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Wang Y, Jiang C, Zhang X, Yan H, Yin Z, Sun X, Gao F, Zhao Y, Liu W, Han S, Zhang J, Zhang Y, Zhang Z, Zhang H, Li J, Xie X, Zhao Q, Wang X, Ye G, Li J, Ming R, Li Z. Upland rice genomic signatures of adaptation to drought resistance and navigation to molecular design breeding. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:662-677. [PMID: 37909415 PMCID: PMC10893945 DOI: 10.1111/pbi.14215] [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: 06/06/2023] [Revised: 07/31/2023] [Accepted: 10/16/2023] [Indexed: 11/03/2023]
Abstract
Upland rice is a distinctive drought-aerobic ecotype of cultivated rice highly resistant to drought stress. However, the genetic and genomic basis for the drought-aerobic adaptation of upland rice remains largely unclear due to the lack of genomic resources. In this study, we identified 25 typical upland rice accessions and assembled a high-quality genome of one of the typical upland rice varieties, IRAT109, comprising 384 Mb with a contig N50 of 19.6 Mb. Phylogenetic analysis revealed upland and lowland rice have distinct ecotype differentiation within the japonica subgroup. Comparative genomic analyses revealed that adaptive differentiation of lowland and upland rice is likely attributable to the natural variation of many genes in promoter regions, formation of specific genes in upland rice, and expansion of gene families. We revealed differentiated gene expression patterns in the leaves and roots of the two ecotypes and found that lignin synthesis mediated by the phenylpropane pathway plays an important role in the adaptive differentiation of upland and lowland rice. We identified 28 selective sweeps that occurred during domestication and validated that the qRT9 gene in selective regions can positively regulate drought resistance in rice. Eighty key genes closely associated with drought resistance were appraised for their appreciable potential in drought resistance breeding. Our study enhances the understanding of the adaptation of upland rice and provides a genome navigation map of drought resistance breeding, which will facilitate the breeding of drought-resistant rice and the "blue revolution" in agriculture.
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Affiliation(s)
- Yulong Wang
- Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Conghui Jiang
- Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
- Institute of Wetland Agriculture and EcologyShandong Academy of Agricultural SciencesJinanShandongChina
| | - Xingtan Zhang
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of EducationFujian Agriculture and Forestry UniversityFuzhouFujianChina
- Agricultural Genomics Institute in ShenzhenChinese Academy of Agricultural SciencesShenzhenGuangdongChina
| | - Huimin Yan
- Collaborative Innovation Center of Henan Grain Crops, Henan Key Laboratory of Rice BiologyHenan Agricultural UniversityZhengzhouHenanChina
| | - Zhigang Yin
- Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Xingming Sun
- Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Fenghua Gao
- Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Yan Zhao
- Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Wei Liu
- Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Shichen Han
- Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Jingjing Zhang
- Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Yage Zhang
- Sanya Institute of Hainan Academy of Agricultural SciencesSanyaHainanChina
| | - Zhanying Zhang
- Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Hongliang Zhang
- Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Jinjie Li
- Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Xianzhi Xie
- Institute of Wetland Agriculture and EcologyShandong Academy of Agricultural SciencesJinanShandongChina
| | - Quanzhi Zhao
- Collaborative Innovation Center of Henan Grain Crops, Henan Key Laboratory of Rice BiologyHenan Agricultural UniversityZhengzhouHenanChina
| | - Xiaoning Wang
- Sanya Institute of Hainan Academy of Agricultural SciencesSanyaHainanChina
| | - Guoyou Ye
- Agricultural Genomics Institute in ShenzhenChinese Academy of Agricultural SciencesShenzhenGuangdongChina
- Institution International Rice Research InstituteLos BañosLagunaPhilippines
| | - Junzhou Li
- Collaborative Innovation Center of Henan Grain Crops, Henan Key Laboratory of Rice BiologyHenan Agricultural UniversityZhengzhouHenanChina
| | - Ray Ming
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of EducationFujian Agriculture and Forestry UniversityFuzhouFujianChina
| | - Zichao Li
- Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
- Sanya Institute of Hainan Academy of Agricultural SciencesSanyaHainanChina
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2
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Zhao X, Xu Z, Chen Y, Du Y, Li M, Huang B, Ge Y, Gu M, Tang S, Liu Q, Zhang H. Development of introgression lines and mapping of qGW2, a novel QTL that confers grain width, in rice ( Oryza sativa L.). MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2024; 44:10. [PMID: 38298743 PMCID: PMC10825081 DOI: 10.1007/s11032-024-01453-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 01/19/2024] [Indexed: 02/02/2024]
Abstract
Rice grain size is a key determinant of both grain yield and quality. Identification of favorable alleles for use in rice breeding may help to meet the demand for increased yield. In this study, we developed a set of 210 introgression lines (ILs) by using indica variety Huanghuazhan as the donor parent and erect-panicle japonica rice variety Wuyujing3R as the recurrent parent. A total of 133 ILs were selected for high-throughput sequencing. Using specific-locus amplified fragment (SLAF) sequencing technology, 10,103 high-quality SLAF labels evenly distributed on 12 chromosomes were obtained and selected for subsequent analysis. Using a high-density map, quantitative trait locus (QTL) mapping of grain size-related traits was performed, and a total of 38 QTLs were obtained in two environments. Furthermore, qGW2, a novel QTL that controls grain width on chromosome 2, was validated and delimited to a region of 309 kb via substitution mapping. These findings provide new genetic material and a basis for future fine mapping and cloning of favorable QTLs. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-024-01453-0.
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Affiliation(s)
- Xiangqiang Zhao
- School of Life Sciences, Nantong University, Nantong, 226019 Jiangsu China
| | - Zuopeng Xu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agricultural College of Yangzhou University, Yangzhou, 225009 China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, 225009 China
| | - YiBo Chen
- Guangdong Academy of Agricultural Sciences, Rice Research Institute, Guangzhou, 510640 Guangdong China
| | - Yuanyue Du
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agricultural College of Yangzhou University, Yangzhou, 225009 China
| | - Meng Li
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agricultural College of Yangzhou University, Yangzhou, 225009 China
| | - Benxi Huang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agricultural College of Yangzhou University, Yangzhou, 225009 China
| | - Yongshen Ge
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agricultural College of Yangzhou University, Yangzhou, 225009 China
| | - Minghong Gu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agricultural College of Yangzhou University, Yangzhou, 225009 China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, 225009 China
| | - Shuzhu Tang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agricultural College of Yangzhou University, Yangzhou, 225009 China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, 225009 China
| | - Qiaoquan Liu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agricultural College of Yangzhou University, Yangzhou, 225009 China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, 225009 China
| | - Honggen Zhang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agricultural College of Yangzhou University, Yangzhou, 225009 China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, 225009 China
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Daryani P, Amirbakhtiar N, Soorni J, Loni F, Darzi Ramandi H, Shobbar ZS. Uncovering the Genomic Regions Associated with Yield Maintenance in Rice Under Drought Stress Using an Integrated Meta-Analysis Approach. RICE (NEW YORK, N.Y.) 2024; 17:7. [PMID: 38227151 DOI: 10.1186/s12284-024-00684-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Accepted: 01/03/2024] [Indexed: 01/17/2024]
Abstract
The complex trait of yield is controlled by several quantitative trait loci (QTLs). Given the global water deficit issue, the development of rice varieties suitable for non-flooded cultivation holds significant importance in breeding programs. The powerful approach of Meta-QTL (MQTL) analysis can be used for the genetic dissection of complicated quantitative traits. In the current study, a comprehensive MQTL analysis was conducted to identify consistent QTL regions associated with drought tolerance and yield-related traits under water deficit conditions in rice. In total, 1087 QTLs from 134 rice populations, published between 2000 to 2021, were utilized in the analysis. Distinct MQTL analysis of the relevant traits resulted in the identification of 213 stable MQTLs. The confidence interval (CI) for the detected MQTLs was between 0.12 and 19.7 cM. The average CI of the identified MQTLs (4.68 cM) was 2.74 times narrower compared to the average CI of the initial QTLs. Interestingly, 63 MQTLs coincided with SNP peak positions detected by genome-wide association studies for yield and drought tolerance-associated traits under water deficit conditions in rice. Considering the genes located both in the QTL-overview peaks and the SNP peak positions, 19 novel candidate genes were introduced, which are associated with drought response index, plant height, panicle number, biomass, and grain yield. Moreover, an inclusive MQTL analysis was performed on all the traits to obtain "Breeding MQTLs". This analysis resulted in the identification of 96 MQTLs with a CI ranging from 0.01 to 9.0 cM. The mean CI of the obtained MQTLs (2.33 cM) was 4.66 times less than the mean CI of the original QTLs. Thirteen MQTLs fulfilling the criteria of having more than 10 initial QTLs, CI < 1 cM, and an average phenotypic variance explained greater than 10%, were designated as "Breeding MQTLs". These findings hold promise for assisting breeders in enhancing rice yield under drought stress conditions.
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Affiliation(s)
- Parisa Daryani
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Nazanin Amirbakhtiar
- National Plant Gene Bank of Iran, Seed and Plant Improvement Institute (SPII), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Jahad Soorni
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Fatemeh Loni
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Hadi Darzi Ramandi
- Department of Plant Production and Genetics, Faculty of Agriculture, Bu-Ali Sina University, Hamedan, Iran.
| | - Zahra-Sadat Shobbar
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran.
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4
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Li Y, Tao F, Hao Y, Tong J, Xiao Y, He Z, Reynolds M. Variations in phenological, physiological, plant architectural and yield-related traits, their associations with grain yield and genetic basis. ANNALS OF BOTANY 2023; 131:503-519. [PMID: 36655618 PMCID: PMC10072080 DOI: 10.1093/aob/mcad003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 01/09/2023] [Indexed: 06/17/2023]
Abstract
BACKGROUND AND AIMS Physiological and morphological traits play essential roles in wheat (Triticum aestivum) growth and development. In particular, photosynthesis is a limitation to yield. Increasing photosynthesis in wheat has been identified as an important strategy to increase yield. However, the genotypic variations and the genomic regions governing morphological, architectural and photosynthesis traits remain unexplored. METHODS Here, we conducted a large-scale investigation of the phenological, physiological, plant architectural and yield-related traits, involving 32 traits for 166 wheat lines during 2018-2020 in four environments, and performed a genome-wide association study with wheat 90K and 660K single nucleotide polymorphism (SNP) arrays. KEY RESULTS These traits exhibited considerable genotypic variations in the wheat diversity panel. Higher yield was associated with higher net photosynthetic rate (r = 0.41, P < 0.01), thousand-grain weight (r = 0.36, P < 0.01) and truncated and lanceolate shape, but shorter plant height (r = -0.63, P < 0.01), flag leaf angle (r = -0.49, P < 0.01) and spike number per square metre (r = -0.22, P < 0.01). Genome-wide association mapping discovered 1236 significant stable loci detected in the four environments among the 32 traits using SNP markers. Trait values have a cumulative effect as the number of the favourable alleles increases, and significant progress has been made in determining phenotypic values and favourable alleles over the years. Eleven elite cultivars and 14 traits associated with grain yield per plot (GY) were identified as potential parental lines and as target traits to develop high-yielding cultivars. CONCLUSIONS This study provides new insights into the phenotypic and genetic elucidation of physiological and morphological traits in wheat and their associations with GY, paving the way for discovering their underlying gene control and for developing enhanced ideotypes in wheat breeding.
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Affiliation(s)
- Yibo Li
- Key Laboratory of Land Surface Pattern and Simulation, Institute of Geographic Sciences and Natural Resources Research, CAS, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | | | - Yuanfeng Hao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jingyang Tong
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yonggui Xiao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | | | - Matthew Reynolds
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
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5
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Li Y, Tao F, Hao Y, Tong J, Xiao Y, Zhang H, He Z, Reynolds M. Linking genetic markers with an eco-physiological model to pyramid favourable alleles and design wheat ideotypes. PLANT, CELL & ENVIRONMENT 2023; 46:780-795. [PMID: 36517924 DOI: 10.1111/pce.14518] [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: 08/14/2022] [Accepted: 12/12/2022] [Indexed: 06/17/2023]
Abstract
Genetic markers can be linked with eco-physiological crop models to accurately predict genotype performance and individual markers' contributions in target environments, exploring interactions between genotype and environment. Here, wheat (Triticum aestivum L.) yield was dissected into seven traits corresponding to cultivar genetic coefficients in an eco-physiological model. Loci for these traits were discovered through the genome-wide association studies (GWAS). The cultivar genetic coefficients were derived from the loci using multiple linear regression or random forest, building a marker-based eco-physiological model. It is then applied to simulate wheat yields and design virtual ideotypes. The results indicated that the loci identified through GWAS explained 46%-75% variations in cultivar genetic coefficients. Using the marker-based model, the normalized root mean square error (nRMSE) between the simulated yield and observed yield was 13.95% by multiple linear regression and 13.62% by random forest. The nRMSE between the simulated and observed maturity dates was 1.24% by multiple linear regression and 1.11% by random forest, respectively. Structural equation modelling indicated that variations in grain yield could be well explained by cultivar genetic coefficients and phenological data. In addition, 24 pleiotropic loci in this study were detected on 15 chromosomes. More significant loci were detected by the model-based dissection method than considering yield per se. Ideotypes were identified by higher yield and more favourable alleles of cultivar genetic traits. This study proposes a genotype-to-phenotype approach and demonstrates novel ideas and tools to support the effective breeding of new cultivars with high yield through pyramiding favourable alleles and designing crop ideotypes.
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Affiliation(s)
- Yibo Li
- Key Laboratory of Land Surface Pattern and Simulation, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Fulu Tao
- Key Laboratory of Land Surface Pattern and Simulation, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yuanfeng Hao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jingyang Tong
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yonggui Xiao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - He Zhang
- Key Laboratory of Land Surface Pattern and Simulation, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, China
| | - Zhonghu He
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Matthew Reynolds
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
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6
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Kumar A, Pandey SS, Kumar D, Tripathi BN. Genetic manipulation of photosynthesis to enhance crop productivity under changing environmental conditions. PHOTOSYNTHESIS RESEARCH 2023; 155:1-21. [PMID: 36319887 DOI: 10.1007/s11120-022-00977-w] [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: 06/06/2022] [Accepted: 10/14/2022] [Indexed: 06/16/2023]
Abstract
Current global agricultural production needs to be increased to feed the unconstrained growing population. The changing climatic condition due to anthropogenic activities also makes the conditions more challenging to meet the required crop productivity in the future. The increase in crop productivity in the post green revolution era most likely became stagnant, or no major enhancement in crop productivity observed. In this review article, we discuss the emerging approaches for the enhancement of crop production along with dealing to the future climate changes like rise in temperature, increase in precipitation and decrease in snow and ice level, etc. At first, we discuss the efforts made for the genetic manipulation of chlorophyll metabolism, antenna engineering, electron transport chain, carbon fixation, and photorespiratory processes to enhance the photosynthesis of plants and to develop tolerance in plants to cope with changing environmental conditions. The application of CRISPR to enhance the crop productivity and develop abiotic stress-tolerant plants to face the current changing climatic conditions is also discussed.
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Affiliation(s)
- Abhishek Kumar
- Biotechnology Division, Council of Scientific and Industrial Research (CSIR)-Institute of Himalayan Bioresource Technology, Palampur, 176061, India
| | - Shiv Shanker Pandey
- Biotechnology Division, Council of Scientific and Industrial Research (CSIR)-Institute of Himalayan Bioresource Technology, Palampur, 176061, India.
| | - Dhananjay Kumar
- Laboratory of Algal Biotechnology, Department of Botany and Microbiology, School of Life Sciences, H.N.B. Garhwal University, Srinagar, Garhwal, 246 174, India.
| | - Bhumi Nath Tripathi
- Department of Biotechnology, Indira Gandhi National Tribal University, Amarkantak, 484886, India
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7
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Garassino F, Wijfjes RY, Boesten R, Reyes Marquez F, Becker FFM, Clapero V, van den Hatert I, Holmer R, Schranz ME, Harbinson J, de Ridder D, Smit S, Aarts MGM. The genome sequence of Hirschfeldia incana, a new Brassicaceae model to improve photosynthetic light-use efficiency. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 112:1298-1315. [PMID: 36239071 PMCID: PMC10100226 DOI: 10.1111/tpj.16005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 10/09/2022] [Accepted: 10/12/2022] [Indexed: 06/16/2023]
Abstract
Photosynthesis is a key process in sustaining plant and human life. Improving the photosynthetic capacity of agricultural crops is an attractive means to increase their yields. While the core mechanisms of photosynthesis are highly conserved in C3 plants, these mechanisms are very flexible, allowing considerable diversity in photosynthetic properties. Among this diversity is the maintenance of high photosynthetic light-use efficiency at high irradiance as identified in a small number of exceptional C3 species. Hirschfeldia incana, a member of the Brassicaceae family, is such an exceptional species, and because it is easy to grow, it is an excellent model for studying the genetic and physiological basis of this trait. Here, we present a reference genome of H. incana and confirm its high photosynthetic light-use efficiency. While H. incana has the highest photosynthetic rates found so far in the Brassicaceae, the light-saturated assimilation rates of closely related Brassica rapa and Brassica nigra are also high. The H. incana genome has extensively diversified from that of B. rapa and B. nigra through large chromosomal rearrangements, species-specific transposon activity, and differential retention of duplicated genes. Duplicated genes in H. incana, B. rapa, and B. nigra that are involved in photosynthesis and/or photoprotection show a positive correlation between copy number and gene expression, providing leads into the mechanisms underlying the high photosynthetic efficiency of these species. Our work demonstrates that the H. incana genome serves as a valuable resource for studying the evolution of high photosynthetic light-use efficiency and enhancing photosynthetic rates in crop species.
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Affiliation(s)
| | - Raúl Y. Wijfjes
- Bioinformatics GroupWageningen University & ResearchWageningenNetherlands
- Present address:
Faculty of BiologyLudwig Maximilian University of MunichMunichGermany
| | - René Boesten
- Laboratory of GeneticsWageningen University & ResearchWageningenNetherlands
| | | | - Frank F. M. Becker
- Laboratory of GeneticsWageningen University & ResearchWageningenNetherlands
| | - Vittoria Clapero
- Laboratory of GeneticsWageningen University & ResearchWageningenNetherlands
- Present address:
Max Planck Institute for Molecular Plant PhysiologyGolmGermany
| | | | - Rens Holmer
- Bioinformatics GroupWageningen University & ResearchWageningenNetherlands
| | - M. Eric Schranz
- Biosystematics GroupWageningen University & ResearchWageningenNetherlands
| | - Jeremy Harbinson
- Laboratory of BiophysicsWageningen University & ResearchWageningenNetherlands
| | - Dick de Ridder
- Bioinformatics GroupWageningen University & ResearchWageningenNetherlands
| | - Sandra Smit
- Bioinformatics GroupWageningen University & ResearchWageningenNetherlands
| | - Mark G. M. Aarts
- Laboratory of GeneticsWageningen University & ResearchWageningenNetherlands
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8
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Li Y, Tao F, Hao Y, Tong J, Xiao Y, He Z, Reynolds M. Wheat traits and the associated loci conferring radiation use efficiency. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 112:565-582. [PMID: 36004546 DOI: 10.1111/tpj.15954] [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: 05/02/2022] [Revised: 08/16/2022] [Accepted: 08/20/2022] [Indexed: 06/15/2023]
Abstract
Wheat (Triticum aestivum L.) radiation use efficiency (RUE) must be raised through crop breeding to further increase the yield potential, as the harvest index is now close to its theoretical limit. Field experiments including 209 wheat cultivars which have been widely cultivated in China since the 1940s were conducted in two growing seasons (2018-2019 and 2019-2020) to evaluate the variations of phenological, physiological, plant architectural, and yield-related traits and their contributions to RUE and to identify limiting factors for wheat yield potential. The average annual genetic gain in grain yield was 0.60% (or 45.32 kg ha-1 year-1 ; R2 = 0.44, P < 0.01), mainly attributed to the gain in RUE (r = 0.85, P < 0.01). The net photosynthetic rates were positively and closely correlated with grain RUE and grain yield, suggesting source as a limiting factor to future yield gains. Thirty-four cultivars were identified, exhibiting not only high RUE, but also traits contributing to high RUE and 11 other critical traits - of known genetic basis - as potential parents for breeding to improve yield and RUE. Our findings reveal wheat traits and the associated loci conferring RUE, which are valuable for facilitating marker-assisted breeding to improve wheat RUE and yield potential.
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Affiliation(s)
- Yibo Li
- Key Laboratory of Land Surface Pattern and Simulation, Institute of Geographic Sciences and Natural Resources Research, CAS, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Fulu Tao
- Key Laboratory of Land Surface Pattern and Simulation, Institute of Geographic Sciences and Natural Resources Research, CAS, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Natural Resources Institute Finland (Luke), Helsinki, Finland
| | - Yuanfeng Hao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jingyang Tong
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yonggui Xiao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zhonghu He
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Matthew Reynolds
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
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9
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Yadavalli VR, Balakrishnan D, Surapaneni M, Addanki K, Mesapogu S, Beerelli K, Desiraju S, Voleti SR, Neelamraju S. Mapping QTLs for yield and photosynthesis-related traits in three consecutive backcross populations of Oryza sativa cultivar Cottondora Sannalu (MTU1010) and Oryza rufipogon. PLANTA 2022; 256:71. [PMID: 36070104 DOI: 10.1007/s00425-022-03983-3] [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: 02/11/2022] [Accepted: 08/25/2022] [Indexed: 06/15/2023]
Abstract
Identification of trait enhancing QTLs for yield and photosynthesis-related traits in rice using interspecific mapping population and chromosome segment substitution lines derived from a cross between Oryza sativa and Oryza rufipogon. Wild rice contains novel genes which can help in improving rice yield. Common wild rice Oryza rufipogon is a known source for enhanced photosynthesis and yield-related traits. We developed BC2F2:3:4 mapping populations using O. rufipogon IC309814 with high photosynthetic rate as donor, and elite cultivar MTU1010 as recurrent parent. Evaluation of 238 BC2F2 families for 13 yield-related traits and 208 BC2F2 families for seven photosynthesis-related physiological traits resulted in identification of significantly different lines which performed better than MTU1010 for various yield contributing traits. 49 QTLs were identified for 13 yield traits and 7 QTLs for photosynthesis-related traits in BC2F2. In addition, 34 QTLs in BC2F3 and 26 QTLs in BC2F4 were also detected for yield traits.11 common QTLs were identified in three consecutive generations and their trait-increasing alleles were derived from O. rufipogon. Significantly, one major effect common QTL qTGW3.1 for thousand grain weight with average phenotypic variance 8.1% and one novel QTL qBM7.1 for biomass were identified. Photosynthesis-related QTLs qPN9.1, qPN12.1, qPN12.2 qSPAD1.1 and qSPAD6.1 showed additive effect from O. rufipogon. A set of 145 CSSLs were identified in BC2F2 which together represented 87% of O. rufipogon genome. In addition, 87 of the 145 CSSLs were significantly different than MTU1010 for at least one trait. The major effect QTLs can be fine mapped for gene discovery. CSSLs developed in this study are a good source of novel alleles from O. rufipogon in the background of Cottondora Sannalu for rapid improvement of any trait in rice.
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Affiliation(s)
- Venkateswara Rao Yadavalli
- ICAR National Professor Project, ICAR-Indian Institute of Rice Research, Hyderabad, 500030, Telangana, India
| | - Divya Balakrishnan
- ICAR National Professor Project, ICAR-Indian Institute of Rice Research, Hyderabad, 500030, Telangana, India
- Department of Plant Breeding and Genetics, ICAR-Indian Institute of Rice Research, Hyderabad, 500030, Telangana, India
| | - Malathi Surapaneni
- ICAR National Professor Project, ICAR-Indian Institute of Rice Research, Hyderabad, 500030, Telangana, India
| | - Krishnamraju Addanki
- ICAR National Professor Project, ICAR-Indian Institute of Rice Research, Hyderabad, 500030, Telangana, India
| | - Sukumar Mesapogu
- ICAR National Professor Project, ICAR-Indian Institute of Rice Research, Hyderabad, 500030, Telangana, India
| | - Kavitha Beerelli
- ICAR National Professor Project, ICAR-Indian Institute of Rice Research, Hyderabad, 500030, Telangana, India
| | - Subrahmanyam Desiraju
- Department of Plant Physiology, ICAR-Indian Institute of Rice Research, Hyderabad, 500030, Telangana, India
| | - Sitapati Rao Voleti
- Department of Plant Physiology, ICAR-Indian Institute of Rice Research, Hyderabad, 500030, Telangana, India
| | - Sarla Neelamraju
- ICAR National Professor Project, ICAR-Indian Institute of Rice Research, Hyderabad, 500030, Telangana, India.
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Fang S, Zhao P, Tan Z, Peng Y, Xu L, Jin Y, Wei F, Guo L, Yao X. Combining Physio-Biochemical Characterization and Transcriptome Analysis Reveal the Responses to Varying Degrees of Drought Stress in Brassica napus L. Int J Mol Sci 2022; 23:ijms23158555. [PMID: 35955689 PMCID: PMC9368929 DOI: 10.3390/ijms23158555] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 07/25/2022] [Accepted: 07/28/2022] [Indexed: 02/05/2023] Open
Abstract
Brassica napus L. has become one of the most important oil-bearing crops, and drought stress severely influences its yield and quality. By combining physio-biochemical characterization and transcriptome analysis, we studied the response of B. napus plants to different degrees of drought stress. Some physio-biochemical traits, such as fresh weight (FW), dry weight (DW), abscisic acid (ABA) content, net photosynthetic rate (Pn), stomatal conductance (gs), and transpiration rate (Tr), were measured, and the total content of the epidermal wax/cutin, as well as their compositions, was determined. The results suggest that both stomatal transpiration and cuticular transpiration are affected when B. napus plants are subjected to varying degrees of drought stress. A total of 795 up-regulated genes and 1050 down-regulated genes were identified under severe drought stress by transcriptome analysis. Gene ontology (GO) enrichment analysis of differentially expressed genes (DEGs) revealed that the up-regulated genes were mainly enriched in the stress response processes, such as response to water deprivation and abscisic acid, while the down-regulated genes were mainly enriched in the chloroplast-related parts affecting photosynthesis. Moreover, overexpression of BnaA01.CIPK6, an up-regulated DEG, was found to confer drought tolerance in B. napus. Our study lays a foundation for a better understanding of the molecular mechanisms underlying drought tolerance in B. napus.
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Affiliation(s)
- Shuai Fang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; (S.F.); (P.Z.); (Z.T.); (Y.P.); (L.X.); (Y.J.); (L.G.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Peimin Zhao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; (S.F.); (P.Z.); (Z.T.); (Y.P.); (L.X.); (Y.J.); (L.G.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Zengdong Tan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; (S.F.); (P.Z.); (Z.T.); (Y.P.); (L.X.); (Y.J.); (L.G.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Yan Peng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; (S.F.); (P.Z.); (Z.T.); (Y.P.); (L.X.); (Y.J.); (L.G.)
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Lintang Xu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; (S.F.); (P.Z.); (Z.T.); (Y.P.); (L.X.); (Y.J.); (L.G.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Yutong Jin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; (S.F.); (P.Z.); (Z.T.); (Y.P.); (L.X.); (Y.J.); (L.G.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Fang Wei
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Oilseeds Processing of Ministry of Agriculture and Hubei Key Laboratory of Lipid Chemistry and Nutrition, Wuhan 430062, China;
| | - Liang Guo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; (S.F.); (P.Z.); (Z.T.); (Y.P.); (L.X.); (Y.J.); (L.G.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan 430070, China
| | - Xuan Yao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; (S.F.); (P.Z.); (Z.T.); (Y.P.); (L.X.); (Y.J.); (L.G.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
- Correspondence:
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11
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Niu Y, Chen T, Zheng Z, Zhao C, Liu C, Jia J, Zhou M. A new major QTL for flag leaf thickness in barley (Hordeum vulgare L.). BMC PLANT BIOLOGY 2022; 22:305. [PMID: 35751018 PMCID: PMC9229122 DOI: 10.1186/s12870-022-03694-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 06/14/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Carbohydrate accumulation of photosynthetic organs, mainly leaves, are the primary sources of grain yield in cereals. The flag leaf plays a vital role in seed development, which is probably the most neglected morphological characteristic during traditional selection processes. RESULTS In this experiment, four flag leaf morphological traits and seven yield-related traits were investigated in a DH population derived from a cross between a wild barley and an Australian malting barley cultivar. Flag leaf thickness (FLT) showed significantly positive correlations with grain size. Four QTL, located on chromosomes 1H, 2H, 3H, and 5H, respectively, were identified for FLT. Among them, a major QTL was located on chromosome 3H with a LOD value of 18.4 and determined 32% of the phenotypic variation. This QTL showed close links but not pleiotropism to the previously reported semi-dwarf gene sdw1 from the cultivated barley. This QTL was not reported before and the thick leaf allele from the wild barley could provide a useful source for improving grain yield through breeding. CONCLUSIONS Our results also provided valuable evidence that source traits and sink traits in barley are tightly connected and suggest further improvement of barley yield potential with enhanced and balanced source and sink relationships by exploiting potentialities of the wild barley resources. Moreover, this study will provide a novel sight on understanding the evolution and development of leaf morphology in barley and improving barley production by rewilding for lost superior traits during plant evolution.
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Affiliation(s)
- Yanan Niu
- Tasmanian Institute of Agriculture, University of Tasmania, Private Bag 1375, 7250, Prospect, TAS, Australia
| | - Tianxiao Chen
- Tasmanian Institute of Agriculture, University of Tasmania, Private Bag 1375, 7250, Prospect, TAS, Australia
| | - Zhi Zheng
- CSIRO Agriculture and Food, 4067, St Lucia, QLD, Australia
| | - Chenchen Zhao
- Tasmanian Institute of Agriculture, University of Tasmania, Private Bag 1375, 7250, Prospect, TAS, Australia
| | - Chunji Liu
- CSIRO Agriculture and Food, 4067, St Lucia, QLD, Australia
| | - Jizeng Jia
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 100081, Beijing, China.
| | - Meixue Zhou
- Tasmanian Institute of Agriculture, University of Tasmania, Private Bag 1375, 7250, Prospect, TAS, Australia.
- College of Agronomy, Shanxi Agricultural University, 030801, Taigu, China.
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12
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Struik PC, Driever SM. Intriguing correlations between leaf architecture and intrinsic water-use efficiency enable selective breeding to mitigate climate challenges. PLANT, CELL & ENVIRONMENT 2022; 45:1607-1611. [PMID: 35274305 PMCID: PMC9313581 DOI: 10.1111/pce.14305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 02/25/2022] [Accepted: 03/03/2022] [Indexed: 06/14/2023]
Affiliation(s)
- Paul Christiaan Struik
- Centre for Crop Systems AnalysisWageningen University and ResearchWageningenThe Netherlands
| | - Steven Michiel Driever
- Centre for Crop Systems AnalysisWageningen University and ResearchWageningenThe Netherlands
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13
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Ortiz D, Salas-Fernandez MG. Dissecting the genetic control of natural variation in sorghum photosynthetic response to drought stress. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:3251-3267. [PMID: 34791180 PMCID: PMC9126735 DOI: 10.1093/jxb/erab502] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 11/12/2021] [Indexed: 06/13/2023]
Abstract
Drought stress causes crop yield losses worldwide. Sorghum is a C4 species tolerant to moderate drought stress, and its extensive natural variation for photosynthetic traits under water-limiting conditions can be exploited for developing cultivars with enhanced stress tolerance. The objective of this study was to discover genes/genomic regions that control the sorghum photosynthetic capacity under pre-anthesis water-limiting conditions. We performed a genome-wide association study for seven photosynthetic gas exchange and chlorophyll fluorescence traits during three periods of contrasting soil volumetric water content (VWC): control (30% VWC), drought (15% VWC), and recovery (30% VWC). Water stress was imposed with an automated irrigation system that generated a controlled dry-down period for all plants, to perform an unbiased genotypic comparison. A total of 60 genomic regions were associated with natural variation in one or more photosynthetic traits in a particular treatment or with derived variables. We identified 33 promising candidate genes with predicted functions related to stress signaling, oxidative stress protection, hormonal response to stress, and dehydration protection. Our results provide new knowledge about the natural variation and genetic control of sorghum photosynthetic response to drought with the ultimate goal of improving its adaptation and productivity under water stress scenarios.
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Affiliation(s)
- Diego Ortiz
- Department of Agronomy, Iowa State University, Ames, IA 50011, USA
- Instituto Nacional de Tecnologia Agropecuaria, Manfredi, Cordoba 5988, Argentina
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14
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Yin X, Gu J, Dingkuhn M, Struik PC. A model-guided holistic review of exploiting natural variation of photosynthesis traits in crop improvement. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:3173-3188. [PMID: 35323898 PMCID: PMC9126731 DOI: 10.1093/jxb/erac109] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 03/22/2022] [Indexed: 05/18/2023]
Abstract
Breeding for improved leaf photosynthesis is considered as a viable approach to increase crop yield. Whether it should be improved in combination with other traits has not been assessed critically. Based on the quantitative crop model GECROS that interconnects various traits to crop productivity, we review natural variation in relevant traits, from biochemical aspects of leaf photosynthesis to morpho-physiological crop characteristics. While large phenotypic variations (sometimes >2-fold) for leaf photosynthesis and its underlying biochemical parameters were reported, few quantitative trait loci (QTL) were identified, accounting for a small percentage of phenotypic variation. More QTL were reported for sink size (that feeds back on photosynthesis) or morpho-physiological traits (that affect canopy productivity and duration), together explaining a much greater percentage of their phenotypic variation. Traits for both photosynthetic rate and sustaining it during grain filling were strongly related to nitrogen-related traits. Much of the molecular basis of known photosynthesis QTL thus resides in genes controlling photosynthesis indirectly. Simulation using GECROS demonstrated the overwhelming importance of electron transport parameters, compared with the maximum Rubisco activity that largely determines the commonly studied light-saturated photosynthetic rate. Exploiting photosynthetic natural variation might significantly improve crop yield if nitrogen uptake, sink capacity, and other morpho-physiological traits are co-selected synergistically.
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Affiliation(s)
- Xinyou Yin
- Centre for Crop Systems Analysis, Wageningen University & Research, PO Box 430, 6700 AK Wageningen, The Netherlands
- Correspondence:
| | - Junfei Gu
- College of Agriculture, Yangzhou University, 48 Wenhui East Road, Yangzhou, Jiangsu 225009, China
| | | | - Paul C Struik
- Centre for Crop Systems Analysis, Wageningen University & Research, PO Box 430, 6700 AK Wageningen, The Netherlands
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15
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Tanaka M, Keira M, Yoon DK, Mae T, Ishida H, Makino A, Ishiyama K. Photosynthetic Enhancement, Lifespan Extension, and Leaf Area Enlargement in Flag Leaves Increased the Yield of Transgenic Rice Plants Overproducing Rubisco Under Sufficient N Fertilization. RICE (NEW YORK, N.Y.) 2022; 15:10. [PMID: 35138458 PMCID: PMC8828814 DOI: 10.1186/s12284-022-00557-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Accepted: 01/31/2022] [Indexed: 06/07/2023]
Abstract
BACKGROUND Improvement in photosynthesis is one of the most promising approaches to increase grain yields. Transgenic rice plants overproducing Rubisco by 30% (RBCS-sense rice plants) showed up to 28% increase in grain yields under sufficient nitrogen (N) fertilization using an isolated experimental paddy field (Yoon et al. in Nat Food 1:134-139, 2020). The plant N contents above-ground sections and Rubisco contents of the flag leaves were higher in the RBCS-sense plants than in the wild-type rice plants during the ripening period, which may be reasons for the increased yields. However, some imprecise points were left in the previous research, such as contributions of photosynthesis of leaves below the flag leaves to the yield, and maintenance duration of high photosynthesis of RBCS-sense rice plants during ripening periods. RESULT In this research, the photosynthetic capacity and canopy architecture were analyzed to explore factors for the increased yields of RBCS-sense rice plants. It was found that N had already been preferentially distributed into the flag leaves at the early ripening stage, contributing to maintaining higher Rubisco content levels in the enlarged flag leaves and extending the lifespan of the flag leaves of RBCS-sense rice plants throughout ripening periods under sufficient N fertilization. The higher amounts of Rubisco also improved the photosynthetic activity in the flag leaves throughout the ripening period. Although the enlarged flag leaves of the RBCS-sense rice plants occupied large spatial areas of the uppermost layer in the canopy, no significant prevention of light penetration to leaves below the flag leaves was observed. Additionally, since the CO2 assimilation rates of lower leaves between wild-type and RBCS-sense rice plants were the same at the early ripening stage, the lower leaves did not contribute to an increase in yields of the RBCS-sense rice plants. CONCLUSION We concluded that improvements in the photosynthetic capacity by higher leaf N and Rubisco contents, enlarged leaf area and extended lifespan of flag leaves led to an increase in grain yields of RBCS-sense rice plants grown under sufficient N fertilization.
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Affiliation(s)
- Marin Tanaka
- Graduate School of Agricultural Science, Tohoku University, 468-1 Aramaki-Aoba, Aoba-ku, Sendai, 980-8572, Japan
| | - Mamoru Keira
- Graduate School of Agricultural Science, Tohoku University, 468-1 Aramaki-Aoba, Aoba-ku, Sendai, 980-8572, Japan
| | - Dong-Kyung Yoon
- Graduate School of Agricultural Science, Tohoku University, 468-1 Aramaki-Aoba, Aoba-ku, Sendai, 980-8572, Japan
| | - Tadahiko Mae
- Graduate School of Agricultural Science, Tohoku University, 468-1 Aramaki-Aoba, Aoba-ku, Sendai, 980-8572, Japan
| | - Hiroyuki Ishida
- Graduate School of Agricultural Science, Tohoku University, 468-1 Aramaki-Aoba, Aoba-ku, Sendai, 980-8572, Japan
| | - Amane Makino
- Graduate School of Agricultural Science, Tohoku University, 468-1 Aramaki-Aoba, Aoba-ku, Sendai, 980-8572, Japan
| | - Keiki Ishiyama
- Graduate School of Agricultural Science, Tohoku University, 468-1 Aramaki-Aoba, Aoba-ku, Sendai, 980-8572, Japan.
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16
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Yang Y, Wang L, Che Z, Wang R, Cui R, Xu H, Chu S, Jiao Y, Zhang H, Yu D, Zhang D. Novel target sites for soybean yield enhancement by photosynthesis. JOURNAL OF PLANT PHYSIOLOGY 2022; 268:153580. [PMID: 34871989 DOI: 10.1016/j.jplph.2021.153580] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 11/23/2021] [Accepted: 11/24/2021] [Indexed: 06/13/2023]
Abstract
Photosynthesis plays an important role in plant growth and development. Increasing photosynthetic rate is a main objective of improving crop productivity. Chlorophyll fluorescence is an effective method for quickly evaluating photosynthesis. In this study, four representative chlorophyll fluorescence parameters, that is, maximum quantum efficiency of photosystem II, quantum efficiency of PSII, photochemical quenching, and non-photochemical quenching, of 219 diverse soybean accessions were measured across three environments. The underlying genetic architecture was analyzed by genome-wide association study. Forty-eight SNPs were detected to associate with the four traits and explained 10.43-20.41% of the phenotypic variation. Nine candidate genes in the stable QTLs were predicted. Great differences in the expression levels of the candidate genes existed between the high photosynthetic efficiency accessions and low photosynthetic efficiency accessions. In all, we uncover 17 QTLs associated with photosynthesis-related traits and nine genes that may participate in the regulation of photosynthesis, which can provide references for revealing the genetic mechanism of photosynthesis. These QTLs and candidate genes will provide new targets for crop yield improvement through increasing photosynthesis.
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Affiliation(s)
- Yuming Yang
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450006, China
| | - Li Wang
- National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, 210014, China
| | - Zhijun Che
- Ningxia University, Yinchuan, 750021, China
| | - Ruiyang Wang
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450006, China
| | - Ruifang Cui
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450006, China
| | - Huanqing Xu
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450006, China
| | - Shanshan Chu
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450006, China
| | - Yongqing Jiao
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450006, China
| | - Hengyou Zhang
- Northeast Institute of Geography and Agroecology, Key Laboratory of Soybean Molecular Design Breeding, Chinese Academy of Sciences, Harbin, 150081, China
| | - Deyue Yu
- National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, 210014, China.
| | - Dan Zhang
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450006, China.
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17
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Quero G, Bonnecarrère V, Simondi S, Santos J, Fernández S, Gutierrez L, Garaycochea S, Borsani O. Genetic architecture of photosynthesis energy partitioning as revealed by a genome-wide association approach. PHOTOSYNTHESIS RESEARCH 2021; 150:97-115. [PMID: 32072456 DOI: 10.1007/s11120-020-00721-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 02/10/2020] [Indexed: 06/10/2023]
Abstract
The photosynthesis process is determined by the intensity level and spectral quality of the light; therefore, leaves need to adapt to a changing environment. The incident energy absorbed can exceed the sink capability of the photosystems, and, in this context, photoinhibition may occur in both photosystem II (PSII) and photosystem I (PSI). Quantum yield parameters analyses reveal how the energy is managed. These parameters are genotype-dependent, and this genotypic variability is a good opportunity to apply mapping association strategies to identify genomic regions associated with photosynthesis energy partitioning. An experimental and mathematical approach is proposed for the determination of an index which estimates the energy per photon flux for each spectral bandwidth (Δλ) of the light incident (QI index). Based on the QI, the spectral quality of the plant growth, environmental lighting, and the actinic light of PAM were quantitatively very similar which allowed an accurate phenotyping strategy of a rice population. A total of 143 genomic single regions associated with at least one trait of chlorophyll fluorescence were identified. Moreover, chromosome 5 gathers most of these regions indicating the importance of this chromosome in the genetic regulation of the photochemistry process. Through a GWAS strategy, 32 genes of rice genome associated with the main parameters of the photochemistry process of photosynthesis in rice were identified. Association between light-harvesting complexes and the potential quantum yield of PSII, as well as the relationship between coding regions for PSI-linked proteins in energy distribution during the photochemical process of photosynthesis is analyzed.
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Affiliation(s)
- Gastón Quero
- Departamento de Biología Vegetal, Facultad de Agronomía, Universidad de la República, Garzón 809, Montevideo, Uruguay.
| | - Victoria Bonnecarrère
- Unidad de Biotecnología, Estación Experimental Wilson Ferreira Aldunate, Instituto Nacional de Investigación Agropecuaria (INIA), Ruta 48, Km 10, Rincón del Colorado, 90200, Canelones, Uruguay
| | - Sebastián Simondi
- Área de Matemática, Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo (FCEN-UNCuyo), Padre Contreras 1300, Mendoza, Argentina
| | - Jorge Santos
- Área de Física, Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo (FCEN-UNCuyo), Padre Contreras 1300, Mendoza, Argentina
| | - Sebastián Fernández
- Facultad de Ingeniería, Instituto de Ingeniería Eléctrica, Universidad de La República, Julio Herrera y Reissig 565, Montevideo, Uruguay
| | - Lucía Gutierrez
- Department of Agronomy, University of Wisconsin-Madison, 1575 Linden Dr., Madison, WI, 53706, USA
- Departamento de Biometría, Estadística y Cómputos, Facultad de Agronomía, Universidad de la República, Garzón 780, Montevideo, Uruguay
| | - Silvia Garaycochea
- Unidad de Biotecnología, Estación Experimental Wilson Ferreira Aldunate, Instituto Nacional de Investigación Agropecuaria (INIA), Ruta 48, Km 10, Rincón del Colorado, 90200, Canelones, Uruguay
| | - Omar Borsani
- Departamento de Biología Vegetal, Facultad de Agronomía, Universidad de la República, Garzón 809, Montevideo, Uruguay
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18
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Meta-Analysis of Quantitative Traits Loci (QTL) Identified in Drought Response in Rice ( Oryza sativa L.). PLANTS 2021; 10:plants10040716. [PMID: 33917162 PMCID: PMC8067883 DOI: 10.3390/plants10040716] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 03/30/2021] [Accepted: 04/02/2021] [Indexed: 11/17/2022]
Abstract
Rice is an important grain that is the staple food for most of the world's population. Drought is one of the major stresses that negatively affects rice yield. The nature of drought tolerance in rice is complex as it is determined by various components and has low heritability. Therefore, to ensure success in breeding programs for drought tolerant rice, QTLs (quantitative trait loci) of interest must be stable in a variety of plant genotypes and environments. This study identified stable QTLs in rice chromosomes in a variety of backgrounds and environments and conducted a meta-QTL analysis of stable QTLs that have been reported by previous research for use in breeding programs. A total of 653 QTLs for drought tolerance in rice from 27 genetic maps were recorded for analysis. The QTLs recorded were related to 13 traits in rice that respond to drought. Through the use of BioMercartor V4.2, a consensus map containing QTLs and molecular markers were generated using 27 genetic maps that were extracted from the previous 20 studies and meta-QTL analysis was conducted on the consensus map. A total of 70 MQTLs were identified and a total of 453 QTLs were mapped into the meta-QTL areas. Five meta-QTLs from chromosome 1 (MQTL 1.5 and MQTL 1.6), chromosome 2 (MQTL2.1 and MQTL 2.2) and chromosome 3 (MQTL 3.1) were selected for functional annotation as these regions have high number of QTLs and include many traits in rice that respond to drought. A number of genes in MQTL1.5 (268 genes), MQTL1.6 (640 genes), MQTL 2.1 (319 genes), MQTL 2.2 (19 genes) and MQTL 3.1 (787 genes) were annotated through Blast2GO. Few major proteins that respond to drought stress were identified in the meta-QTL areas which are Abscisic Acid-Insensitive Protein 5 (ABI5), the G-box binding factor 4 (GBF4), protein kinase PINOID (PID), histidine kinase 2 (AHK2), protein related to autophagy 18A (ATG18A), mitochondrial transcription termination factor (MTERF), aquaporin PIP 1-2, protein detoxification 48 (DTX48) and inositol-tetrakisphosphate 1-kinase 2 (ITPK2). These proteins are regulatory proteins involved in the regulation of signal transduction and gene expression that respond to drought stress. The meta-QTLs derived from this study and the genes that have been identified can be used effectively in molecular breeding and in genetic engineering for drought resistance/tolerance in rice.
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Honda S, Ohkubo S, San NS, Nakkasame A, Tomisawa K, Katsura K, Ookawa T, Nagano AJ, Adachi S. Maintaining higher leaf photosynthesis after heading stage could promote biomass accumulation in rice. Sci Rep 2021; 11:7579. [PMID: 33828128 PMCID: PMC8027620 DOI: 10.1038/s41598-021-86983-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Accepted: 03/23/2021] [Indexed: 11/16/2022] Open
Abstract
Leaf photosynthetic rate changes across the growing season as crop plants age. Most studies of leaf photosynthesis focus on a specific growth stage, leaving the question of which pattern of photosynthetic dynamics maximizes crop productivity unanswered. Here we obtained high-frequency data of canopy leaf CO2 assimilation rate (A) of two elite rice (Oryza sativa) cultivars and 76 inbred lines across the whole growing season. The integrated A value after heading was positively associated with crop growth rate (CGR) from heading to harvest, but that before heading was not. A curve-smoothing analysis of A after heading showed that accumulated A at > 80% of its maximum (A80) was positively correlated with CGR in analyses of all lines mixed and of lines grouped by genetic background, while the maximum A and accumulated A at ≤ 80% were less strongly correlated with CGR. We also found a genomic region (~ 12.2 Mb) that may enhance both A80 and aboveground biomass at harvest. We propose that maintaining a high A after heading, rather than having high maximum A, is a potential target for enhancing rice biomass accumulation.
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Affiliation(s)
- Sotaro Honda
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwaicho, Fuchu, Tokyo, 183-8509, Japan
| | - Satoshi Ohkubo
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwaicho, Fuchu, Tokyo, 183-8509, Japan
| | - Nan Su San
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwaicho, Fuchu, Tokyo, 183-8509, Japan
| | - Anothai Nakkasame
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwaicho, Fuchu, Tokyo, 183-8509, Japan
| | - Kazuki Tomisawa
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwaicho, Fuchu, Tokyo, 183-8509, Japan
| | - Keisuke Katsura
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwaicho, Fuchu, Tokyo, 183-8509, Japan
| | - Taiichiro Ookawa
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwaicho, Fuchu, Tokyo, 183-8509, Japan
| | - Atsushi J Nagano
- Faculty of Agriculture, Ryukoku University, Yokotani 1-5, Seta Oe-cho, Otsu, Shiga, 520-2194, Japan
| | - Shunsuke Adachi
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwaicho, Fuchu, Tokyo, 183-8509, Japan.
- College of Agriculture, Ibaraki University, 3-21-1 Chuo, Ami, Inashiki, Ibaraki, 300-0393, Japan.
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Ma X, Fan J, Wu Y, Zhao S, Zheng X, Sun C, Tan L. Whole-genome de novo assemblies reveal extensive structural variations and dynamic organelle-to-nucleus DNA transfers in African and Asian rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 104:596-612. [PMID: 32748498 PMCID: PMC7693357 DOI: 10.1111/tpj.14946] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 07/17/2020] [Accepted: 07/22/2020] [Indexed: 05/05/2023]
Abstract
Asian cultivated rice (Oryza sativa) and African cultivated rice (Oryza glaberrima) originated from the wild rice species Oryza rufipogon and Oryza barthii, respectively. The genomes of both cultivated species have undergone profound changes during domestication. Whole-genome de novo assemblies of O. barthii, O. glaberrima, O. rufipogon and Oryza nivara, produced using PacBio single-molecule real-time (SMRT) and next-generation sequencing (NGS) technologies, showed that Gypsy-like retrotransposons are the major contributors to genome size variation in African and Asian rice. Through the detection of genome-wide structural variations (SVs), we observed that besides 28 shared SV hot spots, another 67 hot spots existed in either the Asian or African rice genomes. Based on gene annotation information of the SVs, we established that organelle-to-nucleus DNA transfers resulted in numerous SVs that participated in the nuclear genome divergence of rice species and subspecies. We detected 52 giant nuclear integrants of organelle DNA (NORGs, defined as >10 kb) in six Oryza AA genomes. In addition, we developed an effective method to genotype giant NORGs, based on genome assembly, and first showed the dynamic change in the distribution of giant NORGs in rice natural population. Interestingly, 16 highly differentiated giant NORGs tended to accumulate in natural populations of Asian rice from higher latitude regions, grown at lower temperatures and light intensities. Our study provides new insight into the genome divergence of African and Asian rice, and establishes that organelle-to-nucleus DNA transfers, as potentially powerful contributors to environmental adaptation during rice evolution, play a major role in producing SVs in rice genomes.
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Affiliation(s)
- Xin Ma
- MOE Key Laboratory of Crop Heterosis and UtilizationNational Center for Evaluation of Agricultural Wild Plants (Rice)Department of Plant Genetics and BreedingChina Agricultural UniversityBeijing100193China
- State Key Laboratory of AgrobiotechnologyChina Agricultural UniversityBeijing100193China
| | - Jinjian Fan
- MOE Key Laboratory of Crop Heterosis and UtilizationNational Center for Evaluation of Agricultural Wild Plants (Rice)Department of Plant Genetics and BreedingChina Agricultural UniversityBeijing100193China
- State Key Laboratory of AgrobiotechnologyChina Agricultural UniversityBeijing100193China
| | - Yongzhen Wu
- MOE Key Laboratory of Crop Heterosis and UtilizationNational Center for Evaluation of Agricultural Wild Plants (Rice)Department of Plant Genetics and BreedingChina Agricultural UniversityBeijing100193China
| | - Shuangshuang Zhao
- MOE Key Laboratory of Crop Heterosis and UtilizationNational Center for Evaluation of Agricultural Wild Plants (Rice)Department of Plant Genetics and BreedingChina Agricultural UniversityBeijing100193China
| | - Xu Zheng
- MOE Key Laboratory of Crop Heterosis and UtilizationNational Center for Evaluation of Agricultural Wild Plants (Rice)Department of Plant Genetics and BreedingChina Agricultural UniversityBeijing100193China
| | - Chuanqing Sun
- MOE Key Laboratory of Crop Heterosis and UtilizationNational Center for Evaluation of Agricultural Wild Plants (Rice)Department of Plant Genetics and BreedingChina Agricultural UniversityBeijing100193China
- State Key Laboratory of Plant Physiology and BiochemistryChina Agricultural UniversityBeijing100193China
| | - Lubin Tan
- MOE Key Laboratory of Crop Heterosis and UtilizationNational Center for Evaluation of Agricultural Wild Plants (Rice)Department of Plant Genetics and BreedingChina Agricultural UniversityBeijing100193China
- State Key Laboratory of AgrobiotechnologyChina Agricultural UniversityBeijing100193China
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Bhandari A, Sandhu N, Bartholome J, Cao-Hamadoun TV, Ahmadi N, Kumari N, Kumar A. Genome-Wide Association Study for Yield and Yield Related Traits under Reproductive Stage Drought in a Diverse indica-aus Rice Panel. RICE (NEW YORK, N.Y.) 2020; 13:53. [PMID: 32761553 PMCID: PMC7410978 DOI: 10.1186/s12284-020-00406-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Accepted: 07/02/2020] [Indexed: 05/08/2023]
Abstract
BACKGROUND Reproductive-stage drought stress is a major impediment to rice production in rainfed areas. Conventional and marker-assisted breeding strategies for developing drought-tolerant rice varieties are being optimized by mining and exploiting adaptive traits, genetic diversity; identifying the alleles, and understanding their interactions with genetic backgrounds for their increased contribution to drought tolerance. Field experiments were conducted in this study to identify marker-trait associations (MTAs) involved in response to yield under reproductive-stage (RS) drought. A diverse set of 280 indica-aus accessions was phenotyped for ten agronomic traits including yield and yield-related traits under normal irrigated condition and under two managed reproductive-stage drought environments. The accessions were genotyped with 215,250 single nucleotide polymorphism markers. RESULTS The study identified a total of 219 significant MTAs for 10 traits and candidate gene analysis within a 200 kb window centred from GWAS identified SNP peaks detected these MTAs within/ in close proximity to 38 genes, 4 earlier reported major grain yield QTLs and 6 novel QTLs for 7 traits out of the 10. The significant MTAs were mainly located on chromosomes 1, 2, 5, 6, 9, 11 and 12 and the percent phenotypic variance captured for these traits ranged from 5 to 88%. The significant positive correlation of grain yield with yield-related and other agronomic traits except for flowering time, observed under different environments point towards their contribution in improving rice yield under drought. Seven promising accessions were identified for use in future genomics-assisted breeding programs targeting grain yield improvement under drought. CONCLUSION These results provide a promising insight into the complex genetic architecture of grain yield under reproductive-stage drought in different environments. Validation of major genomic regions reported in the study will enable their effectiveness to develop drought-tolerant varieties following marker-assisted selection as well as to identify genes and understanding the associated physiological mechanisms.
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Affiliation(s)
- Aditi Bhandari
- Rice Breeding Platform, International Rice Research Institute, DAPO Box, 7777, Metro Manila, Philippines
- Banasthali Vidyapith, Banasthali, 304022, India
| | - Nitika Sandhu
- Rice Breeding Platform, International Rice Research Institute, DAPO Box, 7777, Metro Manila, Philippines
- Punjab Agricultural University, Ludhiana, 141004, India
| | - Jérôme Bartholome
- Rice Breeding Platform, International Rice Research Institute, DAPO Box, 7777, Metro Manila, Philippines
- CIRAD, UMR, AGAP, Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montepellier, France
| | - Tuong-Vi Cao-Hamadoun
- CIRAD, UMR, AGAP, Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montepellier, France
| | - Nourollah Ahmadi
- CIRAD, UMR, AGAP, Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montepellier, France
| | | | - Arvind Kumar
- Rice Breeding Platform, International Rice Research Institute, DAPO Box, 7777, Metro Manila, Philippines.
- IRRI South Asia Regional Centre, Varanasi, 221006, India.
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Baslam M, Mitsui T, Hodges M, Priesack E, Herritt MT, Aranjuelo I, Sanz-Sáez Á. Photosynthesis in a Changing Global Climate: Scaling Up and Scaling Down in Crops. FRONTIERS IN PLANT SCIENCE 2020; 11:882. [PMID: 32733499 PMCID: PMC7357547 DOI: 10.3389/fpls.2020.00882] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 05/29/2020] [Indexed: 05/06/2023]
Abstract
Photosynthesis is the major process leading to primary production in the Biosphere. There is a total of 7000bn tons of CO2 in the atmosphere and photosynthesis fixes more than 100bn tons annually. The CO2 assimilated by the photosynthetic apparatus is the basis of crop production and, therefore, of animal and human food. This has led to a renewed interest in photosynthesis as a target to increase plant production and there is now increasing evidence showing that the strategy of improving photosynthetic traits can increase plant yield. However, photosynthesis and the photosynthetic apparatus are both conditioned by environmental variables such as water availability, temperature, [CO2], salinity, and ozone. The "omics" revolution has allowed a better understanding of the genetic mechanisms regulating stress responses including the identification of genes and proteins involved in the regulation, acclimation, and adaptation of processes that impact photosynthesis. The development of novel non-destructive high-throughput phenotyping techniques has been important to monitor crop photosynthetic responses to changing environmental conditions. This wealth of data is being incorporated into new modeling algorithms to predict plant growth and development under specific environmental constraints. This review gives a multi-perspective description of the impact of changing environmental conditions on photosynthetic performance and consequently plant growth by briefly highlighting how major technological advances including omics, high-throughput photosynthetic measurements, metabolic engineering, and whole plant photosynthetic modeling have helped to improve our understanding of how the photosynthetic machinery can be modified by different abiotic stresses and thus impact crop production.
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Affiliation(s)
- Marouane Baslam
- Laboratory of Biochemistry, Faculty of Agriculture, Niigata University, Niigata, Japan
| | - Toshiaki Mitsui
- Laboratory of Biochemistry, Faculty of Agriculture, Niigata University, Niigata, Japan
- Graduate School of Science and Technology, Niigata University, Niigata, Japan
| | - Michael Hodges
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRAE, Université Paris-Saclay, Université Evry, Université Paris Diderot, Paris, France
| | - Eckart Priesack
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Matthew T. Herritt
- USDA-ARS Plant Physiology and Genetics Research, US Arid-Land Agricultural Research Center, Maricopa, AZ, United States
| | - Iker Aranjuelo
- Agrobiotechnology Institute (IdAB-CSIC), Consejo Superior de Investigaciones Científicas-Gobierno de Navarra, Mutilva, Spain
| | - Álvaro Sanz-Sáez
- Department of Crop, Soil, and Environmental Sciences, Auburn University, Auburn, AL, United States
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Generation of High Yielding and Fragrant Rice ( Oryza sativa L.) Lines by CRISPR/Cas9 Targeted Mutagenesis of Three Homoeologs of Cytochrome P450 Gene Family and OsBADH2 and Transcriptome and Proteome Profiling of Revealed Changes Triggered by Mutations. PLANTS 2020; 9:plants9060788. [PMID: 32586052 PMCID: PMC7355857 DOI: 10.3390/plants9060788] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 06/19/2020] [Accepted: 06/19/2020] [Indexed: 12/12/2022]
Abstract
The significant increase in grain yield and quality are often antagonistic but a constant demand for breeders and consumers. Some genes related to cytochrome P450 family are known for rice organ growth but their role in controlling grain yield is still unknown. Here, we generated new rice mutants with high yield and improved aroma by simultaneously editing three cytochrome P450 homoeologs (Os03g0603100, Os03g0568400, and GL3.2) and OsBADH2 with the CRISPR/Cas9 system, and RNA-sequencing and proteomic analysis were performed to unveil the subsequent changes. High mutation efficiency was achieved in both target sites of each gene and the mutations were predominantly only deletions, while insertions were rare, and no mutations were detected in the five most likely off-target sites against each sgRNA. Mutants exhibited increased grain size, 2-acetyl-1-pyrroline (2AP) content, and grain cell numbers while there was no change in other agronomic traits. Transgene-DNA-free mutant lines appeared with a frequency of 44.44% and homozygous mutations were stably transmitted, and bi-allelic and heterozygous mutations followed Mendelian inheritance, while the inheritance of chimeric mutations was unpredictable. Deep RNA sequencing and proteomic results revealed the regulation of genes and proteins related to cytochrome P450 family, grain size and development, and cell cycle. The KEGG and hub-gene and protein network analysis showed that the gene and proteins related to ribosomal and photosynthesis pathways were mainly enriched, respectively. Our findings provide a broad and detailed basis to understand the role of CRISPR/Cas9 in rice yield and quality improvement.
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Lana-Costa J, de Oliveira Silva FM, Batista-Silva W, Carolino DC, Senra RL, Medeiros DB, Martins SCV, Gago J, Araújo WL, Nunes-Nesi A. High Photosynthetic Rates in a Solanum pennellii Chromosome 2 QTL Is Explained by Biochemical and Photochemical Changes. FRONTIERS IN PLANT SCIENCE 2020; 11:794. [PMID: 32595679 PMCID: PMC7303335 DOI: 10.3389/fpls.2020.00794] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 05/19/2020] [Indexed: 05/09/2023]
Abstract
Enhanced photosynthesis is strictly associated with to productivity and it can be accomplished by genetic approaches through identification of genetic variation. By using a Solanum pennellii introgression lines (ILs) population, it was previously verified that, under normal (CO2), IL 2-5 and 2-6 display increased photosynthetic rates by up to 20% in comparison with their parental background (M82). However, the physiological mechanisms involved in the enhanced CO2 assimilation exhibited by these lines remained unknown, precluding their use for further biotechnological applications. Thereby, here we attempted to uncover the physiological factors involved in the upregulation of photosynthesis in ILs 2-5 and 2-6 under normal (CO2) as well as under elevated (CO2). The results provide evidence for increased biochemical capacity (higher maximum carboxylation velocity and maximum electron transport rate) in plants from IL 2-5 and 2-6, whereas the diffusive components (stomatal and mesophyll conductances) were unaltered in these ILs in comparison to M82. Our analyses revealed that the higher photosynthetic rate observed in these ILs was associated with higher levels of starch as well as total protein levels, specially increased RuBisCO content. Further analyses performed in plants under high (CO2) confirmed that biochemical properties are involved in genetic variation on chromosome 2 related to enhanced photosynthesis.
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Affiliation(s)
- Jaciara Lana-Costa
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Brazil
| | | | | | - Diego Costa Carolino
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Renato Lima Senra
- Departamento de Bioquímica Aplicada, Universidade Federal de Viçosa, Viçosa, Brazil
| | - David B. Medeiros
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Brazil
| | | | - Jorge Gago
- Departament de Biologia, Institute of Agro-Environmental Research and Water Economy – INAGEA, Universitat de les Illes Balears, Palma, Spain
| | - Wagner L. Araújo
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Adriano Nunes-Nesi
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Brazil
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Wang L, Yang Y, Zhang S, Che Z, Yuan W, Yu D. GWAS reveals two novel loci for photosynthesis-related traits in soybean. Mol Genet Genomics 2020; 295:705-716. [PMID: 32166500 DOI: 10.1007/s00438-020-01661-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 02/27/2020] [Indexed: 10/24/2022]
Abstract
Photosynthesis plays an extremely important role throughout the life cycle of plants. Improving the photosynthetic rate is a major target for increasing crop productivity. This study was conducted to identify single nucleotide polymorphisms (SNPs) associated with the net photosynthetic rate (Pn), stomatal conductance (Cond), intercellular carbon dioxide concentration (Ci) and transpiration rate (Trmmol) through genome-wide association study (GWAS) and to inspect the relationships among these traits in soybean (Glycine max (L.) Merr.). A population of 219 soybean accessions was used in this research. A total of 12 quantitative trait loci (QTLs) associated with Pn, Cond, Ci and Trmmol were detected and distributed on chromosomes 1, 2, 6, 7, 9, 11, 12, 13, 15, 16, 18, and 19, and some of these QTL overlapped with previously reported QTLs. Furthermore, four candidate genes were identified, and there were significantly different expression levels between the high-light-efficiency accessions and low-light-efficiency accessions. These putative genes may participate in the regulation of photosynthesis through different metabolic pathways. Therefore, the associated novel QTLs and candidate genes detected in this study will provide a theoretical basis for genetic studies of photosynthesis and provide new avenues for crop improvement.
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Affiliation(s)
- Li Wang
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yuming Yang
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shuyu Zhang
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhijun Che
- School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
| | - Wenjie Yuan
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Deyue Yu
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China.
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Furbank RT, Sharwood R, Estavillo GM, Silva-Perez V, Condon AG. Photons to food: genetic improvement of cereal crop photosynthesis. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:2226-2238. [PMID: 32083680 PMCID: PMC7135014 DOI: 10.1093/jxb/eraa077] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 02/17/2020] [Indexed: 05/05/2023]
Abstract
Photosynthesis has become a major trait of interest for cereal yield improvement as breeders appear to have reached the theoretical genetic limit for harvest index, the mass of grain as a proportion of crop biomass. Yield improvements afforded by the adoption of green revolution dwarfing genes to wheat and rice are becoming exhausted, and improvements in biomass and radiation use efficiency are now sought in these crops. Exploring genetic diversity in photosynthesis is now possible using high-throughput techniques, and low-cost genotyping facilitates discovery of the genetic architecture underlying this variation. Photosynthetic traits have been shown to be highly heritable, and significant variation is present for these traits in available germplasm. This offers hope that breeding for improved photosynthesis and radiation use efficiency in cereal crops is tractable and a useful shorter term adjunct to genetic and genome engineering to boost yield potential.
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Affiliation(s)
- Robert T Furbank
- ARC Centre of Excellence for Translational Photosynthesis, Research School of Biology, The Australian National University, Canberra, ACT, Australia
- CSIRO Agriculture and Food, Canberra, ACT, Australia
| | - Robert Sharwood
- ARC Centre of Excellence for Translational Photosynthesis, Research School of Biology, The Australian National University, Canberra, ACT, Australia
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Du T, Meng P, Huang J, Peng S, Xiong D. Fast photosynthesis measurements for phenotyping photosynthetic capacity of rice. PLANT METHODS 2020; 16:6. [PMID: 31998402 PMCID: PMC6979334 DOI: 10.1186/s13007-020-0553-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 01/10/2020] [Indexed: 06/10/2023]
Abstract
BACKGROUND Over the past decades, the structural and functional genomics of rice have been deeply studied, and high density of molecular genetic markers have been developed. However, the genetic variation in leaf photosynthesis, the most important trait for rice yield improvement, was rarely studied. The lack of photosynthesis phenotyping tools is one of the bottlenecks, as traditional direct photosynthesis measurements are very low-throughput, and recently developed high-throughput methods are indirect measurements. Hence, there is an urgent need for a fast, accurate and direct measurement approach. RESULT We reported a fast photosynthesis measurement (FPM) method for phenotyping photosynthetic capacity of rice, which measures photosynthesis of excised tillers in environment-controlled lab conditions. The light response curves measured using FPM approach coped well with that the curves measured using traditional gas exchange approach. Importantly, the FPM technique achieved an average throughput of 5.4 light response curves per hour, which was 3 times faster than the 1.8 light response curves per hour using the traditional method. Tillers sampled at early morning had the highest photosynthesis, stomatal conductance and the lowest variability. In addition, even 12 h after sampling, there was no significant difference of photosynthesis rate between excised tillers and in situ. We finally investigated the genetic variations of photosynthetic traits across 568 F2 lines using the FPM technique and discussed the logistics of screening several hundred samples per day per instrumental unit using FPM to generate a wealth of photosynthetic phenotypic data, which might help to improve the selection power in large populations of rice with the ultimate aim of improving yield through improved photosynthesis. CONCLUSIONS Here we developed a high-throughput method that can measure the rice leaf photosynthetic capacity approximately 10 times faster than traditional gas exchange approaches. Importantly, this method can overcome measurement errors caused by environmental heterogeneity under field conditions, and it is possible to measure 12 or more hours per day under lab conditions.
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Affiliation(s)
- Tingting Du
- National Key Laboratory of Crop Genetic Improvement, MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, Huazhong Agricultural University, Wuhan, 430070 Hubei China
| | - Ping Meng
- National Key Laboratory of Crop Genetic Improvement, MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, Huazhong Agricultural University, Wuhan, 430070 Hubei China
| | - Jianliang Huang
- National Key Laboratory of Crop Genetic Improvement, MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, Huazhong Agricultural University, Wuhan, 430070 Hubei China
| | - Shaobing Peng
- National Key Laboratory of Crop Genetic Improvement, MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, Huazhong Agricultural University, Wuhan, 430070 Hubei China
| | - Dongliang Xiong
- National Key Laboratory of Crop Genetic Improvement, MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, Huazhong Agricultural University, Wuhan, 430070 Hubei China
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Morales F, Ancín M, Fakhet D, González-Torralba J, Gámez AL, Seminario A, Soba D, Ben Mariem S, Garriga M, Aranjuelo I. Photosynthetic Metabolism under Stressful Growth Conditions as a Bases for Crop Breeding and Yield Improvement. PLANTS (BASEL, SWITZERLAND) 2020; 9:E88. [PMID: 31936732 PMCID: PMC7020424 DOI: 10.3390/plants9010088] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 12/23/2019] [Accepted: 01/02/2020] [Indexed: 01/04/2023]
Abstract
Increased periods of water shortage and higher temperatures, together with a reduction in nutrient availability, have been proposed as major factors that negatively impact plant development. Photosynthetic CO2 assimilation is the basis of crop production for animal and human food, and for this reason, it has been selected as a primary target for crop phenotyping/breeding studies. Within this context, knowledge of the mechanisms involved in the response and acclimation of photosynthetic CO2 assimilation to multiple changing environmental conditions (including nutrients, water availability, and rising temperature) is a matter of great concern for the understanding of plant behavior under stress conditions, and for the development of new strategies and tools for enhancing plant growth in the future. The current review aims to analyze, from a multi-perspective approach (ranging across breeding, gas exchange, genomics, etc.) the impact of changing environmental conditions on the performance of the photosynthetic apparatus and, consequently, plant growth.
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Affiliation(s)
- Fermín Morales
- Instituto de Agrobiotecnología (IdAB), Consejo Superior de Investigaciones Científicas (CSIC)-Gobierno de Navarra, Av. Pamplona 123, 31192 Mutilva, Spain; (F.M.); (M.A.); (D.F.); (A.L.G.); (A.S.); (D.S.); (S.B.M.)
- Dpto. Nutrición Vegetal, Estación Experimental de Aula Dei (EEAD), CSIC, Apdo. 13034, 50080 Zaragoza, Spain
| | - María Ancín
- Instituto de Agrobiotecnología (IdAB), Consejo Superior de Investigaciones Científicas (CSIC)-Gobierno de Navarra, Av. Pamplona 123, 31192 Mutilva, Spain; (F.M.); (M.A.); (D.F.); (A.L.G.); (A.S.); (D.S.); (S.B.M.)
| | - Dorra Fakhet
- Instituto de Agrobiotecnología (IdAB), Consejo Superior de Investigaciones Científicas (CSIC)-Gobierno de Navarra, Av. Pamplona 123, 31192 Mutilva, Spain; (F.M.); (M.A.); (D.F.); (A.L.G.); (A.S.); (D.S.); (S.B.M.)
| | - Jon González-Torralba
- Institute for Multidisciplinary Applied Biology, Dpto. Agronomía, Biotecnología y Alimentación, Universidad Pública de Navarra, Campus Arrosadia, 31006 Pamplona, Spain;
| | - Angie L. Gámez
- Instituto de Agrobiotecnología (IdAB), Consejo Superior de Investigaciones Científicas (CSIC)-Gobierno de Navarra, Av. Pamplona 123, 31192 Mutilva, Spain; (F.M.); (M.A.); (D.F.); (A.L.G.); (A.S.); (D.S.); (S.B.M.)
| | - Amaia Seminario
- Instituto de Agrobiotecnología (IdAB), Consejo Superior de Investigaciones Científicas (CSIC)-Gobierno de Navarra, Av. Pamplona 123, 31192 Mutilva, Spain; (F.M.); (M.A.); (D.F.); (A.L.G.); (A.S.); (D.S.); (S.B.M.)
| | - David Soba
- Instituto de Agrobiotecnología (IdAB), Consejo Superior de Investigaciones Científicas (CSIC)-Gobierno de Navarra, Av. Pamplona 123, 31192 Mutilva, Spain; (F.M.); (M.A.); (D.F.); (A.L.G.); (A.S.); (D.S.); (S.B.M.)
| | - Sinda Ben Mariem
- Instituto de Agrobiotecnología (IdAB), Consejo Superior de Investigaciones Científicas (CSIC)-Gobierno de Navarra, Av. Pamplona 123, 31192 Mutilva, Spain; (F.M.); (M.A.); (D.F.); (A.L.G.); (A.S.); (D.S.); (S.B.M.)
| | - Miguel Garriga
- Centro de Mejoramiento Genético y Fenómica Vegetal, Facultad de Ciencias Agrarias, Universidad de Talca, Talca 3460000, Chile;
| | - Iker Aranjuelo
- Instituto de Agrobiotecnología (IdAB), Consejo Superior de Investigaciones Científicas (CSIC)-Gobierno de Navarra, Av. Pamplona 123, 31192 Mutilva, Spain; (F.M.); (M.A.); (D.F.); (A.L.G.); (A.S.); (D.S.); (S.B.M.)
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Adachi S, Yamamoto T, Nakae T, Yamashita M, Uchida M, Karimata R, Ichihara N, Soda K, Ochiai T, Ao R, Otsuka C, Nakano R, Takai T, Ikka T, Kondo K, Ueda T, Ookawa T, Hirasawa T. Genetic architecture of leaf photosynthesis in rice revealed by different types of reciprocal mapping populations. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:5131-5144. [PMID: 31257428 PMCID: PMC6793464 DOI: 10.1093/jxb/erz303] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 06/18/2019] [Indexed: 05/18/2023]
Abstract
The improvement of leaf net photosynthetic rate (An) is a major challenge in enhancing crop productivity. However, the genetic control of An among natural genetic accessions is still poorly understood. The high-yielding indica cultivar Takanari has the highest An of all rice cultivars, 20-30% higher than that of the high-quality japonica cultivar Koshihikari. By using reciprocal backcross inbred lines and chromosome segment substitution lines derived from a cross between Takanari and Koshihikari, we identified three quantitative trait loci (QTLs) where the Takanari alleles enhanced An in plants with a Koshihikari genetic background and five QTLs where the Koshihikari alleles enhanced An in plants with a Takanari genetic background. Two QTLs were expressed in plants with both backgrounds (type I QTL). The expression of other QTLs depended strongly on genetic background (type II QTL). These beneficial alleles increased stomatal conductance, the initial slope of An versus intercellular CO2 concentration, or An at CO2 saturation. Pyramiding of these alleles consistently increased An. Some alleles positively affected biomass production and grain yield. These alleles associated with photosynthesis and yield can be a valuable tool in rice breeding programs via DNA marker-assisted selection.
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Affiliation(s)
- Shunsuke Adachi
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, Japan
| | - Toshio Yamamoto
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Kannondai, Tsukuba, Ibaraki, Japan
- Present address: Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, Okayama 710-0046, Japan
| | - Toru Nakae
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, Japan
| | - Masahiro Yamashita
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, Japan
| | - Masaki Uchida
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, Japan
| | - Ryoji Karimata
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, Japan
| | - Naoto Ichihara
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, Japan
| | - Kazuya Soda
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, Japan
| | - Takayuki Ochiai
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, Japan
| | - Risako Ao
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, Japan
| | - Chikako Otsuka
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, Japan
| | - Ruri Nakano
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, Japan
| | - Toshiyuki Takai
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Kannondai, Tsukuba, Ibaraki, Japan
- Present address: Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki 305-8686, Japan
| | - Takashi Ikka
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Kannondai, Tsukuba, Ibaraki, Japan
- Present address: Faculty of Agriculture, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan
| | - Katsuhiko Kondo
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Kannondai, Tsukuba, Ibaraki, Japan
- Present address: Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki 305-8686, Japan
| | - Tadamasa Ueda
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Kannondai, Tsukuba, Ibaraki, Japan
| | - Taiichiro Ookawa
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, Japan
| | - Tadashi Hirasawa
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, Japan
- Correspondence:
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Faralli M, Matthews J, Lawson T. Exploiting natural variation and genetic manipulation of stomatal conductance for crop improvement. CURRENT OPINION IN PLANT BIOLOGY 2019; 49:1-7. [PMID: 30851622 PMCID: PMC6692497 DOI: 10.1016/j.pbi.2019.01.003] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 12/21/2018] [Accepted: 01/28/2019] [Indexed: 05/19/2023]
Abstract
Rising global temperatures and more frequent episodes of drought are expected to drive reductions in crop yield, therefore new avenues for improving crop productivity must be exploited. Stomatal conductance (gs) balances plant CO2 uptake and water loss, therefore, greatly impacting the cumulative rate of photosynthesis and water use over the growing season, which are key determinants of crop yield and productivity. Considerable natural variation exists in stomatal anatomy, biochemistry and behavioural characteristics that impact on the kinetics and magnitude of gs and thus gaseous exchange between the plant and atmosphere. Exploiting these differences in stomatal traits could provide novel breeding targets for new crop varieties that are potentially more water use efficient and have the ability to maintain and/or maximize yield in a range of diverse environments. Here we provide an overview of variation in stomatal traits and the impact these have on gs behaviour, as well as the potential to exploit such variation and genetic manipulation for crop improvement.
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Affiliation(s)
- Michele Faralli
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, United Kingdom
| | - Jack Matthews
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, United Kingdom
| | - Tracy Lawson
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, United Kingdom.
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Sabar M, Shabir G, Shah SM, Aslam K, Naveed SA, Arif M. Identification and mapping of QTLs associated with drought tolerance traits in rice by a cross between Super Basmati and IR55419-04. BREEDING SCIENCE 2019; 69:169-178. [PMID: 31086495 PMCID: PMC6507710 DOI: 10.1270/jsbbs.18068] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 11/30/2018] [Indexed: 05/19/2023]
Abstract
Water stress, in a climate change scenario is one of the major threats for sustainable rice productivity. Combining drought resistance with yield and desirable economic traits is the most promising solution for the researchers. Although several studies resulted in the identification of QTLs for drought resistance in rice, but none of them serve as a milestone. Therefore, there is always a quest to find the new QTLs. The present investigation was carried out to map QTLs involved in drought resistance and yield related parameter in a cross of IR55419-04 and Super Basmati. An F2 population of 418 individuals was used as the mapping population. The raised nursery was transplanted in lyzimeters. Two extreme sets of tolerant (23 Nos.) and sensitive (23 Nos.) individuals were selected based on total water uptake under water stress conditions. Two hundred thirty microsatellite markers staggered on the whole genome were used for identifying polymorphic markers between the two parents. The selected 73 polymorphic microsatellites were used to genotype individuals and were scattered on a distance of 1735 cM on all 12 linkage groups. QTL analysis was performed by using the WinQTL Cartographer 2.5 V. A total of 21 QTLs were detected using composite interval mapping. The QTLs relating to drought tolerance at the vegetative stage were found on chromosome 1. Novel genomic regions were detected in the marker interval RM520-RM143 and RM168-RM520. The region has a significant QTL qTWU3.1 for total water uptake. Root morphological trait QTLs were found on chromosome 3. QTLs responsible for additive effects were due to the alleles of the IR55419-04. These novel QTLs can be used for marker assisted breeding to develop new drought-tolerant rice varieties and fine mapping can be used to explore the functional relationship between the QTLs and phenotypic traits.
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Affiliation(s)
- Muhammad Sabar
- Rice Research Institute, Kala Shah Kaku,
Lahore,
Pakistan
| | - Ghulam Shabir
- Institute of Molecular Biology and Biotechnology, Bahauddin Zakariya University,
Multan,
Pakistan
| | - Shahid Masood Shah
- Department of Environmental Sciences, COMSATS University Islamabad, Abbottabad Campus,
Abbottabad, 22010,
Pakistan
- Corresponding author (e-mail: )
| | - Kashif Aslam
- Institute of Molecular Biology and Biotechnology, Bahauddin Zakariya University,
Multan,
Pakistan
| | - Shahzad Amir Naveed
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences,
Beijing,
China
| | - Muhammad Arif
- National Institute for Biotechnology and Genetic Engineering (NIBGE),
Faisalabad, 38000,
Pakistan
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van Bezouw RFHM, Keurentjes JJB, Harbinson J, Aarts MGM. Converging phenomics and genomics to study natural variation in plant photosynthetic efficiency. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 97:112-133. [PMID: 30548574 PMCID: PMC6850172 DOI: 10.1111/tpj.14190] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Revised: 11/27/2018] [Accepted: 11/28/2018] [Indexed: 05/18/2023]
Abstract
In recent years developments in plant phenomic approaches and facilities have gradually caught up with genomic approaches. An opportunity lies ahead to dissect complex, quantitative traits when both genotype and phenotype can be assessed at a high level of detail. This is especially true for the study of natural variation in photosynthetic efficiency, for which forward genetics studies have yielded only a little progress in our understanding of the genetic layout of the trait. High-throughput phenotyping, primarily from chlorophyll fluorescence imaging, should help to dissect the genetics of photosynthesis at the different levels of both plant physiology and development. Specific emphasis should be directed towards understanding the acclimation of the photosynthetic machinery in fluctuating environments, which may be crucial for the identification of genetic variation for relevant traits in food crops. Facilities should preferably be designed to accommodate phenotyping of photosynthesis-related traits in such environments. The use of forward genetics to study the genetic architecture of photosynthesis is likely to lead to the discovery of novel traits and/or genes that may be targeted in breeding or bio-engineering approaches to improve crop photosynthetic efficiency. In the near future, big data approaches will play a pivotal role in data processing and streamlining the phenotype-to-gene identification pipeline.
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Affiliation(s)
- Roel F. H. M. van Bezouw
- Laboratory of GeneticsWageningen University and ResearchDroevendaalsesteeg 16708PBWageningenThe Netherlands
| | - Joost J. B. Keurentjes
- Laboratory of GeneticsWageningen University and ResearchDroevendaalsesteeg 16708PBWageningenThe Netherlands
| | - Jeremy Harbinson
- Horticulture and Product PhysiologyWageningen University and ResearchDroevendaalsesteeg 16708PBWageningenThe Netherlands
| | - Mark G. M. Aarts
- Laboratory of GeneticsWageningen University and ResearchDroevendaalsesteeg 16708PBWageningenThe Netherlands
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Dwivedi SL, Siddique KHM, Farooq M, Thornton PK, Ortiz R. Using Biotechnology-Led Approaches to Uplift Cereal and Food Legume Yields in Dryland Environments. FRONTIERS IN PLANT SCIENCE 2018; 9:1249. [PMID: 30210519 PMCID: PMC6120061 DOI: 10.3389/fpls.2018.01249] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 08/06/2018] [Indexed: 05/29/2023]
Abstract
Drought and heat in dryland agriculture challenge the enhancement of crop productivity and threaten global food security. This review is centered on harnessing genetic variation through biotechnology-led approaches to select for increased productivity and stress tolerance that will enhance crop adaptation in dryland environments. Peer-reviewed literature, mostly from the last decade and involving experiments with at least two seasons' data, form the basis of this review. It begins by highlighting the adverse impact of the increasing intensity and duration of drought and heat stress due to global warming on crop productivity and its impact on food and nutritional security in dryland environments. This is followed by (1) an overview of the physiological and molecular basis of plant adaptation to elevated CO2 (eCO2), drought, and heat stress; (2) the critical role of high-throughput phenotyping platforms to study phenomes and genomes to increase breeding efficiency; (3) opportunities to enhance stress tolerance and productivity in food crops (cereals and grain legumes) by deploying biotechnology-led approaches [pyramiding quantitative trait loci (QTL), genomic selection, marker-assisted recurrent selection, epigenetic variation, genome editing, and transgene) and inducing flowering independent of environmental clues to match the length of growing season; (4) opportunities to increase productivity in C3 crops by harnessing novel variations (genes and network) in crops' (C3, C4) germplasm pools associated with increased photosynthesis; and (5) the adoption, impact, risk assessment, and enabling policy environments to scale up the adoption of seed-technology to enhance food and nutritional security. This synthesis of technological innovations and insights in seed-based technology offers crop genetic enhancers further opportunities to increase crop productivity in dryland environments.
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Affiliation(s)
| | | | - Muhammad Farooq
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
- Department of Crop Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos University, Al Khoud, Oman
- University of Agriculture, Faisalabad, Pakistan
| | - Philip K. Thornton
- CGIAR Research Program on Climate Change, Agriculture and Food Security (CCAFS), International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Rodomiro Ortiz
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
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Tang X, Gong R, Sun W, Zhang C, Yu S. Genetic dissection and validation of candidate genes for flag leaf size in rice (Oryza sativa L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:801-815. [PMID: 29218376 DOI: 10.1007/s00122-017-3036-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2017] [Accepted: 12/01/2017] [Indexed: 05/17/2023]
Abstract
Two major loci with functional candidate genes were identified and validated affecting flag leaf size, which offer desirable genes to improve leaf architecture and photosynthetic capacity in rice. Leaf size is a major determinant of plant architecture and yield potential in crops. However, the genetic and molecular mechanisms regulating leaf size remain largely elusive. In this study, quantitative trait loci (QTLs) for flag leaf length and flag leaf width in rice were detected with high-density single nucleotide polymorphism genotyping of a chromosomal segment substitution line (CSSL) population, in which each line carries one or a few chromosomal segments from the japonica cultivar Nipponbare in a common background of the indica variety Zhenshan 97. In total, 14 QTLs for flag leaf length and nine QTLs for flag leaf width were identified in the CSSL population. Among them, qFW4-2 for flag leaf width was mapped to a 37-kb interval, with the most likely candidate gene being the previously characterized NAL1. Another major QTL for both flag leaf width and length was delimited by substitution mapping to a small region of 13.5 kb that contains a single gene, Ghd7.1. Mutants of Ghd7.1 generated using CRISPR/CAS9 approach showed reduced leaf size. Allelic variation analyses also validated Ghd7.1 as a functional candidate gene for leaf size, photosynthetic capacity and other yield-related traits. These results provide useful genetic information for the improvement of leaf size and yield in rice breeding programs.
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Affiliation(s)
- Xinxin Tang
- National Key Laboratory of Crop Genetic Improvement, Wuhan, 430070, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Rong Gong
- National Key Laboratory of Crop Genetic Improvement, Wuhan, 430070, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Wenqiang Sun
- National Key Laboratory of Crop Genetic Improvement, Wuhan, 430070, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chaopu Zhang
- National Key Laboratory of Crop Genetic Improvement, Wuhan, 430070, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Sibin Yu
- National Key Laboratory of Crop Genetic Improvement, Wuhan, 430070, China.
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.
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de Oliveira Silva FM, Lichtenstein G, Alseekh S, Rosado-Souza L, Conte M, Suguiyama VF, Lira BS, Fanourakis D, Usadel B, Bhering LL, DaMatta FM, Sulpice R, Araújo WL, Rossi M, de Setta N, Fernie AR, Carrari F, Nunes-Nesi A. The genetic architecture of photosynthesis and plant growth-related traits in tomato. PLANT, CELL & ENVIRONMENT 2018; 41:327-341. [PMID: 29044606 DOI: 10.1111/pce.13084] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 09/22/2017] [Accepted: 09/23/2017] [Indexed: 05/22/2023]
Abstract
To identify genomic regions involved in the regulation of fundamental physiological processes such as photosynthesis and respiration, a population of Solanum pennellii introgression lines was analyzed. We determined phenotypes for physiological, metabolic, and growth related traits, including gas exchange and chlorophyll fluorescence parameters. Data analysis allowed the identification of 208 physiological and metabolic quantitative trait loci with 33 of these being associated to smaller intervals of the genomic regions, termed BINs. Eight BINs were identified that were associated with higher assimilation rates than the recurrent parent M82. Two and 10 genomic regions were related to shoot and root dry matter accumulation, respectively. Nine genomic regions were associated with starch levels, whereas 12 BINs were associated with the levels of other metabolites. Additionally, a comprehensive and detailed annotation of the genomic regions spanning these quantitative trait loci allowed us to identify 87 candidate genes that putatively control the investigated traits. We confirmed 8 of these at the level of variance in gene expression. Taken together, our results allowed the identification of candidate genes that most likely regulate photosynthesis, primary metabolism, and plant growth and as such provide new avenues for crop improvement.
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Affiliation(s)
| | - Gabriel Lichtenstein
- Instituto de Biotecnología, Instituto Nacional de Tecnología Agropecuaría, and Consejo Nacional de Investigaciones Científicas y Técnicas, B1712WAA, Castelar, Argentina
| | - Saleh Alseekh
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam, Germany
| | - Laise Rosado-Souza
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam, Germany
| | - Mariana Conte
- Instituto de Biotecnología, Instituto Nacional de Tecnología Agropecuaría, and Consejo Nacional de Investigaciones Científicas y Técnicas, B1712WAA, Castelar, Argentina
| | | | - Bruno Silvestre Lira
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, 05508-900, Brazil
| | - Dimitrios Fanourakis
- Department of Viticulture, Floriculture, Vegetable Crops and Plant Protection, GR, 71307, Heraklion, Greece
| | - Björn Usadel
- IBMG: Institute for Biology I, RWTH Aachen University, Worringer Weg 2, 52074, Aachen, Germany
- Forschungszentrum Jülich, IBG-2 Plant Sciences, Wilhelm-Johnen-Straße, 52425, Jülich, Germany
| | - Leonardo Lopes Bhering
- Departamento de Biologia Geral, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil
| | - Fábio M DaMatta
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil
| | - Ronan Sulpice
- Plant Systems Biology Lab, Plant and AgriBiosciences Research Centre, Plant & Agribiosiences, National University of Ireland Galway, H91 TK33, Galway, Ireland
| | - Wagner L Araújo
- Max-Planck Partner Group, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil
| | - Magdalena Rossi
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, 05508-900, Brazil
| | - Nathalia de Setta
- Universidade Federal do ABC, 09606070, São Bernardo do Campo, São Paulo, Brazil
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam, Germany
| | - Fernando Carrari
- Instituto de Biotecnología, Instituto Nacional de Tecnología Agropecuaría, and Consejo Nacional de Investigaciones Científicas y Técnicas, B1712WAA, Castelar, Argentina
| | - Adriano Nunes-Nesi
- Max-Planck Partner Group, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil
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Ortiz D, Hu J, Salas Fernandez MG. Genetic architecture of photosynthesis in Sorghum bicolor under non-stress and cold stress conditions. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:4545-4557. [PMID: 28981780 PMCID: PMC5853419 DOI: 10.1093/jxb/erx276] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 07/15/2017] [Indexed: 05/18/2023]
Abstract
Sorghum (Sorghum bicolor L. Moench) is a C4 species sensitive to the cold spring conditions that occur at northern latitudes, especially when coupled with excessive light, and that greatly affect the photosynthetic rate. The objective of this study was to discover genes/genomic regions that control the capacity to cope with excessive energy under low temperature conditions during the vegetative growth period. A genome-wide association study (GWAS) was conducted for seven photosynthetic gas exchange and chlorophyll fluorescence traits under three consecutive temperature treatments: control (28 °C/24 °C), cold (15 °C/15 °C), and recovery (28 °C/24 °C). Cold stress significantly reduced the rate of photosynthetic CO2 uptake of sorghum plants, and a total of 143 unique genomic regions were discovered associated with at least one trait in a particular treatment or with derived variables. Ten regions on chromosomes 3, 4, 6, 7, and 8 that harbor multiple significant markers in linkage disequilibrium (LD) were consistently identified in gas exchange and chlorophyll fluorescence traits. Several candidate genes within those intervals have predicted functions related to carotenoids, phytohormones, thioredoxin, components of PSI, and antioxidants. These regions represent the most promising results for future validation and with potential application for the improvement of crop productivity under cold stress.
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Affiliation(s)
- Diego Ortiz
- Department of Agronomy, Iowa State University, Ames, IA, USA
| | - Jieyun Hu
- Department of Agronomy, Iowa State University, Ames, IA, USA
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Gu J, Zhou Z, Li Z, Chen Y, Wang Z, Zhang H, Yang J. Photosynthetic Properties and Potentials for Improvement of Photosynthesis in Pale Green Leaf Rice under High Light Conditions. FRONTIERS IN PLANT SCIENCE 2017; 8:1082. [PMID: 28676818 PMCID: PMC5476740 DOI: 10.3389/fpls.2017.01082] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2016] [Accepted: 06/06/2017] [Indexed: 05/24/2023]
Abstract
Light is the driving force of plant growth, providing the energy required for photosynthesis. However, photosynthesis is also vulnerable to light-induced damage caused by the production of reactive oxygen species (ROS). Plants have therefore evolved various protective mechanisms such as non-photochemical quenching (NPQ) to dissipate excessively absorbed solar energy as heat; however, photoinhibition and NPQ represent a significant loss in solar energy and photosynthetic efficiency, which lowers the yield potential in crops. To estimate light capture and light energy conversion in rice, a genotype with pale green leaves (pgl) and a normally pigmented control (Z802) were subjected to high (HL) and low light (LL). Chlorophyll content, light absorption, chloroplast micrographs, abundance of light-harvesting complex (LHC) binding proteins, electron transport rates (ETR), photochemical and non-photochemical quenching, and generation of ROS were subsequently examined. Pgl had a smaller size of light-harvesting chlorophyll antenna and absorbed less photons than Z802. NPQ and the generation of ROS were also low, while photosystem II efficiency and ETR were high, resulting in improved photosynthesis and less photoinhibition in pgl than Z802. Chlorophyll synthesis and solar conversion efficiency were higher in pgl under HL compared to LL treatment, while Z802 showed an opposite trend due to the high level of photoinhibition under HL. In Z802, excessive absorption of solar energy not only increased the generation of ROS and NPQ, but also exacerbated the effects of increases in temperature, causing midday depression in photosynthesis. These results suggest that photosynthesis and yield potential in rice could be enhanced by truncated light-harvesting chlorophyll antenna size.
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Affiliation(s)
- Junfei Gu
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou UniversityYangzhou, China
| | - Zhenxiang Zhou
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou UniversityYangzhou, China
| | - Zhikang Li
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou UniversityYangzhou, China
| | - Ying Chen
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou UniversityYangzhou, China
| | - Zhiqin Wang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou UniversityYangzhou, China
| | - Hao Zhang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou UniversityYangzhou, China
| | - Jianchang Yang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou UniversityYangzhou, China
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De Leon TB, Linscombe S, Subudhi PK. Identification and validation of QTLs for seedling salinity tolerance in introgression lines of a salt tolerant rice landrace 'Pokkali'. PLoS One 2017; 12:e0175361. [PMID: 28388633 PMCID: PMC5384751 DOI: 10.1371/journal.pone.0175361] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2016] [Accepted: 03/26/2017] [Indexed: 12/20/2022] Open
Abstract
Salinity is a major threat to rice production worldwide. Several studies have been conducted to elucidate the molecular basis of salinity tolerance in rice. However, the genetic information such as quantitative trait loci (QTLs) and molecular markers, emanating from these studies, were rarely exploited for marker-assisted breeding. To better understand salinity tolerance and to validate previously reported QTLs at seedling stage, a set of introgression lines (ILs) of a salt tolerant donor line ‘Pokkali’ developed in a susceptible high yielding rice cultivar ‘Bengal’ background was evaluated for several morphological and physiological traits under salt stress. Both SSR and genotyping-by-sequencing (GBS) derived SNP markers were utilized to characterize the ILs and identify QTLs for traits related to salinity tolerance. A total of eighteen and thirty-two QTLs were detected using SSR and SNP markers, respectively. At least fourteen QTLs detected in the RIL population developed from the same cross were validated in IL population. Analysis of phenotypic responses, genomic composition, and QTLs present in the tolerant ILs suggested that the mechanisms of tolerance could be Na+ dilution in leaves, vacuolar Na+ compartmentation, and possibly synthesis of compatible solutes. Our results emphasize the use of salt injury score (SIS) QTLs in marker-assisted breeding to improve salinity tolerance. The tolerant lines identified in this study will serve as improved breeding materials for transferring salinity tolerance without the undesirable traits of Pokkali. Additionally, the lines will be useful for fine mapping and map-based cloning of genes responsible for salinity tolerance.
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Affiliation(s)
- Teresa B. De Leon
- School of Plant, Environmental, and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA, United States of America
| | - Steven Linscombe
- Rice Research Station, Louisiana State University Agricultural Center, Rayne, LA, United States of America
| | - Prasanta K. Subudhi
- School of Plant, Environmental, and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA, United States of America
- * E-mail:
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Kim TH, Hur YJ, Han SI, Cho JH, Kim KM, Lee JH, Song YC, Kwon YU, Shin D. Drought-tolerant QTL qVDT11 leads to stable tiller formation under drought stress conditions in rice. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2017; 256:131-138. [PMID: 28167026 DOI: 10.1016/j.plantsci.2016.11.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 10/23/2016] [Accepted: 11/21/2016] [Indexed: 05/27/2023]
Abstract
Drought is an important limiting factor for rice production, but the genetic mechanisms of drought tolerance is poorly understood. Here, we screened 218 rice varieties to identify 32 drought-tolerant varieties. The variety Samgang exhibited strong drought tolerance and stable yield in rain-fed conditions and was selected for further study. To identify QTLs for drought tolerance, we examined visual drought tolerance (VDT) and relative water content (RWC) phenotypes in a doubled haploid (DH) population of 101 individuals derived from a cross between Samgang and Nagdong (a drought-sensitive variety). Three QTLs from Samgang were identified for VDT and explained 41.8% of the phenotypic variance. In particular, qVDT11 contributed 20.3% of the phenotypic variance for RWC. To determine QTL effects on drought tolerance in rain-fed paddy conditions, seven DH lines were selected according to the number of QTLs they contained. Of the drought-tolerance-associated QTLs, qVDT2 and qVDT6 did not affect tiller formation, but qVDT11 increased tiller number. Tiller formation was most stable when qVDT2 and qVDT11 were combined. DH lines with both of these drought-tolerance-associated QTLs exhibited the most stable tiller formation. Together, these results suggest that qVDT11 is important for drought tolerance and stable tiller formation in rain-fed paddy fields.
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Affiliation(s)
- Tae-Heon Kim
- Department of Southern Area Crop Science, National Institute of Crop Science, Rural Development Administration, Miryang 50424, Republic of Korea.
| | - Yeon-Jae Hur
- Department of Southern Area Crop Science, National Institute of Crop Science, Rural Development Administration, Miryang 50424, Republic of Korea.
| | - Sang-Ik Han
- Department of Southern Area Crop Science, National Institute of Crop Science, Rural Development Administration, Miryang 50424, Republic of Korea.
| | - Jun-Hyun Cho
- Department of Southern Area Crop Science, National Institute of Crop Science, Rural Development Administration, Miryang 50424, Republic of Korea.
| | - Kyung-Min Kim
- College of Agriculture and Life Science, Kyungpook National University, Daegu 41566, Republic of Korea.
| | - Jong-Hee Lee
- Research Policy Bureau, Rural Development Administration, Jeonju 54875, Republic of Korea.
| | - You-Chun Song
- Department of Southern Area Crop Science, National Institute of Crop Science, Rural Development Administration, Miryang 50424, Republic of Korea.
| | - Yeong-Up Kwon
- Department of Southern Area Crop Science, National Institute of Crop Science, Rural Development Administration, Miryang 50424, Republic of Korea.
| | - Dongjin Shin
- Department of Southern Area Crop Science, National Institute of Crop Science, Rural Development Administration, Miryang 50424, Republic of Korea.
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Adachi S, Yoshikawa K, Yamanouchi U, Tanabata T, Sun J, Ookawa T, Yamamoto T, Sage RF, Hirasawa T, Yonemaru J. Fine Mapping of Carbon Assimilation Rate 8, a Quantitative Trait Locus for Flag Leaf Nitrogen Content, Stomatal Conductance and Photosynthesis in Rice. FRONTIERS IN PLANT SCIENCE 2017; 8:60. [PMID: 28197156 PMCID: PMC5282472 DOI: 10.3389/fpls.2017.00060] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2016] [Accepted: 01/11/2017] [Indexed: 05/19/2023]
Abstract
Increasing the rate of leaf photosynthesis is one important approach for increasing grain yield in rice (Oryza sativa). Exploiting the natural variation in CO2 assimilation rate (A) between rice cultivars using quantitative genetics is one promising means to identify genes contributing to higher photosynthesis. In this study, we determined precise location of Carbon Assimilation Rate 8 (CAR8) by crossing a high-yielding indica cultivar with a Japanese commercial cultivar. Fine mapping suggested that CAR8 encodes a putative Heme Activator Protein 3 (OsHAP3) subunit of a CCAAT-box-binding transcription factor called OsHAP3H. Sequencing analysis revealed that the indica allele of CAR8 has a 1-bp deletion at 322 bp from the start codon, resulting in a truncated protein of 125 amino acids. In addition, CAR8 is identical to DTH8/Ghd8/LHD1, which was reported to control rice flowering date. The increase of A is largely due to an increase of RuBP regeneration rate via increased leaf nitrogen content, and partially explained by reduced stomatal limitation via increased stomatal conductance relative to A. This allele also increases hydraulic conductivity, which would promote higher stomatal conductance. This indicates that CAR8 affects multiple physiological aspects relating to photosynthesis. The detailed analysis of molecular functions of CAR8 would help to understand the association between photosynthesis and flowering and demonstrate specific genetic mechanisms that can be exploited to improve photosynthesis in rice and potentially other crops.
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Affiliation(s)
- Shunsuke Adachi
- Department of Biological Production Science, Graduate School of Agriculture, Tokyo University of Agriculture and TechnologyFuchu, Japan
- Institute of Global Innovation Research, Tokyo University of Agriculture and TechnologyFuchu, Japan
- Precursory Research for Embryonic Science and Technology, Japan Science and Technology AgencyKawaguchi, Japan
| | - Kazuaki Yoshikawa
- Department of Biological Production Science, Graduate School of Agriculture, Tokyo University of Agriculture and TechnologyFuchu, Japan
| | - Utako Yamanouchi
- Institute of Crop Science, National Agriculture and Food Research OrganizationTsukuba, Japan
| | - Takanari Tanabata
- Department of Frontier Research, Kazusa DNA Research InstituteKisarazu, Japan
| | - Jian Sun
- Institute of Crop Science, National Agriculture and Food Research OrganizationTsukuba, Japan
- Rice Research Institute, Shenyang Agricultural UniversityShenyang, China
| | - Taiichiro Ookawa
- Department of Biological Production Science, Graduate School of Agriculture, Tokyo University of Agriculture and TechnologyFuchu, Japan
- Institute of Global Innovation Research, Tokyo University of Agriculture and TechnologyFuchu, Japan
| | - Toshio Yamamoto
- Institute of Crop Science, National Agriculture and Food Research OrganizationTsukuba, Japan
| | - Rowan F. Sage
- Institute of Global Innovation Research, Tokyo University of Agriculture and TechnologyFuchu, Japan
- Department of Ecology and Evolutionary Biology, University of TorontoToronto, ON, Canada
| | - Tadashi Hirasawa
- Department of Biological Production Science, Graduate School of Agriculture, Tokyo University of Agriculture and TechnologyFuchu, Japan
- Institute of Global Innovation Research, Tokyo University of Agriculture and TechnologyFuchu, Japan
| | - Junichi Yonemaru
- Institute of Crop Science, National Agriculture and Food Research OrganizationTsukuba, Japan
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Meacham K, Sirault X, Quick WP, von Caemmerer S, Furbank R. Diurnal Solar Energy Conversion and Photoprotection in Rice Canopies. PLANT PHYSIOLOGY 2017; 173:495-508. [PMID: 27895208 PMCID: PMC5210756 DOI: 10.1104/pp.16.01585] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 11/24/2016] [Indexed: 05/06/2023]
Abstract
Genetic improvement of photosynthetic performance of cereal crops and increasing the efficiency with which solar radiation is converted into biomass has recently become a major focus for crop physiologists and breeders. The pulse amplitude modulated chlorophyll fluorescence technique (PAM) allows quantitative leaf level monitoring of the utilization of energy for photochemical light conversion and photoprotection in natural environments, potentially over the entire crop lifecycle. Here, the diurnal relationship between electron transport rate (ETR) and irradiance was measured in five cultivars of rice (Oryza sativa) in canopy conditions with PAM fluorescence under natural solar radiation. This relationship differed substantially from that observed for conventional short term light response curves measured under controlled actinic light with the same leaves. This difference was characterized by a reduced curvature factor when curve fitting was used to model this diurnal response. The engagement of photoprotective processes in chloroplast electron transport in leaves under canopy solar radiation was shown to be a major contributor to this difference. Genotypic variation in the irradiance at which energy flux into photoprotective dissipation became greater than ETR was observed. Cultivars capable of higher ETR at midrange light intensities were shown to produce greater leaf area over time, estimated by noninvasive imaging.
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Affiliation(s)
- Katherine Meacham
- ARC Centre of Excellence for Translational Photosynthesis, Australian National University, Canberra, Australian Capital Territory 2601, Australia (K.M., X.S., S.v.C., R.F.)
- High Resolution Plant Phenomics Centre, Commonwealth Scientific and Industrial Research Organization (CSIRO), CSIRO Agriculture and Food, Canberra, Australian Capital Territory 2601, Australia (K.M., X.S., R.F.)
- International Rice Research Institute, Los Baños, 4031 Laguna, Philippines (W.P.Q.); and
- University of Sheffield, Western Bank, Sheffield S10 2TN, United Kingdom (W.P.Q.)
| | - Xavier Sirault
- ARC Centre of Excellence for Translational Photosynthesis, Australian National University, Canberra, Australian Capital Territory 2601, Australia (K.M., X.S., S.v.C., R.F.)
- High Resolution Plant Phenomics Centre, Commonwealth Scientific and Industrial Research Organization (CSIRO), CSIRO Agriculture and Food, Canberra, Australian Capital Territory 2601, Australia (K.M., X.S., R.F.)
- International Rice Research Institute, Los Baños, 4031 Laguna, Philippines (W.P.Q.); and
- University of Sheffield, Western Bank, Sheffield S10 2TN, United Kingdom (W.P.Q.)
| | - W Paul Quick
- ARC Centre of Excellence for Translational Photosynthesis, Australian National University, Canberra, Australian Capital Territory 2601, Australia (K.M., X.S., S.v.C., R.F.)
- High Resolution Plant Phenomics Centre, Commonwealth Scientific and Industrial Research Organization (CSIRO), CSIRO Agriculture and Food, Canberra, Australian Capital Territory 2601, Australia (K.M., X.S., R.F.)
- International Rice Research Institute, Los Baños, 4031 Laguna, Philippines (W.P.Q.); and
- University of Sheffield, Western Bank, Sheffield S10 2TN, United Kingdom (W.P.Q.)
| | - Susanne von Caemmerer
- ARC Centre of Excellence for Translational Photosynthesis, Australian National University, Canberra, Australian Capital Territory 2601, Australia (K.M., X.S., S.v.C., R.F.)
- High Resolution Plant Phenomics Centre, Commonwealth Scientific and Industrial Research Organization (CSIRO), CSIRO Agriculture and Food, Canberra, Australian Capital Territory 2601, Australia (K.M., X.S., R.F.)
- International Rice Research Institute, Los Baños, 4031 Laguna, Philippines (W.P.Q.); and
- University of Sheffield, Western Bank, Sheffield S10 2TN, United Kingdom (W.P.Q.)
| | - Robert Furbank
- ARC Centre of Excellence for Translational Photosynthesis, Australian National University, Canberra, Australian Capital Territory 2601, Australia (K.M., X.S., S.v.C., R.F.);
- High Resolution Plant Phenomics Centre, Commonwealth Scientific and Industrial Research Organization (CSIRO), CSIRO Agriculture and Food, Canberra, Australian Capital Territory 2601, Australia (K.M., X.S., R.F.);
- International Rice Research Institute, Los Baños, 4031 Laguna, Philippines (W.P.Q.); and
- University of Sheffield, Western Bank, Sheffield S10 2TN, United Kingdom (W.P.Q.)
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de Oliveira Silva FM, de Ávila Silva L, Araújo WL, Zsögön A, Nunes-Nesi A. Exploiting Natural Variation to Discover Candidate Genes Involved in Photosynthesis-Related Traits. Methods Mol Biol 2017; 1653:125-135. [PMID: 28822130 DOI: 10.1007/978-1-4939-7225-8_9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Naturally occurring genetic variation in plants can be very useful to dissect the complex regulation of primary metabolism as well as of physiological traits such as photosynthesis and photorespiration. The physiological and genetic mechanisms underlying natural variation in closely related species or accessions may provide important information that can be used to improve crop yield. In this chapter we describe in detail the use of a population of introgression lines (ILs), with the Solanum pennellii IL population as a study case, as a tool for the identification of genomic regions involved in the control of photosynthetic efficiency.
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Affiliation(s)
| | - Lucas de Ávila Silva
- Departmento de Biologia Vegetal, Universidade Federal de Viçosa, Campus UFR, Viçosa, MG, 36570-000, Brazil
| | - Wagner L Araújo
- Departmento de Biologia Vegetal, Universidade Federal de Viçosa, Campus UFR, Viçosa, MG, 36570-000, Brazil
| | - Agustin Zsögön
- Departmento de Biologia Vegetal, Universidade Federal de Viçosa, Campus UFR, Viçosa, MG, 36570-000, Brazil
| | - Adriano Nunes-Nesi
- Departmento de Biologia Vegetal, Universidade Federal de Viçosa, Campus UFR, Viçosa, MG, 36570-000, Brazil.
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Čepl J, Holá D, Stejskal J, Korecký J, Kočová M, Lhotáková Z, Tomášková I, Palovská M, Rothová O, Whetten RW, Kaňák J, Albrechtová J, Lstibůrek M. Genetic variability and heritability of chlorophyll a fluorescence parameters in Scots pine (Pinus sylvestris L.). TREE PHYSIOLOGY 2016; 36:883-895. [PMID: 27126227 DOI: 10.1093/treephys/tpw028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 03/12/2016] [Indexed: 06/05/2023]
Abstract
Current knowledge of the genetic mechanisms underlying the inheritance of photosynthetic activity in forest trees is generally limited, yet it is essential both for various practical forestry purposes and for better understanding of broader evolutionary mechanisms. In this study, we investigated genetic variation underlying selected chlorophyll a fluorescence (ChlF) parameters in structured populations of Scots pine (Pinus sylvestris L.) grown on two sites under non-stress conditions. These parameters were derived from the OJIP part of the ChlF kinetics curve and characterize individual parts of primary photosynthetic processes associated, for example, with the exciton trapping by light-harvesting antennae, energy utilization in photosystem II (PSII) reaction centers (RCs) and its transfer further down the photosynthetic electron-transport chain. An additive relationship matrix was estimated based on pedigree reconstruction, utilizing a set of highly polymorphic single sequence repeat markers. Variance decomposition was conducted using the animal genetic evaluation mixed-linear model. The majority of ChlF parameters in the analyzed pine populations showed significant additive genetic variation. Statistically significant heritability estimates were obtained for most ChlF indices, with the exception of DI0/RC, φD0 and φP0 (Fv/Fm) parameters. Estimated heritabilities varied around the value of 0.15 with the maximal value of 0.23 in the ET0/RC parameter, which indicates electron-transport flux from QA to QB per PSII RC. No significant correlation was found between these indices and selected growth traits. Moreover, no genotype × environment interaction (G × E) was detected, i.e., no differences in genotypes' performance between sites. The absence of significant G × E in our study is interesting, given the relatively low heritability found for the majority of parameters analyzed. Therefore, we infer that polygenic variability of these indices is selectively neutral.
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Affiliation(s)
- Jaroslav Čepl
- Faculty of Forestry and Wood Sciences, Czech University of Life Sciences, Kamýcká 1176, 165 21 Praha 6 - Suchdol, Czech Republic
| | - Dana Holá
- Faculty of Science, Charles University in Prague, Viničná 5, 128 43 Praha 2 - Nové Město, Czech Republic
| | - Jan Stejskal
- Faculty of Forestry and Wood Sciences, Czech University of Life Sciences, Kamýcká 1176, 165 21 Praha 6 - Suchdol, Czech Republic
| | - Jiří Korecký
- Faculty of Forestry and Wood Sciences, Czech University of Life Sciences, Kamýcká 1176, 165 21 Praha 6 - Suchdol, Czech Republic
| | - Marie Kočová
- Faculty of Science, Charles University in Prague, Viničná 5, 128 43 Praha 2 - Nové Město, Czech Republic
| | - Zuzana Lhotáková
- Faculty of Science, Charles University in Prague, Viničná 5, 128 43 Praha 2 - Nové Město, Czech Republic
| | - Ivana Tomášková
- Faculty of Forestry and Wood Sciences, Czech University of Life Sciences, Kamýcká 1176, 165 21 Praha 6 - Suchdol, Czech Republic
| | - Markéta Palovská
- Faculty of Science, Charles University in Prague, Viničná 5, 128 43 Praha 2 - Nové Město, Czech Republic
| | - Olga Rothová
- Faculty of Science, Charles University in Prague, Viničná 5, 128 43 Praha 2 - Nové Město, Czech Republic
| | - Ross W Whetten
- Department of Forestry & Environmental Resources, North Carolina State University, Raleigh, NC 27695-8008, USA
| | - Jan Kaňák
- Arboretum Sofronka, Plaská 877, 323 00 Plzeň-Bolevec, Czech Republic
| | - Jana Albrechtová
- Faculty of Science, Charles University in Prague, Viničná 5, 128 43 Praha 2 - Nové Město, Czech Republic
| | - Milan Lstibůrek
- Faculty of Forestry and Wood Sciences, Czech University of Life Sciences, Kamýcká 1176, 165 21 Praha 6 - Suchdol, Czech Republic
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Quantitative Trait Loci and Inter-Organ Partitioning for Essential Metal and Toxic Analogue Accumulation in Barley. PLoS One 2016; 11:e0153392. [PMID: 27078500 PMCID: PMC4831800 DOI: 10.1371/journal.pone.0153392] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 03/29/2016] [Indexed: 12/25/2022] Open
Abstract
The concentrations of both essential nutrients and chemically similar toxic analogues accumulated in cereal grains have a major impact on the nutritional quality and safety of crops. Naturally occurring genetic diversity can be exploited for the breeding of improved varieties through introgression lines (ILs). In this study, multi-element analysis was conducted on vegetative leaves, senesced flag leaves and mature grains of a set of 54 ILs of the wild ancestral Hordeum vulgare ssp. spontaneum in the cultivated variety Hordeum vulgare ssp. vulgare cv. Scarlett. Plants were cultivated on an anthropogenically heavy metal-contaminated soil collected in an agricultural field, thus allowing simultaneous localization of quantitative trait loci (QTL) for the accumulation of both essential nutrients and toxic trace elements in barley as a model cereal crop. For accumulation of the micronutrients Fe and Zn and the interfering toxin Cd, we identified 25, 16 and 5 QTL, respectively. By examining the gene content of the introgressions, we associated QTL with candidate genes based on homology to known metal homeostasis genes of Arabidopsis and rice. Global comparative analyses suggested the preferential remobilization of Cu and Fe, over Cd, from the flag leaf to developing grains. Our data identifies grain micronutrient filling as a regulated and nutrient-specific process, which operates differently from vegetative micronutrient homoeostasis. In summary, this study provides novel QTL for micronutrient accumulation in the presence of toxic analogues and supports a higher degree of metal specificity of trace element partitioning during grain filling in barley than previously reported for other cereals.
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Comparative transcriptome analysis highlights the crucial roles of photosynthetic system in drought stress adaptation in upland rice. Sci Rep 2016; 6:19349. [PMID: 26777777 PMCID: PMC4726002 DOI: 10.1038/srep19349] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Accepted: 12/01/2015] [Indexed: 11/19/2022] Open
Abstract
Drought stress is one of the major adverse environmental factors reducing plant growth. With the aim to elucidate the underlying molecular basis of rice response to drought stress, comparative transcriptome analysis was conducted between drought susceptible rice cultivar Zhenshan97 and tolerant cultivar IRAT109 at the seedling stage. 436 genes showed differential expression and mainly enriched in the Gene Ontology (GO) terms of stress defence. A large number of variations exist between these two genotypes including 2564 high-quality insertion and deletions (INDELs) and 70,264 single nucleotide polymorphism (SNPs). 1041 orthologous gene pairs show the ratio of nonsynonymous nucleotide substitution rate to synonymous nucleotide substitutions rate (Ka/Ks) larger than 1.5, indicating the rapid adaptation to different environments during domestication. GO and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of positive selection genes suggested that photosynthesis represents the most significant category. The collocation of positively selected genes with the QTLs of photosynthesis and the different photosynthesis performance of these two cultivars further illuminate the crucial function of photosynthesis in rice adaptation to drought stress. Our results also provide fruitful functional markers and candidate genes for future genetic research and improvement of drought tolerance in rice.
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Prince SJ, Beena R, Gomez SM, Senthivel S, Babu RC. Mapping Consistent Rice (Oryza sativa L.) Yield QTLs under Drought Stress in Target Rainfed Environments. RICE (NEW YORK, N.Y.) 2015; 8:53. [PMID: 26206756 PMCID: PMC4513014 DOI: 10.1186/s12284-015-0053-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Accepted: 05/22/2015] [Indexed: 05/26/2023]
Abstract
BACKGROUND Drought stress is a major limitation to rainfed rice production and yield stability. Identifying yield-associated quantitative trait loci (QTLs) that are consistent under drought stress predominant in target production environments, as well as across different genetic backgrounds, will help to develop high-yielding rice cultivars suitable for water-limited environments through marker-assisted breeding (MAB). Considerable progress has been made in mapping QTLs for drought resistance traits in rice; however, few have been successfully used in MAB. RESULTS Recombinant inbred lines of IR20 × Nootripathu, two indica cultivars adapted to rainfed target populations of environments (TPEs), were evaluated in one and two seasons under managed stress and in a rainfed target drought stress environment, respectively. In the managed stress environment, the severity of the stress meant that measurements could be made only on secondary traits and biomass. In the target environment, the lines experienced varying timings, durations, and intensities of drought stress. The rice recombinant inbred lines exhibited significant genotypic variation for physio-morphological, phenological, and plant production traits under drought. Nine and 24 QTLs for physio-morphological and plant production traits were identified in managed and natural drought stress conditions in the TPEs, respectively. Yield QTLs that were consistent in the target environment over seasons were identified on chromosomes 1, 4, and 6, which could stabilize the productivity in high-yielding rice lines in a water-limited rainfed ecosystem. These yield QTLs also govern highly heritable key secondary traits, such as leaf drying, canopy temperature, panicle harvest index and harvest index. CONCLUSION Three QTL regions on chromosome 1 (RM8085), chromosome 4 (I12S), and chromosome 6 (RM6836) harbor significant additive QTLs for various physiological and yield traits under drought stress. The similar chromosomal region on 4 and 6 were found to harbor QTLs for canopy temperature and leaf drying under drought stress conditions. Thus, the identified large effect yield QTLs could be introgressed to develop rice lines with stable yields under varying natural drought stress predominant in TPEs.
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Affiliation(s)
- Silvas J Prince
- Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University (TNAU), Coimbatore, 641 003 India
| | - R Beena
- Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University (TNAU), Coimbatore, 641 003 India
| | - S Michael Gomez
- International Center for Tropical Agriculture (CIAT), Colombia, 6713 Colombia
| | - S Senthivel
- Agricultural Research Station, Tamil Nadu Agricultural University (TNAU), Paramakudi, 623707 India
| | - R Chandra Babu
- Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University (TNAU), Coimbatore, 641 003 India
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Gu L, Wei B, Fan R, Jia X, Wang X, Zhang X. Development, identification and utilization of introgression lines using Chinese endemic and synthetic wheat as donors. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2015; 57:688-697. [PMID: 25545589 DOI: 10.1111/jipb.12324] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 12/22/2014] [Indexed: 06/04/2023]
Abstract
Chromosome segmental introgression lines (ILs) are an effective way to utilize germplasm resources in crops. To improve agronomic traits of wheat cultivar (Triticum aestivum) Shi 4185, four sets of ILs were developed. The donors were Chinese endemic subspecies accessions Yunnan wheat (T. aestivum ssp. yunnanense) YN3, Tibetan semi-wild wheat (T. aestivum ssp. tibetanum) XZ-ZM19450, and Xinjiang wheat (T. aestivum ssp. petropavlovskyi) XJ5, and synthetic wheat HC-XM1620 derived from a cross between T. durum acc. D67.2/P66.270 with Aegilops tauschii acc. 218. Totals of 356, 366, 445 and 457 simple sequence repeat (SSR) markers were polymorphic between Shi 4185 and YN3, XZ-ZM19450, XJ5 and HC-XM1620, respectively. In total, 991 ILs were identified, including 300 derived from YN3, covering 95% of the genome of Shi 4185, 218 from XZ-ZM19450 (79%), 279 from XJ5 (97%), and 194 from HC-ZX1620 (84%). The sizes and locations of each introgression were determined from a consensus SSR linkage map. Using the ILs, 11 putative quantitative trait loci (QTLs) were identified for plant height (PH), spike length (SL) and grain number per spike (GNS). Comparative analyses of 24 elite ILs with the parents revealed that the four donor parents could be important resources to improve wheat SL and GNS. Our work offers a case for utilizing endemic landraces for QTL mapping and improvement of wheat cultivars using introgression lines.
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Affiliation(s)
- Liqing Gu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing, 100101, China
| | - Bo Wei
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing, 100101, China
| | - Renchun Fan
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing, 100101, China
| | - Xu Jia
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing, 100101, China
| | - Xianping Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing, 100101, China
| | - Xiangqi Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing, 100101, China
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Dhanapal AP, Ray JD, Singh SK, Hoyos-Villegas V, Smith JR, Purcell LC, Andy King C, Cregan PB, Song Q, Fritschi FB. Genome-wide association study (GWAS) of carbon isotope ratio (δ13C) in diverse soybean [Glycine max (L.) Merr.] genotypes. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2015. [PMID: 25367378 DOI: 10.1007/s00122-014-2419-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Using genome-wide association studies, 39 SNP markers likely tagging 21 different loci for carbon isotope ratio (δ (13) C) were identified in soybean. Water deficit stress is a major factor limiting soybean [Glycine max (L.) Merr.] yield. Soybean genotypes with improved water use efficiency (WUE) may be used to develop cultivars with increased yield under drought. A collection of 373 diverse soybean genotypes was grown in four environments (2 years and two locations) and characterized for carbon isotope ratio (δ(13)C) as a surrogate measure of WUE. Population structure was assessed based on 12,347 single nucleotide polymorphisms (SNPs), and genome-wide association studies (GWAS) were conducted to identify SNPs associated with δ(13)C. Across all four environments, δ(13)C ranged from a minimum of -30.55‰ to a maximum of -27.74‰. Although δ(13)C values were significantly different between the two locations in both years, results were consistent among genotypes across years and locations. Diversity analysis indicated that eight subpopulations could contain all individuals and revealed that within-subpopulation diversity, rather than among-subpopulation diversity, explained most (80%) of the diversity among the 373 genotypes. A total of 39 SNPs that showed a significant association with δ(13)C in at least two environments or for the average across all environments were identified by GWAS. Fifteen of these SNPs were located within a gene. The 39 SNPs likely tagged 21 different loci and demonstrated that markers for δ(13)C can be identified in soybean using GWAS. Further research is necessary to confirm the marker associations identified and to evaluate their usefulness for selecting genotypes with increased WUE.
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Li X, Wang W, Wang Z, Li K, Lim YP, Piao Z. Construction of chromosome segment substitution lines enables QTL mapping for flowering and morphological traits in Brassica rapa. FRONTIERS IN PLANT SCIENCE 2015; 6:432. [PMID: 26106405 PMCID: PMC4460309 DOI: 10.3389/fpls.2015.00432] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2015] [Accepted: 05/27/2015] [Indexed: 05/04/2023]
Abstract
Chromosome segment substitution lines (CSSLs) represent a powerful method for precise quantitative trait loci (QTL) detection of complex agronomical traits in plants. In this study, we used a marker-assisted backcrossing strategy to develop a population consisting of 63 CSSLs, derived from backcrossing of the F1 generated from a cross between two Brassica rapa subspecies: "Chiifu" (ssp. pekinensis), the Brassica "A" genome-represented line used as the donor, and "49caixin" (ssp. parachinensis), a non-heading cultivar used as the recipient. The 63 CSSLs covered 87.95% of the B. rapa genome. Among them, 39 lines carried a single segment; 15 lines, two segments; and nine lines, three or more segments of the donor parent chromosomes. To verify the potential advantage of these CSSL lines, we used them to locate QTL for six morphology-related traits. A total of 58 QTL were located on eight chromosomes for all six traits: 17 for flowering time, 14 each for bolting time and plant height, six for plant diameter, two for leaf width, and five for flowering stalk diameter. Co-localized QTL were mainly distributed on eight genomic regions in A01, A02, A05, A06, A08, A09, and A10, present in the corresponding CSSLs. Moreover, new chromosomal fragments that harbored QTL were identified using the findings of previous studies. The CSSL population constructed in our study paves the way for fine mapping and cloning of candidate genes involved in late bolting, flowering, and plant architecture-related traits in B. rapa. Furthermore, it has great potential for future marker-aided gene/QTL pyramiding of other interesting traits in B. rapa breeding.
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Affiliation(s)
- Xiaonan Li
- Department of Horticulture, Shenyang Agricultural UniversityShenyang, China
- Molecular Genetics and Genomics Lab, Department of Horticulture, Chungnam National UniversityDaejeon, South Korea
| | - Wenke Wang
- Department of Horticulture, Shenyang Agricultural UniversityShenyang, China
| | - Zhe Wang
- Department of Horticulture, Shenyang Agricultural UniversityShenyang, China
| | - Kangning Li
- Department of Horticulture, Shenyang Agricultural UniversityShenyang, China
| | - Yong Pyo Lim
- Molecular Genetics and Genomics Lab, Department of Horticulture, Chungnam National UniversityDaejeon, South Korea
- *Correspondence: Yong Pyo Lim, Department of Horticulture, Chungnam National University, Gung-Dong, Yuseong-Gu, Daejeon 305-764, South Korea
| | - Zhongyun Piao
- Department of Horticulture, Shenyang Agricultural UniversityShenyang, China
- Zhongyun Piao, Department of Horticulture, Shenyang Agricultural University, #120 Dongling Road, Shenyang, Liaoning 110866, China
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