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Calayugan MIC, Hore TK, Palanog AD, Amparado A, Inabangan-Asilo MA, Joshi G, Chintavaram B, Swamy BPM. Deciphering the genetic basis of agronomic, yield, and nutritional traits in rice (Oryza sativa L.) using a saturated GBS-based SNP linkage map. Sci Rep 2024; 14:18024. [PMID: 39098874 PMCID: PMC11298551 DOI: 10.1038/s41598-024-67543-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Accepted: 07/12/2024] [Indexed: 08/06/2024] Open
Abstract
Developing high-yielding rice varieties that possess favorable agronomic characteristics and enhanced grain Zn content is crucial in ensuring food security and addressing nutritional needs. This research employed ICIM, IM, and multi-parent population QTL mapping methods to identify important genetic regions associated with traits such as DF, PH, NT, NP, PL, YLD, TGW, GL, GW, Zn, and Fe. Two populations of recombinant inbred lines consisting of 373 lines were phenotyped for agronomic, yield and grain micronutrient traits for three seasons at IRRI, and genotyped by sequencing. Most of the traits demonstrated moderate to high broad-sense heritability. There was a positive relationship between Zn and Fe contents. The principal components and correlation results revealed a significant negative association between YLD and Zn/Fe. ICIM identified 81 QTLs, while IM detected 36 QTLs across populations. The multi-parent population analysis detected 27 QTLs with six of them consistently detected across seasons. We shortlisted eight candidate genes associated with yield QTLs, 19 genes with QTLs for agronomic traits, and 26 genes with Zn and Fe QTLs. Notable candidate genes included CL4 and d35 for YLD, dh1 for DF, OsIRX10, HDT702, sd1 for PH, OsD27 for NP, whereas WFP and OsIPI1 were associated with PL, OsRSR1 and OsMTP1 were associated to TGW. The OsNAS1, OsRZFP34, OsHMP5, OsMTP7, OsC3H33, and OsHMA1 were associated with Fe and Zn QTLs. We identified promising RILs with acceptable yield potential and high grain Zn content from each population. The major effect QTLs, genes and high Zn RILs identified in our study are useful for efficient Zn biofortification of rice.
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Affiliation(s)
- Mark Ian C Calayugan
- Rice Breeding and Innovation Department, International Rice Research Institute, DAPO 7777, Metro Manila, Philippines
- Institute of Crop Science, College of Agriculture and Food Science, University of the Philippines Los Baños (UPLB), 4031, College, Laguna, Philippines
| | - Tapas Kumer Hore
- Rice Breeding and Innovation Department, International Rice Research Institute, DAPO 7777, Metro Manila, Philippines
- Institute of Crop Science, College of Agriculture and Food Science, University of the Philippines Los Baños (UPLB), 4031, College, Laguna, Philippines
- Bangladesh Rice Research Institute (BRRI), Gazipur, Bangladesh
| | - Alvin D Palanog
- Rice Breeding and Innovation Department, International Rice Research Institute, DAPO 7777, Metro Manila, Philippines
- Institute of Crop Science, College of Agriculture and Food Science, University of the Philippines Los Baños (UPLB), 4031, College, Laguna, Philippines
- PhilRice Negros, Philippine Rice Research Institute, Murcia, Negros, Philippines
| | - Amery Amparado
- Rice Breeding and Innovation Department, International Rice Research Institute, DAPO 7777, Metro Manila, Philippines
| | - Mary Ann Inabangan-Asilo
- Rice Breeding and Innovation Department, International Rice Research Institute, DAPO 7777, Metro Manila, Philippines
| | - Gaurav Joshi
- Rice Breeding and Innovation Department, International Rice Research Institute, DAPO 7777, Metro Manila, Philippines
| | - Balachiranjeevi Chintavaram
- Rice Breeding and Innovation Department, International Rice Research Institute, DAPO 7777, Metro Manila, Philippines
| | - B P Mallikarjuna Swamy
- Rice Breeding and Innovation Department, International Rice Research Institute, DAPO 7777, Metro Manila, Philippines.
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Liu H, Zhang X, Shang Y, Zhao S, Li Y, Zhou X, Huo X, Qiao P, Wang X, Dai K, Li H, Guo J, Shi W. Genome-wide association study reveals genetic loci for ten trace elements in foxtail millet (Setaria italica). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:186. [PMID: 39017920 DOI: 10.1007/s00122-024-04690-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Accepted: 07/03/2024] [Indexed: 07/18/2024]
Abstract
KEY MESSAGE One hundred and fifty-five QTL for trace element concentrations in foxtail millet were identified using a genome-wide association study, and a candidate gene associated with Ni-Co-Cr concentrations was detected. Foxtail millet (Setaria italica) is an important regional crop known for its rich mineral nutrient content, which has beneficial effects on human health. We assessed the concentrations of ten trace elements (Ba, Co, Cr, Cu, Fe, Mn, Ni, Pb, Sr, and Zn) in the grain of 408 foxtail millet accessions. Significant differences in the concentrations of five elements (Ba, Co, Ni, Sr, and Zn) were observed between two subpopulations of spring- and summer-sown foxtail millet varieties. Moreover, 84.4% of the element pairs exhibited significant correlations. To identify the genetic factors influencing trace element accumulation, a comprehensive genome-wide association study was conducted, identifying 155 quantitative trait locus (QTL) for the ten trace elements across three different environments. Among them, ten QTL were consistently detected in multiple environments, including qZn2.1, qZn4.4, qCr4.1, qFe6.3, qFe6.5, qCo6.1, qPb7.3, qPb7.5, qBa9.1, and qNi9.1. Thirteen QTL clusters were detected for multiple elements, which partially explained the correlations between elements. Additionally, the different concentrations of five elements between foxtail millet subpopulations were caused by the different frequencies of high-concentration alleles associated with important marker-trait associations. Haplotype analysis identified a candidate gene SETIT_036676mg associated with Ni accumulation, with the GG haplotype significantly increasing Ni-Co-Cr concentrations in foxtail millet. A cleaved amplified polymorphic sequence marker (cNi6676) based on the two haplotypes of SETIT_036676mg was developed and validated. Results of this study provide valuable reference information for the genetic research and improvement of trace element content in foxtail millet.
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Affiliation(s)
- Hanxiao Liu
- College of Agronomy, Key Laboratory of Sustainable Dryland Agriculture (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shanxi Agricultural University, Jinzhong, 030801, China
| | - Xin Zhang
- College of Agronomy, Key Laboratory of Sustainable Dryland Agriculture (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shanxi Agricultural University, Jinzhong, 030801, China
| | - Yuping Shang
- College of Agronomy, Key Laboratory of Sustainable Dryland Agriculture (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shanxi Agricultural University, Jinzhong, 030801, China
| | - Shaoxing Zhao
- College of Agronomy, Key Laboratory of Sustainable Dryland Agriculture (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shanxi Agricultural University, Jinzhong, 030801, China
| | - Yingjia Li
- College of Agronomy, Key Laboratory of Sustainable Dryland Agriculture (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shanxi Agricultural University, Jinzhong, 030801, China
| | - Xutao Zhou
- College of Agronomy, Key Laboratory of Sustainable Dryland Agriculture (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shanxi Agricultural University, Jinzhong, 030801, China
| | - Xiaoyu Huo
- College of Agronomy, Key Laboratory of Sustainable Dryland Agriculture (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shanxi Agricultural University, Jinzhong, 030801, China
| | - Pengfei Qiao
- College of Agronomy, Key Laboratory of Sustainable Dryland Agriculture (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shanxi Agricultural University, Jinzhong, 030801, China
| | - Xin Wang
- College of Agronomy, Key Laboratory of Sustainable Dryland Agriculture (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shanxi Agricultural University, Jinzhong, 030801, China
| | - Keli Dai
- College of Agronomy, Key Laboratory of Sustainable Dryland Agriculture (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shanxi Agricultural University, Jinzhong, 030801, China
| | - Huixia Li
- Millet Research Institute, Shanxi Agricultural University, Changzhi, 046000, China
| | - Jie Guo
- College of Agronomy, Key Laboratory of Sustainable Dryland Agriculture (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shanxi Agricultural University, Jinzhong, 030801, China.
| | - Weiping Shi
- College of Agronomy, Key Laboratory of Sustainable Dryland Agriculture (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shanxi Agricultural University, Jinzhong, 030801, China.
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Bukomarhe CB, Kimwemwe PK, Githiri SM, Mamati EG, Kimani W, Mutai C, Nganga F, Nguezet PMD, Mignouna J, Civava RM, Fofana M. Association Mapping of Candidate Genes Associated with Iron and Zinc Content in Rice ( Oryza sativa L.) Grains. Genes (Basel) 2023; 14:1815. [PMID: 37761955 PMCID: PMC10530939 DOI: 10.3390/genes14091815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 08/22/2023] [Accepted: 08/24/2023] [Indexed: 09/29/2023] Open
Abstract
Micronutrient deficiencies, particularly of iron (Fe) and zinc (Zn), in the diet contribute to health issues and hidden hunger. Enhancing the Fe and Zn content in globally staple food crops like rice is necessary to address food malnutrition. A Genome-Wide Association Study (GWAS) was conducted using 85 diverse rice accessions from the Democratic Republic of Congo (DRC) to identify genomic regions associated with grain Fe and Zn content. The Fe content ranged from 0.95 to 8.68 mg/100 g on a dry weight basis (dwb) while Zn content ranged from 0.87 to 3.8 mg/100 g (dwb). Using MLM and FarmCPU models, we found 10 significant SNPs out of which one SNP on chromosome 11 was associated with the variation in Fe content and one SNP on chromosome 4 was associated with the Zn content, and both were commonly detected by the two models. Candidate genes belonging to transcription regulator activities, including the bZIP family genes and MYB family genes, as well as transporter activities involved in Fe and Zn homeostasis were identified in the vicinity of the SNP markers and selected. The identified SNP markers hold promise for marker-assisted selection in rice breeding programs aimed at enhancing Fe and Zn content in rice. This study provides valuable insights into the genetic factors controlling Fe and Zn uptake and their transport and accumulation in rice, offering opportunities for developing biofortified rice varieties to combat malnutrition among rice consumers.
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Affiliation(s)
- Chance Bahati Bukomarhe
- Department of Horticulture and Food Security, Jomo Kenyatta University of Agriculture and Technology (JKUAT), Nairobi P.O. Box 62000-00200, Kenya; (P.K.K.); (S.M.G.); (E.G.M.)
- Olusegun O. Research Campus, International Institute of Tropical Agriculture (IITA), Bukavu P.O. Box 1222, Democratic Republic of the Congo; (J.M.); (M.F.)
- Institut National Pour l’Etude et la Recherche Agronomiques (INERA), Kinshasa P.O. Box 2037, Democratic Republic of the Congo;
| | - Paul Kitenge Kimwemwe
- Department of Horticulture and Food Security, Jomo Kenyatta University of Agriculture and Technology (JKUAT), Nairobi P.O. Box 62000-00200, Kenya; (P.K.K.); (S.M.G.); (E.G.M.)
- Olusegun O. Research Campus, International Institute of Tropical Agriculture (IITA), Bukavu P.O. Box 1222, Democratic Republic of the Congo; (J.M.); (M.F.)
- Institut National Pour l’Etude et la Recherche Agronomiques (INERA), Kinshasa P.O. Box 2037, Democratic Republic of the Congo;
- Faculty of Agriculture and Environmental Sciences, Université de Kalemie (UNIKAL), Kalemie P.O. Box 570, Democratic Republic of the Congo
| | - Stephen Mwangi Githiri
- Department of Horticulture and Food Security, Jomo Kenyatta University of Agriculture and Technology (JKUAT), Nairobi P.O. Box 62000-00200, Kenya; (P.K.K.); (S.M.G.); (E.G.M.)
| | - Edward George Mamati
- Department of Horticulture and Food Security, Jomo Kenyatta University of Agriculture and Technology (JKUAT), Nairobi P.O. Box 62000-00200, Kenya; (P.K.K.); (S.M.G.); (E.G.M.)
| | - Wilson Kimani
- International Livestock Research Institute (ILRI), Nairobi P.O. Box 30709-00100, Kenya; (C.M.); (F.N.)
| | - Collins Mutai
- International Livestock Research Institute (ILRI), Nairobi P.O. Box 30709-00100, Kenya; (C.M.); (F.N.)
| | - Fredrick Nganga
- International Livestock Research Institute (ILRI), Nairobi P.O. Box 30709-00100, Kenya; (C.M.); (F.N.)
| | - Paul-Martin Dontsop Nguezet
- International Institute of Tropical Agriculture (IITA), Kalemie P.O. Box 570, Democratic Republic of the Congo;
| | - Jacob Mignouna
- Olusegun O. Research Campus, International Institute of Tropical Agriculture (IITA), Bukavu P.O. Box 1222, Democratic Republic of the Congo; (J.M.); (M.F.)
| | - René Mushizi Civava
- Institut National Pour l’Etude et la Recherche Agronomiques (INERA), Kinshasa P.O. Box 2037, Democratic Republic of the Congo;
- Faculty of Agriculture and Environmental Sciences, Université Evangélique en Afrique (UEA), Bukavu P.O. Box 3323, Democratic Republic of the Congo
| | - Mamadou Fofana
- Olusegun O. Research Campus, International Institute of Tropical Agriculture (IITA), Bukavu P.O. Box 1222, Democratic Republic of the Congo; (J.M.); (M.F.)
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Kamal NM, Gorafi YSA, Tomemori H, Kim JS, Elhadi GMI, Tsujimoto H. Genetic variation for grain nutritional profile and yield potential in sorghum and the possibility of selection for drought tolerance under irrigated conditions. BMC Genomics 2023; 24:515. [PMID: 37660014 PMCID: PMC10474746 DOI: 10.1186/s12864-023-09613-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 08/22/2023] [Indexed: 09/04/2023] Open
Abstract
BACKGROUND Increasing grain nutritional value in sorghum (Sorghum bicolor) is a paramount breeding objective, as is increasing drought resistance (DR), because sorghum is grown mainly in drought-prone areas. The genetic basis of grain nutritional traits remains largely unknown. Marker-assisted selection using significant loci identified through genome-wide association study (GWAS) shows potential for selecting desirable traits in crops. This study assessed natural variation available in sorghum accessions from around the globe to identify novel genes or genomic regions with potential for improving grain nutritional value, and to study associations between DR traits and grain weight and nutritional composition. RESULTS We dissected the genetic architecture of grain nutritional composition, protein content, thousand-kernel weight (TKW), and plant height (PH) in sorghum through GWAS of 163 unique African and Asian accessions under irrigated and post-flowering drought conditions. Several QTLs were detected. Some were significantly associated with DR, TKW, PH, protein, and Zn, Mn, and Ca contents. Genomic regions on chromosomes 1, 2, 4, 8, 9, and 10 were associated with TKW, nutritional, and DR traits; colocalization patterns of these markers indicate potential for simultaneous improvement of these traits. In African accessions, markers associated with TKW were mapped to six regions also associated with protein, Zn, Ca, Mn, Na, and DR, suggesting the potential for simultaneous selection for higher grain nutrition and TKW. Our results indicate that it may be possible to select for increased DR on the basis of grain nutrition and weight potential. CONCLUSIONS This study provides a valuable resource for selecting landraces for use in plant breeding programs and for identifying loci that may contribute to grain nutrition and weight with the hope of producing cultivars that combine improved yield traits, nutrition, and DR.
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Affiliation(s)
- Nasrein Mohamed Kamal
- Arid Land Research Center, Tottori University, Tottori, 680-0001, Japan.
- Agricultural Research Corporation, PO Box 126, Wad Medani, Sudan.
| | - Yasir Serag Alnor Gorafi
- Agricultural Research Corporation, PO Box 126, Wad Medani, Sudan
- International Platform for Dryland Research and Education, Tottori University, Tottori, Japan
| | - Hisashi Tomemori
- Arid Land Research Center, Tottori University, Tottori, 680-0001, Japan
| | - June-Sik Kim
- RIKEN Center for Sustainable Resource Science, Yokohama, 230-0045, Japan
- Institute of Plant Science and Resources, Okayama University, Kurashiki, 710-0046, Japan
| | | | - Hisashi Tsujimoto
- Arid Land Research Center, Tottori University, Tottori, 680-0001, Japan.
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Liu T, Hu W, Weng L, Deng L, Li J, Yu J, Zhou Z, Liu Y, Chen C, Sheng T, Zhao Z, Xiao G. Phenotypic and genetic dissection of the contents of important metallic elements in hybrid rice grown in cadmium-contaminated paddy fields. Heliyon 2023; 9:e19919. [PMID: 37809877 PMCID: PMC10559331 DOI: 10.1016/j.heliyon.2023.e19919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 09/04/2023] [Accepted: 09/05/2023] [Indexed: 10/10/2023] Open
Abstract
Rice (Oryza sativa L.) is a staple food that feeds over half of the world's population, and the contents of metallic elements in rice grain play important roles in human nutrition. In this study, the contents of important metallic elements were determined by ICP-OES, and included cadmium (Cd), zinc (Zn), manganese (Mn), copper (Cu), iron (Fe), nickel (Ni), calcium (Ca), and magnesium (Mg) in brown rice, in the first node from the top (Node 1), in the second node from the top (Node 2), and in roots of 55 hybrids and their parental lines. The heritability of metallic element contents (MECs), the general combining ability (GCA) for MEC, and the correlation between MECs in different organs/tissues of hybrids were also analyzed. The results indicated that: (1) there was a positive correlation between the contents of Cd and Zn in nodes and roots, but a negative correlation between the contents of Cd and Zn in brown rice of the hybrids(2) the GCA for MECs can be used to evaluate the ability of the parental lines to improve the metal contents in brown rice of the hybrids(3) the contents of Cd, Zn, Ca, and Mg in brown rice were mainly affected by additive genetic effects(4) the restorer lines R2292 and R2265 can be used to cultivate hybrids with high Zn and low Cd contents in the brown rice.
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Affiliation(s)
- Tengfei Liu
- Hunan Rice Research Institute, Hunan Academy of Agricultural Sciences, Changsha, 410125, China
| | - Wenbin Hu
- Hunan Rice Research Institute, Hunan Academy of Agricultural Sciences, Changsha, 410125, China
| | - Lvshui Weng
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, 410125, China
| | - Lihua Deng
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, 410125, China
| | - Jinjiang Li
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, 410125, China
| | - Jianghui Yu
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, 410125, China
| | - Zheng Zhou
- Hunan Rice Research Institute, Hunan Academy of Agricultural Sciences, Changsha, 410125, China
| | - Ye Liu
- Hunan Rice Research Institute, Hunan Academy of Agricultural Sciences, Changsha, 410125, China
| | - Caiyan Chen
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, 410125, China
- Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Teng Sheng
- Laboratory of Photosynthesis and Environmental Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zhenghong Zhao
- Hunan Rice Research Institute, Hunan Academy of Agricultural Sciences, Changsha, 410125, China
| | - Guoying Xiao
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, 410125, China
- Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
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Senguttuvel P, G P, C J, D SR, CN N, V J, P B, R G, J AK, SV SP, LV SR, AS H, K S, D S, RM S, Govindaraj M. Rice biofortification: breeding and genomic approaches for genetic enhancement of grain zinc and iron contents. FRONTIERS IN PLANT SCIENCE 2023; 14:1138408. [PMID: 37332714 PMCID: PMC10272457 DOI: 10.3389/fpls.2023.1138408] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 04/25/2023] [Indexed: 06/20/2023]
Abstract
Rice is a highly consumed staple cereal cultivated predominantly in Asian countries, which share 90% of global rice production. Rice is a primary calorie provider for more than 3.5 billion people across the world. Preference and consumption of polished rice have increased manifold, which resulted in the loss of inherent nutrition. The prevalence of micronutrient deficiencies (Zn and Fe) are major human health challenges in the 21st century. Biofortification of staples is a sustainable approach to alleviating malnutrition. Globally, significant progress has been made in rice for enhancing grain Zn, Fe, and protein. To date, 37 biofortified Fe, Zn, Protein and Provitamin A rich rice varieties are available for commercial cultivation (16 from India and 21 from the rest of the world; Fe > 10 mg/kg, Zn > 24 mg/kg, protein > 10% in polished rice as India target while Zn > 28 mg/kg in polished rice as international target). However, understanding the micronutrient genetics, mechanisms of uptake, translocation, and bioavailability are the prime areas that need to be strengthened. The successful development of these lines through integrated-genomic technologies can accelerate deployment and scaling in future breeding programs to address the key challenges of malnutrition and hidden hunger.
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Affiliation(s)
- P. Senguttuvel
- Crop Improvement Section, ICAR - Indian Institute of Rice Research (ICAR - IIRR), Hyderabad, India
| | - Padmavathi G
- Crop Improvement Section, ICAR - Indian Institute of Rice Research (ICAR - IIRR), Hyderabad, India
| | - Jasmine C
- Crop Improvement Section, ICAR - Indian Institute of Rice Research (ICAR - IIRR), Hyderabad, India
- Genetics and Plant Breeding, Professor Jayashankar Telangana State Agricultural University (PJTSAU), Hyderabad, India
| | - Sanjeeva Rao D
- Crop Improvement Section, ICAR - Indian Institute of Rice Research (ICAR - IIRR), Hyderabad, India
| | - Neeraja CN
- Crop Improvement Section, ICAR - Indian Institute of Rice Research (ICAR - IIRR), Hyderabad, India
| | - Jaldhani V
- Crop Improvement Section, ICAR - Indian Institute of Rice Research (ICAR - IIRR), Hyderabad, India
| | - Beulah P
- Crop Improvement Section, ICAR - Indian Institute of Rice Research (ICAR - IIRR), Hyderabad, India
| | - Gobinath R
- Crop Improvement Section, ICAR - Indian Institute of Rice Research (ICAR - IIRR), Hyderabad, India
| | - Aravind Kumar J
- Crop Improvement Section, ICAR - Indian Institute of Rice Research (ICAR - IIRR), Hyderabad, India
| | - Sai Prasad SV
- Crop Improvement Section, ICAR - Indian Institute of Rice Research (ICAR - IIRR), Hyderabad, India
| | - Subba Rao LV
- Crop Improvement Section, ICAR - Indian Institute of Rice Research (ICAR - IIRR), Hyderabad, India
| | - Hariprasad AS
- Crop Improvement Section, ICAR - Indian Institute of Rice Research (ICAR - IIRR), Hyderabad, India
| | - Sruthi K
- Crop Improvement Section, ICAR - Indian Institute of Rice Research (ICAR - IIRR), Hyderabad, India
| | - Shivani D
- Genetics and Plant Breeding, Professor Jayashankar Telangana State Agricultural University (PJTSAU), Hyderabad, India
| | - Sundaram RM
- Crop Improvement Section, ICAR - Indian Institute of Rice Research (ICAR - IIRR), Hyderabad, India
| | - Mahalingam Govindaraj
- HarvestPlus, Alliance of Bioversity International and the International Center for Tropical Agriculture (CIAT), Cali, Colombia
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Identifying the Genetic Basis of Mineral Elements in Rice Grain Using Genome-Wide Association Mapping. Genes (Basel) 2022; 13:genes13122330. [PMID: 36553597 PMCID: PMC9777918 DOI: 10.3390/genes13122330] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 12/07/2022] [Accepted: 12/09/2022] [Indexed: 12/14/2022] Open
Abstract
Mineral malnutrition is a major problem in many rice-consuming countries. It is essential to know the genetic mechanisms of accumulation of mineral elements in the rice grain to provide future solutions for this issue. This study was conducted to identify the genetic basis of six mineral elements (Cu, Fe, K, Mg, Mn, and Zn) by using three models for single-locus and six models for multi-locus analysis of a genome-wide association study (GWAS) using 174 diverse rice accessions and 6565 SNP markers. To declare a SNP as significant, -log10(P) ≥ 3.0 and 15% FDR significance cut-off values were used for single-locus models, while LOD ≥ 3.0 was used for multi-locus models. Using these criteria, 147 SNPs were detected by one or two GWAS methods at -log10(P) ≥ 3.0, 48 of which met the 15% FDR significance cut-off value. Single-locus models outperformed multi-locus models before applying multi-test correction, but once applied, multi-locus models performed better. While 14 (~29%) of the identified quantitative trait loci (QTLs) after multiple test correction co-located with previously reported genes/QTLs and marker associations, another 34 trait-associated SNPs were novel. After mining genes within 250 kb of the 48 significant SNP loci, in silico and gene enrichment analyses were conducted to predict their potential functions. These shortlisted genes with their functions could guide future experimental validation, helping us to understand the complex molecular mechanisms controlling rice grain mineral elements.
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Xue J, Jiang T, Chen X, Liu H, Yang J. Multi-mineral fingerprinting analysis of the Chinese mitten crab (Eriocheir sinensis) in Yangcheng Lake during the year-round culture period. Food Chem 2022; 390:133167. [PMID: 35597091 DOI: 10.1016/j.foodchem.2022.133167] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 04/29/2022] [Accepted: 05/04/2022] [Indexed: 11/29/2022]
Abstract
Chinese mitten crabs (Eriocheir sinensis), originating from Yangcheng Lake, are valuable aquatic products in China. To characterize changes in nutrients in this species in Yangcheng Lake during the year-round culture period, the contents of ten mineral elements in the third pereiopod were evaluated. Principal component analysis revealed that mineral elements changed substantially in the first three months. Thereafter, the elemental "fingerprint" stabilized, and samples could not be accurately distinguished. This pattern was supported by linear discriminant analysis and self-organizing map analysis. These results demonstrate that a long period of time is required for element characteristics to stabilize, suggesting that short-term breeding is insufficient to obtain the natural elemental "fingerprint." In addition, our findings provide a basis for verifying the origin of Chinese mitten crab and other aquatic taxa in Yangcheng Lake.
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Affiliation(s)
- Junren Xue
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China
| | - Tao Jiang
- Key Laboratory of Fishery Ecological Environment Assessment and Resource Conservation in Middle and Lower Reaches of the Yangtze River, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| | - Xiubao Chen
- Key Laboratory of Fishery Ecological Environment Assessment and Resource Conservation in Middle and Lower Reaches of the Yangtze River, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| | - Hongbo Liu
- Key Laboratory of Fishery Ecological Environment Assessment and Resource Conservation in Middle and Lower Reaches of the Yangtze River, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| | - Jian Yang
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China; Key Laboratory of Fishery Ecological Environment Assessment and Resource Conservation in Middle and Lower Reaches of the Yangtze River, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China.
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9
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Singh B, Goutam U, Kukreja S, Sharma J, Sood S, Bhardwaj V. Potato biofortification: an effective way to fight global hidden hunger. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:2297-2313. [PMID: 34744367 PMCID: PMC8526655 DOI: 10.1007/s12298-021-01081-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 09/16/2021] [Accepted: 09/22/2021] [Indexed: 06/03/2023]
Abstract
Hidden hunger is leading to extensive health problems in the developing world. Several strategies could be used to reduce the micronutrient deficiencies by increasing the dietary uptake of essential micronutrients. These include diet diversification, pharmaceutical supplementation, food fortification and crop biofortification. Among all, crop biofortification is the most sustainable and acceptable strategy to overcome the global issue of hidden hunger. Since most of the people suffering from micronutrient deficiencies, have monetary issues and are dependent on staple crops to fulfil their recommended daily requirements of various essential micronutrients. Therefore, increasing the micronutrient concentrations in cost effective staple crops seems to be an effective solution. Potato being the world's most consumed non-grain staple crop with enormous industrial demand appears to be an ideal candidate for biofortification. It can be grown in different climatic conditions, provide high yield, nutrition and dry matter in lesser time. In addition, huge potato germplasm have natural variations related to micronutrient concentrations, which can be utilized for its biofortification. This review discuss the current scenario of micronutrient malnutrition and various strategies that could be used to overcome it. The review also shed a light on the genetic variations present in potato germplasm and suggest effective ways to incorporate them into modern high yielding potato varieties.
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Affiliation(s)
- Baljeet Singh
- Division of Crop Improvement and Seed Technology, Central Potato Research Institute, Shimla, India
- School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, India
| | - Umesh Goutam
- School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, India
| | - Sarvjeet Kukreja
- Department of Agronomy, Lovely Professional University, Phagwara, India
| | - Jagdev Sharma
- Division of Crop Production, Central Potato Research Institute, Shimla, India
| | - Salej Sood
- Division of Crop Improvement and Seed Technology, Central Potato Research Institute, Shimla, India
| | - Vinay Bhardwaj
- Division of Crop Improvement and Seed Technology, Central Potato Research Institute, Shimla, India
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10
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A high-resolution genome-wide association study of the grain ionome and agronomic traits in rice Oryza sativa subsp. indica. Sci Rep 2021; 11:19230. [PMID: 34584121 PMCID: PMC8478900 DOI: 10.1038/s41598-021-98573-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 09/09/2021] [Indexed: 02/08/2023] Open
Abstract
This study presents a comprehensive study of the genetic bases controlling variation in the rice ionome employing genome-wide association studies (GWAS) with a diverse panel of indica accessions, each genotyped with 5.2 million markers. GWAS was performed for twelve elements including B, Ca, Co, Cu, Fe, K, Mg, Mn, Mo, Na, P, and Zn and four agronomic traits including days to 50% flowering, grain yield, plant height and thousand grain weight. GWAS identified 128 loci associated with the grain elements and 57 associated with the agronomic traits. There were sixteen co-localization regions containing QTL for two or more traits. Fourteen grain element quantitative trait loci were stable across growing environments, which can be strong candidates to be used in marker-assisted selection to improve the concentrations of nutritive elements in rice grain. Potential candidate genes were revealed including OsNAS3 linked to the locus that controls the variation of Zn and Co concentrations. The effects of starch synthesis and grain filling on multiple grain elements were elucidated through the likely involvement of OsSUS1 and OsGSSB1 genes. Overall, our study provides crucial insights into the genetic basis of ionomic variations in rice and will facilitate improvement in breeding for trace mineral content.
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11
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Ma L, Qing C, Zhang M, Zou C, Pan G, Shen Y. GWAS with a PCA uncovers candidate genes for accumulations of microelements in maize seedlings. PHYSIOLOGIA PLANTARUM 2021; 172:2170-2180. [PMID: 34028036 DOI: 10.1111/ppl.13466] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Revised: 05/03/2021] [Accepted: 05/18/2021] [Indexed: 05/13/2023]
Abstract
Microelements are necessary for plant growth and development, they control key processes of physiological metabolism. Herein, we evaluated three accumulation-related performances for each of the four microelements (Fe, Zn, Cu, and Mn) among 305 inbred maize lines. Quantification of these microelements in maize roots and shoots revealed abundant phenotypic variations in the association panel, with the variation coefficients ranging from 0.31 to 0.76. Principal component analysis (PCA) of the three related traits (concentration in root, concentration in shoot, and transport coefficient) showed that PC1 and PC2 explained >95% of phenotypic variations for each element. The scores of PC1 and PC2 were thereby used for a genome-wide association study by combining 44,134 SNPs of this panel. A total of 27, 1, 5, and 3 SNPs were significantly (P < .05) associated with Zn-PC1, Zn-PC2, Cu-PC1, and Mn-PC2, respectively, with 11 genes closely linked (r2 > 0.8) to these SNPs. Of them, GRMZM2G142870, GRMZM2G045531, and GRMZM2G143512 were individually annotated as ABC transporter C family member 14, zinc transporter 3, and heavy metal ATPase10. A candidate gene association analysis further verified that GRMZM2G142870 and GRMZM2G045531 affect Zn and Mn accumulations, respectively. Evaluation of contrasting allele ratios in elite lines indicated that the majority of the alleles correlating with higher Zn or Cu had not been utilized in maize breeding. Integration of more "higher-accumulation" alleles in the elite lines will be practical for improving Zn and Cu accumulations in maize. Our findings contribute to genetic revelation and molecular marker-assisted selection of microelement accumulations in maize.
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Affiliation(s)
- Langlang Ma
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Chunyan Qing
- Mianyang Academy of Agricultural Sciences, Mianyang, China
| | - Minyan Zhang
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Chaoying Zou
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Guangtang Pan
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yaou Shen
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, China
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12
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Pawar S, Pandit E, Mohanty IC, Saha D, Pradhan SK. Population genetic structure and association mapping for iron toxicity tolerance in rice. PLoS One 2021; 16:e0246232. [PMID: 33647046 PMCID: PMC7920388 DOI: 10.1371/journal.pone.0246232] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 11/11/2020] [Indexed: 02/01/2023] Open
Abstract
Iron (Fe) toxicity is a major abiotic stress which severely reduces rice yield in many countries of the world. Genetic variation for this stress tolerance exists in rice germplasms. Mapping of gene(s)/QTL controlling the stress tolerance and transfer of the traits into high yielding rice varieties are essential for improvement against the stress. A panel population of 119 genotypes from 352 germplasm lines was constituted for detecting the candidate gene(s)/QTL through association mapping. STRUCTURE, GenAlEx and Darwin softwares were used to classify the population. The marker-trait association was detected by considering both the Generalized Linear Model (GLM) and Mixed Linear Model (MLM) analyses. Wide genetic variation was observed among the genotypes present in the panel population for the stress tolerance. Linkage disequilibrium was detected in the population for iron toxicity tolerance. The population was categorized into three genetic structure groups. Marker-trait association study considering both the Generalized Linear Model (GLM) and Mixed Linear Model (MLM) showed significant association of leaf browning index (LBI) with markers RM471, RM3, RM590 and RM243. Three novel QTL controlling Fe-toxicity tolerance were detected and designated as qFeTox4.3, qFeTox6.1 and qFeTox10.1. A QTL reported earlier in the marker interval of C955-C885 on chromosome 1 is validated using this panel population. The present study showed that QTL controlling Fe-toxicity tolerance to be co-localized with the QTL for Fe-biofortification of rice grain indicating involvement of common pathway for Fe toxicity tolerance and Fe content in rice grain. Fe-toxicity tolerance QTL qFeTox6.1 was co-localized with grain Fe-biofortification QTLs qFe6.1 and qFe6.2 on chromosome 6, whereas qFeTox10.1 was co-localized with qFe10.1 on chromosome 10. The Fe-toxicity tolerance QTL detected from this mapping study will be useful in marker-assisted breeding programs.
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Affiliation(s)
- S. Pawar
- Crop Improvement Division, ICAR-National Rice Research Institute, Cuttack, Odisha, India
| | - E. Pandit
- Crop Improvement Division, ICAR-National Rice Research Institute, Cuttack, Odisha, India
- Department of Bio-Science and Bio-Technology, Fakir Mohan University, Balasore, Odisha, India
| | - I. C. Mohanty
- Department of Biotechnology, College of Agriculture, OUAT, Bhubaneswar, Odisha, India
| | - D. Saha
- Department of Biotechnology, College of Agriculture, OUAT, Bhubaneswar, Odisha, India
| | - S. K. Pradhan
- Crop Improvement Division, ICAR-National Rice Research Institute, Cuttack, Odisha, India
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13
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Babu PM, Neeraja CN, Rathod S, Suman K, Uttam GA, Chakravartty N, Lachagari VBR, Chaitanya U, Rao LVS, Voleti SR. Stable SNP Allele Associations With High Grain Zinc Content in Polished Rice ( Oryza sativa L.) Identified Based on ddRAD Sequencing. Front Genet 2020; 11:763. [PMID: 32849786 PMCID: PMC7432318 DOI: 10.3389/fgene.2020.00763] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 06/29/2020] [Indexed: 01/01/2023] Open
Abstract
Polished rice is widely consumed staple food across the globe, however, it contains limited nutrients especially iron (Fe) and zinc (Zn). To identify promising genotypes for grain Zn, a total of 40 genotypes consisting 20 rice landraces, and 20 released high yielding rice varieties were evaluated in three environments (wet seasons 2014, 2015 and 2016) for nine traits including days to 50% flowering (DFF), plant height (PH), panicle length (PL), total number of tillers (TNT), single plant yield (SPY), Fe and Zn in brown (IBR, ZBR) and polished rice (IPR, ZPR). Additive Main Effect and Multiplicative Interaction (AMMI), Genotype and Genotype × Environment Interaction (GGE) analyses identified genotypes G22 (Edavankudi Pokkali), G17 (Taraori Basmati), G27 (Chittimuthyalu) and G26 (Kalanamak) stable for ZPR and G8 (Savitri) stable for SPY across three environments. Significant negative correlation between yield and grain Zn was reaffirmed. Regression analysis indicated the contribution of traits toward ZPR and SPY and also desirable level of grain Zn in brown rice. A total of 39,137 polymorphic single nucleotide polymorphisms (SNPs) were obtained through double digest restriction site associated DNA (dd-RAD) sequencing of 40 genotypes. Association analyses with nine phenotypic traits revealed 188 stable SNPs with six traits across three environments. ZPR was associated with SNPs located in three putative candidate genes (LOC_Os03g47980, LOC_Os07g47950 and LOC_Os07g48050) on chromosomes 3 and 7. The genomic region of chromosome 7 co localized with reported genomic regions (rMQTL7.1) and OsNAS3 candidate gene. SPY was found to be associated with 12 stable SNPs located in 11 putative candidate genes on chromosome 1, 6, and 12. Characterization of rice landraces and varieties in terms of stability for their grain Zn and yield identified promising donors and recipients along with genomic regions in the present study to be deployed rice Zn biofortification breeding program.
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Affiliation(s)
- P Madhu Babu
- ICAR-Indian Institute of Rice Research, Hyderabad, India
| | - C N Neeraja
- ICAR-Indian Institute of Rice Research, Hyderabad, India
| | | | - K Suman
- ICAR-Indian Institute of Rice Research, Hyderabad, India
| | - G Anurag Uttam
- ICAR-Indian Institute of Rice Research, Hyderabad, India
| | | | | | - U Chaitanya
- ICAR-Indian Institute of Rice Research, Hyderabad, India
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14
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Liu X, Fan F, Liu M, Long W, Yu Y, Yuan H, Pan G, Li N, Li S, Liu J. Quantitative Trait Loci Mapping of Mineral Element Contents in Brown Rice Using Backcross Inbred Lines Derived From Oryza longistaminata. FRONTIERS IN PLANT SCIENCE 2020; 11:1229. [PMID: 32903403 PMCID: PMC7434966 DOI: 10.3389/fpls.2020.01229] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 07/27/2020] [Indexed: 06/11/2023]
Abstract
Mineral elements play an extremely important role in human health, and are worthy of study in rice grain. Wild rice is an important gene pool for rice improvement including grain yield, disease, and pest resistance as well as mineral elements. In this study, we identified 33 quantitative trait loci (QTL) for Fe, Zn, Se, Cd, Hg, and As contents in wild rice Oryza longistaminata. Of which, 29 QTLs were the first report, and 12 QTLs were overlapped to form five clusters as qSe1/qCd1 on chromosome 1, qCd4.2/qHg4 on chromosome 4, qFe5.2/qZn5.2 on chromosome 5, qFe9/qHg9.2/qAs9.2 on chromosome 9, and qCd10/qHg10 on chromosome 10. Importantly, qSe1/qCd1, can significantly improve the Se content while reduce the Cd content, and qFe5.2/qZn5.2 can significantly improve both the Fe and Zn contents, they were delimited to an interval about 53.8 Kb and 26.2 Kb, respectively. These QTLs detected from Oryza longistaminata not only establish the basis for subsequent gene cloning to decipher the genetic mechanism of mineral element accumulation, but also provide new genetic resource for rice quality improvement.
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Affiliation(s)
- Xingdan Liu
- College of Agronomy, Hunan Agricultural University, Changsha, China
| | - Fengfeng Fan
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Science, Wuhan University, Wuhan, China
| | - Manman Liu
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Science, Wuhan University, Wuhan, China
| | - Weixiong Long
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Science, Wuhan University, Wuhan, China
| | - Yajie Yu
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Science, Wuhan University, Wuhan, China
| | - Huanran Yuan
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Science, Wuhan University, Wuhan, China
| | - Guojing Pan
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Science, Wuhan University, Wuhan, China
| | - Nengwu Li
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Science, Wuhan University, Wuhan, China
| | - Shaoqing Li
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Science, Wuhan University, Wuhan, China
| | - Jianfeng Liu
- College of Agronomy, Hunan Agricultural University, Changsha, China
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15
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Islam MZ, Arifuzzaman M, Banik S, Hossain MA, Ferdous J, Khalequzzaman M, Pittendrigh BR, Tomita M, Ali MP. Mapping QTLs underpin nutrition components in aromatic rice germplasm. PLoS One 2020; 15:e0234395. [PMID: 32525930 PMCID: PMC7289389 DOI: 10.1371/journal.pone.0234395] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 05/22/2020] [Indexed: 12/22/2022] Open
Abstract
As rice is an important staple food globally, research for development and enhancement of its nutritional value it is an imperative task. Identification of nutrient enriched rice germplasm and exploiting them for breeding programme is the easiest way to develop better quality rice. In this study, we analyzed 113 aromatic rice germplasm in order to identify quantitative trait loci (QTL) underpinning nutrition components and determined by measuring the normal frequency distribution for Fe, Zn, amylose, and protein content in those rice germplasm. Comparatively, the germplasm Radhuni pagal, Kalobakri, Thakurbhog (26.6 ppm) and Hatisail exhibited the highest mean values for Fe (16.9 ppm), Zn (34.1 ppm), amylose (26.6 ppm) and protein content (11.0 ppm), respectively. Moreover, a significant linear relationship (R2 = 0.693) was observed between Fe and Zn contents. Cluster analysis based on Mahalanobis D2 distances revealed four major clusters of 113 rice germplasm, with cluster III containing a maximum 37 germplasm and a maximum inter-cluster distance between clusters III and IV. The 45 polymorphic SSRs and four trait associations exhibited eight significant quantitative trait loci (QTL) located on eight different chromosomes using composite interval mapping (CIM). The highly significant QTL (variance 7.89%, LOD 2.02) for protein content (QTL.pro.1) was observed on chromosome 1 at 94.9cM position. Also, four QTLs for amylose content were observed with the highly significant QTL.amy.8 located on chromosome 8 exhibiting 7.2% variance with LOD 1.83. Only one QTL (QTL.Fe.9) for Fe content was located on chromosome 9 (LOD 1.24), and two (QTL.Zn.4 and QTL.Zn.5) for Zn on chromosome 4 (LOD 1.71) and 5 (LOD 1.18), respectively. Overall, germplasm from clusters III and IV might offer higher heterotic response with the identified QTLs playing a significant role in any rice biofortification breeding program and released with development of new varieties.
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Affiliation(s)
- M. Z. Islam
- Genetic Resources and Seed Division, Bangladesh Rice Research Institute (BRRI), Gazipur, Bangladesh
- * E-mail: (MZI); (MPA); (MT)
| | - M. Arifuzzaman
- Department of Genetics and Plant Breeding, Hajee Mohammad Danesh Science and Technology University, Dinajpur, Bangladesh
| | - S. Banik
- Grain Quality and Nutrition Division, Bangladesh Rice Research Institute (BRRI), Gazipur, Bangladesh
| | - M. A. Hossain
- Regional Station, Barisal, Bangladesh Rice Research Institute, Gazipur, Bangladesh
| | - J. Ferdous
- Biotechnology Division, Bangladesh Rice Research Institute (BRRI), Gazipur, Bangladesh
| | - M. Khalequzzaman
- Genetic Resources and Seed Division, Bangladesh Rice Research Institute (BRRI), Gazipur, Bangladesh
| | - B. R. Pittendrigh
- Department of Entomology, Michigan State University, East Lansing, Michigan, United States of America
| | - M. Tomita
- Genetics and Genome Engineering Laboratory, Green Biology Research Division, Research Institute of Green Science and Technology, Shizuoka University, Shizuoka City, Shizuoka, Japan
- * E-mail: (MZI); (MPA); (MT)
| | - M. P. Ali
- Entomolgy Division, Bangladesh Rice Research Institute (BRRI), Gazipur, Bangladesh
- * E-mail: (MZI); (MPA); (MT)
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16
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Zhang Z, Gao S, Chu C. Improvement of nutrient use efficiency in rice: current toolbox and future perspectives. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1365-1384. [PMID: 31919537 DOI: 10.1007/s00122-019-03527-6] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 12/24/2019] [Indexed: 05/03/2023]
Abstract
Modern agriculture relies heavily on chemical fertilizers, especially in terms of cereal production. The excess application of fertilizers not only increases production cost, but also causes severe environmental problems. As one of the major cereal crops, rice (Oryza sativa L.) provides the staple food for nearly half of population worldwide, especially in developing countries. Therefore, improving rice yield is always the priority for rice breeding. Macronutrients, especially nitrogen (N) and phosphorus (P), are two most important players for the grain yield of rice. However, with economic development and improved living standard, improving nutritional quality such as micronutrient contents in grains has become a new goal in order to solve the "hidden hunger." Micronutrients, such as iron (Fe), zinc (Zn), and selenium (Se), are critical nutritional elements for human health. Therefore, breeding the rice varieties with improved nutrient use efficiency (NUE) is thought to be one of the most feasible ways to increase both grain yield and nutritional quality with limited fertilizer input. In this review, we summarized the progresses in molecular dissection of genes for NUE by reverse genetics on macronutrients (N and P) and micronutrients (Fe, Zn, and Se), exploring natural variations for improving NUE in rice; and also, the current genetic toolbox and future perspectives for improving rice NUE are discussed.
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Affiliation(s)
- Zhihua Zhang
- School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Shaopei Gao
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Chengcai Chu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.
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17
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Ram H, Gandass N, Sharma A, Singh A, Sonah H, Deshmukh R, Pandey AK, Sharma TR. Spatio-temporal distribution of micronutrients in rice grains and its regulation. Crit Rev Biotechnol 2020; 40:490-507. [DOI: 10.1080/07388551.2020.1742647] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Hasthi Ram
- Department of Agri-Biotechnology, National Agri-Food Biotechnology Institute (NABI), Mohali, India
| | - Nishu Gandass
- Department of Agri-Biotechnology, National Agri-Food Biotechnology Institute (NABI), Mohali, India
| | - Ankita Sharma
- Department of Agri-Biotechnology, National Agri-Food Biotechnology Institute (NABI), Mohali, India
| | - Anmol Singh
- Department of Agri-Biotechnology, National Agri-Food Biotechnology Institute (NABI), Mohali, India
| | - Humira Sonah
- Department of Agri-Biotechnology, National Agri-Food Biotechnology Institute (NABI), Mohali, India
| | - Rupesh Deshmukh
- Department of Agri-Biotechnology, National Agri-Food Biotechnology Institute (NABI), Mohali, India
| | - Ajay Kumar Pandey
- Department of Agri-Biotechnology, National Agri-Food Biotechnology Institute (NABI), Mohali, India
| | - Tilak Raj Sharma
- Department of Agri-Biotechnology, National Agri-Food Biotechnology Institute (NABI), Mohali, India
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18
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Tan Y, Zhou J, Wang J, Sun L. The Genetic Architecture for Phenotypic Plasticity of the Rice Grain Ionome. FRONTIERS IN PLANT SCIENCE 2020; 11:12. [PMID: 32158453 PMCID: PMC7052182 DOI: 10.3389/fpls.2020.00012] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 01/08/2020] [Indexed: 05/26/2023]
Abstract
The ionome of the rice grain is crucial for the health of populations that consume rice as a staple food. However, the contribution of phenotypic plasticity to the variation of rice grain ionome and the genetic architecture of phenotypic plasticity are poorly understood. In this study, we investigated the rice grain ionome of a rice diversity panel in up to eight environments. A considerable proportion of phenotypic variance can be attributed to phenotypic plasticity. Then, phenotypic plasticity and mean phenotype were quantified using Bayesian Finlay-Wilkinson regression, and a significant correlation between them was observed. However, the genetic architecture of mean phenotype was distinct from that of phenotypic plasticity. Also, the correlation between them was mainly attributed to the phenotypic divergence between rice subspecies. Furthermore, the results of whole-genome regression analysis showed that the genetic loci related to phenotypic plasticity can explain a considerable proportion of the phenotypic variance in some environments, especially for Cd, Cu, Mn, and Zn. Our study not only sheds light on the genetic architecture of phenotypic plasticity of the rice grain ionome but also suggests that the genetic loci which related to phenotypic plasticity are valuable in rice grain ionome improvement breeding.
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Affiliation(s)
- Yongjun Tan
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
- University of Chinese Academy of Science, Beijing, China
| | - Jieqiang Zhou
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
- College of Agronomy, Hunan Agricultural University, Changsha, China
| | - Jiurong Wang
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
| | - Liang Sun
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
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19
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Tan Y, Sun L, Song Q, Mao D, Zhou J, Jiang Y, Wang J, Fan T, Zhu Q, Huang D, Xiao H, Chen C. Genetic architecture of subspecies divergence in trace mineral accumulation and elemental correlations in the rice grain. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:529-545. [PMID: 31734869 DOI: 10.1007/s00122-019-03485-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 11/11/2019] [Indexed: 05/12/2023]
Abstract
Genome differentiation has shaped the divergence in element concentration between rice subspecies and contributed to the correlation among trace minerals in the rice grain. The balance between trace minerals in rice, a staple food for more than half of the world's population, is crucial for human health. However, the genetic basis underlying the correlation between trace minerals has not been fully elucidated. To address this issue, we first quantified the concentrations of 11 trace minerals in the grains of a diversity panel of 575 rice cultivars. We found that eight elements were accumulated at significantly different levels between the indica and japonica subspecies, and we also observed significant correlation patterns among a number of elements. Further, using a genome-wide association study, we identified a total of 96 significant association loci (SALs). The differentiation of the major-effect SALs along with the different number of high-concentration alleles present in the two subspecies shaped the different element performance in indica and japonica varieties. Only a few SALs located in clusters and the majority of SALs showed subspecies/subgroup differentiation, indicating that the correlations between elements in the diversity panel were mainly caused by genome differentiation instead of shared genetic basis. The genetic architecture unveiled in this study will facilitate improvement in breeding for trace mineral content.
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Affiliation(s)
- Yongjun Tan
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Innovation Academy for Seed Design, Chinese Academy of Sciences, Changsha, 410125, Hunan, China
- University of Chinese Academy of Science, Beijing, 100049, China
| | - Liang Sun
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Innovation Academy for Seed Design, Chinese Academy of Sciences, Changsha, 410125, Hunan, China
| | - Qingnan Song
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Science, Beijing, 100049, China
| | - Donghai Mao
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Innovation Academy for Seed Design, Chinese Academy of Sciences, Changsha, 410125, Hunan, China
| | - Jieqiang Zhou
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Innovation Academy for Seed Design, Chinese Academy of Sciences, Changsha, 410125, Hunan, China
| | - Youru Jiang
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Innovation Academy for Seed Design, Chinese Academy of Sciences, Changsha, 410125, Hunan, China
| | - Jiurong Wang
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Innovation Academy for Seed Design, Chinese Academy of Sciences, Changsha, 410125, Hunan, China
| | - Tony Fan
- University of Toronto, Toronto, M5S2E5, Canada
| | - Qihong Zhu
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Innovation Academy for Seed Design, Chinese Academy of Sciences, Changsha, 410125, Hunan, China
| | - Daoyou Huang
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Innovation Academy for Seed Design, Chinese Academy of Sciences, Changsha, 410125, Hunan, China
| | - Han Xiao
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Caiyan Chen
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Innovation Academy for Seed Design, Chinese Academy of Sciences, Changsha, 410125, Hunan, China.
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20
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Raza Q, Riaz A, Sabar M, Atif RM, Bashir K. Meta-analysis of grain iron and zinc associated QTLs identified hotspot chromosomal regions and positional candidate genes for breeding biofortified rice. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 288:110214. [PMID: 31521222 DOI: 10.1016/j.plantsci.2019.110214] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 07/13/2019] [Accepted: 08/06/2019] [Indexed: 05/09/2023]
Abstract
Biofortification of staple crops with essential micronutrients is the sustainable way to overcome the hidden hunger. A large number of quantitative trait loci (QTL) linked with grain micronutrient contents have been reported in different mapping studies. Identification of consistent QTLs across diverse genetic backgrounds is useful for candidate gene analysis and marker assisted selection of target traits. In this study, an up to date meta-analysis of grain iron and zinc associated QTLs was performed and 48 meta-QTLs (MQTLs) distributed across 12 rice chromosomes were identified. The 95% confidence intervals of identified genomic regions were significantly narrower than the average of their corresponding original QTLs. A total of 9308 genes/transcripts physically located within or near MQTL regions were retrieved and through prioritization of candidate genes (CGs) 663 non-redundant iron and zinc CGs were selected and studied in detailed. Several functionally characterized iron and zinc homoeostasis related genes e.g OsATM3, OsDMAS1, OsFRO2, OsNAS1-3, OsVIT2, OsYSL16, OsZIP3 and OsZIP7 were also included in our MQTL analysis. More than 64% genes were enriched with zinc and iron binding gene ontology terms and were involved in oxidation reduction process, carbohydrate metabolic process, regulation of transcription, trans-membrane transport, response to oxidative stress, cell redox homeostasis and proteolysis etc. In-silico transcriptomic analysis of rice identified 260 CGs which were regulated in response to iron and zinc stresses. We also identified at least 37 genes which were differentially expressed under both stress conditions and majority of these have not been studied in detailed before. Our results strongly indicate that majority of the MQTLs identified in this study are hotspots for grain iron and zinc concentration and are worth of intensive functional studies in near future.
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Affiliation(s)
- Qasim Raza
- Molecular Breeding Laboratory, Division of Plant Breeding and Genetics, Rice Research Institute, Kala Shah Kaku, Sheikhupura, Pakistan.
| | - Awais Riaz
- Molecular Breeding Laboratory, Division of Plant Breeding and Genetics, Rice Research Institute, Kala Shah Kaku, Sheikhupura, Pakistan
| | - Muhammad Sabar
- Molecular Breeding Laboratory, Division of Plant Breeding and Genetics, Rice Research Institute, Kala Shah Kaku, Sheikhupura, Pakistan
| | - Rana Muhammad Atif
- Department of Plant Breeding and Genetics, University of Agriculture Faisalabad, Pakistan; US-Pak Centre for Advanced Studies in Food and Agricultural Security, University of Agriculture Faisalabad, Pakistan
| | - Khurram Bashir
- Plant Genomic Network Research Team, Center for Sustainable Resource Science, RIKEN, Yokohama Campus, Yokohama, Japan.
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21
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Descalsota-Empleo GI, Noraziyah AAS, Navea IP, Chung C, Dwiyanti MS, Labios RJD, Ikmal AM, Juanillas VM, Inabangan-Asilo MA, Amparado A, Reinke R, Cruz CMV, Chin JH, Swamy BPM. Genetic Dissection of Grain Nutritional Traits and Leaf Blight Resistance in Rice. Genes (Basel) 2019; 10:E30. [PMID: 30626141 PMCID: PMC6356647 DOI: 10.3390/genes10010030] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Revised: 12/27/2018] [Accepted: 12/28/2018] [Indexed: 11/16/2022] Open
Abstract
Colored rice is rich in nutrition and also a good source of valuable genes/quantitative trait loci (QTL) for nutrition, grain quality, and pest and disease resistance traits for use in rice breeding. Genome-wide association analysis using high-density single nucleotide polymorphism (SNP) is useful in precisely detecting QTLs and genes. We carried out genome-wide association analysis in 152 colored rice accessions, using 22,112 SNPs to map QTLs for nutritional, agronomic, and bacterial leaf blight (BLB) resistance traits. Wide variations and normal frequency distributions were observed for most of the traits except anthocyanin content and BLB resistance. The structural and principal component analysis revealed two subgroups. The linkage disequilibrium (LD) analysis showed 74.3% of the marker pairs in complete LD, with an average LD distance of 1000 kb and, interestingly, 36% of the LD pairs were less than 5 Kb, indicating high recombination in the panel. In total, 57 QTLs were identified for ten traits at p < 0.0001, and the phenotypic variance explained (PVE) by these QTLs varied from 9% to 18%. Interestingly, 30 (53%) QTLs were co-located with known or functionally-related genes. Some of the important candidate genes for grain Zinc (Zn) and BLB resistance were OsHMA9, OsMAPK6, OsNRAMP7, OsMADS13, and OsZFP252, and Xa1, Xa3, xa5, xa13 and xa26, respectively. Red rice genotype, Sayllebon, which is high in both Zn and anthocyanin content, could be a valuable material for a breeding program for nutritious rice. Overall, the QTLs identified in our study can be used for QTL pyramiding as well as genomic selection. Some of the novel QTLs can be further validated by fine mapping and functional characterization. The results show that pigmented rice is a valuable resource for mineral elements and antioxidant compounds; it can also provide novel alleles for disease resistance as well as for yield component traits. Therefore, large opportunities exist to further explore and exploit more colored rice accessions for use in breeding.
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Affiliation(s)
- Gwen Iris Descalsota-Empleo
- International Rice Research Institute (IRRI), Laguna 4031, Philippines.
- University of the Southern Mindanao, Kabacan, Cotabato 9407, Philippines.
| | | | - Ian Paul Navea
- International Rice Research Institute (IRRI), Laguna 4031, Philippines.
- Nousbo Corp. #4-107, 89 Seohoro, Gwonsun, Suwon 16614, Gyeonggi, Korea.
| | - Chongtae Chung
- Chungcheongnam-do Agricultural Research and Extension Services, 167, Chusa-ro, Shinam-myeon, Yesan-gun 32418, Chungcheongnam-do, Korea.
| | - Maria Stefanie Dwiyanti
- International Rice Research Institute (IRRI), Laguna 4031, Philippines.
- Applied Plant Genome Laboratory, Hokkaido University, Kita 9, Nishi 9, Kita-ku, Sapporo 060-8589, Japan.
| | | | - Asmuni Mohd Ikmal
- Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia.
| | | | | | - Amery Amparado
- International Rice Research Institute (IRRI), Laguna 4031, Philippines.
| | - Russell Reinke
- International Rice Research Institute (IRRI), Laguna 4031, Philippines.
| | | | - Joong Hyoun Chin
- Department of Integrative Bio-Industrial Engineering, Sejong University, 209, Neungdong-ro, Gwangjin-gu, Seoul 05006, Korea.
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22
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Shen S, Zhang H, Huang K, Chen H, Shen W, Fang X. Differentiation of cultivation areas and crop years of milled rice using single grain mass spectrometry. NEW J CHEM 2019. [DOI: 10.1039/c8nj02740d] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
A method for the rapid detection of fatty acids in single rice grain would make the evaluation of rice quality easier.
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Affiliation(s)
- Susu Shen
- State Key Laboratory of Inorganic Synthesis and Preparative Chemistry
- College of Chemistry
- Jilin University
- Changchun 130012
- P. R. China
| | - Hua Zhang
- State Key Laboratory of Inorganic Synthesis and Preparative Chemistry
- College of Chemistry
- Jilin University
- Changchun 130012
- P. R. China
| | - Keke Huang
- State Key Laboratory of Inorganic Synthesis and Preparative Chemistry
- College of Chemistry
- Jilin University
- Changchun 130012
- P. R. China
| | - Huanwen Chen
- State Key Laboratory of Inorganic Synthesis and Preparative Chemistry
- College of Chemistry
- Jilin University
- Changchun 130012
- P. R. China
| | - Wenxin Shen
- Jiangxi Institute of Analysis and Testing
- Nanchang 330029
- P. R. China
| | - Xiaowei Fang
- Jiangxi Key Laboratory for Mass Spectrometry and Instrumentation
- East China University of Technology
- Nanchang 330013
- P. R. China
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23
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Yang M, Lu K, Zhao FJ, Xie W, Ramakrishna P, Wang G, Du Q, Liang L, Sun C, Zhao H, Zhang Z, Liu Z, Tian J, Huang XY, Wang W, Dong H, Hu J, Ming L, Xing Y, Wang G, Xiao J, Salt DE, Lian X. Genome-Wide Association Studies Reveal the Genetic Basis of Ionomic Variation in Rice. THE PLANT CELL 2018; 30:2720-2740. [PMID: 30373760 PMCID: PMC6305983 DOI: 10.1105/tpc.18.00375] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 09/28/2018] [Accepted: 10/24/2018] [Indexed: 05/18/2023]
Abstract
Rice (Oryza sativa) is an important dietary source of both essential micronutrients and toxic trace elements for humans. The genetic basis underlying the variations in the mineral composition, the ionome, in rice remains largely unknown. Here, we describe a comprehensive study of the genetic architecture of the variation in the rice ionome performed using genome-wide association studies (GWAS) of the concentrations of 17 mineral elements in rice grain from a diverse panel of 529 accessions, each genotyped at ∼6.4 million single nucleotide polymorphism loci. We identified 72 loci associated with natural ionomic variations, 32 that are common across locations and 40 that are common within a single location. We identified candidate genes for 42 loci and provide evidence for the causal nature of three genes, the sodium transporter gene Os-HKT1;5 for sodium, Os-MOLYBDATE TRANSPORTER1;1 for molybdenum, and Grain number, plant height, and heading date7 for nitrogen. Comparison of GWAS data from rice versus Arabidopsis (Arabidopsis thaliana) also identified well-known as well as new candidates with potential for further characterization. Our study provides crucial insights into the genetic basis of ionomic variations in rice and serves as an important foundation for further studies on the genetic and molecular mechanisms controlling the rice ionome.
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Affiliation(s)
- Meng Yang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Kai Lu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
- Center of Applied Biotechnology, Wuhan Institute of Bioengineering, Wuhan 430415, 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
| | - Weibo Xie
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Priya Ramakrishna
- Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, United Kingdom
| | - Guangyuan Wang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Qingqing Du
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Limin Liang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Cuiju Sun
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Hu Zhao
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Zhanyi Zhang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Zonghao Liu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Jingjing Tian
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Xin-Yuan Huang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Wensheng Wang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Huaxia Dong
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Jintao Hu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Luchang Ming
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Yongzhong Xing
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Gongwei Wang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Jinhua Xiao
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - David E Salt
- Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, United Kingdom
| | - Xingming Lian
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
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24
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Descalsota GIL, Swamy BPM, Zaw H, Inabangan-Asilo MA, Amparado A, Mauleon R, Chadha-Mohanty P, Arocena EC, Raghavan C, Leung H, Hernandez JE, Lalusin AB, Mendioro MS, Diaz MGQ, Reinke R. Genome-Wide Association Mapping in a Rice MAGIC Plus Population Detects QTLs and Genes Useful for Biofortification. FRONTIERS IN PLANT SCIENCE 2018; 9:1347. [PMID: 30294335 PMCID: PMC6158342 DOI: 10.3389/fpls.2018.01347] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2018] [Accepted: 08/27/2018] [Indexed: 05/19/2023]
Abstract
The development of rice genotypes with micronutrient-dense grains and disease resistance is one of the major priorities in rice improvement programs. We conducted Genome-wide association studies (GWAS) using a Multi-parent Advanced Generation Inter-Cross (MAGIC) Plus population to identify QTLs and SNP markers that could potentially be integrated in biofortification and disease resistance breeding. We evaluated 144 MAGIC Plus lines for agronomic and biofortification traits over two locations for two seasons, while disease resistance was screened for one season in the screen house. X-ray fluorescence technology was used to measure grain Fe and Zn concentrations. Genotyping was carried out by genotype by sequencing and a total of 14,242 SNP markers were used in the association analysis. We used Mixed linear model (MLM) with kinship and detected 57 significant genomic regions with a -log10 (P-value) ≥ 3.0. The PH 1.1 and Zn 7.1 were consistently identified in all the four environments, ten QTLs qDF 3.1, qDF 6.2 qDF 9.1 qPH 5.1 qGL 3.1, qGW 3.1, qGW 11.1, and qZn 6.2 were detected in two environments, while two major loci qBLB 11.1 and qBLB 5.1 were identified for Bacterial Leaf Blight (BLB) resistance. The associated SNP markers were found to co-locate with known major genes and QTLs such as OsMADS50 for days to flowering, osGA20ox2 for plant height, and GS3 for grain length. Similarly, Xa4 and xa5 genes were identified for BLB resistance and Pi5(t), Pi28(t), and Pi30(t) genes were identified for Blast resistance. A number of metal homeostasis genes OsMTP6, OsNAS3, OsMT2D, OsVIT1, and OsNRAMP7 were co-located with QTLs for Fe and Zn. The marker-trait relationships from Bayesian network analysis showed consistency with the results of GWAS. A number of promising candidate genes reported in our study can be further validated. We identified several QTLs/genes pyramided lines with high grain Zn and acceptable yield potential, which are a good resource for further evaluation to release as varieties as well as for use in breeding programs.
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Affiliation(s)
- Gwen Iris L. Descalsota
- Strategic Innovation Platform, International Rice Research Institute, Manila, Philippines
- University of Southern Mindanao, Kabacan, Philippines
| | | | - Hein Zaw
- Strategic Innovation Platform, International Rice Research Institute, Manila, Philippines
| | | | - Amery Amparado
- Strategic Innovation Platform, International Rice Research Institute, Manila, Philippines
| | - Ramil Mauleon
- Strategic Innovation Platform, International Rice Research Institute, Manila, Philippines
| | | | - Emily C. Arocena
- Philippine Rice Research Institute, Science City of Muñoz, Philippines
| | - Chitra Raghavan
- Strategic Innovation Platform, International Rice Research Institute, Manila, Philippines
| | - Hei Leung
- Strategic Innovation Platform, International Rice Research Institute, Manila, Philippines
| | | | | | | | | | - Russell Reinke
- Strategic Innovation Platform, International Rice Research Institute, Manila, Philippines
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25
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Zhang GM, Zheng TQ, Chen Z, Wang YL, Wang Y, Shi YM, Wang CC, Zhang LY, Ma JT, Deng LW, Li W, Xu TT, Liang CZ, Xu JL, Li ZK. Joint Exploration of Favorable Haplotypes for Mineral Concentrations in Milled Grains of Rice ( Oryza sativa L.). FRONTIERS IN PLANT SCIENCE 2018; 9:447. [PMID: 29706977 PMCID: PMC5906679 DOI: 10.3389/fpls.2018.00447] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 03/22/2018] [Indexed: 05/23/2023]
Abstract
Grain minerals in rice, especially those in milled grains, are important sources of micro-nutrition elements, such as iron (Fe), zinc (Zn), manganese (Mn), copper (Cu), and selenium (Se), and of toxic heavy metal elements, especially cadmium (Cd), for populations consuming a rice diet. To date, the genetic mechanism underlying grain mineral concentrations (GMCs) in milled grain remains largely unknown. In this report, we adopted a set of 698 germplasms consisting of two subsets [indica/Xian (X-set) and japonica/Geng (G-set)], to detect quantitative trait loci (QTL) affecting GMC traits of Fe, Zn, Cd, Mn, Cu, and Se in milled grains. A total of 47 QTL regions, including 18 loci and 29 clusters (covering 62 Cd loci), responsible for the GMCs in milled grains were detected throughout the genome. A joint exploration of favorable haplotypes of candidate genes was carried out as follows: (1) By comparative mapping, 10 chromosome regions were found to be consistent with our previously detected QTL from linkage mapping. (2) Within eight of these regions on chromosomes 1, 4, 6, 7, and 8, candidate genes were identified in the genome annotation database. (3) A total of 192 candidate genes were then submitted to further haplotype analysis using million-scale single nucleotide polymorphisms (SNPs) from the X-set and the G-set. (4) Finally, 37 genes (19.3%) were found to be significant in the association between the QTL targeting traits and the haplotype variations by pair-wise comparison. (5) The phenotypic values for the haplotypes of each candidate were plotted. Three zinc finger (like) genes within two candidate QTL regions (qFe6-2 and qZn7), and three major GMC traits (Fe, Zn, and Cd) were picked as sample cases, in addition to non-exhausted cross validations, to elucidate this kind of association by trait value plotting. Taken together, our results, especially the 37 genes with favorable haplotype variations, will be useful for rice biofortification molecular breeding.
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Affiliation(s)
- Guo-Min Zhang
- Northern Japonica Rice Molecular Breeding Joint Research Center, Chinese Academy of Sciences, Haerbin, China
| | - Tian-Qing Zheng
- Institute of Crop Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhuo Chen
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Yong-Li Wang
- Northern Japonica Rice Molecular Breeding Joint Research Center, Chinese Academy of Sciences, Haerbin, China
| | - Ying Wang
- Northern Japonica Rice Molecular Breeding Joint Research Center, Chinese Academy of Sciences, Haerbin, China
| | - Yu-Min Shi
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Chun-Chao Wang
- Institute of Crop Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Li-Yan Zhang
- Northern Japonica Rice Molecular Breeding Joint Research Center, Chinese Academy of Sciences, Haerbin, China
| | - Jun-Tao Ma
- Northern Japonica Rice Molecular Breeding Joint Research Center, Chinese Academy of Sciences, Haerbin, China
| | - Ling-Wei Deng
- Northern Japonica Rice Molecular Breeding Joint Research Center, Chinese Academy of Sciences, Haerbin, China
| | - Wan Li
- Northern Japonica Rice Molecular Breeding Joint Research Center, Chinese Academy of Sciences, Haerbin, China
| | - Tian-Tian Xu
- Institute of Crop Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Cheng-Zhi Liang
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Jian-Long Xu
- Institute of Crop Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China
- Shenzhen Institute of Breeding for Innovation, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Zhi-Kang Li
- Institute of Crop Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China
- Shenzhen Institute of Breeding for Innovation, Chinese Academy of Agricultural Sciences, Shenzhen, China
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26
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Kakar KU, Nawaz Z, Cui Z, Almoneafy AA, Ullah R, Shu QY. Rhizosphere-associated Alcaligenes and Bacillus strains that induce resistance against blast and sheath blight diseases, enhance plant growth and improve mineral content in rice. J Appl Microbiol 2018; 124:779-796. [PMID: 29280555 DOI: 10.1111/jam.13678] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 11/21/2017] [Accepted: 12/19/2017] [Indexed: 11/30/2022]
Abstract
AIMS To examine the biocontrol activities of five rhizobacterial strains (i.e. Alcaligenes faecalis strains Bk1 and P1, Bacillus amyloliquefaciens strain Bk7 and Brevibacillus laterosporus stains B4 and S5), to control the rice blast and sheath blight diseases in greenhouse and to study their possible modes of action. METHODS AND RESULTS Five potential plant growth-promoting rhizobacterial (PGPR) strains isolated from rice rhizospheres were tested for in vitro antifungal activities against Magnaporthe oryzae, Rhizoctonia solani, Botrytis cinerea and Fusarium graminearum. In vitro trials showed that three strains, Bk1, P1 and Bk7, were able to unanimously suppress the mycelial growth of the target pathogens. In greenhouse, the application of these three PGPR strains significantly suppressed the incidences of rice blast and sheath blight diseases. At 2 weeks after pathogen inoculation, the highest percentages of disease suppression were noted for Alc. faecalis strain Bk1 (72%) for rice blast, Alc. faecalis strain P1 (71%) for sheath blight, followed by B. amyloliquefaciens strain Bk7. Moreover, these strains significantly improved the plant growth, enriched the content of mineral nutrients in seedlings and increased the expression of major defence-related rice genes. All three strains were marked positive for phosphate solubilization, the production of indoleacetic acid, ammonia and siderophores and catalase activity. In addition, these strains were able to form biofilms and carried multiple lipopeptide biosynthetic genes as revealed by multiplex PCR. CONCLUSION This study reports new potential biocontrol agents for blast and sheath blight diseases of rice. SIGNIFICANCE AND IMPACT OF THE STUDY This study contributes to better understanding of the mechanisms involved in interaction between beneficial rhizobacteria, fungal pathogens and host plants.
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Affiliation(s)
- K U Kakar
- State Key Laboratory of Rice Biology, Institution of Crop Science, Zhejiang University, Hangzhou, China.,Molecular Genetics Key Laboratory of China Tobacco, Guizhou Academy of Tobacco Science, Guiyang, China
| | - Z Nawaz
- Molecular Genetics Key Laboratory of China Tobacco, Guizhou Academy of Tobacco Science, Guiyang, China
| | - Z Cui
- Department of Plant Pathology and Ecology, The Connecticut Agricultural Experimental Station, New Haven, CT, USA.,Department of Biological Sciences, University of Wisconsin, Milwaukee, WI, USA
| | - A A Almoneafy
- Department of Biological Sciences, College of Education and Science, Albaydaa University, Rada'a, Yemen
| | - R Ullah
- Department of Environmental Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Q-Y Shu
- State Key Laboratory of Rice Biology, Institution of Crop Science, Zhejiang University, Hangzhou, China
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27
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Characterization of a major QTL for manganese accumulation in rice grain. Sci Rep 2017; 7:17704. [PMID: 29255144 PMCID: PMC5735179 DOI: 10.1038/s41598-017-18090-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 12/06/2017] [Indexed: 11/13/2022] Open
Abstract
Some diets lack sufficient manganese (Mn), an essential mineral. Increasing Mn in grain by biofortification could prevent Mn deficiency, but may increase levels of the toxic element cadmium (Cd). Here, we investigated Mn in rice (Oryza sativa) grains in recombinant inbred lines (RILs) from the cross of 93–11 (low grain Mn) with PA64s (high grain Mn). Quantitative trait locus (QTL) analysis to identify loci controlling grain Mn identified a major QTL, qGMN7.1, on the short arm of chromosome 7; qGMN7.1 explained 15.6% and 22.8% of the phenotypic variation in the RIL populations grown in two distinct environments. We validated the QTL with a chromosome segment substitution line (CSSL), CSSL-qGMN7.1, in the 93–11 background harboring qGMN7.1 from PA64s. Compared to 93–11, CSSL-qGMN7.1 grain had increased Mn and decreased Cd concentrations; CSSL-qGMN7.1 roots also showed enhanced Mn uptake. Fine mapping delimited qGMN7.1 to a 49.3-kb region containing OsNRAMP5, a gene responsible for Mn and Cd uptake. Sequence variations in the OsNRAMP5 promoter caused changes in its transcript level, and in grain Mn levels. Our study thus cloned a major QTL for grain Mn concentration in rice, and identified materials for breeding rice for high Mn and low Cd concentrations in the grain.
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Khazaei H, Podder R, Caron CT, Kundu SS, Diapari M, Vandenberg A, Bett KE. Marker-Trait Association Analysis of Iron and Zinc Concentration in Lentil ( Lens culinaris Medik.) Seeds. THE PLANT GENOME 2017; 10. [PMID: 28724070 DOI: 10.3835/plantgenome2017.02.0007] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Lentil ( Medik.) seeds are relatively rich in iron (Fe) and zinc (Zn), making lentil a potential crop to aid in the global battle against human micronutrient deficiency. Understanding the genetic basis for uptake of seed Fe and Zn is required to increase sustainable concentrations of these minerals in seeds. The objectives of this study were to characterize genetic variation in seed Fe and Zn concentration and to identify molecular markers associated with these traits across diverse lentil accessions. A set of 138 cultivated lentil accessions from 34 countries were evaluated in four environments (2 sites × 2 yr) in Saskatchewan, Canada. The collection was genotyped using 1150 single-nucleotide polymorphism (SNP) markers that are distributed across the lentil genome. The germplasm tested exhibited a wide range of variation for seed Fe and Zn concentration. The marker-trait association analysis detected two SNP markers tightly linked to seed Fe and one linked to seed Zn concentration (-log10 ≥ 4.36). Additional markers were detected at -log10 ≥ 3.06. A number of putative candidate genes underlying detected loci encode Fe- and Zn-related functions. This study provides insight into the genetics of seed Fe and Zn concentration of lentil and opportunities for marker-assisted selection to improve micronutrient concentration as part of micronutrient biofortification programs.
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Jia C, Wu X, Chen M, Wang Y, Liu X, Gong P, Xu Q, Wang X, Gao H, Wang Z. Identification of genetic loci associated with crude protein and mineral concentrations in alfalfa (Medicago sativa) using association mapping. BMC PLANT BIOLOGY 2017; 17:97. [PMID: 28583066 PMCID: PMC5460482 DOI: 10.1186/s12870-017-1047-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 05/25/2017] [Indexed: 05/04/2023]
Abstract
BACKGROUND Alfalfa (Medicago sativa) is one of the most important legume forage species in China and many other countries of the world. It provides a quality source of proteins and minerals to animals. Genetic underpinnings for these important traits, however, are elusive. An alfalfa (M. sativa) association mapping study for six traits, namely crude protein (CP), rumen undegraded protein (RUP), and four mineral elements (Ca, K, Mg and P), was conducted in three consecutive years using a large collection encompassing 336 genotypes genotyped with 85 simple sequence repeat (SSR) markers. RESULTS All the traits were significantly influenced by genotype, environment, and genotype × environment interaction. Eight-five significant associations (P < 0.005) were identified. Among these, five associations with Ca were repeatedly observed and six co-localized associations were identified. CONCLUSIONS The identified marker alleles significantly associated with the traits provided important information for understanding genetic controls of alfalfa quality. The markers could be used in assisting selection for the individual traits in breeding populations for developing new alfalfa cultivars.
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Affiliation(s)
- Congjun Jia
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Xinming Wu
- Institute of Animal Husbandry and Veterinary Science, Shanxi Academy of Agricultural Sciences, Taiyuan, 030032 China
| | - Min Chen
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Yunqi Wang
- Institute of Animal Husbandry and Veterinary Science, Shanxi Academy of Agricultural Sciences, Taiyuan, 030032 China
| | - Xiqiang Liu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Pan Gong
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Qingfang Xu
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu, 030801 China
| | - Xuemin Wang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Hongwen Gao
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Zan Wang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
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dos Santos RS, de Araujo AT, Pegoraro C, de Oliveira AC. Dealing with iron metabolism in rice: from breeding for stress tolerance to biofortification. Genet Mol Biol 2017; 40:312-325. [PMID: 28304072 PMCID: PMC5452141 DOI: 10.1590/1678-4685-gmb-2016-0036] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 09/22/2016] [Indexed: 12/23/2022] Open
Abstract
Iron is a well-known metal. Used by humankind since ancient times in many different ways, this element is present in all living organisms, where, unfortunately, it represents a two-way problem. Being an essential block in the composition of different proteins and metabolic pathways, iron is a vital component for animals and plants. That is why iron deficiency has a severe impact on the lives of different organisms, including humans, becoming a major concern, especially in developing countries where access to adequate nutrition is still difficult. On the other hand, this metal is also capable of causing damage when present in excess, becoming toxic to cells and affecting the whole organism. Because of its importance, iron absorption, transport and storage mechanisms have been extensively investigated in order to design alternatives that may solve this problem. As the understanding of the strategies that plants use to control iron homeostasis is an important step in the generation of improved plants that meet both human agricultural and nutritional needs, here we discuss some of the most important points about this topic.
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Affiliation(s)
- Railson Schreinert dos Santos
- Plant Genomics and Breeding Center (CGF), Universidade Federal de
Pelotas, Pelotas, RS, Brazil
- Technology Development Center (CDTec), Universidade Federal de
Pelotas, Pelotas, RS, Brazil
| | | | - Camila Pegoraro
- Plant Genomics and Breeding Center (CGF), Universidade Federal de
Pelotas, Pelotas, RS, Brazil
| | - Antonio Costa de Oliveira
- Plant Genomics and Breeding Center (CGF), Universidade Federal de
Pelotas, Pelotas, RS, Brazil
- Technology Development Center (CDTec), Universidade Federal de
Pelotas, Pelotas, RS, Brazil
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Zhang W, Yan C, Li M, Yang L, Ma B, Meng H, Xie L, Chen J. Transcriptome Analysis Reveals the Response of Iron Homeostasis to Early Feeding by Small Brown Planthopper in Rice. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2017; 65:1093-1101. [PMID: 28112511 DOI: 10.1021/acs.jafc.6b04674] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
It has been documented that planthopper attacks change iron (Fe) content of rice plants. To investigate whether planthopper attacks change rice Fe homeostasis at the molecular level, the response of rice Fe homeostasis to early feeding by small brown planthopper (SBPH) was examined by transcriptome profiling. Results showed that the concentration of Fe and nicotianamine decreased in resistant rice genotype and increased in susceptible rice genotype after attack by SBPH. Transcriptome profiling showed that 13 and 21 Fe homeostasis-related genes encoded enzymes that were involved in phytosiderophore biosynthesis and that Fe transporters and regulators displayed altered expression in resistant and susceptible rice genotypes, respectively, after attack by SBPH. This revealing response of Fe homeostasis to planthopper attack in rice at the molecular level provided new insight into rice plants' response to planthopper attack and uncovered a novel physiological response of rice to planthopper attack, which extended our knowledge of the early interaction between rice and SBPH.
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Affiliation(s)
- Weilin Zhang
- College of Chemistry and Life Sciences, Zhejiang Normal University , Jinhua 321004, P. R. China
| | - Chengqi Yan
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Ministry of China Key Laboratory of Biotechnology in Plant Protection, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences , Hangzhou 310021, P. R. China
| | - Mei Li
- Analysis Center of Agrobiology and Environmental Sciences, Zhejiang University , Hangzhou 310058, P. R. China
| | - Ling Yang
- College of Chemistry and Life Sciences, Zhejiang Normal University , Jinhua 321004, P. R. China
| | - Bojun Ma
- College of Chemistry and Life Sciences, Zhejiang Normal University , Jinhua 321004, P. R. China
| | - Hongyu Meng
- College of Chemistry and Life Sciences, Zhejiang Normal University , Jinhua 321004, P. R. China
| | - Li Xie
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Ministry of China Key Laboratory of Biotechnology in Plant Protection, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences , Hangzhou 310021, P. R. China
| | - Jianping Chen
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Ministry of China Key Laboratory of Biotechnology in Plant Protection, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences , Hangzhou 310021, P. R. China
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Anuradha N, Satyavathi CT, Bharadwaj C, Nepolean T, Sankar SM, Singh SP, Meena MC, Singhal T, Srivastava RK. Deciphering Genomic Regions for High Grain Iron and Zinc Content Using Association Mapping in Pearl Millet. FRONTIERS IN PLANT SCIENCE 2017; 8:412. [PMID: 28507551 PMCID: PMC5410614 DOI: 10.3389/fpls.2017.00412] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 03/10/2017] [Indexed: 05/11/2023]
Abstract
Micronutrient malnutrition, especially deficiency of two mineral elements, iron [Fe] and zinc [Zn] in the developing world needs urgent attention. Pearl millet is one of the best crops with many nutritional properties and is accessible to the poor. We report findings of the first attempt to mine favorable alleles for grain iron and zinc content through association mapping in pearl millet. An association mapping panel of 130 diverse lines was evaluated at Delhi, Jodhpur and Dharwad, representing all the three pearl millet growing agro-climatic zones of India, during 2014 and 2015. Wide range of variation was observed for grain iron (32.3-111.9 ppm) and zinc (26.6-73.7 ppm) content. Genotyping with 114 representative polymorphic SSRs revealed 0.35 mean gene diversity. STRUCTURE analysis revealed presence of three sub-populations which was further supported by Neighbor-Joining method of clustering and principal coordinate analysis (PCoA). Marker-trait associations (MTAs) were analyzed with 267 markers (250 SSRs and 17 genic markers) in both general linear model (GLM) and mixed linear model (MLM), however, MTAs resulting from MLM were considered for more robustness of the associations. After appropriate Bonferroni correction, Xpsmp 2261 (13.34% R2-value), Xipes 0180 (R2-value of 11.40%) and Xipes 0096 (R2-value of 11.38%) were consistently associated with grain iron and zinc content for all the three locations. Favorable alleles and promising lines were identified for across and specific environments. PPMI 1102 had highest number (7) of favorable alleles, followed by four each for PPMFeZMP 199 and PPMI 708 for across the environment performance for both grain Fe and Zn content, while PPMI 1104 had alleles specific to Dharwad for grain Fe and Zn content. When compared with the reference genome Tift 23D2B1-P1-P5, Xpsmp 2261 amplicon was identified in intergenic region on pseudomolecule 5, while the other marker, Xipes 0810 was observed to be overlapping with aspartic proteinase (Asp) gene on pseudomolecule 3. Thus, this study can help in breeding new lines with enhanced micronutrient content using marker-assisted selection (MAS) in pearl millet leading to improved well-being especially for women and children.
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Affiliation(s)
- N. Anuradha
- Division of Genetics, ICAR-Indian Agricultural Research InstituteNew Delhi, India
| | - C. Tara Satyavathi
- Division of Genetics, ICAR-Indian Agricultural Research InstituteNew Delhi, India
- *Correspondence: C. Tara Satyavathi
| | - C. Bharadwaj
- Division of Genetics, ICAR-Indian Agricultural Research InstituteNew Delhi, India
| | - T. Nepolean
- Division of Genetics, ICAR-Indian Agricultural Research InstituteNew Delhi, India
| | - S. Mukesh Sankar
- Division of Genetics, ICAR-Indian Agricultural Research InstituteNew Delhi, India
| | - Sumer P. Singh
- Division of Genetics, ICAR-Indian Agricultural Research InstituteNew Delhi, India
| | - Mahesh C. Meena
- Division of Soil Science and Agricultural Chemistry, ICAR-Indian Agricultural Research InstituteNew Delhi, India
| | - Tripti Singhal
- Division of Genetics, ICAR-Indian Agricultural Research InstituteNew Delhi, India
| | - Rakesh K. Srivastava
- International Crops Research Institute for the Semi-Arid TropicsPatancheru, India
- Rakesh K. Srivastava
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Huang Y, Sun C, Min J, Chen Y, Tong C, Bao J. Association Mapping of Quantitative Trait Loci for Mineral Element Contents in Whole Grain Rice (Oryza sativa L.). JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2015; 63:10885-92. [PMID: 26641542 DOI: 10.1021/acs.jafc.5b04932] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Mineral elements in brown rice grain play an important role in human health. In this study, variations in the content of iron (Fe), zinc (Zn), selenium (Se), cadmium (Cd), and lead (Pb) in 378 accessions of brown rice were investigated, and association mapping was used to detect the quantitative trait loci (QTLs) responsible for the variation. Among seven subpopulations, the mean values of Zn and Cd in the japonica group were significantly higher than in the indica groups. The population structure accounted for from 5.7% (Se) to 22.1% (Pb) of the total variation. Correlation analyses showed that Pb was positively correlated with the other minerals (P < 0.001) except for Se. For the five mineral elements investigated, 20 QTLs, including some previously reported and new candidate loci, were identified. Particularly, three cases of QTL colocalization, i.e. Cd and Pb on chromosome 5, Zn and Pb on chromosome 7, and Se and Pb on chromosome 11, were observed. This study suggested that the identified markers could feasibly be used to enhance desired micronutrients while reducing the heavy metal content in whole rice grain by marker-assisted selection (MAS).
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Affiliation(s)
- Yan Huang
- Institute of Nuclear Agricultural Science, College of Agriculture and Biotechnology, Zhejiang University , Huajiachi Campus, Hangzhou 310029, China
| | - Chengxiao Sun
- Rice Product Quality Inspection and Supervision Center, China National Rice Research Institute , Hangzhou 310006, China
| | - Jie Min
- Rice Product Quality Inspection and Supervision Center, China National Rice Research Institute , Hangzhou 310006, China
| | - Yaling Chen
- Institute of Nuclear Agricultural Science, College of Agriculture and Biotechnology, Zhejiang University , Huajiachi Campus, Hangzhou 310029, China
| | - Chuan Tong
- Institute of Nuclear Agricultural Science, College of Agriculture and Biotechnology, Zhejiang University , Huajiachi Campus, Hangzhou 310029, China
| | - Jinsong Bao
- Institute of Nuclear Agricultural Science, College of Agriculture and Biotechnology, Zhejiang University , Huajiachi Campus, Hangzhou 310029, China
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