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Liu H, Zhang X, Shang Y, Zhao S, Li Y, Zhou X, Huo X, Qiao P, Wang X, Dai K, Li H, Guo J, Shi W. Genome-wide association study reveals genetic loci for ten trace elements in foxtail millet (Setaria italica). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:186. [PMID: 39017920 DOI: 10.1007/s00122-024-04690-1] [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: 05/10/2024] [Accepted: 07/03/2024] [Indexed: 07/18/2024]
Abstract
KEY MESSAGE One hundred and fifty-five QTL for trace element concentrations in foxtail millet were identified using a genome-wide association study, and a candidate gene associated with Ni-Co-Cr concentrations was detected. Foxtail millet (Setaria italica) is an important regional crop known for its rich mineral nutrient content, which has beneficial effects on human health. We assessed the concentrations of ten trace elements (Ba, Co, Cr, Cu, Fe, Mn, Ni, Pb, Sr, and Zn) in the grain of 408 foxtail millet accessions. Significant differences in the concentrations of five elements (Ba, Co, Ni, Sr, and Zn) were observed between two subpopulations of spring- and summer-sown foxtail millet varieties. Moreover, 84.4% of the element pairs exhibited significant correlations. To identify the genetic factors influencing trace element accumulation, a comprehensive genome-wide association study was conducted, identifying 155 quantitative trait locus (QTL) for the ten trace elements across three different environments. Among them, ten QTL were consistently detected in multiple environments, including qZn2.1, qZn4.4, qCr4.1, qFe6.3, qFe6.5, qCo6.1, qPb7.3, qPb7.5, qBa9.1, and qNi9.1. Thirteen QTL clusters were detected for multiple elements, which partially explained the correlations between elements. Additionally, the different concentrations of five elements between foxtail millet subpopulations were caused by the different frequencies of high-concentration alleles associated with important marker-trait associations. Haplotype analysis identified a candidate gene SETIT_036676mg associated with Ni accumulation, with the GG haplotype significantly increasing Ni-Co-Cr concentrations in foxtail millet. A cleaved amplified polymorphic sequence marker (cNi6676) based on the two haplotypes of SETIT_036676mg was developed and validated. Results of this study provide valuable reference information for the genetic research and improvement of trace element content in foxtail millet.
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Affiliation(s)
- Hanxiao Liu
- College of Agronomy, Key Laboratory of Sustainable Dryland Agriculture (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shanxi Agricultural University, Jinzhong, 030801, China
| | - Xin Zhang
- College of Agronomy, Key Laboratory of Sustainable Dryland Agriculture (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shanxi Agricultural University, Jinzhong, 030801, China
| | - Yuping Shang
- College of Agronomy, Key Laboratory of Sustainable Dryland Agriculture (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shanxi Agricultural University, Jinzhong, 030801, China
| | - Shaoxing Zhao
- College of Agronomy, Key Laboratory of Sustainable Dryland Agriculture (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shanxi Agricultural University, Jinzhong, 030801, China
| | - Yingjia Li
- College of Agronomy, Key Laboratory of Sustainable Dryland Agriculture (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shanxi Agricultural University, Jinzhong, 030801, China
| | - Xutao Zhou
- College of Agronomy, Key Laboratory of Sustainable Dryland Agriculture (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shanxi Agricultural University, Jinzhong, 030801, China
| | - Xiaoyu Huo
- College of Agronomy, Key Laboratory of Sustainable Dryland Agriculture (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shanxi Agricultural University, Jinzhong, 030801, China
| | - Pengfei Qiao
- College of Agronomy, Key Laboratory of Sustainable Dryland Agriculture (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shanxi Agricultural University, Jinzhong, 030801, China
| | - Xin Wang
- College of Agronomy, Key Laboratory of Sustainable Dryland Agriculture (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shanxi Agricultural University, Jinzhong, 030801, China
| | - Keli Dai
- College of Agronomy, Key Laboratory of Sustainable Dryland Agriculture (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shanxi Agricultural University, Jinzhong, 030801, China
| | - Huixia Li
- Millet Research Institute, Shanxi Agricultural University, Changzhi, 046000, China
| | - Jie Guo
- College of Agronomy, Key Laboratory of Sustainable Dryland Agriculture (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shanxi Agricultural University, Jinzhong, 030801, China.
| | - Weiping Shi
- College of Agronomy, Key Laboratory of Sustainable Dryland Agriculture (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shanxi Agricultural University, Jinzhong, 030801, China.
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Li MZ, Hu DW, Liu XQ, Zhang R, Liu H, Tang Z, Zhao FJ, Huang XY. The OsZIP2 transporter is involved in root-to-shoot translocation and intervascular transfer of cadmium in rice. PLANT, CELL & ENVIRONMENT 2024. [PMID: 38828861 DOI: 10.1111/pce.14993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 05/09/2024] [Accepted: 05/23/2024] [Indexed: 06/05/2024]
Abstract
Cadmium (Cd) is a toxic metal that poses serious threats to human health. Rice is a major source of dietary Cd but how rice plants transport Cd to the grain is not fully understood. Here, we characterize the function of the ZIP (ZRT, IRT-like protein) family protein, OsZIP2, in the root-to-shoot translocation of Cd and intervascular transfer of Cd in nodes. OsZIP2 is localized at the plasma membrane and exhibited Cd2+ transport activity when heterologously expressed in yeast. OsZIP2 is strongly expressed in xylem parenchyma cells in roots and in enlarged vascular bundles in nodes. Knockout of OsZIP2 significantly enhanced root-to-shoot translocation of Cd and alleviated the inhibition of root elongation by excess Cd stress; whereas overexpression of OsZIP2 decreased Cd translocation to shoots and resulted in Cd sensitivity. Knockout of OsZIP2 increased Cd allocation to the flag leaf but decreased Cd allocation to the panicle and grain. We further reveal that the variation of OsZIP2 expression level contributes to grain Cd concentration among rice germplasms. Our results demonstrate that OsZIP2 functions in root-to-shoot translocation of Cd in roots and intervascular transfer of Cd in nodes, which can be used for breeding low Cd rice varieties.
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Affiliation(s)
- Meng-Zhen Li
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Da-Wei Hu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Xiang-Qian Liu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Rui Zhang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Huan Liu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Zhong Tang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Fang-Jie Zhao
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Xin-Yuan Huang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
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Liu X, Li Q, Yin B, Yan H, Wang Y. Assessment of macro, trace and toxic element intake from rice: differences between cultivars, pigmented and non-pigmented rice. Sci Rep 2024; 14:10398. [PMID: 38710769 DOI: 10.1038/s41598-024-58411-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 03/28/2024] [Indexed: 05/08/2024] Open
Abstract
Pigmented and non-pigmented rice varieties (grown in different areas) were collected in China, Yunnan, to investigate the content of macro-, trace elements and potentially toxic elements (PTEs), and to assess the health risk associated with dietary intake. The order of elemental concentrations in rice was Mn > Zn > Fe > Cu > Se for trace elements, P > K > Mg > Ca > Na for macro elements, and Cr > As > Cd for PTEs. Rice with a high concentration of essential elements also associated with a high content of PTEs. In addition, higher content of Cr, Mn and Na were found in pigmented rice. The health risk assessment showed that the daily intake of all elements was below the tolerable limit (UL). Moreover the intake of Fe, Zn and Se was far from sufficient for the nutrient requirement. The PTEs in rice dominated the health risk. Of concern is that this rice consumption is likely to contribute to carcinogenic risks in the long term and that adults are at higher health risk from pigmented rice compared to non-pigmented rice. This study confirms that the lack of essential micronutrients in rice and the health risk associated with rice diets should remain a concern.
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Affiliation(s)
- Xingyong Liu
- Institute of Quality Standards and Testing Technology, Yunnan Academy of Agricultural Sciences, Kunming, 650000, China
| | - Qian Li
- Institute of Quality Standards and Testing Technology, Yunnan Academy of Agricultural Sciences, Kunming, 650000, China
| | - Benlin Yin
- Institute of Quality Standards and Testing Technology, Yunnan Academy of Agricultural Sciences, Kunming, 650000, China
| | - Hongmei Yan
- Institute of Quality Standards and Testing Technology, Yunnan Academy of Agricultural Sciences, Kunming, 650000, China.
| | - Yunmei Wang
- Institute of Quality Standards and Testing Technology, Yunnan Academy of Agricultural Sciences, Kunming, 650000, China.
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Liu T, Hu W, Weng L, Deng L, Li J, Yu J, Zhou Z, Liu Y, Chen C, Sheng T, Zhao Z, Xiao G. Phenotypic and genetic dissection of the contents of important metallic elements in hybrid rice grown in cadmium-contaminated paddy fields. Heliyon 2023; 9:e19919. [PMID: 37809877 PMCID: PMC10559331 DOI: 10.1016/j.heliyon.2023.e19919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 09/04/2023] [Accepted: 09/05/2023] [Indexed: 10/10/2023] Open
Abstract
Rice (Oryza sativa L.) is a staple food that feeds over half of the world's population, and the contents of metallic elements in rice grain play important roles in human nutrition. In this study, the contents of important metallic elements were determined by ICP-OES, and included cadmium (Cd), zinc (Zn), manganese (Mn), copper (Cu), iron (Fe), nickel (Ni), calcium (Ca), and magnesium (Mg) in brown rice, in the first node from the top (Node 1), in the second node from the top (Node 2), and in roots of 55 hybrids and their parental lines. The heritability of metallic element contents (MECs), the general combining ability (GCA) for MEC, and the correlation between MECs in different organs/tissues of hybrids were also analyzed. The results indicated that: (1) there was a positive correlation between the contents of Cd and Zn in nodes and roots, but a negative correlation between the contents of Cd and Zn in brown rice of the hybrids(2) the GCA for MECs can be used to evaluate the ability of the parental lines to improve the metal contents in brown rice of the hybrids(3) the contents of Cd, Zn, Ca, and Mg in brown rice were mainly affected by additive genetic effects(4) the restorer lines R2292 and R2265 can be used to cultivate hybrids with high Zn and low Cd contents in the brown rice.
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Affiliation(s)
- Tengfei Liu
- Hunan Rice Research Institute, Hunan Academy of Agricultural Sciences, Changsha, 410125, China
| | - Wenbin Hu
- Hunan Rice Research Institute, Hunan Academy of Agricultural Sciences, Changsha, 410125, China
| | - Lvshui Weng
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, 410125, China
| | - Lihua Deng
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, 410125, China
| | - Jinjiang Li
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, 410125, China
| | - Jianghui Yu
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, 410125, China
| | - Zheng Zhou
- Hunan Rice Research Institute, Hunan Academy of Agricultural Sciences, Changsha, 410125, China
| | - Ye Liu
- Hunan Rice Research Institute, Hunan Academy of Agricultural Sciences, Changsha, 410125, China
| | - Caiyan Chen
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, 410125, China
- Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Teng Sheng
- Laboratory of Photosynthesis and Environmental Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zhenghong Zhao
- Hunan Rice Research Institute, Hunan Academy of Agricultural Sciences, Changsha, 410125, China
| | - Guoying Xiao
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, 410125, China
- Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
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Huang Z, Li S, Lv Z, Tian Y, Chen Y, Zhu Y, Wang J, Deng H, Sun L, Tang W. Identification of subspecies-divergent genetic loci responsible for mineral accumulation in rice grains. Front Genet 2023; 14:1133600. [PMID: 36824439 PMCID: PMC9941327 DOI: 10.3389/fgene.2023.1133600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 01/27/2023] [Indexed: 02/10/2023] Open
Abstract
Rice (Oryza sativa L.) is a major staple food that provides not only dietary calories but also trace elements for the global inhabitants. The insufficiency of mineral nutrients and the potential accumulation of excessive toxic elements in grains pose risks to human health. The substantial natural variations in mineral accumulation in rice grains presents potentials for genetic improvements of rice via biofortifications of essential mineral nutrients and eliminations of toxic elements in grains. However, the genetic mechanisms underlying the natural variations in mineral accumulation have not been fully explored to date owing to unstable phenotypic variations, which are attributed to poor genetic performance and strong environmental effects. In this study, we first compared the genetic performance of different normalization approaches in determining the grain-Cd, grain-Mn, and grain-Zn variations in rice in different genetic populations. Then through quantitative trait loci (QTLs) identification in two rice inter-ectype populations, three QTLs, including qCd7, qMn3, and qZn7, were identified and the QTLs were found to exhibit allelic differentiation in the different ecotypes. Our results were expected to broaden our understanding for mineral accumulation in rice and propose the potential functional alleles that can be explored for further genetic improvement of rice.
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Affiliation(s)
- Zijian Huang
- College of Agronomy, Hunan Agricultural University, Changsha, China
| | - Sai Li
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
| | - Zhaokun Lv
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
| | - Yan Tian
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, China
| | - Yibo Chen
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
| | - Yuxing Zhu
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
| | - Jiurong Wang
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
| | - Huabing Deng
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
| | - Liang Sun
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China,*Correspondence: Wenbang Tang, ; Liang Sun,
| | - Wenbang Tang
- College of Agronomy, Hunan Agricultural University, Changsha, China,State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, China,*Correspondence: Wenbang Tang, ; Liang Sun,
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Identifying the Genetic Basis of Mineral Elements in Rice Grain Using Genome-Wide Association Mapping. Genes (Basel) 2022; 13:genes13122330. [PMID: 36553597 PMCID: PMC9777918 DOI: 10.3390/genes13122330] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 12/07/2022] [Accepted: 12/09/2022] [Indexed: 12/14/2022] Open
Abstract
Mineral malnutrition is a major problem in many rice-consuming countries. It is essential to know the genetic mechanisms of accumulation of mineral elements in the rice grain to provide future solutions for this issue. This study was conducted to identify the genetic basis of six mineral elements (Cu, Fe, K, Mg, Mn, and Zn) by using three models for single-locus and six models for multi-locus analysis of a genome-wide association study (GWAS) using 174 diverse rice accessions and 6565 SNP markers. To declare a SNP as significant, -log10(P) ≥ 3.0 and 15% FDR significance cut-off values were used for single-locus models, while LOD ≥ 3.0 was used for multi-locus models. Using these criteria, 147 SNPs were detected by one or two GWAS methods at -log10(P) ≥ 3.0, 48 of which met the 15% FDR significance cut-off value. Single-locus models outperformed multi-locus models before applying multi-test correction, but once applied, multi-locus models performed better. While 14 (~29%) of the identified quantitative trait loci (QTLs) after multiple test correction co-located with previously reported genes/QTLs and marker associations, another 34 trait-associated SNPs were novel. After mining genes within 250 kb of the 48 significant SNP loci, in silico and gene enrichment analyses were conducted to predict their potential functions. These shortlisted genes with their functions could guide future experimental validation, helping us to understand the complex molecular mechanisms controlling rice grain mineral elements.
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Lee SB, Kim GJ, Shin JD, Chung W, Park SK, Choi GH, Park SW, Park YJ. Genome-Scale Profiling and High-Throughput Analyses Unravel the Genetic Basis of Arsenic Content Variation in Rice. FRONTIERS IN PLANT SCIENCE 2022; 13:905842. [PMID: 35958208 PMCID: PMC9361212 DOI: 10.3389/fpls.2022.905842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 06/15/2022] [Indexed: 06/15/2023]
Abstract
Ionomics, the study of the composition of mineral nutrients and trace elements in organisms that represent the inorganic component of cells and tissues, has been widely studied to explore to unravel the molecular mechanism regulating the elemental composition of plants. However, the genetic factors of rice subspecies in the interaction between arsenic and functional ions have not yet been explained. Here, the correlation between As and eight essential ions in a rice core collection was analyzed, taking into account growing condition and genetic factors. The results demonstrated that the correlation between As and essential ions was affected by genetic factors and growing condition, but it was confirmed that the genetic factor was slightly larger with the heritability for arsenic content at 53%. In particular, the cluster coefficient of japonica (0.428) was larger than that of indica (0.414) in the co-expression network analysis for 23 arsenic genes, and it was confirmed that the distance between genes involved in As induction and detoxification of japonica was far than that of indica. These findings provide evidence that japonica populations could accumulate more As than indica populations. In addition, the cis-eQTLs of AIR2 (arsenic-induced RING finger protein) were isolated through transcriptome-wide association studies, and it was confirmed that AIR2 expression levels of indica were lower than those of japonica. This was consistent with the functional haplotype results for the genome sequence of AIR2, and finally, eight rice varieties with low AIR2 expression and arsenic content were selected. In addition, As-related QTLs were identified on chromosomes 5 and 6 under flooded and intermittently flooded conditions through genome-scale profiling. Taken together, these results might assist in developing markers and breeding plans to reduce toxic element content and breeding high-quality rice varieties in future.
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Affiliation(s)
- Sang-Beom Lee
- Crop Foundation Research Division, National Institute of Crop Science, Wanju, South Korea
| | - Gyeong-Jin Kim
- Residual Agrochemical Assessment Division, National Institute of Agriculture Science, Wanju, South Korea
| | - Jung-Du Shin
- Bio-Technology of Multidisciplinary Sciences Co., Wanju, South Korea
| | - Woojin Chung
- Department of Environmental Energy Engineering, Kyonggi University, Suwon, South Korea
| | - Soo-Kwon Park
- Crop Foundation Research Division, National Institute of Crop Science, Wanju, South Korea
| | - Geun-Hyoung Choi
- Residual Agrochemical Assessment Division, National Institute of Agriculture Science, Wanju, South Korea
| | - Sang-Won Park
- Reserch Policy Bureau, Rural Development Administration, Wanju, South Korea
| | - Yong-Jin Park
- Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan, South Korea
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Deng F, Zeng F, Norton GJ. Editorial: Natural Variations and Genetic Constraints on Plant Nutrition. Front Genet 2022; 13:941118. [PMID: 35812746 PMCID: PMC9264042 DOI: 10.3389/fgene.2022.941118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 06/06/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
- Fenglin Deng
- College of Agriculture, Yangtze University, Jingzhou, China
- *Correspondence: Fenglin Deng,
| | - Fanrong Zeng
- College of Agriculture, Yangtze University, Jingzhou, China
| | - Gareth J. Norton
- School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom
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Li L, Mao D, Sun L, Wang R, Tan L, Zhu Y, Huang H, Peng C, Zhao Y, Wang J, Huang D, Chen C. CF1 reduces grain-cadmium levels in rice (Oryza sativa). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:1305-1318. [PMID: 35293046 DOI: 10.1111/tpj.15736] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 03/06/2022] [Accepted: 03/08/2022] [Indexed: 06/14/2023]
Abstract
Rice (Oryza sativa) is a leading source of dietary cadmium (Cd), a non-essential heavy metal that poses a serious threat to human health. There are significant variations in grain-Cd levels in natural rice populations, which make the breeding of low-Cd rice a cost-effective way to mitigate grain-Cd accumulation. However, the genetic factors that regulate grain-Cd accumulation have yet to be fully established, thereby hindering the development of low-Cd varieties. Here, we reported a low-Cd quantitative trait locus, CF1, that has the potential to reduce Cd accumulation in rice grains. CF1 is allelic to the metal transporter OsYSL2, which transports Fe from the roots to the shoots. However, it is incapable of binding Cd, and thus, reduces grain-Cd levels indirectly rather than directly in the form of upward delivery. Further analysis showed that high expression levels of CF1 improve Fe nutrition in the shoots, subsequently inhibiting Cd uptake by systemically inhibiting expression of the main Cd uptake gene OsNramp5 in the roots. Compared with the CF1 allele from '02428' (CF102428 ), higher expression levels of CF1 from 'TQ' (CF1TQ ) increased the Fe contents and decreased Cd levels in rice grains. In natural rice populations, CF1TQ was found to be a minor allele, while CF102428 is present in most japonica rice, suggesting that CF1TQ could be widely integrated into the japonica rice genome to generate low-Cd varieties. Overall, these results broaden our mechanistic understanding of the natural variation in grain-Cd accumulation, supporting marker-assisted selection of low-Cd rice.
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Affiliation(s)
- Lanying Li
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Innovation Academy for Seed Design, Chinese Academy of Sciences, Changsha, 410125, China
| | - Donghai Mao
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Innovation Academy for Seed Design, Chinese Academy of Sciences, Changsha, 410125, China
| | - Liang Sun
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Innovation Academy for Seed Design, Chinese Academy of Sciences, Changsha, 410125, China
| | - Ruigang Wang
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, China
| | - Longtao Tan
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Innovation Academy for Seed Design, Chinese Academy of Sciences, Changsha, 410125, China
| | - Yuxing Zhu
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Innovation Academy for Seed Design, Chinese Academy of Sciences, Changsha, 410125, China
| | - Han Huang
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Innovation Academy for Seed Design, Chinese Academy of Sciences, Changsha, 410125, China
| | - Can Peng
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Innovation Academy for Seed Design, Chinese Academy of Sciences, Changsha, 410125, China
| | - Yaping Zhao
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, China
| | - Jiurong Wang
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Innovation Academy for Seed Design, Chinese Academy of Sciences, Changsha, 410125, China
| | - Daoyou Huang
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Innovation Academy for Seed Design, Chinese Academy of Sciences, Changsha, 410125, China
| | - Caiyan Chen
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Innovation Academy for Seed Design, Chinese Academy of Sciences, Changsha, 410125, China
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Xue J, Jiang T, Chen X, Liu H, Yang J. Multi-mineral fingerprinting analysis of the Chinese mitten crab (Eriocheir sinensis) in Yangcheng Lake during the year-round culture period. Food Chem 2022; 390:133167. [PMID: 35597091 DOI: 10.1016/j.foodchem.2022.133167] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 04/29/2022] [Accepted: 05/04/2022] [Indexed: 11/29/2022]
Abstract
Chinese mitten crabs (Eriocheir sinensis), originating from Yangcheng Lake, are valuable aquatic products in China. To characterize changes in nutrients in this species in Yangcheng Lake during the year-round culture period, the contents of ten mineral elements in the third pereiopod were evaluated. Principal component analysis revealed that mineral elements changed substantially in the first three months. Thereafter, the elemental "fingerprint" stabilized, and samples could not be accurately distinguished. This pattern was supported by linear discriminant analysis and self-organizing map analysis. These results demonstrate that a long period of time is required for element characteristics to stabilize, suggesting that short-term breeding is insufficient to obtain the natural elemental "fingerprint." In addition, our findings provide a basis for verifying the origin of Chinese mitten crab and other aquatic taxa in Yangcheng Lake.
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Affiliation(s)
- Junren Xue
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China
| | - Tao Jiang
- Key Laboratory of Fishery Ecological Environment Assessment and Resource Conservation in Middle and Lower Reaches of the Yangtze River, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| | - Xiubao Chen
- Key Laboratory of Fishery Ecological Environment Assessment and Resource Conservation in Middle and Lower Reaches of the Yangtze River, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| | - Hongbo Liu
- Key Laboratory of Fishery Ecological Environment Assessment and Resource Conservation in Middle and Lower Reaches of the Yangtze River, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| | - Jian Yang
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China; Key Laboratory of Fishery Ecological Environment Assessment and Resource Conservation in Middle and Lower Reaches of the Yangtze River, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China.
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11
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Xue W, Zhang C, Huang Y, Wang C, Zhang X, Liu Z. Rice organs concentrate cadmium by chelation of amino acids containing dicarboxyl groups and enhance risks to human and environmental health in Cd-contaminated areas. JOURNAL OF HAZARDOUS MATERIALS 2022; 426:128130. [PMID: 34959214 DOI: 10.1016/j.jhazmat.2021.128130] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 12/14/2021] [Accepted: 12/19/2021] [Indexed: 06/14/2023]
Abstract
When rice plants grown in paddy fields with Cd content of 0.3-1.5 mg kg-1, Cd quantities in roots and straws were 2-7 times higher than that in topsoil. Return of these vegetative organs to topsoil aggravated the ecological risk of Cd pollution. Cd content in rice grains was 0.1-1.3 mg kg-1, and hazard quotients for local consumers by intake of these rice were 0.7-8.8. Planting low-Cd-accumulating (LCA) cultivar reduced hazard quotients for consumers by intake of rice, but had similar ecological risks as high-accumulating (HCA) cultivars. LCA cultivar had lower Cd content in grains as well as higher efficiency of altering Cd into insoluble forms in flag leaves and upmost nodes than HCA cultivars. Insoluble Cd content in nodes was linearly increased with soil Cd content, companied by significant decline of 4 amino acids with dicarboxyl groups. Glu or Asp can form a cyclic complex with Cd by two O atoms from α-COO- and side chain-COO-. These results indicate that roots and straws have high potential to concentrate Cd by forming complexes between amino acids and Cd ions, and Cd-enriched straw return to topsoil may aggravate the ecological risk of Cd contamination.
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Affiliation(s)
- Weijie Xue
- Key Laboratory of Original Agro-Environmental Pollution Prevention and Control, Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China
| | - Changbo Zhang
- Key Laboratory of Original Agro-Environmental Pollution Prevention and Control, Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China
| | - Yongchun Huang
- Key Laboratory of Original Agro-Environmental Pollution Prevention and Control, Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China
| | - Changrong Wang
- Key Laboratory of Original Agro-Environmental Pollution Prevention and Control, Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China
| | - Xin Zhang
- Key Laboratory of Original Agro-Environmental Pollution Prevention and Control, Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China
| | - Zhongqi Liu
- Key Laboratory of Original Agro-Environmental Pollution Prevention and Control, Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China.
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12
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Sun L, Wang R, Tang W, Chen Y, Zhou J, Ma H, Li S, Deng H, Han L, Chen Y, Tan Y, Zhu Y, Lin D, Zhu Q, Wang J, Huang D, Chen C. Robust identification of low-Cd rice varieties by boosting the genotypic effect of grain Cd accumulation in combination with marker-assisted selection. JOURNAL OF HAZARDOUS MATERIALS 2022; 424:127703. [PMID: 34799159 DOI: 10.1016/j.jhazmat.2021.127703] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 10/27/2021] [Accepted: 11/01/2021] [Indexed: 05/28/2023]
Abstract
Rice (Oryza sativa L.), a staple for half of the world's population, usually accumulates high levels of cadmium (Cd) in the grain when planted in the Cd-contaminated paddy fields. Genetic improvements using natural variation of grain-Cd accumulation is the most cost-effective way to mitigate the risk of excess Cd accumulation. However, as a complex trait, grain-Cd accumulation is susceptible to environmental variation, which challenges to characterize the genetic nature and subsequently the stable performance of grain-Cd accumulation. To boost the genetic effect on grain-Cd performance, we established an approach of normalization using the comparative grain-Cd value (CCd) following a contrasting field design. Identification of the genetic locus responsible for CCd variation help us develop a low-grain-Cd variety de novo, named 'Lushansimiao', which had lower grain-Cd levels in a large-scale field test and can produce Cd-safe rice following prolonged irrigations in the field with intermediate levels of Cd pollution. Combined CCd evaluating and low-Cd allelic genotyping, another six varieties were also identified as low-grain-Cd rice. Our study paves the way to efficiently quantify the genetic nature of grain-Cd accumulation in rice, and the stable low-Cd rice varieties will help to mitigate the risk of excess Cd accumulation in rice.
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Affiliation(s)
- Liang Sun
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China
| | - Ruigang Wang
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China
| | - Wenbang Tang
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Yuchao Chen
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China; University of Chinese Academy of Science, Beijing 100049, China
| | - Jieqiang Zhou
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China; College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Haoran Ma
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China
| | - Sai Li
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China; University of Chinese Academy of Science, Beijing 100049, China
| | - Hubing Deng
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Lei Han
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China
| | - Yibo Chen
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China; College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Yongjun Tan
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China; University of Chinese Academy of Science, Beijing 100049, China
| | - Yuxing Zhu
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China
| | - Dasong Lin
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China
| | - Qihong Zhu
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China
| | - Jiurong Wang
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China
| | - Daoyou Huang
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China
| | - Caiyan Chen
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China.
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13
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Anwar K, Joshi R, Morales A, Das G, Yin X, Anten NPR, Raghuvanshi S, Bahuguna RN, Singh MP, Singh RK, Zanten M, Sasidharan R, Singla‐Pareek SL, Pareek A. Genetic diversity reveals synergistic interaction between yield components could improve the sink size and yield in rice. Food Energy Secur 2022. [DOI: 10.1002/fes3.334] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Affiliation(s)
- Khalid Anwar
- Stress Physiology and Molecular Biology Laboratory School of Life Sciences Jawaharlal Nehru University New Delhi India
| | - Rohit Joshi
- Stress Physiology and Molecular Biology Laboratory School of Life Sciences Jawaharlal Nehru University New Delhi India
- Division of Biotechnology CSIR‐Institute of Himalayan Bioresource Technology Palampur India
| | - Alejandro Morales
- Centre for Crop Systems Analysis Plant Sciences Group Wageningen University & Research Wageningen The Netherlands
- Molecular Plant Physiology Institute of Environmental Biology Utrecht University Utrecht The Netherlands
- Plant Ecophysiology Institute of Environmental Biology Utrecht University Utrecht The Netherlands
| | - Gourab Das
- Stress Physiology and Molecular Biology Laboratory School of Life Sciences Jawaharlal Nehru University New Delhi India
| | - Xinyou Yin
- Centre for Crop Systems Analysis Plant Sciences Group Wageningen University & Research Wageningen The Netherlands
| | - Niels P. R. Anten
- Centre for Crop Systems Analysis Plant Sciences Group Wageningen University & Research Wageningen The Netherlands
| | - Saurabh Raghuvanshi
- Department of Plant Molecular Biology University of Delhi South Campus New Delhi India
| | - Rajeev N. Bahuguna
- Stress Physiology and Molecular Biology Laboratory School of Life Sciences Jawaharlal Nehru University New Delhi India
- Center for Advance Studies on Climate Change Dr. Rajendra Prasad Central Agricultural University, Pusa Samastipur India
| | - Madan Pal Singh
- Division of Plant Physiology Indian Agricultural Research Institute PUSA New Delhi India
| | - Rakesh K. Singh
- Crop Diversification and Genetics International Center for Biosaline Agriculture Academic City Dubai United Arab Emirates
| | - Martijn Zanten
- Molecular Plant Physiology Institute of Environmental Biology Utrecht University Utrecht The Netherlands
| | - Rashmi Sasidharan
- Plant Ecophysiology Institute of Environmental Biology Utrecht University Utrecht The Netherlands
| | - Sneh L. Singla‐Pareek
- Plant Stress Biology International Centre for Genetic Engineering and Biotechnology New Delhi India
| | - Ashwani Pareek
- Stress Physiology and Molecular Biology Laboratory School of Life Sciences Jawaharlal Nehru University New Delhi India
- National Agri‐Food Biotechnology Institute Mohali India
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14
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Luo JS, Zhang Z. Mechanisms of cadmium phytoremediation and detoxification in plants. ACTA ACUST UNITED AC 2021. [DOI: 10.1016/j.cj.2021.02.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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15
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Chen YB, Chen YC, Zhu YX, Li S, Deng HB, Wang JR, Tang WB, Sun L. Genetic Control Diversity Drives Differences Between Cadmium Distribution and Tolerance in Rice. FRONTIERS IN PLANT SCIENCE 2021; 12:638095. [PMID: 33679853 PMCID: PMC7933448 DOI: 10.3389/fpls.2021.638095] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Accepted: 01/12/2021] [Indexed: 06/12/2023]
Abstract
Rice, a staple crop for nearly half the planet's population, tends to absorb and accumulate excessive cadmium (Cd) when grown in Cd-contaminated fields. Low levels of Cd can degrade the quality of rice grains, while high levels can inhibit the growth of rice plants. There is genotypic diversity in Cd distribution and Cd tolerance in different rice varieties, but their underlying genetic mechanisms are far from elucidated, which hinders genetic improvements. In this study, a joint study of phenotypic investigation with quantitative trait loci (QTLs) analyses of genetic patterns of Cd distribution and Cd tolerance was performed using a biparent population derived from japonica and indica rice varieties. We identified multiple QTLs for each trait and revealed that additive effects from various loci drive the inheritance of Cd distribution, while epistatic effects between various loci contribute to differences in Cd tolerance. One pleiotropic locus, qCddis8, was found to affect the Cd distribution from both roots to shoots and from leaf sheaths to leaf blades. The results expand our understanding of the diversity of genetic control over Cd distribution and Cd tolerance in rice. The findings provide information on potential QTLs for genetic improvement of Cd distribution in rice varieties.
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Affiliation(s)
- Yi-Bo Chen
- College of Agronomy, Hunan Agricultural University, Changsha, China
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
| | - Yu-Chao Chen
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
| | - Yu-Xing Zhu
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
| | - Sai Li
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
| | - Hua-bing Deng
- College of Agronomy, Hunan Agricultural University, Changsha, China
| | - Jiu-Rong Wang
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
| | - Wen-Bang Tang
- College of Agronomy, Hunan Agricultural University, Changsha, China
| | - Liang Sun
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
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16
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Norton GJ, Travis A, Ruang-areerate P, Nicol GW, Adeosun AA, Hossain M, Islam MR, Douglas A, Price AH. Genetic loci regulating cadmium content in rice grains. EUPHYTICA: NETHERLANDS JOURNAL OF PLANT BREEDING 2021; 217:35. [PMID: 33627887 PMCID: PMC7875855 DOI: 10.1007/s10681-020-02752-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 12/15/2020] [Indexed: 06/12/2023]
Abstract
UNLABELLED It has been estimated that up to 90% of human exposure to cadmium is through food, and that cadmium within rice grains can be a major contributor to that dietary source. In this study genome wide association mapping was conducted on the Bengal and Assam Aus Panel (BAAP) of rice to identify quantitative trait loci and candidate genes for lowering grain cadmium. Field experiments were conducted over two years under two different irrigation systems: continually flooded and alternate wetting and drying (AWD). There was significant effects of water treatment, genotype, and genotype by water treatment interaction. Importantly, AWD increased grain cadmium, on average, by 49.6% and 108.8% in year 1 and 2 respectively. There was between 4.6 and 28 fold variation in cadmium concentration. A total of 58 QTLs were detected but no loci are clearly specific to one water regime despite approximately 20% of variation attributable to genotype by water regime interaction. A number of QTLs were consistent across most water treatments and years. These included QTLs on chromosome 7 (7.23-7.61, 8.93-9.04, and 29.12-29.14 Mbp), chromosome 5 (8.66-8.72 Mbp), and chromosome 9 (11.46-11.64 Mbp). Further analysis of the loci on chromosome 7 (8.93-9.04 Mbp), identified the candidate gene OsNRAMP1, where cultivars with a deletion upstream of the gene had higher concentrations of cadmium compared to the cultivars that did not have the deletion. The distribution of alleles within the BAAP suggest this QTL is easily detected in this population because it is composed of aus cultivars. Local genome cluster analysis suggest high Cd alleles are uncommon, but should be avoided in breeding. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at (10.1007/s10681-020-02752-1).
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Affiliation(s)
- Gareth J. Norton
- School of Biological Sciences, University of Aberdeen, Aberdeen, AB24 3UU UK
| | - Anthony Travis
- School of Biological Sciences, University of Aberdeen, Aberdeen, AB24 3UU UK
| | - Panthita Ruang-areerate
- School of Biological Sciences, University of Aberdeen, Aberdeen, AB24 3UU UK
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120 Thailand
| | - Graeme W. Nicol
- Laboratoire Ampère, École Centrale de Lyon, Université de Lyon, 36 avenue Guy de Collongue, 69134 Ecully Cedex, France
| | - Ayotunde A. Adeosun
- School of Biological Sciences, University of Aberdeen, Aberdeen, AB24 3UU UK
| | - Mahmud Hossain
- Department of Soil Science, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - M. Rafiq Islam
- Department of Soil Science, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Alex Douglas
- School of Biological Sciences, University of Aberdeen, Aberdeen, AB24 3UU UK
| | - Adam H. Price
- School of Biological Sciences, University of Aberdeen, Aberdeen, AB24 3UU UK
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17
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Liu H, Long SX, Pinson SRM, Tang Z, Guerinot ML, Salt DE, Zhao FJ, Huang XY. Univariate and Multivariate QTL Analyses Reveal Covariance Among Mineral Elements in the Rice Ionome. Front Genet 2021; 12:638555. [PMID: 33569081 PMCID: PMC7868434 DOI: 10.3389/fgene.2021.638555] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 01/06/2021] [Indexed: 11/27/2022] Open
Abstract
Rice provides more than one fifth of daily calories for half of the world’s human population, and is a major dietary source of both essential mineral nutrients and toxic elements. Rice grains are generally poor in some essential nutrients but may contain unsafe levels of some toxic elements under certain conditions. Identification of quantitative trait loci (QTLs) controlling the concentrations of mineral nutrients and toxic trace metals (the ionome) in rice will facilitate development of nutritionally improved rice varieties. However, QTL analyses have traditionally considered each element separately without considering their interrelatedness. In this study, we performed principal component analysis (PCA) and multivariate QTL analyses to identify the genetic loci controlling the covariance among mineral elements in the rice ionome. We resequenced the whole genomes of a rice recombinant inbred line (RIL) population, and performed univariate and multivariate QTL analyses for the concentrations of 16 elements in grains, shoots and roots of the RIL population grown in different conditions. We identified a total of 167 unique elemental QTLs based on analyses of individual elemental concentrations as separate traits, 53 QTLs controlling covariance among elemental concentrations within a single environment/tissue (PC-QTLs), and 152 QTLs which determined covariation among elements across environments/tissues (aPC-QTLs). The candidate genes underlying the QTL clusters with elemental QTLs, PC-QTLs and aPC-QTLs co-localized were identified, including OsHMA4 and OsNRAMP5. The identification of both elemental QTLs and PC QTLs will facilitate the cloning of underlying causal genes and the dissection of the complex regulation of the ionome in rice.
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Affiliation(s)
- Huan Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Su-Xian Long
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Shannon R M Pinson
- USDA-ARS Dale Bumpers National Rice Research Center, Stuttgart, AR, United States
| | - Zhong Tang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Mary Lou Guerinot
- Department of Biological Sciences, Dartmouth College, Hanover, NH, United States
| | - David E Salt
- Future Food Beacon of Excellence and the School of Biosciences, University of Nottingham, Loughborough, United Kingdom
| | - Fang-Jie Zhao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Xin-Yuan Huang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
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18
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Babu PM, Neeraja CN, Rathod S, Suman K, Uttam GA, Chakravartty N, Lachagari VBR, Chaitanya U, Rao LVS, Voleti SR. Stable SNP Allele Associations With High Grain Zinc Content in Polished Rice ( Oryza sativa L.) Identified Based on ddRAD Sequencing. Front Genet 2020; 11:763. [PMID: 32849786 PMCID: PMC7432318 DOI: 10.3389/fgene.2020.00763] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 06/29/2020] [Indexed: 01/01/2023] Open
Abstract
Polished rice is widely consumed staple food across the globe, however, it contains limited nutrients especially iron (Fe) and zinc (Zn). To identify promising genotypes for grain Zn, a total of 40 genotypes consisting 20 rice landraces, and 20 released high yielding rice varieties were evaluated in three environments (wet seasons 2014, 2015 and 2016) for nine traits including days to 50% flowering (DFF), plant height (PH), panicle length (PL), total number of tillers (TNT), single plant yield (SPY), Fe and Zn in brown (IBR, ZBR) and polished rice (IPR, ZPR). Additive Main Effect and Multiplicative Interaction (AMMI), Genotype and Genotype × Environment Interaction (GGE) analyses identified genotypes G22 (Edavankudi Pokkali), G17 (Taraori Basmati), G27 (Chittimuthyalu) and G26 (Kalanamak) stable for ZPR and G8 (Savitri) stable for SPY across three environments. Significant negative correlation between yield and grain Zn was reaffirmed. Regression analysis indicated the contribution of traits toward ZPR and SPY and also desirable level of grain Zn in brown rice. A total of 39,137 polymorphic single nucleotide polymorphisms (SNPs) were obtained through double digest restriction site associated DNA (dd-RAD) sequencing of 40 genotypes. Association analyses with nine phenotypic traits revealed 188 stable SNPs with six traits across three environments. ZPR was associated with SNPs located in three putative candidate genes (LOC_Os03g47980, LOC_Os07g47950 and LOC_Os07g48050) on chromosomes 3 and 7. The genomic region of chromosome 7 co localized with reported genomic regions (rMQTL7.1) and OsNAS3 candidate gene. SPY was found to be associated with 12 stable SNPs located in 11 putative candidate genes on chromosome 1, 6, and 12. Characterization of rice landraces and varieties in terms of stability for their grain Zn and yield identified promising donors and recipients along with genomic regions in the present study to be deployed rice Zn biofortification breeding program.
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Affiliation(s)
- P Madhu Babu
- ICAR-Indian Institute of Rice Research, Hyderabad, India
| | - C N Neeraja
- ICAR-Indian Institute of Rice Research, Hyderabad, India
| | | | - K Suman
- ICAR-Indian Institute of Rice Research, Hyderabad, India
| | - G Anurag Uttam
- ICAR-Indian Institute of Rice Research, Hyderabad, India
| | | | | | - U Chaitanya
- ICAR-Indian Institute of Rice Research, Hyderabad, India
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19
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Liu C, Ding S, Zhang A, Hong K, Jiang H, Yang S, Ruan B, Zhang B, Dong G, Guo L, Zeng D, Qian Q, Gao Z. Development of nutritious rice with high zinc/selenium and low cadmium in grains through QTL pyramiding. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2020; 62:349-359. [PMID: 31957138 DOI: 10.1111/jipb.12909] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 01/17/2020] [Indexed: 06/10/2023]
Abstract
Enriching zinc (Zn) and selenium (Se) levels, while reducing cadmium (Cd) concentration in rice grains is of great benefit for human diet and health. Large natural variations in grain Zn, Se, and Cd concentrations in different rice accessions enable Zn/Se-biofortification and Cd-minimization through molecular breeding. Here, we report the development of new elite varieties by pyramiding major quantitative trait loci (QTLs) that significantly contribute to high Zn/Se and low Cd accumulation in grains. A chromosome segment substitution line CSSLGCC7 with the PA64s-derived GCC7 allele in the 93-11 background, exhibited steadily higher Mn and lower Cd concentrations in grains than those of 93-11. This elite chromosome segment substitution line (CSSL) was used as the core breeding material to cross with CSSLs harboring other major QTLs for essential mineral elements, especially CSSLGZC6 for grain Zn concentration and CSSLGSC5 for grain Se concentration. The CSSLGCC7+GZC6 and CSSLGCC7+GSC5 exhibited lower Cd concentration with higher Zn and Se concentrations in grains, respectively. Our study thus provides elite materials for rice breeding targeting high Zn/Se and low Cd concentrations in grains.
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Affiliation(s)
- Chaolei Liu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Shilin Ding
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Anpeng Zhang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Kai Hong
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Hongzhen Jiang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Shenglong Yang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Banpu Ruan
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Bin Zhang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Guojun Dong
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Longbiao Guo
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Dali Zeng
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Qian Qian
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Zhenyu Gao
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
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20
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Tan Y, Zhou J, Wang J, Sun L. The Genetic Architecture for Phenotypic Plasticity of the Rice Grain Ionome. FRONTIERS IN PLANT SCIENCE 2020; 11:12. [PMID: 32158453 PMCID: PMC7052182 DOI: 10.3389/fpls.2020.00012] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 01/08/2020] [Indexed: 05/26/2023]
Abstract
The ionome of the rice grain is crucial for the health of populations that consume rice as a staple food. However, the contribution of phenotypic plasticity to the variation of rice grain ionome and the genetic architecture of phenotypic plasticity are poorly understood. In this study, we investigated the rice grain ionome of a rice diversity panel in up to eight environments. A considerable proportion of phenotypic variance can be attributed to phenotypic plasticity. Then, phenotypic plasticity and mean phenotype were quantified using Bayesian Finlay-Wilkinson regression, and a significant correlation between them was observed. However, the genetic architecture of mean phenotype was distinct from that of phenotypic plasticity. Also, the correlation between them was mainly attributed to the phenotypic divergence between rice subspecies. Furthermore, the results of whole-genome regression analysis showed that the genetic loci related to phenotypic plasticity can explain a considerable proportion of the phenotypic variance in some environments, especially for Cd, Cu, Mn, and Zn. Our study not only sheds light on the genetic architecture of phenotypic plasticity of the rice grain ionome but also suggests that the genetic loci which related to phenotypic plasticity are valuable in rice grain ionome improvement breeding.
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Affiliation(s)
- Yongjun Tan
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
- University of Chinese Academy of Science, Beijing, China
| | - Jieqiang Zhou
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
- College of Agronomy, Hunan Agricultural University, Changsha, China
| | - Jiurong Wang
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
| | - Liang Sun
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
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