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Imran M, Junaid M, Shafiq S, Liu S, Chen X, Wang J, Tang X. Multiomics analysis reveals a substantial decrease in nanoplastics uptake and associated impacts by nano zinc oxide in fragrant rice (Oryza sativa L.). JOURNAL OF HAZARDOUS MATERIALS 2024; 474:134640. [PMID: 38810581 DOI: 10.1016/j.jhazmat.2024.134640] [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: 03/16/2024] [Revised: 04/28/2024] [Accepted: 05/16/2024] [Indexed: 05/31/2024]
Abstract
Nanoplastics (NPs) have emerged as global environmental pollutants with concerning implications for sustainable agriculture. Understanding the underlying mechanisms of NPs toxicity and devising strategies to mitigate their impact is crucial for crop growth and development. Here, we investigated the nanoparticles of zinc oxide (nZnO) to mitigate the adverse effects of 80 nm NPs on fragrant rice. Our results showed that optimized nZnO (25 mg L-1) concentration rescued root length and structural deficits by improving oxidative stress response, antioxidant defense mechanism and balanced nutrient levels, compared to seedlings subjected only to NPs stress (50 mg L-1). Consequently, microscopy observations, Zeta potential and Fourier transform infrared (FTIR) results revealed that NPs were mainly accumulated on the initiation joints of secondary roots and between cortical cells that blocks the nutrients uptake, while the supplementation of nZnO led to the formation of aggregates with NPs, which effectively impedes the uptake of NPs by the roots of fragrant rice. Transcriptomic analysis identified a total of 3973, 3513 and 3380 differentially expressed genes (DEGs) in response to NPs, nZnO and NPs+nZnO, respectively, compared to the control. Moreover, DEGs were significantly enriched in multiple pathways including biosynthesis of secondary metabolite, phenylpropanoid biosynthesis, amino sugar and nucleotide sugar metabolism, carotenoid biosynthesis, plant-pathogen interactions, MAPK signaling pathway, starch and sucrose metabolism, and plant hormone signal transduction. These pathways could play a significant role in alleviating NPs toxicity and restoring fragrant rice roots. Furthermore, metabolomic analysis demonstrated that nZnO application restored 2-acetyl-1-pyrroline (2-AP) pathways genes expression, enzymatic activities, and the content of essential precursors related to 2-AP biosynthesis under NPs toxicity, which ultimately led to the restoration of 2-AP content in the leaves. In conclusion, this study shows that optimized nZnO application effectively alleviates NPs toxic effects and restores both root structure and aroma production in fragrant rice leaves. This research offers a sustainable and practical strategy to enhance crop production under NPs toxicity while emphasizing the pivotal role of essential micronutrient nanomaterials in agriculture.
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Affiliation(s)
- Muhammad Imran
- Department of Crop Science and Technology, College of Agriculture, South China Agricultural University, Guangzhou 510642, China.
| | - Muhammad Junaid
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Sarfraz Shafiq
- Department of Crop Science and Technology, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Shulin Liu
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Xiaoyuan Chen
- Department of Crop Science and Technology, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Jun Wang
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Xiangru Tang
- Department of Crop Science and Technology, College of Agriculture, South China Agricultural University, Guangzhou 510642, China.
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Huang S, Ashraf U, Duan M, Ren Y, Xing P, Yan Z, Tang X. Ultrasonic seed treatment improved seed germination, growth, and yield of rice by modulating associated physio-biochemical mechanisms. ULTRASONICS SONOCHEMISTRY 2024; 104:106821. [PMID: 38387222 PMCID: PMC10901143 DOI: 10.1016/j.ultsonch.2024.106821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 02/18/2024] [Accepted: 02/19/2024] [Indexed: 02/24/2024]
Abstract
Ultrasonic seed (US) treatment could alter seed germination mechanism, however, US induced alterations in morph-physiological attributes and yield of fragrant rice were rarely reported. In the present study, the seeds of three fragrant rice cultivars viz., Xiangyaxiangzhan, Meixiangzhan 2, Ruanhuayou 6100 and one non-fragrant rice viz., Wufengyou 615 were exposed to ultrasonic waves at 20-40 kHz for 1.5 min (T) whereas the seeds without exposure were taken as control (CK). Results showed that US treatment caused minor cracks on seed surface while improved seed germination rate (1.79 %-11.09 %) and 3-indoleacetic acid (IAA) (3.36 %-46.91 %). Furthermore, peroxidase (POD) activity and methionine sulfoxide reductase activity was increased by 29.15 %-74.13 % and 11.26 %-20.87 %, respectively; however, methionine sulfoxide reductase related protein repairing gene MSRA4 was down-regulated by 17.93 % -41.04 % under T, compared to CK. Besides, US treatment also improved soluble protein in flag leaf (0.92 %-40.79 %), photosynthesis (3.37 %-16.46 %), biomass (5.17 %-31.87 %), as well as 2-acetyl-1-pyrroline content (4.77 %-15.48 %) in rice grains. In addition, multivariate analysis showed that the dry weight at the maturity stage were significantly related to the POD, glutathione reductase (GR) activity, IAA, and abscisic acid (ABA) content while germination rate was positively related to the GR activity, ABA content, and yield, but which were negatively related to the IAA and gibberellic acid content.
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Affiliation(s)
- Suihua Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agricultural Bioresources, South China Agricultural University, Guangzhou 510642, China; Institute of Quality Standard and Monitoring Technology for Agro-Products of Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Umair Ashraf
- Department of Botany, Division of Science and Technology, University of Education, Lahore 54770, Punjab, Pakistan
| | - Meiyang Duan
- State Key Laboratory for Conservation and Utilization of Subtropical Agricultural Bioresources, South China Agricultural University, Guangzhou 510642, China
| | - Yong Ren
- Guangxi Key Laboratory of Agricultural Resources Chemistry and Biotechnology, Yulin Normal University, 537000, China
| | - Pipeng Xing
- State Key Laboratory for Conservation and Utilization of Subtropical Agricultural Bioresources, South China Agricultural University, Guangzhou 510642, China
| | - Zhuosheng Yan
- Guangzhou Golden Rice Agricultural Science & Technology Co., Ltd., Guangzhou 510900, China
| | - Xiangru Tang
- State Key Laboratory for Conservation and Utilization of Subtropical Agricultural Bioresources, South China Agricultural University, Guangzhou 510642, China.
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Sun Y, Li M, Li X, Du J, Li W, Lin Y, Zhang Y, Wang Y, He W, Chen Q, Zhang Y, Wang X, Luo Y, Xiong A, Tang H. Characterization of Volatile Organic Compounds in Five Celery ( Apium graveolens L.) Cultivars with Different Petiole Colors by HS-SPME-GC-MS. Int J Mol Sci 2023; 24:13343. [PMID: 37686147 PMCID: PMC10488006 DOI: 10.3390/ijms241713343] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 08/17/2023] [Accepted: 08/24/2023] [Indexed: 09/10/2023] Open
Abstract
Celery (Apium graveolens L.) is an important vegetable crop cultivated worldwide for its medicinal properties and distinctive flavor. Volatile organic compound (VOC) analysis is a valuable tool for the identification and classification of species. Currently, less research has been conducted on aroma compounds in different celery varieties and colors. In this study, five different colored celery were quantitatively analyzed for VOCs using HS-SPME, GC-MS determination, and stoichiometry methods. The result revealed that γ-terpinene, d-limonene, 2-hexenal,-(E)-, and β-myrcene contributed primarily to the celery aroma. The composition of compounds in celery exhibited a correlation not only with the color of the variety, with green celery displaying a higher concentration compared with other varieties, but also with the specific organ, whereby the content and distribution of volatile compounds were primarily influenced by the leaf rather than the petiole. Seven key genes influencing terpenoid synthesis were screened to detect expression levels. Most of the genes exhibited higher expression in leaves than petioles. In addition, some genes, particularly AgDXS and AgIDI, have higher expression levels in celery than other genes, thereby influencing the regulation of terpenoid synthesis through the MEP and MVA pathways, such as hydrocarbon monoterpenes. This study identified the characteristics of flavor compounds and key aroma components in different colored celery varieties and explored key genes involved in the regulation of terpenoid synthesis, laying a theoretical foundation for understanding flavor chemistry and improving its quality.
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Affiliation(s)
- Yue Sun
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (Y.S.); (M.L.); (X.L.); (J.D.); (W.L.); (Y.L.); (Y.Z.); (Y.W.); (W.H.); (Q.C.); (Y.Z.); (X.W.); (Y.L.)
| | - Mengyao Li
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (Y.S.); (M.L.); (X.L.); (J.D.); (W.L.); (Y.L.); (Y.Z.); (Y.W.); (W.H.); (Q.C.); (Y.Z.); (X.W.); (Y.L.)
| | - Xiaoyan Li
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (Y.S.); (M.L.); (X.L.); (J.D.); (W.L.); (Y.L.); (Y.Z.); (Y.W.); (W.H.); (Q.C.); (Y.Z.); (X.W.); (Y.L.)
| | - Jiageng Du
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (Y.S.); (M.L.); (X.L.); (J.D.); (W.L.); (Y.L.); (Y.Z.); (Y.W.); (W.H.); (Q.C.); (Y.Z.); (X.W.); (Y.L.)
| | - Weilong Li
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (Y.S.); (M.L.); (X.L.); (J.D.); (W.L.); (Y.L.); (Y.Z.); (Y.W.); (W.H.); (Q.C.); (Y.Z.); (X.W.); (Y.L.)
| | - Yuanxiu Lin
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (Y.S.); (M.L.); (X.L.); (J.D.); (W.L.); (Y.L.); (Y.Z.); (Y.W.); (W.H.); (Q.C.); (Y.Z.); (X.W.); (Y.L.)
| | - Yunting Zhang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (Y.S.); (M.L.); (X.L.); (J.D.); (W.L.); (Y.L.); (Y.Z.); (Y.W.); (W.H.); (Q.C.); (Y.Z.); (X.W.); (Y.L.)
| | - Yan Wang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (Y.S.); (M.L.); (X.L.); (J.D.); (W.L.); (Y.L.); (Y.Z.); (Y.W.); (W.H.); (Q.C.); (Y.Z.); (X.W.); (Y.L.)
| | - Wen He
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (Y.S.); (M.L.); (X.L.); (J.D.); (W.L.); (Y.L.); (Y.Z.); (Y.W.); (W.H.); (Q.C.); (Y.Z.); (X.W.); (Y.L.)
| | - Qing Chen
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (Y.S.); (M.L.); (X.L.); (J.D.); (W.L.); (Y.L.); (Y.Z.); (Y.W.); (W.H.); (Q.C.); (Y.Z.); (X.W.); (Y.L.)
| | - Yong Zhang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (Y.S.); (M.L.); (X.L.); (J.D.); (W.L.); (Y.L.); (Y.Z.); (Y.W.); (W.H.); (Q.C.); (Y.Z.); (X.W.); (Y.L.)
| | - Xiaorong Wang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (Y.S.); (M.L.); (X.L.); (J.D.); (W.L.); (Y.L.); (Y.Z.); (Y.W.); (W.H.); (Q.C.); (Y.Z.); (X.W.); (Y.L.)
| | - Ya Luo
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (Y.S.); (M.L.); (X.L.); (J.D.); (W.L.); (Y.L.); (Y.Z.); (Y.W.); (W.H.); (Q.C.); (Y.Z.); (X.W.); (Y.L.)
| | - Aisheng Xiong
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China;
| | - Haoru Tang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (Y.S.); (M.L.); (X.L.); (J.D.); (W.L.); (Y.L.); (Y.Z.); (Y.W.); (W.H.); (Q.C.); (Y.Z.); (X.W.); (Y.L.)
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Abbas F, Yu Y, Bendahmane M, Wang HC. Plant volatiles and color compounds: From biosynthesis to function. PHYSIOLOGIA PLANTARUM 2023; 175:e13947. [PMID: 37357979 DOI: 10.1111/ppl.13947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 06/05/2023] [Indexed: 06/27/2023]
Affiliation(s)
- Farhat Abbas
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops-South China/Guangdong Litchi Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Yixun Yu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops-South China/Guangdong Litchi Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Mohammed Bendahmane
- Laboratoire Reproduction et Development des Plantes, INRA-CNRS-Lyon1-ENS, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Hui-Cong Wang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops-South China/Guangdong Litchi Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou, China
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Imran M, Shafiq S, Ashraf U, Qi J, Mo Z, Tang X. Biosynthesis of 2-Acetyl-1-pyrroline in Fragrant Rice: Recent Insights into Agro-management, Environmental Factors, and Functional Genomics. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:4201-4215. [PMID: 36880506 DOI: 10.1021/acs.jafc.2c07934] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Rice is a staple food for more than half of the world's population, and rice fragrance is a key quality attribute which is highly desired by consumers and attracts premium prices in the international market. There are around 200 volatile compounds involved in rice fragrance, but 2-acetyl-1-pyrroline (2-AP) has been considered a master regulator of aroma in fragrant rice. Consequently, efforts were made to increase the 2-AP contents in the grain by managing agronomical practices or by using modern functional genomic tools, which successfully converted nonfragrant cultivars to fragrant rice. Furthermore, environmental factors were also reported to influence the 2-AP contents. However, a comprehensive analysis of 2-AP biosynthesis in response to agro-management practices, environmental factors, and the application of functional genomic tools for fragrant rice production was missing. In this Review, we summarize how micro/macronutrients, cultivation practices, amino acid precursors, growth regulators, and environmental factors, such as drought, salinity, light, and temperature, influence the 2-AP biosynthesis to modulate the aroma of fragrant rice. Furthermore, we also summarized the successful conversion of nonfragrant rice cultivars to fragrant rice using modern gene editing tools, such as RNAi, TALENS, and CRISPR-Cas9. Finally, we discussed and highlighted the future perspective and challenges related to the aroma of fragrant rice.
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Affiliation(s)
- Muhammad Imran
- Department of Crop Science and Technology, College of Agriculture, South China Agricultural University, Guangzhou 510642, P. R. China
- Scientific Observing and Experimental Station of Crop Cultivation in South China, Ministry of Agriculture, Guangzhou 510642, P. R. China
- Yingdong College of Biology and Agriculture, Shaoguan University, Shaoguan 512005, P. R. China
| | - Sarfraz Shafiq
- Department of Anatomy and Cell Biology, University of Western Ontario, 1151 Richmond St., London, ON N6A5B8, Canada
| | - Umair Ashraf
- Department of Botany, Division of Science and Technology, University of Education, Lahore 54770, Pakistan
| | - Jianying Qi
- Department of Crop Science and Technology, College of Agriculture, South China Agricultural University, Guangzhou 510642, P. R. China
- Scientific Observing and Experimental Station of Crop Cultivation in South China, Ministry of Agriculture, Guangzhou 510642, P. R. China
| | - Zhaowen Mo
- Department of Crop Science and Technology, College of Agriculture, South China Agricultural University, Guangzhou 510642, P. R. China
- Scientific Observing and Experimental Station of Crop Cultivation in South China, Ministry of Agriculture, Guangzhou 510642, P. R. China
| | - Xiangru Tang
- Department of Crop Science and Technology, College of Agriculture, South China Agricultural University, Guangzhou 510642, P. R. China
- Scientific Observing and Experimental Station of Crop Cultivation in South China, Ministry of Agriculture, Guangzhou 510642, P. R. China
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Deng L, Yang X, Qiu Y, Luo J, Wu H, Liu X, Zhao G, Gong H, Zheng X, Li J. Metabolic and molecular mechanisms underlying the foliar Zn application induced increase of 2-acetyl-1-pyrroline conferring the 'taro-like' aroma in pumpkin leaves. FRONTIERS IN PLANT SCIENCE 2023; 14:1127032. [PMID: 36778711 PMCID: PMC9909474 DOI: 10.3389/fpls.2023.1127032] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 01/11/2023] [Indexed: 06/18/2023]
Abstract
INTRODUCTION Fresh pumpkin leaf is popular vegetable for its rich nutrition. The pleasant taro-like odour is important aroma quality of crops, and mostly contributed by 2-acetyl-1-pyrroline in pumpkin. Element Zn can impact metabolite biosynthesis in plants, including aroma formation. However, Zn-induced biochemical responses, especially 2-acetyl-1-pyrroline formation in pumpkin, haven't been elucidated. METHODS This study integrated metabolome and transcriptome to explore molecular fluctuations in pumpkin leaves at different time intervals after foliar Zn treatment. RESULT AND DISCUSSION We first identified more than one thousand metabolites from pumpkin leaves by integrating different mass spectrometry methods according to the form in which a metabolite exists. Comparative metabolomic analysis revealed there were separately 25 out of 50 and 286 out of 963 metabolites that were respectively identified by gas chromatography-mass spectrometry and liquid chromatography-tandem mass spectrometry, differentially regulated by Zn treatment. Our findings revealed that 50mg/L of Zn significantly enhanced 2-acetyl-1-pyrroline production by more than 38%, which was contributed by increased biosynthesis of its precursors, including ornithine and proline. The following transcriptome analysis discovered 30,574 genes, including 953 novel genes. Zn treatment induced the differential expression of 41.6% of identified genes which were supposed to regulate the downstream metabolite changes in a time-dependent manner. Pathway analysis indicated that alternations in primary metabolism, including carbon metabolism and biosynthesis of amino acids, were vital to the fluctuated aromatic compound generation. Phytohormones and transcription factors may regulate the expression of gene P5CS and proline biosynthesis, which, therefore, affect 2-acetyl-1-pyrroline production. This research reveals molecular mechanisms of 2-acetyl-1-pyrroline formation in pumpkin, which will provide the molecular basis for desired aroma compound production through metabolite engineering.
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Affiliation(s)
- Liting Deng
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China
| | - Xian Yang
- College of Horticulture, South China Agricultural University, Guangzhou, Guangdong, China
| | - Yuehan Qiu
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China
- College of Horticulture, South China Agricultural University, Guangzhou, Guangdong, China
| | - Jianning Luo
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China
| | - Haibin Wu
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China
| | - Xiaoxi Liu
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China
| | - Gangjun Zhao
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China
| | - Hao Gong
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China
| | - Xiaoming Zheng
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China
| | - Junxing Li
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China
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Imran M, Shafiq S, Ilahi S, Ghahramani A, Bao G, Dessoky ES, Widemann E, Pan S, Mo Z, Tang X. Post-transcriptional regulation of 2-acetyl-1-pyrroline (2-AP) biosynthesis pathway, silicon, and heavy metal transporters in response to Zn in fragrant rice. FRONTIERS IN PLANT SCIENCE 2022; 13:948884. [PMID: 36061781 PMCID: PMC9428631 DOI: 10.3389/fpls.2022.948884] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 07/25/2022] [Indexed: 06/15/2023]
Abstract
Fragrant rice (Oryza sativa L.) has a high economic and nutritional value, and the application of micronutrients regulates 2-acetyl-1-pyrroline (2-AP) production, which is responsible for aroma in fragrant rice. Alternative splicing (AS) is an important post-transcriptional regulatory mechanism to generate transcript variability and proteome diversity in plants. However, no systematic investigation of AS events in response to micronutrients (Zn) has been performed in fragrant rice. Furthermore, the post-transcriptional regulation of genes involved in 2-AP biosynthesis is also not known. In this study, a comprehensive analysis of AS events under two gradients of Zn treatment in two different fragrant rice cultivars (Meixiangzhan-2 and Xiangyaxiangzhan) was performed based on RNA-seq analysis. A total of 386 and 598 significant AS events were found in Meixiangzhan-2 treated with low and high doses of Zn, respectively. In Xiangyaxiangzhan, a total of 449 and 598 significant AS events were found in low and high doses of Zn, respectively. Go analysis indicated that these genes were highly enriched in physiological processes, metabolism, and cellular processes in both cultivars. However, genotype and dose-dependent AS events were also detected in both cultivars. By comparing differential AS (DAS) events with differentially expressed genes (DEGs), we found a weak overlap among DAS and DEGs in both fragrant rice cultivars indicating that only a few genes are post-transcriptionally regulated in response to Zn treatment. We further report that Zn differentially regulates the expression of 2-AP biosynthesis-related genes in both cultivars and Zn treatment altered the editing frequency of single nucleotide polymorphism (SNPs) in the genes involved in 2-AP biosynthesis. Finally, we showed that epigenetic modifications associated with active gene transcription are generally enriched over 2-AP biosynthesis-related genes. Similar to the 2-AP pathway, we found that heavy metal transporters (genes related to silicon, iron, Zn and other metal transport) are also regulated at transcriptional and post-transcriptional levels in response to Zn in fragrant rice. Taken together, our results provide evidence of the post-transcriptional gene regulation in fragrant rice in response to Zn treatment and highlight that the 2-AP biosynthesis pathway and heavy metal transporters may also be regulated through epigenetic modifications. These findings will serve as a cornerstone for further investigation to understand the molecular mechanisms of 2-AP biosynthesis and regulation of heavy metal transporters in fragrant rice.
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Affiliation(s)
- Muhammad Imran
- Department of Crop Science and Technology, College of Agriculture, South China Agricultural University, Guangzhou, China
- Scientific Observing and Experimental Station of Crop Cultivation in South China, Ministry of Agriculture, Guangzhou, China
| | - Sarfraz Shafiq
- Department of Anatomy and Cell Biology, University of Western Ontario, London, ON, Canada
| | - Sara Ilahi
- Department of Economics, Lahore College for Women University, Lahore, Pakistan
| | - Alireza Ghahramani
- Department of Anatomy and Cell Biology, University of Western Ontario, London, ON, Canada
| | - Gegen Bao
- Department of Crop Science and Technology, College of Agriculture, South China Agricultural University, Guangzhou, China
- Scientific Observing and Experimental Station of Crop Cultivation in South China, Ministry of Agriculture, Guangzhou, China
| | - Eldessoky S. Dessoky
- Department of Plant Genetic Transformation, Agricultural Genetic Engineering Research Institute, Agricultural Research Center, Giza, Egypt
| | - Emilie Widemann
- Institut de Biologie Moléculaire des Plantes, CNRS-Université de Strasbourg, Strasbourg, France
| | - Shenggang Pan
- Department of Crop Science and Technology, College of Agriculture, South China Agricultural University, Guangzhou, China
- Scientific Observing and Experimental Station of Crop Cultivation in South China, Ministry of Agriculture, Guangzhou, China
| | - Zhaowen Mo
- Department of Crop Science and Technology, College of Agriculture, South China Agricultural University, Guangzhou, China
- Scientific Observing and Experimental Station of Crop Cultivation in South China, Ministry of Agriculture, Guangzhou, China
| | - Xiangru Tang
- Department of Crop Science and Technology, College of Agriculture, South China Agricultural University, Guangzhou, China
- Scientific Observing and Experimental Station of Crop Cultivation in South China, Ministry of Agriculture, Guangzhou, China
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