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Pasion EA, Misra G, Kohli A, Sreenivasulu N. Unraveling the genetics underlying micronutrient signatures of diversity panel present in brown rice through genome-ionome linkages. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 113:749-771. [PMID: 36573652 PMCID: PMC10952705 DOI: 10.1111/tpj.16080] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 12/18/2022] [Accepted: 12/21/2022] [Indexed: 06/17/2023]
Abstract
Rice (Oryza sativa) is an important staple crop to address the Hidden Hunger problem not only in Asia but also in Africa where rice is fast becoming an important source of calories. The brown rice (whole grain with bran) is known to be more nutritious due to elevated mineral composition. The genetics underlying brown rice ionome (sum total of such mineral composition) remains largely unexplored. Hence, we conducted a comprehensive study to dissect the genetic architecture of the brown rice ionome. We used genome-wide association studies, gene set analysis, and targeted association analysis for 12 micronutrients in the brown rice grains. A diverse panel of 300 resequenced indica accessions, with more than 1.02 million single nucleotide polymorphisms, was used. We identified 109 candidate genes with 5-20% phenotypic variation explained for the 12 micronutrients and identified epistatic interactions with multiple micronutrients. Pooling all candidate genes per micronutrient exhibited phenotypic variation explained values ranging from 11% to almost 40%. The key donor lines with larger concentrations for most of the micronutrients possessed superior alleles, which were absent in the breeding lines. Through gene regulatory networks we identified enriched functional pathways for central regulators that were detected as key candidate genes through genome-wide association studies. This study provided important insights on the ionome variations in rice, on the genetic basis of the genome-ionome relationships and on the molecular mechanisms underlying micronutrient signatures.
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Affiliation(s)
| | - Gopal Misra
- International Rice Research InstituteLos BañosLaguna4030Philippines
| | - Ajay Kohli
- International Rice Research InstituteLos BañosLaguna4030Philippines
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Wang W, Xie Y, Liu L, King GJ, White P, Ding G, Wang S, Cai H, Wang C, Xu F, Shi L. Genetic Control of Seed Phytate Accumulation and the Development of Low-Phytate Crops: A Review and Perspective. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:3375-3390. [PMID: 35275483 DOI: 10.1021/acs.jafc.1c06831] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Breeding low phytic acid (lpa) crops is a strategy that has potential to both improve the nutritional quality of food and feed and contribute to the sustainability of agriculture. Here, we review the lipid-independent and -dependent pathways of phytate synthesis and their regulatory mechanisms in plants. We compare the genetic variation of the phytate concentration and distribution in seeds between dicot and monocot species as well as the associated temporal and spatial expression patterns of the genes involved in phytate synthesis and transport. Quantitative trait loci or significant single nucleotide polymorphisms for the seed phytate concentration have been identified in different plant species by linkage and association mapping, and some genes have been cloned from lpa mutants. We summarize the effects of various lpa mutations on important agronomic traits in crop plants and propose SULTR3;3 and SULTR3;4 as optimal target genes for lpa crop breeding.
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Affiliation(s)
- Wei Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, People's Republic of China
- Microelement Research Center, Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, Hubei 430070, People's Republic of China
| | - Yiwen Xie
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, People's Republic of China
- Microelement Research Center, Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, Hubei 430070, People's Republic of China
| | - Lei Liu
- Southern Cross Plant Science, Southern Cross University, Lismore New South Wales 2480, Australia
| | - Graham J King
- Southern Cross Plant Science, Southern Cross University, Lismore New South Wales 2480, Australia
| | - Philip White
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, People's Republic of China
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom
| | - Guangda Ding
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, People's Republic of China
- Microelement Research Center, Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, Hubei 430070, People's Republic of China
| | - Sheliang Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, People's Republic of China
- Microelement Research Center, Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, Hubei 430070, People's Republic of China
| | - Hongmei Cai
- Microelement Research Center, Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, Hubei 430070, People's Republic of China
| | - Chuang Wang
- Microelement Research Center, Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, Hubei 430070, People's Republic of China
| | - Fangsen Xu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, People's Republic of China
- Microelement Research Center, Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, Hubei 430070, People's Republic of China
| | - Lei Shi
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, People's Republic of China
- Microelement Research Center, Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, Hubei 430070, People's Republic of China
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Wang R, Guo S. Phytic acid and its interactions: Contributions to protein functionality, food processing, and safety. Compr Rev Food Sci Food Saf 2021; 20:2081-2105. [DOI: 10.1111/1541-4337.12714] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 12/15/2020] [Accepted: 01/06/2021] [Indexed: 12/16/2022]
Affiliation(s)
- Ruican Wang
- Department of Food Science University of Wisconsin‐Madison Madison Wisconsin USA
| | - Shuntang Guo
- Beijing Key Laboratory of Plant Protein and Cereal Processing, College of Food Science & Nutritional Engineering China Agricultural University Beijing China
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Qamar ZU, Hameed A, Ashraf M, Rizwan M, Akhtar M. Development and Molecular Characterization of Low Phytate Basmati Rice Through Induced Mutagenesis, Hybridization, Backcross, and Marker Assisted Breeding. FRONTIERS IN PLANT SCIENCE 2019; 10:1525. [PMID: 31850026 PMCID: PMC6901921 DOI: 10.3389/fpls.2019.01525] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 11/01/2019] [Indexed: 06/10/2023]
Abstract
Breeding low phytate crops is the most viable solution to tackle mineral deficiencies. The objective of the present study was to develop high yielding, low phytate (lpa) basmati rice cultivars. Three homozygous lpa mutants, Lpa5, Lpa9, and Lpa59, were developed through induced mutations (gamma rays 60Co) and identified by colorimetric and High Performance Liquid Chromatography (HPLC) analysis. These mutants showed 54%-63% reduction in phytic acid but had poor germination and yield. To improve these traits, hybridization and back cross breeding involving Lpa5, Lpa59, and parent cultivar Super Basmati were performed and F2:3, F3:4, BC1F2:3, and BC1F3:4 generations were developed and screened to target the objective. Within the F2:3, homozygous (226), heterozygous (65), and wild type (46) lpa recombinants were identified. Within the homozygous lpa category, four recombinants (Lpa5, Lpa6, Lpa7, and Lpa30) showed improved germination. Within the F3:4 generation, 86 homozygous lpa recombinants were identified. Further selection, on the basis of better plant type and the low phytate trait resulted in the selection of 38 recombinants. Grain quality and cooking characteristics of these selected recombinants were comparable as compared to parent cultivar. Within the BC1F2:3 generations, two homozygous Lpa recombinant lines, Lpa141, and Lpa205, were selected out of 220. Screening of the BC1F3:4 generation for the desirable agronomic and low phytate trait also resulted in the selection of two homozygous lines. Finally, seven recombinants i.e. Lpa12-3, Lpa111-1, Lpa141, Lpa56-3, Lpa53-4, Lpa99-2, and Lpa205-4 out of 42 homozygous low phytate lines were selected on the basis of yield improvement (4%-18%) as compared to parent cultivar. Association analysis suggested that further selection based on primary branches per plant, panicle length and productive tillers per plant would further improve the paddy yield. For molecular characterization of the Lpa trait, previously reported Lpa1-CAPS and Lpa1-InDel and functional molecular markers were applied. Results indicated the absence of the Z9B-Lpa allele and XS-Lpa mutation in the OsMRP5 gene in tested mutants, possibly suggesting that there may be new mutations or novel alleles in tested mutants that need to be identified and then fine mapped for subsequent utilization. To our knowledge, this is the first report of low phytic acid rice mutant development and their improved germination and yield through backcross breeding in basmati rice.
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Affiliation(s)
- Zia-ul- Qamar
- Plant Breeding and Genetics Division, Nuclear Institute for Agriculture and Biology (NIAB), Faisalabad, Pakistan
| | - Amjad Hameed
- Plant Breeding and Genetics Division, Nuclear Institute for Agriculture and Biology (NIAB), Faisalabad, Pakistan
| | - Muhammad Ashraf
- Plant Breeding and Genetics Division, Nuclear Institute for Agriculture and Biology (NIAB), Faisalabad, Pakistan
| | - Muhammad Rizwan
- Plant Breeding and Genetics Division, Nuclear Institute of Agriculture (NIA), Tando Jam (Sindh), Pakistan
| | - Muhammad Akhtar
- Soil and Environmental Sciences Division, Nuclear Institute for Agriculture and Biology (NIAB), Faisalabad, Pakistan
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Thavarajah D, Thavarajah P, Amarakoon D, Fenlason A, Johnson CR, Knutson P, Warkentin TD. Changes in Inositol Phosphates in Low Phytic Acid Field Pea (<i>Pisum sativum</i> L.) Lines during Germination and in Response to Fertilization. ACTA ACUST UNITED AC 2013. [DOI: 10.4236/ajps.2013.42033] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Synthesis of inositol phosphate ligands of plant hormone-receptor complexes: pathways of inositol hexakisphosphate turnover. Biochem J 2012; 444:601-9. [PMID: 22429240 DOI: 10.1042/bj20111811] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Reduction of phytate is a major goal of plant breeding programs to improve the nutritional quality of crops. Remarkably, except for the storage organs of crops such as barley, maize and soybean, we know little of the stereoisomeric composition of inositol phosphates in plant tissues. To investigate the metabolic origins of higher inositol phosphates in photosynthetic tissues, we have radiolabelled leaf tissue of Solanum tuberosum with myo-[2-3H]inositol, undertaken a detailed analysis of inositol phosphate stereoisomerism and permeabilized mesophyll protoplasts in media containing inositol phosphates. We describe the inositol phosphate composition of leaf tissue and identify pathways of inositol phosphate metabolism that we reveal to be common to other kingdoms. Our results identify the metabolic origins of a number of higher inositol phosphates including ones that are precursors of cofactors, or cofactors of plant hormone-receptor complexes. The present study affords alternative explanations of the effects of disruption of inositol phosphate metabolism reported in other species, and identifies different inositol phosphates from that described in photosynthetic tissue of the monocot Spirodela polyrhiza. We define the pathways of inositol hexakisphosphate turnover and shed light on the occurrence of a number of inositol phosphates identified in animals, for which metabolic origins have not been defined.
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