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Zulfiqar U, Khokhar A, Maqsood MF, Shahbaz M, Naz N, Sara M, Maqsood S, Sahar S, Hussain S, Ahmad M. Genetic biofortification: advancing crop nutrition to tackle hidden hunger. Funct Integr Genomics 2024; 24:34. [PMID: 38365972 DOI: 10.1007/s10142-024-01308-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 01/26/2024] [Accepted: 01/29/2024] [Indexed: 02/18/2024]
Abstract
Malnutrition, often termed "hidden hunger," represents a pervasive global issue carrying significant implications for health, development, and socioeconomic conditions. Addressing the challenge of inadequate essential nutrients, despite sufficient caloric intake, is crucial. Biofortification emerges as a promising solution by enhance the presence of vital nutrients like iron, zinc, iodine, and vitamin A in edible parts of different crop plants. Crop biofortification can be attained through either agronomic methods or genetic breeding techniques. Agronomic strategies for biofortification encompass the application of mineral fertilizers through foliar or soil methods, as well as leveraging microbe-mediated mechanisms to enhance nutrient uptake. On the other hand, genetic biofortification involves the strategic crossing of plants to achieve a desired combination of genes, promoting balanced nutrient uptake and bioavailability. Additionally, genetic biofortification encompasses innovative methods such as speed breeding, transgenic approaches, genome editing techniques, and integrated omics approaches. These diverse strategies collectively contribute to enhancing the nutritional profile of crops. This review highlights the above-said genetic biofortification strategies and it also covers the aspect of reduction in antinutritional components in food through genetic biofortification.
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Affiliation(s)
- Usman Zulfiqar
- Department of Agronomy, Faculty of Agriculture and Environment, The Islamia University of Bahawalpur, Bahawalpur, 63100, Pakistan.
| | - Amman Khokhar
- Department of Botany, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | | | - Muhammad Shahbaz
- Department of Botany, University of Agriculture, Faisalabad, Pakistan
| | - Nargis Naz
- Department of Botany, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Maheen Sara
- Department of Nutritional Sciences, Government College Women University, Faisalabad, Pakistan
| | - Sana Maqsood
- Department of Botany, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Sajila Sahar
- Department of Plant Breeding & Genetics, University of Agriculture, Faisalabad, Pakistan
| | - Saddam Hussain
- Department of Agronomy, University of Agriculture, Faisalabad, Pakistan
| | - Muhammad Ahmad
- Department of Agronomy, University of Agriculture, Faisalabad, Pakistan
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Cong W, Li N, Miao Y, Huang Y, Zhao W, Kang Y, Zhang B, Wang J, Zhang J, Lv Y, Li J, Zhang J, Gong L, Liu B, Ou X. DNA hypomethylation-associated transcriptional rewiring enables resistance to heavy metal mercury (Hg) stress in rice. JOURNAL OF HAZARDOUS MATERIALS 2024; 461:132649. [PMID: 37783144 DOI: 10.1016/j.jhazmat.2023.132649] [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: 12/26/2022] [Revised: 06/17/2023] [Accepted: 09/26/2023] [Indexed: 10/04/2023]
Abstract
Mercury (Hg) is an important hazardous pollutant that can cause phytotoxicity and harm human health through the food chain. Recently, rice (Oryza sativa L.) has been confirmed as a potential Hg bioaccumulator. Although the genetic and molecular mechanisms involved in heavy metal absorption and translocation in rice have been investigated for several heavy metals, Hg is largely neglected. Here, we analyzed one Hg-resistant line in rice (RHg) derived from a DNA methyltransferase-coding gene, OsMET1-2 heterozygous mutant. Compared with its isogenic wild-type (WT), RHg exhibited a significantly higher survival rate after Hg treatment, ameliorated oxidative damage, and lower Hg uptake and translocation. RNAseq-based comparative transcriptomic analysis identified 34 potential Hg resistance-related genes involved in phytohormone signaling, abiotic stress response, and zinc (Zn) transport. Importantly, the elevated expression of Hg resistance-related genes in RHg was highly correlated with DNA hypomethylation in their putative promoter regions. An ionomic analysis unraveled a negative correlation between Zn and Hg in roots. Moreover, Hg concentration was effectively decreased by exogenous application of Zn in Hg-stressed rice plants. Our findings indicate an epigenetic basis of Hg resistance and reveal an antagonistic relationship between Hg and Zn, providing new hints towards Hg detoxification in plants. ENVIRONMENTAL IMPLICATION: Mercury (Hg) as an important hazardous pollutant adversely impacts the environment and jeopardizes human health, due to its chronicity, transferability, persistence, bioaccumulation and toxicity. In this paper, we identified 34 potential genes that may significantly contribute to Hg resistance in rice. We find the expression of Hg resistance-related genes was highly correlated with DNA hypomethylation in their putative promoter regions. Our results also revealed an antagonistic relationship between Hg and Zinc (Zn), providing new hints towards Hg detoxification in plants. Together, findings of this study extend our current understanding of Hg tolerance in rice and are informative to breed seed non-accumulating rice cultivars.
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Affiliation(s)
- Weixuan Cong
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China; Faculty of Agronomy, Jilin Agricultural University, Changchun 130118, China
| | - Ning Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Yiling Miao
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun 130062, China
| | - Yuxi Huang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Wenhao Zhao
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Ying Kang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Bingqi Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Jinbin Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Jiayu Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Yinhe Lv
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Jiamo Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Jian Zhang
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130118, China
| | - Lei Gong
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China.
| | - Xiufang Ou
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China.
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Zhu H, Lai R, Chen W, Lu C, Chachar Z, Lu S, Lin H, Fan L, Hu Y, An Y, Li X, Zhang X, Qi Y. Genetic dissection of maize (Zea maysL.) trace element traits using genome-wide association studies. BMC PLANT BIOLOGY 2023; 23:631. [PMID: 38062375 PMCID: PMC10704835 DOI: 10.1186/s12870-023-04643-8] [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: 06/02/2023] [Accepted: 11/29/2023] [Indexed: 12/18/2023]
Abstract
Maize (Zea mays L.) is an important food and feed crop worldwide and serves as a a vital source of biological trace elements, which are important breeding targets. In this study, 170 maize materials were used to detect QTNs related to the content of Mn, Fe and Mo in maize grains through two GWAS models, namely MLM_Q + K and MLM_PCA + K. The results identified 87 (Mn), 205 (Fe), and 310 (Mo) QTNs using both methods in the three environments. Considering comprehensive factors such as co-location across multiple environments, strict significance threshold, and phenotypic value in multiple environments, 8 QTNs related to Mn, 10 QTNs related to Fe, and 26 QTNs related to Mo were used to identify 44 superior alleles. Consequently, three cross combinations with higher Mn element, two combinations with higher Fe element, six combinations with higher Mo element, and two combinations with multiple element (Mn/Fe/Mo) were predicted to yield offspring with higher numbers of superior alleles, thereby increasing the likelihood of enriching the corresponding elements. Additionally, the candidate genes identified 100 kb downstream and upstream the QTNs featured function and pathways related to maize elemental transport and accumulation. These results are expected to facilitate the screening and development of high-quality maize varieties enriched with trace elements, establish an important theoretical foundation for molecular marker assisted breeding and contribute to a better understanding of the regulatory network governing trace elements in maize.
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Affiliation(s)
- Hang Zhu
- Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, Guangdong, China
- Institute of Nanfan & Seed Industry, Guangdong Academy of Science, Guangzhou, 510316, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, Guangdong, China
- College of Agriculture, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Ruiqiang Lai
- Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, Guangdong, China
- Institute of Nanfan & Seed Industry, Guangdong Academy of Science, Guangzhou, 510316, Guangdong, China
| | - Weiwei Chen
- Institute of Nanfan & Seed Industry, Guangdong Academy of Science, Guangzhou, 510316, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, Guangdong, China
- Heyuan Provincial Academy of Sciences Research Institute, Guangdong Academy of Sciences, GDAS, Heyuan, 517001, Guangdong, China
| | - Chuanli Lu
- Institute of Nanfan & Seed Industry, Guangdong Academy of Science, Guangzhou, 510316, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, Guangdong, China
- Heyuan Provincial Academy of Sciences Research Institute, Guangdong Academy of Sciences, GDAS, Heyuan, 517001, Guangdong, China
| | - Zaid Chachar
- Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, Guangdong, China
| | - Siqi Lu
- Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, Guangdong, China
- Institute of Nanfan & Seed Industry, Guangdong Academy of Science, Guangzhou, 510316, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, Guangdong, China
| | - Huanzhang Lin
- Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, Guangdong, China
- Institute of Nanfan & Seed Industry, Guangdong Academy of Science, Guangzhou, 510316, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, Guangdong, China
| | - Lina Fan
- Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, Guangdong, China
- Institute of Nanfan & Seed Industry, Guangdong Academy of Science, Guangzhou, 510316, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, Guangdong, China
| | - Yuanqiang Hu
- Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, Guangdong, China
- Institute of Nanfan & Seed Industry, Guangdong Academy of Science, Guangzhou, 510316, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, Guangdong, China
| | - Yuxing An
- Institute of Nanfan & Seed Industry, Guangdong Academy of Science, Guangzhou, 510316, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, Guangdong, China
- Heyuan Provincial Academy of Sciences Research Institute, Guangdong Academy of Sciences, GDAS, Heyuan, 517001, Guangdong, China
| | - Xuhui Li
- Institute of Nanfan & Seed Industry, Guangdong Academy of Science, Guangzhou, 510316, Guangdong, China.
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, Guangdong, China.
- Heyuan Provincial Academy of Sciences Research Institute, Guangdong Academy of Sciences, GDAS, Heyuan, 517001, Guangdong, China.
| | - Xiangbo Zhang
- Institute of Nanfan & Seed Industry, Guangdong Academy of Science, Guangzhou, 510316, Guangdong, China.
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, Guangdong, China.
- Heyuan Provincial Academy of Sciences Research Institute, Guangdong Academy of Sciences, GDAS, Heyuan, 517001, Guangdong, China.
| | - Yongwen Qi
- Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, Guangdong, China.
- Institute of Nanfan & Seed Industry, Guangdong Academy of Science, Guangzhou, 510316, Guangdong, China.
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, Guangdong, China.
- College of Agriculture, Yangtze University, Jingzhou, 434025, Hubei, China.
- Heyuan Provincial Academy of Sciences Research Institute, Guangdong Academy of Sciences, GDAS, Heyuan, 517001, Guangdong, China.
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Alam M, Wang Y, Chen J, Lou G, Yang H, Zhou Y, Luitel S, Jiang G, He Y. QTL detection for rice grain storage protein content and genetic effect verifications. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2023; 43:89. [PMID: 38059164 PMCID: PMC10695898 DOI: 10.1007/s11032-023-01436-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 11/21/2023] [Indexed: 12/08/2023]
Abstract
Rice grain quality is a multifarious attribute mainly governed by multiple nutritional factors. Grain protein is the central component of rice grain nutrition dominantly affecting eating-cooking qualities. Grain protein content is quantitatively influenced by its protein fractions. Genetic quantification of five protein fractions-albumins, globulins, prolamins, glutelin, and grain protein content-were evaluated by exploiting two BC3F2 mapping populations, derived from Kongyu131/TKM9 (population-I) and Kongyu131/Bg94-1 (population-II), which were grown in a single environment. Correlation studies among protein fractions and grain protein content were thoroughly investigated. A genetic linkage map was developed by using 146 single sequence repeat (SSR) markers in population-I and 167 markers in population-II. In total, 40 QTLs were delineated for five traits in both populations. Approximately 22 QTLs were dissected in population-I, derived from Kongyu131/TKM9, seven QTLs for albumin content, four QTLs for globulin content, three QTLs for prolamin content, four QTLs for glutelin content, and four QTLs for grain protein content. In total, 18 QTLs were detected in population-II, derived from Kongyu131/Bg94-1, five QTLs for albumin content, three QTLs for globulin content, four QTLs for prolamin content, two QTLs for glutelin content, and four QTLs for grain protein content. Three QTLs, qAlb7.1, Alb7.2, and qGPC7.2, derived from population-II (Kongyu131/Bg94-1) for albumin and grain protein content were successfully validated in the near isogenic line (NIL) populations. The localized chromosomal locus of the validated QTLs could be helpful for fine mapping via map-based cloning to discover underlying candidate genes. The functional insights of the underlying candidate gene would furnish novel perceptivity for the foundation of rice grain protein content and trigger the development of nutritionally important rice cultivars by combining marker-assisted selection (MAS) breeding. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-023-01436-7.
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Affiliation(s)
- Mufid Alam
- National Key Laboratory of Crop Genetic Improvement and National Center of Crop Molecular Breeding, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070 Hubei China
| | - YingYing Wang
- National Key Laboratory of Crop Genetic Improvement and National Center of Crop Molecular Breeding, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070 Hubei China
| | - Jianxian Chen
- National Key Laboratory of Crop Genetic Improvement and National Center of Crop Molecular Breeding, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070 Hubei China
| | - Guangming Lou
- National Key Laboratory of Crop Genetic Improvement and National Center of Crop Molecular Breeding, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070 Hubei China
| | - Hanyuan Yang
- National Key Laboratory of Crop Genetic Improvement and National Center of Crop Molecular Breeding, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070 Hubei China
| | - Yin Zhou
- National Key Laboratory of Crop Genetic Improvement and National Center of Crop Molecular Breeding, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070 Hubei China
| | - Saurav Luitel
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070 Hubei China
| | - Gonghao Jiang
- College of Life Science, Heilongjiang University, Haerbin, 150080 Heilongjiang China
| | - Yuqing He
- National Key Laboratory of Crop Genetic Improvement and National Center of Crop Molecular Breeding, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070 Hubei China
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Debnath S, Dey A, Khanam R, Saha S, Sarkar D, Saha JK, Coumar MV, Patra BC, Biswas T, Ray M, Radhika MS, Mandal B. Historical shifting in grain mineral density of landmark rice and wheat cultivars released over the past 50 years in India. Sci Rep 2023; 13:21164. [PMID: 38036556 PMCID: PMC10689764 DOI: 10.1038/s41598-023-48488-5] [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: 05/22/2023] [Accepted: 11/27/2023] [Indexed: 12/02/2023] Open
Abstract
The 'Green Revolution (GR)' has been successful in meeting food sufficiency in India, but compromising its nutritional security. In a first, we report altered grain nutrients profile of modern-bred rice and wheat cultivars diminishing their mineral dietary significance to the Indian population. To substantiate, we evaluated grain nutrients profile of historical landmark high-yielding cultivars of rice and wheat released in succeeding decades since the GR and its impacts on mineral diet quality and human health, with a prediction for decades ahead. Analysis of grain nutrients profile shows a downward trend in concentrations of essential and beneficial elements, but an upward in toxic elements in past 50 y in both rice and wheat. For example, zinc (Zn) and iron (Fe) concentration in grains of rice decreased by ~ 33.0 (P < 0.001) and 27.0% (P < 0.0001); while for wheat it decreased by ~ 30.0 (P < 0.0001) and 19.0% (P < 0.0001) in past more than 50 y, respectively. A proposed mineral-diet quality index (M-DQI) significantly (P < 0.0001) decreased ~ 57.0 and 36.0% in the reported time span (1960-2010) in rice and wheat, respectively. The impoverished M-DQI could impose hostile effects on non-communicable diseases (NCDs) like iron-deficiency anemia, respiratory, cardiovascular, and musculoskeletal among the Indian population by 2040. Our research calls for an urgency of grain nutrients profiling before releasing a cultivar of staples like rice and wheat in the future.
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Affiliation(s)
- Sovan Debnath
- Directorate of Research, Bidhan Chandra Krishi Viswavidyalaya, Kalyani, West Bengal, 741 235, India
- Department of Agricultural Chemistry and Soil Science, Faculty of Agriculture, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, West Bengal, 741 252, India
- Indian Council of Agricultural Research (ICAR)-Central Institute of Temperate Horticulture, Regional Station Mukteshwar, Nainital, Uttarakhand, 263 138, India
- ICAR-Central Agroforestry Research Institute, Jhansi, Uttar Pradesh, 284 003, India
| | - Ahana Dey
- Department of Agricultural Chemistry and Soil Science, Faculty of Agriculture, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, West Bengal, 741 252, India
| | - Rubina Khanam
- ICAR-National Rice Research Institute, Cuttack, Odisha, 753 006, India
| | - Susmit Saha
- College of Agriculture, Bidhan Chandra Krishi Viswavidyalaya, Burdwan Sadar, West Bengal, 713 101, India
| | - Dibyendu Sarkar
- Directorate of Research, Bidhan Chandra Krishi Viswavidyalaya, Kalyani, West Bengal, 741 235, India
- Department of Agricultural Chemistry and Soil Science, Faculty of Agriculture, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, West Bengal, 741 252, India
| | - Jayanta K Saha
- Division of Environmental Soil Science, ICAR-Indian Institute of Soil Science, Bhopal, Madhya Pradesh, 462 038, India
| | - Mounissamy V Coumar
- Division of Environmental Soil Science, ICAR-Indian Institute of Soil Science, Bhopal, Madhya Pradesh, 462 038, India
| | - Bhaskar C Patra
- ICAR-National Rice Research Institute, Cuttack, Odisha, 753 006, India
| | - Tufleuddin Biswas
- Department of Agricultural Statistics, Faculty of Agriculture, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, West Bengal, 741 252, India
- Department of Agricultural Economics and Statistics, M.S. Swaminathan School of Agriculture, Centurion University of Technology and Management, Bhubaneswar, Odisha, 761 211, India
| | - Mrinmoy Ray
- Division of Forecasting and Agricultural Systems Modeling, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110 012, India
| | - Madhari S Radhika
- Department of Dietetics, Indian Council of Medical Research-National Institute of Nutrition, Hyderabad, Telangana, 500 007, India
| | - Biswapati Mandal
- Directorate of Research, Bidhan Chandra Krishi Viswavidyalaya, Kalyani, West Bengal, 741 235, India.
- Department of Agricultural Chemistry and Soil Science, Faculty of Agriculture, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, West Bengal, 741 252, India.
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Senguttuvel P, G P, C J, D SR, CN N, V J, P B, R G, J AK, SV SP, LV SR, AS H, K S, D S, RM S, Govindaraj M. Rice biofortification: breeding and genomic approaches for genetic enhancement of grain zinc and iron contents. FRONTIERS IN PLANT SCIENCE 2023; 14:1138408. [PMID: 37332714 PMCID: PMC10272457 DOI: 10.3389/fpls.2023.1138408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 04/25/2023] [Indexed: 06/20/2023]
Abstract
Rice is a highly consumed staple cereal cultivated predominantly in Asian countries, which share 90% of global rice production. Rice is a primary calorie provider for more than 3.5 billion people across the world. Preference and consumption of polished rice have increased manifold, which resulted in the loss of inherent nutrition. The prevalence of micronutrient deficiencies (Zn and Fe) are major human health challenges in the 21st century. Biofortification of staples is a sustainable approach to alleviating malnutrition. Globally, significant progress has been made in rice for enhancing grain Zn, Fe, and protein. To date, 37 biofortified Fe, Zn, Protein and Provitamin A rich rice varieties are available for commercial cultivation (16 from India and 21 from the rest of the world; Fe > 10 mg/kg, Zn > 24 mg/kg, protein > 10% in polished rice as India target while Zn > 28 mg/kg in polished rice as international target). However, understanding the micronutrient genetics, mechanisms of uptake, translocation, and bioavailability are the prime areas that need to be strengthened. The successful development of these lines through integrated-genomic technologies can accelerate deployment and scaling in future breeding programs to address the key challenges of malnutrition and hidden hunger.
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Affiliation(s)
- P. Senguttuvel
- Crop Improvement Section, ICAR - Indian Institute of Rice Research (ICAR - IIRR), Hyderabad, India
| | - Padmavathi G
- Crop Improvement Section, ICAR - Indian Institute of Rice Research (ICAR - IIRR), Hyderabad, India
| | - Jasmine C
- Crop Improvement Section, ICAR - Indian Institute of Rice Research (ICAR - IIRR), Hyderabad, India
- Genetics and Plant Breeding, Professor Jayashankar Telangana State Agricultural University (PJTSAU), Hyderabad, India
| | - Sanjeeva Rao D
- Crop Improvement Section, ICAR - Indian Institute of Rice Research (ICAR - IIRR), Hyderabad, India
| | - Neeraja CN
- Crop Improvement Section, ICAR - Indian Institute of Rice Research (ICAR - IIRR), Hyderabad, India
| | - Jaldhani V
- Crop Improvement Section, ICAR - Indian Institute of Rice Research (ICAR - IIRR), Hyderabad, India
| | - Beulah P
- Crop Improvement Section, ICAR - Indian Institute of Rice Research (ICAR - IIRR), Hyderabad, India
| | - Gobinath R
- Crop Improvement Section, ICAR - Indian Institute of Rice Research (ICAR - IIRR), Hyderabad, India
| | - Aravind Kumar J
- Crop Improvement Section, ICAR - Indian Institute of Rice Research (ICAR - IIRR), Hyderabad, India
| | - Sai Prasad SV
- Crop Improvement Section, ICAR - Indian Institute of Rice Research (ICAR - IIRR), Hyderabad, India
| | - Subba Rao LV
- Crop Improvement Section, ICAR - Indian Institute of Rice Research (ICAR - IIRR), Hyderabad, India
| | - Hariprasad AS
- Crop Improvement Section, ICAR - Indian Institute of Rice Research (ICAR - IIRR), Hyderabad, India
| | - Sruthi K
- Crop Improvement Section, ICAR - Indian Institute of Rice Research (ICAR - IIRR), Hyderabad, India
| | - Shivani D
- Genetics and Plant Breeding, Professor Jayashankar Telangana State Agricultural University (PJTSAU), Hyderabad, India
| | - Sundaram RM
- Crop Improvement Section, ICAR - Indian Institute of Rice Research (ICAR - IIRR), Hyderabad, India
| | - Mahalingam Govindaraj
- HarvestPlus, Alliance of Bioversity International and the International Center for Tropical Agriculture (CIAT), Cali, Colombia
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7
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Shuochen J, Lihe Z, Fenqin H, Xiangru T, Bin D. Zinc supplementation and light intensity affect 2-acetyl-1-pyrroline (2AP) formation in fragrant rice. BMC PLANT BIOLOGY 2023; 23:194. [PMID: 37041465 PMCID: PMC10088174 DOI: 10.1186/s12870-022-03954-6] [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: 06/15/2022] [Accepted: 11/21/2022] [Indexed: 06/19/2023]
Abstract
BACKGROUND Improving the yield and aroma content of fragrant rice is the focus of fragrant rice research. Light and Zinc (Zn) management generally cause regulations in the 2-acetyl-1-pyrroline (2AP) accumulation in fragrant rice. In addition, Zn promotes rice growth and improves rice yield, which has the potential to compensate for the negative impact of low light on fragrant rice yield. However, the potential of Zn to improve fragrant rice yield and 2AP content under shading conditions has not been verified. METHODS Field experiments were conducted in the rice season (May-September) in 2019 to 2021. Two light i.e., normal light (NL) and low light (LL) and four Zn levels i.e., 0 kg Zn ha- 1 (N0), 1 kg Zn ha- 1 (Zn1), 2 kg Zn ha- 1(Zn2), and 3 kg Zn ha- 1 (Zn3), which applied at booting stage was set up. The grain yield, 2AP contents, Zn content in polished rice, photosynthesis related indicators, MDA content, antioxidant enzyme activity and the biochemical parameters related to 2AP formation were investigated. RESULTS Shading reduced yield by 8.74% and increased 2AP content by 24.37%. In addition, shading reduced net photosynthetic rate (Pn), superoxide dismutase (SOD), peroxidase (POD) and catalase (CAT), and increased proline, γ-aminobutyric acid (GABA), and pyrroline-5-carboxylic acid (P5C), proline dehydrogenase (PDH), △1-pyrroline-5-carboxylic acid synthetase (P5CS), malondialdehyde (MDA). With increasing Zn application levels, yield, 2AP, Zn content in polished rice, Pn, proline, P5C, GABA, PDH, P5CS, SOD, CAT and POD increased, and MDA decreased. Significant Light and Zn interaction effect on 2AP content was detected, and both shading and increasing Zn application increased the 2AP content. CONCLUSION Shading can increase the 2AP content but reduce the yield of fragrant rice. Increasing Zn application under shading conditions can further promote the biosynthesis of 2AP, but the effect of improving yield is limited.
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Affiliation(s)
- Jiang Shuochen
- College of Agriculture, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Zhang Lihe
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 434007, Guangdong, China
| | - Hu Fenqin
- College of Agriculture, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Tang Xiangru
- College of Agriculture, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Du Bin
- College of Agriculture, South China Agricultural University, Guangzhou, 510642, Guangdong, China.
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8
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Palanog AD, Nha CT, Descalsota-Empleo GIL, Calayugan MI, Swe ZM, Amparado A, Inabangan-Asilo MA, Hernandez JE, Sta. Cruz PC, Borromeo TH, Lalusin AG, Mauleon R, McNally KL, Swamy BPM. Molecular dissection of connected rice populations revealed important genomic regions for agronomic and biofortification traits. FRONTIERS IN PLANT SCIENCE 2023; 14:1157507. [PMID: 37035067 PMCID: PMC10073715 DOI: 10.3389/fpls.2023.1157507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 02/20/2023] [Indexed: 06/19/2023]
Abstract
Breeding staple crops with increased micronutrient concentration is a sustainable approach to address micronutrient malnutrition. We carried out Multi-Cross QTL analysis and Inclusive Composite Interval Mapping for 11 agronomic, yield and biofortification traits using four connected RILs populations of rice. Overall, MC-156 QTLs were detected for agronomic (115) and biofortification (41) traits, which were higher in number but smaller in effects compared to single population analysis. The MC-QTL analysis was able to detect important QTLs viz: qZn5.2, qFe7.1, qGY10.1, qDF7.1, qPH1.1, qNT4.1, qPT4.1, qPL1.2, qTGW5.1, qGL3.1 , and qGW6.1 , which can be used in rice genomics assisted breeding. A major QTL (qZn5.2 ) for grain Zn concentration has been detected on chromosome 5 that accounted for 13% of R2. In all, 26 QTL clusters were identified on different chromosomes. qPH6.1 epistatically interacted with qZn5.1 and qGY6.2 . Most of QTLs were co-located with functionally related candidate genes indicating the accuracy of QTL mapping. The genomic region of qZn5.2 was co-located with putative genes such as OsZIP5, OsZIP9, and LOC_OS05G40490 that are involved in Zn uptake. These genes included polymorphic functional SNPs, and their promoter regions were enriched with cis-regulatory elements involved in plant growth and development, and biotic and abiotic stress tolerance. Major effect QTL identified for biofortification and agronomic traits can be utilized in breeding for Zn biofortified rice varieties.
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Affiliation(s)
- Alvin D. Palanog
- Rice Breeding Innovations Platform, International Rice Research Institute, Los Baños, Laguna, Philippines
- College of Agriculture and Food Science, University of the Philippines, Los Baños, Laguna, Philippines
- PhilRice Negros Branch Station, Philippine Rice Research Institute, Murcia, Negros Occidental, Philippines
| | | | | | - Mark Ian Calayugan
- College of Agriculture and Food Science, University of the Philippines, Los Baños, Laguna, Philippines
| | - Zin Mar Swe
- Rice Breeding Innovations Platform, International Rice Research Institute, Los Baños, Laguna, Philippines
| | - Amery Amparado
- Rice Breeding Innovations Platform, International Rice Research Institute, Los Baños, Laguna, Philippines
| | - Mary Ann Inabangan-Asilo
- Rice Breeding Innovations Platform, International Rice Research Institute, Los Baños, Laguna, Philippines
| | - Jose E. Hernandez
- College of Agriculture and Food Science, University of the Philippines, Los Baños, Laguna, Philippines
| | - Pompe C. Sta. Cruz
- College of Agriculture and Food Science, University of the Philippines, Los Baños, Laguna, Philippines
| | - Teresita H. Borromeo
- College of Agriculture and Food Science, University of the Philippines, Los Baños, Laguna, Philippines
| | - Antonio G. Lalusin
- College of Agriculture and Food Science, University of the Philippines, Los Baños, Laguna, Philippines
| | - Ramil Mauleon
- Rice Breeding Innovations Platform, International Rice Research Institute, Los Baños, Laguna, Philippines
- College of Agriculture, University of Southern Mindanao, Kabacan, North Cotabato, Philippines
| | - Kenneth L. McNally
- Rice Breeding Innovations Platform, International Rice Research Institute, Los Baños, Laguna, Philippines
| | - B. P. Mallikarjuna Swamy
- Rice Breeding Innovations Platform, International Rice Research Institute, Los Baños, Laguna, Philippines
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Kudapa H, Barmukh R, Vemuri H, Gorthy S, Pinnamaneni R, Vetriventhan M, Srivastava RK, Joshi P, Habyarimana E, Gupta SK, Govindaraj M. Genetic and genomic interventions in crop biofortification: Examples in millets. FRONTIERS IN PLANT SCIENCE 2023; 14:1123655. [PMID: 36950360 PMCID: PMC10025513 DOI: 10.3389/fpls.2023.1123655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 02/20/2023] [Indexed: 06/18/2023]
Abstract
Micronutrient malnutrition is a serious threat to the developing world's human population, which largely relies on a cereal-based diet that lacks diversity and micronutrients. Besides major cereals, millets represent the key sources of energy, protein, vitamins, and minerals for people residing in the dryland tropics and drought-prone areas of South Asia and sub-Saharan Africa. Millets serve as multi-purpose crops with several salient traits including tolerance to abiotic stresses, adaptation to diverse agro-ecologies, higher productivity in nutrient-poor soils, and rich nutritional characteristics. Considering the potential of millets in empowering smallholder farmers, adapting to changing climate, and transforming agrifood systems, the year 2023 has been declared by the United Nations as the International Year of Millets. In this review, we highlight recent genetic and genomic innovations that can be explored to enhance grain micronutrient density in millets. We summarize the advances made in high-throughput phenotyping to accurately measure grain micronutrient content in cereals. We shed light on genetic diversity in millet germplasm collections existing globally that can be exploited for developing nutrient-dense and high-yielding varieties to address food and nutritional security. Furthermore, we describe the progress made in the fields of genomics, proteomics, metabolomics, and phenomics with an emphasis on enhancing the grain nutritional content for designing competitive biofortified varieties for the future. Considering the close genetic-relatedness within cereals, upcoming research should focus on identifying the genetic and genomic basis of nutritional traits in millets and introgressing them into major cereals through integrated omics approaches. Recent breakthroughs in the genome editing toolbox would be crucial for mainstreaming biofortification in millets.
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Affiliation(s)
- Himabindu Kudapa
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Telangana, India
| | - Rutwik Barmukh
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Telangana, India
| | - Hindu Vemuri
- International Maize and Wheat Improvement Center (CIMMYT), Patancheru, Telangana, India
| | - Sunita Gorthy
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Telangana, India
| | | | - Mani Vetriventhan
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Telangana, India
| | - Rakesh K. Srivastava
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Telangana, India
| | - Priyanka Joshi
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Telangana, India
| | - Ephrem Habyarimana
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Telangana, India
| | - S. K. Gupta
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Telangana, India
| | - Mahalingam Govindaraj
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Telangana, India
- HarvestPlus Program, Alliance of Bioversity International and the International Center for Tropical Agriculture (CIAT), Cali, Colombia
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10
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Hou J, Chen H, Zhang K, Liu W, Cao C, Ruan Y, Deng Y, Liu Y, Yuan X, Sun C, Fu Y. The GZnC1 variant from common wild rice influences grain Zn content. PLANT MOLECULAR BIOLOGY 2023; 111:263-273. [PMID: 36414883 DOI: 10.1007/s11103-022-01325-1] [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: 08/18/2022] [Accepted: 11/11/2022] [Indexed: 06/16/2023]
Abstract
Zinc (Zn) deficiency, caused by inadequate Zn intake in the human diet, has serious health implications. Rice (Oryza sativa) is the staple food in regions with a high incidence of Zn deficiency, so raising Zn levels in rice grain could help alleviate Zn deficiency. The wild relatives of cultivated rice vary widely in grain Zn content and thus are suitable resources for improving this trait. However, few loci underlying grain Zn content have been identified in wild rice relatives. Here, we identified a major quantitative trait locus for grain Zn content, Grain Zn Content 1 (qGZnC1), from Yuanjiang common wild rice (Oryza rufipogon Griff.) using map-based cloning. Down-regulating GZnC1 expression reduced the grain Zn content, whereas the presence of GZnC1 had the opposite effect, indicating that GZnC1 is involved in grain Zn content in rice. Notably, GZnC1 is identical to a previously reported gene, EMBRYO SAC ABORTION 1 (ESA1), involved in seed setting rate. The mutation in GZnC1/ESA1 at position 1819 (T1819C) causes delayed termination of protein translation. In addition, GZnC1 is specifically expressed in developing panicles. Several genes related to Zn-transporter genes were up-regulated in the presence of GZnC1. Our results suggest that GZnC1 activates Zn transporters to promote Zn distribution in panicles. Our work thus sheds light on the genetic mechanism of Zn accumulation in rice grain and provides a new genetic resource for improving Zn content in rice.
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Affiliation(s)
- Jingjing Hou
- MOE Key Laboratory of Crop Heterosis and Utilization, National Center for Evaluation of Agricultural Wild Plants (Rice), Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Hao Chen
- Institute of Crop Sciences, Fujian Academy of Agricultural Sciences; Fujian Engineering Research Center for Characteristic Upland Crops Breeding; Fujian Engineering Laboratory of Crop Molecular Breeding, Fuzhou, 350013, China
| | - Kun Zhang
- MOE Key Laboratory of Crop Heterosis and Utilization, National Center for Evaluation of Agricultural Wild Plants (Rice), Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Wenjing Liu
- Institute of Agricultural Quality Standards and Testing Technology Research, Fujian Academy of Agricultural Sciences; Fujian Key Laboratory of Agro-Products Quality and Safety, Fuzhou, 350003, China
| | - Caihong Cao
- MOE Key Laboratory of Crop Heterosis and Utilization, National Center for Evaluation of Agricultural Wild Plants (Rice), Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Yini Ruan
- MOE Key Laboratory of Crop Heterosis and Utilization, National Center for Evaluation of Agricultural Wild Plants (Rice), Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Yanyan Deng
- MOE Key Laboratory of Crop Heterosis and Utilization, National Center for Evaluation of Agricultural Wild Plants (Rice), Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Yaxin Liu
- MOE Key Laboratory of Crop Heterosis and Utilization, National Center for Evaluation of Agricultural Wild Plants (Rice), Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Xuzhao Yuan
- MOE Key Laboratory of Crop Heterosis and Utilization, National Center for Evaluation of Agricultural Wild Plants (Rice), Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Chuanqing Sun
- MOE Key Laboratory of Crop Heterosis and Utilization, National Center for Evaluation of Agricultural Wild Plants (Rice), Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Yongcai Fu
- MOE Key Laboratory of Crop Heterosis and Utilization, National Center for Evaluation of Agricultural Wild Plants (Rice), Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China.
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11
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Rezvi HUA, Tahjib‐Ul‐Arif M, Azim MA, Tumpa TA, Tipu MMH, Najnine F, Dawood MFA, Skalicky M, Brestič M. Rice and food security: Climate change implications and the future prospects for nutritional security. Food Energy Secur 2022. [DOI: 10.1002/fes3.430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Affiliation(s)
| | - Md. Tahjib‐Ul‐Arif
- Department of Biochemistry and Molecular Biology Bangladesh Agricultural University Mymensingh Bangladesh
| | - Md. Abdul Azim
- Biotechnology Division Bangladesh Sugarcrop Research Institute Pabna Bangladesh
| | - Toufica Ahmed Tumpa
- Department of Entomology Bangladesh Agricultural University Mymensingh Bangladesh
| | | | - Farhana Najnine
- Food Science and Engineering South China University of Technology Guangdong Guangzhou China
| | - Mona F. A. Dawood
- Botany and Microbiology Department, Faculty of Science Assiut University Assiut Egypt
| | - Milan Skalicky
- Department of Botany and Plant Physiology, Faculty of Agrobiology, Food and Natural Resources Czech University of Life Sciences Prague Prague Czech Republic
| | - Marián Brestič
- Department of Botany and Plant Physiology, Faculty of Agrobiology, Food and Natural Resources Czech University of Life Sciences Prague Prague Czech Republic
- Institute of Plant and Environmental Sciences Faculty of Agrobiology and Food Resources Slovak University of Agriculture Nitra Slovakia
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12
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Viana VE, Maltzahn LE, Costa de Oliveira A, Pegoraro C. Genetic Approaches for Iron and Zinc Biofortification and Arsenic Decrease in Oryza sativa L. Grains. Biol Trace Elem Res 2022; 200:4505-4523. [PMID: 34773578 DOI: 10.1007/s12011-021-03018-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 11/04/2021] [Indexed: 12/29/2022]
Abstract
Rice is the staple diet to half of the world's population, being a major source of carbohydrates, vitamins, and some essential elements. However, rice naturally contains low amounts of essential minerals such as iron (Fe) and zinc (Zn), which are drastically decreased after milling. Thus, populations that consume mostly rice may have micronutrient deficiency, which is associated with different diseases. On the other hand, rice irrigated by flooding has a high ability to accumulate arsenic (As) in the grain. Therefore, when rice is grown in areas with contaminated soil or irrigation water, it represents a risk factor for consumers, since As is associated with cancer and other diseases. Different strategies have been used to mitigate micronutrient deficiencies such as Fe and Zn and to prevent As from entering the food chain. Each strategy has its positive and its negative sides. The development of genetically biofortified rice plants with Fe and Zn and with low As accumulation is one of the most promising strategies, since it does not represent an additional cost for farmers, and gives benefits to consumers as well. Considering the importance of genetic improvement (traditional or molecular) to decrease the impact of micronutrient deficiencies such as Fe and Zn and contamination with As, this review aimed to summarize the major efforts, advances, and challenges for genetic biofortification of Fe and Zn and decrease in As content in rice grains.
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Affiliation(s)
- Vívian Ebeling Viana
- Centro de Genômica E Fitomelhoramento, Departamento de Fitotecnia, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas, Capão Do Leão, Brazil
| | - Latóia Eduarda Maltzahn
- Centro de Genômica E Fitomelhoramento, Departamento de Fitotecnia, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas, Capão Do Leão, Brazil
| | - Antonio Costa de Oliveira
- Centro de Genômica E Fitomelhoramento, Departamento de Fitotecnia, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas, Capão Do Leão, Brazil
| | - Camila Pegoraro
- Centro de Genômica E Fitomelhoramento, Departamento de Fitotecnia, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas, Capão Do Leão, Brazil.
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13
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Rakotondramanana M, Tanaka R, Pariasca-Tanaka J, Stangoulis J, Grenier C, Wissuwa M. Genomic prediction of zinc-biofortification potential in rice gene bank accessions. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:2265-2278. [PMID: 35618915 PMCID: PMC9271118 DOI: 10.1007/s00122-022-04110-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 04/19/2022] [Indexed: 06/15/2023]
Abstract
A genomic prediction model successfully predicted grain Zn concentrations in 3000 gene bank accessions and this was verified experimentally with selected potential donors having high on-farm grain-Zn in Madagascar. Increasing zinc (Zn) concentrations in edible parts of food crops, an approach termed Zn-biofortification, is a global breeding objective to alleviate micro-nutrient malnutrition. In particular, infants in countries like Madagascar are at risk of Zn deficiency because their dominant food source, rice, contains insufficient Zn. Biofortified rice varieties with increased grain Zn concentrations would offer a solution and our objective is to explore the genotypic variation present among rice gene bank accessions and to possibly identify underlying genetic factors through genomic prediction and genome-wide association studies (GWAS). A training set of 253 rice accessions was grown at two field sites in Madagascar to determine grain Zn concentrations and grain yield. A multi-locus GWAS analysis identified eight loci. Among these, QTN_11.3 had the largest effect and a rare allele increased grain Zn concentrations by 15%. A genomic prediction model was developed from the above training set to predict Zn concentrations of 3000 sequenced rice accessions. Predicted concentrations ranged from 17.1 to 40.2 ppm with a prediction accuracy of 0.51. An independent confirmation with 61 gene bank seed samples provided high correlations (r = 0.74) between measured and predicted values. Accessions from the aus sub-species had the highest predicted grain Zn concentrations and these were confirmed in additional field experiments, with one potential donor having more than twice the grain Zn compared to a local check variety. We conclude utilizing donors from the aus sub-species and employing genomic selection during the breeding process is the most promising approach to raise grain Zn concentrations in rice.
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Affiliation(s)
- Mbolatantely Rakotondramanana
- Rice Research Department, The National Center for Applied Research on Rural Development (FOFIFA), 101, Antananarivo, Madagascar
| | - Ryokei Tanaka
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo, 113-8657, Japan
| | - Juan Pariasca-Tanaka
- Crop, Livestock and Environment Division, Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki, 305-8686, Japan
| | - James Stangoulis
- College of Science and Engineering, Flinders University, Bedford Park, SA, 5042, Australia
| | - Cécile Grenier
- CIRAD, INRAE, Institut Agro, UMR AGAP Institut, Univ Montpellier, 34398, Montpellier, France
| | - Matthias Wissuwa
- Crop, Livestock and Environment Division, Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki, 305-8686, Japan.
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14
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Badoni S, Parween S, Henry RJ, Sreenivasulu N. Systems seed biology to understand and manipulate rice grain quality and nutrition. Crit Rev Biotechnol 2022:1-18. [PMID: 35723584 DOI: 10.1080/07388551.2022.2058460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Rice is one of the most essential crops since it meets the calorific needs of 3 billion people around the world. Rice seed development initiates upon fertilization, leading to the establishment of two distinct filial tissues, the endosperm and embryo, which accumulate distinct seed storage products, such as starch, storage proteins, and lipids. A range of systems biology tools deployed in dissecting the spatiotemporal dynamics of transcriptome data, methylation, and small RNA based regulation operative during seed development, influencing the accumulation of storage products was reviewed. Studies of other model systems are also considered due to the limited information on the rice transcriptome. This review highlights key genes identified through a holistic view of systems biology targeted to modify biochemical composition and influence rice grain quality and nutritional value with the target of improving rice as a functional food.
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Affiliation(s)
- Saurabh Badoni
- Consumer-Driven Grain Quality and Nutrition Unit, International Rice Research Institute (IRRI), Manila, Philippines
| | - Sabiha Parween
- Consumer-Driven Grain Quality and Nutrition Unit, International Rice Research Institute (IRRI), Manila, Philippines
| | - Robert J Henry
- Centre for Crop Science, Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Australia
| | - Nese Sreenivasulu
- Consumer-Driven Grain Quality and Nutrition Unit, International Rice Research Institute (IRRI), Manila, Philippines
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15
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Upadhayay VK, Singh AV, Khan A, Singh J, Pareek N, Raghav A. FE-SEM/EDX Based Zinc Mobilization Analysis of Burkholderia cepacia and Pantoea rodasii and Their Functional Annotation in Crop Productivity, Soil Quality, and Zinc Biofortification of Paddy. Front Microbiol 2022; 13:852192. [PMID: 35602065 PMCID: PMC9120762 DOI: 10.3389/fmicb.2022.852192] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 03/15/2022] [Indexed: 11/13/2022] Open
Abstract
The experimental study was contrived to characterize two zinc-solubilizing bacteria (ZSB), namely BMRR126 and BMAR64, and their role in zinc (Zn) biofortification of rice. These bacteria solubilized Zn profoundly, determined qualitatively by halo-zone formation on a solid medium and quantitatively in a liquid broth by AAS and SEM-EDX. The lowering of pH and contact angle assessment of the liquid broth unveiled the establishment of the acidic conditions in a medium suitable for Zn solubilization. The characterization of both isolates on the basis of 16S rRNA gene analysis was identified as Burkholderia cepacia and Pantoea rodasii, respectively. These strains were also found to have some plant probiotic traits namely phosphate solubilization, production of siderophore, indole acetic acid (IAA), exopolysaccharide (EPS), and ammonia. The field experiments were performed at two diverse locations and under all treatments; the simultaneous use of BMRR126 and BMAR64 with zinc oxide (ZnO) resulted in the highest growth and productivity of the paddy crop. The utmost Zn achievement in the grain was estimated in a treatment (T9) (25.07 mg/kg) containing a consortium of BMRR126 and BMAR64 along with ZnO for the Terai region. The treatment containing single ZSB bioinoculant BMRR126 (T7) showed an elevated Zn amount in the rice grain (33.25 mg/kg) for the Katchar region. The soil parameters (pH, EC, organic carbon, NPK, available Zn, and dehydrogenase activity) were also positively influenced under all bacterial treatments compared to the uninoculated control. Our study clearly accentuates the need for Zn solubilizing bacteria (ZSB) to provide the benefits of Zn-biofortification in different regions.
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Affiliation(s)
- Viabhav Kumar Upadhayay
- Department of Microbiology, College of Basic Sciences and Humanities, G. B. Pant University of Agriculture and Technology, Pantnagar, India
| | - Ajay Veer Singh
- Department of Microbiology, College of Basic Sciences and Humanities, G. B. Pant University of Agriculture and Technology, Pantnagar, India
- *Correspondence: Ajay Veer Singh,
| | - Amir Khan
- Department of Microbiology, College of Basic Sciences and Humanities, G. B. Pant University of Agriculture and Technology, Pantnagar, India
| | - Jyoti Singh
- Department of Microbiology, College of Basic Sciences and Humanities, G. B. Pant University of Agriculture and Technology, Pantnagar, India
| | - Navneet Pareek
- Department of Soil Science, College of Agriculture, G. B. Pant University of Agriculture and Technology, Pantnagar, India
| | - Alok Raghav
- Multidisciplinary Research Unit, Department of Health Research, Ministry of Health and Family Welfare, Ganesh Shankar Vidyarthi Memorial Medical College, Kanpur, India
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16
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Amini S, Arsova B, Hanikenne M. The molecular basis of zinc homeostasis in cereals. PLANT, CELL & ENVIRONMENT 2022; 45:1339-1361. [PMID: 35037265 DOI: 10.1111/pce.14257] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 11/12/2021] [Accepted: 12/16/2021] [Indexed: 06/14/2023]
Abstract
Plants require zinc (Zn) as an essential cofactor for diverse molecular, cellular and physiological functions. Zn is crucial for crop yield, but is one of the most limiting micronutrients in soils. Grasses like rice, wheat, maize and barley are crucial sources of food and nutrients for humans. Zn deficiency in these species therefore not only reduces annual yield but also directly results in Zn malnutrition of more than two billion people in the world. There has been good progress in understanding Zn homeostasis and Zn deficiency mechanisms in plants. However, our current knowledge of monocots, including grasses, remains insufficient. In this review, we provide a summary of our knowledge of molecular Zn homeostasis mechanisms in monocots, with a focus on important cereal crops. We additionally highlight divergences in Zn homeostasis of monocots and the dicot model Arabidopsis thaliana, as well as important gaps in our knowledge that need to be addressed in future research on Zn homeostasis in cereal monocots.
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Affiliation(s)
- Sahand Amini
- InBioS-PhytoSystems, Translational Plant Biology, University of Liège, Liège, Belgium
| | - Borjana Arsova
- Root Dynamics Group, IBG-2 - Plant Sciences, Institut für Bio- und Geowissenschaften (IBG), Forschungszentrum, Jülich, Germany
| | - Marc Hanikenne
- InBioS-PhytoSystems, Translational Plant Biology, University of Liège, Liège, Belgium
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Assessment of Genetic Variability and Bran Oil Characters of New Developed Restorer Lines of Rice (Oryza sativa L.). Genes (Basel) 2022; 13:genes13030509. [PMID: 35328063 PMCID: PMC8951205 DOI: 10.3390/genes13030509] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 03/04/2022] [Accepted: 03/11/2022] [Indexed: 02/01/2023] Open
Abstract
Rice is one of the most important crops in Egypt. Due to the gap between the demand and the availability of the local edible oils, there is need to raise the nutritional value of rice and, therefore, to improve the nutritional value of the consumer. This research was carried out at the Experimental Farm of Sakha Agricultural Research Station, Sakha, Kafr El-Sheikh, Egypt, during the 2019 and 2020 seasons. Five newly developed genotypes of rice, namely NRL 63, NRL 64, NRL 65, NRL 66, and Giza 178 as check variety (control), were used to evaluate the analytical characterization of raw rice bran and rice bran oil from rice bran, study the genetic variability and genetic advance for various quantitative and qualitative traits in rice as well as, rice bran oil. The genotypes were evaluated in a randomized complete block design (RCBD) with three replications. Analysis of variance revealed highly significant variations among the genotypes for all the studied characters. Data revealed that high estimates of the phenotypic coefficient of variance (PCV%) and genotypic coefficient of variance (GCV%) were observed for amylose content percentage, peroxide value (meq/kg oil), myristic C14:0, and arachidic C20:0, indicating that they all interacted with the environment to some extent. The line NRL66 and NRL64 showed the highest and high values of mean performance for grain yield (t/h), grain type (shape), amylose content percentage, crude protein, ether extract and ash of milled rice, crude protein, ether extract, ash, phosphorus, magnesium, manganese, zinc, and iron of stabilized rice bran oil. Genetic advance as a percentage of mean was high for most of the studied traits. It indicates that most likely, the heritability is due to additive gene effects, and selection may be effective. The percentage of advantage over the Giza 178 as the commercial variety was significant and highly significant among the genotypes for all the characters studied in the two years, indicating that the selection is effective in the genetic improvements for these traits.
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18
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Current Status and Potential of Biofortification to Enhance Crop Nutritional Quality: An Overview. SUSTAINABILITY 2022. [DOI: 10.3390/su14063301] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Around 2 billion people are suffering from chronic malnutrition or “hidden hunger”, which is the result of many diseases and disorders, including cognitive degeneration, stunting growth, and mortality. Thus, biofortification of staple food crops enriched with micronutrients is a more sustainable option for providing nutritional supplements and managing malnutrition in a society. Since 2001, when the concept of biofortification came to light, different research activities have been carried out, like the development of target populations, breeding or genetic engineering, and the release of biofortified cultivars, in addition to conducting nutritional efficacy trials and delivery plan development. Although, being a cost-effective intervention, it still faces many challenges, like easy accessibility of biofortified cultivars, stakeholders’ acceptance, and the availability of biofortified germplasm in the public domain, which varies from region to region. Hence, this review is focused on the recent potential, efforts made to crop biofortification, impacts analysis on human health, cost-effectiveness, and future perspectives to further strengthen biofortification programs. Through regular interventions of sustainable techniques and methodologies, biofortification holds huge potential to solve the malnutrition problem through regular interventions of nutrient-enriched staple food options for billions of people globally.
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Stanton C, Sanders D, Krämer U, Podar D. Zinc in plants: Integrating homeostasis and biofortification. MOLECULAR PLANT 2022; 15:65-85. [PMID: 34952215 DOI: 10.1016/j.molp.2021.12.008] [Citation(s) in RCA: 50] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 12/07/2021] [Accepted: 12/21/2021] [Indexed: 05/24/2023]
Abstract
Zinc plays many essential roles in life. As a strong Lewis acid that lacks redox activity under environmental and cellular conditions, the Zn2+ cation is central in determining protein structure and catalytic function of nearly 10% of most eukaryotic proteomes. While specific functions of zinc have been elucidated at a molecular level in a number of plant proteins, wider issues abound with respect to the acquisition and distribution of zinc by plants. An important challenge is to understand how plants balance between Zn supply in soil and their own nutritional requirement for zinc, particularly where edaphic factors lead to a lack of bioavailable zinc or, conversely, an excess of zinc that bears a major risk of phytotoxicity. Plants are the ultimate source of zinc in the human diet, and human Zn deficiency accounts for over 400 000 deaths annually. Here, we review the current understanding of zinc homeostasis in plants from the molecular and physiological perspectives. We provide an overview of approaches pursued so far in Zn biofortification of crops. Finally, we outline a "push-pull" model of zinc nutrition in plants as a simplifying concept. In summary, this review discusses avenues that can potentially deliver wider benefits for both plant and human Zn nutrition.
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Affiliation(s)
| | - Dale Sanders
- John Innes Centre, Colney Lane, Norwich, NR4 7UH, UK
| | - Ute Krämer
- Molecular Genetics and Physiology of Plants, Ruhr University Bochum, 44801 Bochum, Germany.
| | - Dorina Podar
- Department of Molecular Biology and Biotechnology and Centre for Systems Biology, Biodiversity and Bioresources, Babes-Bolyai University, 400084 Cluj-Napoca, Romania.
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Sanghamitra P, Bose LK, Bagchi TB, Kumar A, Roy PS, Moharana N, Patra BC, Padmavati G, Chattopadhyay K. Characterization and exploring genetic potential of landraces from Odisha with special emphasis on grain micronutrient content for benefaction of biofortification in rice. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2022; 28:203-221. [PMID: 35221580 PMCID: PMC8847517 DOI: 10.1007/s12298-021-01119-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 12/08/2021] [Accepted: 12/09/2021] [Indexed: 06/14/2023]
Abstract
UNLABELLED Assessing genetic variability of micronutrient content in association with qualitative and quantitative traits in germplasm is prerequisite for effective biofortification programme. Odisha, a state of eastern India is considered as one of the most potential hot spot of diversity of cultivated rice for grain yield and nutritional traits. Significant variability for most of the qualitative and quantitative traits including Fe and Zn content was observed in a set of 293 germplasm with varying kernel colour encompassing 14 districts of Odisha. Mostly these landraces were low yielding with some exception (Haldigundi: AC 36454, 50.08 g/plant). These landraces were mostly represented by medium Fe (10-20 ppm)-medium Zn group (20-30 ppm). Fe and Zn content had positive association with each other and also with grain size. Landraces with red kernel colour were observed to have slightly higher average Zn content (26.30 ppm) as compared to white (25.87 ppm) grains. Diversity analysis of 14 districts revealed that Nayagarh, a south-eastern district was rich in Fe content while Deogarh, Keonjhar and Mayurbhanj, all north-western districts were rich in Zn content. This study identified 10 superior micronutrient dense genotypes with medium to high Fe and Zn content. This set of donors for micronutrient content was validated in another year. Champeisiali (AC 43368) and Gedemalati (AC 34306) with highest Fe (44.1 ppm) and Zn (40.48 ppm) content, respectively were detected over the environments. Identified donors and associated traits could be utilized in biofortificaion programme using appropriate breeding methodologies for enhancing micronutrients in high yielding background. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-021-01119-7.
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Affiliation(s)
| | - Lotan Kumar Bose
- ICAR-National Rice Research Institute, Cuttack, Odisha 753006 India
| | | | - Awadhesh Kumar
- ICAR-National Rice Research Institute, Cuttack, Odisha 753006 India
| | | | - Nutan Moharana
- ICAR-National Rice Research Institute, Cuttack, Odisha 753006 India
| | | | - G. Padmavati
- ICAR-Indian Institute of Rice Research, Hyderabad, India
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Verma V, Vishal B, Kohli A, Kumar PP. Systems-based rice improvement approaches for sustainable food and nutritional security. PLANT CELL REPORTS 2021; 40:2021-2036. [PMID: 34591154 DOI: 10.1007/s00299-021-02790-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 09/15/2021] [Indexed: 06/13/2023]
Abstract
An integrated research approach to ensure sustainable rice yield increase of a crop grown by 25% of the world's farmers in 10% of cropland is essential for global food security. Rice, being a global staple crop, feeds about 56% of the world population and sustains 40% of the world's poor. At ~ $200 billion, it also accounts for 13% of the annual crop value. With hunger and malnutrition rampant among the poor, rice research for development is unique in global food and nutrition security. A systems-based, sustainable increase in rice quantity and quality is imperative for environmental and biodiversity benefits. Upstream 'discovery' through biotechnology, midstream 'development' through breeding and agronomy, downstream 'dissemination and deployment' must be 'demand-driven' for 'distinct socio-economic transformational impacts'. Local agro-ecology and livelihood nexus must drive the research agenda for targeted benefits. This necessitates sustained long-term investments by government, non-government and private sectors to secure the future food, nutrition, environment, prosperity and equity status.
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Affiliation(s)
- Vivek Verma
- Department of Biotechnology, School of Life Sciences, Central University of Rajasthan, Ajmer, 305817, Rajasthan, India.
| | - Bhushan Vishal
- School of Biological Sciences, Nanyang Technological University, Singapore, 639798, Republic of Singapore
| | - Ajay Kohli
- Strategic Innovation Platform, International Rice Research Institute, DAPO 7777, Metro Manila, Philippines
| | - Prakash P Kumar
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, 117543, Republic of Singapore.
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22
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Bao G, Ashraf U, Wan X, Zhou Q, Li S, Wang C, He L, Tang X. Transcriptomic Analysis Provides Insights into Foliar Zinc Application Induced Upregulation in 2-Acetyl-1-pyrroline and Related Transcriptional Regulatory Mechanism in Fragrant Rice. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:11350-11360. [PMID: 34528806 DOI: 10.1021/acs.jafc.1c03655] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The involvement of zinc (Zn) in terms of aroma formation has been rarely investigated. This study shows that the regulation of 2-acetyl-1-pyrroline (2AP) biosynthesis was evaluated in two different rice cultivars under foliar Zn application. The results showed that the 2AP and Zn contents in leaves and grains were improved substantially under foliar Zn application. The 2AP content was positively related to the expression P5CS2 gene, contents of proline, 1-pyrroline, and Δ1-pyrroline-5-carboxylate (P5C), and the activity of pyrroline-5-carboxylate synthase (P5CS) under Zn application in fragrant rice. Multiple transcription factors (TFs) were differently expressed, such as bZIPs, NACs, and MYBs, to play a role under Zn treatments in fragrant rice, suggesting the crucial role of 46 differently expressed TFs in 2AP improvements in fragrant rice. Furthermore, this study showed that the optimal foliar Zn application at a concentration of 30 mg L-1 could increase the 2AP content of aromatic rice and keep the yield stable or increase the yield. TFs were involved in regulating to promote the 2AP formation in aromatic rice under the foliar Zn application. However, the relationship between 2AP biosynthesis pathway genes and TFs in fragrant rice remains to be further studied.
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Affiliation(s)
- Gegen Bao
- Department of Crop Science and Technology, College of Agriculture, South China Agricultural University, Guangzhou 510642, P. R. China
- Guangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, P. R. China
- Scientific Observing and Experimental Station of Crop Cultivation in South China, Ministry of Agriculture, Guangzhou 510642, P. R. China
| | - Umair Ashraf
- Department of Botany, Division of Science and Technology, University of Education, Lahore 54770, Punjab, Pakistan
| | - Xiaorong Wan
- Guangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, P. R. China
| | - Qi Zhou
- Guangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, P. R. China
| | - Shengyu Li
- Guangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, P. R. China
| | - Chunling Wang
- Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, Guangdong, P. R. China
| | - Longxin He
- Department of Crop Science and Technology, College of Agriculture, South China Agricultural University, Guangzhou 510642, P. R. China
- Scientific Observing and Experimental Station of Crop Cultivation in South China, Ministry of Agriculture, Guangzhou 510642, P. R. China
| | - Xiangru Tang
- Department of Crop Science and Technology, College of Agriculture, South China Agricultural University, Guangzhou 510642, P. R. China
- Scientific Observing and Experimental Station of Crop Cultivation in South China, Ministry of Agriculture, Guangzhou 510642, P. R. China
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Ogasawara M, Miyazaki N, Monden G, Taniko K, Lim S, Iwata M, Ishii T, Ma JF, Ishikawa R. Role of qGZn9a in controlling grain zinc concentration in rice, Oryza sativa L. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:3013-3022. [PMID: 34110432 PMCID: PMC8190762 DOI: 10.1007/s00122-021-03873-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 05/25/2021] [Indexed: 06/12/2023]
Abstract
A candidate gene responsible for higher grain zinc accumulation in rice was identified, which was probably associated with a partial defect in anther dehiscence. Zinc (Zn) is an essential mineral element in many organisms. Zn deficiency in humans causes various health problems; therefore, an adequate dietary Zn intake is required daily. Rice, Oryza sativa, is one of the main crops cultivated in Asian countries, and one of the breeding scopes of rice is to increase the grain Zn levels. Previously, we found that an Australian wild rice strain, O. meridionalis W1627, exhibits higher grain Zn levels than cultivated rice, O. sativa Nipponbare, and identified responsible genomic loci. An increase in grain Zn levels caused by one of the loci, qGZn9a, is associated with fertility reduction, but how this negative effect on grain productivity is regulated remains unknown. In this study, we artificially trimmed spikelets on the flowering day and found that a reduction in number of seeds was associated with an increase in the grain Zn levels. We also found that a partial defect in anther dehiscence correlated with the increase in grain Zn levels in plants carrying the W1627 chromosomal segment at qGZn9a in a Nipponbare genetic background. Among eight candidate genes in the qGZn9a region, three were absent from the corresponding region of W1627; one of these, Os09g0384900, encoding a DUF295 protein with an unknown function, was found to be specifically expressed in the developing anther, thereby suggesting that the gene may be involved in the regulation of anther dehiscence. As fertility and grain Zn levels are essential agronomic traits in rice, our results highlight the importance of balancing these two traits.
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Affiliation(s)
- Miki Ogasawara
- Laboratory of Plant Breeding, Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, 657-8501, Japan
| | - Naoya Miyazaki
- Laboratory of Plant Breeding, Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, 657-8501, Japan
| | - Gotaro Monden
- Laboratory of Plant Breeding, Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, 657-8501, Japan
| | - Kenta Taniko
- Laboratory of Plant Breeding, Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, 657-8501, Japan
| | - Sathya Lim
- Laboratory of Plant Breeding, Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, 657-8501, Japan
| | - Masahide Iwata
- Laboratory of Plant Breeding, Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, 657-8501, Japan
| | - Takashige Ishii
- Laboratory of Plant Breeding, Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, 657-8501, Japan
| | - Jian Feng Ma
- Institute of Plant Science and Resources, Okayama University, Chuo 2-20-1, Kurashiki, 710-0046, Japan
| | - Ryo Ishikawa
- Laboratory of Plant Breeding, Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, 657-8501, Japan.
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Saengwilai P, Meeinkuirt W. Cadmium (Cd) and zinc (Zn) accumulation by Thai rice varieties and health risk assessment in a Cd-Zn co-contaminated paddy field: Effect of soil amendments. ENVIRONMENTAL GEOCHEMISTRY AND HEALTH 2021; 43:3659-3674. [PMID: 33630197 DOI: 10.1007/s10653-021-00858-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 02/05/2021] [Indexed: 06/12/2023]
Abstract
Zinc mining and smelting activities result in cadmium (Cd) and zinc (Zn) contamination in rice grains, causing deleterious impacts on human health and local economies. Here, we investigated the effects of soil amendments, including mixtures of dicalcium phosphate with cattle manure (T1) and leonardite (T2), on soil physicochemical properties as well as growth performance and accumulation of Cd and Zn among three commercial Thai rice varieties: Khao Dok Mali 105 (KDML105), Phitsanulok2 (PSL2) and RD3, grown in a Cd-Zn co-contaminated paddy field. Human health risk was assessed using the health risk index (HRI) and Daily Intake of Metal (DIM). Application of the amendments, particularly T1, decreased Cd and Zn bioavailability by 60% and 39%, respectively, increased biomass production in PSL2 and RD3 varieties, and substantially reduced Cd uptake in the KDML105 variety by 47%. While levels of Zn in whole plant tissues of all treatments did not exceed maximum levels of undesirable substances in fodder, Cd contents in grain of PSL2 and RD3 exceeded the maximum allowable concentration of 0.2 mg kg-1. The HRI values for Cd of PSL2 and RD3 varieties were relatively high and are considered to pose a potential risk to human health. KDML105 in the T1 treatment had the lowest HRI value (0.05 ± 0.03), which was within acceptable limits. Our results suggest that Cd and Zn accumulation in rice and associated human health risks could be reduced by application of amendments to paddy soils, but the effectiveness depends on amendment types, rice varieties and soil physicochemical properties.
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Affiliation(s)
- Patompong Saengwilai
- Department of Biology, Faculty of Science, Mahidol University, Rama VI Road, Bangkok, 10400, Thailand
- Center of Excellence On Environmental Health and Toxicology (EHT), CHE, Ministry of Education, Bangkok, Thailand
| | - Weeradej Meeinkuirt
- Water and Soil Environmental Research Unit, Nakhonsawan Campus, Mahidol University, Nakhonsawan, 60130, Thailand.
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Verma PK, Verma S, Chakrabarty D, Pandey N. Biotechnological Approaches to Enhance Zinc Uptake and Utilization Efficiency in Cereal Crops. JOURNAL OF SOIL SCIENCE AND PLANT NUTRITION 2021; 21:2412-2424. [DOI: 10.1007/s42729-021-00532-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 06/08/2021] [Indexed: 06/27/2023]
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Liu J, Zhan J, Chen J, Lu X, Zhi S, Ye G. Validation of Genes Affecting Rice Grain Zinc Content Through Candidate Gene-Based Association Analysis. Front Genet 2021; 12:701658. [PMID: 34434221 PMCID: PMC8381382 DOI: 10.3389/fgene.2021.701658] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 07/02/2021] [Indexed: 11/27/2022] Open
Abstract
Several key genes governing Zn homeostasis and grain zinc content (GZC) have been functionally characterized. However, the effects of these genes in diverse breeding populations have not been evaluated; thus, their availability in breeding is unclear. In this study, the effects of 65 genes related to rice zinc responses on GZC were evaluated using two panels of breeding lines, and the superior haplotypes were identified. One panel consisted of mega varieties from the International Rice Research Institute (IRRI), South Asia, and Southeast Asia (SEA), and the other panel is breeding lines/varieties from South China (SC). In addition, a multiparent advanced generation intercross (MAGIC) population, named as DC1, was also employed. Three analytical methods, single-locus mixed linear model (SL-MLM), multilocus random-SNP-effect mixed linear model (mrMLM), and haplotype-based association analysis (Hap-AA), were applied. OsIDEF1 (which explained 12.3% of the phenotypic variance) and OsZIFL7 (8.3-9.1%), OsZIP7 (18.9%), and OsIRT1 (17.9%) were identified by SL-MLM in SEA and SC, respectively, whereas no gene was significantly associated with GZC in DC1. In total, five (OsNRAMP6, OsYSL15, OsIRT1, OsIDEF1, and OsZIFL7, 7.70-15.39%), three (OsFRDL1, OsIRT1, and OsZIP7, 11.87-17.99%), and two (OsYSL7 and OsZIP7, 9.85-10.57%) genes were detected to be significantly associated with GZC in SEA, SC, and DC1 by mrMLM, respectively. Hap-AA indicated that Hap1-OsNRAMP5, Hap5-OsZIP4, Hap1-OsIRT1, Hap3-OsNRAMP6, Hap6-OsMTP1, and Hap6-OsYSL15 had the largest effects for GZC in SEA, whereas Hap3-OsOPT7, Hap4-OsIRT2, Hap4-OsZIP7, Hap5-OsIRT1, and Hap5-OsSAMS1 were the most significant in the SC population. Besides, superior alleles were also identified for the significant genes. The genes significantly associated with GZC and their superior haplotypes identified in different panels could be used in enhancing GZC through molecular breeding, which could further address the problem of Zn malnutrition among rice consumers.
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Affiliation(s)
- Jindong Liu
- Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Junhui Zhan
- Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Jingguang Chen
- Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- School of Agriculture, Sun Yat-sen University, Guangzhou, China
| | - Xiang Lu
- Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Shuai Zhi
- Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Guoyou Ye
- Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Strategic Innovation Platform, International Rice Research Institute, Makati, Philippines
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Baseggio M, Murray M, Wu D, Ziegler G, Kaczmar N, Chamness J, Hamilton JP, Buell CR, Vatamaniuk OK, Buckler ES, Smith ME, Baxter I, Tracy WF, Gore MA. Genome-wide association study suggests an independent genetic basis of zinc and cadmium concentrations in fresh sweet corn kernels. G3 (BETHESDA, MD.) 2021; 11:6287658. [PMID: 34849806 PMCID: PMC8496296 DOI: 10.1093/g3journal/jkab186] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 05/25/2021] [Indexed: 01/05/2023]
Abstract
Despite being one of the most consumed vegetables in the United States, the elemental profile of sweet corn (Zea mays L.) is limited in its dietary contributions. To address this through genetic improvement, a genome-wide association study was conducted for the concentrations of 15 elements in fresh kernels of a sweet corn association panel. In concordance with mapping results from mature maize kernels, we detected a probable pleiotropic association of zinc and iron concentrations with nicotianamine synthase5 (nas5), which purportedly encodes an enzyme involved in synthesis of the metal chelator nicotianamine. In addition, a pervasive association signal was identified for cadmium concentration within a recombination suppressed region on chromosome 2. The likely causal gene underlying this signal was heavy metal ATPase3 (hma3), whose counterpart in rice, OsHMA3, mediates vacuolar sequestration of cadmium and zinc in roots, whereby regulating zinc homeostasis and cadmium accumulation in grains. In our association panel, hma3 associated with cadmium but not zinc accumulation in fresh kernels. This finding implies that selection for low cadmium will not affect zinc levels in fresh kernels. Although less resolved association signals were detected for boron, nickel, and calcium, all 15 elements were shown to have moderate predictive abilities via whole-genome prediction. Collectively, these results help enhance our genomics-assisted breeding efforts centered on improving the elemental profile of fresh sweet corn kernels.
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Affiliation(s)
- Matheus Baseggio
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Matthew Murray
- Department of Agronomy, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Di Wu
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Gregory Ziegler
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
| | - Nicholas Kaczmar
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - James Chamness
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - John P Hamilton
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
| | - C Robin Buell
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Olena K Vatamaniuk
- Soil and Crop Sciences Section, Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Edward S Buckler
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA.,Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853, USA.,US Department of Agriculture-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, NY 14853, USA
| | - Margaret E Smith
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Ivan Baxter
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
| | - William F Tracy
- Department of Agronomy, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Michael A Gore
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
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Wu D, Tanaka R, Li X, Ramstein GP, Cu S, Hamilton JP, Buell CR, Stangoulis J, Rocheford T, Gore MA. High-resolution genome-wide association study pinpoints metal transporter and chelator genes involved in the genetic control of element levels in maize grain. G3-GENES GENOMES GENETICS 2021; 11:6156830. [PMID: 33677522 PMCID: PMC8759812 DOI: 10.1093/g3journal/jkab059] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 02/21/2021] [Indexed: 12/18/2022]
Abstract
Despite its importance to plant function and human health, the genetics underpinning element levels in maize grain remain largely unknown. Through a genome-wide association study in the maize Ames panel of nearly 2,000 inbred lines that was imputed with ∼7.7 million SNP markers, we investigated the genetic basis of natural variation for the concentration of 11 elements in grain. Novel associations were detected for the metal transporter genes rte2 (rotten ear2) and irt1 (iron-regulated transporter1) with boron and nickel, respectively. We also further resolved loci that were previously found to be associated with one or more of five elements (copper, iron, manganese, molybdenum, and/or zinc), with two metal chelator and five metal transporter candidate causal genes identified. The nas5 (nicotianamine synthase5) gene involved in the synthesis of nicotianamine, a metal chelator, was found associated with both zinc and iron and suggests a common genetic basis controlling the accumulation of these two metals in the grain. Furthermore, moderate predictive abilities were obtained for the 11 elemental grain phenotypes with two whole-genome prediction models: Bayesian Ridge Regression (0.33–0.51) and BayesB (0.33–0.53). Of the two models, BayesB, with its greater emphasis on large-effect loci, showed ∼4–10% higher predictive abilities for nickel, molybdenum, and copper. Altogether, our findings contribute to an improved genotype-phenotype map for grain element accumulation in maize.
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Affiliation(s)
- Di Wu
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Ryokei Tanaka
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Xiaowei Li
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | | | - Suong Cu
- College of Science and Engineering, Flinders University, Bedford Park, SA 5042, Australia
| | - John P Hamilton
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
| | - C Robin Buell
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
| | - James Stangoulis
- College of Science and Engineering, Flinders University, Bedford Park, SA 5042, Australia
| | - Torbert Rocheford
- Department of Agronomy, Purdue University, West Lafayette, IN 47907, USA
| | - Michael A Gore
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
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Swamy BPM, Marathi B, Ribeiro-Barros AIF, Calayugan MIC, Ricachenevsky FK. Iron Biofortification in Rice: An Update on Quantitative Trait Loci and Candidate Genes. FRONTIERS IN PLANT SCIENCE 2021; 12:647341. [PMID: 34122472 PMCID: PMC8187908 DOI: 10.3389/fpls.2021.647341] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 04/15/2021] [Indexed: 05/06/2023]
Abstract
Rice is the most versatile model for cereals and also an economically relevant food crop; as a result, it is the most suitable species for molecular characterization of Fe homeostasis and biofortification. Recently there have been significant efforts to dissect genes and quantitative trait loci (QTL) associated with Fe translocation into rice grains; such information is highly useful for Fe biofortification of cereals but very limited in other species, such as maize (Zea mays) and wheat (Triticum aestivum). Given rice's centrality as a model for Poaceae species, we review the current knowledge on genes playing important roles in Fe transport, accumulation, and distribution in rice grains and QTLs that might explain the variability in Fe concentrations observed in different genotypes. More than 90 Fe QTLs have been identified over the 12 rice chromosomes. From these, 17 were recorded as stable, and 25 harbored Fe-related genes nearby or within the QTL. Among the candidate genes associated with Fe uptake, translocation, and loading into rice grains, we highlight the function of transporters from the YSL and ZIP families; transporters from metal-binding molecules, such as nicotianamine and deoxymugineic acid; vacuolar iron transporters; citrate efflux transporters; and others that were shown to play a role in steps leading to Fe delivery to seeds. Finally, we discuss the application of these QTLs and genes in genomics assisted breeding for fast-tracking Fe biofortification in rice and other cereals in the near future.
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Affiliation(s)
| | - Balram Marathi
- Agricultural College, Warangal, Professor Jayashankar Telangana State Agricultural University, Hyderabad, India
| | - Ana I. F. Ribeiro-Barros
- Forest Research Centre (CEF), Instituto Superior de Agronomia, Universidade de Lisboa, Lisbon, Portugal
| | - Mark Ian C. Calayugan
- Institute of Crop Science, University of the Philippines Los Baños, Laguna, Philippines
| | - Felipe Klein Ricachenevsky
- Departamento de Botânica, Instituto de Biociências, e Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
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Kasote D, Sreenivasulu N, Acuin C, Regina A. Enhancing health benefits of milled rice: current status and future perspectives. Crit Rev Food Sci Nutr 2021; 62:8099-8119. [PMID: 34036858 DOI: 10.1080/10408398.2021.1925629] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Milled rice is an essential part of the regular diet for approximately half of the world's population. Its remarkable commercial value and consumer acceptance are mostly due to its promising cooking qualities, appealing sensory properties, and longer shelf life. However, the significant loss of the nutrient-rich bran layer during milling makes it less nutritious than the whole grain. Thus, enhancing the nutritive value of milled rice is vital in improving the health and wellbeing of rice consumers, particularly for those residing in the low-economic zones where rice is the primary source of calories and nutrition. This article provides a critical review on multiple frontiers of recent interventions, such as (1) infusing the genetic diversity to enrich amylose and resistant starch to reduce glycaemic index, (2) enhancing the minerals and vitamins through complementary fortification and biofortification as short and long-term interventions, and (3) developing transgenic solutions to improve the nutrient levels of milled rice. Additionally, the review highlights the benefits of functional ingredients of milled rice to human health and the potential of enhancing them in rice to address the triple burden of malnutrition. The potential merit of milled rice concerning food safety is also reviewed in this article.
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Affiliation(s)
- Deepak Kasote
- Centre of Excellence in Rice Value Addition (CERVA), International Rice Research Institute (IRRI), South Asia Regional Centre, Varanasi, Uttar Pradesh (U.P.), India
| | - Nese Sreenivasulu
- Rice Breeding and Innovation Platform, International Rice Research Institute (IRRI), Los Baños, Laguna, Philippines
| | - Cecilia Acuin
- Rice Breeding and Innovation Platform, International Rice Research Institute (IRRI), Los Baños, Laguna, Philippines
| | - Ahmed Regina
- Centre of Excellence in Rice Value Addition (CERVA), International Rice Research Institute (IRRI), South Asia Regional Centre, Varanasi, Uttar Pradesh (U.P.), India
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Grain Fe and Zn content, heterosis, combining ability and its association with grain yield in irrigated and aerobic rice. Sci Rep 2021; 11:10579. [PMID: 34011978 PMCID: PMC8134482 DOI: 10.1038/s41598-021-90038-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 05/04/2021] [Indexed: 11/24/2022] Open
Abstract
Genetic improvement of rice for grain micronutrients, viz., iron (Fe) and zinc (Zn) content is one of the important breeding objectives, in addition to yield improvement under the irrigated and aerobic ecosystems. In view of developing genetic resources for aerobic conditions, line (L) × tester (T) analysis was conducted with four restorers, four CMS lines and 16 hybrids. Both hybrids and parental lines were evaluated in irrigated and aerobic field conditions for grain yield, grain Fe and Zn content. General Combining Ability (GCA) effects of parents and Specific Combining Ability (SCA) effects of hybrids were observed to be contrasting for the micronutrient content in both the growing environments. The grain Fe and Zn content for parental lines were negatively correlated with grain yield in both the contrasting growing conditions. However, hybrids exhibited positive correlation for grain Fe and Zn with grain yield under limited water conditions. The magnitude of SCA mean squares was much higher than GCA mean squares implying preponderance of dominance gene action and also role of complementary non-allelic gene(s) interaction of parents and suitability of hybrids to the aerobic system. The testers HHZ12-SAL8-Y1-SAL1 (T1) and HHZ17-Y16-Y3-Y2 (T2) were identified as good combiners for grain Zn content under irrigated and aerobic conditions respectively.
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32
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Mapping QTLs for yield component traits using overwintering cultivated rice. J Genet 2021. [DOI: 10.1007/s12041-021-01279-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Green Labelled Rice Shows a Higher Nutritional and Physiochemical Quality Than Conventional Rice in China. Foods 2021; 10:foods10050915. [PMID: 33919454 PMCID: PMC8143485 DOI: 10.3390/foods10050915] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 04/17/2021] [Accepted: 04/19/2021] [Indexed: 11/20/2022] Open
Abstract
In China, green food refers to a wide array of certified agricultural and processed edible commodities that are produced strictly following defined standard protocols and labelled with a specified “Green Food” logo. The demand for green labelled rice is rapidly growing due to its higher quality and adherence to safety standards compared to conventional rice. Therefore, the physicochemical and nutritional quality of green rice needs to be further investigated for consumers’ benefits. Using Daohuaxiang 2, one of the most famous types of green rice, we found that green rice was significantly superior to conventional rice in terms of thousand kernel weight, chalkiness, amylose content, and rheological properties. Green rice contained lower levels of heavy metals than conventional rice due to a dramatic reduction in chemical inputs during its cultivation. The concentrations of Cr, As, Cd, Pb in green rice decreased, respectively, from 98.7 to 180.1 μg/kg, 49.8 to 62.3 μg/kg, 7.8 to 9.1 μg/kg, and 29.0 to 42.8 μg/kg on average. Gas chromatography coupled with mass spectrometry (GC–MS)-based metabolomics, in combination with multivariate analysis, revealed that 15 metabolites differentially accumulated when comparing green and conventional rice. Among these, 12 metabolites showed a high accumulation in green rice, including seven amino acids, two sugars, and three fatty acids. Overall, our results suggest the superior quality of a type of green rice that is popular in China, which may boost green rice consumption and facilitate the further expansion of green rice production in China.
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Swamy BPM, Marathi B, Ribeiro-Barros AIF, Ricachenevsky FK. Editorial: Development of Healthy and Nutritious Cereals: Recent Insights on Molecular Advances in Breeding. Front Genet 2021; 12:635006. [PMID: 33868374 PMCID: PMC8044956 DOI: 10.3389/fgene.2021.635006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Accepted: 02/23/2021] [Indexed: 11/13/2022] Open
Affiliation(s)
| | - Balram Marathi
- Department of Genetics and Plant Breeding, Professor Jayashankar Telangana State Agricultural University, Hyderabad, India
| | - Ana I F Ribeiro-Barros
- Forest Research Centre (CEF), Instituto Superior de Agronomia, Universidade de Lisboa, Lisbon, Portugal
| | - Felipe Klein Ricachenevsky
- Departamento de Botânica, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.,Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
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35
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Lu X, Liu S, Zhi S, Chen J, Ye G. Comparative transcriptome profile analysis of rice varieties with different tolerance to zinc deficiency. PLANT BIOLOGY (STUTTGART, GERMANY) 2021; 23:375-390. [PMID: 33296551 DOI: 10.1111/plb.13227] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 11/30/2020] [Indexed: 06/12/2023]
Abstract
Zinc (Zn) is an indispensable element for rice growth. Zn deficiency results in brown blotches and streaks 2-3 weeks after transplanting, as well as stunting, reduced tillering, and low productivity of rice plants. These processes are controlled by different families of expressed genes. A comparative transcriptome profile analysis was conducted using the roots of two Zn deficiency tolerant varieties (UCP122 and KALIBORO26) and two sensitive varieties (IR26 and IR64) by merging data from untreated control (CK) and Zn deficiency treated samples. Results revealed a total of 4,688 differentially expressed genes (DEGs) between the normal Zn and deficient conditions, with 2,702 and 1,489 unique DEGs upregulated and downregulated, respectively. Functional enrichment analysis identified transcription factors (TFs), such as WRKY, MYB, ERF, and bHLH which are important in the regulation of the Zn deficiency response. Furthermore, chitinases, jasmonic acid, and phenylpropanoid pathways were found to be important in the Zn deficiency response. The metal tolerance protein (MTP) genes also appeared to play an important role in conferring tolerance to Zn deficiency. A heavy metal-associated domain-containing protein 7 was associated with tolerance to Zn deficiency and negatively regulated downstream genes. Collectively, our findings provide valuable expression patterns and candidate genes for the study of molecular mechanisms underlying the response to Zn deficiency and for improvements in breeding for tolerance to Zn deficiency in rice.
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Affiliation(s)
- X Lu
- CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute in Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - S Liu
- CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute in Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Group of Crop Genetics and Breeding, Jiangxi Agricultural University, Nanchang, China
| | - S Zhi
- CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute in Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- College of Resources and Environment, Henan Agricultural University, Zhengzhou, China
| | - J Chen
- CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute in Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - G Ye
- CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute in Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Group of Crop Genetics and Breeding, Jiangxi Agricultural University, Nanchang, China
- Strategic Innovation Platform, International Rice Research Institute, Metro Manila, Philippines
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Suman K, Neeraja CN, Madhubabu P, Rathod S, Bej S, Jadhav KP, Kumar JA, Chaitanya U, Pawar SC, Rani SH, Subbarao LV, Voleti SR. Identification of Promising RILs for High Grain Zinc Through Genotype × Environment Analysis and Stable Grain Zinc QTL Using SSRs and SNPs in Rice ( Oryza sativa L.). FRONTIERS IN PLANT SCIENCE 2021; 12:587482. [PMID: 33679823 PMCID: PMC7930840 DOI: 10.3389/fpls.2021.587482] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Accepted: 01/06/2021] [Indexed: 05/09/2023]
Abstract
Polished rice is one of the commonly consumed staple foods across the world. However, it contains limited nutrients especially iron (Fe) and zinc (Zn). To identify promising recombinant inbred lines (RILs) for grain Zn and single plant yield, 190 RILs developed from PR116 and Ranbir Basmati were evaluated in two environments (E1 and E2). A subset of 44 contrasting RILs for grain Zn was screened in another two environments (E3 and E4). Phenotypic data was collected for 10 traits, viz., days to 50% flowering, plant height, panicle length, number of tillers, single plant yield (SPY), test weight, Fe and Zn in brown (IBR, ZBR), and polished rice (IPR, ZPR). Stepwise regression analysis of trait data in 190 RILs and a subset of 44 RILs revealed the interdependence of ZPR, ZBR, IPR, and IBR and the negative association of grain Zn with single plant yield. Based on the additive main effect and multiplicative interaction (AMMI) and genotype and genotype × environment interaction (GGE) analyses of the subset of 44 RILs across four environments (E1-E4), six promising RILs were identified for ZPR with >28 ppm. Mapping of 190 RILs with 102 simple sequence repeats (SSRs) resulted in 13 QTLs for best linear unbiased estimates (BLUEs) of traits including advantage over check (AOC). Using genotype-based sequencing (GBS), the subset of 44 RILs was mapped with 1035 single-nucleotide polymorphisms (SNPs) and 21 QTLs were identified. More than 100 epistatic interactions were observed. A major QTL qZPR.1.1 (PV 37.84%) and another QTL qZPR.11.1 (PV 15.47%) were identified for grain Zn in polished rice. A common major QTL (qZBR.2.1 and qZPR.2.1) was also identified on chromosome 2 for grain Zn content across SSR and SNP maps. Two potential candidate genes related to transporters were identified based on network analyses in the genomic regions of QTL < 3 Mb. The RILs identified for grain Zn and SPY were nominated for national evaluation as under rice biofortification, and two QTLs identified based on BLUEs could be used in the rice biofortification breeding programs.
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Affiliation(s)
- K. Suman
- ICAR–Indian Institute of Rice Research, Hyderabad, India
- Department of Genetics & Biotechnology, Osmania University, Hyderabad, India
| | - C. N. Neeraja
- ICAR–Indian Institute of Rice Research, Hyderabad, India
- *Correspondence: C. N. Neeraja,
| | - P. Madhubabu
- ICAR–Indian Institute of Rice Research, Hyderabad, India
| | | | - Sonali Bej
- ICAR–Indian Institute of Rice Research, Hyderabad, India
| | - K. P. Jadhav
- ICAR–Indian Institute of Rice Research, Hyderabad, India
| | | | - U. Chaitanya
- ICAR–Indian Institute of Rice Research, Hyderabad, India
| | - Smita C. Pawar
- Department of Genetics & Biotechnology, Osmania University, Hyderabad, India
| | - Surekha H. Rani
- Department of Genetics & Biotechnology, Osmania University, Hyderabad, India
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Gupta PK, Balyan HS, Sharma S, Kumar R. Biofortification and bioavailability of Zn, Fe and Se in wheat: present status and future prospects. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:1-35. [PMID: 33136168 DOI: 10.1007/s00122-020-03709-7] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 10/13/2020] [Indexed: 05/02/2023]
Abstract
Knowledge of genetic variation, genetics, physiology/molecular basis and breeding (including biotechnological approaches) for biofortification and bioavailability for Zn, Fe and Se will help in developing nutritionally improved wheat. Biofortification of wheat cultivars for micronutrients is a priority research area for wheat geneticists and breeders. It is known that during breeding of wheat cultivars for productivity and quality, a loss of grain micronutrient contents occurred, leading to decline in nutritional quality of wheat grain. Keeping this in view, major efforts have been made during the last two decades for achieving biofortification and bioavailability of wheat grain for micronutrients including Zn, Fe and Se. The studies conducted so far included evaluation of gene pools for contents of not only grain micronutrients as above, but also for phytic acid (PA) or phytate and phytase, so that, while breeding for the micronutrients, bioavailability is also improved. For this purpose, QTL interval mapping and GWAS were carried out to identify QTLs/genes and associated markers that were subsequently used for marker-assisted selection (MAS) during breeding for biofortification. Studies have also been conducted to understand the physiology and molecular basis of biofortification, which also allowed identification of genes for uptake, transport and storage of micronutrients. Transgenics using transgenes have also been produced. The breeding efforts led to the development of at least a dozen cultivars with improved contents of grain micronutrients, although land area occupied by these biofortified cultivars is still marginal. In this review, the available information on different aspects of biofortification and bioavailability of micronutrients including Zn, Fe and Se in wheat has been reviewed for the benefit of those, who plan to start work or already conducting research in this area.
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Affiliation(s)
- P K Gupta
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, U.P, 250004, India.
| | - H S Balyan
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, U.P, 250004, India
| | - Shailendra Sharma
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, U.P, 250004, India
| | - Rahul Kumar
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, U.P, 250004, India
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Hirschi KD. Genetically Modified Plants: Nutritious, Sustainable, yet Underrated. J Nutr 2020; 150:2628-2634. [PMID: 32725215 PMCID: PMC7549299 DOI: 10.1093/jn/nxaa220] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 05/11/2020] [Accepted: 07/07/2020] [Indexed: 12/16/2022] Open
Abstract
Combating malnutrition is one of the greatest global health challenges. Plant-based foods offer an assortment of nutrients that are essential for adequate nutrition and can promote good health. Unfortunately, the majority of widely consumed crops are deficient in some of these nutrients. Biofortification is the umbrella term for the process by which the nutritional quality of food crops is enhanced. Traditional agricultural breeding approaches for biofortification are time consuming but can enhance the nutritional value of some foods; however, advances in molecular biology are rapidly being exploited to biofortify various crops. Globally, genetically modified organisms are a controversial topic for consumers and governmental agencies, with a vast majority of people apprehensive about the technology. Golden Rice has been genetically modified to contain elevated β-carotene concentrations and is the bellwether for both the promise and angst of agricultural biotechnology. Although there are numerous other nutritional targets of genetically biofortified crops, here I briefly summarize the work to elevate iron and folate concentrations. In addition, the possibility of using modified foods to affect the gut microbiota is examined. For several decades, plant biotechnology has measured changes in nutrient concentrations; however, the bioavailability of nutrients from many biofortified crops has not been demonstrated.
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Affiliation(s)
- Kendal D Hirschi
- Department of Pediatrics, Children's Nutrition Research Center, Baylor College of Medicine, Houston, TX, USA
- Department of Human and Molecular Genetics, Children's Nutrition Research Center, Baylor College of Medicine, Houston, TX, USA
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Raza Q, Riaz A, Saher H, Bibi A, Raza MA, Ali SS, Sabar M. Grain Fe and Zn contents linked SSR markers based genetic diversity in rice. PLoS One 2020; 15:e0239739. [PMID: 32986755 PMCID: PMC7521695 DOI: 10.1371/journal.pone.0239739] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 09/12/2020] [Indexed: 12/15/2022] Open
Abstract
Rice is critical for sustainable food and nutritional security; however, nominal micronutrient quantities in grains aggravate malnutrition in rice-eating poor populations. In this study, we evaluated genetic diversity in grain iron (Fe) and zinc (Zn) contents using trait-linked simple sequence repeat (SSR) markers in the representative subset of a large collection of local and exotic rice germplasm. Results demonstrated that aromatic fine grain accessions contained relatively higher Fe and Zn contents in brown rice (BR) than coarse grain accessions and a strong positive correlation between both mineral elements. Genotyping with 24 trait-linked SSR markers identified 21 polymorphic markers, among which 17 demonstrated higher gene diversity and polymorphism information content (PIC) values, strongly indicating that markers used in current research were moderate to highly informative for evaluating the genetic diversity. Population structure, principal coordinate and phylogenetic analyses classified studied rice accessions into two fine grain specific and one fine and coarse grain admixture subpopulations. Single marker analysis recognized four ZnBR and single FeBR significant marker-trait associations (MTAs) contributing 15.41-39.72% in total observed phenotypic variance. Furthermore, high grain Fe and Zn contents linked marker alleles from significant MTAs were also identified. Collectively, these results indicate a wide genetic diversity exist in grain Fe and Zn contents of studied rice accessions and reveal perspective for marker-assisted biofortification breeding.
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Affiliation(s)
- Qasim Raza
- Molecular Breeding Laboratory, Rice Research Institute, Kala Shah Kaku, Sheikhupura, Punjab, Pakistan
| | - Awais Riaz
- Molecular Breeding Laboratory, Rice Research Institute, Kala Shah Kaku, Sheikhupura, Punjab, Pakistan
| | - Hira Saher
- Molecular Breeding Laboratory, Rice Research Institute, Kala Shah Kaku, Sheikhupura, Punjab, Pakistan
| | - Ayesha Bibi
- Plant Pathology Laboratory, Rice Research Institute, Kala Shah Kaku, Sheikhupura, Punjab, Pakistan
| | - Mohsin Ali Raza
- Rice Technology Laboratory, Rice Research Institute, Kala Shah Kaku, Sheikhupura, Punjab Pakistan
| | - Syed Sultan Ali
- Molecular Breeding Laboratory, Rice Research Institute, Kala Shah Kaku, Sheikhupura, Punjab, Pakistan
| | - Muhammad Sabar
- Molecular Breeding Laboratory, Rice Research Institute, Kala Shah Kaku, Sheikhupura, Punjab, Pakistan
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Naik SM, Raman AK, Nagamallika M, Venkateshwarlu C, Singh SP, Kumar S, Singh SK, Das SP, Prasad K, Izhar T, Mandal NP, Singh NK, Yadav S, Reinke R, Swamy BPM, Virk P, Kumar A. Genotype × environment interactions for grain iron and zinc content in rice. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2020; 100:4150-4164. [PMID: 32421211 DOI: 10.1002/jsfa.10454] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 02/26/2020] [Accepted: 05/18/2020] [Indexed: 05/12/2023]
Abstract
BACKGROUND Nutrient deficiency in humans, especially in children and lactating women, is a major concern. Increasing the micronutrient concentration in staple crops like rice is one way to overcome this. The micronutrient content in rice, especially the iron (Fe) and zinc (Zn) content, is highly variable. The identification of rice genotypes in which there are naturally high Fe and Zn concentrations across environments is an important target towards the production of biofortified rice. RESULTS Phenotypic correlations between grain Fe and Zn content were positive and significant in all environments but a significant negative association was observed between grain yield and grain Fe and Zn. Promising breeding lines with higher Zn or Fe content, or both, were: IR 82475-110-2-2-1-2 (Zn: 20.24-37.33 mg kg-1 ; Fe: 7.47-14.65 mg kg-1 ); IR 83294-66-2-2-3-2 (Zn: 22-37-41.97 mg kg-1 ; Fe: 9.43-17.16); IR 83668-35-2-2-2 (Zn: 27.15-42.73 mg kg-1 ; Fe: 6.01-14.71); IR 68144-2B-2-2-3-1-166 (Zn: 23.53-40.30 mg kg-1 ; Fe: 10.53-17.80 mg kg-1 ) and RP Bio 5478-185M7 (Zn: 22.60-40.07 mg kg-1 ; Fe: 7.64-14.73 mg kg-1 ). Among these, IR82475-110-2-2-1-2 (Zn: 20.24-37.33 mg kg-1 ; Fe: 7.47-14.65 mg kg-1 ) is also high yielding with 3.75 t ha-1 . Kelhrie Cha (Zn: 17.76-36.45 mg kg-1 ; Fe: 7.17-14.77 mg kg-1 ), Dzuluorhe (Zn: 17.48-39.68 mg kg-1 ; Fe: 7.89-19.90 mg kg-1 ), Nedu (Zn: 18.97-43.55 mg kg-1 Fe: 8.01-19.51 mg kg-1 ), Kuhusoi-Ri-Sareku (Zn: 17.37-44.14 mg kg-1 ; Fe: 8.99-14.30 mg kg-1 ) and Mima (Zn: 17.10-45.64 mg kg-1 ; Fe: 9.97-17.40 mg kg-1 ) were traditional donor genotypes that possessed both high grain Fe and high Zn content. CONCLUSION Significant genotype × location (G × L) effects were observed in all traits except Fe. Genetic variance was significant and was considerably larger than the variance of G × L for grain Zn and Fe content traits, except grain yield. The G × L × year variance component was significant in all cases. © 2020 Society of Chemical Industry.
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Affiliation(s)
- Shilpa M Naik
- International Rice Research Institute, South Asia Hub, ICRISAT, Patancheru, India
| | - Anitha K Raman
- International Rice Research Institute, South Asia Hub, ICRISAT, Patancheru, India
| | - Minnuru Nagamallika
- International Rice Research Institute, South Asia Hub, ICRISAT, Patancheru, India
| | | | - Suresh Prasad Singh
- Department of Genetics and Plant Breeding, Bihar Agricultural University, Sabour, India
| | - Santosh Kumar
- Division of Crop Research, ICAR Research Complex for Eastern Region, Patna, India
| | - Shravan Kumar Singh
- Department of Genetics and Plant Breeding, Institute of Agricultural Science, Banaras Hindu University, Varanasi, India
| | - Sankar Prasad Das
- Division of Plant Breeding, ICAR Research Complex for NEH Region, Lembucherra, India
| | - Krishna Prasad
- Department of Genetics and Plant Breeding, Birsa Agricultural University, Ranchi, India
| | - Tajwar Izhar
- Department of Genetics and Plant Breeding, Birsa Agricultural University, Ranchi, India
| | - Nimmai P Mandal
- Central Rainfed Upland Rice Research Station, National Rice Research Institute, Hazaribagh, India
| | - Nitendra Kumar Singh
- Department of Genetics and Plant Breeding, Dr. Rajendra Prasad Agricultural University, Samastipur, India
| | - Shailesh Yadav
- Rice Breeding Platform, International Rice Research Institute, Metro Manila, Philippines
| | - Russell Reinke
- Rice Breeding Platform, International Rice Research Institute, Metro Manila, Philippines
| | | | - Parminder Virk
- HarvestPlus, International Crop Research Institute for Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Arvind Kumar
- Rice Breeding Platform, International Rice Research Institute, Metro Manila, Philippines
- IRRI South Asia Regional Center (ISARC), Varanasi, India
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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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Yang M, Li Y, Liu Z, Tian J, Liang L, Qiu Y, Wang G, Du Q, Cheng D, Cai H, Shi L, Xu F, Lian X. A high activity zinc transporter OsZIP9 mediates zinc uptake in rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:1695-1709. [PMID: 32449251 DOI: 10.1111/tpj.14855] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 05/12/2020] [Accepted: 05/15/2020] [Indexed: 05/24/2023]
Abstract
Zinc (Zn) is an essential micronutrient for most organisms including humans, and Zn deficiency is widespread in human populations, particularly in underdeveloped regions. Cereals such as rice (Oryza sativa) are the major dietary source of Zn for most people. However, the molecular mechanism underlying Zn uptake in rice is still not fully understood. Here, we report that a member of the ZIP (ZRT, IRT-like protein) family, OsZIP9, contributes to Zn uptake in rice. It was expressed in the epidermal and exodermal cells of lateral roots, localized in the plasma membrane and induced during Zn deficiency. Yeast-expressed OsZIP9 showed much higher Zn influx transport activity than other rice ZIP proteins in a wide range of Zn concentrations. OsZIP9 knockout rice plants showed a significant reduction in growth at low Zn concentrations, but could be rescued by a high Zn supply. Compared with the wild type, accumulation of Zn in root, shoot and grain was much lower in knockout lines, particularly with a low supply of Zn under both hydroponic and paddy soil conditions. OsZIP9 also showed Co uptake activity. Natural variation of OsZIP9 expression level is highly associated with Zn content in milled grain among rice varieties in the germplasm collection. Taken together, these results show that OsZIP9 is an important influx transporter responsible for the take up of Zn and Co from external media into root cells.
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Affiliation(s)
- Meng Yang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
- Shuanshui Shuanglü Institute, Huazhong Agricultural University, Wuhan, 430070, China
- Microelement Research Centre, Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yutong Li
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
- Shuanshui Shuanglü Institute, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zonghao Liu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
- Shuanshui Shuanglü Institute, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jingjing Tian
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
- Shuanshui Shuanglü Institute, Huazhong Agricultural University, Wuhan, 430070, China
| | - Limin Liang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
- Shuanshui Shuanglü Institute, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yu Qiu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
- Shuanshui Shuanglü Institute, Huazhong Agricultural University, Wuhan, 430070, China
| | - Guangyuan Wang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
- Shuanshui Shuanglü Institute, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qingqing Du
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
- Shuanshui Shuanglü Institute, Huazhong Agricultural University, Wuhan, 430070, China
| | - Deng Cheng
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
- Shuanshui Shuanglü Institute, Huazhong Agricultural University, Wuhan, 430070, China
| | - Hongmei Cai
- Microelement Research Centre, Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, 430070, China
| | - Lei Shi
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
- Microelement Research Centre, Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, 430070, China
| | - Fangsen Xu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
- Microelement Research Centre, Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xingming Lian
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
- Shuanshui Shuanglü Institute, Huazhong Agricultural University, Wuhan, 430070, China
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Das P, Adak S, Lahiri Majumder A. Genetic Manipulation for Improved Nutritional Quality in Rice. Front Genet 2020; 11:776. [PMID: 32793287 PMCID: PMC7393646 DOI: 10.3389/fgene.2020.00776] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 06/30/2020] [Indexed: 01/10/2023] Open
Abstract
Food with higher nutritional value is always desired for human health. Rice is the prime staple food in more than thirty developing countries, providing at least 20% of dietary protein, 3% of dietary fat and other essential nutrients. Several factors influence the nutrient content of rice which includes agricultural practices, post-harvest processing, cultivar type as well as manipulations followed by selection through breeding and genetic means. In addition to mutation breeding, genetic engineering approach also contributed significantly for the generation of nutrition added varieties of rice in the last decade or so. In the present review, we summarize the research update on improving the nutritional characteristics of rice by using genetic engineering and mutation breeding approach. We also compare the conventional breeding techniques of rice with modern molecular breeding techniques toward the generation of nutritionally improved rice variety as compared to other cereals in areas of micronutrients and availability of essential nutrients such as folate and iron. In addition to biofortification, our focus will be on the efforts to generate low phytate in seeds, increase in essential fatty acids or addition of vitamins (as in golden rice) all leading to the achievements in rice nutrition science. The superiority of biotechnology over conventional breeding being already established, it is essential to ascertain that there are no serious negative agronomic consequences for consumers with any difference in grain size or color or texture, when a nutritionally improved variety of rice is generated through genetic engineering technology.
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Roda FA, Marques I, Batista-Santos P, Esquível MG, Ndayiragije A, Lidon FC, Swamy BPM, Ramalho JC, Ribeiro-Barros AI. Rice Biofortification With Zinc and Selenium: A Transcriptomic Approach to Understand Mineral Accumulation in Flag Leaves. Front Genet 2020; 11:543. [PMID: 32733530 PMCID: PMC7359728 DOI: 10.3389/fgene.2020.00543] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Accepted: 05/05/2020] [Indexed: 11/13/2022] Open
Abstract
Human malnutrition due to micronutrient deficiencies, particularly with regards to Zinc (Zn) and Selenium (Se), affects millions of people around the world, and the enrichment of staple foods through biofortification has been successfully used to fight hidden hunger. Rice (Oryza sativa L.) is one of the staple foods most consumed in countries with high levels of malnutrition. However, it is poor in micronutrients, which are often removed during grain processing. In this study, we have analyzed the transcriptome of rice flag leaves biofortified with Zn (900 g ha-1), Se (500 g ha-1), and Zn-Se. Flag leaves play an important role in plant photosynthesis and provide sources of metal remobilization for developing grains. A total of 3170 differentially expressed genes (DEGs) were identified. The expression patterns and gene ontology of DEGs varied among the three sets of biofortified plants and were limited to specific metabolic pathways related to micronutrient mobilization and to the specific functions of Zn (i.e., its enzymatic co-factor/coenzyme function in the biosynthesis of nitrogenous compounds, carboxylic acids, organic acids, and amino acids) and Se (vitamin biosynthesis and ion homeostasis). The success of this approach should be followed in future studies to understand how landraces and other cultivars respond to biofortification.
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Affiliation(s)
- Faustino Adriano Roda
- Ministério de Agricultura e Segurança Alimentar, Instituto de Investigação Agrária de Moçambique, Centro Zonal Noroeste, Lichinga, Mozambique
- Universidade Eduardo Mondlane-Centro de Biotechnologia, Maputo, Mozambique
- PlantStress&Biodiversity Lab, Forest Research Center (IM, JCR, AIRB) and Linking, Landscape, Environment, Agriculture and Food (PBS, MGE), Instituto Superior de Agronomia, Universidade de Lisboa, Lisbon, Portugal
| | - Isabel Marques
- PlantStress&Biodiversity Lab, Forest Research Center (IM, JCR, AIRB) and Linking, Landscape, Environment, Agriculture and Food (PBS, MGE), Instituto Superior de Agronomia, Universidade de Lisboa, Lisbon, Portugal
| | - Paula Batista-Santos
- PlantStress&Biodiversity Lab, Forest Research Center (IM, JCR, AIRB) and Linking, Landscape, Environment, Agriculture and Food (PBS, MGE), Instituto Superior de Agronomia, Universidade de Lisboa, Lisbon, Portugal
| | - Maria Glória Esquível
- PlantStress&Biodiversity Lab, Forest Research Center (IM, JCR, AIRB) and Linking, Landscape, Environment, Agriculture and Food (PBS, MGE), Instituto Superior de Agronomia, Universidade de Lisboa, Lisbon, Portugal
| | - Alexis Ndayiragije
- International Rice Research Institute, Maputo, Mozambique
- International Rice Research Institute, Laguna, Philippines
| | - Fernando Cebola Lidon
- Unidade de Geobiociências, Geoengenharias e Geotecnologias, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Caparica, Portugal
| | - B. P. Mallikarjuna Swamy
- International Rice Research Institute, Maputo, Mozambique
- International Rice Research Institute, Laguna, Philippines
| | - José Cochicho Ramalho
- PlantStress&Biodiversity Lab, Forest Research Center (IM, JCR, AIRB) and Linking, Landscape, Environment, Agriculture and Food (PBS, MGE), Instituto Superior de Agronomia, Universidade de Lisboa, Lisbon, Portugal
- Unidade de Geobiociências, Geoengenharias e Geotecnologias, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Ana I. Ribeiro-Barros
- PlantStress&Biodiversity Lab, Forest Research Center (IM, JCR, AIRB) and Linking, Landscape, Environment, Agriculture and Food (PBS, MGE), Instituto Superior de Agronomia, Universidade de Lisboa, Lisbon, Portugal
- Unidade de Geobiociências, Geoengenharias e Geotecnologias, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Caparica, Portugal
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Islam MZ, Arifuzzaman M, Banik S, Hossain MA, Ferdous J, Khalequzzaman M, Pittendrigh BR, Tomita M, Ali MP. Mapping QTLs underpin nutrition components in aromatic rice germplasm. PLoS One 2020; 15:e0234395. [PMID: 32525930 PMCID: PMC7289389 DOI: 10.1371/journal.pone.0234395] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 05/22/2020] [Indexed: 12/22/2022] Open
Abstract
As rice is an important staple food globally, research for development and enhancement of its nutritional value it is an imperative task. Identification of nutrient enriched rice germplasm and exploiting them for breeding programme is the easiest way to develop better quality rice. In this study, we analyzed 113 aromatic rice germplasm in order to identify quantitative trait loci (QTL) underpinning nutrition components and determined by measuring the normal frequency distribution for Fe, Zn, amylose, and protein content in those rice germplasm. Comparatively, the germplasm Radhuni pagal, Kalobakri, Thakurbhog (26.6 ppm) and Hatisail exhibited the highest mean values for Fe (16.9 ppm), Zn (34.1 ppm), amylose (26.6 ppm) and protein content (11.0 ppm), respectively. Moreover, a significant linear relationship (R2 = 0.693) was observed between Fe and Zn contents. Cluster analysis based on Mahalanobis D2 distances revealed four major clusters of 113 rice germplasm, with cluster III containing a maximum 37 germplasm and a maximum inter-cluster distance between clusters III and IV. The 45 polymorphic SSRs and four trait associations exhibited eight significant quantitative trait loci (QTL) located on eight different chromosomes using composite interval mapping (CIM). The highly significant QTL (variance 7.89%, LOD 2.02) for protein content (QTL.pro.1) was observed on chromosome 1 at 94.9cM position. Also, four QTLs for amylose content were observed with the highly significant QTL.amy.8 located on chromosome 8 exhibiting 7.2% variance with LOD 1.83. Only one QTL (QTL.Fe.9) for Fe content was located on chromosome 9 (LOD 1.24), and two (QTL.Zn.4 and QTL.Zn.5) for Zn on chromosome 4 (LOD 1.71) and 5 (LOD 1.18), respectively. Overall, germplasm from clusters III and IV might offer higher heterotic response with the identified QTLs playing a significant role in any rice biofortification breeding program and released with development of new varieties.
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Affiliation(s)
- M. Z. Islam
- Genetic Resources and Seed Division, Bangladesh Rice Research Institute (BRRI), Gazipur, Bangladesh
- * E-mail: (MZI); (MPA); (MT)
| | - M. Arifuzzaman
- Department of Genetics and Plant Breeding, Hajee Mohammad Danesh Science and Technology University, Dinajpur, Bangladesh
| | - S. Banik
- Grain Quality and Nutrition Division, Bangladesh Rice Research Institute (BRRI), Gazipur, Bangladesh
| | - M. A. Hossain
- Regional Station, Barisal, Bangladesh Rice Research Institute, Gazipur, Bangladesh
| | - J. Ferdous
- Biotechnology Division, Bangladesh Rice Research Institute (BRRI), Gazipur, Bangladesh
| | - M. Khalequzzaman
- Genetic Resources and Seed Division, Bangladesh Rice Research Institute (BRRI), Gazipur, Bangladesh
| | - B. R. Pittendrigh
- Department of Entomology, Michigan State University, East Lansing, Michigan, United States of America
| | - M. Tomita
- Genetics and Genome Engineering Laboratory, Green Biology Research Division, Research Institute of Green Science and Technology, Shizuoka University, Shizuoka City, Shizuoka, Japan
- * E-mail: (MZI); (MPA); (MT)
| | - M. P. Ali
- Entomolgy Division, Bangladesh Rice Research Institute (BRRI), Gazipur, Bangladesh
- * E-mail: (MZI); (MPA); (MT)
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Sanjeeva Rao D, Neeraja CN, Madhu Babu P, Nirmala B, Suman K, Rao LVS, Surekha K, Raghu P, Longvah T, Surendra P, Kumar R, Babu VR, Voleti SR. Zinc Biofortified Rice Varieties: Challenges, Possibilities, and Progress in India. Front Nutr 2020; 7:26. [PMID: 32318582 PMCID: PMC7154074 DOI: 10.3389/fnut.2020.00026] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 02/25/2020] [Indexed: 11/17/2022] Open
Abstract
Zinc malnutrition is a major issue in developing countries where polished rice is a staple food. With the existing significant genetic variability for high zinc in polished rice, the development of biofortified rice varieties was targeted in India with support from HarvestPlus, Department of Biotechnology, and Indian Council of Agricultural Research of Government of India. Indian Institute of Rice Research (IIRR) facilitates rice varietal release through All India Coordinated Rice Improvement Project (AICRIP) and also supports rice biofortification program in India. Various germplasm sets of several national institutions were characterized at IIRR for their zinc content in brown rice using energy-dispersive X-ray fluorescence spectroscopy indicating the range of zinc to be 7.3 to 52.7 mg/kg. Evaluation of different mapping populations involving wild germplasm, landraces, and varieties for their zinc content showed the feasibility of favorable recombination of high zinc content and yield. Ninety-nine genotypes from germplasm and 344 lines from mapping populations showed zinc content of ≥28 mg/kg in polished rice meeting the target zinc content set by HarvestPlus. Through AICRIP biofortification trial constituted since 2013, 170 test entries were nominated by various national institutions until 2017, and four biofortified rice varieties were released. Only the test entry with target zinc content, yield, and quality parameters is promoted to the next year; thus, each test entry is evaluated for 3 years across 17 to 27 locations for their performance. Multilocation studies of two mapping populations and AICRIP biofortification trials indicated the zinc content to be highly influenced by environment. The bioavailability of a released biofortified rice variety, viz., DRR Dhan 45 was found to twice that of control IR64. The technology efficacy of the four released varieties developed through conventional breeding ranged from 48 to 75% with zinc intake of 38 to be 47% and 46 to 57% of the RDA for male and female, respectively. The observations from the characterization of germplasm and mapping populations for zinc content and development of national evaluation system for the release of biofortified rice varieties have been discussed in the context of the five criteria set by biofortification program.
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Affiliation(s)
- D Sanjeeva Rao
- ICAR-Indian Institute of Rice Research, Hyderabad, India
| | - C N Neeraja
- ICAR-Indian Institute of Rice Research, Hyderabad, India
| | - P Madhu Babu
- ICAR-Indian Institute of Rice Research, Hyderabad, India
| | - B Nirmala
- ICAR-Indian Institute of Rice Research, Hyderabad, India
| | - K Suman
- ICAR-Indian Institute of Rice Research, Hyderabad, India
| | - L V Subba Rao
- ICAR-Indian Institute of Rice Research, Hyderabad, India
| | - K Surekha
- ICAR-Indian Institute of Rice Research, Hyderabad, India
| | - P Raghu
- ICMR-National Institute of Nutrition, Hyderabad, India
| | - T Longvah
- ICMR-National Institute of Nutrition, Hyderabad, India
| | - P Surendra
- Agricultural Research Station, University of Agricultural Sciences-D, Bangalore, India
| | - Rajesh Kumar
- Department of Plant Breeding and Genetics, AICRIP (Rice), Rajendra Agricultural University, Samastipur, India
| | | | - S R Voleti
- ICAR-Indian Institute of Rice Research, Hyderabad, India
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Phung LD, Pham DV, Sasaki Y, Masuda S, Takakai F, Kaku N, Watanabe T. Continuous Sub-Irrigation with Treated Municipal Wastewater for Protein-Rich Rice Production with Reduced Emissions of CH 4 and N 2O. Sci Rep 2020; 10:5485. [PMID: 32218473 PMCID: PMC7099058 DOI: 10.1038/s41598-020-62247-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 02/03/2020] [Indexed: 11/27/2022] Open
Abstract
Herein, we introduce continuous sub-irrigation with treated municipal wastewater (TWW) as a novel cultivation system to promote resource recycling and cost-effective forage rice production in Japan. However, both TWW irrigation and forage rice cultivation were previously considered to intensify CH4 and N2O emissions. In the present study, therefore, we evaluate the emissions of greenhouse gases (GHGs) and yielding capacity of forage rice between conventional cultivation and continuous sub-irrigation systems employing different water supply rates. Results indicated that continuous sub-irrigation with TWW resulted in high rice yields (10.4–11 t ha−1) with superior protein content (11.3–12.8%) compared with conventional cultivation (8.6 t ha−1 and 9.2%, respectively). All TWW irrigation systems considerably reduced CH4 emissions, while higher continuous supply rates significantly increased N2O emissions compared with the conventional cultivation. Only the continuous irrigation regime employing suitable supply rates at appropriate timings to meet the N demand of rice plants decreased both CH4 and N2O emissions by 84% and 28%, respectively. Overall, continuous sub-irrigation with TWW provides high yields of protein-rich forage rice without the need for synthetic fertilisers and effectively mitigated GHG emissions from paddy fields.
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Affiliation(s)
- Luc Duc Phung
- The United Graduate School of Agricultural Sciences, Iwate University, 3-18-8 Ueda, Morioka, Iwate, 020-8550, Japan.
| | - Dung Viet Pham
- Faculty of Agriculture, Yamagata University, 1-23 Wakaba-machi, Tsuruoka, Yamagata, 997-8555, Japan
| | - Yuka Sasaki
- Faculty of Agriculture, Yamagata University, 1-23 Wakaba-machi, Tsuruoka, Yamagata, 997-8555, Japan
| | - Shuhei Masuda
- Department of Civil and Environmental Engineering, National Institute of Technology, Akita College, 1-1 Bunkyo-cho, Iijima, Akita, 011-8555, Japan
| | - Fumiaki Takakai
- Faculty of Bioresource Sciences, Akita Prefectural University, 241-438 Aza Kaidobata-Nishi, Shimoshinjo Nakano, Akita, 010-0195, Japan
| | - Nobuo Kaku
- Faculty of Agriculture, Yamagata University, 1-23 Wakaba-machi, Tsuruoka, Yamagata, 997-8555, Japan
| | - Toru Watanabe
- Faculty of Agriculture, Yamagata University, 1-23 Wakaba-machi, Tsuruoka, Yamagata, 997-8555, Japan.
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48
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Calayugan MIC, Formantes AK, Amparado A, Descalsota-Empleo GI, Nha CT, Inabangan-Asilo MA, Swe ZM, Hernandez JE, Borromeo TH, Lalusin AG, Mendioro MS, Diaz MGQ, Viña CBD, Reinke R, Swamy BPM. Genetic Analysis of Agronomic Traits and Grain Iron and Zinc Concentrations in a Doubled Haploid Population of Rice (Oryza sativa L.). Sci Rep 2020; 10:2283. [PMID: 32042046 PMCID: PMC7010768 DOI: 10.1038/s41598-020-59184-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 01/24/2020] [Indexed: 12/28/2022] Open
Abstract
The development of micronutrient dense rice varieties with good agronomic traits is one of the sustainable and cost-effective approaches for reducing malnutrition. Identification of QTLs for high grain Fe and Zn, yield and yield components helps in precise and faster development of high Fe and Zn rice. We carried out a three-season evaluation using IR05F102 x IR69428 derived doubled-haploid population at IRRI. Inclusive composite interval mapping was carried out using SNP markers and Best Linear Unbiased Estimates of the phenotypic traits. A total of 23 QTLs were identified for eight agronomic traits and grain Fe and Zn concentration that explained 7.2 to 22.0% PV. A QTL by environment interaction analysis confirmed the stability of nine QTLs, including two QTLs for Zn on chromosomes 5 and 12. One epistatic interaction for plant height was significant with 28.4% PVE. Moreover, five QTLs were identified for Fe and Zn that harbor several candidate genes, e.g. OsZIP6 on QTL qZn5.1. A number of QTLs were associated with a combination of greater yield and increased grain Zn levels. These results are useful for development of new rice varieties with good agronomic traits and high grain Zn using MAS, and identification of genetic resources with the novel QTLs for grain Zn.
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Affiliation(s)
- Mark Ian C Calayugan
- International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines.,University of the Philippines Los Baños, Laguna, 4031, Philippines
| | - Andrea Kariza Formantes
- International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines.,University of the Philippines Los Baños, Laguna, 4031, Philippines
| | - Amery Amparado
- International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines
| | - Gwen Iris Descalsota-Empleo
- International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines.,University of the Philippines Los Baños, Laguna, 4031, Philippines.,University of the Southern Mindanao, Kabacan, Cotabato, 9407, Philippines
| | - Chau Thanh Nha
- International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines.,Cuu Long Delta Rice Research Institute (CLRRI), Cần Thơ, Vietnam
| | | | - Zin Mar Swe
- International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines.,Department of Agriculture, Yezin, Myanmar
| | - Jose E Hernandez
- University of the Philippines Los Baños, Laguna, 4031, Philippines
| | | | | | | | | | | | - Russell Reinke
- International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines
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Pradhan SK, Pandit E, Pawar S, Naveenkumar R, Barik SR, Mohanty SP, Nayak DK, Ghritlahre SK, Sanjiba Rao D, Reddy JN, Patnaik SSC. Linkage disequilibrium mapping for grain Fe and Zn enhancing QTLs useful for nutrient dense rice breeding. BMC PLANT BIOLOGY 2020; 20:57. [PMID: 32019504 PMCID: PMC7001215 DOI: 10.1186/s12870-020-2262-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 01/20/2020] [Indexed: 05/23/2023]
Abstract
BACKGROUND High yielding rice varieties are usually low in grain iron (Fe) and zinc (Zn) content. These two micronutrients are involved in many enzymatic activities, lack of which cause many disorders in human body. Bio-fortification is a cheaper and easier way to improve the content of these nutrients in rice grain. RESULTS A population panel was prepared representing all the phenotypic classes for grain Fe-Zn content from 485 germplasm lines. The panel was studied for genetic diversity, population structure and association mapping of grain Fe-Zn content in the milled rice. The population showed linkage disequilibrium showing deviation of Hardy-Weinberg's expectation for Fe-Zn content in rice. Population structure at K = 3 categorized the panel population into distinct sub-populations corroborating with their grain Fe-Zn content. STRUCTURE analysis revealed a common primary ancestor for each sub-population. Novel quantitative trait loci (QTLs) namely qFe3.3 and qFe7.3 for grain Fe and qZn2.2, qZn8.3 and qZn12.3 for Zn content were detected using association mapping. Four QTLs, namely qFe3.3, qFe7.3, qFe8.1 and qFe12.2 for grain Fe content were detected to be co-localized with qZn3.1, qZn7, qZn8.3 and qZn12.3 QTLs controlling grain Zn content, respectively. Additionally, some Fe-Zn controlling QTLs were co-localized with the yield component QTLs, qTBGW, OsSPL14 and qPN. The QTLs qFe1.1, qFe3.1, qFe5.1, qFe7.1, qFe8.1, qZn6, qZn7 and gRMm9-1 for grain Fe-Zn content reported in earlier studies were validated in this study. CONCLUSION Novel QTLs, qFe3.3 and qFe7.3 for grain Fe and qZn2.2, qZn8.3 and qZn12.3 for Zn content were detected for these two traits. Four Fe-Zn controlling QTLs and few yield component QTLs were detected to be co-localized. The QTLs, qFe1.1, qFe3.1, qFe5.1, qFe7.1, qFe8.1, qFe3.3, qFe7.3, qZn6, qZn7, qZn2.2, qZn8.3 and qZn12.3 will be useful for biofortification of the micronutrients. Simultaneous enhancement of Fe-Zn content may be possible with yield component traits in rice.
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Affiliation(s)
- S. K. Pradhan
- ICAR-National Rice Research Institute, Cuttack, Odisha India
| | - E. Pandit
- ICAR-National Rice Research Institute, Cuttack, Odisha India
| | - S. Pawar
- ICAR-National Rice Research Institute, Cuttack, Odisha India
| | - R. Naveenkumar
- ICAR-National Rice Research Institute, Cuttack, Odisha India
| | - S. R. Barik
- ICAR-National Rice Research Institute, Cuttack, Odisha India
| | - S. P. Mohanty
- ICAR-National Rice Research Institute, Cuttack, Odisha India
| | - D. K. Nayak
- ICAR-National Rice Research Institute, Cuttack, Odisha India
| | | | - D. Sanjiba Rao
- ICAR-Indian Institute of Rice Research, Hyderabad, India
| | - J. N. Reddy
- ICAR-National Rice Research Institute, Cuttack, Odisha India
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Raza Q, Riaz A, Sabar M, Atif RM, Bashir K. Meta-analysis of grain iron and zinc associated QTLs identified hotspot chromosomal regions and positional candidate genes for breeding biofortified rice. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 288:110214. [PMID: 31521222 DOI: 10.1016/j.plantsci.2019.110214] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 07/13/2019] [Accepted: 08/06/2019] [Indexed: 05/09/2023]
Abstract
Biofortification of staple crops with essential micronutrients is the sustainable way to overcome the hidden hunger. A large number of quantitative trait loci (QTL) linked with grain micronutrient contents have been reported in different mapping studies. Identification of consistent QTLs across diverse genetic backgrounds is useful for candidate gene analysis and marker assisted selection of target traits. In this study, an up to date meta-analysis of grain iron and zinc associated QTLs was performed and 48 meta-QTLs (MQTLs) distributed across 12 rice chromosomes were identified. The 95% confidence intervals of identified genomic regions were significantly narrower than the average of their corresponding original QTLs. A total of 9308 genes/transcripts physically located within or near MQTL regions were retrieved and through prioritization of candidate genes (CGs) 663 non-redundant iron and zinc CGs were selected and studied in detailed. Several functionally characterized iron and zinc homoeostasis related genes e.g OsATM3, OsDMAS1, OsFRO2, OsNAS1-3, OsVIT2, OsYSL16, OsZIP3 and OsZIP7 were also included in our MQTL analysis. More than 64% genes were enriched with zinc and iron binding gene ontology terms and were involved in oxidation reduction process, carbohydrate metabolic process, regulation of transcription, trans-membrane transport, response to oxidative stress, cell redox homeostasis and proteolysis etc. In-silico transcriptomic analysis of rice identified 260 CGs which were regulated in response to iron and zinc stresses. We also identified at least 37 genes which were differentially expressed under both stress conditions and majority of these have not been studied in detailed before. Our results strongly indicate that majority of the MQTLs identified in this study are hotspots for grain iron and zinc concentration and are worth of intensive functional studies in near future.
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Affiliation(s)
- Qasim Raza
- Molecular Breeding Laboratory, Division of Plant Breeding and Genetics, Rice Research Institute, Kala Shah Kaku, Sheikhupura, Pakistan.
| | - Awais Riaz
- Molecular Breeding Laboratory, Division of Plant Breeding and Genetics, Rice Research Institute, Kala Shah Kaku, Sheikhupura, Pakistan
| | - Muhammad Sabar
- Molecular Breeding Laboratory, Division of Plant Breeding and Genetics, Rice Research Institute, Kala Shah Kaku, Sheikhupura, Pakistan
| | - Rana Muhammad Atif
- Department of Plant Breeding and Genetics, University of Agriculture Faisalabad, Pakistan; US-Pak Centre for Advanced Studies in Food and Agricultural Security, University of Agriculture Faisalabad, Pakistan
| | - Khurram Bashir
- Plant Genomic Network Research Team, Center for Sustainable Resource Science, RIKEN, Yokohama Campus, Yokohama, Japan.
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