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Sudan J, Urwat U, Farooq A, Pakhtoon MM, Zaffar A, Naik ZA, Batool A, Bashir S, Mansoor M, Sofi PA, Sofi NUR, Shikari AB, Khan MK, Hossain MA, Henry RJ, Zargar SM. Explicating genetic architecture governing nutritional quality in pigmented rice. PeerJ 2023; 11:e15901. [PMID: 37719119 PMCID: PMC10501373 DOI: 10.7717/peerj.15901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 07/25/2023] [Indexed: 09/19/2023] Open
Abstract
Rice is one of the most important staple plant foods that provide a major source of calories and nutrients for tackling the global hunger index especially in developing countries. In terms of nutritional profile, pigmented rice grains are favoured for their nutritional and health benefits. The pigmented rice varieties are rich sources of flavonoids, anthocyanin and proanthocyanidin that can be readily incorporated into diets to help address various lifestyle diseases. However, the cultivation of pigmented rice is limited due to low productivity and unfavourable cooking qualities. With the advances in genome sequencing, molecular breeding, gene expression analysis and multi-omics approaches, various attempts have been made to explore the genetic architecture of rice grain pigmentation. In this review, we have compiled the current state of knowledge of the genetic architecture and nutritional value of pigmentation in rice based upon the available experimental evidence. Future research areas that can help to deepen our understanding and help in harnessing the economic and health benefits of pigmented rice are also explored.
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Affiliation(s)
- Jebi Sudan
- Proteomics Lab, Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, Jammu and Kashmir, India
| | - Uneeb Urwat
- Proteomics Lab, Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, Jammu and Kashmir, India
| | - Asmat Farooq
- Proteomics Lab, Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, Jammu and Kashmir, India
| | - Mohammad Maqbool Pakhtoon
- Proteomics Lab, Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, Jammu and Kashmir, India
| | - Aaqif Zaffar
- Division of Genetics and Plant Breeding, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir (J&K), Srinagar, Jammu and Kashmir, India
| | - Zafir Ahmad Naik
- Division of Genetics and Plant Breeding, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir (J&K), Srinagar, Jammu and Kashmir, India
| | - Aneesa Batool
- Proteomics Lab, Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, Jammu and Kashmir, India
| | - Saika Bashir
- Proteomics Lab, Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, Jammu and Kashmir, India
| | - Madeeha Mansoor
- Proteomics Lab, Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, Jammu and Kashmir, India
| | - Parvaze A. Sofi
- Division of Genetics and Plant Breeding, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir (J&K), Srinagar, Jammu and Kashmir, India
| | - Najeebul Ul Rehman Sofi
- Mountain Research Centre for Field Crops, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Khudwani, Jammu and Kashmir, India
| | - Asif B. Shikari
- Division of Genetics and Plant Breeding, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir (J&K), Srinagar, Jammu and Kashmir, India
| | - Mohd. Kamran Khan
- Department of Soil Sciences and Plant Nutrition, Faculty of Agriculture, Selcuk University, Konya, Turkey
| | - Mohammad Anwar Hossain
- Department of Genetics and Plant Breeding, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Robert J. Henry
- Queensland Alliance for Agriculture and Food Innovation, Queensland University, Brisbane, Australia
| | - Sajad Majeed Zargar
- Proteomics Lab, Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, Jammu and Kashmir, India
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Melnick RL, Jarvis L, Hendley P, Garcia-Alonso M, Metzger MJ, Ramankutty N, Teem JL, Roberts A. GEnZ explorer: a tool for visualizing agroclimate to inform research and regulatory risk assessment. Transgenic Res 2023; 32:321-337. [PMID: 37278871 PMCID: PMC10409678 DOI: 10.1007/s11248-023-00354-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 05/16/2023] [Indexed: 06/07/2023]
Abstract
Confined field trials (CFT) of genetically engineered (GE) crops are used to generate data to inform environmental risk assessments (ERA). ERAs are required by regulatory authorities before novel GE crops can be released for cultivation. The transportability of CFT data to inform risk assessment in countries other than those where the CFT was conducted has been discussed previously in an analysis showing that the primary difference between CFT locations potentially impacting trial outcomes is the physical environment, particularly the agroclimate. This means that data from trials carried out in similar agroclimates could be considered relevant and sufficient to satisfy regulatory requirements for CFT data, irrespective of the country where the CFTs are conducted. This paper describes the development of an open-source tool to assist in determining the transportability of CFT data. This tool provides agroclimate together with overall crop production information to assist regulators and applicants in making informed choices on whether data from previous CFTs can inform an environmental risk assessment in a new country, as well as help developers determine optimal locations for planning future CFTs. The GEnZ Explorer is a freely available, thoroughly documented, and open-source tool that allows users to identify the agroclimate zones that are relevant for the production of 21 major crops and crop categories or to determine the agroclimatic zone at a specific location. This tool will help provide additional scientific justification for CFT data transportability, along with spatial visualization, to help ensure regulatory transparency.
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Affiliation(s)
| | - Larissa Jarvis
- McGill University, 845 Sherbrooke Street West, Montréal, QC, Canada
| | - Paul Hendley
- Phasera Ltd., 7 Kenilworth Avenue, Bracknell, Berkshire, UK
| | | | - Marc J Metzger
- School of Geosciences, Geography and the Lived Environment, The University of Edinburgh, Edinburgh, Scotland
| | - Navin Ramankutty
- School of Public Policy and Global Affairs, The University of British Columbia, Vancouver, BC, Canada
| | - John L Teem
- Genetic Biocontrols LLC, Tallahassee, FL, USA
| | - Andrew Roberts
- Agriculture and Food Systems Institute, Washington, DC, USA.
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Palanog AD, Nha CT, Descalsota-Empleo GIL, Calayugan MI, Swe ZM, Amparado A, Inabangan-Asilo MA, Hernandez JE, Sta. Cruz PC, Borromeo TH, Lalusin AG, Mauleon R, McNally KL, Swamy BPM. Molecular dissection of connected rice populations revealed important genomic regions for agronomic and biofortification traits. FRONTIERS IN PLANT SCIENCE 2023; 14:1157507. [PMID: 37035067 PMCID: PMC10073715 DOI: 10.3389/fpls.2023.1157507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 02/20/2023] [Indexed: 06/19/2023]
Abstract
Breeding staple crops with increased micronutrient concentration is a sustainable approach to address micronutrient malnutrition. We carried out Multi-Cross QTL analysis and Inclusive Composite Interval Mapping for 11 agronomic, yield and biofortification traits using four connected RILs populations of rice. Overall, MC-156 QTLs were detected for agronomic (115) and biofortification (41) traits, which were higher in number but smaller in effects compared to single population analysis. The MC-QTL analysis was able to detect important QTLs viz: qZn5.2, qFe7.1, qGY10.1, qDF7.1, qPH1.1, qNT4.1, qPT4.1, qPL1.2, qTGW5.1, qGL3.1 , and qGW6.1 , which can be used in rice genomics assisted breeding. A major QTL (qZn5.2 ) for grain Zn concentration has been detected on chromosome 5 that accounted for 13% of R2. In all, 26 QTL clusters were identified on different chromosomes. qPH6.1 epistatically interacted with qZn5.1 and qGY6.2 . Most of QTLs were co-located with functionally related candidate genes indicating the accuracy of QTL mapping. The genomic region of qZn5.2 was co-located with putative genes such as OsZIP5, OsZIP9, and LOC_OS05G40490 that are involved in Zn uptake. These genes included polymorphic functional SNPs, and their promoter regions were enriched with cis-regulatory elements involved in plant growth and development, and biotic and abiotic stress tolerance. Major effect QTL identified for biofortification and agronomic traits can be utilized in breeding for Zn biofortified rice varieties.
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Affiliation(s)
- Alvin D. Palanog
- Rice Breeding Innovations Platform, International Rice Research Institute, Los Baños, Laguna, Philippines
- College of Agriculture and Food Science, University of the Philippines, Los Baños, Laguna, Philippines
- PhilRice Negros Branch Station, Philippine Rice Research Institute, Murcia, Negros Occidental, Philippines
| | | | | | - Mark Ian Calayugan
- College of Agriculture and Food Science, University of the Philippines, Los Baños, Laguna, Philippines
| | - Zin Mar Swe
- Rice Breeding Innovations Platform, International Rice Research Institute, Los Baños, Laguna, Philippines
| | - Amery Amparado
- Rice Breeding Innovations Platform, International Rice Research Institute, Los Baños, Laguna, Philippines
| | - Mary Ann Inabangan-Asilo
- Rice Breeding Innovations Platform, International Rice Research Institute, Los Baños, Laguna, Philippines
| | - Jose E. Hernandez
- College of Agriculture and Food Science, University of the Philippines, Los Baños, Laguna, Philippines
| | - Pompe C. Sta. Cruz
- College of Agriculture and Food Science, University of the Philippines, Los Baños, Laguna, Philippines
| | - Teresita H. Borromeo
- College of Agriculture and Food Science, University of the Philippines, Los Baños, Laguna, Philippines
| | - Antonio G. Lalusin
- College of Agriculture and Food Science, University of the Philippines, Los Baños, Laguna, Philippines
| | - Ramil Mauleon
- Rice Breeding Innovations Platform, International Rice Research Institute, Los Baños, Laguna, Philippines
- College of Agriculture, University of Southern Mindanao, Kabacan, North Cotabato, Philippines
| | - Kenneth L. McNally
- Rice Breeding Innovations Platform, International Rice Research Institute, Los Baños, Laguna, Philippines
| | - B. P. Mallikarjuna Swamy
- Rice Breeding Innovations Platform, International Rice Research Institute, Los Baños, Laguna, Philippines
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