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Jyoti SD, Singh G, Pradhan AK, Tarpley L, Septiningsih EM, Talukder SK. Rice breeding for low input agriculture. FRONTIERS IN PLANT SCIENCE 2024; 15:1408356. [PMID: 38974981 PMCID: PMC11224470 DOI: 10.3389/fpls.2024.1408356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Accepted: 05/24/2024] [Indexed: 07/09/2024]
Abstract
A low-input-based farming system can reduce the adverse effects of modern agriculture through proper utilization of natural resources. Modern varieties often need to improve in low-input settings since they are not adapted to these systems. In addition, rice is one of the most widely cultivated crops worldwide. Enhancing rice performance under a low input system will significantly reduce the environmental concerns related to rice cultivation. Traits that help rice to maintain yield performance under minimum inputs like seedling vigor, appropriate root architecture for nutrient use efficiency should be incorporated into varieties for low input systems through integrated breeding approaches. Genes or QTLs controlling nutrient uptake, nutrient assimilation, nutrient remobilization, and root morphology need to be properly incorporated into the rice breeding pipeline. Also, genes/QTLs controlling suitable rice cultivars for sustainable farming. Since several variables influence performance under low input conditions, conventional breeding techniques make it challenging to work on many traits. However, recent advances in omics technologies have created enormous opportunities for rapidly improving multiple characteristics. This review highlights current research on features pertinent to low-input agriculture and provides an overview of alternative genomics-based breeding strategies for enhancing genetic gain in rice suitable for low-input farming practices.
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Affiliation(s)
- Subroto Das Jyoti
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States
| | - Gurjeet Singh
- Texas A&M AgriLife Research Center, Beaumont, TX, United States
| | | | - Lee Tarpley
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States
- Texas A&M AgriLife Research Center, Beaumont, TX, United States
| | - Endang M. Septiningsih
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States
| | - Shyamal K. Talukder
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States
- Texas A&M AgriLife Research Center, Beaumont, TX, United States
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Mai NTP, Nguyen LTT, Tran SG, To HTM. Genome-wide association study reveals useful QTL and genes controlling the fatty acid composition in rice bran oil using Vietnamese rice landraces. Funct Integr Genomics 2023; 23:150. [PMID: 37156920 DOI: 10.1007/s10142-023-01080-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 04/25/2023] [Accepted: 04/28/2023] [Indexed: 05/10/2023]
Abstract
In rice (Oryza sativa L.), rice bran contains valuable nutritional constituents, such as high unsaturated fat content, tocotrienols, inositol, γ-oryzanol, and phytosterols, all of which are of nutritional and pharmaceuticals interest. There is now a rising market demand for rice bran oil, which makes research into their content and fatty acid profile an area of interest. As it is evident that lipid content has a substantial impact on the eating, cooking, and storage quality of rice, an understanding of the genetic mechanisms that determine oil content in rice is of great importance, equal to that of rice quality. Therefore, in this study, we performed a genome-wide association study on the composition and oil concentration of 161 Vietnamese rice varieties. Five categories of fatty acids in rice bran were discovered and the bran oil concentration profile in different rice accessions was identified. We also identified 229 important markers related to the fatty acid composition of bran oil, distributed mainly on chromosomes 1 and 7. Seven quantitative trait loci and five potential genes related to unsaturated fatty acid content were detected, including OsKASI, OsFAD, OsARF, OsGAPDH, and OsMADS29. These results provide insights into the genetic basis of rice bran oil composition, which is pivotal to the metabolic engineering of rice plants with desirable bran oil content through candidate genes selection.
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Affiliation(s)
- Nga T P Mai
- University of Sciences and Technology of Hanoi (USTH), Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Cau Giay, 10000, Ha Noi City, Vietnam
| | - Linh Thi Thuy Nguyen
- University of Sciences and Technology of Hanoi (USTH), Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Cau Giay, 10000, Ha Noi City, Vietnam
| | - Son Giang Tran
- University of Sciences and Technology of Hanoi (USTH), Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Cau Giay, 10000, Ha Noi City, Vietnam
| | - Huong Thi Mai To
- University of Sciences and Technology of Hanoi (USTH), Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Cau Giay, 10000, Ha Noi City, Vietnam.
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Van-Anh Le T, Mai Nga TP, Nhi Nguyen P, Kieu-Oanh Nguyen T. Genotypic and Phenotypic Diversity of Endemic Golden Camellias Collected from the North of Vietnam. Chem Biodivers 2023; 20:e202200843. [PMID: 36574472 DOI: 10.1002/cbdv.202200843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 12/13/2022] [Indexed: 12/28/2022]
Abstract
Golden Camellias have recently been used as a food, cosmetic, and traditional medicine in China and Vietnam. Forty-two species have natural distribution in Vietnam, of which thirty-two species were considered endemic species of this country. The morphology of leaves and flowers of these species were similar; therefore, their taxonomic identification usually needed experts and the authentication has often been confused among species. Our study aims to describe the genetic diversity and the relationship of six species Camellia phanii, Camellia tamdaoensis, Camellia tienii, Camellia flava, Camellia petelotii and Camellia euphlebia by using three chloroplast DNA-barcodes: matK, rbcL and trnH-psbA. We also clarified the significant differences in anatomical characteristics of midvein and blade of their leaves, which suggested the possibility to use these criteria in taxonomy. In addition, preliminary chemical profiles of the methanolic extracts of leaves from six Golden Camellias such as total phenolic content (TPC), total flavonoid content (TFC), total anthocyanin content (TAC) and chlorogenic acids content (TCGAs) also showed the diversity among them. Interestingly, the discrimination on the catechins profile among six species followed the same tendency with the genetic distance on the phylogeny tree suggesting that catechins (i. e., discriminative catechins) can be biomarkers for the chemotaxonomy of these six Golden Camellias.
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Affiliation(s)
- T Van-Anh Le
- Department of Life Sciences, University of Science and Technology of Hanoi, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet - Cau Giay, Hanoi, Vietnam
| | - T P Mai Nga
- Department of Life Sciences, University of Science and Technology of Hanoi, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet - Cau Giay, Hanoi, Vietnam
| | - P Nhi Nguyen
- Department of Life Sciences, University of Science and Technology of Hanoi, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet - Cau Giay, Hanoi, Vietnam
| | - T Kieu-Oanh Nguyen
- Department of Life Sciences, University of Science and Technology of Hanoi, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet - Cau Giay, Hanoi, Vietnam
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Ojeda-Rivera JO, Alejo-Jacuinde G, Nájera-González HR, López-Arredondo D. Prospects of genetics and breeding for low-phosphate tolerance: an integrated approach from soil to cell. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:4125-4150. [PMID: 35524816 PMCID: PMC9729153 DOI: 10.1007/s00122-022-04095-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 03/31/2022] [Indexed: 05/04/2023]
Abstract
Improving phosphorus (P) crop nutrition has emerged as a key factor toward achieving a more resilient and sustainable agriculture. P is an essential nutrient for plant development and reproduction, and phosphate (Pi)-based fertilizers represent one of the pillars that sustain food production systems. To meet the global food demand, the challenge for modern agriculture is to increase food production and improve food quality in a sustainable way by significantly optimizing Pi fertilizer use efficiency. The development of genetically improved crops with higher Pi uptake and Pi-use efficiency and higher adaptability to environments with low-Pi availability will play a crucial role toward this end. In this review, we summarize the current understanding of Pi nutrition and the regulation of Pi-starvation responses in plants, and provide new perspectives on how to harness the ample repertoire of genetic mechanisms behind these adaptive responses for crop improvement. We discuss on the potential of implementing more integrative, versatile, and effective strategies by incorporating systems biology approaches and tools such as genome editing and synthetic biology. These strategies will be invaluable for producing high-yielding crops that require reduced Pi fertilizer inputs and to develop a more sustainable global agriculture.
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Affiliation(s)
- Jonathan Odilón Ojeda-Rivera
- Department of Plant and Soil Science, Institute of Genomics for Crop Abiotic Stress Tolerance, Texas Tech University, Lubbock, TX, USA
| | - Gerardo Alejo-Jacuinde
- Department of Plant and Soil Science, Institute of Genomics for Crop Abiotic Stress Tolerance, Texas Tech University, Lubbock, TX, USA
| | - Héctor-Rogelio Nájera-González
- Department of Plant and Soil Science, Institute of Genomics for Crop Abiotic Stress Tolerance, Texas Tech University, Lubbock, TX, USA
| | - Damar López-Arredondo
- Department of Plant and Soil Science, Institute of Genomics for Crop Abiotic Stress Tolerance, Texas Tech University, Lubbock, TX, USA.
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Deep polygenic neural network for predicting and identifying yield-associated genes in Indonesian rice accessions. Sci Rep 2022; 12:13823. [PMID: 35970979 PMCID: PMC9378700 DOI: 10.1038/s41598-022-16075-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 07/04/2022] [Indexed: 11/12/2022] Open
Abstract
As the fourth most populous country in the world, Indonesia must increase the annual rice production rate to achieve national food security by 2050. One possible solution comes from the nanoscopic level: a genetic variant called Single Nucleotide Polymorphism (SNP), which can express significant yield-associated genes. The prior benchmark of this study utilized a statistical genetics model where no SNP position information and attention mechanism were involved. Hence, we developed a novel deep polygenic neural network, named the NucleoNet model, to address these obstacles. The NucleoNets were constructed with the combination of prominent components that include positional SNP encoding, the context vector, wide models, Elastic Net, and Shannon’s entropy loss. This polygenic modeling obtained up to 2.779 of Mean Squared Error (MSE) with 47.156% of Symmetric Mean Absolute Percentage Error (SMAPE), while revealing 15 new important SNPs. Furthermore, the NucleoNets reduced the MSE score up to 32.28% compared to the Ordinary Least Squares (OLS) model. Through the ablation study, we learned that the combination of Xavier distribution for weights initialization and Normal distribution for biases initialization sparked more various important SNPs throughout 12 chromosomes. Our findings confirmed that the NucleoNet model was successfully outperformed the OLS model and identified important SNPs to Indonesian rice yields.
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Hibbert L, Taylor G. Improving phosphate use efficiency in the aquatic crop watercress (Nasturtium officinale). HORTICULTURE RESEARCH 2022; 9:uhac011. [PMID: 35147194 PMCID: PMC8969064 DOI: 10.1093/hr/uhac011] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 11/30/2021] [Indexed: 06/14/2023]
Abstract
Watercress is a nutrient-dense leafy green crop, traditionally grown in aquatic outdoor systems and increasingly seen as well-suited for indoor hydroponic systems. However, there is concern that this crop has a detrimental impact on the environment through direct phosphate additions causing environmental pollution. Phosphate-based fertilisers are supplied to enhanced crop yield, but their use may contribute to eutrophication of waterways downstream of traditional watercress farms. One option is to develop a more phosphate use efficient (PUE) crop. This review identifies the key traits for this aquatic crop (the ideotype), for future selection, marker development and breeding. Traits identified as important for PUE are (i) increased root surface area through prolific root branching and adventitious root formation, (ii) aerenchyma formation and root hair growth. Functional genomic traits for improved PUE are (iii) efficacious phosphate remobilisation and scavenging strategies and (iv) the use of alternative metabolic pathways. Key genomic targets for this aquatic crop are identified as: PHT phosphate transporter genes, global transcriptional regulators such as those of the SPX family and genes involved in galactolipid and sulfolipid biosynthesis such as MGD2/3, PECP1, PSR2, PLDζ1/2 and SQD2. Breeding for enhanced PUE in watercress will be accelerated by improved molecular genetic resources such as a full reference genome sequence that is currently in development.
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Affiliation(s)
- Lauren Hibbert
- School of Biological Sciences, University of Southampton, Southampton, Hampshire, SO17 1BJ, UK
- Department of Plant Sciences, UC Davis, Davis, CA, 95616, USA
| | - Gail Taylor
- School of Biological Sciences, University of Southampton, Southampton, Hampshire, SO17 1BJ, UK
- Department of Plant Sciences, UC Davis, Davis, CA, 95616, USA
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Higgins J, Santos B, Khanh TD, Trung KH, Duong TD, Doai NTP, Khoa NT, Ha DTT, Diep NT, Dung KT, Phi CN, Thuy TT, Tuan NT, Tran HD, Trung NT, Giang HT, Nhung TK, Tran CD, Lang SV, Nghia LT, Van Giang N, Xuan TD, Hall A, Dyer S, Ham LH, Caccamo M, De Vega JJ. Resequencing of 672 Native Rice Accessions to Explore Genetic Diversity and Trait Associations in Vietnam. RICE (NEW YORK, N.Y.) 2021; 14:52. [PMID: 34110541 PMCID: PMC8192651 DOI: 10.1186/s12284-021-00481-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 04/07/2021] [Indexed: 05/28/2023]
Abstract
BACKGROUND Vietnam possesses a vast diversity of rice landraces due to its geographical situation, latitudinal range, and a variety of ecosystems. This genetic diversity constitutes a highly valuable resource at a time when the highest rice production areas in the low-lying Mekong and Red River Deltas are enduring increasing threats from climate changes, particularly in rainfall and temperature patterns. RESULTS We analysed 672 Vietnamese rice genomes, 616 newly sequenced, that encompass the range of rice varieties grown in the diverse ecosystems found throughout Vietnam. We described four Japonica and five Indica subpopulations within Vietnam likely adapted to the region of origin. We compared the population structure and genetic diversity of these Vietnamese rice genomes to the 3000 genomes of Asian cultivated rice. The named Indica-5 (I5) subpopulation was expanded in Vietnam and contained lowland Indica accessions, which had very low shared ancestry with accessions from any other subpopulation and were previously overlooked as admixtures. We scored phenotypic measurements for nineteen traits and identified 453 unique genotype-phenotype significant associations comprising twenty-one QTLs (quantitative trait loci). The strongest associations were observed for grain size traits, while weaker associations were observed for a range of characteristics, including panicle length, heading date and leaf width. CONCLUSIONS We showed how the rice diversity within Vietnam relates to the wider Asian rice diversity by using a number of approaches to provide a clear picture of the novel diversity present within Vietnam, mainly around the Indica-5 subpopulation. Our results highlight differences in genome composition and trait associations among traditional Vietnamese rice accessions, which are likely the product of adaption to multiple environmental conditions and regional preferences in a very diverse country. Our results highlighted traits and their associated genomic regions that are a potential source of novel loci and alleles to breed a new generation of low input sustainable and climate resilient rice.
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Affiliation(s)
- Janet Higgins
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
| | - Bruno Santos
- NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK
| | - Tran Dang Khanh
- Agriculture Genetics Institute (AGI), Hanoi, Vietnam
- Vietnam National University of Agriculture, Hanoi, 131000, Vietnam
| | | | | | | | | | | | | | - Kieu Thi Dung
- Agriculture Genetics Institute (AGI), Hanoi, Vietnam
| | | | - Tran Thi Thuy
- Agriculture Genetics Institute (AGI), Hanoi, Vietnam
| | | | - Hoang Dung Tran
- Faculty of Biotechnology, Nguyen Tat Thanh University, Ho Chi Minh, 72820, Vietnam
| | - Nguyen Thanh Trung
- Faculty of Pharmacy, Duy Tan University, Da Nang, 550000, Vietnam
- Institute of Research and Development, Duy Tan University, Da Nang, 550000, Vietnam
| | | | - Ta Kim Nhung
- Agriculture Genetics Institute (AGI), Hanoi, Vietnam
| | | | - Son Vi Lang
- Agriculture Genetics Institute (AGI), Hanoi, Vietnam
| | - La Tuan Nghia
- Plant Resource Center, An Khanh, Hoai Duc, Hanoi, 152900, Vietnam
| | - Nguyen Van Giang
- Vietnam National University of Agriculture, Hanoi, 131000, Vietnam
| | - Tran Dang Xuan
- Graduate School of Advanced Science and Engineering, Hiroshima University, Hiroshima, 739-8529, Japan
| | - Anthony Hall
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
| | - Sarah Dyer
- NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK
| | - Le Huy Ham
- Agriculture Genetics Institute (AGI), Hanoi, Vietnam
| | - Mario Caccamo
- NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK
| | - Jose J De Vega
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK.
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