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Zheng H, Tang W, Yang T, Zhou M, Guo C, Cheng T, Cao W, Zhu Y, Zhang Y, Yao X. Grain Protein Content Phenotyping in Rice via Hyperspectral Imaging Technology and a Genome-Wide Association Study. PLANT PHENOMICS (WASHINGTON, D.C.) 2024; 6:0200. [PMID: 38978968 PMCID: PMC11227985 DOI: 10.34133/plantphenomics.0200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 05/18/2024] [Indexed: 07/10/2024]
Abstract
Efficient and accurate acquisition of the rice grain protein content (GPC) is important for selecting high-quality rice varieties, and remote sensing technology is an attractive potential method for this task. However, the majority of multispectral sensors are poor predictors of GPC due to their broad spectral bands. Hyperspectral technology provides a new analytical technology for bridging the gap between phenomics and genomics. However, the small size of typical datasets is a constraint for model construction for estimating GPC, limiting their accuracy and reducing their ability to generalize to a wide range of varieties. In this study, we used hyperspectral data of rice grains from 515 japonica varieties and deep convolution generative adversarial networks (DCGANs) to generate simulated data to improve the model accuracy. Features sensitive to GPC were extracted after applying a continuous wavelet transform (CWT), and the estimated GPC model was constructed by partial least squares regression (PLSR). Finally, a genome-wide association study (GWAS) was applied to the measured and generated datasets to detect GPC loci. The results demonstrated that the simulated GPC values generated after 8,000 epochs were closest to the measured values. The wavelet feature (WF1743, 2), obtained from the data with the addition of 200 simulated samples, exhibited the highest GPC estimation accuracy (R 2 = 0.58 and RRMSE = 6.70%). The GWAS analysis showed that the estimated values based on the simulated data detected the same loci as the measured values, including the OsmtSSB1L gene related to grain storage protein. This study provides a new technique for the efficient genetic study of phenotypic traits in rice based on hyperspectral technology.
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Affiliation(s)
- Hengbiao Zheng
- National Engineering and Technology Center for Information Agriculture (NETCIA), MARA Key Laboratory of Crop System Analysis and Decision Making, MOE Engineering Research Center of Smart Agriculture, Jiangsu Key Laboratory for Information Agriculture, Institute of Smart Agriculture,
Nanjing Agricultural University, Nanjing, Jiangsu, China
- Zhongshan Biological Breeding Laboratory,Nanjing, China
| | - Weijie Tang
- Zhongshan Biological Breeding Laboratory,Nanjing, China
- Provincial Key Laboratory of Agrobiology, Institute of Germplasm Resources and Biotechnology,
Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu, China
| | - Tao Yang
- National Engineering and Technology Center for Information Agriculture (NETCIA), MARA Key Laboratory of Crop System Analysis and Decision Making, MOE Engineering Research Center of Smart Agriculture, Jiangsu Key Laboratory for Information Agriculture, Institute of Smart Agriculture,
Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Meng Zhou
- National Engineering and Technology Center for Information Agriculture (NETCIA), MARA Key Laboratory of Crop System Analysis and Decision Making, MOE Engineering Research Center of Smart Agriculture, Jiangsu Key Laboratory for Information Agriculture, Institute of Smart Agriculture,
Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Caili Guo
- National Engineering and Technology Center for Information Agriculture (NETCIA), MARA Key Laboratory of Crop System Analysis and Decision Making, MOE Engineering Research Center of Smart Agriculture, Jiangsu Key Laboratory for Information Agriculture, Institute of Smart Agriculture,
Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Tao Cheng
- National Engineering and Technology Center for Information Agriculture (NETCIA), MARA Key Laboratory of Crop System Analysis and Decision Making, MOE Engineering Research Center of Smart Agriculture, Jiangsu Key Laboratory for Information Agriculture, Institute of Smart Agriculture,
Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Weixing Cao
- National Engineering and Technology Center for Information Agriculture (NETCIA), MARA Key Laboratory of Crop System Analysis and Decision Making, MOE Engineering Research Center of Smart Agriculture, Jiangsu Key Laboratory for Information Agriculture, Institute of Smart Agriculture,
Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Yan Zhu
- National Engineering and Technology Center for Information Agriculture (NETCIA), MARA Key Laboratory of Crop System Analysis and Decision Making, MOE Engineering Research Center of Smart Agriculture, Jiangsu Key Laboratory for Information Agriculture, Institute of Smart Agriculture,
Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Yunhui Zhang
- Zhongshan Biological Breeding Laboratory,Nanjing, China
- Provincial Key Laboratory of Agrobiology, Institute of Germplasm Resources and Biotechnology,
Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu, China
| | - Xia Yao
- National Engineering and Technology Center for Information Agriculture (NETCIA), MARA Key Laboratory of Crop System Analysis and Decision Making, MOE Engineering Research Center of Smart Agriculture, Jiangsu Key Laboratory for Information Agriculture, Institute of Smart Agriculture,
Nanjing Agricultural University, Nanjing, Jiangsu, China
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Zhou R, Song Y, Xue X, Xue R, Jiang H, Zhou Y, Qi X, Wang Y. Differential Transcription Profiling Reveals the MicroRNAs Involved in Alleviating Damage to Photosynthesis under Drought Stress during the Grain Filling Stage in Wheat. Int J Mol Sci 2024; 25:5518. [PMID: 38791558 PMCID: PMC11122533 DOI: 10.3390/ijms25105518] [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: 04/04/2024] [Revised: 05/09/2024] [Accepted: 05/15/2024] [Indexed: 05/26/2024] Open
Abstract
To explore the possible novel microRNA (miRNA) regulatory pathways in Zhengmai 1860, a newly cultivated drought-tolerant wheat (Triticum aestivum L.) cultivar, miRNA transcriptome sequencing of the flag leaves of Zhengmai 1860, drought-sensitive variety Zhoumai 18, and drought-resistant variety Bainong 207 was performed during the grain filling stage. We also observed changes in the chloroplast ultrastructure, phytohormone levels, and antioxidant- and photosynthesis-related physiological indicators in three wheat varieties. The results showed that the flag leaves of the drought-tolerant variety Zhengmai 1860 had higher chlorophyll contents and net photosynthetic rates than those of Zhoumai 18 under drought stress during the grain filling stage; in addition, the chloroplast structure was more complete. However, there was no significant difference between Zhengmai 1860 and Bainong 207. MiRNA transcriptome analysis revealed that the differential expression of the miRNAs and mRNAs exhibited variable specificity. The KEGG pathway enrichment results indicated that most of the genes were enriched in the MAPK signaling pathway, plant hormone signal transduction, photosynthetic antennae protein, and amino acid and carbohydrate metabolism. In the drought-tolerant cultivar Zhengmai 1860, tae-miR408 was targeted to regulate the allene oxide synthase (AOS) gene, inhibit its expression, reduce the AOS content, and decrease the synthesis of jasmonic acid (JA) and abscisic acid (ABA). The results of this study suggest that Zhengmai 1860 could improve the photosynthetic performance of flag leaves by inhibiting the expression of genes involved in the JA pathway through miRNAs under drought conditions. Moreover, multiple miRNAs may target chlorophyll, antioxidant enzymes, phytohormone signal transduction, and other related pathways; thus, it is possible to provide a more theoretical basis for wheat molecular breeding.
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Affiliation(s)
- Ruixiang Zhou
- College of Life Sciences, Henan Agricultural University, 218 Ping’an Avenue, Zhengzhou 450046, China
| | - Yuhang Song
- College of Life Sciences, Henan Agricultural University, 218 Ping’an Avenue, Zhengzhou 450046, China
| | - Xinyu Xue
- College of Life Sciences, Henan Agricultural University, 218 Ping’an Avenue, Zhengzhou 450046, China
| | - Ruili Xue
- College of Life Sciences, Henan Agricultural University, 218 Ping’an Avenue, Zhengzhou 450046, China
| | - Haifang Jiang
- College of Life Sciences, Henan Agricultural University, 218 Ping’an Avenue, Zhengzhou 450046, China
| | - Yi Zhou
- College of Life Sciences, Henan Agricultural University, 218 Ping’an Avenue, Zhengzhou 450046, China
| | - Xueli Qi
- Henan Academy of Crop Molecular Breeding, Zhengzhou 450002, China
| | - Yuexia Wang
- College of Life Sciences, Henan Agricultural University, 218 Ping’an Avenue, Zhengzhou 450046, China
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Wang S, Fang R, Yuan X, Chen J, Mi K, Wang R, Zhang H, Zhang H. Foliar Spraying of ZnO Nanoparticles Enhanced the Yield, Quality, and Zinc Enrichment of Rice Grains. Foods 2023; 12:3677. [PMID: 37835330 PMCID: PMC10572805 DOI: 10.3390/foods12193677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 09/18/2023] [Accepted: 09/26/2023] [Indexed: 10/15/2023] Open
Abstract
Zinc deficiency in rice can lead to reduced nutritional value and taste. This study investigates the potential of zinc oxide nanoparticles (ZnO NPs) as a foliar fertilizer during the jointing stage to improve rice yield, quality, and grain zinc enrichment. Over a two-year field experiment (2019-2020), six doses of ZnO NPs (ranging from 0 to 12 kg hm-2) were applied during the jointing stage (46 days after transplanting). The results revealed that foliar spraying of ZnO NPs increased the number of spikelets per spike and the thousand-grain weight by 7.4% to 9.2% and 4.2% to 7.1%, respectively, resulting in a substantial increase in rice yield. Furthermore, it led to a reduction in chalky white and chalky whiteness by 6.23% to 23.6% and 2.2% to 27.9%. ZnO NPs effectively boosted zinc content in rice grains while decreasing the phytic acid to zinc ratio, indicating improved zinc enrichment. Remarkably, protein and amylose content remained unaffected. These findings underscore the potential of ZnO NPs as a foliar fertilizer to enhance rice production, quality, and zinc enrichment. Further research can explore optimal application strategies and long-term effects for sustainable rice production.
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Affiliation(s)
| | | | | | | | | | | | - Haipeng Zhang
- Jiangsu Key Laboratory of Crop Cultivation and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops/Innovation Center of Rice Cultivation Technology in Yangtze Valley, Ministry of Agriculture and Rural Affairs, Research Institute of Rice Industrial Engineering Technology, Yangzhou University, Yangzhou 225009, China; (S.W.); (R.F.); (X.Y.); (J.C.); (K.M.); (R.W.); (H.Z.)
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Rodríguez AA, Vilas JM, Sartore GD, Bezus R, Colazo J, Maiale SJ. Field and genetic evidence support the photosynthetic performance index (PI ABS) as an indicator of rice grain yield. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 201:107897. [PMID: 37487369 DOI: 10.1016/j.plaphy.2023.107897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 07/12/2023] [Accepted: 07/14/2023] [Indexed: 07/26/2023]
Abstract
The rice breeding process for grain yield could be effectively enhanced by developing efficient tools that accelerate plant selection through the rapid determination of reliable predictors. In this study, we have described various associations between grain yield and photosynthetic parameters, which can be easily and quickly obtained using a non-invasive technique on the flag leaf during the anthesis stage. Among the analyzed photosynthetic parameters, the photosynthetic performance index (PIABS) stood out due to its strong association with grain yield. A genome-wide association analysis conducted on plants from a rice diversity panel at the tillering stage revealed the presence of a quantitative trait locus on chromosome 9. This locus was characterized by a group of candidate chloroplastic genes that exhibited contrasting haplotypes for PIABS. An analysis of these haplotypes revealed a clear division into two groups. One group consisted of haplotypes linked to high values of PIABS, which were predominantly associated with Japonica spp. subpopulations. The other group consisted of haplotypes linked to low values of PIABS, which were exclusively associated with Indica spp. subpopulations. Japonica spp. genotypes exhibited higher values in the yield component panicle weight compared with the Indica spp. genotypes. The findings of this study indicate that PIABS could serve as an early predictor of yield parameters during the tillering stage in rice breeding processes.
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Affiliation(s)
- Andrés Alberto Rodríguez
- Laboratorio de Fisiología y Asistencia al Mejoramiento Vegetal, Instituto Tecnológico de Chascomús (CONICET-UNSAM), Escuela de Bio y Nanotecnologías (UNSAM), Argentina.
| | - Juan Manuel Vilas
- Laboratorio de Fisiología y Asistencia al Mejoramiento Vegetal, Instituto Tecnológico de Chascomús (CONICET-UNSAM), Escuela de Bio y Nanotecnologías (UNSAM), Argentina.
| | - Gustavo Daniel Sartore
- Facultad de Ciencias Agrarias y Forestales, Universidad Nacional de la Plata, 60 y 119, La Plata, Pcia. Bs. As., Argentina.
| | - Rodolfo Bezus
- Facultad de Ciencias Agrarias y Forestales, Universidad Nacional de la Plata, 60 y 119, La Plata, Pcia. Bs. As., Argentina.
| | - José Colazo
- EEA INTA Concepción del Uruguay, Ruta 39 Km 143, Concepción del Uruguay, Pcia. de Entre Ríos, Argentina.
| | - Santiago Javier Maiale
- Laboratorio de Fisiología y Asistencia al Mejoramiento Vegetal, Instituto Tecnológico de Chascomús (CONICET-UNSAM), Escuela de Bio y Nanotecnologías (UNSAM), Argentina.
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Shi S, Zhao D, Pan K, Ma Y, Zhang G, Li L, Cao C, Jiang Y. Combination of near-infrared spectroscopy and key wavelength-based screening algorithm for rapid determination of rice protein content. J Food Compost Anal 2023. [DOI: 10.1016/j.jfca.2023.105216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/13/2023]
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Cohen M, Hertweck K, Itkin M, Malitsky S, Dassa B, Fischer AM, Fluhr R. Enhanced proteostasis, lipid remodeling, and nitrogen remobilization define barley flag leaf senescence. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:6816-6837. [PMID: 35918065 DOI: 10.1093/jxb/erac329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 07/28/2022] [Indexed: 06/15/2023]
Abstract
Leaf senescence is a developmental process allowing nutrient remobilization to sink organs. We characterized flag leaf senescence at 7, 14, and 21 d past anthesis in two near-isogenic barley lines varying in the allelic state of the HvNAM1 transcription factor gene, which influences senescence timing. Metabolomics and microscopy indicated that, as senescence progressed, thylakoid lipids were transiently converted to neutral lipids accumulating in lipid droplets. Senescing leaves also exhibited an accumulation of sugars including glucose, while nitrogen compounds (nucleobases, nucleotides, and amino acids) decreased. RNA-Seq analysis suggested lipid catabolism via β-oxidation and the glyoxylate cycle, producing carbon skeletons and feeding respiration as a replacement of the diminished carbon supply from photosynthesis. Comparison of the two barley lines highlighted a more prominent up-regulation of heat stress transcription factor- and chaperone-encoding genes in the late-senescing line, suggesting a role for these genes in the control of leaf longevity. While numerous genes with putative roles in nitrogen remobilization were up-regulated in both lines, several peptidases, nucleases, and nitrogen transporters were more highly induced in the early-senescing line; this finding identifies processes and specific candidates which may affect nitrogen remobilization from senescing barley leaves, downstream of the HvNAM1 transcription factor.
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Affiliation(s)
- Maja Cohen
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Kendra Hertweck
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, USA
| | - Maxim Itkin
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Sergey Malitsky
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Bareket Dassa
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Andreas M Fischer
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, USA
| | - Robert Fluhr
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
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