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Gogoi S, Singh S, Swamy BPM, Das P, Sarma D, Sarma RN, Acharjee S, Deka SD. Grain iron and zinc content is independent of anthocyanin accumulation in pigmented rice genotypes of Northeast region of India. Sci Rep 2024; 14:4128. [PMID: 38374189 PMCID: PMC10876706 DOI: 10.1038/s41598-024-53534-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 02/01/2024] [Indexed: 02/21/2024] Open
Abstract
The traditional rice genotypes of Assam are considered to have biological value due to the presence of several bioactive compounds like flavonoids, polyphenols, and anthocyanins, which have antioxidant, anti-cancer, anti-diabetic, and anti-aging properties. The pigmented genotypes are considered to have high iron (Fe) content. However, the effect of Fe and Zinc (Zn) accumulation on anthocyanin content is yet to be studied in pigmented rice of Assam. We studied the Fe, Zn, and anthocyanin content in grains of 204 traditional rice of Assam, which are traditionally preferred for their nutraceutical properties. We performed phenotypic and biochemical compositional analyses of 204 genotypes to identify those having high Fe, Zn, and anthocyanin. We also carried out the differential expression of a few selected Fe and Zn transporter genes along with the expression of anthocyanin biosynthesis genes. Interestingly, all pigmented rice genotypes contained a higher amount of phenolic compound than the non-pigmented form of rice. We found the highest (32.73 g) seed yield per plant for genotype Jengoni followed by Kajoli chokuwa and Khau Pakhi 1. We also listed 30 genotypes having high levels of Fe and Zn content. The genotype Jengoni accumulated the highest (186.9 μg g-1) Fe, while the highest Zn (119.9 μg g-1) content was measured in genotype Bora (Nagaon), The levels of Ferritin 2 gene expression were found to be significantly higher in Bora (Nagaon) (> 2-fold). For Zn accumulation, the genotype DRR Dhan-45, which was released as a high Zn content variety, showed significant up-regulation of the ZIP4 gene at booting (> 7-fold), post-anthesis (7.8-fold) and grain filling (> 5-fold) stages followed by Bora (Nagaon) (> 3-fold) at post-anthesis. Anthocyanidin synthase gene, Flavanone 3-dioxygenase 1-like (FDO1), and Chalcone-flavanone isomerase-like genes were up-regulated in highly pigmented genotype Bora (Nagaon) followed by Jengoni. Based on our data there was no significant correlation between iron and zinc content on the accumulation of anthocyanin. This challenges the present perception of the higher nutritive value in terms of the micronutrient content of the colored rice of Assam. This is the first report on the detailed characterization of traditional rice genotypes inclusive of phenotypic, biochemical, nutritional, and molecular attributes, which would be useful for designing the breeding program to improve Fe, Zn, or anthocyanin content in rice.
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Affiliation(s)
- Smrita Gogoi
- Department of Plant Breeding and Genetics, Assam Agricultural University, Jorhat, 785013, India
| | - Sanjay Singh
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, 785013, India
| | - B P Mallikarjuna Swamy
- Plant Breeding Division, International Rice Research Institute (IRRI), Metro Manila, Philippines
| | - Priyanka Das
- Department of Biochemistry and Agricultural Chemistry, Assam Agricultural University, Jorhat, 785013, India
| | - Debojit Sarma
- Department of Plant Breeding and Genetics, Assam Agricultural University, Jorhat, 785013, India
| | - Ramendra Nath Sarma
- Department of Plant Breeding and Genetics, Assam Agricultural University, Jorhat, 785013, India
| | - Sumita Acharjee
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, 785013, India.
| | - Sharmila Dutta Deka
- Department of Plant Breeding and Genetics, Assam Agricultural University, Jorhat, 785013, India.
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Joshi G, Soe YP, Palanog A, Hore TK, Nha CT, Calayugan MI, Inabangan-Asilo MA, Amparado A, Pandey ID, Cruz PCS, Hernandez JE, Swamy BPM. Meta-QTL s and haplotypes for efficient zinc biofortification of rice. Plant Genome 2023; 16:e20315. [PMID: 36896580 DOI: 10.1002/tpg2.20315] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 01/23/2023] [Indexed: 06/18/2023]
Abstract
Biofortification of rice with improved grain zinc (Zn) content is the most sustainable and cost-effective approach to address Zn malnutrition in Asia. Genomics-assisted breeding using precise and consistent Zn quantitative trait loci (QTLs), genes, and haplotypes can fast-track the development of Zn biofortified rice varieties. We conducted the meta-analysis of 155 Zn QTLs reported from 26 different studies. Results revealed 57 meta-QTLs with a significant reduction of 63.2% and 80% in the number and confidence interval of the Zn QTLs, respectively. Meta-quantitative trait loci (MQTLs) regions were found to be enriched with diverse metal homeostasis genes; at least 11 MQTLs were colocated with 20 known major genes involved in the production of root exudates, metal uptake, transport, partitioning, and loading into grains in rice. These genes were differentially expressed in vegetative and reproductive tissues, and a complex web of interactions were observed among them. We identified superior haplotypes and their combinations for nine candidate genes (CGs), and the frequency and allelic effects of superior haplotypes varied in different subgroups. The precise MQTLs with high phenotypic variance, CGs, and superior haplotypes identified in our study are useful for an efficient Zn biofortification of rice and to ensure Zn as an essential component of all the future rice varieties through mainstreaming of Zn breeding.
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Affiliation(s)
- Gaurav Joshi
- Rice Genetic Design and Validation Unit, International Rice Research Institute, Los Baños, Philippines
- Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, Uttarakhand, India
| | | | | | - Tapas Kumer Hore
- Rice Genetic Design and Validation Unit, International Rice Research Institute, Los Baños, Philippines
| | - Chau Thanh Nha
- Philippines Rice Research Institute, Muñoz, Nueva Ecija, Philippines
| | | | - Mary Ann Inabangan-Asilo
- Rice Genetic Design and Validation Unit, International Rice Research Institute, Los Baños, Philippines
| | - Amery Amparado
- Rice Genetic Design and Validation Unit, International Rice Research Institute, Los Baños, Philippines
| | - Indra Deo Pandey
- Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, Uttarakhand, India
| | | | | | - B P Mallikarjuna Swamy
- Rice Genetic Design and Validation Unit, International Rice Research Institute, Los Baños, Philippines
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Palanog AD, Nha CT, Descalsota-Empleo GIL, Calayugan MI, Swe ZM, Amparado A, Inabangan-Asilo MA, Hernandez JE, Sta. Cruz PC, Borromeo TH, Lalusin AG, Mauleon R, McNally KL, Swamy BPM. Molecular dissection of connected rice populations revealed important genomic regions for agronomic and biofortification traits. Front Plant Sci 2023; 14:1157507. [PMID: 37035067 PMCID: PMC10073715 DOI: 10.3389/fpls.2023.1157507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 02/20/2023] [Indexed: 06/19/2023]
Abstract
Breeding staple crops with increased micronutrient concentration is a sustainable approach to address micronutrient malnutrition. We carried out Multi-Cross QTL analysis and Inclusive Composite Interval Mapping for 11 agronomic, yield and biofortification traits using four connected RILs populations of rice. Overall, MC-156 QTLs were detected for agronomic (115) and biofortification (41) traits, which were higher in number but smaller in effects compared to single population analysis. The MC-QTL analysis was able to detect important QTLs viz: qZn5.2, qFe7.1, qGY10.1, qDF7.1, qPH1.1, qNT4.1, qPT4.1, qPL1.2, qTGW5.1, qGL3.1 , and qGW6.1 , which can be used in rice genomics assisted breeding. A major QTL (qZn5.2 ) for grain Zn concentration has been detected on chromosome 5 that accounted for 13% of R2. In all, 26 QTL clusters were identified on different chromosomes. qPH6.1 epistatically interacted with qZn5.1 and qGY6.2 . Most of QTLs were co-located with functionally related candidate genes indicating the accuracy of QTL mapping. The genomic region of qZn5.2 was co-located with putative genes such as OsZIP5, OsZIP9, and LOC_OS05G40490 that are involved in Zn uptake. These genes included polymorphic functional SNPs, and their promoter regions were enriched with cis-regulatory elements involved in plant growth and development, and biotic and abiotic stress tolerance. Major effect QTL identified for biofortification and agronomic traits can be utilized in breeding for Zn biofortified rice varieties.
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Affiliation(s)
- Alvin D. Palanog
- Rice Breeding Innovations Platform, International Rice Research Institute, Los Baños, Laguna, Philippines
- College of Agriculture and Food Science, University of the Philippines, Los Baños, Laguna, Philippines
- PhilRice Negros Branch Station, Philippine Rice Research Institute, Murcia, Negros Occidental, Philippines
| | | | | | - Mark Ian Calayugan
- College of Agriculture and Food Science, University of the Philippines, Los Baños, Laguna, Philippines
| | - Zin Mar Swe
- Rice Breeding Innovations Platform, International Rice Research Institute, Los Baños, Laguna, Philippines
| | - Amery Amparado
- Rice Breeding Innovations Platform, International Rice Research Institute, Los Baños, Laguna, Philippines
| | - Mary Ann Inabangan-Asilo
- Rice Breeding Innovations Platform, International Rice Research Institute, Los Baños, Laguna, Philippines
| | - Jose E. Hernandez
- College of Agriculture and Food Science, University of the Philippines, Los Baños, Laguna, Philippines
| | - Pompe C. Sta. Cruz
- College of Agriculture and Food Science, University of the Philippines, Los Baños, Laguna, Philippines
| | - Teresita H. Borromeo
- College of Agriculture and Food Science, University of the Philippines, Los Baños, Laguna, Philippines
| | - Antonio G. Lalusin
- College of Agriculture and Food Science, University of the Philippines, Los Baños, Laguna, Philippines
| | - Ramil Mauleon
- Rice Breeding Innovations Platform, International Rice Research Institute, Los Baños, Laguna, Philippines
- College of Agriculture, University of Southern Mindanao, Kabacan, North Cotabato, Philippines
| | - Kenneth L. McNally
- Rice Breeding Innovations Platform, International Rice Research Institute, Los Baños, Laguna, Philippines
| | - B. P. Mallikarjuna Swamy
- Rice Breeding Innovations Platform, International Rice Research Institute, Los Baños, Laguna, Philippines
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Swamy BPM, Marathi B, Ribeiro-Barros AIF, Calayugan MIC, Ricachenevsky FK. Iron Biofortification in Rice: An Update on Quantitative Trait Loci and Candidate Genes. Front Plant Sci 2021; 12:647341. [PMID: 34122472 PMCID: PMC8187908 DOI: 10.3389/fpls.2021.647341] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 04/15/2021] [Indexed: 05/06/2023]
Abstract
Rice is the most versatile model for cereals and also an economically relevant food crop; as a result, it is the most suitable species for molecular characterization of Fe homeostasis and biofortification. Recently there have been significant efforts to dissect genes and quantitative trait loci (QTL) associated with Fe translocation into rice grains; such information is highly useful for Fe biofortification of cereals but very limited in other species, such as maize (Zea mays) and wheat (Triticum aestivum). Given rice's centrality as a model for Poaceae species, we review the current knowledge on genes playing important roles in Fe transport, accumulation, and distribution in rice grains and QTLs that might explain the variability in Fe concentrations observed in different genotypes. More than 90 Fe QTLs have been identified over the 12 rice chromosomes. From these, 17 were recorded as stable, and 25 harbored Fe-related genes nearby or within the QTL. Among the candidate genes associated with Fe uptake, translocation, and loading into rice grains, we highlight the function of transporters from the YSL and ZIP families; transporters from metal-binding molecules, such as nicotianamine and deoxymugineic acid; vacuolar iron transporters; citrate efflux transporters; and others that were shown to play a role in steps leading to Fe delivery to seeds. Finally, we discuss the application of these QTLs and genes in genomics assisted breeding for fast-tracking Fe biofortification in rice and other cereals in the near future.
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Affiliation(s)
| | - Balram Marathi
- Agricultural College, Warangal, Professor Jayashankar Telangana State Agricultural University, Hyderabad, India
| | - Ana I. F. Ribeiro-Barros
- Forest Research Centre (CEF), Instituto Superior de Agronomia, Universidade de Lisboa, Lisbon, Portugal
| | - Mark Ian C. Calayugan
- Institute of Crop Science, University of the Philippines Los Baños, Laguna, Philippines
| | - Felipe Klein Ricachenevsky
- Departamento de Botânica, Instituto de Biociências, e Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
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Swamy BPM, Marathi B, Ribeiro-Barros AIF, Ricachenevsky FK. Editorial: Development of Healthy and Nutritious Cereals: Recent Insights on Molecular Advances in Breeding. Front Genet 2021; 12:635006. [PMID: 33868374 PMCID: PMC8044956 DOI: 10.3389/fgene.2021.635006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Accepted: 02/23/2021] [Indexed: 11/13/2022] Open
Affiliation(s)
| | - Balram Marathi
- Department of Genetics and Plant Breeding, Professor Jayashankar Telangana State Agricultural University, Hyderabad, India
| | - Ana I F Ribeiro-Barros
- Forest Research Centre (CEF), Instituto Superior de Agronomia, Universidade de Lisboa, Lisbon, Portugal
| | - Felipe Klein Ricachenevsky
- Departamento de Botânica, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.,Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
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Biswas PS, Swamy BPM, Kader MA, Hossain MA, Boncodin R, Samia M, Hassan ML, Wazuddin M, MacKenzie D, Reinke R. Development and Field Evaluation of Near-Isogenic Lines of GR2-EBRRI dhan29 Golden Rice. Front Plant Sci 2021; 12:619739. [PMID: 33719290 PMCID: PMC7947304 DOI: 10.3389/fpls.2021.619739] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 01/11/2021] [Indexed: 06/07/2023]
Abstract
Vitamin A deficiency remains a common public health problem among the rice-dependent poor people in the developing countries of Asia. Conventional milled rice does not contain provitamin A (β-carotene) in is edible part (endosperm) and is also deficient in essential minerals, such as iron and zinc. Transgenic Golden Rice event GR2E, which produces β-carotene in its endosperm, was used as a parent to introgress the transgene locus conferring β-carotene biosynthesis into a widely grown rice variety, BRRI dhan29, which covers around 26.1% of the irrigated rice area (4.901 Mha) of Bangladesh in the dry season. The current study reports the introgression process and field performance of GR2E BRRI dhan29 Golden Rice. The background recovery of GR2E BRRI dhan29 lines at BC5F2 generation was more than 98% with a 6K SNP-chip set. The transgenic GR2E BRRI dhan29 yielded 6.2 t/ha to 7.7 t/ha with an average of 7.0 ± 0.38 t/ha, while the non-transgenic BRRI dhan29 yielded 7.0 t/ha under confined field conditions in Bangladesh. Moreover, no significant difference between GR2-E BRRI dhan29 Golden Rice and non-transgenic BRRI dhan29 in any measured trait was observed in the multi-location trials conducted at five locations across the country. Furthermore, the appearance of cooked and uncooked rice was similar to that of BRRI dhan29 except for the yellow color indicating the presence of carotenoids. Total carotenoid content in the selected introgression lines ranged from 8.5 to 12.5 μg/g with an average of 10.6 ± 1.16 μg/g. This amount is sufficient to deliver approximately 66 and 80% of the recommended daily intake of vitamin A for children and women, respectively, assuming complete substitution of white rice in the diet with Golden Rice. However, the lead selected line(s) need further evaluation at open field conditions before deciding for commercial cultivation. A large-scale feeding trial among the malnourished community with this newly developed GR2-E BRRI dhan29 Golden Rice is also required to validate its efficacy in alleviating vitamin A deficiency.
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Affiliation(s)
- Partha S. Biswas
- Plant Breeding Division, Bangladesh Rice Research Institute, Gazipur, Bangladesh
| | | | - Md. Abdul Kader
- Plant Breeding Division, Bangladesh Rice Research Institute, Gazipur, Bangladesh
| | - Md. Alamgir Hossain
- Plant Breeding Division, Bangladesh Rice Research Institute, Gazipur, Bangladesh
| | - Raul Boncodin
- International Rice Research Institute, Los Baños, Philippines
| | - Mercy Samia
- International Rice Research Institute, Los Baños, Philippines
| | - Md. Lutful Hassan
- Department of Genetics and Plant Breeding, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - M. Wazuddin
- Department of Genetics and Plant Breeding, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Donald MacKenzie
- Donald Danforth Plant Science Center, Saint Louis, MO, United States
| | - Russell Reinke
- International Rice Research Institute, Los Baños, Philippines
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Mallikarjuna Swamy BP, Marundan S, Samia M, Ordonio RL, Rebong DB, Miranda R, Alibuyog A, Rebong AT, Tabil MA, Suralta RR, Alfonso AA, Biswas PS, Kader MA, Reinke RF, Boncodin R, MacKenzie DJ. Development and characterization of GR2E Golden rice introgression lines. Sci Rep 2021; 11:2496. [PMID: 33510272 PMCID: PMC7843986 DOI: 10.1038/s41598-021-82001-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 01/14/2021] [Indexed: 12/11/2022] Open
Abstract
Golden Rice with β-carotene in the grain helps to address the problem of vitamin A deficiency. Prior to commercialize Golden Rice, several performance and regulatory checkpoints must be achieved. We report results of marker assisted backcross breeding of the GR2E trait into three popular rice varieties followed by a series of confined field tests of event GR2E introgression lines to assess their agronomic performance and carotenoid expression. Results from confined tests in the Philippines and Bangladesh have shown that GR2E introgression lines matched the performance of the recurrent parents for agronomic and yield performance, and the key components of grain quality. Moreover, no differences were observed in terms of pest and disease reaction. The best performing lines identified in each genetic background had significant amounts of carotenoids in the milled grains. These lines can supply 30–50% of the estimated average requirements of vitamin A.
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Affiliation(s)
| | - Severino Marundan
- International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines
| | - Mercy Samia
- International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines
| | - Reynante L Ordonio
- Philippines Rice Research Institute (PhilRice), Maligaya, Science City of Munoz, Philippines
| | - Democrito B Rebong
- Philippines Rice Research Institute (PhilRice), Maligaya, Science City of Munoz, Philippines
| | - Ronalyn Miranda
- Philippines Rice Research Institute (PhilRice), Maligaya, Science City of Munoz, Philippines
| | - Anielyn Alibuyog
- Philippines Rice Research Institute (PhilRice), Maligaya, Science City of Munoz, Philippines
| | - Anna Theresa Rebong
- Philippines Rice Research Institute (PhilRice), Maligaya, Science City of Munoz, Philippines
| | - Ma Angela Tabil
- Philippines Rice Research Institute (PhilRice), Maligaya, Science City of Munoz, Philippines
| | - Roel R Suralta
- Philippines Rice Research Institute (PhilRice), Maligaya, Science City of Munoz, Philippines
| | - Antonio A Alfonso
- Philippines Rice Research Institute (PhilRice), Maligaya, Science City of Munoz, Philippines
| | - Partha Sarathi Biswas
- Plant Breeding Division, Bangladesh Rice Research Institute (BRRI), Gazipur, Bangladesh
| | - Md Abdul Kader
- Plant Breeding Division, Bangladesh Rice Research Institute (BRRI), Gazipur, Bangladesh
| | - Russell F Reinke
- International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines
| | - Raul Boncodin
- International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines
| | - Donald J MacKenzie
- Institute for International Crop Improvement, Donald Danforth Plant Science Center, Saint Louis, MO, USA
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Roda FA, Marques I, Batista-Santos P, Esquível MG, Ndayiragije A, Lidon FC, Swamy BPM, Ramalho JC, Ribeiro-Barros AI. Rice Biofortification With Zinc and Selenium: A Transcriptomic Approach to Understand Mineral Accumulation in Flag Leaves. Front Genet 2020; 11:543. [PMID: 32733530 PMCID: PMC7359728 DOI: 10.3389/fgene.2020.00543] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Accepted: 05/05/2020] [Indexed: 11/13/2022] Open
Abstract
Human malnutrition due to micronutrient deficiencies, particularly with regards to Zinc (Zn) and Selenium (Se), affects millions of people around the world, and the enrichment of staple foods through biofortification has been successfully used to fight hidden hunger. Rice (Oryza sativa L.) is one of the staple foods most consumed in countries with high levels of malnutrition. However, it is poor in micronutrients, which are often removed during grain processing. In this study, we have analyzed the transcriptome of rice flag leaves biofortified with Zn (900 g ha-1), Se (500 g ha-1), and Zn-Se. Flag leaves play an important role in plant photosynthesis and provide sources of metal remobilization for developing grains. A total of 3170 differentially expressed genes (DEGs) were identified. The expression patterns and gene ontology of DEGs varied among the three sets of biofortified plants and were limited to specific metabolic pathways related to micronutrient mobilization and to the specific functions of Zn (i.e., its enzymatic co-factor/coenzyme function in the biosynthesis of nitrogenous compounds, carboxylic acids, organic acids, and amino acids) and Se (vitamin biosynthesis and ion homeostasis). The success of this approach should be followed in future studies to understand how landraces and other cultivars respond to biofortification.
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Affiliation(s)
- Faustino Adriano Roda
- Ministério de Agricultura e Segurança Alimentar, Instituto de Investigação Agrária de Moçambique, Centro Zonal Noroeste, Lichinga, Mozambique
- Universidade Eduardo Mondlane-Centro de Biotechnologia, Maputo, Mozambique
- PlantStress&Biodiversity Lab, Forest Research Center (IM, JCR, AIRB) and Linking, Landscape, Environment, Agriculture and Food (PBS, MGE), Instituto Superior de Agronomia, Universidade de Lisboa, Lisbon, Portugal
| | - Isabel Marques
- PlantStress&Biodiversity Lab, Forest Research Center (IM, JCR, AIRB) and Linking, Landscape, Environment, Agriculture and Food (PBS, MGE), Instituto Superior de Agronomia, Universidade de Lisboa, Lisbon, Portugal
| | - Paula Batista-Santos
- PlantStress&Biodiversity Lab, Forest Research Center (IM, JCR, AIRB) and Linking, Landscape, Environment, Agriculture and Food (PBS, MGE), Instituto Superior de Agronomia, Universidade de Lisboa, Lisbon, Portugal
| | - Maria Glória Esquível
- PlantStress&Biodiversity Lab, Forest Research Center (IM, JCR, AIRB) and Linking, Landscape, Environment, Agriculture and Food (PBS, MGE), Instituto Superior de Agronomia, Universidade de Lisboa, Lisbon, Portugal
| | - Alexis Ndayiragije
- International Rice Research Institute, Maputo, Mozambique
- International Rice Research Institute, Laguna, Philippines
| | - Fernando Cebola Lidon
- Unidade de Geobiociências, Geoengenharias e Geotecnologias, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Caparica, Portugal
| | - B. P. Mallikarjuna Swamy
- International Rice Research Institute, Maputo, Mozambique
- International Rice Research Institute, Laguna, Philippines
| | - José Cochicho Ramalho
- PlantStress&Biodiversity Lab, Forest Research Center (IM, JCR, AIRB) and Linking, Landscape, Environment, Agriculture and Food (PBS, MGE), Instituto Superior de Agronomia, Universidade de Lisboa, Lisbon, Portugal
- Unidade de Geobiociências, Geoengenharias e Geotecnologias, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Ana I. Ribeiro-Barros
- PlantStress&Biodiversity Lab, Forest Research Center (IM, JCR, AIRB) and Linking, Landscape, Environment, Agriculture and Food (PBS, MGE), Instituto Superior de Agronomia, Universidade de Lisboa, Lisbon, Portugal
- Unidade de Geobiociências, Geoengenharias e Geotecnologias, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Caparica, Portugal
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Calayugan MIC, Formantes AK, Amparado A, Descalsota-Empleo GI, Nha CT, Inabangan-Asilo MA, Swe ZM, Hernandez JE, Borromeo TH, Lalusin AG, Mendioro MS, Diaz MGQ, Viña CBD, Reinke R, Swamy BPM. Genetic Analysis of Agronomic Traits and Grain Iron and Zinc Concentrations in a Doubled Haploid Population of Rice (Oryza sativa L.). Sci Rep 2020; 10:2283. [PMID: 32042046 PMCID: PMC7010768 DOI: 10.1038/s41598-020-59184-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 01/24/2020] [Indexed: 12/28/2022] Open
Abstract
The development of micronutrient dense rice varieties with good agronomic traits is one of the sustainable and cost-effective approaches for reducing malnutrition. Identification of QTLs for high grain Fe and Zn, yield and yield components helps in precise and faster development of high Fe and Zn rice. We carried out a three-season evaluation using IR05F102 x IR69428 derived doubled-haploid population at IRRI. Inclusive composite interval mapping was carried out using SNP markers and Best Linear Unbiased Estimates of the phenotypic traits. A total of 23 QTLs were identified for eight agronomic traits and grain Fe and Zn concentration that explained 7.2 to 22.0% PV. A QTL by environment interaction analysis confirmed the stability of nine QTLs, including two QTLs for Zn on chromosomes 5 and 12. One epistatic interaction for plant height was significant with 28.4% PVE. Moreover, five QTLs were identified for Fe and Zn that harbor several candidate genes, e.g. OsZIP6 on QTL qZn5.1. A number of QTLs were associated with a combination of greater yield and increased grain Zn levels. These results are useful for development of new rice varieties with good agronomic traits and high grain Zn using MAS, and identification of genetic resources with the novel QTLs for grain Zn.
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Affiliation(s)
- Mark Ian C Calayugan
- International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines.,University of the Philippines Los Baños, Laguna, 4031, Philippines
| | - Andrea Kariza Formantes
- International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines.,University of the Philippines Los Baños, Laguna, 4031, Philippines
| | - Amery Amparado
- International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines
| | - Gwen Iris Descalsota-Empleo
- International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines.,University of the Philippines Los Baños, Laguna, 4031, Philippines.,University of the Southern Mindanao, Kabacan, Cotabato, 9407, Philippines
| | - Chau Thanh Nha
- International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines.,Cuu Long Delta Rice Research Institute (CLRRI), Cần Thơ, Vietnam
| | | | - Zin Mar Swe
- International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines.,Department of Agriculture, Yezin, Myanmar
| | - Jose E Hernandez
- University of the Philippines Los Baños, Laguna, 4031, Philippines
| | | | | | | | | | | | - Russell Reinke
- International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines
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10
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Oliva N, Florida Cueto-Reaño M, Trijatmiko KR, Samia M, Welsch R, Schaub P, Beyer P, Mackenzie D, Boncodin R, Reinke R, Slamet-Loedin I, Mallikarjuna Swamy BP. Molecular characterization and safety assessment of biofortified provitamin A rice. Sci Rep 2020; 10:1376. [PMID: 31992721 PMCID: PMC6987151 DOI: 10.1038/s41598-020-57669-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 12/30/2019] [Indexed: 11/09/2022] Open
Abstract
Part of the studies involved in safety assessment of genetically engineered crops includes characterizing the organization, integrity, and stability of the inserted DNA and evaluating the potential allergenicity and toxicity of newly-expressed proteins. Molecular characterization of the introduced DNA in provitamin A biofortified rice event GR2E confirmed insertion of a single copy of the transfer-DNA in the genome and its inheritance as a single locus. Nucleotide sequencing of the inserted DNA confirmed it was introduced without modifications. The phytoene synthase, and carotene desaturase proteins did not display sequence similarity with allergens or toxins. Both proteins were rapidly digested in simulated gastric fluid and their enzymatic activity was inhibited upon heat treatment. Acute oral toxicity testing of the protein in mice demonstrated lack of adverse effects. These evidences substantiated the lack of any identifiable hazards for both proteins and in combination with other existing comparative analyses provided assurance that food derived from this rice is safe. This conclusion is in line with those of the regulatory agencies of US Food and Drug Administration, Health Canada and Food Standard Australia and New Zealand.
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Affiliation(s)
- Norman Oliva
- Strategic Innovation Platform, International Rice Research Institute (IRRI), Metro Manila, Philippines
| | - Maria Florida Cueto-Reaño
- Strategic Innovation Platform, International Rice Research Institute (IRRI), Metro Manila, Philippines
| | - Kurniawan R Trijatmiko
- Strategic Innovation Platform, International Rice Research Institute (IRRI), Metro Manila, Philippines
| | - Mercy Samia
- Strategic Innovation Platform, International Rice Research Institute (IRRI), Metro Manila, Philippines
| | - Ralf Welsch
- Faculty of Biology, Cell Biology, University of Freiburg, Freiburg, Germany
| | - Patrick Schaub
- Faculty of Biology, Cell Biology, University of Freiburg, Freiburg, Germany
| | - Peter Beyer
- Faculty of Biology, Cell Biology, University of Freiburg, Freiburg, Germany
| | - Donald Mackenzie
- Institute for International Crop Improvement, Donald Danforth Plant Science Center, Saint Louis, Missouri, USA.
| | - Raul Boncodin
- Strategic Innovation Platform, International Rice Research Institute (IRRI), Metro Manila, Philippines
| | - Russell Reinke
- Strategic Innovation Platform, International Rice Research Institute (IRRI), Metro Manila, Philippines
| | - Inez Slamet-Loedin
- Strategic Innovation Platform, International Rice Research Institute (IRRI), Metro Manila, Philippines.
| | - B P Mallikarjuna Swamy
- Strategic Innovation Platform, International Rice Research Institute (IRRI), Metro Manila, Philippines.
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11
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Swamy BPM, Samia M, Boncodin R, Marundan S, Rebong DB, Ordonio RL, Miranda RT, Rebong ATO, Alibuyog AY, Adeva CC, Reinke R, MacKenzie DJ. Compositional Analysis of Genetically Engineered GR2E "Golden Rice" in Comparison to That of Conventional Rice. J Agric Food Chem 2019; 67:7986-7994. [PMID: 31282158 PMCID: PMC6646955 DOI: 10.1021/acs.jafc.9b01524] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 06/12/2019] [Accepted: 06/17/2019] [Indexed: 05/23/2023]
Abstract
Compositional analyses were performed on samples of rice grain, straw, and derived bran obtained from golden rice event GR2E and near-isogenic control PSBRc82 rice grown at four locations in the Philippines during 2015 and 2016. Grain samples were analyzed for key nutritional components, including proximates, fiber, polysaccharides, fatty acids, amino acids, minerals, vitamins, and antinutrients. Samples of straw and bran were analyzed for proximates and minerals. The only biologically meaningful difference between GR2E and control rice was in levels of β-carotene and other provitamin A carotenoids in the grain. Except for β-carotene and related carotenoids, the compositional parameters of GR2E rice were within the range of natural variability of those components in conventional rice varieties with a history of safe consumption. Mean provitamin A concentrations in milled rice of GR2E can contribute up to 89-113% and 57-99% of the estimated average requirement for vitamin A for preschool children in Bangladesh and the Philippines, respectively.
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Affiliation(s)
| | - Mercy Samia
- International
Rice Research Institute, Los Banos, Laguna 4031, Philippines
| | - Raul Boncodin
- International
Rice Research Institute, Los Banos, Laguna 4031, Philippines
| | - Severino Marundan
- International
Rice Research Institute, Los Banos, Laguna 4031, Philippines
| | - Democrito B. Rebong
- The
Philippines Rice Research Institute, Science City of Munoz, 3119 Nueva Ecija, Philippines
| | - Reynante L. Ordonio
- The
Philippines Rice Research Institute, Science City of Munoz, 3119 Nueva Ecija, Philippines
| | - Ronalyn T. Miranda
- The
Philippines Rice Research Institute, Science City of Munoz, 3119 Nueva Ecija, Philippines
| | - Anna T. O. Rebong
- The
Philippines Rice Research Institute, Science City of Munoz, 3119 Nueva Ecija, Philippines
| | - Anielyn Y. Alibuyog
- The
Philippines Rice Research Institute, Science City of Munoz, 3119 Nueva Ecija, Philippines
| | - Cheryl C. Adeva
- The
Philippines Rice Research Institute, Science City of Munoz, 3119 Nueva Ecija, Philippines
| | | | - Donald J. MacKenzie
- Donald
Danforth Plant Science Center, Saint Louis, Missouri 63132, United States
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12
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Palanog AD, Calayugan MIC, Descalsota-Empleo GI, Amparado A, Inabangan-Asilo MA, Arocena EC, Sta. Cruz PC, Borromeo TH, Lalusin A, Hernandez JE, Acuin C, Reinke R, Swamy BPM. Zinc and Iron Nutrition Status in the Philippines Population and Local Soils. Front Nutr 2019; 6:81. [PMID: 31231657 PMCID: PMC6568233 DOI: 10.3389/fnut.2019.00081] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Accepted: 05/20/2019] [Indexed: 12/11/2022] Open
Abstract
The Philippines is one of the major rice-producing and rice-consuming countries of Asia. A large portion of its population depends on rice for their daily caloric intake and nutritional needs. The lack of dietary diversity among poor communities has led to nutritional consequences, particularly micronutrient deficiencies. Iron-deficiency anemia (IDA) and zinc deficiency (ZnD) are two serious nutritional problems that affect the health and economic sector of the country. Since rice dominates the Filipino diet by default, biofortification of rice will help improve the micronutrient status. The Philippine government has proactively initiated various programs and policies to address micronutrient deficiencies, particularly through fortification of basic food commodities. Biofortification, the fortification of rice with micronutrients through breeding, is considered the most sustainable and cost-effective strategy that can benefit large vulnerable populations. However, developing promising genotypes with micronutrient-enriched grains should be coupled with improving micronutrient bioavailability in the soil in order to optimize biofortification. This review documents the prevailing soil Zn-deficiency problems in the major rice production areas in the Philippines that may influence the Zn nutritional status of the population. The article also reports on the biofortification efforts that have resulted in the development of two biofortified varieties approved for commercial release in the Philippines. As nutritional security is increasingly recognized as a priority area, greater efforts are required to develop biofortified rice varieties that suit both farmers' and consumers' preferences, and that can address these critical needs for human health in a sustainable and cost-effective manner.
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Affiliation(s)
- Alvin D. Palanog
- Strategic Innovation Platform, International Rice Research Institute, Los Baños, Philippines
- College of Agriculture and Food Science, University of the Philippines, Los Baños, Philippines
- PhilRice Negros, Philippine Rice Research Institute, Science City of Muñoz, Philippines
| | - Mark Ian C. Calayugan
- Strategic Innovation Platform, International Rice Research Institute, Los Baños, Philippines
- College of Agriculture and Food Science, University of the Philippines, Los Baños, Philippines
| | - Gwen Iris Descalsota-Empleo
- Strategic Innovation Platform, International Rice Research Institute, Los Baños, Philippines
- College of Agriculture, University of Southern Mindanao, Kabacan, Philippines
| | - Amery Amparado
- Strategic Innovation Platform, International Rice Research Institute, Los Baños, Philippines
| | | | - Emily C. Arocena
- PhilRice Negros, Philippine Rice Research Institute, Science City of Muñoz, Philippines
| | - Pompe C. Sta. Cruz
- College of Agriculture and Food Science, University of the Philippines, Los Baños, Philippines
| | - Teresita H. Borromeo
- College of Agriculture and Food Science, University of the Philippines, Los Baños, Philippines
| | - Antonio Lalusin
- College of Agriculture and Food Science, University of the Philippines, Los Baños, Philippines
| | - Jose E. Hernandez
- College of Agriculture and Food Science, University of the Philippines, Los Baños, Philippines
| | - Cecilia Acuin
- Strategic Innovation Platform, International Rice Research Institute, Los Baños, Philippines
| | - Russell Reinke
- Strategic Innovation Platform, International Rice Research Institute, Los Baños, Philippines
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13
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Mahender A, Swamy BPM, Anandan A, Ali J. Tolerance of Iron-Deficient and -Toxic Soil Conditions in Rice. Plants (Basel) 2019; 8:E31. [PMID: 30696039 PMCID: PMC6409647 DOI: 10.3390/plants8020031] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 01/21/2019] [Accepted: 01/23/2019] [Indexed: 01/04/2023]
Abstract
Iron (Fe) deficiency and toxicity are the most widely prevalent soil-related micronutrient disorders in rice (Oryza sativa L.). Progress in rice cultivars with improved tolerance has been hampered by a poor understanding of Fe availability in the soil, the transportation mechanism, and associated genetic factors for the tolerance of Fe toxicity soil (FTS) or Fe deficiency soil (FDS) conditions. In the past, through conventional breeding approaches, rice varieties were developed especially suitable for low- and high-pH soils, which indirectly helped the varieties to tolerate FTS and FDS conditions. Rice-Fe interactions in the external environment of soil, internal homeostasis, and transportation have been studied extensively in the past few decades. However, the molecular and physiological mechanisms of Fe uptake and transport need to be characterized in response to the tolerance of morpho-physiological traits under Fe-toxic and -deficient soil conditions, and these traits need to be well integrated into breeding programs. A deeper understanding of the several factors that influence Fe absorption, uptake, and transport from soil to root and above-ground organs under FDS and FTS is needed to develop tolerant rice cultivars with improved grain yield. Therefore, the objective of this review paper is to congregate the different phenotypic screening methodologies for prospecting tolerant rice varieties and their responsible genetic traits, and Fe homeostasis related to all the known quantitative trait loci (QTLs), genes, and transporters, which could offer enormous information to rice breeders and biotechnologists to develop rice cultivars tolerant of Fe toxicity or deficiency. The mechanism of Fe regulation and transport from soil to grain needs to be understood in a systematic manner along with the cascade of metabolomics steps that are involved in the development of rice varieties tolerant of FTS and FDS. Therefore, the integration of breeding with advanced genome sequencing and omics technologies allows for the fine-tuning of tolerant genotypes on the basis of molecular genetics, and the further identification of novel genes and transporters that are related to Fe regulation from FTS and FDS conditions is incredibly important to achieve further success in this aspect.
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Affiliation(s)
- Anumalla Mahender
- Rice Breeding Platform, International Rice Research Institute (IRRI), Los Baños, Laguna 4031, Philippines.
| | - B P Mallikarjuna Swamy
- Rice Breeding Platform, International Rice Research Institute (IRRI), Los Baños, Laguna 4031, Philippines.
| | - Annamalai Anandan
- ICAR-National Rice Research Institute, Cuttack, Odisha 753006, India.
| | - Jauhar Ali
- Rice Breeding Platform, International Rice Research Institute (IRRI), Los Baños, Laguna 4031, Philippines.
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14
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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:genes10010030. [PMID: 30626141 PMCID: PMC6356647 DOI: 10.3390/genes10010030] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [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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15
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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. Front Plant Sci 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] [What about the content of this article? (0)] [Affiliation(s)] [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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16
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Swamy BPM, Descalsota GIL, Nha CT, Amparado A, Inabangan-Asilo MA, Manito C, Tesoro F, Reinke R. Identification of genomic regions associated with agronomic and biofortification traits in DH populations of rice. PLoS One 2018; 13:e0201756. [PMID: 30096168 PMCID: PMC6086416 DOI: 10.1371/journal.pone.0201756] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 07/20/2018] [Indexed: 01/21/2023] Open
Abstract
Rice provides energy and nutrition to more than half of the world’s population. Breeding rice varieties with the increased levels of bioavailable micronutrients is one of the most sustainable approaches to tackle micronutrient malnutrition. So, high zinc and iron content in the grain are primary targets in rice biofortification breeding. In this study, we conducted QTL mapping using doubled haploid (DH) populations, PSBRc82 x Joryeongbyeo and PSBRc82 x IR69428, phenotyped for agronomic traits and micronutrients during two growing seasons and using genotypic information from analysis with the 6K SNP chip. A number of DH lines were identified as having high grain Zn and Fe content in polished rice. Importantly, we identified 20 QTLs for agronomic traits and 59 QTLs for a number of biofortification traits. Of the 79 QTLs, 12 were large-effect QTLs (>25% PVE), nine QTLs were consistent across seasons in either population, and one QTL was identified in both populations. Moreover, at least two QTLs were clustered in defined regions of chromosomes 1, 2, 3, 4, 5, 7 and 9. Eight epistatic interactions were detected for Cu, Mg, Na, and Zn in population 1. Furthermore, we identified several candidate genes near QTLs for grain Zn (OsNRAMP, OsNAS, OsZIP, OsYSL, OsFER, and OsZIFL family) and grain yield (OsSPL14 and OsSPL16). These new QTLs and candidate genes help to further elucidate the genetic basis for grain micronutrient concentration, and may prove useful for marker assisted breeding for this important trait.
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Affiliation(s)
- B. P. Mallikarjuna Swamy
- Plant Breeding Platform, International Rice Research Institute (IRRI), Metro Manila, Philippines
| | - Gwen Iris L. Descalsota
- Plant Breeding Platform, International Rice Research Institute (IRRI), Metro Manila, Philippines
- University of Southern Mindanao, Kabacan, Cotabato, Philippines
| | - Chau Thanh Nha
- Cuu Long Delta Rice Research Institute (CLRRI), Can Tho, Vietnam
| | - Amery Amparado
- Plant Breeding Platform, International Rice Research Institute (IRRI), Metro Manila, Philippines
| | - Mary Ann Inabangan-Asilo
- Plant Breeding Platform, International Rice Research Institute (IRRI), Metro Manila, Philippines
| | - Christine Manito
- Plant Breeding Platform, International Rice Research Institute (IRRI), Metro Manila, Philippines
| | - Frances Tesoro
- Plant Breeding Platform, International Rice Research Institute (IRRI), Metro Manila, Philippines
| | - Russell Reinke
- Plant Breeding Platform, International Rice Research Institute (IRRI), Metro Manila, Philippines
- * E-mail:
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17
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Swamy BPM, Shamsudin NAA, Rahman SNA, Mauleon R, Ratnam W, Sta. Cruz MT, Kumar A. Association Mapping of Yield and Yield-related Traits Under Reproductive Stage Drought Stress in Rice (Oryza sativa L.). Rice (N Y) 2017; 10:21. [PMID: 28523639 PMCID: PMC5436998 DOI: 10.1186/s12284-017-0161-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 05/09/2017] [Indexed: 05/05/2023]
Abstract
BACKGROUND The identification and introgression of major-effect QTLs for grain yield under drought are some of the best and well-proven approaches for improving the drought tolerance of rice varieties. In the present study, we characterized Malaysian rice germplasm for yield and yield-related traits and identified significant trait marker associations by structured association mapping. RESULTS The drought screening was successful in screening germplasm with a yield reduction of up to 60% and heritability for grain yield under drought was up to 78%. There was a wider phenotypic and molecular diversity within the panel, indicating the suitability of the population for quantitative trait loci (QTL) mapping. Structure analyses clearly grouped the accessions into three subgroups with admixtures. Linkage disequilibrium (LD) analysis revealed that LD decreased with an increase in distance between marker pairs and the LD decay varied from 5-20 cM. The Mixed Linear model-based structured association mapping identified 80 marker trait associations (MTA) for grain yield (GY), plant height (PH) and days to flowering (DTF). Seven MTA were identified for GY under drought stress, four of these MTA were consistently identified in at least two of the three analyses. Most of these MTA identified were on chromosomes 2, 5, 10, 11 and 12, and their phenotypic variance (PV) varied from 5% to 19%. The in silico analysis of drought QTL regions revealed the association of several drought-responsive genes conferring drought tolerance. The major-effect QTLs are useful in marker-assisted QTL pyramiding to improve drought tolerance. CONCLUSION The results have clearly shown that structured association mapping is one of the feasible options to identify major-effect QTLs for drought tolerance-related traits in rice.
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Affiliation(s)
- B. P. Mallikarjuna Swamy
- Plant Breeding Division, International Rice Research Institute (IRRI), DAPO Box 7777 Metro Manila, Philippines
| | - Noraziyah Abd Aziz Shamsudin
- Plant Breeding Division, International Rice Research Institute (IRRI), DAPO Box 7777 Metro Manila, Philippines
- Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor Malaysia
| | - Site Noorzuraini Abd Rahman
- Plant Breeding Division, International Rice Research Institute (IRRI), DAPO Box 7777 Metro Manila, Philippines
- MARDI, Seberang Perai, P.O. Box No. 203, 13200 Kepala Batas, Pulau Pinang Malaysia
| | - Ramil Mauleon
- Plant Breeding Division, International Rice Research Institute (IRRI), DAPO Box 7777 Metro Manila, Philippines
| | - Wickneswari Ratnam
- Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor Malaysia
| | - Ma. Teressa Sta. Cruz
- Plant Breeding Division, International Rice Research Institute (IRRI), DAPO Box 7777 Metro Manila, Philippines
| | - Arvind Kumar
- Plant Breeding Division, International Rice Research Institute (IRRI), DAPO Box 7777 Metro Manila, Philippines
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18
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Swamy BPM, Shamsudin NAA, Rahman SNA, Mauleon R, Ratnam W, Sta Cruz MT, Kumar A. Association Mapping of Yield and Yield-related Traits Under Reproductive Stage Drought Stress in Rice (Oryza sativa L.). Rice (N Y) 2017. [PMID: 28523639 DOI: 10.1186/s12284-017-0161-6©] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
BACKGROUND The identification and introgression of major-effect QTLs for grain yield under drought are some of the best and well-proven approaches for improving the drought tolerance of rice varieties. In the present study, we characterized Malaysian rice germplasm for yield and yield-related traits and identified significant trait marker associations by structured association mapping. RESULTS The drought screening was successful in screening germplasm with a yield reduction of up to 60% and heritability for grain yield under drought was up to 78%. There was a wider phenotypic and molecular diversity within the panel, indicating the suitability of the population for quantitative trait loci (QTL) mapping. Structure analyses clearly grouped the accessions into three subgroups with admixtures. Linkage disequilibrium (LD) analysis revealed that LD decreased with an increase in distance between marker pairs and the LD decay varied from 5-20 cM. The Mixed Linear model-based structured association mapping identified 80 marker trait associations (MTA) for grain yield (GY), plant height (PH) and days to flowering (DTF). Seven MTA were identified for GY under drought stress, four of these MTA were consistently identified in at least two of the three analyses. Most of these MTA identified were on chromosomes 2, 5, 10, 11 and 12, and their phenotypic variance (PV) varied from 5% to 19%. The in silico analysis of drought QTL regions revealed the association of several drought-responsive genes conferring drought tolerance. The major-effect QTLs are useful in marker-assisted QTL pyramiding to improve drought tolerance. CONCLUSION The results have clearly shown that structured association mapping is one of the feasible options to identify major-effect QTLs for drought tolerance-related traits in rice.
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Affiliation(s)
- B P Mallikarjuna Swamy
- Plant Breeding Division, International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines
| | - Noraziyah Abd Aziz Shamsudin
- Plant Breeding Division, International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines
- Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
| | - Site Noorzuraini Abd Rahman
- Plant Breeding Division, International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines
- MARDI, Seberang Perai, P.O. Box No. 203, 13200, Kepala Batas, Pulau Pinang, Malaysia
| | - Ramil Mauleon
- Plant Breeding Division, International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines
| | - Wickneswari Ratnam
- Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
| | - Ma Teressa Sta Cruz
- Plant Breeding Division, International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines
| | - Arvind Kumar
- Plant Breeding Division, International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines.
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Rahman MA, Bimpong IK, Bizimana JB, Pascual ED, Arceta M, Swamy BPM, Diaw F, Rahman MS, Singh RK. Mapping QTLs using a novel source of salinity tolerance from Hasawi and their interaction with environments in rice. Rice (N Y) 2017; 10:47. [PMID: 29098463 PMCID: PMC5668218 DOI: 10.1186/s12284-017-0186-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 10/23/2017] [Indexed: 05/21/2023]
Abstract
BACKGROUND Salinity is one of the most severe and widespread abiotic stresses that affect rice production. The identification of major-effect quantitative trait loci (QTLs) for traits related to salinity tolerance and understanding of QTL × environment interactions (QEIs) can help in more precise and faster development of salinity-tolerant rice varieties through marker-assisted breeding. Recombinant inbred lines (RILs) derived from IR29/Hasawi (a novel source of salinity) were screened for salinity tolerance in the IRRI phytotron in the Philippines (E1) and in two other diverse environments in Senegal (E2) and Tanzania (E3). QTLs were mapped for traits related to salinity tolerance at the seedling stage. RESULTS The RILs were genotyped using 194 polymorphic SNPs (single nucleotide polymorphisms). After removing segregation distortion markers (SDM), a total of 145 and 135 SNPs were used to construct a genetic linkage map with a length of 1655 and 1662 cM, with an average marker density of 11.4 cM in E1 and 12.3 cM in E2 and E3, respectively. A total of 34 QTLs were identified on 10 chromosomes for five traits using ICIM-ADD and segregation distortion locus (SDL) mapping (IM-ADD) under salinity stress across environments. Eight major genomic regions on chromosome 1 between 170 and 175 cM (qSES1.3, qSES1.4, qSL1.2, qSL1.3, qRL1.1, qRL1.2, qFWsht1.2, qDWsht1.2), chromosome 4 at 32 cM (qSES4.1, qFWsht4.2, qDWsht4.2), chromosome 6 at 115 cM (qFWsht6.1, qDWsht6.1), chromosome 8 at 105 cM (qFWsht8.1, qDWsht8.1), and chromosome 12 at 78 cM (qFWsht12.1, qDWsht12.1) have co-localized QTLs for the multiple traits that might be governing seedling stage salinity tolerance through multiple traits in different phenotyping environments, thus suggesting these as hot spots for tolerance of salinity. Forty-nine and 30 significant pair-wise epistatic interactions were detected between QTL-linked and QTL-unlinked regions using single-environment and multi-environment analyses. CONCLUSIONS The identification of genomic regions for salinity tolerance in the RILs showed that Hasawi possesses alleles that are novel for salinity tolerance. The common regions for the multiple QTLs across environments as co-localized regions on chromosomes 1, 4, 6, 8, and 12 could be due to linkage or pleiotropic effect, which might be helpful for multiple QTL introgression for marker-assisted breeding programs to improve the salinity tolerance of adaptive and popular but otherwise salinity-sensitive rice varieties.
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Affiliation(s)
- M Akhlasur Rahman
- International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines
- Bangladesh Rice Research Institute, Gazipur, 1701, Bangladesh
| | | | | | - Evangeline D Pascual
- Institute of Biological Sciences, University of the Philippines at Los Baños, Laguna, Philippines
| | - Marydee Arceta
- International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines
| | | | - Faty Diaw
- Africa Rice Center, Sahel Regional Station, BP 96, St Louis, Senegal
| | | | - R K Singh
- International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines.
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Shamsudin NAA, Swamy BPM, Ratnam W, Sta Cruz MT, Sandhu N, Raman AK, Kumar A. Pyramiding of drought yield QTLs into a high quality Malaysian rice cultivar MRQ74 improves yield under reproductive stage drought. Rice (N Y) 2016; 9:21. [PMID: 27164982 PMCID: PMC4864745 DOI: 10.1186/s12284-016-0093-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 04/22/2016] [Indexed: 05/03/2023]
Abstract
BACKGROUND With the objective of improving the grain yield (GY) of the Malaysian high quality rice cultivar MRQ74 under reproductive stage drought stress (RS), three drought yield QTLs, viz. qDTY 2.2, qDTY 3.1 , and qDTY 12.1 were pyramided by marker assisted breeding (MAB). Foreground selection using QTL specific markers, recombinant selection using flanking markers, and background selections were performed in every generation. BC1F3 derived pyramided lines (PLs) with different combinations of qDTY 2.2, qDTY 3.1 , and qDTY 12.1 were evaluated under both RS and non-stress (NS) during the dry season (DS) of 2013 and 2014 at IRRI. RESULTS The GY reductions in RS trials compared to NS trials ranged from 79 to 99 %. Plant height (PH) was reduced and days to flowering (DTF) was delayed under RS. Eleven BC1F5 MRQ74 PLs with yield advantages of 1009 to 3473 kg ha(-1) under RS and with yields equivalent to MRQ74 under NS trials were identified as promising drought tolerance PLs. Five best PLs, IR 98010-126-708-1-4, IR 98010-126-708-1-3, IR 98010-126-708-1-5, IR 99616-44-94-1-1, and IR 99616-44-94-1-2 with a yield advantage of more than 1000 kg ha(-1) under RS and with yield potential equivalent to that of MRQ74 under NS were selected. The effect of three drought grain yield QTLs under RS in MRQ74 was validated. Under NS, PLs with two qDTY combinations (qDTY 2.2 + qDTY 12.1 ) performed better than PLs with other qDTY combinations, indicating the presence of a positive interaction between qDTY 2.2 and qDTY 12.1 in the MRQ74 background. CONCLUSION Drought tolerant MRQ74 PLs with a yield advantage of more than 1000 kg ha(-1) under RS were developed. Differential yield advantages of different combinations of the qDTYs indicate a differential synergistic relationship among qDTYs.
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Affiliation(s)
- Noraziyah Abd Aziz Shamsudin
- Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
- Plant Breeding, Genetics, and Biotechnology Division, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - B P Mallikarjuna Swamy
- Plant Breeding, Genetics, and Biotechnology Division, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Wickneswari Ratnam
- Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
| | - Ma Teressa Sta Cruz
- Plant Breeding, Genetics, and Biotechnology Division, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Nitika Sandhu
- Plant Breeding, Genetics, and Biotechnology Division, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Anitha K Raman
- Plant Breeding, Genetics, and Biotechnology Division, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Arvind Kumar
- Plant Breeding, Genetics, and Biotechnology Division, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines.
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Swamy BPM, Rahman MA, Inabangan-Asilo MA, Amparado A, Manito C, Chadha-Mohanty P, Reinke R, Slamet-Loedin IH. Advances in breeding for high grain Zinc in Rice. Rice (N Y) 2016; 9:49. [PMID: 27671163 PMCID: PMC5037106 DOI: 10.1186/s12284-016-0122-5] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2016] [Accepted: 09/16/2016] [Indexed: 05/18/2023]
Abstract
Zinc (Zn) is one of the most essential micronutrients required for the growth and development of human beings. More than one billion people, particularly children and pregnant women suffer from Zn deficiency related health problems in Asia. Rice is the major staple food for Asians, but the presently grown popular high yielding rice varieties are poor supplier of Zn in their polished form. Breeding rice varieties with high grain Zn has been suggested to be a sustainable, targeted, food-based and cost effective approach in alleviating Zn deficiency. The physiological, genetic and molecular mechanisms of Zn homeostasis have been well studied, but these mechanisms need to be characterized from a biofortification perspective and should be well integrated with the breeding processes. There is a significant variation for grain Zn in rice germplasm and efforts are being directed at exploiting this variation through breeding to develop high Zn rice varieties. Several QTLs and gene specific markers have been identified for grain Zn and there is a great potential to use them in Marker-Assisted Breeding. A thorough characterization of genotype and environmental interactions is essential to identify key environmental factors influencing grain Zn. Agronomic biofortification has shown inconsistent results, but a combination of genetic and agronomic biofortification strategies may be more effective. Significant progress has been made in developing high Zn rice lines for release in target countries. A holistic breeding approach involving high Zn trait development, high Zn product development, product testing and release, including bioefficacy and bioavailability studies is essential for successful Zn biofortification.
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Affiliation(s)
- B. P. Mallikarjuna Swamy
- Plant Breeding, Genetics, and Biotechnology Division, International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines
| | - Mohammad Akhlasur Rahman
- Plant Breeding, Genetics, and Biotechnology Division, International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines
- Plant Breeding Division, Bangladesh Rice Research Institute (BRRI), Gazipur, Bangladesh
| | - Mary Ann Inabangan-Asilo
- Plant Breeding, Genetics, and Biotechnology Division, International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines
| | - Amery Amparado
- Plant Breeding, Genetics, and Biotechnology Division, International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines
| | - Christine Manito
- Plant Breeding, Genetics, and Biotechnology Division, International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines
| | - Prabhjit Chadha-Mohanty
- Plant Breeding, Genetics, and Biotechnology Division, International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines
| | - Russell Reinke
- Plant Breeding, Genetics, and Biotechnology Division, International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines
| | - Inez H. Slamet-Loedin
- Plant Breeding, Genetics, and Biotechnology Division, International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines
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Vikram P, Swamy BPM, Dixit S, Trinidad J, Sta Cruz MT, Maturan PC, Amante M, Kumar A. Linkages and Interactions Analysis of Major Effect Drought Grain Yield QTLs in Rice. PLoS One 2016; 11:e0151532. [PMID: 27018583 PMCID: PMC4809569 DOI: 10.1371/journal.pone.0151532] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 02/28/2016] [Indexed: 02/01/2023] Open
Abstract
Quantitative trait loci conferring high grain yield under drought in rice are important genomic resources for climate resilient breeding. Major and consistent drought grain yield QTLs usually co-locate with flowering and/or plant height QTLs, which could be due to either linkage or pleiotropy. Five mapping populations used for the identification of major and consistent drought grain yield QTLs underwent multiple-trait, multiple-interval mapping test (MT-MIM) to estimate the significance of pleiotropy effects. Results indicated towards possible linkages between the drought grain yield QTLs with co-locating flowering and/or plant height QTLs. Linkages of days to flowering and plant height were eliminated through a marker-assisted breeding approach. Drought grain yield QTLs also showed interaction effects with flowering QTLs. Drought responsiveness of the flowering locus on chromosome 3 (qDTY3.2) has been revealed through allelic analysis. Considering linkage and interaction effects associated with drought QTLs, a comprehensive marker-assisted breeding strategy was followed to develop rice genotypes with improved grain yield under drought stress.
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Affiliation(s)
- Prashant Vikram
- Plant Breeding Genetics and Biotechnology Division, International Rice Research Institute (IRRI), Los Baños, Metro Manila, Philippines
- * E-mail: (AK); (PV)
| | - B. P. Mallikarjuna Swamy
- Plant Breeding Genetics and Biotechnology Division, International Rice Research Institute (IRRI), Los Baños, Metro Manila, Philippines
| | - Shalabh Dixit
- Plant Breeding Genetics and Biotechnology Division, International Rice Research Institute (IRRI), Los Baños, Metro Manila, Philippines
| | - Jennylyn Trinidad
- Plant Breeding Genetics and Biotechnology Division, International Rice Research Institute (IRRI), Los Baños, Metro Manila, Philippines
| | - Ma Teresa Sta Cruz
- Plant Breeding Genetics and Biotechnology Division, International Rice Research Institute (IRRI), Los Baños, Metro Manila, Philippines
| | - Paul C. Maturan
- Plant Breeding Genetics and Biotechnology Division, International Rice Research Institute (IRRI), Los Baños, Metro Manila, Philippines
| | - Modesto Amante
- Plant Breeding Genetics and Biotechnology Division, International Rice Research Institute (IRRI), Los Baños, Metro Manila, Philippines
| | - Arvind Kumar
- Plant Breeding Genetics and Biotechnology Division, International Rice Research Institute (IRRI), Los Baños, Metro Manila, Philippines
- * E-mail: (AK); (PV)
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Shamsudin NAA, Swamy BPM, Ratnam W, Sta Cruz MT, Raman A, Kumar A. Marker assisted pyramiding of drought yield QTLs into a popular Malaysian rice cultivar, MR219. BMC Genet 2016; 17:30. [PMID: 26818269 PMCID: PMC4729146 DOI: 10.1186/s12863-016-0334-0] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 01/14/2016] [Indexed: 11/15/2022] Open
Abstract
Background Three drought yield QTLs, qDTY2.2, qDTY3.1, and qDTY12.1 with consistent effect on grain yield under reproductive stage drought stress were pyramided through marker assisted breeding with the objective of improving the grain yield of the elite Malaysian rice cultivar MR219 under reproductive stage drought stress. Foreground selection using QTL specific markers, recombinant selection using flanking markers, and background selection were performed. BC1F3-derived lines with different combinations of qDTY2.2, qDTY3.1, and qDTY12.1 were evaluated under both reproductive stage drought stress and non-stress during the dry seasons of 2013 and 2014 at IRRI. Results The grain yield reductions in the stress trials compared to non-stress trials ranged from 79 to 93 %. In the stress trials, delay in days to flowering and reduction in plant height were observed. In both seasons, MR219 did not produce any yield under stress, however it produced a yield of 5917 kg ha−1 during the 2013 dry season and 8319 kg ha−1 during the 2014 dry season under non-stress. Selected introgressed lines gave a yield advantage of 903 to 2500 kg ha−1 over MR219 under reproductive stage drought stress and a yield of more than 6900 kg ha−1 under non-stress during the 2014 dry season. Among lines with single qDTY, lines carrying qDTY2.2 provided a higher yield advantage under reproductive stage drought stress in the MR219 background. Two-qDTY combinations (qDTY3.1+qDTY2.2 and qDTY3.1+qDTY12.1) performed better than lines with three qDTY combinations, indicating the absence of positive interactions between the three qDTYs. Conclusion We successfully developed drought-tolerant MR219 pyramided lines with a yield advantage of more than 1500 kg ha−1. Differential yield advantages of different combinations of the qDTYs indicate a differential synergistic relationship among qDTYs. This is the first report on the successful effect of qDTYs in increasing the yield under drought in genetic backgrounds other than those in which the qDTYs were earlier identified.
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Affiliation(s)
- Noraziyah Abd Aziz Shamsudin
- Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia. .,International Rice Research Institute, Los Banos, DAPO BOX 7777, Metro Manila, Philippines.
| | - B P Mallikarjuna Swamy
- International Rice Research Institute, Los Banos, DAPO BOX 7777, Metro Manila, Philippines.
| | - Wickneswari Ratnam
- Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia.
| | - Ma Teressa Sta Cruz
- International Rice Research Institute, Los Banos, DAPO BOX 7777, Metro Manila, Philippines.
| | - Anitha Raman
- International Rice Research Institute, Los Banos, DAPO BOX 7777, Metro Manila, Philippines.
| | - Arvind Kumar
- International Rice Research Institute, Los Banos, DAPO BOX 7777, Metro Manila, Philippines.
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Vikram P, Swamy BPM, Dixit S, Singh R, Singh BP, Miro B, Kohli A, Henry A, Singh NK, Kumar A. Drought susceptibility of modern rice varieties: an effect of linkage of drought tolerance with undesirable traits. Sci Rep 2015; 5:14799. [PMID: 26458744 PMCID: PMC4602206 DOI: 10.1038/srep14799] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 09/02/2015] [Indexed: 12/15/2022] Open
Abstract
Green Revolution (GR) rice varieties are high yielding but typically drought sensitive. This is partly due to the tight linkage between the loci governing plant height and drought tolerance. This linkage is illustrated here through characterization of qDTY1.1, a QTL for grain yield under drought that co-segregates with the GR gene sd1 for semi-dwarf plant height. We report that the loss of the qDTY1.1 allele during the GR was due to its tight linkage in repulsion with the sd1 allele. Other drought-yield QTLs (qDTY) also showed tight linkage with traits rejected in GR varieties. Genetic diversity analysis for 11 different qDTY regions grouped GR varieties separately from traditional drought-tolerant varieties, and showed lower frequency of drought tolerance alleles. The increased understanding and breaking of the linkage between drought tolerance and undesirable traits has led to the development of high-yielding drought-tolerant dwarf lines with positive qDTY alleles and provides new hope for extending the benefits of the GR to drought-prone rice-growing regions.
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Affiliation(s)
- Prashant Vikram
- Plant Breeding, Genetics, and Biotechnology Division, International Rice Research Institute, Los Baños, Philippines
| | - B. P. Mallikarjuna Swamy
- Plant Breeding, Genetics, and Biotechnology Division, International Rice Research Institute, Los Baños, Philippines
| | - Shalabh Dixit
- Plant Breeding, Genetics, and Biotechnology Division, International Rice Research Institute, Los Baños, Philippines
| | - Renu Singh
- National Research Center for Plant Biology, Indian Agricultural Research Institute, New Delhi, India 110012
| | - Bikram P. Singh
- National Research Center for Plant Biology, Indian Agricultural Research Institute, New Delhi, India 110012
| | - Berta Miro
- Plant Breeding, Genetics, and Biotechnology Division, International Rice Research Institute, Los Baños, Philippines
| | - Ajay Kohli
- Plant Breeding, Genetics, and Biotechnology Division, International Rice Research Institute, Los Baños, Philippines
| | - Amelia Henry
- Crop and Environmental Sciences Division, International Rice Research Institute, Los Baños, Philippines
| | - N. K. Singh
- National Research Center for Plant Biology, Indian Agricultural Research Institute, New Delhi, India 110012
| | - Arvind Kumar
- Plant Breeding, Genetics, and Biotechnology Division, International Rice Research Institute, Los Baños, Philippines
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Swamy BPM, Kaladhar K, Reddy GA, Viraktamath BC, Sarla N. Mapping and introgression of QTL for yield and related traits in two backcross populations derived from Oryza sativa cv. Swarna and two accessions of O. nivara. J Genet 2015; 93:643-54. [PMID: 25572223 DOI: 10.1007/s12041-014-0420-x] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Advanced backcross QTL (AB-QTL) analysis was carried out in two Oryza nivara-derived BC2F2 populations. For nine traits, we identified 28 QTL in population 1 and 26 QTL in population 2. The two most significant yield-enhancing QTL, yldp9.1 and yldp2.1 showed an additive effect of 16 and 7 g per plant in population 1, while yld2.1 and yld11.1 showed an additive effect of 11 and 10 g per plant in population 2. At least one O. nivara-derived QTL with a phenotypic variance of >15% was detected for seven traits in population 1 and three traits in population 2. The O. nivara-derived QTL ph1.1, nt12.1, nsp1.1, nfg1.1, bm11.1, yld2.1 and yld11.1 were conserved at the same chromosomal locations in both populations. Two major QTL clusters were detected at the marker intervals RM488-RM431 and RM6-RM535 on chromosomes 1 and 2, respectively. The colocation of O. nivara-derived yield QTL with yield meta-QTL on chromosomes 1, 2 and 9 indicates their accuracy and consistency. The major-effect QTL reported in this study are useful for marker-assisted breeding and are also suitable for further fine mapping and candidate gene identification.
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Henry A, Swamy BPM, Dixit S, Torres RD, Batoto TC, Manalili M, Anantha MS, Mandal NP, Kumar A. Physiological mechanisms contributing to the QTL-combination effects on improved performance of IR64 rice NILs under drought. J Exp Bot 2015; 66:1787-99. [PMID: 25680791 PMCID: PMC4378621 DOI: 10.1093/jxb/eru506] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Revised: 11/26/2014] [Accepted: 12/01/2014] [Indexed: 05/04/2023]
Abstract
Characterizing the physiological mechanisms behind major-effect drought-yield quantitative trait loci (QTLs) can provide an understanding of the function of the QTLs-as well as plant responses to drought in general. In this study, we characterized rice (Oryza sativa L.) genotypes with QTLs derived from drought-tolerant traditional variety AdaySel that were introgressed into drought-susceptible high-yielding variety IR64, one of the most popular megavarieties in South Asian rainfed lowland systems. Of the different combinations of the four QTLs evaluated, genotypes with two QTLs (qDTY 2.2 + qDTY 4.1 ) showed the greatest degree of improvement under drought compared with IR64 in terms of yield, canopy temperature, and normalized difference vegetation index (NDVI). Furthermore, qDTY 2.2 and qDTY 4.1 showed a potential for complementarity in that they were each most effective under different severities of drought stress. Multiple drought-response mechanisms were observed to be conferred in the genotypes with the two-QTL combination: higher root hydraulic conductivity and in some cases greater root growth at depth. As evidenced by multiple leaf water status and plant growth indicators, these traits affected transpiration but not transpiration efficiency or harvest index. The results from this study highlight the complex interactions among major-effect drought-yield QTLs and the drought-response traits they confer, and the need to evaluate the optimal combinations of QTLs that complement each other when present in a common genetic background.
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Affiliation(s)
- Amelia Henry
- International Rice Research Institute, Los Baños, Laguna 4031, Philippines
| | | | - Shalabh Dixit
- International Rice Research Institute, Los Baños, Laguna 4031, Philippines
| | - Rolando D Torres
- International Rice Research Institute, Los Baños, Laguna 4031, Philippines
| | - Tristram C Batoto
- International Rice Research Institute, Los Baños, Laguna 4031, Philippines
| | - Mervin Manalili
- International Rice Research Institute, Los Baños, Laguna 4031, Philippines
| | - M S Anantha
- Central Rainfed Upland Rice Research Station, Hazaribag, Jharkand 825 301, India
| | - N P Mandal
- Central Rainfed Upland Rice Research Station, Hazaribag, Jharkand 825 301, India
| | - Arvind Kumar
- Central Rainfed Upland Rice Research Station, Hazaribag, Jharkand 825 301, India
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Swamy BPM, Kumar A. Genomics-based precision breeding approaches to improve drought tolerance in rice. Biotechnol Adv 2013; 31:1308-18. [PMID: 23702083 DOI: 10.1016/j.biotechadv.2013.05.004] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2012] [Revised: 04/23/2013] [Accepted: 05/08/2013] [Indexed: 12/15/2022]
Abstract
Rice (Oryza sativa L.), the major staple food crop of the world, faces a severe threat from widespread drought. The development of drought-tolerant rice varieties is considered a feasible option to counteract drought stress. The screening of rice germplasm under drought and its characterization at the morphological, genetic, and molecular levels revealed the existence of genetic variation for drought tolerance within the rice gene pool. The improvements made in managed drought screening and selection for grain yield under drought have significantly contributed to progress in drought breeding programs. The availability of rice genome sequence information, genome-wide molecular markers, and low-cost genotyping platforms now makes it possible to routinely apply marker-assisted breeding approaches to improve grain yield under drought. Grain yield QTLs with a large and consistent effect under drought have been indentified and successfully pyramided in popular rice mega-varieties. Various rice functional genomics resources, databases, tools, and recent advances in "-omics" are facilitating the characterization of genes and pathways involved in drought tolerance, providing the basis for candidate gene identification and allele mining. The transgenic approach is successful in generating drought tolerance in rice under controlled conditions, but field-level testing is necessary. Genomics-assisted drought breeding approaches hold great promise, but a well-planned integration with standardized phenotyping is highly essential to exploit their full potential.
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Swamy BPM, Ahmed HU, Henry A, Mauleon R, Dixit S, Vikram P, Tilatto R, Verulkar SB, Perraju P, Mandal NP, Variar M, Robin S, Chandrababu R, Singh ON, Dwivedi JL, Das SP, Mishra KK, Yadaw RB, Aditya TL, Karmakar B, Satoh K, Moumeni A, Kikuchi S, Leung H, Kumar A. Genetic, physiological, and gene expression analyses reveal that multiple QTL enhance yield of rice mega-variety IR64 under drought. PLoS One 2013; 8:e62795. [PMID: 23667521 PMCID: PMC3648568 DOI: 10.1371/journal.pone.0062795] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Accepted: 03/25/2013] [Indexed: 01/30/2023] Open
Abstract
Background Rice (Oryza sativa L.) is a highly drought sensitive crop, and most semi dwarf rice varieties suffer severe yield losses from reproductive stage drought stress. The genetic complexity of drought tolerance has deterred the identification of agronomically relevant quantitative trait loci (QTL) that can be deployed to improve rice yield under drought in rice. Convergent evidence from physiological characterization, genetic mapping, and multi-location field evaluation was used to address this challenge. Methodology/Principal Findings Two pairs of backcross inbred lines (BILs) from a cross between drought-tolerant donor Aday Sel and high-yielding but drought-susceptible rice variety IR64 were produced. From six BC4F3 mapping populations produced by crossing the +QTL BILs with the −QTL BILs and IR64, four major-effect QTL - one each on chromosomes 2, 4, 9, and 10 - were identified. Meta-analysis of transcriptome data from the +QTL/−QTL BILs identified differentially expressed genes (DEGs) significantly associated with QTL on chromosomes 2, 4, 9, and 10. Physiological characterization of BILs showed increased water uptake ability under drought. The enrichment of DEGs associated with root traits points to differential regulation of root development and function as contributing to drought tolerance in these BILs. BC4F3-derived lines with the QTL conferred yield advantages of 528 to 1875 kg ha−1 over IR64 under reproductive-stage drought stress in the targeted ecosystems of South Asia. Conclusions/Significance Given the importance of rice in daily food consumption and the popularity of IR64, the BC4F3 lines with multiple QTL could provide higher livelihood security to farmers in drought-prone environments. Candidate genes were shortlisted for further characterization to confirm their role in drought tolerance. Differential yield advantages of different combinations of the four QTL reported here indicate that future research should include optimizing QTL combinations in different genetic backgrounds to maximize yield advantage under drought.
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Dixit S, Swamy BPM, Vikram P, Ahmed HU, Sta Cruz MT, Amante M, Atri D, Leung H, Kumar A. Fine mapping of QTLs for rice grain yield under drought reveals sub-QTLs conferring a response to variable drought severities. Theor Appl Genet 2012; 125:155-69. [PMID: 22361948 DOI: 10.1007/s00122-012-1823-9] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2011] [Accepted: 02/03/2012] [Indexed: 05/19/2023]
Abstract
Fine-mapping studies on four QTLs, qDTY(2.1), qDTY(2.2), qDTY(9.1) and qDTY(12.1), for grain yield (GY) under drought were conducted using four different backcross-derived populations screened in 16 experiments from 2006 to 2010. Composite and bayesian interval mapping analyses resolved the originally identified qDTY(2.1) region of 42.3 cM into a segment of 1.6 cM, the qDTY(2.2) region of 31.0 cM into a segment of 6.7 cM, the qDTY(9.1) region of 32.1 cM into two segments of 9.4 and 2.4 cM and the qDTY(12.1) region of 10.6 cM into two segments of 3.1 and 0.4 cM. Two of the four QTLs (qDTY(9.1) and qDTY(12.1)) having effects under varying degrees of stress severity showed the presence of more than one region within the original QTL. The study found the presence of a donor allele at RM262 within qDTY(2.1) and RM24334 within qDTY(9.1) showing a negative effect on GY under drought, indicating the necessity of precise fine mapping of QTL regions before using them in marker-assisted selection (MAS). However, the presence of sub-QTLs together in close vicinity to each other provides a unique opportunity to breeders to introgress such regions together as a unit into high-yielding drought-susceptible varieties through MAS.
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Affiliation(s)
- Shalabh Dixit
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
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Swamy BPM, Kaladhar K, Shobha Rani N, Prasad GSV, Viraktamath BC, Reddy GA, Sarla N. QTL analysis for grain quality traits in 2 BC2F2 populations derived from crosses between Oryza sativa cv Swarna and 2 accessions of O. nivara. ACTA ACUST UNITED AC 2012; 103:442-52. [PMID: 22312119 DOI: 10.1093/jhered/esr145] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The appearance and cooking quality of rice determine its acceptability and price to a large extent. Quantitative trait loci (QTLs) for 12 grain quality traits were mapped in 2 mapping populations derived from Oryza sativa cv Swarna × O. nivara. The BC(2)F(2) population of the cross Swarna × O. nivara IRGC81848 (population 1) was evaluated during 2005 and that from Swarna × O. nivara IRGC81832 (population 2) was evaluated during 2006. Linkage maps were constructed using 100 simple sequence repeat (SSR) markers in population 1 and 75 SSR markers in population 2. In all, 21 QTLs were identified in population 1 (43% from O. nivara) and 37 in population 2 (38% QTLs from O. nivara). The location of O. nivara-derived QTLs mp1.2 for milling percent, kw6.1 for kernel width, and klac12.1 for kernel length after cooking coincided in the 2 populations and appear to be useful for Marker Assisted Selection (MAS). Four QTLs for milling percent, 1 QTL each for amylose content, water uptake, elongation ratio, 2 QTLs for kernel width, and 3 QTLs for gel consistency, each explained more than 20% phenotypic variance. Three QTL clusters for grain quality traits were close to the genes/QTLs for shattering and seed dormancy. QTLs for 4 quality traits were associated with 5 of the 7 major yield QTLs reported in the same 2 mapping populations. Useful introgression lines have been developed for several agronomic traits. It emerges that 40% O. nivara alleles were trait enhancing in both populations, and QTLs for grain quality overlapped with yield meta-QTLs and QTLs for dormancy and seed shattering.
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Vikram P, Swamy BPM, Dixit S, Ahmed HU, Teresa Sta Cruz M, Singh AK, Kumar A. qDTY₁.₁, a major QTL for rice grain yield under reproductive-stage drought stress with a consistent effect in multiple elite genetic backgrounds. BMC Genet 2011; 12:89. [PMID: 22008150 PMCID: PMC3234187 DOI: 10.1186/1471-2156-12-89] [Citation(s) in RCA: 140] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2011] [Accepted: 10/18/2011] [Indexed: 12/15/2022] Open
Abstract
Background Drought is one of the most important abiotic stresses causing drastic reductions in yield in rainfed rice environments. The suitability of grain yield (GY) under drought as a selection criterion has been reported in the past few years. Most of the quantitative trait loci (QTLs) for GY under drought in rice reported so far has been in the background of low-yielding susceptible varieties. Such QTLs have not shown a similar effect in multiple high- yielding drought-susceptible varieties, thus limiting their use in marker-assisted selection. Genetic control of GY under reproductive-stage drought stress (RS) in elite genetic backgrounds was studied in three F3:4 mapping populations derived from crosses of N22, a drought-tolerant aus cultivar, with Swarna, IR64, and MTU1010, three high-yielding popular mega-varieties, with the aim to identify QTLs for GY under RS that show a consistent effect in multiple elite genetic backgrounds. Three populations were phenotyped under RS in the dry seasons (DS) of 2009 and 2010 at IRRI. For genotyping, whole-genome scans for N22/MTU1010 and bulked segregant analysis for N22/Swarna and N22/IR64 were employed using SSR markers. Results A major QTL for GY under RS, qDTY1.1, was identified on rice chromosome 1 flanked by RM11943 and RM431 in all three populations. In combined analysis over two years, qDTY1.1 showed an additive effect of 29.3%, 24.3%, and 16.1% of mean yield in N22/Swarna, N22/IR64, and N22/MTU1010, respectively, under RS. qDTY1.1 also showed a positive effect on GY in non-stress (NS) situations in N22/Swarna, N22/IR64 over both years, and N22/MTU1010 in DS2009. Conclusions This is the first reported QTL in rice with a major and consistent effect in multiple elite genetic backgrounds under both RS and NS situations. Consistency of the QTL effect across different genetic backgrounds makes it a suitable candidate for use in marker-assisted breeding.
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Affiliation(s)
- Prashant Vikram
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
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Swamy BPM, Vikram P, Dixit S, Ahmed HU, Kumar A. Meta-analysis of grain yield QTL identified during agricultural drought in grasses showed consensus. BMC Genomics 2011; 12:319. [PMID: 21679437 PMCID: PMC3155843 DOI: 10.1186/1471-2164-12-319] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2010] [Accepted: 06/16/2011] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND In the last few years, efforts have been made to identify large effect QTL for grain yield under drought in rice. However, identification of most precise and consistent QTL across the environments and genetics backgrounds is essential for their successful use in Marker-assisted Selection. In this study, an attempt was made to locate consistent QTL regions associated with yield increase under drought by applying a genome-wide QTL meta-analysis approach. RESULTS The integration of 15 maps resulted in a consensus map with 531 markers and a total map length of 1821 cM. Fifty-three yield QTL reported in 15 studies were projected on a consensus map and meta-analysis was performed. Fourteen meta-QTL were obtained on seven chromosomes. MQTL1.2, MQTL1.3, MQTL1.4, and MQTL12.1 were around 700 kb and corresponded to a reasonably small genetic distance of 1.8 to 5 cM and they are suitable for use in marker-assisted selection (MAS). The meta-QTL for grain yield under drought coincided with at least one of the meta-QTL identified for root and leaf morphology traits under drought in earlier reports. Validation of major-effect QTL on a panel of random drought-tolerant lines revealed the presence of at least one major QTL in each line. DTY12.1 was present in 85% of the lines, followed by DTY4.1 in 79% and DTY1.1 in 64% of the lines. Comparative genomics of meta-QTL with other cereals revealed that the homologous regions of MQTL1.4 and MQTL3.2 had QTL for grain yield under drought in maize, wheat, and barley respectively. The genes in the meta-QTL regions were analyzed by a comparative genomics approach and candidate genes were deduced for grain yield under drought. Three groups of genes such as stress-inducible genes, growth and development-related genes, and sugar transport-related genes were found in clusters in most of the meta-QTL. CONCLUSIONS Meta-QTL with small genetic and physical intervals could be useful in Marker-assisted selection individually and in combinations. Validation and comparative genomics of the major-effect QTL confirmed their consistency within and across the species. The shortlisted candidate genes can be cloned to unravel the molecular mechanism regulating grain yield under drought.
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Reddy CS, Babu AP, Swamy BPM, Kaladhar K, Sarla N. ISSR markers based on GA and AG repeats reveal genetic relationship among rice varieties tolerant to drought, flood, or salinity. J Zhejiang Univ Sci B 2009; 10:133-41. [PMID: 19235272 DOI: 10.1631/jzus.b0820183] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Drought, flood, salinity, or a combination of these limits rice production. Several rice varieties are well known for their tolerance to specific abiotic stresses. We determined genetic relationship among 12 rice varieties including 9 tolerant to drought, flood, or salinity using inter-simple sequence repeat (ISSR) markers. Based on all markers, the nine tolerant varieties formed one cluster distinct from the cluster of three control varieties. The salt-tolerant varieties were closest to two flood-tolerant varieties, and together they were distinct from the drought-tolerant varieties. (GA)(8)YG was the most informative primer, showing the highest polymorphic information content (PIC) and resolving power (Rp). The drought-, flood-, and salt-tolerant varieties grouped in three distinct clusters within the group of tolerant varieties, when (GA)(8)YG was used. Sabita was the only exception. The two aus varieties, Nagina22 and FR13A, were separated and grouped with the drought- and flood-tolerant varieties, respectively, but they were together in dendrograms based on other primers. The results show that ISSR markers associated with (GA)(8)YG delineated the three groups of stress-tolerant varieties from each other and can be used to identify genes/new alleles associated with the three abiotic stresses in rice germplasm.
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Affiliation(s)
- Ch Surendhar Reddy
- Biotechnology Laboratory, Crop Improvement Section, Directorate of Rice Research, Rajendranagar, Hyderabad 500030, India
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