenues for integrative systems biological analyses and help to nominate systems information supported (prime) candidate genes. In the present study, we capitalise on a diverse canola population with 477 spring-type lines which was previously analysed by high-throughput phenotyping of growth-related traits and by RNA sequencing and metabolite profiling for multi-omics-based hybrid performance prediction. We deepened the phenotypic data analysis, now providing 123 time-resolved image-based traits, to gain insight into the complex relations during early vegetative growth and reanalysed the transcriptome data based on the latest Darmor-bzh v10 genome assembly. Genome-wide association testing revealed 61 298 robust quantitative trait loci (QTL) including 187 metabolite QTL, 56814 expression QTL and 4297 phenotypic QTL, many clustered in pronounced hotspots. Combining information about QTL colocalisation across omics layers and correlations between omics features allowed us to discover prime candidate genes for metabolic and vegetative growth variation. Prioritised candidate genes for early biomass accumulation include A06p05760.1_BnaDAR (PIAL1), A10p16280.1_BnaDAR, C07p48260.1_BnaDAR (PRL1) and C07p48510.1_BnaDAR (CLPR4). Moreover, we observed unequal effects of the Brassica A and C subgenomes on early biomass production.
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Affiliation(s)
- Dominic Knoch
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466, Corrensstrasse 3, Seeland OT, Gatersleben, Germany
| | - Rhonda C Meyer
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466, Corrensstrasse 3, Seeland OT, Gatersleben, Germany
| | - Marc C Heuermann
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466, Corrensstrasse 3, Seeland OT, Gatersleben, Germany
| | - David Riewe
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466, Corrensstrasse 3, Seeland OT, Gatersleben, Germany
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Ecological Chemistry, Plant Analysis and Stored Product Protection, 14195, Berlin, Germany
| | - Fritz F Peleke
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466, Corrensstrasse 3, Seeland OT, Gatersleben, Germany
| | - Jędrzej Szymański
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466, Corrensstrasse 3, Seeland OT, Gatersleben, Germany
- Institute of Bio- and Geosciences IBG-4: Bioinformatics, Forschungszentrum Jülich, 52428, Jülich, Germany
| | - Amine Abbadi
- NPZ Innovation GmbH, Hohenlieth, 24363, Holtsee, Germany
- Norddeutsche Pflanzenzucht Hans-Georg Lembke KG, Hohenlieth, 24363, Holtsee, Germany
| | - Rod J Snowdon
- Department of Plant Breeding, Research Centre for Biosystems, Land Use and Nutrition (iFZ), Justus-Liebig-University Giessen, 35392, Giessen, Germany
| | - Thomas Altmann
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466, Corrensstrasse 3, Seeland OT, Gatersleben, Germany
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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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Farooq N, Khan MO, Ahmed MZ, Fatima S, Nawaz MA, Abideen Z, Nielsen BL, Ahmad N. Salt-Induced Modulation of Ion Transport and PSII Photoprotection Determine the Salinity Tolerance of Amphidiploid Brassicas. PLANTS (BASEL, SWITZERLAND) 2023; 12:2590. [PMID: 37514204 PMCID: PMC10386101 DOI: 10.3390/plants12142590] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 07/06/2023] [Accepted: 07/06/2023] [Indexed: 07/30/2023]
Abstract
Brassica species show varying levels of resistance to salt stress. To understand the genetics underlying these differential stress tolerance patterns in Brassicas, we exposed two widely cultivated amphidiploid Brassica species having different genomes, Brassica juncea (AABB, n = 18) and Brassica napus (AACC, n = 19), to elevated levels of NaCl concentration (300 mM, half the salinity of seawater). B. juncea produced more biomass, an increased chlorophyll content, and fewer accumulated sodium (Na+) and chloride (Cl-) ions in its photosynthesizing tissues. Chlorophyll fluorescence assays revealed that the reaction centers of PSII of B. juncea were more photoprotected and hence more active than those of B. napus under NaCl stress, which, in turn, resulted in a better PSII quantum efficiency, better utilization of photochemical energy with significantly reduced energy loss, and higher electron transport rates, even under stressful conditions. The expression of key genes responsible for salt tolerance (NHX1 and AVP1, which are nuclear-encoded) and photosynthesis (psbA, psaA, petB, and rbcL, which are chloroplast-encoded) were monitored for their genetic differences underlying stress tolerance. Under NaCl stress, the expression of NHX1, D1, and Rubisco increased several folds in B. juncea plants compared to B. napus, highlighting differences in genetics between these two Brassicas. The higher photosynthetic potential under stress suggests that B. juncea is a promising candidate for genetic modifications and its cultivation on marginal lands.
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Affiliation(s)
- Nisma Farooq
- National Institute for Biotechnology and Genetic Engineering College (NIBGE-C), Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad 38000, Pakistan; (N.F.); (M.O.K.); (S.F.); (M.A.N.)
| | - Muhammad Omar Khan
- National Institute for Biotechnology and Genetic Engineering College (NIBGE-C), Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad 38000, Pakistan; (N.F.); (M.O.K.); (S.F.); (M.A.N.)
| | - Muhammad Zaheer Ahmed
- Dr Muhammad Ajmal Khan Institute of Sustainable Halophyte Utilization, University of Karachi, Karachi 75270, Pakistan; (M.Z.A.); (Z.A.)
| | - Samia Fatima
- National Institute for Biotechnology and Genetic Engineering College (NIBGE-C), Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad 38000, Pakistan; (N.F.); (M.O.K.); (S.F.); (M.A.N.)
| | - Muhammad Asif Nawaz
- National Institute for Biotechnology and Genetic Engineering College (NIBGE-C), Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad 38000, Pakistan; (N.F.); (M.O.K.); (S.F.); (M.A.N.)
| | - Zainul Abideen
- Dr Muhammad Ajmal Khan Institute of Sustainable Halophyte Utilization, University of Karachi, Karachi 75270, Pakistan; (M.Z.A.); (Z.A.)
| | - Brent L. Nielsen
- Microbiology & Molecular Biology, Brigham Young University, Provo, UT 84602, USA
| | - Niaz Ahmad
- National Institute for Biotechnology and Genetic Engineering College (NIBGE-C), Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad 38000, Pakistan; (N.F.); (M.O.K.); (S.F.); (M.A.N.)
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Zhang Y, Zhang Q, Wang H, Tao S, Cao H, Shi Y, Bakirov A, Xu A, Huang Z. Discovery of common loci and candidate genes for controlling salt-alkali tolerance and yield-related traits in Brassica napus L. PLANT CELL REPORTS 2023; 42:1039-1057. [PMID: 37076701 DOI: 10.1007/s00299-023-03011-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Accepted: 03/27/2023] [Indexed: 05/03/2023]
Abstract
KEY MESSAGE Common loci and candidate genes for controlling salt-alkali tolerance and yield-related traits were identified in Brassica napus combining QTL mapping with transcriptome under salt and alkaline stresses. The yield of rapeseed (Brassica napus L.) is determined by multiple yield-related traits, which are susceptible to environmental factors. Many yield-related quantitative trait loci (QTLs) have been reported in Brassica napus; however, no studies have been conducted to investigate both salt-alkali tolerance and yield-related traits simultaneously. Here, specific-locus amplified fragment sequencing (SLAF-seq) technologies were utilized to map the QTLs for salt-alkali tolerance and yield-related traits. A total of 65 QTLs were identified, including 30 QTLs for salt-alkali tolerance traits and 35 QTLs for yield-related traits, accounting for 7.61-27.84% of the total phenotypic variations. Among these QTLs, 18 unique QTLs controlling two to four traits were identified by meta-analysis. Six novel and unique QTLs were detected for salt-alkali tolerance traits. By comparing these unique QTLs for salt-alkali tolerance traits with those previously reported QTLs for yield-related traits, seven co-localized chromosomal regions were identified on A09 and A10. Combining QTL mapping with transcriptome of two parents under salt and alkaline stresses, thirteen genes were identified as the candidates controlling both salt-alkali tolerance and yield. These findings provide useful information for future breeding of high-yield cultivars resistant to alkaline and salt stresses.
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Affiliation(s)
- Yan Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Qi Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Han Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Shunxian Tao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Hanming Cao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Yiji Shi
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Aldiyar Bakirov
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Aixia Xu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Zhen Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China.
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Chen B, Bian X, Tu M, Yu T, Jiang L, Lu Y, Chen X. Moderate Salinity Stress Increases the Seedling Biomass in Oilseed Rape ( Brassica napus L.). PLANTS (BASEL, SWITZERLAND) 2023; 12:1650. [PMID: 37111872 PMCID: PMC10144440 DOI: 10.3390/plants12081650] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 03/30/2023] [Accepted: 04/05/2023] [Indexed: 06/19/2023]
Abstract
Oilseed rape (Brassica napus L.), an important oil crop of the world, suffers various abiotic stresses including salinity stress during the growth stage. While most of the previous studies paid attention to the adverse effects of high salinity stress on plant growth and development, as well as their underlying physiological and molecular mechanisms, less attention was paid to the effects of moderate or low salinity stress. In this study, we first tested the effects of different concentrations of NaCl solution on the seedling growth performance of two oilseed rape varieties (CH336, a semi-winter type, and Bruttor, a spring type) in pot cultures. We found that moderate salt concentrations (25 and 50 mmol L-1 NaCl) can stimulate seedling growth by a significant increase (10~20%, compared to controls) in both above- and underground biomasses, as estimated at the early flowering stage. We then performed RNA-seq analyses of shoot apical meristems (SAMs) from six-leaf-aged seedlings under control (CK), low (LS, 25 mmol L-1), and high (HS, 180 mmol L-1) salinity treatments in the two varieties. The GO and KEGG enrichment analyses of differentially expressed genes (DEGs) demonstrated that such a stimulating effect on seedling growth by low salinity stress may be caused by a more efficient capacity for photosynthesis as compensation, accompanied by a reduced energy loss for the biosynthesis of secondary metabolites and redirecting of energy to biomass formation. Our study provides a new perspective on the cultivation of oilseed rape in saline regions and new insights into the molecular mechanisms of salt tolerance in Brassica crops. The candidate genes identified in this study can serve as targets for molecular breeding selection and genetic engineering toward enhancing salt tolerance in B. napus.
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Affiliation(s)
- Beini Chen
- Institute of Crop Science, Jinhua Academy of Agricultural Sciences, Zhihe Road 1158, Jinhua 321017, China (T.Y.)
- Institute of Crop Science, Zhejiang University, Yu-Hang-Tang Road 866, Hangzhou 310058, China
| | - Xiaobo Bian
- Institute of Crop Science, Jinhua Academy of Agricultural Sciences, Zhihe Road 1158, Jinhua 321017, China (T.Y.)
| | - Mengxin Tu
- Institute of Crop Science, Zhejiang University, Yu-Hang-Tang Road 866, Hangzhou 310058, China
| | - Tao Yu
- Institute of Crop Science, Jinhua Academy of Agricultural Sciences, Zhihe Road 1158, Jinhua 321017, China (T.Y.)
| | - Lixi Jiang
- Institute of Crop Science, Zhejiang University, Yu-Hang-Tang Road 866, Hangzhou 310058, China
| | - Yunhai Lu
- Institute of Crop Science, Zhejiang University, Yu-Hang-Tang Road 866, Hangzhou 310058, China
| | - Xiaoyang Chen
- Institute of Crop Science, Jinhua Academy of Agricultural Sciences, Zhihe Road 1158, Jinhua 321017, China (T.Y.)
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8
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Genome-Wide Association Studies of Salt Tolerance at the Seed Germination Stage and Yield-Related Traits in Brassica napus L. Int J Mol Sci 2022; 23:ijms232415892. [PMID: 36555533 PMCID: PMC9785822 DOI: 10.3390/ijms232415892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 12/11/2022] [Accepted: 12/12/2022] [Indexed: 12/15/2022] Open
Abstract
Salt stress severely affects crop growth and development and reduces the yield of Brassica napus. Exploring natural genetic variations for high salt tolerance in B. napus seedlings is an effective approach to improve productivity under salt stress. Using 10,658 high-quality single nucleotide polymorphic (SNP) markers developed by specific-locus amplified fragment sequencing (SLAF-seq) technology, genome-wide association studies (GWAS) were performed to investigate the genetic basis of salt tolerance and yield-related traits of B. napus. The results revealed that 77 and 497 SNPs were significantly associated with salt tolerance and yield-related traits, of which 40 and 58 SNPs were located in previously reported QTLs/SNPs, respectively. We identified nineteen candidate genes orthologous with Arabidopsis genes known to be associated with salt tolerance and seven potential candidates controlling both salt tolerance and yield. Our study provides a novel genetic resource for the breeding of high-yield cultivars resistant to salt stress.
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Khan MN, Li Y, Fu C, Hu J, Chen L, Yan J, Khan Z, Wu H, Li Z. CeO 2 Nanoparticles Seed Priming Increases Salicylic Acid Level and ROS Scavenging Ability to Improve Rapeseed Salt Tolerance. GLOBAL CHALLENGES (HOBOKEN, NJ) 2022; 6:2200025. [PMID: 35860396 PMCID: PMC9284644 DOI: 10.1002/gch2.202200025] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 05/10/2022] [Indexed: 05/05/2023]
Abstract
Soil salinity is a major issue limiting efficient crop production. Seed priming with nanomaterials (nanopriming) is a cost-effective technology to improve seed germination under salinity; however, the underlying mechanisms still need to be explored. Here, polyacrylic acid coated nanoceria (cerium oxide nanoparticles) (PNC, 9.2 nm, -38.7 mV) are synthesized and characterized. The results show that under salinity, PNC priming significantly increases rapeseed shoot length (41.5%), root length (93%), and seedling dry weight (78%) compared to the no-nanoparticle (NNP) priming group. Confocal imaging results show that compared with NNP group, PNC priming significantly reduces reactive oxygen species (ROS) level in leaf (94.3% of H2O2, 56.4% of •O2 -) and root (38.4% of H2O2, 41.3% of •O2 -) of salt stressed rapeseed seedlings. Further, the results show that compared with the NNP group, PNC priming not only increases salicylic acid (SA) content in shoot (51.3%) and root (78.4%), but also upregulates the expression of SA biosynthesis related genes in salt stressed rapeseed. Overall, PNC nanopriming improved rapeseed salt tolerance is associated with both the increase of ROS scavenging ability and the increase of salicylic acid. The results add more information to understand the complexity of mechanisms behind nanoceria priming improved plant salt tolerance.
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Affiliation(s)
- Mohammad Nauman Khan
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze RiverCollege of Plant Science and TechnologyHuazhong Agricultural UniversityWuhan430070China
| | - Yanhui Li
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze RiverCollege of Plant Science and TechnologyHuazhong Agricultural UniversityWuhan430070China
| | - Chengcheng Fu
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze RiverCollege of Plant Science and TechnologyHuazhong Agricultural UniversityWuhan430070China
| | - Jin Hu
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze RiverCollege of Plant Science and TechnologyHuazhong Agricultural UniversityWuhan430070China
| | - Linlin Chen
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze RiverCollege of Plant Science and TechnologyHuazhong Agricultural UniversityWuhan430070China
| | - Jiasen Yan
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze RiverCollege of Plant Science and TechnologyHuazhong Agricultural UniversityWuhan430070China
| | - Zaid Khan
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze RiverCollege of Plant Science and TechnologyHuazhong Agricultural UniversityWuhan430070China
| | - Honghong Wu
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze RiverCollege of Plant Science and TechnologyHuazhong Agricultural UniversityWuhan430070China
- Hongshan LaboratoryWuhanHubei430070China
- College of Agronomy and BiotechnologyChina Agricultural UniversityBeijing100083China
| | - Zhaohu Li
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze RiverCollege of Plant Science and TechnologyHuazhong Agricultural UniversityWuhan430070China
- Hongshan LaboratoryWuhanHubei430070China
- College of Agronomy and BiotechnologyChina Agricultural UniversityBeijing100083China
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10
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Shahzad B, Rehman A, Tanveer M, Wang L, Park SK, Ali A. Salt Stress in Brassica: Effects, Tolerance Mechanisms, and Management. JOURNAL OF PLANT GROWTH REGULATION 2022. [PMID: 0 DOI: 10.1007/s00344-021-10338-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
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11
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Zhang G, Peng Y, Zhou J, Tan Z, Jin C, Fang S, Zhong S, Jin C, Wang R, Wen X, Li B, Lu S, Zhou G, Fu T, Guo L, Yao X. Genome-Wide Association Studies of Salt-Alkali Tolerance at Seedling and Mature Stages in Brassica napus. FRONTIERS IN PLANT SCIENCE 2022; 13:857149. [PMID: 35574128 PMCID: PMC9094488 DOI: 10.3389/fpls.2022.857149] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 03/28/2022] [Indexed: 05/19/2023]
Abstract
Most plants are sensitive to salt-alkali stress, and the degree of tolerance to salt-alkali stress varies from different species and varieties. In order to explore the salt-alkali stress adaptability of Brassica napus, we collected the phenotypic data of 505 B. napus accessions at seedling and mature stages under control, low and high salt-alkali soil stress conditions in Inner Mongolia of China. Six resistant and 5 sensitive materials, respectively, have been identified both in Inner Mongolia and Xinjiang Uygur Autonomous Region of China. Genome-wide association studies (GWAS) for 15 absolute values and 10 tolerance coefficients (TCs) of growth and agronomic traits were applied to investigate the genetic basis of salt-alkali tolerance of B. napus. We finally mapped 9 significant QTLs related to salt-alkali stress response and predicted 20 candidate genes related to salt-alkali stress tolerance. Some important candidate genes, including BnABA4, BnBBX14, BnVTI12, BnPYL8, and BnCRR1, were identified by combining sequence variation annotation and expression differences. The identified valuable loci and germplasms could be useful for breeding salt-alkali-tolerant B.napus varieties. This study laid a foundation for understanding molecular mechanism of salt-alkali stress adaptation and provides rich genetic resources for the large-scale production of B. napus on salt-alkali land in the future.
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Affiliation(s)
- Guofang Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Yan Peng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Jinzhi Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Zengdong Tan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Cheng Jin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Shuai Fang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Shengzhu Zhong
- Agriculture and Animal Husbandry Technology Promotion Center, Inner Mongolia, China
| | - Cunwang Jin
- Green Industry Development Center, Inner Mongolia, China
| | - Ruizhen Wang
- Agriculture and Animal Husbandry Technology Promotion Center, Inner Mongolia, China
| | - Xiaoliang Wen
- Agriculture and Animal Husbandry Technology Promotion Center, Inner Mongolia, China
| | - Binrui Li
- Agriculture and Animal Husbandry Technology Promotion Center, Inner Mongolia, China
| | - Shaoping Lu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Guangsheng Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Tingdong Fu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Liang Guo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Xuan Yao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
- *Correspondence: Xuan Yao
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12
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Zhou T, Yue CP, Liu Y, Zhang TY, Huang JY, Hua YP. Multiomics reveal pivotal roles of sodium translocation and compartmentation in regulating salinity resistance in allotetraploid rapeseed. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:5687-5708. [PMID: 33989425 DOI: 10.1093/jxb/erab215] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Accepted: 05/12/2021] [Indexed: 05/20/2023]
Abstract
The large size and complexity of the allotetraploid rapeseed (Brassica napus) genome present huge challenges for understanding salinity resistance in this important crop. In this study, we identified two rapeseed genotypes with significantly different degrees of salinity resistance and examined the underlying mechanisms using an integrated analysis of phenomics, ionomics, genomics, and transcriptomics. Under salinity, a higher accumulation of osmoregulation substances and better root-system architecture was observed in the resistant genotype, H159, than in the sensitive one, L339. A lower shoot Na+ concentration and a higher root vacuolar Na+ concentration indicated lower root-to-shoot translocation and higher compartmentation in H159 than in L339. Whole-genome re-sequencing (WGRS) and transcriptome sequencing identified numerous DNA variants and differentially expressed genes involved in abiotic stress responses and ion transport. Combining ionomics with transcriptomics identified plasma membrane-localized BnaC2.HKT1;1 and tonoplast-localized BnaC5.NHX2 as the central factors regulating differential root xylem unloading and vacuolar sequestration of Na+ between the two genotypes. Identification of polymorphisms by WGRS and PCR revealed two polymorphic MYB-binding sites in the promoter regions that might determine the differential gene expression of BnaC2.HKT1;1 and BnaC5.NHX2. Our multiomics approach thus identified core transporters involved in Na+ translocation and compartmentation that regulate salinity resistance in rapeseed. Our results may provide elite gene resources for the improvement of salinity resistance in this crop, and our multiomics approach can be applied to other similar studies.
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Affiliation(s)
- Ting Zhou
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Cai-Peng Yue
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Ying Liu
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Tian-Yu Zhang
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Jin-Yong Huang
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Ying-Peng Hua
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
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13
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Quezada-Martinez D, Addo Nyarko CP, Schiessl SV, Mason AS. Using wild relatives and related species to build climate resilience in Brassica crops. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:1711-1728. [PMID: 33730183 PMCID: PMC8205867 DOI: 10.1007/s00122-021-03793-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 02/12/2021] [Indexed: 05/18/2023]
Abstract
Climate change will have major impacts on crop production: not just increasing drought and heat stress, but also increasing insect and disease loads and the chance of extreme weather events and further adverse conditions. Often, wild relatives show increased tolerances to biotic and abiotic stresses, due to reduced stringency of selection for yield and yield-related traits under optimum conditions. One possible strategy to improve resilience in our modern-day crop cultivars is to utilize wild relative germplasm in breeding, and attempt to introgress genetic factors contributing to greater environmental tolerances from these wild relatives into elite crop types. However, this approach can be difficult, as it relies on factors such as ease of hybridization and genetic distance between the source and target, crossover frequencies and distributions in the hybrid, and ability to select for desirable introgressions while minimizing linkage drag. In this review, we outline the possible effects that climate change may have on crop production, introduce the Brassica crop species and their wild relatives, and provide an index of useful traits that are known to be present in each of these species that may be exploitable through interspecific hybridization-based approaches. Subsequently, we outline how introgression breeding works, what factors affect the success of this approach, and how this approach can be optimized so as to increase the chance of recovering the desired introgression lines. Our review provides a working guide to the use of wild relatives and related crop germplasm to improve biotic and abiotic resistances in Brassica crop species.
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Affiliation(s)
- Daniela Quezada-Martinez
- Plant Breeding Department, Justus Liebig University, 35392, Giessen, Germany
- Plant Breeding Department, The University of Bonn, Katzenburgweg 5, 53115, Bonn, Germany
| | - Charles P Addo Nyarko
- Plant Breeding Department, Justus Liebig University, 35392, Giessen, Germany
- Plant Breeding Department, The University of Bonn, Katzenburgweg 5, 53115, Bonn, Germany
| | - Sarah V Schiessl
- Plant Breeding Department, Justus Liebig University, 35392, Giessen, Germany
| | - Annaliese S Mason
- Plant Breeding Department, Justus Liebig University, 35392, Giessen, Germany.
- Plant Breeding Department, The University of Bonn, Katzenburgweg 5, 53115, Bonn, Germany.
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14
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Quezada-Martinez D, Addo Nyarko CP, Schiessl SV, Mason AS. Using wild relatives and related species to build climate resilience in Brassica crops. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:1711-1728. [PMID: 33730183 DOI: 10.1007/s00122-021-03793-3.pdf] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 02/12/2021] [Indexed: 05/24/2023]
Abstract
Climate change will have major impacts on crop production: not just increasing drought and heat stress, but also increasing insect and disease loads and the chance of extreme weather events and further adverse conditions. Often, wild relatives show increased tolerances to biotic and abiotic stresses, due to reduced stringency of selection for yield and yield-related traits under optimum conditions. One possible strategy to improve resilience in our modern-day crop cultivars is to utilize wild relative germplasm in breeding, and attempt to introgress genetic factors contributing to greater environmental tolerances from these wild relatives into elite crop types. However, this approach can be difficult, as it relies on factors such as ease of hybridization and genetic distance between the source and target, crossover frequencies and distributions in the hybrid, and ability to select for desirable introgressions while minimizing linkage drag. In this review, we outline the possible effects that climate change may have on crop production, introduce the Brassica crop species and their wild relatives, and provide an index of useful traits that are known to be present in each of these species that may be exploitable through interspecific hybridization-based approaches. Subsequently, we outline how introgression breeding works, what factors affect the success of this approach, and how this approach can be optimized so as to increase the chance of recovering the desired introgression lines. Our review provides a working guide to the use of wild relatives and related crop germplasm to improve biotic and abiotic resistances in Brassica crop species.
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Affiliation(s)
- Daniela Quezada-Martinez
- Plant Breeding Department, Justus Liebig University, 35392, Giessen, Germany
- Plant Breeding Department, The University of Bonn, Katzenburgweg 5, 53115, Bonn, Germany
| | - Charles P Addo Nyarko
- Plant Breeding Department, Justus Liebig University, 35392, Giessen, Germany
- Plant Breeding Department, The University of Bonn, Katzenburgweg 5, 53115, Bonn, Germany
| | - Sarah V Schiessl
- Plant Breeding Department, Justus Liebig University, 35392, Giessen, Germany
| | - Annaliese S Mason
- Plant Breeding Department, Justus Liebig University, 35392, Giessen, Germany.
- Plant Breeding Department, The University of Bonn, Katzenburgweg 5, 53115, Bonn, Germany.
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Quan X, Liu J, Zhang N, Xie C, Li H, Xia X, He W, Qin Y. Genome-Wide Association Study Uncover the Genetic Architecture of Salt Tolerance-Related Traits in Common Wheat ( Triticum aestivum L.). Front Genet 2021; 12:663941. [PMID: 34093656 PMCID: PMC8172982 DOI: 10.3389/fgene.2021.663941] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 03/24/2021] [Indexed: 01/13/2023] Open
Abstract
Soil salinity is a serious threat to wheat yield affecting sustainable agriculture. Although salt tolerance is important for plant establishment at seedling stage, its genetic architecture remains unclear. In the present study, we have evaluated eight salt tolerance-related traits at seedling stage and identified the loci for salt tolerance by genome-wide association study (GWAS). This GWAS panel comprised 317 accessions and was genotyped with the wheat 90 K single-nucleotide polymorphism (SNP) chip. In total, 37 SNPs located at 16 unique loci were identified, and each explained 6.3 to 18.6% of the phenotypic variations. Among these, six loci were overlapped with previously reported genes or quantitative trait loci, whereas the other 10 were novel. Besides, nine loci were detected for two or more traits, indicating that the salt-tolerance genetic architecture is complex. Furthermore, five candidate genes were identified for salt tolerance-related traits, including kinase family protein, E3 ubiquitin-protein ligase-like protein, and transmembrane protein. SNPs identified in this study and the accessions with more favorable alleles could further enhance salt tolerance in wheat breeding. Our results are useful for uncovering the genetic mechanism of salt tolerance in wheat at seeding stage.
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Affiliation(s)
- Xiaoyan Quan
- Department of Biological Science, School of Biological Science and Technology, University of Jinan, Jinan, China
| | - Jindong Liu
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.,Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ning Zhang
- Department of Biological Science, School of Biological Science and Technology, University of Jinan, Jinan, China
| | - Chunjuan Xie
- Department of Biological Science, School of Biological Science and Technology, University of Jinan, Jinan, China
| | - Hongmei Li
- Department of Biological Science, School of Biological Science and Technology, University of Jinan, Jinan, China
| | - Xianchun Xia
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wenxing He
- Department of Biological Science, School of Biological Science and Technology, University of Jinan, Jinan, China
| | - Yuxiang Qin
- Department of Biological Science, School of Biological Science and Technology, University of Jinan, Jinan, China
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Raza A, Razzaq A, Mehmood SS, Hussain MA, Wei S, He H, Zaman QU, Xuekun Z, Hasanuzzaman M. Omics: The way forward to enhance abiotic stress tolerance in Brassica napus L. GM CROPS & FOOD 2021; 12:251-281. [PMID: 33464960 PMCID: PMC7833762 DOI: 10.1080/21645698.2020.1859898] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Plant abiotic stresses negative affects growth and development, causing a massive reduction in global agricultural production. Rapeseed (Brassica napus L.) is a major oilseed crop because of its economic value and oilseed production. However, its productivity has been reduced by many environmental adversities. Therefore, it is a prime need to grow rapeseed cultivars, which can withstand numerous abiotic stresses. To understand the various molecular and cellular mechanisms underlying the abiotic stress tolerance and improvement in rapeseed, omics approaches have been extensively employed in recent years. This review summarized the recent advancement in genomics, transcriptomics, proteomics, metabolomics, and their imploration in abiotic stress regulation in rapeseed. Some persisting bottlenecks have been highlighted, demanding proper attention to fully explore the omics tools. Further, the potential prospects of the CRISPR/Cas9 system for genome editing to assist molecular breeding in developing abiotic stress-tolerant rapeseed genotypes have also been explained. In short, the combination of integrated omics, genome editing, and speed breeding can alter rapeseed production worldwide.
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Affiliation(s)
- Ali Raza
- Key Lab of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences (CAAS) , Wuhan, China
| | - Ali Razzaq
- Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture , Faisalabad, Pakistan
| | - Sundas Saher Mehmood
- Key Lab of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences (CAAS) , Wuhan, China
| | - Muhammad Azhar Hussain
- Key Lab of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences (CAAS) , Wuhan, China
| | - Su Wei
- Key Lab of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences (CAAS) , Wuhan, China
| | - Huang He
- Key Lab of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences (CAAS) , Wuhan, China
| | - Qamar U Zaman
- Key Lab of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences (CAAS) , Wuhan, China
| | - Zhang Xuekun
- College of Agriculture, Engineering Research Center of Ecology and Agricultural Use of Wetland of Ministry of Education, Yangtze University Jingzhou , China
| | - Mirza Hasanuzzaman
- Department of Agronomy, Faculty of Agriculture, Sher-e-Bangla Agricultural University , Dhaka, Bangladesh
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17
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Identification of genetic variation for salt tolerance in Brassica napus using genome-wide association mapping. Mol Genet Genomics 2021; 296:391-408. [DOI: 10.1007/s00438-020-01749-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 12/07/2020] [Indexed: 12/31/2022]
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Zhang G, Zhou J, Peng Y, Tan Z, Li L, Yu L, Jin C, Fang S, Lu S, Guo L, Yao X. Genome-Wide Association Studies of Salt Tolerance at Seed Germination and Seedling Stages in Brassica napus. FRONTIERS IN PLANT SCIENCE 2021; 12:772708. [PMID: 35069628 PMCID: PMC8766642 DOI: 10.3389/fpls.2021.772708] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 11/25/2021] [Indexed: 05/19/2023]
Abstract
Most crops are sensitive to salt stress, but their degree of susceptibility varies among species and cultivars. In order to understand the salt stress adaptability of Brassica napus to salt stress, we collected the phenotypic data of 505 B. napus accessions at the germination stage under 150 or 215 mM sodium chloride (NaCl) and at the seedling stage under 215 mM NaCl. Genome-wide association studies (GWAS) of 16 salt tolerance coefficients (STCs) were applied to investigate the genetic basis of salt stress tolerance of B. napus. In this study, we mapped 31 salts stress-related QTLs and identified 177 and 228 candidate genes related to salt stress tolerance were detected at germination and seedling stages, respectively. Overexpression of two candidate genes, BnCKX5 and BnERF3 overexpression, were found to increase the sensitivity to salt and mannitol stresses at the germination stage. This study demonstrated that it is a feasible method to dissect the genetic basis of salt stress tolerance at germination and seedling stages in B. napus by GWAS, which provides valuable loci for improving the salt stress tolerance of B. napus. Moreover, these candidate genes are rich genetic resources for the following exploration of molecular mechanisms in adaptation to salt stress in B. napus.
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Affiliation(s)
- Guofang Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Jinzhi Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Yan Peng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Zengdong Tan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Long Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Liangqian Yu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Cheng Jin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Shuai Fang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Shaoping Lu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Liang Guo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Xuan Yao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
- *Correspondence: Xuan Yao,
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Shah AN, Tanveer M, Abbas A, Fahad S, Baloch MS, Ahmad MI, Saud S, Song Y. Targeting salt stress coping mechanisms for stress tolerance in Brassica: A research perspective. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 158:53-64. [PMID: 33296846 DOI: 10.1016/j.plaphy.2020.11.044] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 11/18/2020] [Indexed: 05/02/2023]
Abstract
Brassica genus comprises numerous cultivated brassica species with various economic importance. Salt stress is an overwhelming problem causing serious losses in Brassica species (e.g. B. napus, B. rapa, B. oleracea, B. juncea) growth and grain yield production by inducing ionic and ROS toxicity. Given that a significant variation exists in salt tolerance level in Brassica genus, Brassica species exhibited numerous salt tolerance mechanisms which were either overlooked or given less importance to improve and understand innate salt stress tolerance mechanism in Brassica species. In this review, we tried to highlight the importance and recent findings relating to some overlooked and potential mechanisms such as role of neurotransmitters, and role of cytosolic Ca2+ and ROS as signaling elements to enhance salt stress tolerance. Studies revealed that salt tolerant brassica species retained more K+ in leaf mesophyll which confers overall salinity tolerance in salt tolerance brassica species. Neurotransmitter such as melatonin, dopamiane and eATP regulates K+ and Ca2+ permeable ion channels and plays a very crucial role in ionic homeostasis under salinity stress in brassica. At the end, the numerous possible salt stress agronomic strategies were also discussed to mitigate the severity of the salt stress in Brassica species.
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Affiliation(s)
- Adnan Noor Shah
- School of Agronomy, Anhui Agricultural University, Hefei, 230036, China
| | - Mohsin Tanveer
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, Australia
| | - Asad Abbas
- School of Horticulture, Anhui Agricultural University, Hefei, 230036, China
| | - Shah Fahad
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou, 570228, Hainan, China; Department of Agronomy, The University of Haripur, Haripur, 22620, Pakistan
| | - Mohammad Safdar Baloch
- Department of Agronomy, Faculty of Agriculture, Gomal University, Dera Ismail Khan, 29050, KPK, Pakistan
| | | | - Shah Saud
- Department of Horticulture, Northeast Agricultural University, Harbin, 150030, China
| | - Youhong Song
- School of Agronomy, Anhui Agricultural University, Hefei, 230036, China.
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Zhang F, Xiao X, Xu K, Cheng X, Xie T, Hu J, Wu X. Genome-wide association study (GWAS) reveals genetic loci of lead (Pb) tolerance during seedling establishment in rapeseed (Brassica napus L.). BMC Genomics 2020; 21:139. [PMID: 32041524 PMCID: PMC7011513 DOI: 10.1186/s12864-020-6558-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Accepted: 02/05/2020] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Lead (Pb) pollution in soil has become one of the major environmental threats to plant growth and human health. Safe utilization of Pb contaminated soil by phytoremediation require Pb-tolerant rapeseed (Brassica napus L.) accessions. However, breeding of new B. napus cultivars tolerance to Pb stress has been restricted by limited knowledge on molecular mechanisms involved in Pb tolerance. This work was carried out to identify genetic loci related to Pb tolerance during seedling establishment in rapeseed. RESULTS Pb tolerance, which was assessed by quantifying radicle length (RL) under 0 or 100 mg/L Pb stress condition, shown an extensive variation in 472 worldwide-collected rapeseed accessions. Based on the criterion of relative RL > 80%, six Pb-tolerant genotypes were selected. Four quantitative trait loci (QTLs) associated with Pb tolerance were identified by Genome-wide association study. The expression level of nine promising candidate genes, including GSTUs, BCATs, UBP13, TBR and HIPP01, located in these four QTL regions, were significantly higher or induced by Pb in Pb-tolerant accessions in comparison to Pb-sensitive accessions. CONCLUSION To our knowledge, this is the first study on Pb-tolerant germplasms and genomic loci in B. napus. The findings can provide valuable genetic resources for the breeding of Pb-tolerant B. napus cultivars and understanding of Pb tolerance mechanism in Brassica species.
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Affiliation(s)
- Fugui Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Xudong 2nd Road, Wuhan, 430062, Hubei, China
| | - Xin Xiao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Xudong 2nd Road, Wuhan, 430062, Hubei, China
| | - Kun Xu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Xudong 2nd Road, Wuhan, 430062, Hubei, China
| | - Xi Cheng
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Xudong 2nd Road, Wuhan, 430062, Hubei, China
| | - Ting Xie
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Xudong 2nd Road, Wuhan, 430062, Hubei, China
| | - Jihong Hu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Xudong 2nd Road, Wuhan, 430062, Hubei, China
| | - Xiaoming Wu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Xudong 2nd Road, Wuhan, 430062, Hubei, China.
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Knoch D, Abbadi A, Grandke F, Meyer RC, Samans B, Werner CR, Snowdon RJ, Altmann T. Strong temporal dynamics of QTL action on plant growth progression revealed through high-throughput phenotyping in canola. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:68-82. [PMID: 31125482 PMCID: PMC6920335 DOI: 10.1111/pbi.13171] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 05/13/2019] [Accepted: 05/15/2019] [Indexed: 05/08/2023]
Abstract
A major challenge of plant biology is to unravel the genetic basis of complex traits. We took advantage of recent technical advances in high-throughput phenotyping in conjunction with genome-wide association studies to elucidate genotype-phenotype relationships at high temporal resolution. A diverse Brassica napus population from a commercial breeding programme was analysed by automated non-invasive phenotyping. Time-resolved data for early growth-related traits, including estimated biovolume, projected leaf area, early plant height and colour uniformity, were established and complemented by fresh and dry weight biomass. Genome-wide SNP array data provided the framework for genome-wide association analyses. Using time point data and relative growth rates, multiple robust main effect marker-trait associations for biomass and related traits were detected. Candidate genes involved in meristem development, cell wall modification and transcriptional regulation were detected. Our results demonstrate that early plant growth is a highly complex trait governed by several medium and many small effect loci, most of which act only during short phases. These observations highlight the importance of taking the temporal patterns of QTL/allele actions into account and emphasize the need for detailed time-resolved analyses to effectively unravel the complex and stage-specific contributions of genes affecting growth processes that operate at different developmental phases.
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Affiliation(s)
- Dominic Knoch
- Molecular Genetics/HeterosisLeibniz Institute of Plant Genetics and Crop Plant Research (IPK)SeelandGermany
| | - Amine Abbadi
- Norddeutsche Pflanzenzucht Innovation GmbH (NPZi)HoltseeGermany
| | - Fabian Grandke
- Department of Plant BreedingResearch Centre for BiosystemsLand Use and Nutrition (iFZ)Justus‐Liebig‐University GiessenGiessenGermany
| | - Rhonda C. Meyer
- Molecular Genetics/HeterosisLeibniz Institute of Plant Genetics and Crop Plant Research (IPK)SeelandGermany
| | - Birgit Samans
- Department of Plant BreedingResearch Centre for BiosystemsLand Use and Nutrition (iFZ)Justus‐Liebig‐University GiessenGiessenGermany
- Present address:
Technische Hochschule Mittelhessen (THM), University of Applied SciencesFachbereich Gesundheit35390GiessenGermany
| | - Christian R. Werner
- Department of Plant BreedingResearch Centre for BiosystemsLand Use and Nutrition (iFZ)Justus‐Liebig‐University GiessenGiessenGermany
- Present address:
The Roslin InstituteUniversity of EdinburghEaster Bush CampusMidlothianEH25 9RGUK
| | - Rod J. Snowdon
- Department of Plant BreedingResearch Centre for BiosystemsLand Use and Nutrition (iFZ)Justus‐Liebig‐University GiessenGiessenGermany
| | - Thomas Altmann
- Molecular Genetics/HeterosisLeibniz Institute of Plant Genetics and Crop Plant Research (IPK)SeelandGermany
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22
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Kang Y, Torres‐Jerez I, An Z, Greve V, Huhman D, Krom N, Cui Y, Udvardi M. Genome-wide association analysis of salinity responsive traits in Medicago truncatula. PLANT, CELL & ENVIRONMENT 2019; 42:1513-1531. [PMID: 30593671 PMCID: PMC6850670 DOI: 10.1111/pce.13508] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 12/16/2018] [Indexed: 05/19/2023]
Abstract
Salinity stress is an important cause of crop yield loss in many parts of the world. Here, we performed genome-wide association studies of salinity-stress responsive traits in 132 HapMap genotypes of the model legume Medicago truncatula. Plants grown in soil were subjected to a step-wise increase in NaCl concentration, from 0 through 0.5% and 1.0% to 1.5%, and the following traits were measured: vigor, shoot biomass, shoot water content, leaf chlorophyll content, leaf size, and leaf and root concentrations of proline and major ions (Na+ , Cl- , K+ , Ca2+ , etc.). Genome-wide association studies were carried out using 2.5 million single nucleotide polymorphisms, and 12 genomic regions associated with at least four traits each were identified. Transcript-level analysis of the top eight candidate genes in five extreme genotypes revealed association between salinity tolerance and transcript-level changes for seven of the genes, encoding a vacuolar H+ -ATPase, two transcription factors, two proteins involved in vesicle trafficking, one peroxidase, and a protein of unknown function. Earlier functional studies on putative orthologues of two of the top eight genes (a vacuolar H+ -ATPase and a peroxidase) demonstrated their involvement in plant salinity tolerance.
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Affiliation(s)
- Yun Kang
- Noble Research InstituteArdmoreOklahoma73401
| | | | - Zewei An
- State Center for Rubber Breeding and Rubber Research InstituteDanzhouHainan571700China
| | - Veronica Greve
- College of Biological SciencesUniversity of MinnesotaHuntsvilleAlabama35806
| | | | | | - Yuehua Cui
- Department of Statistics and ProbabilityMichigan State UniversityEast LansingMichigan48824
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23
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Wang Y, Zeng X, Xu Q, Mei X, Yuan H, Jiabu D, Sang Z, Nyima T. Metabolite profiling in two contrasting Tibetan hulless barley cultivars revealed the core salt-responsive metabolome and key salt-tolerance biomarkers. AOB PLANTS 2019; 11:plz021. [PMID: 31037214 PMCID: PMC6482114 DOI: 10.1093/aobpla/plz021] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 03/27/2019] [Indexed: 05/18/2023]
Abstract
Salinity stress represents one of the most harmful abiotic stresses for agricultural productivity. Tibetan hulless barley is an important economic crop widely grown in highly stressful conditions in the Qinghai-Tibet Plateau and is often challenged by salinity stress. To investigate the temporal metabolic responses to salinity stress in hulless barley, we performed a widely targeted metabolomic analysis of 72 leaf samples from two contrasting cultivars. We identified 642 compounds 57 % of which were affected by salt stress in the two cultivars, principally amino acids and derivatives, organic acids, nucleotides, and derivatives and flavonoids. A total of 13 stress-related metabolites including piperidine, L-tryptophan, L-glutamic acid, L-saccharopine, L-phenylalanine, 6-methylcoumarin, cinnamic acid, inosine 5'-monophosphate, aminomalonic acid, 6-aminocaproic acid, putrescine, tyramine and abscisic acid (ABA) represent the core metabolome responsive to salinity stress in hulless barley regardless of the tolerance level. In particular, we found that the ABA signalling pathway is essential to salt stress response in hulless barley. The high tolerance of the cultivar 0119 is due to a metabolic reprogramming at key stress times. During the early salt stress stages (0-24 h), 0119 tended to save energy through reduced glycolysis, nucleotide metabolism and amino acid synthesis, while increased antioxidant compounds such as flavonoids. Under prolonged stress (48-72 h), 0119 significantly enhanced energy production and amino acid synthesis. In addition, some important compatible solutes were strongly accumulated. By comparing the two cultivars, nine salt-tolerance biomarkers, mostly unreported salt-tolerance compounds in plants, were uncovered. Our study indicated that the salt tolerant hulless barley cultivar invokes a tolerance strategy which is conserved in other plant species. Overall, we provide for the first time some extensive metabolic data and some important salt-tolerance biomarkers which may assist in efforts to improve hulless barley tolerance to salinity stress.
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Affiliation(s)
- Yulin Wang
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, China
- Institute of Agricultural Research, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| | - Xingquan Zeng
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, China
- Institute of Agricultural Research, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| | - Qijun Xu
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, China
- Institute of Agricultural Research, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| | - Xiao Mei
- Wuhan Metware Biotechnology Co., Ltd, Wuhan, China
| | - Hongjun Yuan
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, China
- Institute of Agricultural Research, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| | - Dunzhu Jiabu
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, China
- Institute of Agricultural Research, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| | - Zha Sang
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, China
- Institute of Agricultural Research, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| | - Tashi Nyima
- Institute of Agricultural Research, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
- Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet, China
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24
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Zhang W, Hu D, Raman R, Guo S, Wei Z, Shen X, Meng J, Raman H, Zou J. Investigation of the Genetic Diversity and Quantitative Trait Loci Accounting for Important Agronomic and Seed Quality Traits in Brassica carinata. FRONTIERS IN PLANT SCIENCE 2017; 8:615. [PMID: 28484482 PMCID: PMC5401912 DOI: 10.3389/fpls.2017.00615] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2017] [Accepted: 04/04/2017] [Indexed: 05/21/2023]
Abstract
Brassica carinata (BBCC) is an allotetraploid in Brassicas with unique alleles for agronomic traits and has huge potential as source for biodiesel production. To investigate the genome-wide molecular diversity, population structure and linkage disequilibrium (LD) pattern in this species, we genotyped a panel of 81 accessions of B. carinata with genotyping by sequencing approach DArTseq, generating a total of 54,510 polymorphic markers. Two subpopulations were exhibited in the B. carinata accessions. The average distance of LD decay (r2 = 0.1) in B subgenome (0.25 Mb) was shorter than that of C subgenome (0.40 Mb). Genome-wide association analysis (GWAS) identified a total of seven markers significantly associated with five seed quality traits in two experiments. To further identify the quantitative trait loci (QTL) for important agronomic and seed quality traits, we phenotyped a doubled haploid (DH) mapping population derived from the "YW" cross between two parents (Y-BcDH64 and W-BcDH76) representing from the two subpopulations. The YW DH population and its parents were grown in three contrasting environments; spring (Hezheng and Xining, China), semi-winter (Wuhan, China), and spring (Wagga Wagga, Australia) across 5 years for QTL mapping. Genetic bases of phenotypic variation in seed yield and its seven related traits, and six seed quality traits were determined. A total of 282 consensus QTL accounting for these traits were identified including nine major QTL for flowering time, oleic acid, linolenic acid, pod number of main inflorescence, and seed weight. Of these, 109 and 134 QTL were specific to spring and semi-winter environment, respectively, while 39 consensus QTL were identified in both contrasting environments. Two QTL identified for linolenic acid (B3) and erucic acid (C7) were validated in the diverse lines used for GWAS. A total of 25 QTL accounting for flowering time, erucic acid, and oleic acid were aligned to the homologous QTL or candidate gene regions in the C genome of B. napus. These results would not only provide insights for genetic improvement of this species, but will also identify useful genetic variation hidden in the Cc subgenome of B. carinata to improve canola cultivars.
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Affiliation(s)
- Wenshan Zhang
- National Key Laboratory of Crop Genetic Improvement, Key Laboratory of Rapeseed Genetic Improvement, Ministry of Agriculture China, Huazhong Agricultural UniversityWuhan, China
| | - Dandan Hu
- National Key Laboratory of Crop Genetic Improvement, Key Laboratory of Rapeseed Genetic Improvement, Ministry of Agriculture China, Huazhong Agricultural UniversityWuhan, China
| | - Rosy Raman
- Graham Centre for Agricultural Innovation (an Alliance between the Charles Sturt University and NSW Department of Primary Industries), Wagga Wagga Agricultural InstituteWagga Wagga, NSW, Australia
| | - Shaomin Guo
- National Key Laboratory of Crop Genetic Improvement, Key Laboratory of Rapeseed Genetic Improvement, Ministry of Agriculture China, Huazhong Agricultural UniversityWuhan, China
| | - Zili Wei
- National Key Laboratory of Crop Genetic Improvement, Key Laboratory of Rapeseed Genetic Improvement, Ministry of Agriculture China, Huazhong Agricultural UniversityWuhan, China
| | - Xueqi Shen
- National Key Laboratory of Crop Genetic Improvement, Key Laboratory of Rapeseed Genetic Improvement, Ministry of Agriculture China, Huazhong Agricultural UniversityWuhan, China
| | - Jinling Meng
- National Key Laboratory of Crop Genetic Improvement, Key Laboratory of Rapeseed Genetic Improvement, Ministry of Agriculture China, Huazhong Agricultural UniversityWuhan, China
| | - Harsh Raman
- Graham Centre for Agricultural Innovation (an Alliance between the Charles Sturt University and NSW Department of Primary Industries), Wagga Wagga Agricultural InstituteWagga Wagga, NSW, Australia
| | - Jun Zou
- National Key Laboratory of Crop Genetic Improvement, Key Laboratory of Rapeseed Genetic Improvement, Ministry of Agriculture China, Huazhong Agricultural UniversityWuhan, China
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25
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Wan H, Chen L, Guo J, Li Q, Wen J, Yi B, Ma C, Tu J, Fu T, Shen J. Genome-Wide Association Study Reveals the Genetic Architecture Underlying Salt Tolerance-Related Traits in Rapeseed ( Brassica napus L.). FRONTIERS IN PLANT SCIENCE 2017; 8:593. [PMID: 28491067 PMCID: PMC5405135 DOI: 10.3389/fpls.2017.00593] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 03/31/2017] [Indexed: 05/02/2023]
Abstract
Soil salinity is a serious threat to agriculture sustainability worldwide. Salt tolerance at the seedling stage is crucial for plant establishment and high yield in saline soils; however, little information is available on rapeseed (Brassica napus L.) salt tolerance. We evaluated salt tolerance in different rapeseed accessions and conducted a genome-wide association study (GWAS) to identify salt tolerance-related quantitative trait loci (QTL). A natural population comprising 368 B. napus cultivars and inbred lines was genotyped with a Brassica 60K Illumina Infinium SNP array. The results revealed that 75 single-nucleotide polymorphisms (SNPs) distributed across 14 chromosomes were associated with four salt tolerance-related traits. These SNPs integrated into 25 QTLs that explained 4.21-9.23% of the phenotypic variation in the cultivars. Additionally, 38 possible candidate genes were identified in genomic regions associated with salt tolerance indices. These genes fell into several functional groups that are associated with plant salt tolerance, including transcription factors, aquaporins, transporters, and enzymes. Thus, salt tolerance in rapeseed involves complex molecular mechanisms. Our results provide valuable information for studying the genetic control of salt tolerance in B. napus seedlings and may facilitate marker-based breeding for rapeseed salt tolerance.
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26
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Khalil C, El Houssei B, Hassan B, Fouad M. Comparative Salt Tolerance Study of Some Acacia Species at Seed Germination Stage. ACTA ACUST UNITED AC 2016. [DOI: 10.3923/ajps.2016.66.74] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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27
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Zhu M, Monroe JG, Suhail Y, Villiers F, Mullen J, Pater D, Hauser F, Jeon BW, Bader JS, Kwak JM, Schroeder JI, McKay JK, Assmann SM. Molecular and systems approaches towards drought-tolerant canola crops. THE NEW PHYTOLOGIST 2016; 210:1169-1189. [PMID: 26879345 DOI: 10.1111/nph.13866] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2015] [Accepted: 12/14/2015] [Indexed: 06/05/2023]
Abstract
1169 I. 1170 II. 1170 III. 1172 IV. 1176 V. 1181 VI. 1182 1183 References 1183 SUMMARY: Modern agriculture is facing multiple challenges including the necessity for a substantial increase in production to meet the needs of a burgeoning human population. Water shortage is a deleterious consequence of both population growth and climate change and is one of the most severe factors limiting global crop productivity. Brassica species, particularly canola varieties, are cultivated worldwide for edible oil, animal feed, and biodiesel, and suffer dramatic yield loss upon drought stress. The recent release of the Brassica napus genome supplies essential genetic information to facilitate identification of drought-related genes and provides new information for agricultural improvement in this species. Here we summarize current knowledge regarding drought responses of canola, including physiological and -omics effects of drought. We further discuss knowledge gained through translational biology based on discoveries in the closely related reference species Arabidopsis thaliana and through genetic strategies such as genome-wide association studies and analysis of natural variation. Knowledge of drought tolerance/resistance responses in canola together with research outcomes arising from new technologies and methodologies will inform novel strategies for improvement of drought tolerance and yield in this and other important crop species.
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Affiliation(s)
- Mengmeng Zhu
- Biology Department, Pennsylvania State University, University Park, PA, 16802, USA
| | - J Grey Monroe
- Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, 80523, USA
| | - Yasir Suhail
- Department of Biomedical Engineering, The Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
| | - Florent Villiers
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20740, USA
| | - Jack Mullen
- Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, 80523, USA
| | - Dianne Pater
- Division of Biological Sciences, Cell and Developmental Biology Section, Food and Fuel for the 21st Century Center, University of California San Diego, La Jolla, CA, 92093-016, USA
| | - Felix Hauser
- Division of Biological Sciences, Cell and Developmental Biology Section, Food and Fuel for the 21st Century Center, University of California San Diego, La Jolla, CA, 92093-016, USA
| | - Byeong Wook Jeon
- Biology Department, Pennsylvania State University, University Park, PA, 16802, USA
| | - Joel S Bader
- Department of Biomedical Engineering, The Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
- School of Medicine, The Johns Hopkins University, Baltimore, MD, 21205, USA
| | - June M Kwak
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20740, USA
- Center for Plant Aging Research, Institute for Basic Science, Department of New Biology, DGIST, Daegu, 42988, Korea
| | - Julian I Schroeder
- Division of Biological Sciences, Cell and Developmental Biology Section, Food and Fuel for the 21st Century Center, University of California San Diego, La Jolla, CA, 92093-016, USA
| | - John K McKay
- Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, 80523, USA
| | - Sarah M Assmann
- Biology Department, Pennsylvania State University, University Park, PA, 16802, USA
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28
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Genc Y, Oldach K, Taylor J, Lyons GH. Uncoupling of sodium and chloride to assist breeding for salinity tolerance in crops. THE NEW PHYTOLOGIST 2016; 210:145-56. [PMID: 26607560 DOI: 10.1111/nph.13757] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 10/14/2015] [Indexed: 05/08/2023]
Abstract
The separation of toxic effects of sodium (Na(+)) and chloride (Cl(-)) by the current methods of mixed salts and subsequent determination of their relevance to breeding has been problematic. We report a novel method (Na(+) humate) to study the ionic effects of Na(+) toxicity without interference from Cl(-), and ionic and osmotic effects when combined with salinity (NaCl). Three cereal species (Hordeum vulgare, Triticum aestivum and Triticum turgidum ssp. durum with and without the Na(+) exclusion gene Nax2) differing in Na(+) exclusion were grown in a potting mix under sodicity (Na(+) humate) and salinity (NaCl), and water use, leaf nutrient profiles and yield were determined. Under sodicity, Na(+)-excluding bread wheat and durum wheat with the Nax2 gene had higher yield than Na(+)-accumulating barley and durum wheat without the Nax2 gene. However, under salinity, despite a 100-fold difference in leaf Na(+), all species yielded similarly, indicating that osmotic stress negated the benefits of Na(+) exclusion. In conclusion, Na(+) exclusion can be an effective mechanism for sodicity tolerance, while osmoregulation and tissue tolerance to Na(+) and/or Cl(-) should be the main foci for further improvement of salinity tolerance in cereals. This represents a paradigm shift for breeding cereals with salinity tolerance.
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Affiliation(s)
- Yusuf Genc
- South Australian Research and Development Institute, Plant Genomics Centre, Waite Campus, Glen Osmond, SA, 5064, Australia
- School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Glen Osmond, SA, 5064, Australia
| | - Klaus Oldach
- South Australian Research and Development Institute, Plant Genomics Centre, Waite Campus, Glen Osmond, SA, 5064, Australia
- School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Glen Osmond, SA, 5064, Australia
| | - Julian Taylor
- School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Glen Osmond, SA, 5064, Australia
| | - Graham H Lyons
- South Australian Research and Development Institute, Plant Genomics Centre, Waite Campus, Glen Osmond, SA, 5064, Australia
- School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Glen Osmond, SA, 5064, Australia
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