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Fan J, Zhang H, Shi Y, Li Y, He Y, Wang Q, Liu S, Yao Y, Zhou X, Liao J, Huang Y, Wang Z. Systematic identification and characterization of microRNAs with target genes involved in high night temperature stress at the filling stage of rice. PHYSIOLOGIA PLANTARUM 2024; 176:e14305. [PMID: 38659134 DOI: 10.1111/ppl.14305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 04/07/2024] [Accepted: 04/10/2024] [Indexed: 04/26/2024]
Abstract
High night temperature stress is one of the main environmental factors affecting rice yield and quality. More and more evidence shows that microRNA (miRNA) plays an important role in various abiotic stresses. However, the molecular network of miRNA regulation on rice tolerance to high night temperatures remains unclear. Here, small RNA, transcriptome and degradome sequencing were integrated to identify differentially expressed miRNAs, genes, and key miRNA-target gene pairs in rice heat-sensitive and heat-tolerant lines at the filling stage suffering from high night temperature stress. It was discovered that there were notable differences in the relative expression of 102 miRNAs between the two rice lines under stress. Meanwhile, 5263 and 5405 mRNAs were differentially expressed in the heat-sensitive line and heat-tolerant line, and functional enrichment analysis revealed that these genes were involved in heat-related processes and pathways. The miRNAs-mRNAs target relationship was further verified by degradome sequencing. Eventually, 49 miRNAs-222 mRNAs target pairs with reverse expression patterns showed significant relative expression changes between the heat-tolerant and the heat-sensitive line, being suggested to be responsible for the heat tolerance difference of these two rice lines. Functional analysis of these 222 mRNA transcripts showed that high night temperature-responsive miRNAs targeted these mRNAs involved in many heat-related biological processes, such as transcription regulation, chloroplast regulation, mitochondrion regulation, protein folding, hormone regulation and redox process. This study identified possible miRNA-mRNA regulation relationships in response to high night temperature stress in rice and potentially contributed to heat resistance breeding of rice in the future.
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Affiliation(s)
- Jiangmin Fan
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding (Jiangxi Agricultural University), Ministry of Education of the P.R. China, Nanchang, Jiangxi Province, China
- Key Laboratory of Agriculture Responding to Climate Change (Jiangxi Agricultural University), Nanchang, Jiangxi Province, China
| | - Hongyu Zhang
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding (Jiangxi Agricultural University), Ministry of Education of the P.R. China, Nanchang, Jiangxi Province, China
- Key Laboratory of Agriculture Responding to Climate Change (Jiangxi Agricultural University), Nanchang, Jiangxi Province, China
| | - Yan Shi
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding (Jiangxi Agricultural University), Ministry of Education of the P.R. China, Nanchang, Jiangxi Province, China
- Key Laboratory of Agriculture Responding to Climate Change (Jiangxi Agricultural University), Nanchang, Jiangxi Province, China
| | - Yuewu Li
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding (Jiangxi Agricultural University), Ministry of Education of the P.R. China, Nanchang, Jiangxi Province, China
- Key Laboratory of Agriculture Responding to Climate Change (Jiangxi Agricultural University), Nanchang, Jiangxi Province, China
| | - Yuxiang He
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding (Jiangxi Agricultural University), Ministry of Education of the P.R. China, Nanchang, Jiangxi Province, China
- Key Laboratory of Agriculture Responding to Climate Change (Jiangxi Agricultural University), Nanchang, Jiangxi Province, China
| | - Qiang Wang
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding (Jiangxi Agricultural University), Ministry of Education of the P.R. China, Nanchang, Jiangxi Province, China
- Key Laboratory of Agriculture Responding to Climate Change (Jiangxi Agricultural University), Nanchang, Jiangxi Province, China
| | - Siyi Liu
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding (Jiangxi Agricultural University), Ministry of Education of the P.R. China, Nanchang, Jiangxi Province, China
- Key Laboratory of Agriculture Responding to Climate Change (Jiangxi Agricultural University), Nanchang, Jiangxi Province, China
| | - Youmin Yao
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding (Jiangxi Agricultural University), Ministry of Education of the P.R. China, Nanchang, Jiangxi Province, China
- Key Laboratory of Agriculture Responding to Climate Change (Jiangxi Agricultural University), Nanchang, Jiangxi Province, China
| | - Xiaoya Zhou
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding (Jiangxi Agricultural University), Ministry of Education of the P.R. China, Nanchang, Jiangxi Province, China
- Key Laboratory of Agriculture Responding to Climate Change (Jiangxi Agricultural University), Nanchang, Jiangxi Province, China
| | - Jianglin Liao
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding (Jiangxi Agricultural University), Ministry of Education of the P.R. China, Nanchang, Jiangxi Province, China
- Key Laboratory of Agriculture Responding to Climate Change (Jiangxi Agricultural University), Nanchang, Jiangxi Province, China
| | - Yingjin Huang
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding (Jiangxi Agricultural University), Ministry of Education of the P.R. China, Nanchang, Jiangxi Province, China
- Key Laboratory of Agriculture Responding to Climate Change (Jiangxi Agricultural University), Nanchang, Jiangxi Province, China
| | - Zhaohai Wang
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding (Jiangxi Agricultural University), Ministry of Education of the P.R. China, Nanchang, Jiangxi Province, China
- Key Laboratory of Agriculture Responding to Climate Change (Jiangxi Agricultural University), Nanchang, Jiangxi Province, China
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Bedford JA, Carine M, Chapman MA. Detection of locally adapted genomic regions in wild rice (Oryza rufipogon) using environmental association analysis. G3 (BETHESDA, MD.) 2023; 13:jkad194. [PMID: 37619981 PMCID: PMC10542315 DOI: 10.1093/g3journal/jkad194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 08/14/2023] [Accepted: 08/17/2023] [Indexed: 08/26/2023]
Abstract
Oryza rufipogon is the wild progenitor of cultivated rice Oryza sativa and exhibits high levels of genetic diversity across its distribution, making it a useful resource for the identification of abiotic stress-tolerant varieties and genes that could limit future climate-changed-induced yield losses. To investigate local adaptation in O. rufipogon, we analyzed single nucleotide polymorphism (SNP) data from a panel of 286 samples located across a diverse range of climates. Environmental association analysis (EAA), a genome-wide association study (GWAS)-based method, was used and revealed 15 regions of the genome significantly associated with various climate factors. Genes within these environmentally associated regions have putative functions in abiotic stress response, phytohormone signaling, and the control of flowering time. This provides an insight into potential local adaptation in O. rufipogon and reveals possible locally adaptive genes that may provide opportunities for breeding novel rice varieties with climate change-resilient phenotypes.
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Affiliation(s)
- James A Bedford
- Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
- Life Sciences, The Natural History Museum, London SW7 5BD, UK
| | - Mark Carine
- Life Sciences, The Natural History Museum, London SW7 5BD, UK
| | - Mark A Chapman
- Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
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Kumar A, Thomas J, Gill N, Dwiningsih Y, Ruiz C, Famoso A, Pereira A. Molecular mapping and characterization of QTLs for grain quality traits in a RIL population of US rice under high nighttime temperature stress. Sci Rep 2023; 13:4880. [PMID: 36966148 PMCID: PMC10039871 DOI: 10.1038/s41598-023-31399-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 03/10/2023] [Indexed: 03/27/2023] Open
Abstract
Elevated nighttime temperatures resulting from climate change significantly impact the rice crop worldwide. The rice (Oryza sativa L.) plant is highly sensitive to high nighttime temperature (HNT) during grain-filling (reproductive stage). HNT stress negatively affects grain quality traits and has a major impact on the value of the harvested rice crop. In addition, along with grain dimensions determining rice grain market classes, the grain appearance and quality traits determine the rice grain market value. During the last few years, there has been a major concern for rice growers and the rice industry over the prevalence of rice grains opacity and the reduction of grain dimensions affected by HNT stress. Hence, the improvement of heat-stress tolerance to maintain grain quality of the rice crop under HNT stress will bolster future rice value in the market. In this study, 185 F12-recombinant inbred lines (RILs) derived from two US rice cultivars, Cypress (HNT-tolerant) and LaGrue (HNT-sensitive) were screened for the grain quality traits grain length (GL), grain width (GW), and percent chalkiness (%chalk) under control and HNT stress conditions and evaluated to identify the genomic regions associated with the grain quality traits. In total, there were 15 QTLs identified; 6 QTLs represented under control condition explaining 3.33% to 8.27% of the phenotypic variation, with additive effects ranging from - 0.99 to 0.0267 on six chromosomes and 9 QTLs represented under HNT stress elucidating 6.39 to 51.53% of the phenotypic variation, with additive effects ranging from - 8.8 to 0.028 on nine chromosomes for GL, GW, and % chalk. These 15 QTLs were further characterized and scanned for natural genetic variation in a japonica diversity panel (JDP) to identify candidate genes for GL, GW, and %chalk. We found 6160 high impact single nucleotide polymorphisms (SNPs) characterized as such depending on their type, region, functional class, position, and proximity to the gene and/or gene features, and 149 differentially expressed genes (DEGs) in the 51 Mbp genomic region comprising of the 15 QTLs. Out of which, 11 potential candidate genes showed high impact SNP associations. Therefore, the analysis of the mapped QTLs and their genetic dissection in the US grown Japonica rice genotypes at genomic and transcriptomic levels provide deep insights into genetic variation beneficial to rice breeders and geneticists for understanding the mechanisms related to grain quality under heat stress in rice.
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Affiliation(s)
- Anuj Kumar
- Departemnt of Crop, Soil, & Environmental Sciences, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Julie Thomas
- Departemnt of Crop, Soil, & Environmental Sciences, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Navdeep Gill
- Department of Biological Sciences, Nova Southeastern University, Fort Lauderdale, FL, 33314, USA
| | - Yheni Dwiningsih
- Departemnt of Crop, Soil, & Environmental Sciences, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Charles Ruiz
- Departemnt of Crop, Soil, & Environmental Sciences, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Adam Famoso
- H. Rouse Caffey Rice Research Station, Louisiana State University Agricultural Center, Rayne, LA, 70578, USA
| | - Andy Pereira
- Departemnt of Crop, Soil, & Environmental Sciences, University of Arkansas, Fayetteville, AR, 72701, USA.
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Asaf S, Jan R, Khan MA, Khan AL, Asif S, Bilal S, Ahmad W, Waqas M, Kim KM, Al-Harrasi A, Lee IJ. Unraveling the mutualistic interaction between endophytic Curvularia lunata CSL1 and tomato to mitigate cadmium (Cd) toxicity via transcriptomic insights. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 861:160542. [PMID: 36493827 DOI: 10.1016/j.scitotenv.2022.160542] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 11/06/2022] [Accepted: 11/23/2022] [Indexed: 06/17/2023]
Abstract
In this study, endophytic fungus Curvularia lunata strain SL1 was used to explore its bioremediation potential and growth restoration of tomato (Solanum lycopersicum) under cadmium (Cd) stress. Our findings demonstrate that SL1 establishes a symbiotic relationship with tomato plants, which modulates the antioxidant system, secondary metabolites, and gene expression in tomato plants exposed to Cd stress. Under Cd stress, tomato seedling growth was significantly reduced by up to 42.8 %, although this reduction was mitigated by up to 25 % after SL1 inoculation. Similar to this, SLI inoculation inhibits Cd absorption and translocation to the upper parts of the plant. Additionally, during Cd stress, phytohormones related to stress, including jasmonic acid (JA), abscisic acid (ABA), and ethylene (ET), were elevated; however, SL1 inoculation lowered their level. RNA-Seq data revealed that the highest number of differentially expressed genes (DEGs) was detected in the comparison between control and 1 mM Cd, followed by 2 mM Cd stress. These DEGs were mostly related to oxidoreductase activity, catalytic activity, plant hormones transduction, and photosynthesis. The findings also suggested that SL1 could improve tomato tolerance to Cd stress by modulating Ca2+ signaling, phytohormone biosynthesis, MAPK signaling pathway, and some transcription factors.
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Affiliation(s)
- Sajjad Asaf
- Natural and Medical Sciences Research Center, University of Nizwa, 616 Nizwa, Oman
| | - Rahmatullah Jan
- Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Muhammad Aaqil Khan
- Department of Chemical and Life Science, Qurtaba University of Science and Technology, Peshawar, Pakistan
| | - Abdul Latif Khan
- Department of Engineering Technology, University of Houston, Sugar Land, TX, 77479, USA
| | - Saleem Asif
- Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Saqib Bilal
- Natural and Medical Sciences Research Center, University of Nizwa, 616 Nizwa, Oman
| | - Waqar Ahmad
- Department of Engineering Technology, University of Houston, Sugar Land, TX, 77479, USA
| | - Muhammad Waqas
- Department of Agriculture Extension, Government of Khyber Pakhtunkhwa, Mardan, Pakistan
| | - Kyung-Min Kim
- Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea.
| | - Ahmed Al-Harrasi
- Natural and Medical Sciences Research Center, University of Nizwa, 616 Nizwa, Oman.
| | - In-Jung Lee
- Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea.
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Tu D, Jiang Y, Salah A, Xi M, Cai M, Cheng B, Sun X, Cao C, Wu W. Variation of rice starch structure and physicochemical properties in response to high natural temperature during the reproductive stage. FRONTIERS IN PLANT SCIENCE 2023; 14:1136347. [PMID: 36866379 PMCID: PMC9971927 DOI: 10.3389/fpls.2023.1136347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 01/31/2023] [Indexed: 06/18/2023]
Abstract
Climate warming affects rice growth at different phenological stages, thereby increasing rice chalkiness and protein content and reducing eating and cooking quality (ECQ). The structural and physicochemical properties of rice starch played important roles in determining rice quality. However, differences in their response to high temperature during the reproductive stage have been rarely studied. In the present study, they were evaluated and compared between two contrasting natural temperature field conditions, namely, high seasonal temperature (HST) and low seasonal temperature (LST), during the reproductive stage of rice in 2017 and 2018. Compared with LST, HST significantly deteriorated rice quality, including increased grain chalkiness, setback, consistence, and pasting temperature and reduced taste values. HST considerably reduced the total starch and increased the protein content. Likewise, HST significantly reduced the short amylopectin chains [degree of polymerization (DP) <12] and increased the long amylopectin chains (DP > 12) and relative crystallinity. The starch structure, total starch content, and protein content explained 91.4%, 90.4%, and 89.2% of the total variations in pasting properties, taste value, and grain chalkiness degree, respectively. In conclusion, we suggested that rice quality variations were closely associated with the changes in chemical composition content (total starch and protein content) and starch structure in response to HST. These results indicated that we should improve the resistance of rice to high temperature during the reproductive stage to improve the fine structure of rice starch in further breeding and practice.
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Affiliation(s)
- Debao Tu
- Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei, China
- National Key Laboratory of Crop Genetic Improvement, MOA Key Laboratory of Crop Physiology, Ecology and Cultivation (The Middle Reaches of Yangtze River), Huazhong Agricultural University, Wuhan, China
| | - Yang Jiang
- National Key Laboratory of Crop Genetic Improvement, MOA Key Laboratory of Crop Physiology, Ecology and Cultivation (The Middle Reaches of Yangtze River), Huazhong Agricultural University, Wuhan, China
| | - Akram Salah
- National Key Laboratory of Crop Genetic Improvement, MOA Key Laboratory of Crop Physiology, Ecology and Cultivation (The Middle Reaches of Yangtze River), Huazhong Agricultural University, Wuhan, China
| | - Min Xi
- Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Mingli Cai
- National Key Laboratory of Crop Genetic Improvement, MOA Key Laboratory of Crop Physiology, Ecology and Cultivation (The Middle Reaches of Yangtze River), Huazhong Agricultural University, Wuhan, China
| | - Bo Cheng
- National Key Laboratory of Crop Genetic Improvement, MOA Key Laboratory of Crop Physiology, Ecology and Cultivation (The Middle Reaches of Yangtze River), Huazhong Agricultural University, Wuhan, China
| | - Xiaosong Sun
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University, Yangzhou, China
| | - Cougui Cao
- National Key Laboratory of Crop Genetic Improvement, MOA Key Laboratory of Crop Physiology, Ecology and Cultivation (The Middle Reaches of Yangtze River), Huazhong Agricultural University, Wuhan, China
| | - Wenge Wu
- Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei, China
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Khan I, Asaf S, Jan R, Bilal S, Lubna, Khan AL, Kim KM, Al-Harrasi A. Genome-wide annotation and expression analysis of WRKY and bHLH transcriptional factor families reveal their involvement under cadmium stress in tomato ( Solanum lycopersicum L.). FRONTIERS IN PLANT SCIENCE 2023; 14:1100895. [PMID: 36760632 PMCID: PMC9905835 DOI: 10.3389/fpls.2023.1100895] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 01/04/2023] [Indexed: 08/12/2023]
Abstract
The WRKY and bHLH transcription factors have been implicated in the regulation of gene expression during various physiological processes in plants, especially in plant stress responses. However, little information about the heavy metal-responsive SlWRKY and SlbHLH in tomato (Solanum lycopersicum) is available. We performed a genome-wide investigation for these two TF families in S. lycopersicum and determined their role in cadmium (Cd) stress tolerance. Furthermore, ortholog analysis with the Arabidopsis genome led to classifying WRKY and bHLH ortholog genes into nine and 11 clusters, respectively. The comparative phylogenetic analysis revealed duplication events and gene loss in Arabidopsis and S. lycopersicum, which occurred during evolution both before and after the last common ancestor of the two species. Orthologous relationships are also supported by additional evidence, such as gene structure, conserved motif compositions, and protein-protein interaction networks for the majority of genes, suggesting their similar functions. A comprehensive transcriptomics analysis revealed that both WRKY and bHLH genes were differentially expressed in response to cadmium stress as compared with control plants. A gene ontology analysis revealed that most WRKYs and bHLHs are DNA-binding essential proteins that regulate gene expression positively and negatively. Analyses of interaction networks revealed that both WRKYs and bHLHs mediate networks implicated in several stress-signaling pathways. The findings of this work may help us to comprehend the intricate transcriptional control of WRKY and bHLH genes and identify potential stress-responsive genes relevant to tomato genetic improvement. Moreover, identifying heavy metal stress-responsive WRKY and bHLH genes in S. lycopersicum will provide fundamental insights for developing new heavy metal stress-tolerant varieties of tomato crops.
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Affiliation(s)
- Ibrahim Khan
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, Oman
| | - Sajjad Asaf
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, Oman
| | - Rahmatullah Jan
- Department of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
| | - Saqib Bilal
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, Oman
| | - Lubna
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, Oman
| | - Abdul Latif Khan
- Department of Engineering Technology, University of Houston, Sugar Land, TX, United States
| | - Kyung-Min Kim
- Department of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
| | - Ahmed Al-Harrasi
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, Oman
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Genome and Transcriptome-Wide Analysis of OsWRKY and OsNAC Gene Families in Oryza sativa and Their Response to White-Backed Planthopper Infestation. Int J Mol Sci 2022; 23:ijms232315396. [PMID: 36499722 PMCID: PMC9739594 DOI: 10.3390/ijms232315396] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 11/27/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022] Open
Abstract
Plants are threatened by a wide variety of herbivorous insect assaults, and display a variety of inherent and induced defenses that shield them against herbivore attacks. Looking at the massive damage caused by the white-backed planthopper (WBPH), Sogatella furcifera, we undertook a study to identify and functionally annotate OsWRKY and OsNAC transcription factors (TFs) in rice, especially their involvement in WBPH stress. OsWRKY and OsNAC TFs are involved in various developmental processes and responses to biotic and abiotic stresses. However, no comprehensive reports are available on the specific phycological functions of most of the OsWRKY and OsNAC genes in rice during WBPH infestation. The current study aimed to comprehensively explore the OsWRKY and OsNAC genes by analyzing their phylogenetic relationships, subcellular localizations, exon-intron arrangements, conserved motif identities, chromosomal allocations, interaction networks and differential gene expressions during stress conditions. Comparative phylogenetic trees of 101 OsWRKY with 72 AtWRKY genes, and 121 OsNAC with 110 AtNAC genes were constructed to study relationships among these TFs across species. Phylogenetic relationships classified OsWRKY and OsNAC into eight and nine clades, respectively. Most TFs in the same clade had similar genomic features that represented similar functions, and had a high degree of co-expression. Some OsWRKYs (Os09g0417800 (OsWRKY62), Os11g0117600 (OsWRKY50), Os11g0117400 (OsWRKY104) and OsNACs (Os05g0442700, Os12g0630800, Os01g0862800 and Os12g0156100)) showed significantly higher expressions under WBPH infestation, based on transcriptome datasets. This study provides valuable information and clues about predicting the potential roles of OsWRKYs and OsNACs in rice, by combining their genome-wide characterization, expression profiling, protein-protein interactions and gene expressions under WBPH stress. These findings may require additional investigation to understand their metabolic and expression processes, and to develop rice cultivars that are resistant to WBPH.
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Jan R, Asaf S, Lubna, Asif S, Kim EG, Jang YH, Kim N, Al-Harrasi A, Lee GS, Kim KM. Enhancing the Expression of the OsF3H Gene in Oryza sativa Leads to the Regulation of Multiple Biosynthetic Pathways and Transcriptomic Changes That Influence Insect Resistance. Int J Mol Sci 2022; 23:15308. [PMID: 36499636 PMCID: PMC9737463 DOI: 10.3390/ijms232315308] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 11/29/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022] Open
Abstract
The white-backed planthopper (WBPH) is a major pest of rice crops and causes severe loss of yield. We previously developed the WBPH-resistant rice cultivar "OxF3H" by overexpressing the OsF3H gene. Although there was a higher accumulation of the flavonoids kaempferol (Kr) and quercetin (Qu) as well as salicylic acid (SA) in OxF3H transgenic (OsF3H or Trans) plants compared to the wild type (WT), it is still unclear how OsF3H overexpression affects these WBPH resistant-related changes in gene expression in OxF3H plants. In this study, we analyze RNA-seq data from OxF3H and WT at several points (0 h, 3 h, 12 h, and 24 h) after WBPH infection to explain how overall changes in gene expression happen in these two cultivars. RT-qPCR further validated a number of the genes. Results revealed that the highest number of DEGs (4735) between the two genotypes was detected after 24 h of infection. Interestingly, it was found that several of the DEGs between the WT and OsF3H under control conditions were also differentially expressed in OsF3H in response to WBPH infestation. These results indicate that significant differences in gene expression between the "OxF3H" and "WT" exist as the infection time increases. Many of these DEGs were related to oxidoreductase activity, response to stress, salicylic acid biosynthesis, metabolic process, defense response to pathogen, cellular response to toxic substance, and regulation of hormone levels. Moreover, genes involved in salicylic acid (SA) and ethylene (Et) biosynthesis were upregulated in OxF3H plants, while jasmonic acid (JA), brassinosteroid (Br), and abscisic acid (ABA) signaling pathways were found downregulated in OxF3H plants during WBPH infestation. Interestingly, many DEGs related to pathogenesis, such as OsPR1, OsPR1b, OsNPR1, OsNPR3, and OsNPR5, were found to be significantly upregulated in OxF3H plants. Additionally, genes related to the MAPKs pathway and about 30 WRKY genes involved in different pathways were upregulated in OxF3H plants after WBPH infestation. This suggests that overexpression of the OxF3H gene leads to multiple transcriptomic changes and impacts plant hormones and pathogenic-related and secondary-metabolites-related genes, enhancing the plant's resistance to WBPH infestation.
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Affiliation(s)
- Rahmatullah Jan
- Department of Applied Biosciences, Graduate School, Kyungpook National University, Daegu 41566, Republic of Korea
- Coastal Agriculture Research Institute, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Sajjad Asaf
- Natural and Medical Science Research Center, University of Nizwa, Nizwa 611, Oman
| | - Lubna
- Department of Botany, Garden Campus, Abdul Wali Khan University, Mardan 23200, Pakistan
| | - Saleem Asif
- Department of Applied Biosciences, Graduate School, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Eun-Gyeong Kim
- Department of Applied Biosciences, Graduate School, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Yoon-Hee Jang
- Department of Applied Biosciences, Graduate School, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Nari Kim
- Department of Applied Biosciences, Graduate School, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Ahmed Al-Harrasi
- Natural and Medical Science Research Center, University of Nizwa, Nizwa 611, Oman
| | - Gang-Seob Lee
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Republic of Korea
| | - Kyung-Min Kim
- Department of Applied Biosciences, Graduate School, Kyungpook National University, Daegu 41566, Republic of Korea
- Coastal Agriculture Research Institute, Kyungpook National University, Daegu 41566, Republic of Korea
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Liang Z, Myers ZA, Petrella D, Engelhorn J, Hartwig T, Springer NM. Mapping responsive genomic elements to heat stress in a maize diversity panel. Genome Biol 2022; 23:234. [PMID: 36345007 PMCID: PMC9639295 DOI: 10.1186/s13059-022-02807-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 10/29/2022] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND Many plant species exhibit genetic variation for coping with environmental stress. However, there are still limited approaches to effectively uncover the genomic region that regulates distinct responsive patterns of the gene across multiple varieties within the same species under abiotic stress. RESULTS By analyzing the transcriptomes of more than 100 maize inbreds, we reveal many cis- and trans-acting eQTLs that influence the expression response to heat stress. The cis-acting eQTLs in response to heat stress are identified in genes with differential responses to heat stress between genotypes as well as genes that are only expressed under heat stress. The cis-acting variants for heat stress-responsive expression likely result from distinct promoter activities, and the differential heat responses of the alleles are confirmed for selected genes using transient expression assays. Global footprinting of transcription factor binding is performed in control and heat stress conditions to document regions with heat-enriched transcription factor binding occupancies. CONCLUSIONS Footprints enriched near proximal regions of characterized heat-responsive genes in a large association panel can be utilized for prioritizing functional genomic regions that regulate genotype-specific responses under heat stress.
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Affiliation(s)
- Zhikai Liang
- grid.17635.360000000419368657Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN 55108 USA
| | - Zachary A. Myers
- grid.17635.360000000419368657Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN 55108 USA
| | - Dominic Petrella
- grid.17635.360000000419368657Department of Horticulture, University of Minnesota, Saint Paul, MN 55108 USA ,grid.261331.40000 0001 2285 7943Present address: Agricultural Technical Institute, The Ohio State University, Wooster, OH 44691 USA
| | - Julia Engelhorn
- grid.419498.90000 0001 0660 6765Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany ,grid.411327.20000 0001 2176 9917Heinrich-Heine University, 40225 Dusseldorf, Germany
| | - Thomas Hartwig
- grid.419498.90000 0001 0660 6765Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany ,grid.411327.20000 0001 2176 9917Heinrich-Heine University, 40225 Dusseldorf, Germany
| | - Nathan M. Springer
- grid.17635.360000000419368657Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN 55108 USA
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10
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Lee SB, Kim GJ, Shin JD, Chung W, Park SK, Choi GH, Park SW, Park YJ. Genome-Scale Profiling and High-Throughput Analyses Unravel the Genetic Basis of Arsenic Content Variation in Rice. FRONTIERS IN PLANT SCIENCE 2022; 13:905842. [PMID: 35958208 PMCID: PMC9361212 DOI: 10.3389/fpls.2022.905842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 06/15/2022] [Indexed: 06/15/2023]
Abstract
Ionomics, the study of the composition of mineral nutrients and trace elements in organisms that represent the inorganic component of cells and tissues, has been widely studied to explore to unravel the molecular mechanism regulating the elemental composition of plants. However, the genetic factors of rice subspecies in the interaction between arsenic and functional ions have not yet been explained. Here, the correlation between As and eight essential ions in a rice core collection was analyzed, taking into account growing condition and genetic factors. The results demonstrated that the correlation between As and essential ions was affected by genetic factors and growing condition, but it was confirmed that the genetic factor was slightly larger with the heritability for arsenic content at 53%. In particular, the cluster coefficient of japonica (0.428) was larger than that of indica (0.414) in the co-expression network analysis for 23 arsenic genes, and it was confirmed that the distance between genes involved in As induction and detoxification of japonica was far than that of indica. These findings provide evidence that japonica populations could accumulate more As than indica populations. In addition, the cis-eQTLs of AIR2 (arsenic-induced RING finger protein) were isolated through transcriptome-wide association studies, and it was confirmed that AIR2 expression levels of indica were lower than those of japonica. This was consistent with the functional haplotype results for the genome sequence of AIR2, and finally, eight rice varieties with low AIR2 expression and arsenic content were selected. In addition, As-related QTLs were identified on chromosomes 5 and 6 under flooded and intermittently flooded conditions through genome-scale profiling. Taken together, these results might assist in developing markers and breeding plans to reduce toxic element content and breeding high-quality rice varieties in future.
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Affiliation(s)
- Sang-Beom Lee
- Crop Foundation Research Division, National Institute of Crop Science, Wanju, South Korea
| | - Gyeong-Jin Kim
- Residual Agrochemical Assessment Division, National Institute of Agriculture Science, Wanju, South Korea
| | - Jung-Du Shin
- Bio-Technology of Multidisciplinary Sciences Co., Wanju, South Korea
| | - Woojin Chung
- Department of Environmental Energy Engineering, Kyonggi University, Suwon, South Korea
| | - Soo-Kwon Park
- Crop Foundation Research Division, National Institute of Crop Science, Wanju, South Korea
| | - Geun-Hyoung Choi
- Residual Agrochemical Assessment Division, National Institute of Agriculture Science, Wanju, South Korea
| | - Sang-Won Park
- Reserch Policy Bureau, Rural Development Administration, Wanju, South Korea
| | - Yong-Jin Park
- Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan, South Korea
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11
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Zhou R, Jiang F, Niu L, Song X, Yu L, Yang Y, Wu Z. Increase Crop Resilience to Heat Stress Using Omic Strategies. FRONTIERS IN PLANT SCIENCE 2022; 13:891861. [PMID: 35656008 PMCID: PMC9152541 DOI: 10.3389/fpls.2022.891861] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 04/04/2022] [Indexed: 06/15/2023]
Abstract
Varieties of various crops with high resilience are urgently needed to feed the increased population in climate change conditions. Human activities and climate change have led to frequent and strong weather fluctuation, which cause various abiotic stresses to crops. The understanding of crops' responses to abiotic stresses in different aspects including genes, RNAs, proteins, metabolites, and phenotypes can facilitate crop breeding. Using multi-omics methods, mainly genomics, transcriptomics, proteomics, metabolomics, and phenomics, to study crops' responses to abiotic stresses will generate a better, deeper, and more comprehensive understanding. More importantly, multi-omics can provide multiple layers of information on biological data to understand plant biology, which will open windows for new opportunities to improve crop resilience and tolerance. However, the opportunities and challenges coexist. Interpretation of the multidimensional data from multi-omics and translation of the data into biological meaningful context remained a challenge. More reasonable experimental designs starting from sowing seed, cultivating the plant, and collecting and extracting samples were necessary for a multi-omics study as the first step. The normalization, transformation, and scaling of single-omics data should consider the integration of multi-omics. This review reports the current study of crops at abiotic stresses in particular heat stress using omics, which will help to accelerate crop improvement to better tolerate and adapt to climate change.
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Affiliation(s)
- Rong Zhou
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
- Department of Food Science, Aarhus University, Aarhus, Denmark
| | - Fangling Jiang
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Lifei Niu
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Xiaoming Song
- College of Life Sciences, North China University of Science and Technology, Tangshan, China
| | - Lu Yu
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Yuwen Yang
- Excellence and Innovation Center, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Zhen Wu
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
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12
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Transcriptome Analysis of Populus euphratica under Salt Treatment and PeERF1 Gene Enhances Salt Tolerance in Transgenic Populus alba × Populus glandulosa. Int J Mol Sci 2022; 23:ijms23073727. [PMID: 35409087 PMCID: PMC8998595 DOI: 10.3390/ijms23073727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 03/24/2022] [Accepted: 03/24/2022] [Indexed: 12/02/2022] Open
Abstract
Populus euphratica is mainly distributed in desert environments with dry and hot climate in summer and cold in winter. Compared with other poplars, P. euphratica is more resistant to salt stress. It is critical to investigate the transcriptome and molecular basis of salt tolerance in order to uncover stress-related genes. In this study, salt-tolerant treatment of P. euphratica resulted in an increase in osmo-regulatory substances and recovery of antioxidant enzymes. To improve the mining efficiency of candidate genes, the analysis combining both the transcriptome WGCNA and the former GWAS results was selected, and a range of key regulatory factors with salt resistance were found. The PeERF1 gene was highly connected in the turquoise modules with significant differences in salt stress traits, and the expression levels were significantly different in each treatment. For further functional verification of PeERF1, we obtained stable overexpression and dominant suppression transgenic lines by transforming into Populus alba × Populusglandulosa. The growth and physiological characteristics of the PeERF1 overexpressed plants were better than that of the wild type under salt stress. Transcriptome analysis of leaves of transgenic lines and WT revealed that highly enriched GO terms in DEGs were associated with stress responses, including abiotic stimuli responses, chemical responses, and oxidative stress responses. The result is helpful for in-depth analysis of the salt tolerance mechanism of poplar. This work provides important genes for poplar breeding with salt tolerance.
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Poór P, Nawaz K, Gupta R, Ashfaque F, Khan MIR. Ethylene involvement in the regulation of heat stress tolerance in plants. PLANT CELL REPORTS 2022; 41:675-698. [PMID: 33713206 DOI: 10.1007/s00299-021-02675-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 02/14/2021] [Indexed: 05/12/2023]
Abstract
Because of the rise in global temperature, heat stress has become a major concern for crop production. Heat stress deteriorates plant productivity and alters phenological and physiological responses that aid in precise monitoring and sensing of mild-to-severe transient heat stress. Plants have evolved several sophisticated mechanisms including hormone-signaling pathways to sense heat stimuli and acquire heat stress tolerance. In response to heat stress, ethylene, a gaseous hormone, is produced which is indispensable for plant growth and development and tolerance to various abiotic stresses including heat stress. The manipulation of ethylene in developing heat stress tolerance targeting ethylene biosynthesis and signaling pathways has brought promising out comes. Conversely increased ethylene biosynthesis and signaling seem to exhibit inhibitory effects in plant growth responses from primitive to maturity stages. This review mainly focuses on the recent studies of ethylene involvement in plant responses to heat stress and its functional regulation, and molecular mechanism underlying the plant responses in the mitigation of heat-induced damages. Furthermore, this review also describes the crosstalk between ethylene and other signaling molecules under heat stress and approaches to improve heat stress tolerance in plants.
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Affiliation(s)
- Peter Poór
- Department of Plant Biology, University of Szeged, Szeged, Hungary
| | - Kashif Nawaz
- Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Ravi Gupta
- Department of Botany, Jamia Hamdard, New Delhi, India
| | - Farha Ashfaque
- Department of Botany, Aligarh Muslim University, Aligarh, India
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14
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Zhao X, Huang LJ, Sun XF, Zhao LL, Wang PC. Differential Physiological, Transcriptomic, and Metabolomic Responses of Paspalum wettsteinii Under High-Temperature Stress. FRONTIERS IN PLANT SCIENCE 2022; 13:865608. [PMID: 35528933 PMCID: PMC9069066 DOI: 10.3389/fpls.2022.865608] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 04/04/2022] [Indexed: 05/08/2023]
Abstract
Global warming has far-reaching effects on plant growth and development. As a warm-season forage grass, Paspalum wettsteinii is highly adaptable to high temperatures. However, the response mechanism of P. wettsteinii under high-temperature stress is still unclear. Therefore, we investigated the physiological indicators, transcriptome and metabolome of P. wettsteinii under different heat stress treatments. Plant height, the activities of superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT), and the contents of soluble sugar, proline, chlorophyll a, and chlorophyll b increased and then decreased, while the malondialdehyde (MDA) content decreased and then increased with increasing heat stress. Transcriptomic analysis revealed that genes related to energy and carbohydrate metabolism, heat shock proteins (HSPs), and transcription factors (TFs), secondary metabolite biosynthesis and the antioxidant system significantly changed to varying degrees. Metabolomic analysis showed that only free fatty acids were downregulated, while amino acids and their derivatives, organic acids, flavonoids, and sugars were both up- and downregulated under heat stress. These combined analyses revealed that growth was promoted at 25-40°C, while at 45°C, excess reactive oxygen species (ROS) damage reduced antioxidant and osmoregulatory effects and inactivated genes associated with the light and electron transport chains (ETCs), as well as damaged the PS II system and inhibited photosynthesis. A small number of genes and metabolites were upregulated to maintain the basic growth of P. wettsteinii. The physiological and biochemical changes in response to high-temperature stress were revealed, and the important metabolites and key genes involved in the response to high temperature were identified, providing an important reference for the physiological and molecular regulation of high-temperature stress in plants.
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Affiliation(s)
- Xin Zhao
- College of Animal Science, Guizhou University, Guiyang, China
| | - Li-Juan Huang
- College of Animal Science, Guizhou University, Guiyang, China
| | - Xiao-Fu Sun
- College of Animal Science, Guizhou University, Guiyang, China
| | - Li-Li Zhao
- College of Animal Science, Guizhou University, Guiyang, China
- *Correspondence: Li-Li Zhao,
| | - Pu-Chang Wang
- School of Life Sciences, Guizhou Normal University, Guiyang, China
- Pu-Chang Wang,
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15
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Zhang H, Xu H, Jiang Y, Zhang H, Wang S, Wang F, Zhu Y. Genetic Control and High Temperature Effects on Starch Biosynthesis and Grain Quality in Rice. FRONTIERS IN PLANT SCIENCE 2021; 12:757997. [PMID: 34975940 PMCID: PMC8718882 DOI: 10.3389/fpls.2021.757997] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 11/23/2021] [Indexed: 05/29/2023]
Abstract
Grain quality is one of the key targets to be improved for rice breeders and covers cooking, eating, nutritional, appearance, milling, and sensory properties. Cooking and eating quality are mostly of concern to consumers and mainly determined by starch structure and composition. Although many starch synthesis enzymes have been identified and starch synthesis system has been established for a long time, novel functions of some starch synthesis genes have continually been found, and many important regulatory factors for seed development and grain quality control have recently been identified. Here, we summarize the progress in this field as comprehensively as possible and hopefully reveal some underlying molecular mechanisms controlling eating quality in rice. The regulatory network of amylose content (AC) determination is emphasized, as AC is the most important index for rice eating quality (REQ). Moreover, the regulatory mechanism of REQ, especially AC influenced by high temperature which is concerned as a most harmful environmental factor during grain filling is highlighted in this review.
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Affiliation(s)
- Hua Zhang
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Science, Hangzhou, China
| | - Heng Xu
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Science, Hangzhou, China
| | - Yingying Jiang
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Science, Hangzhou, China
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, China
| | - Heng Zhang
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Science, Hangzhou, China
| | - Shiyu Wang
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Science, Hangzhou, China
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, China
| | - Fulin Wang
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Science, Hangzhou, China
| | - Ying Zhu
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Science, Hangzhou, China
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16
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He W, Wang L, Lin Q, Yu F. Rice seed storage proteins: Biosynthetic pathways and the effects of environmental factors. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:1999-2019. [PMID: 34581486 DOI: 10.1111/jipb.13176] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 09/27/2021] [Indexed: 05/02/2023]
Abstract
Rice (Oryza sativa L.) is the most important food crop for at least half of the world's population. Due to improved living standards, the cultivation of high-quality rice for different purposes and markets has become a major goal. Rice quality is determined by the presence of many nutritional components, including seed storage proteins (SSPs), which are the second most abundant nutrient components of rice grains after starch. Rice SSP biosynthesis requires the participation of multiple organelles and is influenced by the external environment, making it challenging to understand the molecular details of SSP biosynthesis and improve rice protein quality. In this review, we highlight the current knowledge of rice SSP biosynthesis, including a detailed description of the key molecules involved in rice SSP biosynthetic processes and the major environmental factors affecting SSP biosynthesis. The effects of these factors on SSP accumulation and their contribution to rice quality are also discussed based on recent findings. This recent knowledge suggests not only new research directions for exploring rice SSP biosynthesis but also innovative strategies for breeding high-quality rice varieties.
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Affiliation(s)
- Wei He
- National Engineering Laboratory for Rice and By-product Deep Processing, Central South University of Forestry and Technology, Changsha, 410004, China
- College of Biology, State Key Laboratory of Chemo/Biosensing and Chemometrics, and Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, 410082, China
| | - Long Wang
- College of Biology, State Key Laboratory of Chemo/Biosensing and Chemometrics, and Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, 410082, China
| | - Qinlu Lin
- National Engineering Laboratory for Rice and By-product Deep Processing, Central South University of Forestry and Technology, Changsha, 410004, China
| | - Feng Yu
- College of Biology, State Key Laboratory of Chemo/Biosensing and Chemometrics, and Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, 410082, China
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17
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Comparative Phosphoproteomic Analysis Reveals the Response of Starch Metabolism to High-Temperature Stress in Rice Endosperm. Int J Mol Sci 2021; 22:ijms221910546. [PMID: 34638888 PMCID: PMC8508931 DOI: 10.3390/ijms221910546] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 09/26/2021] [Accepted: 09/27/2021] [Indexed: 11/30/2022] Open
Abstract
High-temperature stress severely affects rice grain quality. While extensive research has been conducted at the physiological, transcriptional, and protein levels, it is still unknown how protein phosphorylation regulates seed development in high-temperature environments. Here, we explore the impact of high-temperature stress on the phosphoproteome of developing grains from two indica rice varieties, 9311 and Guangluai4 (GLA4), with different starch qualities. A total of 9994 phosphosites from 3216 phosphoproteins were identified in all endosperm samples. We identified several consensus phosphorylation motifs ([sP], [LxRxxs], [Rxxs], [tP]) induced by high-temperature treatment and revealed a core set of protein kinases, splicing factors, and regulatory factors in response to high-temperature stress, especially those involved in starch metabolism. A detailed phosphorylation scenario in the regulation of starch biosynthesis (AGPase, GBSSI, SSIIa, SSIIIa, BEI, BEIIb, ISA1, PUL, PHO1, PTST) in rice endosperm was proposed. Furthermore, the dynamic changes in phosphorylated enzymes related to starch synthesis (SSIIIa-Ser94, BEI-Ser562, BEI-Ser620, BEI-Ser821, BEIIb-Ser685, BEIIb-Ser715) were confirmed by Western blot analysis, which revealed that phosphorylation might play specific roles in amylopectin biosynthesis in response to high-temperature stress. The link between phosphorylation-mediated regulation and starch metabolism will provide new insights into the mechanism underlying grain quality development in response to high-temperature stress.
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18
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Vitoriano CB, Calixto CPG. Reading between the Lines: RNA-seq Data Mining Reveals the Alternative Message of the Rice Leaf Transcriptome in Response to Heat Stress. PLANTS 2021; 10:plants10081647. [PMID: 34451692 PMCID: PMC8400768 DOI: 10.3390/plants10081647] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 06/07/2021] [Accepted: 06/10/2021] [Indexed: 11/21/2022]
Abstract
Rice (Oryza sativa L.) is a major food crop but heat stress affects its yield and grain quality. To identify mechanistic solutions to improve rice yield under rising temperatures, molecular responses of thermotolerance must be understood. Transcriptional and post-transcriptional controls are involved in a wide range of plant environmental responses. Alternative splicing (AS), in particular, is a widespread mechanism impacting the stress defence in plants but it has been completely overlooked in rice genome-wide heat stress studies. In this context, we carried out a robust data mining of publicly available RNA-seq datasets to investigate the extension of heat-induced AS in rice leaves. For this, datasets of interest were subjected to filtering and quality control, followed by accurate transcript-specific quantifications. Powerful differential gene expression (DE) and differential AS (DAS) identified 17,143 and 2162 heat response genes, respectively, many of which are novel. Detailed analysis of DAS genes coding for key regulators of gene expression suggests that AS helps shape transcriptome and proteome diversity in response to heat. The knowledge resulting from this study confirmed a widespread transcriptional and post-transcriptional response to heat stress in plants, and it provided novel candidates for rapidly advancing rice breeding in response to climate change.
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19
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Schaarschmidt S, Lawas LMF, Kopka J, Jagadish SVK, Zuther E. Physiological and molecular attributes contribute to high night temperature tolerance in cereals. PLANT, CELL & ENVIRONMENT 2021; 44:2034-2048. [PMID: 33764557 DOI: 10.1111/pce.14055] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/22/2021] [Accepted: 03/23/2021] [Indexed: 05/24/2023]
Abstract
Asymmetric warming resulting in a faster increase in night compared to day temperatures affects crop yields negatively. Physiological characterization and agronomic findings have been complemented more recently by molecular biology approaches including transcriptomic, proteomic, metabolomic and lipidomic investigations in crops exposed to high night temperature (HNT) conditions. Nevertheless, the understanding of the underlying mechanisms causing yield decline under HNT is still limited. The discovery of significant differences between HNT-tolerant and HNT-sensitive cultivars is one of the main research directions to secure continuous food supply under the challenge of increasing climate change. With this review, we provide a summary of current knowledge on the physiological and molecular basis of contrasting HNT tolerance in rice and wheat cultivars. Requirements for HNT tolerance and the special adaptation strategies of the HNT-tolerant rice cultivar Nagina-22 (N22) are discussed. Putative metabolite markers for HNT tolerance useful for marker-assisted breeding are suggested, together with future research directions aimed at improving food security under HNT conditions.
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Affiliation(s)
| | | | - Joachim Kopka
- Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | | | - Ellen Zuther
- Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
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20
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Rabara RC, Msanne J, Basu S, Ferrer MC, Roychoudhury A. Coping with inclement weather conditions due to high temperature and water deficit in rice: An insight from genetic and biochemical perspectives. PHYSIOLOGIA PLANTARUM 2021; 172:487-504. [PMID: 33179306 DOI: 10.1111/ppl.13272] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 10/13/2020] [Accepted: 11/06/2020] [Indexed: 06/11/2023]
Abstract
Climatic fluctuations, temperature extremes, and water scarcity are becoming increasingly unpredictable with the passage of time. Such environmental atrocities have been the scourge of agriculture over the ages, bringing with them poor harvests and threat of famine. Rice production, owing to its high-water requirement for cultivation, is highly vulnerable to the threat of changing climate, particularly prolonged drought and high temperature, individually or in combination. Amidst all the abiotic stresses, heat and drought are considered as the most important concurrent stressors, largely affecting rice yield and productivity under the current scenario. Such threats heighten the need for new breeding and cultivation strategies in generating abiotic stress-resilient rice varieties with better yield potential. Responses of rice to these stresses can be categorized at the morphological, physiological and biochemical levels. This review examines the physiological and molecular mechanism, in the form of up regulation of several defense machineries of rice varieties to cope with drought stress (DS), high temperature stress (HTS), and their combination (DS-HTS). Genotypic differences among rice varieties in their tolerance ability have also been addressed. The review also appraises research studies conducted in rice regarding various phenotypic traits, genetic loci and response mechanisms to stress conditions to help craft new breeding strategies for improved tolerance to DS and HTS, singly or in combination. The review also encompasses the gene regulatory networks and transcription factors, and their cross-talks in mediating tolerance to such stresses. Understanding the epigenetic regulation, involving DNA methylation and histone modification during such hostile situations, will also play a crucial role in our comprehensive understanding of combinatorial stress responses. Taken together, this review consolidates current research and available information on promising rice cultivars with desirable traits as well as advocates synergistic and complementary approaches in molecular and systems biology to develop new rice breeds that favorably respond to DS-HTS-induced abiotic stress.
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Affiliation(s)
- Roel C Rabara
- Department of Biology, University of Virginia, Charlottesville, Virginia, United States of America
| | - Joseph Msanne
- New Mexico Consortium, Los Alamos, NM, New Mexico, United States of America
| | - Supratim Basu
- New Mexico Consortium, Los Alamos, NM, New Mexico, United States of America
| | - Marilyn C Ferrer
- Genetic Resources Division, Philippine Rice Research Institute, Science City of Muñoz, Nueva Ecija, Philippines
| | - Aryadeep Roychoudhury
- Department of Biotechnology, St. Xavier's College (Autonomous), Kolkata, West Bengal, India
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21
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Lim H, Hwang H, Kim T, Kim S, Chung H, Lee D, Kim S, Park S, Cho W, Ji H, Lee G. Transcriptomic Analysis of Rice Plants Overexpressing PsGAPDH in Response to Salinity Stress. Genes (Basel) 2021; 12:genes12050641. [PMID: 33923067 PMCID: PMC8146104 DOI: 10.3390/genes12050641] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 04/22/2021] [Accepted: 04/22/2021] [Indexed: 01/21/2023] Open
Abstract
In plants, glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is a main enzyme in the glycolytic pathway. It plays an essential role in glycerolipid metabolism and response to various stresses. To examine the function of PsGAPDH (Pleurotus sajor-caju GAPDH) in response to abiotic stress, we generated transgenic rice plants with single-copy/intergenic/homozygous overexpression PsGAPDH (PsGAPDH-OX) and investigated their responses to salinity stress. Seedling growth and germination rates of PsGAPDH-OX were significantly increased under salt stress conditions compared to those of the wild type. To elucidate the role of PsGAPDH-OX in salt stress tolerance of rice, an Illumina HiSeq 2000 platform was used to analyze transcriptome profiles of leaves under salt stress. Analysis results of sequencing data showed that 1124 transcripts were differentially expressed. Using the list of differentially expressed genes (DEGs), functional enrichment analyses of DEGs such as Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were performed. KEGG pathway enrichment analysis revealed that unigenes exhibiting differential expression were involved in starch and sucrose metabolism. Interestingly, trehalose-6-phosphate synthase (TPS) genes, of which expression was enhanced by abiotic stress, showed a significant difference in PsGAPDH-OX. Findings of this study suggest that PsGAPDH plays a role in the adaptation of rice plants to salt stress.
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Affiliation(s)
- Hyemin Lim
- Department of Forest Bioresources, National Institute of Forest Science, Suwon 16631, Korea; (H.L.); (T.K.)
| | - Hyunju Hwang
- Department of Applied Marine Bioresource Science, National Marine Biodiversity Institute of Korea, Seocheon 33662, Korea;
| | - Taelim Kim
- Department of Forest Bioresources, National Institute of Forest Science, Suwon 16631, Korea; (H.L.); (T.K.)
| | - Soyoung Kim
- National Institute of Agricultural Science, Rural Development Administration, Jeonju 54874, Korea; (S.K.); (S.P.); (W.C.); (H.J.)
| | - Hoyong Chung
- 3BIGS CO. LTD., 156 Gwanggyo-ro, Suwon 16429, Korea;
| | - Daewoo Lee
- National Institute of Crop Science, Rural Development Administration, Suwon 16430, Korea;
| | - Soorin Kim
- School of Food Science & Biotechnology, Kyungpook National University, Daegu 41566, Korea;
| | - Soochul Park
- National Institute of Agricultural Science, Rural Development Administration, Jeonju 54874, Korea; (S.K.); (S.P.); (W.C.); (H.J.)
| | - Woosuk Cho
- National Institute of Agricultural Science, Rural Development Administration, Jeonju 54874, Korea; (S.K.); (S.P.); (W.C.); (H.J.)
| | - Hyeonso Ji
- National Institute of Agricultural Science, Rural Development Administration, Jeonju 54874, Korea; (S.K.); (S.P.); (W.C.); (H.J.)
| | - Gangseob Lee
- National Institute of Agricultural Science, Rural Development Administration, Jeonju 54874, Korea; (S.K.); (S.P.); (W.C.); (H.J.)
- Correspondence:
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22
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Genome-wide association study and gene network analyses reveal potential candidate genes for high night temperature tolerance in rice. Sci Rep 2021; 11:6747. [PMID: 33762605 PMCID: PMC7991035 DOI: 10.1038/s41598-021-85921-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 03/08/2021] [Indexed: 12/13/2022] Open
Abstract
High night temperatures (HNT) are shown to significantly reduce rice (Oryza sativa L.) yield and quality. A better understanding of the genetic architecture of HNT tolerance will help rice breeders to develop varieties adapted to future warmer climates. In this study, a diverse indica rice panel displayed a wide range of phenotypic variability in yield and quality traits under control night (24 °C) and higher night (29 °C) temperatures. Genome-wide association analysis revealed 38 genetic loci associated across treatments (18 for control and 20 for HNT). Nineteen loci were detected with the relative changes in the traits between control and HNT. Positive phenotypic correlations and co-located genetic loci with previously cloned grain size genes revealed common genetic regulation between control and HNT, particularly grain size. Network-based predictive models prioritized 20 causal genes at the genetic loci based on known gene/s expression under HNT in rice. Our study provides important insights for future candidate gene validation and molecular marker development to enhance HNT tolerance in rice. Integrated physiological, genomic, and gene network-informed approaches indicate that the candidate genes for stay-green trait may be relevant to minimizing HNT-induced yield and quality losses during grain filling in rice by optimizing source-sink relationships.
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Qin-Di D, Gui-Hua J, Xiu-Neng W, Zun-Guang M, Qing-Yong P, Shiyun C, Yu-Jian M, Shuang-Xi Z, Yong-Xiang H, Yu L. High temperature-mediated disturbance of carbohydrate metabolism and gene expressional regulation in rice: a review. PLANT SIGNALING & BEHAVIOR 2021; 16:1862564. [PMID: 33470154 PMCID: PMC7889029 DOI: 10.1080/15592324.2020.1862564] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 12/07/2020] [Accepted: 12/07/2020] [Indexed: 06/12/2023]
Abstract
Global warming has induced higher frequencies of excessively high-temperature weather episodes, which pose damage risk to rice growth and production. Past studies seldom specified how high temperature-induced carbohydrate metabolism disturbances from both source and sink affect rice fertilization and production. Here we discuss the mechanism of heat-triggered damage to rice quality and production through disturbance of carbohydrate generation and consumption under high temperatures. Furthermore, we provide strong evidence from past studies that rice varieties that maintain high photosynthesis and carbohydrate usage efficiencies under high temperatures will suffer less heat-induced damage during reproductive developmental stages. We also discuss the complexity of expressional regulation of rice genes in response to high temperatures, while highlighting the important roles of heat-inducible post-transcriptional regulations of gene expression. Lastly, we predict future directions in heat-tolerant rice breeding and also propose challenges that need to be conquered in the future.
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Affiliation(s)
- Deng Qin-Di
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang,China
| | - Jian Gui-Hua
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang,China
| | - Wang Xiu-Neng
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang,China
| | - Mo Zun-Guang
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang,China
| | - Peng Qing-Yong
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang,China
| | - Chen Shiyun
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang,China
| | - Mo Yu-Jian
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang,China
| | - Zhou Shuang-Xi
- New Zealand Institute for Plant and Food Research Limited, Hawke’s Bay,New Zealand
| | - Huang Yong-Xiang
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang,China
| | - Ling Yu
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang,China
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24
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Chunduri V, Sharma N, Garg M. A null allele of granule bound starch synthase (Wx-B1) may be one of the major genes controlling chapatti softness. PLoS One 2021; 16:e0246095. [PMID: 33508026 PMCID: PMC7842929 DOI: 10.1371/journal.pone.0246095] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 01/13/2021] [Indexed: 11/19/2022] Open
Abstract
Chapatti (unleavened flatbread) is a staple food in northern India and neighboring countries but the genetics behind its processing quality are poorly understood. To understand the genes determining chapatti quality, differentially expressed genes were selected from microarray data of contrasting chapatti cultivars. From the gene and trait association studies, a null allele of granule bound starch synthase (GBSS; Wx-B1) was found to be associated with low amylose content and good chapatti quality. For validation, near-isogenic lines (NILs) of this allele were created by marker assisted backcross (MAB) breeding. Background screening indicated 88.2 to 96.7% background recovery in 16 selected BC3F5 NILs. Processing quality and sensory evaluation of selected NILs indicated improvement in chapatti making quality. Traits that showed improvement were mouthfeel, tearing strength and softness indicating that the Wx-B1 may be one of the major genes controlling chapatti softness.
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Affiliation(s)
- Venkatesh Chunduri
- Agri-Biotechnology Division, National Agri-Food Biotechnology Institute, Mohali, Punjab, India
| | - Natasha Sharma
- Agri-Biotechnology Division, National Agri-Food Biotechnology Institute, Mohali, Punjab, India
| | - Monika Garg
- Agri-Biotechnology Division, National Agri-Food Biotechnology Institute, Mohali, Punjab, India
- * E-mail: ,
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25
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Chaudhary S, Devi P, Bhardwaj A, Jha UC, Sharma KD, Prasad PVV, Siddique KHM, Bindumadhava H, Kumar S, Nayyar H. Identification and Characterization of Contrasting Genotypes/Cultivars for Developing Heat Tolerance in Agricultural Crops: Current Status and Prospects. FRONTIERS IN PLANT SCIENCE 2020; 11:587264. [PMID: 33193540 PMCID: PMC7642017 DOI: 10.3389/fpls.2020.587264] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Accepted: 09/14/2020] [Indexed: 05/19/2023]
Abstract
Rising global temperatures due to climate change are affecting crop performance in several regions of the world. High temperatures affect plants at various organizational levels, primarily accelerating phenology to limit biomass production and shortening reproductive phase to curtail flower and fruit numbers, thus resulting in severe yield losses. Besides, heat stress also disrupts normal growth, development, cellular metabolism, and gene expression, which alters shoot and root structures, branching patterns, leaf surface and orientation, and anatomical, structural, and functional aspects of leaves and flowers. The reproductive growth stage is crucial in plants' life cycle, and susceptible to high temperatures, as reproductive processes are negatively impacted thus reducing crop yield. Genetic variation exists among genotypes of various crops to resist impacts of heat stress. Several screening studies have successfully phenotyped large populations of various crops to distinguish heat-tolerant and heat-sensitive genotypes using various traits, related to shoots (including leaves), flowers, fruits (pods, spikes, spikelets), and seeds (or grains), which have led to direct release of heat-tolerant cultivars in some cases (such as chickpea). In the present review, we discuss examples of contrasting genotypes for heat tolerance in different crops, involving many traits related to thermotolerance in leaves (membrane thermostability, photosynthetic efficiency, chlorophyll content, chlorophyll fluorescence, stomatal activity), flowers (pollen viability, pollen germination, fertilization, ovule viability), roots (architecture), biomolecules (antioxidants, osmolytes, phytohormones, heat-shock proteins, other stress proteins), and "omics" (phenomics, transcriptomics, genomics) approaches. The traits linked to heat tolerance can be introgressed into high yielding but heat-sensitive genotypes of crops to enhance their thermotolerance. Involving these traits will be useful for screening contrasting genotypes and would pave the way for characterizing the underlying molecular mechanisms, which could be valuable for engineering plants with enhanced thermotolerance. Wherever possible, we discussed breeding and biotechnological approaches for using these traits to develop heat-tolerant genotypes of various food crops.
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Affiliation(s)
| | - Poonam Devi
- Department of Botany, Panjab University, Chandigarh, India
| | | | | | - Kamal Dev Sharma
- Department of Agricultural Biotechnology, Chaudhary Sarwan Kumar Himachal Pradesh (CSK HP) Agricultural University, Palampur, India
| | | | | | - H. Bindumadhava
- World Vegetable Center, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Shiv Kumar
- International Center for Agriculture Research in the Dry Areas (ICARDA), Rabat, Morocco
| | - Harsh Nayyar
- Department of Botany, Panjab University, Chandigarh, India
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26
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He C, Zhang HY, Zhang YX, Fu P, You LL, Xiao WB, Wang ZH, Song HY, Huang YJ, Liao JL. Cytosine methylations in the promoter regions of genes involved in the cellular oxidation equilibrium pathways affect rice heat tolerance. BMC Genomics 2020; 21:560. [PMID: 32799794 PMCID: PMC7430847 DOI: 10.1186/s12864-020-06975-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Accepted: 08/06/2020] [Indexed: 11/15/2022] Open
Abstract
Background High temperatures, particularly at night, decrease rice yield and quality. As high nighttime temperatures (HNTs) become increasingly frequent due to climate change, it is imperative to develop rice crops that tolerate HNTs. DNA methylation may represent a potential avenue for HNT-tolerant rice strain development, as this mechanism regulates gene activity and cellular phenotype in response to adverse environmental conditions without changing the nucleotide sequence. Results After HNT exposure, the methylation patterns of cytosines in the CHH context differed noticeably between two coisogenic rice strains with significantly different levels in heat tolerance. Methylation differences between strains were primarily observed on successive cytosines in the promoter or downstream regions of transcription factors and transposon elements. In contrast to the heat-sensitive rice strain, the regions 358–359 bp and 2–60 bp downstream of two basal transcriptional factors (TFIID subunit 11 and mediator of RNA polymerase II transcription subunit 31, respectively) were fully demethylated in the heat-tolerant strain after HNT exposure. In the heat-tolerant strain, HNTs reversed the methylation patterns of successive cytosines in the promoter regions of various genes involved in abscisic acid (ABA)-related reactive oxygen species (ROS) equilibrium pathways, including the pentatricopeptide repeat domain gene PPR (LOC_Os07g28900) and the homeobox domain gene homeobox (LOC_Os01g19694). Indeed, PRR expression was inhibited in heat-sensitive rice strains, and the methylation rates of the cytosines in the promoter region of PRR were greater in heat-sensitive strains as compared to heat-tolerant strains. Conclusions After HNT exposure, cytosines in the CHH context were more likely than cytosines in other contexts to be methylated differently between the heat-sensitive and heat-tolerant rice strains. Methylation in the promoter regions of the genes associated with ABA-related oxidation and ROS scavenging improved heat tolerance in rice. Our results help to clarify the molecular mechanisms underlying rice heat tolerance.
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Affiliation(s)
- Chao He
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding (Jiangxi Agricultural University), Ministry of Education of China, Nanchang, 330045, China
| | - Hong-Yu Zhang
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding (Jiangxi Agricultural University), Ministry of Education of China, Nanchang, 330045, China
| | - Yong-Xin Zhang
- South Zhejiang Key Laboratory of Crop Breeding, Institute of Crop Research, Wenzhou Academy of Agricultural Sciences, Wenzhou, 325006, China
| | - Pei Fu
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding (Jiangxi Agricultural University), Ministry of Education of China, Nanchang, 330045, China
| | - Li-Li You
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding (Jiangxi Agricultural University), Ministry of Education of China, Nanchang, 330045, China
| | - Wen-Bo Xiao
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding (Jiangxi Agricultural University), Ministry of Education of China, Nanchang, 330045, China
| | - Zhao-Hai Wang
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding (Jiangxi Agricultural University), Ministry of Education of China, Nanchang, 330045, China
| | - Hai-Yan Song
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding (Jiangxi Agricultural University), Ministry of Education of China, Nanchang, 330045, China
| | - Ying-Jin Huang
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding (Jiangxi Agricultural University), Ministry of Education of China, Nanchang, 330045, China. .,Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Changsha, 410128, China.
| | - Jiang-Lin Liao
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding (Jiangxi Agricultural University), Ministry of Education of China, Nanchang, 330045, China. .,Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Changsha, 410128, China.
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27
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Janni M, Gullì M, Maestri E, Marmiroli M, Valliyodan B, Nguyen HT, Marmiroli N. Molecular and genetic bases of heat stress responses in crop plants and breeding for increased resilience and productivity. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:3780-3802. [PMID: 31970395 PMCID: PMC7316970 DOI: 10.1093/jxb/eraa034] [Citation(s) in RCA: 100] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 01/20/2020] [Indexed: 05/21/2023]
Abstract
To ensure the food security of future generations and to address the challenge of the 'no hunger zone' proposed by the FAO (Food and Agriculture Organization), crop production must be doubled by 2050, but environmental stresses are counteracting this goal. Heat stress in particular is affecting agricultural crops more frequently and more severely. Since the discovery of the physiological, molecular, and genetic bases of heat stress responses, cultivated plants have become the subject of intense research on how they may avoid or tolerate heat stress by either using natural genetic variation or creating new variation with DNA technologies, mutational breeding, or genome editing. This review reports current understanding of the genetic and molecular bases of heat stress in crops together with recent approaches to creating heat-tolerant varieties. Research is close to a breakthrough of global relevance, breeding plants fitter to face the biggest challenge of our time.
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Affiliation(s)
- Michela Janni
- Institute of Bioscience and Bioresources (IBBR), National Research Council (CNR), Via Amendola, Bari, Italy
- Institute of Materials for Electronics and Magnetism (IMEM), National Research Council (CNR), Parco Area delle Scienze, Parma, Italy
| | - Mariolina Gullì
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze, Parma, Italy
| | - Elena Maestri
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze, Parma, Italy
| | - Marta Marmiroli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze, Parma, Italy
| | - Babu Valliyodan
- Division of Plant Sciences, University of Missouri, Columbia, MO, USA
- Lincoln University, Jefferson City, MO, USA
| | - Henry T Nguyen
- Division of Plant Sciences, University of Missouri, Columbia, MO, USA
| | - Nelson Marmiroli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze, Parma, Italy
- CINSA Interuniversity Consortium for Environmental Sciences, Parma/Venice, Italy
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28
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Schaarschmidt S, Lawas LMF, Glaubitz U, Li X, Erban A, Kopka J, Jagadish SVK, Hincha DK, Zuther E. Season Affects Yield and Metabolic Profiles of Rice ( Oryza sativa) under High Night Temperature Stress in the Field. Int J Mol Sci 2020; 21:E3187. [PMID: 32366031 PMCID: PMC7247591 DOI: 10.3390/ijms21093187] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 04/23/2020] [Accepted: 04/29/2020] [Indexed: 12/12/2022] Open
Abstract
Rice (Oryza sativa) is the main food source for more than 3.5 billion people in the world. Global climate change is having a strong negative effect on rice production. One of the climatic factors impacting rice yield is asymmetric warming, i.e., the stronger increase in nighttime as compared to daytime temperatures. Little is known of the metabolic responses of rice to high night temperature (HNT) in the field. Eight rice cultivars with contrasting HNT sensitivity were grown in the field during the wet (WS) and dry season (DS) in the Philippines. Plant height, 1000-grain weight and harvest index were influenced by HNT in both seasons, while total grain yield was only consistently reduced in the WS. Metabolite composition was analysed by gas chromatography-mass spectrometry (GC-MS). HNT effects were more pronounced in panicles than in flag leaves. A decreased abundance of sugar phosphates and sucrose, and a higher abundance of monosaccharides in panicles indicated impaired glycolysis and higher respiration-driven carbon losses in response to HNT in the WS. Higher amounts of alanine and cyano-alanine in panicles grown in the DS compared to in those grown in the WS point to an improved N-assimilation and more effective detoxification of cyanide, contributing to the smaller impact of HNT on grain yield in the DS.
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Affiliation(s)
- Stephanie Schaarschmidt
- Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam, Germany; (S.S.); (L.M.F.L.); (U.G.); (X.L.); (A.E.); (J.K.); (D.K.H.)
| | - Lovely Mae F. Lawas
- Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam, Germany; (S.S.); (L.M.F.L.); (U.G.); (X.L.); (A.E.); (J.K.); (D.K.H.)
- International Rice Research Institute, Metro Manila 1301, Philippines;
| | - Ulrike Glaubitz
- Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam, Germany; (S.S.); (L.M.F.L.); (U.G.); (X.L.); (A.E.); (J.K.); (D.K.H.)
| | - Xia Li
- Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam, Germany; (S.S.); (L.M.F.L.); (U.G.); (X.L.); (A.E.); (J.K.); (D.K.H.)
- Institute of Crop Science, Chinese Academy of Agricultural Science, Beijing 100081, China
| | - Alexander Erban
- Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam, Germany; (S.S.); (L.M.F.L.); (U.G.); (X.L.); (A.E.); (J.K.); (D.K.H.)
| | - Joachim Kopka
- Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam, Germany; (S.S.); (L.M.F.L.); (U.G.); (X.L.); (A.E.); (J.K.); (D.K.H.)
| | - S. V. Krishna Jagadish
- International Rice Research Institute, Metro Manila 1301, Philippines;
- Department of Agronomy, Kansas State University, Manhattan, KS 66506, USA
| | - Dirk K. Hincha
- Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam, Germany; (S.S.); (L.M.F.L.); (U.G.); (X.L.); (A.E.); (J.K.); (D.K.H.)
| | - Ellen Zuther
- Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam, Germany; (S.S.); (L.M.F.L.); (U.G.); (X.L.); (A.E.); (J.K.); (D.K.H.)
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29
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Yang T, Tan X, Huang S, Pan X, Shi Q, Zeng Y, Zhang J, Zeng Y. Effects of experimental warming on physicochemical properties of indica rice starch in a double rice cropping system. Food Chem 2020; 310:125981. [PMID: 31835221 DOI: 10.1016/j.foodchem.2019.125981] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 11/25/2019] [Accepted: 11/28/2019] [Indexed: 11/25/2022]
Abstract
To evaluate the actual response of rice starch physicochemical properties to climate warming, a field warming experiment was conducted with four indica rice cultivars using free-air temperature increase (FATI) facility in a double rice cropping system. FATI facility increased rice canopy temperature by 1.4-2.1 °C during the entire growth period. The responses of starch physicochemical properties to experimental warming were basically consistent for both early and late rice. On average, experimental warming increased the starch relative crystallinity, granule average diameter, and amylopectin average chain length by 14.3%, 6.9%, and 2.4%, respectively. These resulted in starch with lower swelling power, water solubility, and pasting viscosity, but higher gelatinization temperatures and gelatinization enthalpy. Our study indicated that experimental warming affected the rice starch physicochemical properties, and would provide some useful information on how to guide the rice starch end use in food and non-food industries under climate warming.
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Affiliation(s)
- Taotao Yang
- Ministry of Education and Jiangxi Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Jiangxi Agricultural University, Nanchang 330045, China
| | - Xueming Tan
- Ministry of Education and Jiangxi Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Jiangxi Agricultural University, Nanchang 330045, China
| | - Shan Huang
- Ministry of Education and Jiangxi Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Jiangxi Agricultural University, Nanchang 330045, China
| | - Xiaohua Pan
- Ministry of Education and Jiangxi Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Jiangxi Agricultural University, Nanchang 330045, China
| | - Qinghua Shi
- Ministry of Education and Jiangxi Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Jiangxi Agricultural University, Nanchang 330045, China
| | - Yongjun Zeng
- Ministry of Education and Jiangxi Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Jiangxi Agricultural University, Nanchang 330045, China
| | - Jun Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yanhua Zeng
- Ministry of Education and Jiangxi Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Jiangxi Agricultural University, Nanchang 330045, China.
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30
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The miRNA-Mediated Post-Transcriptional Regulation of Maize in Response to High Temperature. Int J Mol Sci 2019; 20:ijms20071754. [PMID: 30970661 PMCID: PMC6480492 DOI: 10.3390/ijms20071754] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 04/02/2019] [Accepted: 04/03/2019] [Indexed: 01/20/2023] Open
Abstract
High temperature (HT) has recently become one of the most important abiotic stresses restricting crop production worldwide. MicroRNAs (miRNAs) are important regulators in plant development and stress responses. However, knowledge of miRNAs of maize in response to HT is limited. In this study, we simultaneously adopted miRNA sequencing and transcriptome profiling to analyze the differential expression of miRNAs and mRNAs in maize during exposure to HT stress. Our analysis revealed 61 known miRNAs belonging to 26 miRNA families and 42 novel miRNAs showing significant differential expression, with the majority being downregulated. Meanwhile, the expression of 5450 mRNAs was significantly altered in the same stressed tissues. Differentially expressed transcripts were most significantly associated with response to stress, photosynthesis, biosynthesis of secondary metabolites, and signal transduction pathways. In addition, we discovered 129 miRNA–mRNA pairs that were regulated antagonistically, and further depiction of the targeted mRNAs indicated that several transcription factors, protein kinases, and receptor-like-protein-related transmembrane transport and signaling transduction were profoundly affected. This study has identified potential key regulators of HT-stress response in maize and the subset of genes that are likely to be post-transcriptionally regulated by miRNAs under HT stress.
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31
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Lei G, Zhang HY, Wang ZH, Wei LX, Fu P, Song JB, Fu DH, Huang YJ, Liao JL. High Nighttime Temperature Induces Antioxidant Molecule Perturbations in Heat-Sensitive and Heat-Tolerant Coisogenic Rice ( Oryza sativa) Strains. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:12131-12140. [PMID: 30362740 DOI: 10.1021/acs.jafc.8b04425] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Global warming-associated increases in temperature, particularly at nighttime, are detrimental to rice yield and quality. Metabolomic profiling was used to examine and compare the short-term extreme high nighttime temperature-induced molecular perturbations in rice ( Oryza sativa) coisogenic strains with contrasting heat-tolerances at the first stage of seed ripening. Compared to the heat-sensitive strain, antioxidant molecules were higher in abundance in the heat-tolerant strain, whereas the abundances of molecules involved in photosynthesis, nucleotide catabolism, and the S-adenosylmethionine (SAM) cycle varied only slightly. Thus, we proposed that the high abundance of antioxidant molecules in the heat-tolerant strain alleviated cellular oxidative stress, which protected photosynthesis, nucleotide catabolism, and the SAM cycle, leading to good grain filling.
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Affiliation(s)
- Gang Lei
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding (Jiangxi Agricultural University) , Ministry of Education of China , Nanchang 330045 , Jiangxi Province , China
| | - Hong-Yu Zhang
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding (Jiangxi Agricultural University) , Ministry of Education of China , Nanchang 330045 , Jiangxi Province , China
| | - Zhao-Hai Wang
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding (Jiangxi Agricultural University) , Ministry of Education of China , Nanchang 330045 , Jiangxi Province , China
| | - Ling-Xia Wei
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding (Jiangxi Agricultural University) , Ministry of Education of China , Nanchang 330045 , Jiangxi Province , China
| | - Pei Fu
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding (Jiangxi Agricultural University) , Ministry of Education of China , Nanchang 330045 , Jiangxi Province , China
| | - Jian-Bo Song
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding (Jiangxi Agricultural University) , Ministry of Education of China , Nanchang 330045 , Jiangxi Province , China
| | - Dong-Hui Fu
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding (Jiangxi Agricultural University) , Ministry of Education of China , Nanchang 330045 , Jiangxi Province , China
| | - Ying-Jin Huang
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding (Jiangxi Agricultural University) , Ministry of Education of China , Nanchang 330045 , Jiangxi Province , China
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China , Changsha 410128 , Hunan Province , China
| | - Jiang-Lin Liao
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding (Jiangxi Agricultural University) , Ministry of Education of China , Nanchang 330045 , Jiangxi Province , China
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China , Changsha 410128 , Hunan Province , China
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32
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Zhang H, Xu H, Feng M, Zhu Y. Suppression of OsMADS7 in rice endosperm stabilizes amylose content under high temperature stress. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:18-26. [PMID: 28429576 PMCID: PMC5785353 DOI: 10.1111/pbi.12745] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 04/06/2017] [Accepted: 04/11/2017] [Indexed: 05/03/2023]
Abstract
High temperature significantly alters the amylose content of rice, resulting in mature grains with poor eating quality. However, only few genes and/or quantitative trait loci involved in this process have been isolated and the molecular mechanisms of this effect remain unclear. Here, we describe a floral organ identity gene, OsMADS7, involved in stabilizing rice amylose content at high temperature. OsMADS7 is greatly induced by high temperature at the early filling stage. Constitutive suppression of OsMADS7 stabilizes amylose content under high temperature stress but results in low spikelet fertility. However, rice plants with both stable amylose content at high temperature and normal spikelet fertility can be obtained by specifically suppressing OsMADS7 in endosperm. GBSSI is the major enzyme responsible for amylose biosynthesis. A low filling rate and high expression of GBSSI were detected in OsMADS7 RNAi plants at high temperature, which may be correlated with stabilized amylose content in these transgenic seeds under high temperature. Thus, specific suppression of OsMADS7 in endosperm could improve the stability of rice amylose content at high temperature, and such transgenic materials may be a valuable genetic resource for breeding rice with elite thermal resilience.
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Affiliation(s)
- Hua Zhang
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease ControlKey Laboratory of Creative AgricultureMinistry of AgricultureInstitute of Virology and BiotechnologyZhejiang Academy of Agricultural SciencesHangzhouZhejiangChina
| | - Heng Xu
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease ControlKey Laboratory of Creative AgricultureMinistry of AgricultureInstitute of Virology and BiotechnologyZhejiang Academy of Agricultural SciencesHangzhouZhejiangChina
| | - Mengjie Feng
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease ControlKey Laboratory of Creative AgricultureMinistry of AgricultureInstitute of Virology and BiotechnologyZhejiang Academy of Agricultural SciencesHangzhouZhejiangChina
| | - Ying Zhu
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease ControlKey Laboratory of Creative AgricultureMinistry of AgricultureInstitute of Virology and BiotechnologyZhejiang Academy of Agricultural SciencesHangzhouZhejiangChina
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Zhang HY, Lei G, Zhou HW, He C, Liao JL, Huang YJ. Quantitative iTRAQ-based proteomic analysis of rice grains to assess high night temperature stress. Proteomics 2017; 17. [PMID: 28101936 PMCID: PMC5811895 DOI: 10.1002/pmic.201600365] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Revised: 12/23/2016] [Accepted: 01/13/2017] [Indexed: 12/13/2022]
Abstract
Rice yield and quality are adversely affected by increasing global surface temperature, and are strongly attributed to high night temperature (HNT) than high daytime temperature. However, the molecular mechanism underlying the heat‐tolerant characteristics of rice remains unclear. In the present study, we compared the proteomes of heat‐tolerant and ‐sensitive lines of rice at early milky stage using an iTRAQ method. We have identified 38 differentially expressed proteins between the two lines, of which 32 proteins have been functionally annotated in NCBI and/or the UniProt database. These proteins were then classified into seven functional subgroups, which include signal transduction, transcript regulation, oxidation, defense response, transport, energy metabolism, and biosynthesis. Further analysis indicated that HNT stress could disrupt the redox equilibrium of plant cells, which in turn triggers the calcium‐dependent protein kinase and COP9 signalosome, thereby regulating downstream genes/proteins that are involved in the HNT response. The candidate proteins may provide genetic resources for the improvement of heat‐tolerant characteristics in rice, and the proposed model for signal transduction and transcriptional regulation may facilitate in the elucidation of the molecular mechanism underlying the response to HNT stress in rice.
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Affiliation(s)
- Hong-Yu Zhang
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding (Jiangxi Agricultural University), Ministry of Education, Jiangxi Province, P. R. China
| | - Gang Lei
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding (Jiangxi Agricultural University), Ministry of Education, Jiangxi Province, P. R. China
| | - Hui-Wen Zhou
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding (Jiangxi Agricultural University), Ministry of Education, Jiangxi Province, P. R. China
| | - Chao He
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding (Jiangxi Agricultural University), Ministry of Education, Jiangxi Province, P. R. China
| | - Jiang-Lin Liao
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding (Jiangxi Agricultural University), Ministry of Education, Jiangxi Province, P. R. China
| | - Ying-Jin Huang
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding (Jiangxi Agricultural University), Ministry of Education, Jiangxi Province, P. R. China.,Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Hunan Province, P. R. China
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Glaubitz U, Li X, Schaedel S, Erban A, Sulpice R, Kopka J, Hincha DK, Zuther E. Integrated analysis of rice transcriptomic and metabolomic responses to elevated night temperatures identifies sensitivity- and tolerance-related profiles. PLANT, CELL & ENVIRONMENT 2017; 40:121-137. [PMID: 27761892 DOI: 10.1111/pce.12850] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 10/12/2016] [Accepted: 10/15/2016] [Indexed: 05/05/2023]
Abstract
Transcript and metabolite profiling were performed on leaves from six rice cultivars under high night temperature (HNT) condition. Six genes were identified as central for HNT response encoding proteins involved in transcription regulation, signal transduction, protein-protein interactions, jasmonate response and the biosynthesis of secondary metabolites. Sensitive cultivars showed specific changes in transcript abundance including abiotic stress responses, changes of cell wall-related genes, of ABA signaling and secondary metabolism. Additionally, metabolite profiles revealed a highly activated TCA cycle under HNT and concomitantly increased levels in pathways branching off that could be corroborated by enzyme activity measurements. Integrated data analysis using clustering based on one-dimensional self-organizing maps identified two profiles highly correlated with HNT sensitivity. The sensitivity profile included genes of the functional bins abiotic stress, hormone metabolism, cell wall, signaling, redox state, transcription factors, secondary metabolites and defence genes. In the tolerance profile, similar bins were affected with slight differences in hormone metabolism and transcription factor responses. Metabolites of the two profiles revealed involvement of GABA signaling, thus providing a link to the TCA cycle status in sensitive cultivars and of myo-inositol as precursor for inositol phosphates linking jasmonate signaling to the HNT response specifically in tolerant cultivars.
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Affiliation(s)
- Ulrike Glaubitz
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476, Potsdam, Germany
| | - Xia Li
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476, Potsdam, Germany
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Haidian District, Beijing, 100081, China
| | - Sandra Schaedel
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476, Potsdam, Germany
- ICRC Weyer GmbH, Bölschestraße 35, D-12587, Berlin, Germany
| | - Alexander Erban
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476, Potsdam, Germany
| | - Ronan Sulpice
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476, Potsdam, Germany
- Plant Systems Biology Research Lab, Plant and AgriBiosciences Research Centre, Botany and Plant Science, National University of Galway, Galway, Ireland
| | - Joachim Kopka
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476, Potsdam, Germany
| | - Dirk K Hincha
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476, Potsdam, Germany
| | - Ellen Zuther
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476, Potsdam, Germany
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Hua Y, Zhou T, Ding G, Yang Q, Shi L, Xu F. Physiological, genomic and transcriptional diversity in responses to boron deficiency in rapeseed genotypes. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:5769-5784. [PMID: 27639094 PMCID: PMC5066495 DOI: 10.1093/jxb/erw342] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Allotetraploid rapeseed (Brassica napus L. AnAnCnCn, 2n=4x=38) is highly susceptible to boron (B) deficiency, a widespread limiting factor that causes severe losses in seed yield. The genetic variation in the sensitivity to B deficiency found in rapeseed genotypes emphasizes the complex response architecture. In this research, a B-inefficient genotype, 'Westar 10' ('W10'), responded to B deficiencies during vegetative and reproductive development with an over-accumulation of reactive oxygen species, severe lipid peroxidation, evident plasmolysis, abnormal floral organogenesis, and widespread sterility compared to a B-efficient genotype, 'Qingyou 10' ('QY10'). Whole-genome re-sequencing (WGS) of 'QY10' and 'W10' revealed a total of 1 605 747 single nucleotide polymorphisms and 218 755 insertions/deletions unevenly distributed across the allotetraploid rapeseed genome (~1130Mb). Digital gene expression (DGE) profiling identified more genes related to B transporters, antioxidant enzymes, and the maintenance of cell walls and membranes with higher transcript levels in the roots of 'QY10' than in 'W10' under B deficiency. Furthermore, based on WGS and bulked segregant analysis of the doubled haploid (DH) line pools derived from 'QY10' and 'W10', two significant quantitative trait loci (QTLs) for B efficiency were characterized on chromosome C2, and DGE-assisted QTL-seq analyses then identified a nodulin 26-like intrinsic protein gene and an ATP-binding cassette (ABC) transporter gene as the corresponding candidates regulating B efficiency. This research facilitates a more comprehensive understanding of the differential physiological and transcriptional responses to B deficiency and abundant genetic diversity in rapeseed genotypes, and the DGE-assisted QTL-seq analyses provide novel insights regarding the rapid dissection of quantitative trait genes in plant species with complex genomes.
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Affiliation(s)
- Yingpeng Hua
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China Microelement Research Centre, Huazhong Agricultural University, Wuhan 430070, China
| | - Ting Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China Microelement Research Centre, Huazhong Agricultural University, Wuhan 430070, China
| | - Guangda Ding
- Microelement Research Centre, Huazhong Agricultural University, Wuhan 430070, China
| | - Qingyong Yang
- College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Lei Shi
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China Microelement Research Centre, Huazhong Agricultural University, Wuhan 430070, China
| | - Fangsen Xu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China Microelement Research Centre, Huazhong Agricultural University, Wuhan 430070, China
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Fatihi A, Boulard C, Bouyer D, Baud S, Dubreucq B, Lepiniec L. Deciphering and modifying LAFL transcriptional regulatory network in seed for improving yield and quality of storage compounds. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2016; 250:198-204. [PMID: 27457996 DOI: 10.1016/j.plantsci.2016.06.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2016] [Revised: 06/16/2016] [Accepted: 06/18/2016] [Indexed: 05/11/2023]
Abstract
Increasing yield and quality of seed storage compounds in a sustainable way is a key challenge for our societies. Genome-wide analyses conducted in both monocot and dicot angiosperms emphasized drastic transcriptional switches that occur during seed development. In Arabidopsis thaliana, a reference species, genetic and molecular analyses have demonstrated the key role of LAFL (LEC1, ABI3, FUS3, and LEC2) transcription factors (TFs), in controlling gene expression programs essential to accomplish seed maturation and the accumulation of storage compounds. Here, we summarize recent progress obtained in the characterization of these LAFL proteins, their regulation, partners and target genes. Moreover, we illustrate how these evolutionary conserved TFs can be used to engineer new crops with altered seed compositions and point out the current limitations. Last, we discuss about the interest of investigating further the environmental and epigenetic regulation of this network for the coming years.
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Affiliation(s)
- Abdelhak Fatihi
- IJPB, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78026, Versailles Cedex, France.
| | - Céline Boulard
- IJPB, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78026, Versailles Cedex, France
| | - Daniel Bouyer
- Institut de Biologie de l'ENS, CNRS UMR8197, Ecole Normale Supérieure, 46 rue d'Ulm, 75230, Paris cedex 05, France
| | - Sébastien Baud
- IJPB, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78026, Versailles Cedex, France
| | - Bertrand Dubreucq
- IJPB, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78026, Versailles Cedex, France
| | - Loïc Lepiniec
- IJPB, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78026, Versailles Cedex, France.
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Zhang C, Zhou L, Zhu Z, Lu H, Zhou X, Qian Y, Li Q, Lu Y, Gu M, Liu Q. Characterization of Grain Quality and Starch Fine Structure of Two Japonica Rice (Oryza Sativa) Cultivars with Good Sensory Properties at Different Temperatures during the Filling Stage. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2016; 64:4048-57. [PMID: 27128366 DOI: 10.1021/acs.jafc.6b00083] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Temperature during the growing season is a critical factor affecting grain quality. High temperatures at grain filling affect kernel development, resulting in reduced yield, increased chalkiness, reduced amylose content, and poor milling quality. Here, we investigated the grain quality and starch structure of two japonica rice cultivars with good sensory properties grown at different temperatures during the filling stage under natural field conditions. Compared to those grown under normal conditions, rice grains grown under hot conditions showed significantly reduced eating and cooking qualities, including a higher percentage of grains with chalkiness, lower protein and amylose contents, and higher pasting properties. Under hot conditions, rice starch contained reduced long-chain amylose (MW 10(7.1) to 10(7.4)) and significantly fewer short-chain amylopectin (DP 5-12) but more intermediate- (DP 13-34) and long- (DP 45-60) chain amylopectin than under normal conditions, as well as higher crystallinity and gelatinization properties.
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Affiliation(s)
- Changquan Zhang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University , Yangzhou 225009, China
| | - Lihui Zhou
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University , Yangzhou 225009, China
- Jiangsu High Quality Rice Research and Development Center, Institute of Food Crops, Jiangsu Academy of Agricultural Sciences , Nanjing 210014, China
| | - Zhengbin Zhu
- Suzhou Seed Administration Station , Suzhou 215011, China
| | - Huwen Lu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University , Yangzhou 225009, China
| | - Xingzhong Zhou
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University , Yangzhou 225009, China
| | - Yiting Qian
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University , Yangzhou 225009, China
| | - Qianfeng Li
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University , Yangzhou 225009, China
| | - Yan Lu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University , Yangzhou 225009, China
| | - Minghong Gu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University , Yangzhou 225009, China
| | - Qiaoquan Liu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University , Yangzhou 225009, China
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Transcriptome Analysis of Salt Stress Responsiveness in the Seedlings of Dongxiang Wild Rice (Oryza rufipogon Griff.). PLoS One 2016; 11:e0146242. [PMID: 26752408 PMCID: PMC4709063 DOI: 10.1371/journal.pone.0146242] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 12/15/2015] [Indexed: 11/19/2022] Open
Abstract
Dongxiang wild rice (Oryza rufipogon Griff.) is the progenitor of cultivated rice (Oryza sativa L.), and is well known for its superior level of tolerance against cold, drought and diseases. To date, however, little is known about the salt-tolerant character of Dongxiang wild rice. To elucidate the molecular genetic mechanisms of salt-stress tolerance in Dongxiang wild rice, the Illumina HiSeq 2000 platform was used to analyze the transcriptome profiles of the leaves and roots at the seedling stage under salt stress compared with those under normal conditions. The analysis results for the sequencing data showed that 6,867 transcripts were differentially expressed in the leaves (2,216 up-regulated and 4,651 down-regulated) and 4,988 transcripts in the roots (3,105 up-regulated and 1,883 down-regulated). Among these differentially expressed genes, the detection of many transcription factor genes demonstrated that multiple regulatory pathways were involved in salt stress tolerance. In addition, the differentially expressed genes were compared with the previous RNA-Seq analysis of salt-stress responses in cultivated rice Nipponbare, indicating the possible specific molecular mechanisms of salt-stress responses for Dongxiang wild rice. A large number of the salt-inducible genes identified in this study were co-localized onto fine-mapped salt-tolerance-related quantitative trait loci, providing candidates for gene cloning and elucidation of molecular mechanisms responsible for salt-stress tolerance in rice.
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Wang A, Hu J, Huang X, Li X, Zhou G, Yan Z. Comparative Transcriptome Analysis Reveals Heat-Responsive Genes in Chinese Cabbage (Brassica rapa ssp. chinensis). FRONTIERS IN PLANT SCIENCE 2016; 7:939. [PMID: 27443222 PMCID: PMC4923122 DOI: 10.3389/fpls.2016.00939] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 06/13/2016] [Indexed: 05/20/2023]
Abstract
Chinese cabbage (Brassica rapa ssp. chinensis) is an economically and agriculturally significant vegetable crop and is extensively cultivated throughout the world. Heat stress disturbs cellular homeostasis and causes visible growth inhibition of shoots and roots, severe retardation in growth and development, and even death. However, there are few studies on the transcriptome profiling of heat stress in non-heading Chinese cabbage. In this study, we investigated the transcript profiles of non-heading Chinese cabbage from heat-sensitive and heat-tolerant varieties "GHA" and "XK," respectively, in response to high temperature using RNA sequencing (RNA seq). Approximately 625 genes were differentially expressed between the two varieties. The responsive genes can be divided into three phases along with the time of heat treatment: response to stimulus, programmed cell death and ribosome biogenesis. Differentially expressed genes (DEGs) were identified in the two varieties, including transcription factors (TFs), kinases/phosphatases, genes related to photosynthesis and effectors of homeostasis. Many TFs were involved in the heat stress response of Chinese cabbage, including NAC069 TF which was up-regulated at all the heat treatment stages. And their expression levels were also validated by quantitative real-time-PCR (qRT-PCR). These candidate genes will provide genetic resources for further improving the heat-tolerant characteristics in non-heading Chinese cabbage.
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Affiliation(s)
- Aihua Wang
- Wuhan Vegetable Research Institute, Wuhan Academy of Agricultural Science and TechnologyWuhan, China
| | - Jihong Hu
- State Key Laboratory of Hybrid Rice, College of life Sciences, Wuhan UniversityWuhan, China
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesWuhan, China
| | - Xingxue Huang
- Wuhan Vegetable Research Institute, Wuhan Academy of Agricultural Science and TechnologyWuhan, China
| | - Xia Li
- Wuhan Vegetable Research Institute, Wuhan Academy of Agricultural Science and TechnologyWuhan, China
| | - Guolin Zhou
- Wuhan Vegetable Research Institute, Wuhan Academy of Agricultural Science and TechnologyWuhan, China
- *Correspondence: Guolin Zhou
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