Metabonomic and Transcriptomic Profiling Reveals Amino Acid Metabolism Affects the Quality of Premium Japonica Rice Varieties in Northeast China

Overview

Journal Food Chem (Oxf)

Specialty Biochemistry

Date 2024 Dec 9

PMID 39650206

Authors

Jing Wang

Haitao Guan

Xiaolei Zhang

Changjun Dai

Cuiling Wang

Guofeng Chen

Kun Li

Zhenhua Xu

Ruiying Zhang

Baohai Liu

Hongtao Wen

Affiliations

Soon will be listed here.

Abstract

Rice consumption and demand for premium rice are increasing worldwide. However, the characterizations and how to identify the premium rice are still unclear. Small molecular metabolites have a great advantage in distinguishing subtle differences among similar agricultural products. So, we hypothesized that the metabolites would be the key to identifying the tiny differences in premium rice among similar varieties. In this study, we performed metabolomic and transcriptomic profiles to comprehensively elucidate key metabolites, genes, and formation mechanisms of premium rice. As a result, eight compounds belong to four categories, and 49 different expressional genes were identified in premium rice varieties after comparing with the second-best varieties. Moreover, the integrated analysis confirmed that the amino acid pathway, including 42 expression genes and 11 metabolites, was critical for the premium rice formation. Six genes and two metabolites had significant regulatory effects on the pathways. Furthermore, amino acid quantification confirmed the content of 12 kinds of hydrolytic amino acids, such as aspartic acid and arginine were different between premium and other varieties. These amino acids may serve as potential biomarkers for differentiating premium rice in Northeast China. Our results strongly support the possibility of differentiating premium rice and would provide essential data for premium rice identification and metabolomics-assisted breeding.

References

Li F, Liu Y, Zhang X, Liu L, Yan Y, Ji X . Transcriptome and Metabolome Analyses Reveals the Pathway and Metabolites of Grain Quality Under Phytochrome B in Rice (Oryza sativa L.). Rice (N Y). 2022; 15(1):52. PMC: 9613846. DOI: 10.1186/s12284-022-00600-5. View

Zhao Q, Lin J, Wang C, Yousaf L, Xue Y, Shen Q . Protein structural properties and proteomic analysis of rice during storage at different temperatures. Food Chem. 2021; 361:130028. DOI: 10.1016/j.foodchem.2021.130028. View

Yang Y, Shen Z, Li Y, Xu C, Xia H, Zhuang H . Rapid improvement of rice eating and cooking quality through gene editing toward glutelin as target. J Integr Plant Biol. 2022; 64(10):1860-1865. DOI: 10.1111/jipb.13334. View

Liu Y, Li Y, Peng Y, Yang Y, Wang Q . Detection of fraud in high-quality rice by near-infrared spectroscopy. J Food Sci. 2020; 85(9):2773-2782. DOI: 10.1111/1750-3841.15314. View

Zhu D, Zheng X, Yu J, Chen M, Li M, Shao Y . Effects of Starch Molecular Structure and Physicochemical Properties on Eating Quality of Rice with Similar Apparent Amylose and Protein Contents. Foods. 2023; 12(19). PMC: 10572605. DOI: 10.3390/foods12193535. View

Liu Z, Jiang S, Jiang L, Li W, Tang Y, He W . Transcription factor OsSGL is a regulator of starch synthesis and grain quality in rice. J Exp Bot. 2022; 73(11):3417-3430. DOI: 10.1093/jxb/erac068. View

Doll N, Ingram G . Embryo-Endosperm Interactions. Annu Rev Plant Biol. 2022; 73:293-321. DOI: 10.1146/annurev-arplant-102820-091838. View

Xiong Q, Sun C, Shi H, Cai S, Xie H, Liu F . Analysis of Related Metabolites Affecting Taste Values in Rice under Different Nitrogen Fertilizer Amounts and Planting Densities. Foods. 2022; 11(10). PMC: 9141971. DOI: 10.3390/foods11101508. View

Yang X, Pan Y, Xia X, Qing D, Chen W, Nong B . Molecular basis of genetic improvement for key rice quality traits in Southern China. Genomics. 2023; 115(6):110745. DOI: 10.1016/j.ygeno.2023.110745. View

10.

Rana N, Kumawat S, Kumar V, Bansal R, Mandlik R, Dhiman P . Deciphering Haplotypic Variation and Gene Expression Dynamics Associated with Nutritional and Cooking Quality in Rice. Cells. 2022; 11(7). PMC: 8998046. DOI: 10.3390/cells11071144. View

11.

Yang W, Jiang X, Xie Y, Chen L, Zhao J, Liu B . Transcriptome and Metabolome Analyses Reveal New Insights into the Regulatory Mechanism of Head Milled Rice Rate. Plants (Basel). 2022; 11(21). PMC: 9654032. DOI: 10.3390/plants11212838. View

12.

Zeng T, Fang B, Huang F, Dai L, Tang Z, Tian J . Mass spectrometry-based metabolomics investigation on two different indica rice grains (Oryza sativa L.) under cadmium stress. Food Chem. 2020; 343:128472. DOI: 10.1016/j.foodchem.2020.128472. View

13.

Daygon V, Calingacion M, Forster L, De Voss J, Schwartz B, Ovenden B . Metabolomics and genomics combine to unravel the pathway for the presence of fragrance in rice. Sci Rep. 2017; 7(1):8767. PMC: 5562744. DOI: 10.1038/s41598-017-07693-9. View

14.

Setyaningsih W, Majchrzak T, Dymerski T, Namiesnik J, Palma M . Key-Marker Volatile Compounds in Aromatic Rice () Grains: An HS-SPME Extraction Method Combined with GC×GC-TOFMS. Molecules. 2019; 24(22). PMC: 6891657. DOI: 10.3390/molecules24224180. View

15.

Wang W, Xu D, Sui Y, Ding X, Song X . A multiomic study uncovers a bZIP23-PER1A-mediated detoxification pathway to enhance seed vigor in rice. Proc Natl Acad Sci U S A. 2022; 119(9). PMC: 8892333. DOI: 10.1073/pnas.2026355119. View

16.

Zhao L, Duan X, Liu H, Zhang D, Wang Q, Liu J . A panel of lipid markers for rice discrimination of Wuchang Daohuaxiang in China. Food Res Int. 2022; 159:111511. DOI: 10.1016/j.foodres.2022.111511. View

17.

Xiong Q, Sun C, Wang R, Wang R, Wang X, Zhang Y . The Key Metabolites in Rice Quality Formation of Conventional Varieties. Curr Issues Mol Biol. 2023; 45(2):990-1001. PMC: 9955130. DOI: 10.3390/cimb45020064. View

18.

Duan M, Sun S . Profiling the expression of genes controlling rice grain quality. Plant Mol Biol. 2005; 59(1):165-78. DOI: 10.1007/s11103-004-7507-3. View

19.

Zhang C, Zhu L, Shao K, Gu M, Liu Q . Toward underlying reasons for rice starches having low viscosity and high amylose: physiochemical and structural characteristics. J Sci Food Agric. 2012; 93(7):1543-51. DOI: 10.1002/jsfa.5987. View

20.

Ramalingam A, Mohanavel W, Premnath A, Muthurajan R, Prasad P, Perumal R . Large-Scale Non-Targeted Metabolomics Reveals Antioxidant, Nutraceutical and Therapeutic Potentials of Sorghum. Antioxidants (Basel). 2021; 10(10). PMC: 8532915. DOI: 10.3390/antiox10101511. View