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Nagata K, Nonoue Y, Matsubara K, Mizobuchi R, Ono N, Shibaya T, Ebana K, Ogiso-Tanaka E, Tanabata T, Sugimoto K, Taguchi-Shiobara F, Yonemaru JI, Uga Y, Fukuda A, Ueda T, Yamamoto SI, Yamanouchi U, Takai T, Ikka T, Kondo K, Hoshino T, Yamamoto E, Adachi S, Sun J, Kuya N, Kitomi Y, Iijima K, Nagasaki H, Shomura A, Mizubayashi T, Kitazawa N, Hori K, Ando T, Yamamoto T, Fukuoka S, Yano M. Development of 12 sets of chromosome segment substitution lines that enhance allele mining in Asian cultivated rice. BREEDING SCIENCE 2023; 73:332-342. [PMID: 37840983 PMCID: PMC10570878 DOI: 10.1270/jsbbs.23006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 04/12/2023] [Indexed: 10/17/2023]
Abstract
Many agronomic traits that are important in rice breeding are controlled by multiple genes. The extensive time and effort devoted so far to identifying and selecting such genes are still not enough to target multiple agronomic traits in practical breeding in Japan because of a lack of suitable plant materials in which to efficiently detect and validate beneficial alleles from diverse genetic resources. To facilitate the comprehensive analysis of genetic variation in agronomic traits among Asian cultivated rice, we developed 12 sets of chromosome segment substitution lines (CSSLs) with the japonica background, 11 of them in the same genetic background, using donors representing the genetic diversity of Asian cultivated rice. Using these materials, we overviewed the chromosomal locations of 1079 putative QTLs for seven agronomic traits and their allelic distribution in Asian cultivated rice through multiple linear regression analysis. The CSSLs will allow the effects of putative QTLs in the highly homogeneous japonica background to be validated.
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Affiliation(s)
- Kazufumi Nagata
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Yasunori Nonoue
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Kazuki Matsubara
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Ritsuko Mizobuchi
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Nozomi Ono
- Institute of the Society for Techno-innovation of Agriculture, Forestry and Fisheries, 446-1 Ippaizuka, Kamiyokoba, Tsukuba, Ibaraki 305-0854, Japan
| | - Taeko Shibaya
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Kaworu Ebana
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Eri Ogiso-Tanaka
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Takanari Tanabata
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Kazuhiko Sugimoto
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Fumio Taguchi-Shiobara
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Jun-ichi Yonemaru
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Yusaku Uga
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Atsunori Fukuda
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Tadamasa Ueda
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Shin-ichi Yamamoto
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Utako Yamanouchi
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Toshiyuki Takai
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Takashi Ikka
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Katsuhiko Kondo
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Tomoki Hoshino
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Eiji Yamamoto
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Shunsuke Adachi
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Jian Sun
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Noriyuki Kuya
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Yuka Kitomi
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Ken Iijima
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Hideki Nagasaki
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Ayahiko Shomura
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Tatsumi Mizubayashi
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Noriyuki Kitazawa
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Kiyosumi Hori
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Tsuyu Ando
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Toshio Yamamoto
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Shuichi Fukuoka
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Masahiro Yano
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
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Tang Z, You TT, Li YF, Tang ZX, Bao MQ, Dong G, Xu ZR, Wang P, Zhao FJ. Rapid identification of high and low cadmium (Cd) accumulating rice cultivars using machine learning models with molecular markers and soil Cd levels as input data. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 326:121501. [PMID: 36963454 DOI: 10.1016/j.envpol.2023.121501] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 02/28/2023] [Accepted: 03/21/2023] [Indexed: 06/18/2023]
Abstract
Excessive accumulation of cadmium (Cd) in rice grains threatens food safety and human health. Growing low Cd accumulating rice cultivars is an effective approach to produce low-Cd rice. However, field screening of low-Cd rice cultivars is laborious, time-consuming, and subjected to the influence of environment × genotype interactions. In the present study, we investigated whether machine learning-based methods incorporating genotype and soil Cd concentration can identify high and low-Cd accumulating rice cultivars. One hundred and sixty-seven locally adapted high-yielding rice cultivars were grown in three fields with different soil Cd levels and genotyped using four molecular markers related to grain Cd accumulation. We identified sixteen cultivars as stable low-Cd accumulators with grain Cd concentrations below the 0.2 mg kg-1 food safety limit in all three paddy fields. In addition, we developed eight machine learning-based models to predict low- and high-Cd accumulating rice cultivars with genotypes and soil Cd levels as input data. The optimized model classifies low- or high-Cd cultivars (i.e., the grain Cd concentration below or above 0.2 mg kg-1) with an overall accuracy of 76%. These results indicate that machine learning-based classification models constructed with molecular markers and soil Cd levels can quickly and accurately identify the high- and low-Cd accumulating rice cultivars.
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Affiliation(s)
- Zhong Tang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ting-Ting You
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ya-Fang Li
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhi-Xian Tang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Miao-Qing Bao
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ge Dong
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhong-Rui Xu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Peng Wang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China; Centre for Agriculture and Health, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Fang-Jie Zhao
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
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Zulfiqar U, Jiang W, Xiukang W, Hussain S, Ahmad M, Maqsood MF, Ali N, Ishfaq M, Kaleem M, Haider FU, Farooq N, Naveed M, Kucerik J, Brtnicky M, Mustafa A. Cadmium Phytotoxicity, Tolerance, and Advanced Remediation Approaches in Agricultural Soils; A Comprehensive Review. FRONTIERS IN PLANT SCIENCE 2022; 13:773815. [PMID: 35371142 PMCID: PMC8965506 DOI: 10.3389/fpls.2022.773815] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 02/02/2022] [Indexed: 05/03/2023]
Abstract
Cadmium (Cd) is a major environmental contaminant due to its widespread industrial use. Cd contamination of soil and water is rather classical but has emerged as a recent problem. Cd toxicity causes a range of damages to plants ranging from germination to yield suppression. Plant physiological functions, i.e., water interactions, essential mineral uptake, and photosynthesis, are also harmed by Cd. Plants have also shown metabolic changes because of Cd exposure either as direct impact on enzymes or other metabolites, or because of its propensity to produce reactive oxygen species, which can induce oxidative stress. In recent years, there has been increased interest in the potential of plants with ability to accumulate or stabilize Cd compounds for bioremediation of Cd pollution. Here, we critically review the chemistry of Cd and its dynamics in soil and the rhizosphere, toxic effects on plant growth, and yield formation. To conserve the environment and resources, chemical/biological remediation processes for Cd and their efficacy have been summarized in this review. Modulation of plant growth regulators such as cytokinins, ethylene, gibberellins, auxins, abscisic acid, polyamines, jasmonic acid, brassinosteroids, and nitric oxide has been highlighted. Development of plant genotypes with restricted Cd uptake and reduced accumulation in edible portions by conventional and marker-assisted breeding are also presented. In this regard, use of molecular techniques including identification of QTLs, CRISPR/Cas9, and functional genomics to enhance the adverse impacts of Cd in plants may be quite helpful. The review's results should aid in the development of novel and suitable solutions for limiting Cd bioavailability and toxicity, as well as the long-term management of Cd-polluted soils, therefore reducing environmental and human health hazards.
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Affiliation(s)
- Usman Zulfiqar
- Department of Agronomy, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Wenting Jiang
- College of Life Sciences, Yan’an University, Yan’an, China
| | - Wang Xiukang
- College of Life Sciences, Yan’an University, Yan’an, China
| | - Saddam Hussain
- Department of Agronomy, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Muhammad Ahmad
- Department of Agronomy, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | | | - Nauman Ali
- Agronomic Research Institute, Ayub Agricultural Research Institute, Faisalabad, Pakistan
| | - Muhammad Ishfaq
- Department of Agronomy, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Muhammad Kaleem
- Department of Botany, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Fasih Ullah Haider
- College of Resources and Environmental Sciences, Gansu Agricultural University, Lanzhou, China
| | - Naila Farooq
- Department of Soil and Environmental Science, College of Agriculture, University of Sargodha, Sargodha, Pakistan
| | - Muhammad Naveed
- Institute of Soil and Environmental Science, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Jiri Kucerik
- Institute of Chemistry and Technology of Environmental Protection, Faculty of Chemistry, Brno University of Technology, Brno, Czechia
| | - Martin Brtnicky
- Institute of Chemistry and Technology of Environmental Protection, Faculty of Chemistry, Brno University of Technology, Brno, Czechia
- Department of Agrochemistry, Soil Science, Microbiology and Plant Nutrition, Faculty of AgriSciences, Mendel University in Brno, Brno, Czechia
| | - Adnan Mustafa
- Institute of Chemistry and Technology of Environmental Protection, Faculty of Chemistry, Brno University of Technology, Brno, Czechia
- Department of Agrochemistry, Soil Science, Microbiology and Plant Nutrition, Faculty of AgriSciences, Mendel University in Brno, Brno, Czechia
- Institute for Environmental Studies, Faculty of Science, Charles University in Prague, Prague, Czechia
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Abstract
Cadmium (Cd) is an element that is nonessential and extremely toxic to both plants and human beings. Soil contaminated with Cd has adverse impacts on crop yields and threatens human health via the food chain. Cultivation of low-Cd cultivars has been of particular interest and is one of the most cost-effective and promising approaches to minimize human dietary intake of Cd. Low-Cd crop cultivars should meet particular criteria, including acceptable yield and quality, and their edible parts should have Cd concentrations below maximum permissible concentrations for safe consumption, even when grown in Cd-contaminated soil. Several low-Cd cereal cultivars and genotypes have been developed worldwide through cultivar screening and conventional breeding. Molecular markers are powerful in facilitating the selection of low-Cd cereal cultivars. Modern molecular breeding technologies may have great potential in breeding programs for the development of low-Cd cultivars, especially when coupled with conventional breeding. In this review, we provide a synthesis of low-Cd cereal breeding.
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Affiliation(s)
- Qin Chen
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Fei-Bo Wu
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
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Exploring the Loci Responsible for Awn Development in Rice through Comparative Analysis of All AA Genome Species. PLANTS 2021; 10:plants10040725. [PMID: 33917982 PMCID: PMC8068336 DOI: 10.3390/plants10040725] [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: 03/01/2021] [Revised: 03/31/2021] [Accepted: 04/06/2021] [Indexed: 11/17/2022]
Abstract
Wild rice species have long awns at their seed tips, but this trait has been lost through rice domestication. Awn loss mitigates harvest and seed storage; further, awnlessness increases the grain number and, subsequently, improves grain yield in Asian cultivated rice, highlighting the contribution of the loss of awn to modern rice agriculture. Therefore, identifying the genes regulating awn development would facilitate the elucidation of a part of the domestication process in rice and increase our understanding of the complex mechanism in awn morphogenesis. To identify the novel loci regulating awn development and understand the conservation of genes in other wild rice relatives belonging to the AA genome group, we analyzed the chromosome segment substitution lines (CSSL). In this study, we compared a number of CSSL sets derived by crossing wild rice species in the AA genome group with the cultivated species Oryza sativa ssp. japonica. Two loci on chromosomes 7 and 11 were newly discovered to be responsible for awn development. We also found wild relatives that were used as donor parents of the CSSLs carrying the functional alleles responsible for awn elongation, REGULATOR OF AWN ELONGATION 1 (RAE1) and RAE2. To understand the conserveness of RAE1 and RAE2 in wild rice relatives, we analyzed RAE1 and RAE2 sequences of 175 accessions among diverse AA genome species retrieved from the sequence read archive (SRA) database. Comparative sequence analysis demonstrated that most wild rice AA genome species maintained functional RAE1 and RAE2, whereas most Asian rice cultivars have lost either or both functions. In addition, some different loss-of-function alleles of RAE1 and RAE2 were found in Asian cultivated species. These findings suggest that different combinations of dysfunctional alleles of RAE1 and RAE2 were selected after the speciation of O. sativa, and that two-step loss of function in RAE1 and RAE2 contributed to awnlessness in Asian cultivated rice.
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Validating a segment on chromosome 7 of japonica for establishing low-cadmium accumulating indica rice variety. Sci Rep 2021; 11:6053. [PMID: 33723281 PMCID: PMC7961068 DOI: 10.1038/s41598-021-85324-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 02/23/2021] [Indexed: 11/08/2022] Open
Abstract
Cadmium (Cd) contamination of rice is a serious food safety issue that has recently been gaining significant public attention. Therefore, reduction of Cd accumulation in rice grains is an important objective of rice breeding. The use of favourable alleles of Cd accumulating genes using marker-assisted selection (MAS) is theoretically feasible. In this study, we validated a segment covering OsHMA3-OsNramp5-OsNramp1 on chromosome 7 of japonica for establishing low-cadmium accumulating indica rice variety. The OsHMA3-OsNramp5-OsNramp1jap haplotype significantly decreased grain Cd concentration in middle-season indica genetic background. The improved 9311 carrying the OsHMA3-OsNramp5-OsNramp1jap haplotype with recurrent parent genome recovery of up to 91.6% resulted in approximately 31.8% decrease in Cd accumulation in the grain and with no penalty on yield. There is a genetic linkage-drag between OsHMA3-OsNramp5-OsNramp1 jap and the gene conditioning heading to days (HTD) in the early-season indica genetic background. Because the OsHMA3-OsNramp5-OsNramp1-Ghd7jap haplotype significantly increases grain Cd concentration and prolongs growth duration, the linkage-drag between OsHMA3-OsNramp5-OsNramp1 and Ghd7 should be broken down by large segregating populations or gene editing. A novel allele of OsHMA3 was identified from a wide-compatibility japonica cultivar, the expression differences of OsNramp1 and OsNramp5 in roots might contribute the Cd accumulating variation between japonica and indica variety.
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Chen Q, Tang W, Zeng G, Sheng H, Shi W, Xiao Y. Reduction of cadmium accumulation in the grains of male sterile rice Chuang-5S carrying Pi48 or Pi49 through marker-assisted selection. 3 Biotech 2020; 10:539. [PMID: 33224708 PMCID: PMC7672139 DOI: 10.1007/s13205-020-02533-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 10/29/2020] [Indexed: 10/23/2022] Open
Abstract
To reduce cadmium (Cd) accumulation in the grains of rice Chuang-5S (C5S), a gene OsHMA3 and a QTL qlGCd3 related to low-Cd accumulation were separately introgressed into the recipient parent C5S (male sterile line) by molecular marker-assisted breeding. The recurrent parent C5S was then replaced by NIL (near-isogenic line)-C5S with the blast resistance gene Pi48 or Pi49 to construct the BC2F1 generation. Finally, two groups of improved materials of C5S, which pyramided the gene/QTL associated with low-Cd accumulation and blast resistance gene, were developed. The Cd accumulation, agronomic traits, genetic background and blast resistance of these improved C5S materials were evaluated. The results showed that the average Cd content of improved C5S material carrying OsHMA3 and qlGCd3 was, respectively, reduced by 52.8% and 50.8% compared with that of C5S, indicating that the gene related to low-Cd accumulation was, successfully, transferred to C5S with stable expression. The main agronomic traits of the improved materials were consistent with those of C5S. Besides, the improved C5S lines showed stronger blast resistance than C5S and more than 88% similarity to the genetic background of C5S. These two groups of improved materials may be further utilized for the breeding of advanced male sterile lines or superior hybrid rice.
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Affiliation(s)
- Qiuhong Chen
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops, Hunan Agricultural University, Changsha 410128, China
| | - Wei Tang
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops, Hunan Agricultural University, Changsha 410128, China
| | - Gai Zeng
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops, Hunan Agricultural University, Changsha 410128, China
| | - Haowen Sheng
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops, Hunan Agricultural University, Changsha 410128, China
| | - Weijie Shi
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops, Hunan Agricultural University, Changsha 410128, China
| | - Yinghui Xiao
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops, Hunan Agricultural University, Changsha 410128, China
- Beidahuang Kenfeng Seed Co., Ltd., Harbin, 150090 China
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Mizobuchi R, Fukuoka S, Tsuiki C, Tsushima S, Sato H. Evaluation of major rice cultivars for resistance to bacterial seedling rot caused by Burkholderia glumae and identification of Japanese standard cultivars for resistance assessments. BREEDING SCIENCE 2020; 70:221-230. [PMID: 32523404 PMCID: PMC7272248 DOI: 10.1270/jsbbs.19117] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 11/28/2019] [Indexed: 06/11/2023]
Abstract
Burkholderia glumae causes bacterial seedling rot (BSR) and bacterial grain rot (BGR) in rice (Oryza sativa), both of which are important diseases in Japan. We previously evaluated major Japanese cultivars for BGR resistance and selected standard cultivars for resistance assessments. Here, we assessed the BSR occurrence rate in cultivars from the World Rice Collection (WRC) and other sources and found wide variation in resistance. Next, we evaluated major Japanese cultivars for BSR resistance and found that two Japanese landraces, 'Kujuu' and 'Aikoku', showed "strong" resistance; most others were categorized as "medium" or "medium to weak". We previously developed a near-isogenic line (RBG1-NIL) by introducing the genomic region containing RBG1, a quantitative trait locus (QTL) for BSR resistance, from 'Nona Bokra' (indica) into 'Koshihikari' (temperate japonica). The resistance level of RBG1-NIL was "strong", indicating the effectiveness of RBG1 against BSR. The correlation between BSR and BGR resistance scores was low, indicating that it is necessary to introduce QTLs for resistance from different sources to develop cultivars resistant to both BSR and BGR. On the basis of the screening results, we selected standard cultivars for BSR resistance to cover a range of resistance levels.
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Affiliation(s)
- Ritsuko Mizobuchi
- Institute of Crop Science, NARO (National Agriculture and Food Research Organization), 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Shuichi Fukuoka
- Institute of Crop Science, NARO (National Agriculture and Food Research Organization), 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Chikako Tsuiki
- Institute of Crop Science, NARO (National Agriculture and Food Research Organization), 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Seiya Tsushima
- Department of Molecular Microbiology, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo 156-8502, Japan
| | - Hiroyuki Sato
- Institute of Crop Science, NARO (National Agriculture and Food Research Organization), 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
- Ministry of Agriculture, Forestry and Fisheries, 1-2-1 Kasumigaseki, Chiyoda-ku, Tokyo 100-8950, Japan
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Guo J, Li K, Zhang X, Huang H, Huang F, Zhang L, Wang Y, Li T, Yu H. Genetic properties of cadmium translocation from straw to brown rice in low-grain cadmium rice (Oryza sativa L.) line. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2019; 182:109422. [PMID: 31301594 DOI: 10.1016/j.ecoenv.2019.109422] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 07/02/2019] [Accepted: 07/04/2019] [Indexed: 06/10/2023]
Abstract
Breeding the rice cultivar with high cadmium (Cd) accumulation in straw but with low Cd in brown rice using marker-assisted selection (MAS) based on quantitative trait loci (QTL) is meaningful for phytoremediation as well as safety in production. A restorer rice line, YaHui2816, steadily showed low Cd translocation from straw to brown rice and carried alleles for reducing Cd concentration in brown rice (BRCdC). In this study, one F2 population (C268A/YaHui2816) was used to identify the QTLs for BRCdC in 2016, and other two different F2 populations (Lu98A/YaHui2816 and 5406A/YaHui2816) were used to furtherly validate the QTLs in 2017. Furthermore, a pot experiment was conducted to investigate the relative expression of predicted genes in the regions of these QTLs for BRCdC. Here 4 QTLs for BRCdC were identified, among which, 2 novel QTLs (qBRCdC-9 and qBRCdC-12) were identified on chromosomes 9 and 12 in rice. The YaHui2816 alleles in the QTLs qBRCdC-9 and qBRCdC-12 could effectively reduce BRCdC under different genetic backgrounds. Importantly, the QTL qBRCdC-12 was simultaneously associated with the Cd translocation from shoot to brown rice (T-s-b), genetically explaining that the low T-s-b of the YaHui2816 resulted in its low BRCdC. The interval length of the QTL qBRCdC-12 was only narrowed to 0.28 cM, making it possible to develop molecular markers and excavate genes for reducing BRCdC. It is worth noting that genes existed in these QTL regions have not been reported for regulating the Cd translocation in rice. 6 candidate genes (OS05G0198400, OS05G0178300, OS09G0544400, OS12G0161100, OS12G0162100 and OS12G0165200) up-regulated expressed in nodeⅡof the YaHui2816 in response to Cd treatment, and encoded ZRT/IRT-like protein (ZIP) 4, the protein similar to glutathione transferase (GSTs) 16, heat shock protein Hsp20 domain containing protein, MAP kinase-like protein and Cd tolerant protein 5, respectively.
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Affiliation(s)
- Jingyi Guo
- College of Resource Science & Technology, Sichuan Agricultural University, 211 Huimin Road, Chengdu, Sichuan, 611130, China
| | - Kun Li
- College of Resource Science & Technology, Sichuan Agricultural University, 211 Huimin Road, Chengdu, Sichuan, 611130, China
| | - Xizhou Zhang
- College of Resource Science & Technology, Sichuan Agricultural University, 211 Huimin Road, Chengdu, Sichuan, 611130, China
| | - Huagang Huang
- College of Resource Science & Technology, Sichuan Agricultural University, 211 Huimin Road, Chengdu, Sichuan, 611130, China
| | - Fu Huang
- College of Agronomy, Sichuan Agricultural University, 211 Huimin Road, Chengdu, Sichuan, 611130, China
| | - Lu Zhang
- College of Resource Science & Technology, Sichuan Agricultural University, 211 Huimin Road, Chengdu, Sichuan, 611130, China
| | - Yongdong Wang
- College of Resource Science & Technology, Sichuan Agricultural University, 211 Huimin Road, Chengdu, Sichuan, 611130, China
| | - Tingxuan Li
- College of Resource Science & Technology, Sichuan Agricultural University, 211 Huimin Road, Chengdu, Sichuan, 611130, China.
| | - Haiying Yu
- College of Resource Science & Technology, Sichuan Agricultural University, 211 Huimin Road, Chengdu, Sichuan, 611130, China.
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10
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Clemens S. Safer food through plant science: reducing toxic element accumulation in crops. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:5537-5557. [PMID: 31408148 DOI: 10.1093/jxb/erz366] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 07/31/2019] [Indexed: 05/24/2023]
Abstract
Natural processes and human activities have caused widespread background contamination with non-essential toxic elements. The uptake and accumulation of cadmium (Cd), arsenic (As), and lead (Pb) by crop plants results in chronic dietary exposure and is associated with various health risks. Current human intake levels are close to what is provisionally regarded as safe. This has recently triggered legislative actions to introduce or lower limits for toxic elements in food. Arguably, the most effective way to reduce the risk of slow poisoning is the breeding of crops with much lower accumulation of contaminants. The past years have seen tremendous progress in elucidating molecular mechanisms of toxic element transport. This was achieved in the model systems Arabidopsis thaliana and, most importantly, rice, the major source of exposure to As and Cd for a large fraction of the global population. Many components of entry and sequestration pathways have been identified. This knowledge can now be applied to engineer crops with reduced toxic element accumulation especially in edible organs. Most obvious in the case of Cd, it appears likely that subtle genetic intervention has the potential to reduce human exposure to non-essential toxic elements almost immediately. This review outlines the risks and discusses our current state of knowledge with emphasis on transgenic and gene editing approaches.
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Affiliation(s)
- Stephan Clemens
- Department of Plant Physiology, and Bayreuth Center of Ecology and Environmental Research, University of Bayreuth, Bayreuth, Germany
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11
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Chen J, Zou W, Meng L, Fan X, Xu G, Ye G. Advances in the Uptake and Transport Mechanisms and QTLs Mapping of Cadmium in Rice. Int J Mol Sci 2019; 20:ijms20143417. [PMID: 31336794 PMCID: PMC6678204 DOI: 10.3390/ijms20143417] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 07/10/2019] [Accepted: 07/11/2019] [Indexed: 02/07/2023] Open
Abstract
Cadmium (Cd), as a heavy metal, presents substantial biological toxicity and has harmful effects on human health. To lower the ingress levels of human Cd, it is necessary for Cd content in food crops to be reduced, which is of considerable significance for ensuring food safety. This review will summarize the genetic traits of Cd accumulation in rice and examine the mechanism of Cd uptake and translocation in rice. The status of genes related to Cd stress and Cd accumulation in rice in recent years will be summarized, and the genes related to Cd accumulation in rice will be classified according to their functions. In addition, an overview of quantitative trait loci (QTLs) mapping populations in rice will be introduced, aiming to provide a theoretical reference for the breeding of rice varieties with low Cd accumulation. Finally, existing problems and prospects will be put forward.
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Affiliation(s)
- Jingguang Chen
- CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute in Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Wenli Zou
- CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute in Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Lijun Meng
- CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute in Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China.
| | - Xiaorong Fan
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China.
| | - Guohua Xu
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Guoyou Ye
- CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute in Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- Strategic Innovation Platform, International Rice Research Institute, DAPO Box 7777, Metro Manila 1226, Philippines
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12
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Cao ZZ, Lin XY, Yang YJ, Guan MY, Xu P, Chen MX. Gene identification and transcriptome analysis of low cadmium accumulation rice mutant (lcd1) in response to cadmium stress using MutMap and RNA-seq. BMC PLANT BIOLOGY 2019; 19:250. [PMID: 31185911 PMCID: PMC6560816 DOI: 10.1186/s12870-019-1867-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 06/03/2019] [Indexed: 05/29/2023]
Abstract
BACKGROUND Cadmium (Cd) is a widespread toxic heavy metal pollutant in agricultural soil, and Cd accumulation in rice grains is a major intake source of Cd for Asian populations that adversely affect human health. However, the molecular mechanism underlying Cd uptake, translocation and accumulation has not been fully understood in rice plants. RESULTS In this study, a mutant displaying extremely low Cd accumulation (lcd1) in rice plant and grain was generated by EMS mutagenesis from indica rice cultivar 9311 seeds. The candidate SNPs associated with low Cd accumulation phenotype in the lcd1 mutant were identified by MutMap and the transcriptome changes between lcd1 and WT under Cd exposure were analyzed by RNA-seq. The lcd1 mutant had lower Cd uptake and accumulation in rice root and shoot, as well as less growth inhibition compared with WT in the presence of 5 μM Cd. Genetic analysis showed that lcd1 was a single locus recessive mutation. The SNP responsible for low Cd accumulation in the lcd1 mutant located at position 8,887,787 on chromosome 7, corresponding to the seventh exon of OsNRAMP5. This SNP led to a Pro236Leu amino acid substitution in the highly conserved region of OsNRAMP5 in the lcd1 mutant. A total of 1208 genes were differentially expressed between lcd1 and WT roots under Cd exposure, and DEGs were enriched in transmembrane transport process GO term. Increased OsHMA3 expression probably adds to the effect of OsNRAMP5 mutation to account for the significant decreases in Cd accumulation in rice plant and grain of the lcd1 mutant. CONCLUSIONS An extremely low Cd mutant lcd1 was isolated and identified using MutMap and RNA-seq. A Pro236Leu amino acid substitution in the highly conserved region of OsNRAMP5 is likely responsible for low Cd accumulation in the lcd1 mutant. This work provides more insight into the mechanism of Cd uptake and accumulation in rice, and will be helpful for developing low Cd accumulation rice by marker-assisted breeding.
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Affiliation(s)
- Zhen Zhen Cao
- Rice Product Quality Supervision and Inspection Center, China National Rice Research Institute, Hangzhou 310006, PR, No.28 Shuidaosuo Rd., Fuyang, 311400 Zhejiang China
| | - Xiao Yan Lin
- Rice Product Quality Supervision and Inspection Center, China National Rice Research Institute, Hangzhou 310006, PR, No.28 Shuidaosuo Rd., Fuyang, 311400 Zhejiang China
| | - Yong Jie Yang
- Rice Product Quality Supervision and Inspection Center, China National Rice Research Institute, Hangzhou 310006, PR, No.28 Shuidaosuo Rd., Fuyang, 311400 Zhejiang China
| | - Mei Yan Guan
- Rice Product Quality Supervision and Inspection Center, China National Rice Research Institute, Hangzhou 310006, PR, No.28 Shuidaosuo Rd., Fuyang, 311400 Zhejiang China
| | - Ping Xu
- Rice Product Quality Supervision and Inspection Center, China National Rice Research Institute, Hangzhou 310006, PR, No.28 Shuidaosuo Rd., Fuyang, 311400 Zhejiang China
| | - Ming Xue Chen
- Rice Product Quality Supervision and Inspection Center, China National Rice Research Institute, Hangzhou 310006, PR, No.28 Shuidaosuo Rd., Fuyang, 311400 Zhejiang China
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13
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Sui F, Zhao D, Zhu H, Gong Y, Tang Z, Huang XY, Zhang G, Zhao FJ. Map-based cloning of a new total loss-of-function allele of OsHMA3 causes high cadmium accumulation in rice grain. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:2857-2871. [PMID: 30840768 DOI: 10.1093/jxb/erz093] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2018] [Accepted: 02/12/2019] [Indexed: 05/18/2023]
Abstract
Rice (Oryza sativa) is a major dietary source of the toxic metal cadmium (Cd). Reducing Cd transfer from soil to the rice grain is important for food safety. Rice cultivars vary widely in their Cd accumulation, but the genetic basis for this variation is not fully understood. Based on field and pot experiments comparing 26 rice cultivars, we identified a cultivar with high Cd accumulation in grain (BG367, coded as W4) and a cultivar with low grain Cd accumulation (Huajingxian 74, coded as W0). W4 showed a higher Cd translocation from roots to shoots than W0. Using chromosome single segment substitution lines derived from the two cultivars, we mapped a quantitative trait locus for Cd accumulation in grain to a 400 kb region in chromosome 7. Using yeast expression assays and transgenic complementation, we identified OsHMA3 as the causal gene at this locus. Compared with OsHMA3W0, OsHMA3W4 has a deletion of 14 amino acids predicted to be in the ATP binding domain. OsHMA3W4 showed a complete loss of transport activity for Cd in yeast assays. Taking our findings together, we have identified a new allele of OsHMA3 with a total loss-of-function, resulting in greatly elevated Cd translocation to rice shoots and grain.
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Affiliation(s)
- Fuqing Sui
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Dikun Zhao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Haitao Zhu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
| | - Yongfu Gong
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
| | - Zhong Tang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Xin-Yuan Huang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Guiquan Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
| | - Fang-Jie Zhao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
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14
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Kitazawa N, Shomura A, Mizubayashi T, Ando T, Nagata K, Hayashi N, Takahashi A, Yamanouchi U, Fukuoka S. Rapid DNA-genotyping system targeting ten loci for resistance to blast disease in rice. BREEDING SCIENCE 2019; 69:68-83. [PMID: 31086485 PMCID: PMC6507720 DOI: 10.1270/jsbbs.18143] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 10/13/2018] [Indexed: 06/09/2023]
Abstract
The fungal pathogen Pyricularia oryzae causes blast, a severe disease of rice (Oryza sativa L.). Improving blast resistance is important in rice breeding programs. Inoculation tests have been used to select for resistance genotypes, with DNA marker-based selection becoming an efficient alternative. No comprehensive DNA marker system for race-specific resistance alleles in the Japanese rice breeding program has been developed because some loci contain multiple resistance alleles. Here, we used the Fluidigm SNP genotyping platform to determine a set of 96 single nucleotide polymorphism (SNP) markers for 10 loci with race-specific resistance. The markers were then used to evaluate the presence or absence of 24 resistance alleles in 369 cultivars; results were 93.5% consistent with reported inoculation test-based genotypes in japonica varieties. The evaluation system was successfully applied to high-yield varieties with indica genetic backgrounds. The system includes polymorphisms that distinguish the resistant alleles at the tightly linked Pita and Pita-2 loci, thereby confirming that all the tested cultivars with Pita-2 allele carry Pita allele. We also developed and validated insertion/deletion (InDel) markers for ten resistance loci. Combining SNP and InDel markers is an accurate and efficient strategy for selection for race-specific resistance to blast in breeding programs.
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Affiliation(s)
- Noriyuki Kitazawa
- Institute of Crop Science, National Agriculture and Food Research Organization,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518,
Japan
| | - Ayahiko Shomura
- Institute of Crop Science, National Agriculture and Food Research Organization,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518,
Japan
| | - Tatsumi Mizubayashi
- Institute of Crop Science, National Agriculture and Food Research Organization,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518,
Japan
| | - Tsuyu Ando
- Institute of Crop Science, National Agriculture and Food Research Organization,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518,
Japan
| | - Kazufumi Nagata
- Institute of Crop Science, National Agriculture and Food Research Organization,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518,
Japan
| | - Nagao Hayashi
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518,
Japan
| | - Akira Takahashi
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518,
Japan
| | - Utako Yamanouchi
- Institute of Crop Science, National Agriculture and Food Research Organization,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518,
Japan
| | - Shuichi Fukuoka
- Institute of Crop Science, National Agriculture and Food Research Organization,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518,
Japan
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15
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Mulsanti IW, Yamamoto T, Ueda T, Samadi AF, Kamahora E, Rumanti IA, Thanh VC, Adachi S, Suzuki S, Kanekatsu M, Hirasawa T, Ookawa T. Finding the superior allele of japonica-type for increasing stem lodging resistance in indica rice varieties using chromosome segment substitution lines. RICE 2018; 11:25. [PMID: 29671092 PMCID: PMC5906422 DOI: 10.1186/s12284-018-0216-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 04/04/2018] [Indexed: 05/04/2023]
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16
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Zhao J, Yang W, Zhang S, Yang T, Liu Q, Dong J, Fu H, Mao X, Liu B. Genome-wide association study and candidate gene analysis of rice cadmium accumulation in grain in a diverse rice collection. RICE (NEW YORK, N.Y.) 2018; 11:61. [PMID: 30465288 PMCID: PMC6249348 DOI: 10.1186/s12284-018-0254-x] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 11/14/2018] [Indexed: 05/05/2023]
Abstract
BACKGROUND Cadmium (Cd) accumulation in rice followed by transfer to the food chain causes severe health problems in humans. Breeding of low Cd accumulation varieties is one of the most economical ways to solve the problem. However, information on the identity of rice germplasm with low Cd accumulation is limited, particularly in indica, and the genetic basis of Cd accumulation in rice is not well understood. RESULTS Screening of 312 diverse rice accessions revealed that the grain Cd concentrations of these rice accessions ranged from 0.12 to 1.23 mg/kg, with 24 accessions less than 0.20 mg/kg. Three of the 24 accessions belong to indica. Japonica accumulated significantly less Cd than indica (p < 0.001), while tropical japonica accumulated significantly less Cd than temperate japonica (p < 0.01). GWAS in all accessions identified 14 QTLs for Cd accumulation, with 7 identified in indica and 7 identified in japonica subpopulations. No common QTL was identified between indica and japonica. The previously identified genes (OsHMA3, OsNRAMP1, and OsNRAMP5) from japonica were colocalized with QTLs identified in japonica instead of indica. Expression analysis of OsNRAMP2, the candidate gene of the novel QTL (qCd3-2) identified in the present study, demonstrated that OsNRAMP2 was mainly induced in the shoots of high Cd accumulation accessions after Cd treatment. Four amino acid differences were found in the open reading frame of OsNRAMP2 between high and low Cd accumulation accessions. The allele from low Cd accumulation accessions significantly increased the Cd sensitivity and accumulation in yeast. Subcellular localization analysis demonstrated OsNRAMP2 expressed in the tonoplast of rice protoplast. CONCLUSION The results suggest that grain Cd concentrations are significantly different among subgroups, with Cd concentrations decreasing from indica to temperate japonica to tropical japonica. However, considerable variations exist within subgroups. The fact that no common QTL was identified between indica and japonica implies that there is a different genetic basis for determining Cd accumulation between indica and japonica, or that some QTLs for Cd accumulation in rice are subspecies-specific. Through further integrated analysis, it is speculated that OsNRAMP2 could be a novel functional gene associated with Cd accumulation in rice.
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Affiliation(s)
- Junliang Zhao
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640 China
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
| | - Wu Yang
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640 China
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
| | - Shaohong Zhang
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640 China
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
| | - Tifeng Yang
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640 China
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
| | - Qin Liu
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640 China
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
| | - Jingfang Dong
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640 China
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
| | - Hua Fu
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640 China
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
| | - Xingxue Mao
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640 China
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
| | - Bin Liu
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640 China
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
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17
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Itoh H, Wada KC, Sakai H, Shibasaki K, Fukuoka S, Wu J, Yonemaru JI, Yano M, Izawa T. Genomic adaptation of flowering-time genes during the expansion of rice cultivation area. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 94:895-909. [PMID: 29570873 DOI: 10.1111/tpj.13906] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 03/02/2018] [Accepted: 03/09/2018] [Indexed: 05/04/2023]
Abstract
The diversification of flowering time in response to natural environments is critical for the spread of crops to diverse geographic regions. In contrast with recent advances in understanding the molecular basis of photoperiodic flowering in rice (Oryza sativa), little is known about how flowering-time diversification is structured within rice subspecies. By analyzing genome sequencing data and a set of 429 chromosome segment substitution lines (CSSLs) originating from 10 diverse rice accessions with wide distributions, we revealed diverse effects of allelic variations for common flowering-time quantitative trait loci in the recipient's background. Although functional variations associated with a few loci corresponded to standing variations among subspecies, the identified functional nucleotide polymorphisms occurred recently after rice subgroup differentiation, indicating that the functional diversity of flowering-time gene sequences was not particularly associated with phylogenetic relationship between rice subspecies. Intensive analysis of the Hd1 genomic region identified the signature of an early introgression of the Hd1 with key mutation(s) in aus and temperate japonica accessions. Our data suggested that, after such key introgressions, new mutations were selected and accelerated the flowering-time diversity within subspecies during the expansion of rice cultivation area. This finding may imply that new genome-wide changes for flowering-time adaptation are one of the critical determinants for establishing genomic architecture of local rice subgroups. In-depth analyses of various rice genomes coupling with the genetically confirmed phenotypic changes in a large set of CSSLs enabled us to demonstrate how rice genome dynamics has coordinated with the adaptation of cultivated rice during the expansion of cultivation area.
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Affiliation(s)
- Hironori Itoh
- Functional Plant Research Unit, National Institute of Agrobiological Sciences (NIAS), 2-1-2 Kannondai, 305-8602, Tsukuba, Japan
- National Agriculture and Food Research Organization, Institute of Crop Science, NARO (NICS), Kannondai 2-1-2, 305-8518, Tsukuba, Japan
| | - Kaede C Wada
- Functional Plant Research Unit, National Institute of Agrobiological Sciences (NIAS), 2-1-2 Kannondai, 305-8602, Tsukuba, Japan
- Horticultural Research Institute, Ibaraki Agricultural Center, Ago 3165-1, 319-0292, Kasama, Japan
| | - Hiroaki Sakai
- Agrogenomics Research Center, NIAS, Kannondai 2-1-2, 305-8602, Tsukuba, Japan
- Advanced Analysis Center, NARO, Kannondai 2-1-2, 305-8602, Tsukuba, Japan
| | - Kyohei Shibasaki
- Functional Plant Research Unit, National Institute of Agrobiological Sciences (NIAS), 2-1-2 Kannondai, 305-8602, Tsukuba, Japan
- RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro, Tsurumi, 230-0045, Yokohama, Japan
| | - Shuichi Fukuoka
- National Agriculture and Food Research Organization, Institute of Crop Science, NARO (NICS), Kannondai 2-1-2, 305-8518, Tsukuba, Japan
- Rice Applied Genomics Research Unit, NIAS, 2-1-2 Kannondai, 305-8602, Tsukuba, Japan
| | - Jianzhong Wu
- Agrogenomics Research Center, NIAS, Kannondai 2-1-2, 305-8602, Tsukuba, Japan
- Advanced Analysis Center, NARO, Kannondai 2-1-2, 305-8602, Tsukuba, Japan
| | - Jun-Ichi Yonemaru
- National Agriculture and Food Research Organization, Institute of Crop Science, NARO (NICS), Kannondai 2-1-2, 305-8518, Tsukuba, Japan
- Rice Applied Genomics Research Unit, NIAS, 2-1-2 Kannondai, 305-8602, Tsukuba, Japan
| | - Masahiro Yano
- National Agriculture and Food Research Organization, Institute of Crop Science, NARO (NICS), Kannondai 2-1-2, 305-8518, Tsukuba, Japan
- Rice Applied Genomics Research Unit, NIAS, 2-1-2 Kannondai, 305-8602, Tsukuba, Japan
| | - Takeshi Izawa
- Functional Plant Research Unit, National Institute of Agrobiological Sciences (NIAS), 2-1-2 Kannondai, 305-8602, Tsukuba, Japan
- Faculty of Agriculture, Laboratory of Plant Breeding and Genetics, University of Tokyo, Bunkyo-ku, Yayoi 1-1-1, 113-8657, Tokyo, Japan
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18
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Wang C, Guo W, Cai X, Li R, Ow DW. Engineering low-cadmium rice through stress-inducible expression of OXS3-family member genes. N Biotechnol 2018; 48:29-34. [PMID: 29684657 DOI: 10.1016/j.nbt.2018.04.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Revised: 04/16/2018] [Accepted: 04/17/2018] [Indexed: 11/19/2022]
Abstract
Cadmium (Cd) as a carcinogen poses a great threat to food security and public health through plant-derived foods such as rice, the staple for nearly half of the world's population. We have previously reported that overexpression of truncated gene fragments derived from the rice genes OsO3L2 and OsO3L3 could reduce Cd accumulation in transgenic rice. However, we did not test the full length genes due to prior work in Arabidopsis where overexpression of these genes caused seedling lethality. Here, we report on limiting the overexpression of OsO3L2 and OsO3L3 through the use of the stress- inducible promoter RD29B. However, despite generating 625 putative transformants, only 7 lines survived as T1 seedlings and only 1 line of each overexpressed OsO3L2 or OsO3L3-produced T2 progeny. The T2 homozygotes from these 2 lines showed the same effect of reducing accumulation of Cd in root and shoot as well as in T3 grain. As importantly, the concentrations of essential metals copper (Cu), iron (Fe), manganese (Mn) and zinc (Zn) were unaffected. Analysis of the expression profile suggested that low Cd accumulation may be due to high expression of OsO3L2 and OsO3L3 in the root tip region. Cellular localization of OsO3L2 and OsO3L3 indicate that they are histone H2A interacting nuclear proteins in vascular cells and especially in the root tip region. It is possible that interaction with histone H2A modifies chromatin to regulate downstream gene expression.
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Affiliation(s)
- Changhu Wang
- Plant Gene Engineering Center, Chinese Academy of Sciences Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Weili Guo
- Plant Gene Engineering Center, Chinese Academy of Sciences Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Xingzhe Cai
- Plant Gene Engineering Center, Chinese Academy of Sciences Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Ruyu Li
- Plant Gene Engineering Center, Chinese Academy of Sciences Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - David W Ow
- Plant Gene Engineering Center, Chinese Academy of Sciences Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China.
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19
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Chen L, Wan H, Qian J, Guo J, Sun C, Wen J, Yi B, Ma C, Tu J, Song L, Fu T, Shen J. Genome-Wide Association Study of Cadmium Accumulation at the Seedling Stage in Rapeseed ( Brassica napus L.). FRONTIERS IN PLANT SCIENCE 2018; 9:375. [PMID: 29725340 PMCID: PMC5917214 DOI: 10.3389/fpls.2018.00375] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2017] [Accepted: 03/06/2018] [Indexed: 05/26/2023]
Abstract
Cadmium is a potentially toxic heavy metal to human health. Rapeseed (Brassica napus L.), a vegetable and oilseed crop, might also be a Cd hyperaccumulator, but there is little information on this trait in rapeseed. We evaluated Cd accumulation in different oilseed accessions and employed a genome-wide association study to identify quantitative trait loci (QTLs) related to Cd accumulation. A total of 419 B. napus accessions and inbred lines were genotyped with a 60K Illumina Infinium SNP array of Brassica. Wide genotypic variations in Cd concentration and translocation were found. Twenty-five QTLs integrated with 98 single-nucleotide polymorphisms (SNPs) located at 15 chromosomes were associated with Cd accumulation traits. These QTLs explained 3.49-7.57% of the phenotypic variation observed. Thirty-two candidate genes were identified in these genomic regions, and they were 0.33-497.97 kb away from the SNPs. We found orthologs of Arabidopsis thaliana located near the significant SNPs on the B. napus genome, including NRAMP6 (natural resistance-associated macrophage protein 6), IRT1 (iron-regulated transporter 1), CAD1 (cadmium-sensitive 1), and PCS2 (phytochelatin synthase 2). Of them, four candidate genes were verified by qRT-PCR, the expression levels of which were significantly higher after exposure to Cd than in the controls. Our results might facilitate the study of the genetic basis of Cd accumulation and the cloning of candidate Cd accumulation genes, which could be used to help reduce Cd levels in edible plant parts and/or create more efficient hyperaccumulators.
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Affiliation(s)
- Lunlin Chen
- National Key Laboratory of Crop Genetic Improvement, National Engineering Research Center for Rapeseed, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Nanchang Branch of National Center of Oilcrops Improvement, Jiangxi Province Key Laboratory of Oil Crops Biology, Crops Research Institute of Jiangxi Academy of Agricultural Sciences, Nanchang, China
| | - Heping Wan
- National Key Laboratory of Crop Genetic Improvement, National Engineering Research Center for Rapeseed, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jiali Qian
- National Key Laboratory of Crop Genetic Improvement, National Engineering Research Center for Rapeseed, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jianbin Guo
- National Key Laboratory of Crop Genetic Improvement, National Engineering Research Center for Rapeseed, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Chengming Sun
- National Key Laboratory of Crop Genetic Improvement, National Engineering Research Center for Rapeseed, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jing Wen
- National Key Laboratory of Crop Genetic Improvement, National Engineering Research Center for Rapeseed, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Bin Yi
- National Key Laboratory of Crop Genetic Improvement, National Engineering Research Center for Rapeseed, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Chaozhi Ma
- National Key Laboratory of Crop Genetic Improvement, National Engineering Research Center for Rapeseed, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jinxing Tu
- National Key Laboratory of Crop Genetic Improvement, National Engineering Research Center for Rapeseed, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Laiqiang Song
- Nanchang Branch of National Center of Oilcrops Improvement, Jiangxi Province Key Laboratory of Oil Crops Biology, Crops Research Institute of Jiangxi Academy of Agricultural Sciences, Nanchang, China
| | - Tingdong Fu
- National Key Laboratory of Crop Genetic Improvement, National Engineering Research Center for Rapeseed, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jinxiong Shen
- National Key Laboratory of Crop Genetic Improvement, National Engineering Research Center for Rapeseed, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
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Kobayashi A, Hori K, Yamamoto T, Yano M. Koshihikari: a premium short-grain rice cultivar - its expansion and breeding in Japan. RICE (NEW YORK, N.Y.) 2018; 11:15. [PMID: 29629486 PMCID: PMC5890008 DOI: 10.1186/s12284-018-0207-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2017] [Accepted: 03/11/2018] [Indexed: 05/10/2023]
Abstract
Koshihikari, a Japanese short-grain rice cultivar, was developed in 1956, more than 60 years ago. Despite its age, it has been the most widely grown cultivar in Japan for more than 35 years, making it the most important rice for the Japanese people. In its early days, there was no reason to predict that Koshihikari would become so widely disseminated. However, since the end of the post-World War II food shortage in the 1960s, Japanese preferences changed from high productivity to good eating quality. This triggered wide expansion of Koshihikari cultivation due to the cultivar's excellent taste and texture. With increasing cultivation of Koshihikari in Japan, several good agronomic characteristics beyond its high eating quality became apparent, such as its good adaptation to different environments, tolerance to pre-harvest sprouting, and cold tolerance during the booting stage. These characteristics outweigh drawbacks such as its low blast resistance and low lodging resistance. The popularity of Koshihikari influenced subsequent rice breeding trends at regional agricultural experimental stations, and the characteristics of newly developed rice cultivars in Japan are usually rated relative to Koshihikari, which is used as the benchmark. Koshihikari was the first japonica rice cultivar whose whole genome has been sequenced by means of next-generation sequencing. Furthermore, comparison of the genomes of Koshihikari and Nipponbare has provided detailed insights into the genetic diversity of Japanese rice cultivars relative to that in rice populations elsewhere in the world. Further progress in rice genomics is gradually unlocking the mechanisms that underlie the agronomic characteristics of Koshihikari. To support both research and the development of novel rice cultivars, a series of isogenic and near-isogenic lines in the Koshihikari genetic background have been continuously developed. These new findings and materials will facilitate genomics-assisted rice breeding, eventually leading to superior cultivars.
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Affiliation(s)
- Asako Kobayashi
- Fukui Agricultural Experiment Station, 52-21 Ryomachi, Fukui, 918-8215 Japan
| | - Kiyosumi Hori
- National Agriculture and Food Research Organization (NARO), Institute of Crop Science, 2-1-2, Kannondai, Tsukuba, Ibaraki, 305-8518 Japan
| | - Toshio Yamamoto
- National Agriculture and Food Research Organization (NARO), Institute of Crop Science, 2-1-2, Kannondai, Tsukuba, Ibaraki, 305-8518 Japan
| | - Masahiro Yano
- National Agriculture and Food Research Organization (NARO), Institute of Crop Science, 2-1-2, Kannondai, Tsukuba, Ibaraki, 305-8518 Japan
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Huang DR, Fan YY, Hu BL, Xiao YQ, Chen DZ, Zhuang JY. Assessment and genetic analysis of heavy metal content in rice grain using an Oryza sativa × O. rufipogon backcross inbred line population. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2018; 98:1339-1345. [PMID: 28758676 DOI: 10.1002/jsfa.8598] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Revised: 06/26/2017] [Accepted: 07/23/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND Heavy metal accumulation in rice is a growing concern for public health. Backcross inbred lines derived from an interspecific cross of Oryza sativa × O. rufipogon were grown in two distinct ecological locations (Hangzhou and Lingshui, China). The objective of this study was to characterise the contents of heavy metal in rice grains, and to identify quantitative trait loci (QTLs) for heavy metal contents. RESULTS The contents of Ni, As, Pb, Cr and Hg in milled rice showed a significant decline as compared with those in brown rice, whereas the content of Cd showed little change. The concentration of heavy metal in rice grain varied greatly between the two environments. A total of 24 QTLs responsible for heavy metal contents were detected, including two for both the brown and milled rice, 13 for brown rice only, and nine for milled rice only. All the QTLs except two had the enhancing alleles derived from O. rufipogon. Sixteen QTLs were clustered in six chromosomal regions. CONCLUSION Environmental variation plays an important role in the heavy metal contents in rice grain. QTLs detected in this study might be useful for breeding rice varieties with low heavy metal content. © 2017 Society of Chemical Industry.
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Affiliation(s)
- De-Run Huang
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, China
| | - Ye-Yang Fan
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, China
| | - Biao-Lin Hu
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, China
- Rice Research Institute, Jiangxi Academy of Agricultural Sciences and Nanchang National Sub-center for Rice Improvement, Nanchang, China
| | - Ye-Qing Xiao
- Rice Research Institute, Jiangxi Academy of Agricultural Sciences and Nanchang National Sub-center for Rice Improvement, Nanchang, China
| | - Da-Zhou Chen
- Rice Research Institute, Jiangxi Academy of Agricultural Sciences and Nanchang National Sub-center for Rice Improvement, Nanchang, China
| | - Jie-Yun Zhuang
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, China
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22
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Duan G, Shao G, Tang Z, Chen H, Wang B, Tang Z, Yang Y, Liu Y, Zhao FJ. Genotypic and Environmental Variations in Grain Cadmium and Arsenic Concentrations Among a Panel of High Yielding Rice Cultivars. RICE (NEW YORK, N.Y.) 2017; 10:9. [PMID: 28353179 PMCID: PMC5371165 DOI: 10.1186/s12284-017-0149-2] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 03/17/2017] [Indexed: 05/18/2023]
Abstract
BACKGROUND Rice is a major dietary source of cadmium (Cd) and arsenic (As) for populations consuming rice as the staple food. Excessive Cd and As accumulation in rice grain is of great concern worldwide, especially in South China where soil contamination with heavy metals and metalloids is widespread. It is important to reduce Cd and As accumulation in rice grain through selection and breeding of cultivars accumulating low levels of Cd or As. RESULTS To assess the genetic and environmental variations in the concentrations of Cd and As in rice grains, 471 locally adapted high-yielding rice cultivars were grown at three moderately contaminated sites in South China for two years. Cadmium and As concentrations in brown rice varied by 10 - 32 and 2.5 - 4 fold, respectively. Genotype (G), environment (E) and G x E interactions were highly significant factors explaining the variations. Brown rice Cd concentration was found to correlate positively with the heading date among different cultivars, whereas As concentration and heading date correlated negatively. There was a significant and negative correlation between grain Cd and As concentrations. CONCLUSIONS Eight and 6 rice cultivars were identified as stable low accumulators of Cd and As, respectively, based on the multiple site and season trials. These cultivars are likely to be compliant with the grain Cd or As limits of the Chinese Food Safety Standards when grown in moderately contaminated paddy soils in South China.
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Affiliation(s)
- Guilan Duan
- State Key Laboratory of Urban and Regional Ecology, Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Guosheng Shao
- Chinese National Rice Research Institute, Hangzhou, 310006, China
| | - Zhong Tang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Hongping Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Boxun Wang
- State Key Laboratory of Urban and Regional Ecology, Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Zhu Tang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yuping Yang
- State Key Laboratory of Urban and Regional Ecology, Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Yuechuan Liu
- Youxian Agricultural Bureau of Hunan Province, Hunan, 412300, China
| | - Fang-Jie Zhao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China.
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23
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Gao L, Chang J, Chen R, Li H, Lu H, Tao L, Xiong J. Comparison on cellular mechanisms of iron and cadmium accumulation in rice: prospects for cultivating Fe-rich but Cd-free rice. RICE (NEW YORK, N.Y.) 2016; 9:39. [PMID: 27502932 PMCID: PMC4977236 DOI: 10.1186/s12284-016-0112-7] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 07/31/2016] [Indexed: 05/09/2023]
Abstract
Iron (Fe) is essential for rice growth and humans consuming as their staple food but is often deficient because of insoluble Fe(III) in soil for rice growth and limited assimilation for human bodies, while cadmium (Cd) is non-essential and toxic for rice growth and humans if accumulating at high levels. Over-accumulated Cd can cause damage to human bodies. Selecting and breeding Fe-rich but Cd-free rice cultivars are ambitious, challenging and meaningful tasks for researchers. Although evidences show that the mechanisms of Fe/Cd uptake and accumulation in rice are common to some extent as a result of similar entry routes within rice, an increasing number of researchers have discovered distinct mechanisms between Fe/Cd uptake and accumulation in rice. This comprehensive review systematically elaborates and compares cellular mechanisms of Fe/Cd uptake and accumulation in rice, respectively. Mechanisms for maintaining Fe homeostasis and Cd detoxicification are also elucidated. Then, effects of different fertilizer management on Fe/Cd accumulation in rice are discussed. Finally, this review enumerates various approaches for reducing grain Cd accumulation and enhancing Fe content in rice. In summary, understanding of discrepant cellular mechanisms of Fe/Cd accumulation in rice provides guidance for cultivating Fe-fortified rice and has paved the way to develop rice that are tolerant to Cd stress, aiming at breeding Fe-rich but Cd-free rice.
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Affiliation(s)
- Lei Gao
- College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou, 310018, People's Republic of China
- Zhejinag Province Key Laboratory of Plant Secondary Metabolism and Regulation, Hangzhou, 310018, People's Republic of China
| | - Jiadong Chang
- College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou, 310018, People's Republic of China
- Zhejinag Province Key Laboratory of Plant Secondary Metabolism and Regulation, Hangzhou, 310018, People's Republic of China
| | - Ruijie Chen
- College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou, 310018, People's Republic of China
- Zhejinag Province Key Laboratory of Plant Secondary Metabolism and Regulation, Hangzhou, 310018, People's Republic of China
| | - Hubo Li
- College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou, 310018, People's Republic of China
- Zhejinag Province Key Laboratory of Plant Secondary Metabolism and Regulation, Hangzhou, 310018, People's Republic of China
| | - Hongfei Lu
- College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou, 310018, People's Republic of China
- Zhejinag Province Key Laboratory of Plant Secondary Metabolism and Regulation, Hangzhou, 310018, People's Republic of China
| | - Longxing Tao
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, People's Republic of China
| | - Jie Xiong
- College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou, 310018, People's Republic of China.
- Zhejinag Province Key Laboratory of Plant Secondary Metabolism and Regulation, Hangzhou, 310018, People's Republic of China.
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Sun L, Xu X, Jiang Y, Zhu Q, Yang F, Zhou J, Yang Y, Huang Z, Li A, Chen L, Tang W, Zhang G, Wang J, Xiao G, Huang D, Chen C. Genetic Diversity, Rather than Cultivar Type, Determines Relative Grain Cd Accumulation in Hybrid Rice. FRONTIERS IN PLANT SCIENCE 2016; 7:1407. [PMID: 27708659 PMCID: PMC5030296 DOI: 10.3389/fpls.2016.01407] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 09/02/2016] [Indexed: 05/26/2023]
Abstract
Cadmium (Cd) is a toxic element, and rice is known to be a leading source of dietary Cd for people who consume rice as their main caloric resource. Hybrid rice has dominated rice production in southern China and has been adopted worldwide. The characteristics of high yield heterosis of rice hybrids makes the public think intuitively that the hybrid rice accumulates more Cd in grain than do inbred cultivars. A detailed understanding of the genetic basis of grain Cd accumulation in hybrids and developing Cd-safe rice are one of the top priorities for hybrid rice breeders at present. In this study, we investigated genetic diversity and grain Cd levels in 617 elite rice hybrids collected from the middle and lower Yangtze River Valley in China and 68 inbred cultivars from around the world. We found that there are large variations in grain Cd accumulation in both the hybrids and their inbred counterparts. However, we found grain Cd levels in the rice hybrids to be similar to the levels in indica rice inbreds, suggesting that the hybrids do not accumulate more Cd than do the inbred rice cultivars. Further analysis revealed that the high heritability of Cd accumulation in the grain and the single indica population structure increases the risk of Cd over-accumulation in hybrid rice. The genetic effects of Cd-related QTLs, which have been identified in related Cd-QTL mapping studies, were also determined in the hybrid rice population. Four QTLs were identified as being associated with the variation in grain Cd levels; three of these loci exhibited obvious indica-japonica differentiations. Our study will provide a better understanding of grain Cd accumulations in hybrid rice, and pave the way toward effective breeding for high-yielding, low grain-Cd hybrids in the future.
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Affiliation(s)
- Liang Sun
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of SciencesChangsha, China
| | - Xiaxu Xu
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of SciencesChangsha, China
| | - Youru Jiang
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of SciencesChangsha, China
- Institute of Rice Science, Hunan Agricultural UniversityChangsha, China
| | - Qihong Zhu
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of SciencesChangsha, China
| | - Fei Yang
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of SciencesChangsha, China
| | - Jieqiang Zhou
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of SciencesChangsha, China
- Institute of Rice Science, Hunan Agricultural UniversityChangsha, China
| | - Yuanzhu Yang
- Yuanlongping High-Tech Agriculture Co., LTDChangsha, China
| | - Zhiyuan Huang
- China National Hybrid Rice R&D CenterChangsha, China
| | - Aihong Li
- Lixiahe Agricultural Research Institute of Jiangsu ProvinceYangzhou, China
| | - Lianghui Chen
- Beishan Agricultural Service Center of Changsha CountyChangsha, China
| | - Wenbang Tang
- Institute of Rice Science, Hunan Agricultural UniversityChangsha, China
| | - Guoyu Zhang
- Beishan Agricultural Service Center of Changsha CountyChangsha, China
| | - Jiurong Wang
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of SciencesChangsha, China
| | - Guoying Xiao
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of SciencesChangsha, China
| | - Daoyou Huang
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of SciencesChangsha, China
| | - Caiyan Chen
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of SciencesChangsha, China
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25
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Clemens S, Ma JF. Toxic Heavy Metal and Metalloid Accumulation in Crop Plants and Foods. ANNUAL REVIEW OF PLANT BIOLOGY 2016; 67:489-512. [PMID: 27128467 DOI: 10.1146/annurev-arplant-043015-112301] [Citation(s) in RCA: 503] [Impact Index Per Article: 62.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Arsenic, cadmium, lead, and mercury are toxic elements that are almost ubiquitously present at low levels in the environment because of anthropogenic influences. Dietary intake of plant-derived food represents a major fraction of potentially health-threatening human exposure, especially to arsenic and cadmium. In the interest of better food safety, it is important to reduce toxic element accumulation in crops. A molecular understanding of the pathways responsible for this accumulation can enable the development of crop varieties with strongly reduced concentrations of toxic elements in their edible parts. Such understanding is rapidly progressing for arsenic and cadmium but is in its infancy for lead and mercury. Basic discoveries have been made in Arabidopsis, rice, and other models, and most advances in crops have been made in rice. Proteins mediating the uptake of arsenic and cadmium have been identified, and the speciation and biotransformations of arsenic are now understood. Factors controlling the efficiency of root-to-shoot translocation and the partitioning of toxic elements through the rice node have also been identified.
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Affiliation(s)
- Stephan Clemens
- Department of Plant Physiology, University of Bayreuth, 95440 Bayreuth, Germany;
| | - Jian Feng Ma
- Institute of Plant Science and Resources, Okayama University, Kurashiki 710-0046, Japan;
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26
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Nagata K, Ando T, Nonoue Y, Mizubayashi T, Kitazawa N, Shomura A, Matsubara K, Ono N, Mizobuchi R, Shibaya T, Ogiso-Tanaka E, Hori K, Yano M, Fukuoka S. Advanced backcross QTL analysis reveals complicated genetic control of rice grain shape in a japonica × indica cross. BREEDING SCIENCE 2015; 65:308-18. [PMID: 26366113 PMCID: PMC4542931 DOI: 10.1270/jsbbs.65.308] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Accepted: 05/29/2015] [Indexed: 05/18/2023]
Abstract
Grain shape is an important trait for improving rice yield. A number of quantitative trait loci (QTLs) for this trait have been identified by using primary F2 mapping populations and recombinant inbred lines, in which QTLs with a small effect are harder to detect than they would be in advanced generations. In this study, we developed two advanced mapping populations (chromosome segment substitution lines [CSSLs] and BC4F2 lines consisting of more than 2000 individuals) in the genetic backgrounds of two improved cultivars: a japonica cultivar (Koshihikari) with short, round grains, and an indica cultivar (IR64) with long, slender grains. We compared the ability of these materials to reveal QTLs for grain shape with that of an F2 population. Only 8 QTLs for grain length or grain width were detected in the F2 population, versus 47 in the CSSL population and 65 in the BC4F2 population. These results strongly suggest that advanced mapping populations can reveal QTLs for agronomic traits under complicated genetic control, and that DNA markers linked with the QTLs are useful for choosing superior allelic combinations to enhance grain shape in the Koshihikari and IR64 genetic backgrounds.
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Affiliation(s)
- Kazufumi Nagata
- National Institute of Agrobiological Sciences,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
| | - Tsuyu Ando
- National Institute of Agrobiological Sciences,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
| | - Yasunori Nonoue
- National Institute of Agrobiological Sciences,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
- Institute of the Society for Techno-innovation of Agriculture, Forestry and Fisheries,
446-1 Ippaizuka, Kamiyokoba, Tsukuba, Ibaraki 305-0854,
Japan
| | - Tatsumi Mizubayashi
- National Institute of Agrobiological Sciences,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
| | - Noriyuki Kitazawa
- National Institute of Agrobiological Sciences,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
| | - Ayahiko Shomura
- National Institute of Agrobiological Sciences,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
| | - Kazuki Matsubara
- National Institute of Agrobiological Sciences,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
| | - Nozomi Ono
- Institute of the Society for Techno-innovation of Agriculture, Forestry and Fisheries,
446-1 Ippaizuka, Kamiyokoba, Tsukuba, Ibaraki 305-0854,
Japan
| | - Ritsuko Mizobuchi
- National Institute of Agrobiological Sciences,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
| | - Taeko Shibaya
- National Institute of Agrobiological Sciences,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
| | - Eri Ogiso-Tanaka
- National Institute of Agrobiological Sciences,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
| | - Kiyosumi Hori
- National Institute of Agrobiological Sciences,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
| | - Masahiro Yano
- National Institute of Agrobiological Sciences,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
| | - Shuichi Fukuoka
- National Institute of Agrobiological Sciences,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
- Corresponding author (e-mail: )
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27
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Zhao FJ, Ma Y, Zhu YG, Tang Z, McGrath SP. Soil contamination in China: current status and mitigation strategies. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2015; 49:750-9. [PMID: 25514502 DOI: 10.1021/es5047099] [Citation(s) in RCA: 1031] [Impact Index Per Article: 114.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
China faces great challenges in protecting its soil from contamination caused by rapid industrialization and urbanization over the last three decades. Recent nationwide surveys show that 16% of the soil samples, 19% for the agricultural soils, are contaminated based on China’s soil environmental quality limits, mainly with heavy metals and metalloids. Comparisons with other regions of the world show that the current status of soil contamination, based on the total contaminant concentrations, is not worse in China. However, the concentrations of some heavy metals in Chinese soils appear to be increasing at much greater rates. Exceedance of the contaminant limits in food crops is widespread in some areas, especially southern China, due to elevated inputs of contaminants, acidic nature of the soil and crop species or cultivars prone to heavy metal accumulation. Minimizing the transfer of contaminants from soil to the food chain is a top priority. A number of options are proposed, including identification of the sources of contaminants to agricultural systems, minimization of contaminant inputs, reduction of heavy metal phytoavailability in soil with liming or other immobilizing materials, selection and breeding of low accumulating crop cultivars, adoption of appropriate water and fertilizer management, bioremediation, and change of land use to grow nonfood crops. Implementation of these strategies requires not only technological advances, but also social-economic evaluation and effective enforcement of environmental protection law.
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28
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Fukuoka S, Yamamoto SI, Mizobuchi R, Yamanouchi U, Ono K, Kitazawa N, Yasuda N, Fujita Y, Thi Thanh Nguyen T, Koizumi S, Sugimoto K, Matsumoto T, Yano M. Multiple functional polymorphisms in a single disease resistance gene in rice enhance durable resistance to blast. Sci Rep 2014. [DOI: 10.1038/srep04550] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
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