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Zinta R, Tiwari JK, Buckseth T, Goutam U, Singh RK, Thakur AK, Singh S, Kumar V, Kumar M. Phenotypic and transcriptomics characterization uncovers genes underlying tuber yield traits and gene expression marker development in potato under aeroponics. PLANTA 2024; 260:74. [PMID: 39153022 DOI: 10.1007/s00425-024-04507-x] [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: 05/05/2024] [Accepted: 08/09/2024] [Indexed: 08/19/2024]
Abstract
MAIN CONCLUSION Transcriptome analysis in potato varieties revealed genes associated with tuber yield-related traits and developed gene expression markers. This study aimed to identify genes involved in high tuber yield and its component traits in test potato varieties (Kufri Frysona, Kufri Khyati, and Kufri Mohan) compared to control (Kufri Sutlej). The aeroponic evaluation showed significant differences in yield-related traits in the varieties. Total RNA sequencing was performed using tuber and leaf tissues on the Illumina platform. The high-quality reads (QV > 25) mapping with the reference potato genomes revealed statistically significant (P < 0.05) differentially expressed genes (DEGs) into two categories: up-regulated (> 2 Log2 fold change) and down-regulated (< -2 Log2 fold change). DEGs were characterized by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Collectively, we identified genes participating in sugar metabolism, stress response, transcription factors, phytohormones, kinase proteins, and other genes greatly affecting tuber yield and its related traits. A few selected genes were UDP-glucose glucosyltransferase, glutathion S-transferase, GDSL esterase/lipase, transcription factors (MYB, WRKY, bHLH63, and BURP), phytohormones (auxin-induced protein X10A, and GA20 oxidase), kinase proteins (Kunitz-type tuber invertase inhibitor, BRASSINOSTEROID INSENSITIVE 1-associated receptor kinase 1) and laccase. Based on the selected 17 peptide sequences representing 13 genes, a phylogeny tree and motifs were analyzed. Real time-quantitative polymerase chain reaction (RT-qPCR) analysis was used to validate the RNA-seq results. RT-qPCR based gene expression markers were developed for the genes such as 101 kDa heat shock protein, catechol oxidase B chloroplastic, cysteine protease inhibitor 1, Kunitz-type tuber invertase inhibitor, and laccase to identify high yielding potato genotypes. Thus, our study paved the path for potential genes associated with tuber yield traits in potato under aeroponics.
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Affiliation(s)
- Rasna Zinta
- Indian Council of Agricultural Research-Central Potato Research Institute, Shimla, Himachal Pradesh, India
- School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, Punjab, India
| | - Jagesh Kumar Tiwari
- Indian Council of Agricultural Research-Central Potato Research Institute, Shimla, Himachal Pradesh, India.
- Indian Council of Agricultural Research- Indian Institute of Vegetable Research, Varanasi, Uttar Pradesh, India.
| | - Tanuja Buckseth
- Indian Council of Agricultural Research-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Umesh Goutam
- School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, Punjab, India
| | - Rajesh Kumar Singh
- Indian Council of Agricultural Research-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Ajay Kumar Thakur
- Indian Council of Agricultural Research-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Shwetank Singh
- Indian Council of Agricultural Research- Indian Institute of Vegetable Research, Varanasi, Uttar Pradesh, India
| | - Vinod Kumar
- Indian Council of Agricultural Research-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Manoj Kumar
- Indian Council of Agricultural Research-Central Potato Research Institute, Shimla, Himachal Pradesh, India
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Bhatia N, Tiwari JK, Kumari C, Zinta R, Sharma S, Buckseth T, Thakur AK, Singh RK, Kumar V. Transcriptome analysis reveals genes associated with late blight resistance in potato. Sci Rep 2024; 14:15501. [PMID: 38969681 PMCID: PMC11226683 DOI: 10.1038/s41598-024-60608-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Accepted: 04/25/2024] [Indexed: 07/07/2024] Open
Abstract
Late blight is a serious disease of potato worldwide. Our study aimed to unveil genes involved in late blight resistance in potato by RNA-seq analysis after artificial inoculation under controlled conditions. In this study, two potato somatic hybrids (P7 and Crd6) and three varieties such as Kufri Girdhari, Kufri Jyoti and Kufri Bahar (control) were used. Transcriptiome analysis revealed statistically significant (p < 0.05) differentially expressed genes (DEGs), which were analysed into up-regulated and down-regulated genes. Further, DEGs were functionally characterized by the Gene Ontology annotations and the Kyoto Encyclopedia of Genes and Genomes pathways. Overall, some of the up-regulated genes in resistant genotypes were disease resistance proteins such as CC-NBS-LRR resistance protein, ankyrin repeat family protein, cytochrome P450, leucine-rich repeat family protein/protein kinase family, and MYB transcription factor. Sequence diversity analysis based on 38 peptide sequences representing 18 genes showed distinct variation and the presence of three motifs in 15 amino acid sequences. Selected genes were also validated by real-time quantitative polymerase chain reaction analysis. Interestingly, gene expression markers were developed for late blight resistant genotypes. Our study elucidates genes involved in imparting late blight resistance in potato, which will be beneficial for its management strategies in the future.
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Affiliation(s)
- Nisha Bhatia
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, India
- School of Biotechnology, Shoolini University, Solan, Himachal Pradesh, India
| | - Jagesh Kumar Tiwari
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, India.
- ICAR-Indian Institute of Vegetable Research, Varanasi, Uttar Pradesh, India.
| | - Chandresh Kumari
- School of Biotechnology, Shoolini University, Solan, Himachal Pradesh, India
| | - Rasna Zinta
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, India
- School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, Punjab, India
| | - Sanjeev Sharma
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Tanuja Buckseth
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Ajay K Thakur
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Rajesh K Singh
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Vinod Kumar
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, India
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Kumar S, Bandyopadhyay N, Saxena S, Hajare SN, More V, Tripathi J, Dahia Y, Gautam S. Differential gene expression in irradiated potato tubers contributed to sprout inhibition and quality retention during a commercial scale storage. Sci Rep 2024; 14:13484. [PMID: 38866836 PMCID: PMC11169491 DOI: 10.1038/s41598-024-58949-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 04/04/2024] [Indexed: 06/14/2024] Open
Abstract
Current study is the first ever storage cum market trial of radiation processed (28 tons) of potato conducted in India at a commercial scale. The objective was to affirm the efficacy of very low dose of gamma radiation processing of potato for extended storage with retained quality and to understand the plausible mechanism at the gene modulation level for suppression of potato sprouting. Genes pertaining to abscisic acid (ABA) biosynthesis were upregulated whereas its catabolism was downregulated in irradiated potatoes. Additionally, genes related to auxin buildup were downregulated in irradiated potatoes. The change in the endogenous phytohormone contents in irradiated potato with respect to the control were found to be correlated well with the differential expression level of certain related genes. Irradiated potatoes showed retention of processing attributes including cooking and chip-making qualities, which could be attributed to the elevated expression of invertase inhibitor in these tubers. Further, quality retention in radiation treated potatoes may also be related to inhibition in the physiological changes due to sprout inhibition. Ecological and economical analysis of national and global data showed that successful adoption of radiation processing may gradually replace sprout suppressants like isopropyl N-(3-chlorophenyl) carbamate (CIPC), known to leave residue in the commodity, stabilize the wholesale annual market price, and provide a boost to the industries involved in product manufacturing.
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Affiliation(s)
- Sanjeev Kumar
- Food Technology Division, Bhabha Atomic Research Centre, Mumbai, 400 085, India
| | | | - Sudhanshu Saxena
- Food Technology Division, Bhabha Atomic Research Centre, Mumbai, 400 085, India
| | - Sachin N Hajare
- Food Technology Division, Bhabha Atomic Research Centre, Mumbai, 400 085, India
| | - Varsha More
- Food Technology Division, Bhabha Atomic Research Centre, Mumbai, 400 085, India
| | - Jyoti Tripathi
- Food Technology Division, Bhabha Atomic Research Centre, Mumbai, 400 085, India
| | - Yogesh Dahia
- Natural Storage Solutions Private Limited, Gandhinagar, 382 729, India
| | - Satyendra Gautam
- Food Technology Division, Bhabha Atomic Research Centre, Mumbai, 400 085, India.
- Homi Bhabha National Institute, Mumbai, 400 094, India.
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Bonthala VS, Stich B. StCoExpNet: a global co-expression network analysis facilitates identifying genes underlying agronomic traits in potatoes. PLANT CELL REPORTS 2024; 43:117. [PMID: 38622429 PMCID: PMC11018665 DOI: 10.1007/s00299-024-03201-2] [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: 11/29/2023] [Accepted: 03/18/2024] [Indexed: 04/17/2024]
Abstract
KEY MESSAGE We constructed a gene expression atlas and co-expression network for potatoes and identified several novel genes associated with various agronomic traits. This resource will accelerate potato genetics and genomics research. Potato (Solanum tuberosum L.) is the world's most crucial non-cereal food crop and ranks third in food production after wheat and rice. Despite the availability of several potato transcriptome datasets at public databases like NCBI SRA, an effort has yet to be put into developing a global transcriptome atlas and a co-expression network for potatoes. The objectives of our study were to construct a global expression atlas for potatoes using publicly available transcriptome datasets, identify housekeeping and tissue-specific genes, construct a global co-expression network and identify co-expression clusters, investigate the transcriptional complexity of genes involved in various essential biological processes related to agronomic traits, and provide a web server (StCoExpNet) to easily access the newly constructed expression atlas and co-expression network to investigate the expression and co-expression of genes of interest. In this study, we used data from 2299 publicly available potato transcriptome samples obtained from 15 different tissues to construct a global transcriptome atlas. We found that roughly 87% of the annotated genes exhibited detectable expression in at least one sample. Among these, we identified 281 genes with consistent and stable expression levels, indicating their role as housekeeping genes. Conversely, 308 genes exhibited marked tissue-specific expression patterns. We exemplarily linked some co-expression clusters to important agronomic traits of potatoes, such as self-incompatibility, anthocyanin biosynthesis, tuberization, and defense responses against multiple pathogens. The dataset compiled here constitutes a new resource (StCoExpNet), which can be accessed at https://stcoexpnet.julius-kuehn.de . This transcriptome atlas and the co-expression network will accelerate potato genetics and genomics research.
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Affiliation(s)
- Venkata Suresh Bonthala
- Institute of Quantitative Genetics and Genomics of Plants, Heinrich Heine University of Düsseldorf, Düsseldorf, Germany.
| | - Benjamin Stich
- Institute of Quantitative Genetics and Genomics of Plants, Heinrich Heine University of Düsseldorf, Düsseldorf, Germany
- Julius Kühn-Institut (JKI), Institute for Breeding Research On Agricultural Crops, Rudolf-Schick-Platz 3a, OT Groß Lüsewitz, 18190, Sanitz, Germany
- Max Planck Institute for Plant Breeding Research, Köln, Germany
- Cluster of Excellence On Plant Sciences, From Complex Traits Towards Synthetic Modules, Düsseldorf, Germany
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Zinta R, Tiwari JK, Buckseth T, Goutam U, Singh RK, Kumar V, Thakur AK. Transcriptome profiling and characterization of genes associated with tuberization under high temperature in aeroponics in potato cv. Kufri Anand. Genes Genomics 2024; 46:409-421. [PMID: 38381322 DOI: 10.1007/s13258-024-01503-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Accepted: 02/02/2024] [Indexed: 02/22/2024]
Abstract
BACKGROUND High temperature stress is an important abiotic factor, which affects tuberization and ultimately causes heavy yield reduction in potato. OBJECTIVES Identification and characterization of genes associated with tuberization under high temperature stress is essential for future management through biotechnology. METHODOLOGY Two contrasting potato varieties Kufri Anand (profuse tuber-bearing) versus Kufri Frysona (very less/scanty tuber-bearing, control) were cultivated in aeroponics under high temperature stress, and transcriptomes were analyzed. RESULTS Potato cv. Kufri Anand was found superior over control (Kufri Frysona) for tuber yield and its component traits along with root morphology under aeroponics. Transcriptomes of tuber and leaf tissues were analyzed. Statistically significant (p < 0.05) differentially expressed genes (DEGs) were categorised into up-regulated (> 2 log2 fold change, FC) and down-regulated (< -2 log2 FC) genes. DEGs were annotated by gene ontology and KEGG pathways. A few selected up-regulated genes of both tissues were identified, and phylogeny tree and motif analysis were analysed based on 36 peptide sequences representing 15 selected DEGs in this study. Further, gene expression markers were developed and validated by real time qPCR analysis for the identification of high temperature tolerant genotypes. CONCLUSION A few key genes associated in tuberization under high temperature conditions were heat shock proteins (e.g. 18.5 kDa class I heat shock protein), sugar metabolism (e.g. glucosyltransferase), transcription factor (e.g. WRKY), and phytohormones (e.g. auxin-induced beta-glucosidase). Our study provides an overview of key genes involved in tuberization under high temperature stress in potato cv. Kufri Anand under aeroponics.
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Affiliation(s)
- Rasna Zinta
- Indian Council of Agricultural Research-Central Potato Research Institute, Shimla, Himachal Pradesh, India
- School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, Punjab, India
| | - Jagesh Kumar Tiwari
- Indian Council of Agricultural Research-Central Potato Research Institute, Shimla, Himachal Pradesh, India.
- ICAR-Indian Institute of Vegetable Research Institute, Varanasi, Uttar Pradesh, India.
| | - Tanuja Buckseth
- Indian Council of Agricultural Research-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Umesh Goutam
- School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, Punjab, India
| | - Rajesh Kumar Singh
- Indian Council of Agricultural Research-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Vinod Kumar
- Indian Council of Agricultural Research-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Ajay Kumar Thakur
- Indian Council of Agricultural Research-Central Potato Research Institute, Shimla, Himachal Pradesh, India
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Zhang M, Jian H, Shang L, Wang K, Wen S, Li Z, Liu R, Jia L, Huang Z, Lyu D. Transcriptome Analysis Reveals Novel Genes Potentially Involved in Tuberization in Potato. PLANTS (BASEL, SWITZERLAND) 2024; 13:795. [PMID: 38592791 PMCID: PMC10975680 DOI: 10.3390/plants13060795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Revised: 03/07/2024] [Accepted: 03/07/2024] [Indexed: 04/11/2024]
Abstract
The formation and development of tubers, the primary edible and economic organ of potatoes, directly affect their yield and quality. The regulatory network and mechanism of tuberization have been preliminarily revealed in recent years, but plenty of relevant genes remain to be discovered. A few candidate genes were provided due to the simplicity of sampling and result analysis of previous transcriptomes related to tuberization. We sequenced and thoroughly analyzed the transcriptomes of thirteen tissues from potato plants at the tuber proliferation phase to provide more reference information and gene resources. Among them, eight tissues were stolons and tubers at different developmental stages, which we focused on. Five critical periods of tuberization were selected to perform an analysis of differentially expressed genes (DEGs), according to the results of the tissue correlation. Compared with the unswollen stolons (Sto), 2751, 4897, 6635, and 9700 DEGs were detected in the slightly swollen stolons (Sto1), swollen stolons (Sto2), tubers of proliferation stage 1 (Tu1), and tubers of proliferation stage 4 (Tu4). A total of 854 transcription factors and 164 hormone pathway genes were identified in the DEGs. Furthermore, three co-expression networks associated with Sto-Sto1, Sto2-Tu1, and tubers of proliferation stages two to five (Tu2-Tu5) were built using the weighted gene co-expression network analysis (WGCNA). Thirty hub genes (HGs) and 30 hub transcription factors (HTFs) were screened and focalized in these networks. We found that five HGs were reported to regulate tuberization, and most of the remaining HGs and HTFs co-expressed with them. The orthologs of these HGs and HTFs were reported to regulate processes (e.g., flowering, cell division, hormone synthesis, metabolism and signal transduction, sucrose transport, and starch synthesis) that were also required for tuberization. Such results further support their potential to control tuberization. Our study provides insights and countless candidate genes of the regulatory network of tuberization, laying the foundation for further elucidating the genetic basis of tuber development.
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Affiliation(s)
- Meihua Zhang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing 401329, China; (M.Z.); (H.J.); (L.S.); (S.W.); (Z.L.); (R.L.); (L.J.)
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Hongju Jian
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing 401329, China; (M.Z.); (H.J.); (L.S.); (S.W.); (Z.L.); (R.L.); (L.J.)
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing 400715, China
- Chongqing Key Laboratory of Biology and Genetic Breeding for Tuber and Root Crops, Southwest University, Chongqing 400715, China
| | - Lina Shang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing 401329, China; (M.Z.); (H.J.); (L.S.); (S.W.); (Z.L.); (R.L.); (L.J.)
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Ke Wang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing 401329, China; (M.Z.); (H.J.); (L.S.); (S.W.); (Z.L.); (R.L.); (L.J.)
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Shiqi Wen
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing 401329, China; (M.Z.); (H.J.); (L.S.); (S.W.); (Z.L.); (R.L.); (L.J.)
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Zihan Li
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing 401329, China; (M.Z.); (H.J.); (L.S.); (S.W.); (Z.L.); (R.L.); (L.J.)
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Rongrong Liu
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing 401329, China; (M.Z.); (H.J.); (L.S.); (S.W.); (Z.L.); (R.L.); (L.J.)
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Lijun Jia
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing 401329, China; (M.Z.); (H.J.); (L.S.); (S.W.); (Z.L.); (R.L.); (L.J.)
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Zhenlin Huang
- Chongqing Agricultural Technical Extension Station, Chongqing 401121, China;
| | - Dianqiu Lyu
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing 401329, China; (M.Z.); (H.J.); (L.S.); (S.W.); (Z.L.); (R.L.); (L.J.)
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing 400715, China
- Chongqing Key Laboratory of Biology and Genetic Breeding for Tuber and Root Crops, Southwest University, Chongqing 400715, China
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Kaur G, Jain S, Bhushan S, Das N, Sharma M, Sharma D. Role of microRNAs and their putative mechanism in regulating potato (Solanum tuberosum L.) life cycle and response to various environmental stresses. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 207:108334. [PMID: 38219424 DOI: 10.1016/j.plaphy.2024.108334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 10/31/2023] [Accepted: 01/02/2024] [Indexed: 01/16/2024]
Abstract
The exponentially increasing population and the demand for food is inextricably linked. This has shifted global attention to improving crop plant traits to meet global food demands. Potato (Solanum tuberosum L.) is a major non-grain food crop that is grown all over the world. Currently, some of the major global potato research work focuses on the significance of microRNAs (miRNAs) in potato. miRNAs are a type of non-coding RNAs that regulate the gene expression of their target mRNA genes by cleavage and/or their translational inhibition. This suggests an essential role of miRNAs in a multitude of plant biological processes, including maintenance of genome integrity, plant growth, development and maturation, and initiation of responses to various stress conditions. Therefore, engineering miRNAs to generate stress-resistant varieties of potato may result in high yield and improved nutritional qualities. In this review, we discuss the potato miRNAs specifically known to play an essential role in the various stages of the potato life cycle, conferring stress-resistant characteristics, and modifying gene expression. This review highlights the significance of the miRNA machinery in plants, especially potato, encouraging further research into engineering miRNAs to boost crop yields and tolerance towards stress.
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Affiliation(s)
- Gurpreet Kaur
- Department of Biotechnology, Thapar Institute of Engineering and Technology, Patiala, 147004, Punjab, India
| | - Sahil Jain
- Department of Biochemistry and Molecular Biology, Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, Israel
| | - Sakshi Bhushan
- Department of Botany, Central University of Jammu, Jammu and Kashmir (UT), India
| | - Niranjan Das
- Department of Biotechnology, Thapar Institute of Engineering and Technology, Patiala, 147004, Punjab, India
| | - Munish Sharma
- Department of Plant Science, Central University of Himachal Pradesh, Shahpur Parisar, Kangra, Himachal Pradesh, India.
| | - Deepak Sharma
- Department of Plant Science, University of Manitoba, Winnipeg, MB, Canada.
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Jiang H, Qi CH, Gao HN, Feng ZQ, Wu YT, Xu XX, Cui JY, Wang XF, Lv YH, Gao WS, Jiang YM, You CX, Li YY. MdBT2 regulates nitrogen-mediated cuticular wax biosynthesis via a MdMYB106-MdCER2L1 signalling pathway in apple. NATURE PLANTS 2024; 10:131-144. [PMID: 38172573 DOI: 10.1038/s41477-023-01587-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 11/08/2023] [Indexed: 01/05/2024]
Abstract
Cuticular waxes play important roles in plant development and the interaction between plants and their environment. Researches on wax biosynthetic pathways have been reported in several plant species. Also, wax formation is closely related to environmental condition. However, the regulatory mechanism between wax and environmental factors, especially essential mineral elements, is less studied. Here we found that nitrogen (N) played a negative role in the regulation of wax synthesis in apple. We therefore analysed wax content, composition and crystals in BTB-TAZ domain protein 2 (MdBT2) overexpressing and antisense transgenic apple seedlings and found that MdBT2 could downregulate wax biosynthesis. Furthermore, R2R3-MYB transcription factor 16-like protein (MdMYB106) interacted with MdBT2, and MdBT2 mediated its ubiquitination and degradation through the 26S proteasome pathway. Finally, HXXXD-type acyl-transferase ECERIFERUM 2-like1 (MdCER2L1) was confirmed as a downstream target gene of MdMYB106. Our findings reveal an N-mediated apple wax biosynthesis pathway and lay a foundation for further study of the environmental factors associated with wax regulatory networks in apple.
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Affiliation(s)
- Han Jiang
- National Research Center for Apple Engineering and Technology, Shandong Collaborative Innovation Center of Fruit and Vegetable Quality and Efficient Production, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, China
| | - Chen-Hui Qi
- National Research Center for Apple Engineering and Technology, Shandong Collaborative Innovation Center of Fruit and Vegetable Quality and Efficient Production, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, China
| | - Huai-Na Gao
- National Research Center for Apple Engineering and Technology, Shandong Collaborative Innovation Center of Fruit and Vegetable Quality and Efficient Production, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, China
| | - Zi-Quan Feng
- National Research Center for Apple Engineering and Technology, Shandong Collaborative Innovation Center of Fruit and Vegetable Quality and Efficient Production, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, China
| | - Ya-Ting Wu
- National Research Center for Apple Engineering and Technology, Shandong Collaborative Innovation Center of Fruit and Vegetable Quality and Efficient Production, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, China
| | - Xin-Xiang Xu
- National Research Center for Apple Engineering and Technology, Shandong Collaborative Innovation Center of Fruit and Vegetable Quality and Efficient Production, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, China
- Yantai Academy of Agricultural Sciences, Yantai, China
| | - Jian-Ying Cui
- National Research Center for Apple Engineering and Technology, Shandong Collaborative Innovation Center of Fruit and Vegetable Quality and Efficient Production, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, China
| | - Xiao-Fei Wang
- National Research Center for Apple Engineering and Technology, Shandong Collaborative Innovation Center of Fruit and Vegetable Quality and Efficient Production, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, China
| | - Yan-Hui Lv
- National Research Center for Apple Engineering and Technology, Shandong Collaborative Innovation Center of Fruit and Vegetable Quality and Efficient Production, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, China
| | - Wen-Sheng Gao
- Shandong Agricultural Technology Extension Center, Jinan, China
| | - Yuan-Mao Jiang
- National Research Center for Apple Engineering and Technology, Shandong Collaborative Innovation Center of Fruit and Vegetable Quality and Efficient Production, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, China
| | - Chun-Xiang You
- National Research Center for Apple Engineering and Technology, Shandong Collaborative Innovation Center of Fruit and Vegetable Quality and Efficient Production, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, China
| | - Yuan-Yuan Li
- National Research Center for Apple Engineering and Technology, Shandong Collaborative Innovation Center of Fruit and Vegetable Quality and Efficient Production, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, China.
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Soto-Cerda BJ, Larama G, Cloutier S, Fofana B, Inostroza-Blancheteau C, Aravena G. The Genetic Dissection of Nitrogen Use-Related Traits in Flax ( Linum usitatissimum L.) at the Seedling Stage through the Integration of Multi-Locus GWAS, RNA-seq and Genomic Selection. Int J Mol Sci 2023; 24:17624. [PMID: 38139451 PMCID: PMC10743809 DOI: 10.3390/ijms242417624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 12/10/2023] [Accepted: 12/12/2023] [Indexed: 12/24/2023] Open
Abstract
Nitrogen (N), the most important macro-nutrient for plant growth and development, is a key factor that determines crop yield. Yet its excessive applications pollute the environment and are expensive. Hence, studying nitrogen use efficiency (NUE) in crops is fundamental for sustainable agriculture. Here, an association panel consisting of 123 flax accessions was evaluated for 21 NUE-related traits at the seedling stage under optimum N (N+) and N deficiency (N-) treatments to dissect the genetic architecture of NUE-related traits using a multi-omics approach integrating genome-wide association studies (GWAS), transcriptome analysis and genomic selection (GS). Root traits exhibited significant and positive correlations with NUE under N- conditions (r = 0.33 to 0.43, p < 0.05). A total of 359 QTLs were identified, accounting for 0.11% to 23.1% of the phenotypic variation in NUE-related traits. Transcriptomic analysis identified 1034 differentially expressed genes (DEGs) under contrasting N conditions. DEGs involved in N metabolism, root development, amino acid transport and catabolism and others, were found near the QTLs. GS models to predict NUE stress tolerance index (NUE_STI) trait were tested using a random genome-wide SNP dataset and a GWAS-derived QTLs dataset. The latter produced superior prediction accuracy (r = 0.62 to 0.79) compared to the genome-wide SNP marker dataset (r = 0.11) for NUE_STI. Our results provide insights into the QTL architecture of NUE-related traits, identify candidate genes for further studies, and propose genomic breeding tools to achieve superior NUE in flax under low N input.
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Affiliation(s)
- Braulio J. Soto-Cerda
- Departamento de Ciencias Agropecuarias y Acuícolas, Universidad Católica de Temuco, Rudecindo Ortega 02950, Temuco 4781312, Chile; (C.I.-B.); (G.A.)
- Núcleo de Investigación en Producción Alimentaria, Facultad de Recursos Naturales, Universidad Católica de Temuco, Rudecindo Ortega 02950, Temuco 4781312, Chile
| | - Giovanni Larama
- Center of Plant, Soil Interaction and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco 4811230, Chile;
- Biocontrol Research Laboratory, Universidad de La Frontera, Temuco 4811230, Chile
| | - Sylvie Cloutier
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON K1A 0C6, Canada;
| | - Bourlaye Fofana
- Charlottetown Research and Development Centre, Agriculture and Agri-Food Canada, 440 University Avenue, Charlottetown, PE C1A 4N6, Canada
| | - Claudio Inostroza-Blancheteau
- Departamento de Ciencias Agropecuarias y Acuícolas, Universidad Católica de Temuco, Rudecindo Ortega 02950, Temuco 4781312, Chile; (C.I.-B.); (G.A.)
- Núcleo de Investigación en Producción Alimentaria, Facultad de Recursos Naturales, Universidad Católica de Temuco, Rudecindo Ortega 02950, Temuco 4781312, Chile
| | - Gabriela Aravena
- Departamento de Ciencias Agropecuarias y Acuícolas, Universidad Católica de Temuco, Rudecindo Ortega 02950, Temuco 4781312, Chile; (C.I.-B.); (G.A.)
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Agho CA, Kaurilind E, Tähtjärv T, Runno-Paurson E, Niinemets Ü. Comparative transcriptome profiling of potato cultivars infected by late blight pathogen Phytophthora infestans: Diversity of quantitative and qualitative responses. Genomics 2023; 115:110678. [PMID: 37406973 PMCID: PMC10548088 DOI: 10.1016/j.ygeno.2023.110678] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 06/30/2023] [Accepted: 07/02/2023] [Indexed: 07/07/2023]
Abstract
The Estonia potato cultivar Ando has shown elevated field resistance to Phytophthora infestans, even after being widely grown for over 40 years. A comprehensive transcriptional analysis was performed using RNA-seq from plant leaf tissues to gain insight into the mechanisms activated for the defense after infection. Pathogen infection in Ando resulted in about 5927 differentially expressed genes (DEGs) compared to 1161 DEGs in the susceptible cultivar Arielle. The expression levels of genes related to plant disease resistance such as serine/threonine kinase activity, signal transduction, plant-pathogen interaction, endocytosis, autophagy, mitogen-activated protein kinase (MAPK), and others were significantly enriched in the upregulated DEGs in Ando, whereas in the susceptible cultivar, only the pathway related to phenylpropanoid biosynthesis was enriched in the upregulated DEGs. However, in response to infection, photosynthesis was deregulated in Ando. Multi-signaling pathways of the salicylic-jasmonic-ethylene biosynthesis pathway were also activated in response to Phytophthora infestans infection.
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Affiliation(s)
- C A Agho
- Chair of Crop Science and Plant Biology, Estonian University of Life Sciences, Kreutzwaldi 1, Tartu 51006, Estonia.
| | - E Kaurilind
- Chair of Crop Science and Plant Biology, Estonian University of Life Sciences, Kreutzwaldi 1, Tartu 51006, Estonia
| | - T Tähtjärv
- Centre of Estonian Rural Research and Knowledge, J. Aamisepa 1, 48309 Jõgeva, Estonia
| | - E Runno-Paurson
- Chair of Crop Science and Plant Biology, Estonian University of Life Sciences, Kreutzwaldi 1, Tartu 51006, Estonia
| | - Ü Niinemets
- Chair of Crop Science and Plant Biology, Estonian University of Life Sciences, Kreutzwaldi 1, Tartu 51006, Estonia; Estonian Academy of Sciences, Kohtu 6, Tallinn 10130, Estonia
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Li H, Wang Q, Huang T, Liu J, Zhang P, Li L, Xie H, Wang H, Liu C, Qin P. Transcriptome and Metabolome Analyses Reveal Mechanisms Underlying the Response of Quinoa Seedlings to Nitrogen Fertilizers. Int J Mol Sci 2023; 24:11580. [PMID: 37511340 PMCID: PMC10380953 DOI: 10.3390/ijms241411580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 07/09/2023] [Accepted: 07/14/2023] [Indexed: 07/30/2023] Open
Abstract
Quinoa (Chenopodium quinoa Willd.) is a dicotyledonous annual amaranth herb that belongs to the family Chenopodiaceae. Quinoa can be cultivated across a wide range of climatic conditions. With regard to its cultivation, nitrogen-based fertilizers have a demonstrable effect on the growth and development of quinoa. How crops respond to the application of nitrogen affects grain quality and yield. Therefore, to explore the regulatory mechanisms that underlie the responses of quinoa seedlings to the application of nitrogen, we selected two varieties (i.e., Dianli-1299 and Dianli-71) of quinoa seedlings and analyzed them using metabolomic and transcriptomic techniques. Specifically, we studied the mechanisms underlying the responses of quinoa seedlings to varying concentrations of nitrogen by analyzing the dynamics of metabolites and genes involved in arginine biosynthesis; carbon fixation; and alanine, aspartate, and glutamate biosynthetic pathways. Overall, we found that differentially expressed genes (DEGs) and differentially expressed metabolites (DEMs) of quinoa are affected by the concentration of nitrogen. We detected 1057 metabolites, and 29,012 genes were annotated for the KEGG. We also found that 15 DEMs and 8 DEGs were key determinants of the differences observed in quinoa seedlings under different nitrogen concentrations. These contribute toward a deeper understanding of the metabolic processes of plants under different nitrogen treatments and provide a theoretical basis for improving the nitrogen use efficiency (NUE) of quinoa.
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Affiliation(s)
- Hanxue Li
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China
| | - Qianchao Wang
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China
| | - Tingzhi Huang
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China
| | - Junna Liu
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China
| | - Ping Zhang
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China
| | - Li Li
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China
| | - Heng Xie
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China
| | - Hongxin Wang
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China
| | - Chenghong Liu
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotech Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China
| | - Peng Qin
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China
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Bhatia N, Tiwari JK, Kumari C, Zinta R, Sharma S, Thakur AK, Buckseth T, Dalamu D, Singh RK, Kumar V. Screening of wild species and transcriptome profiling to identify differentially regulated genes in response to late blight resistance in potato. FRONTIERS IN PLANT SCIENCE 2023; 14:1212135. [PMID: 37502703 PMCID: PMC10368984 DOI: 10.3389/fpls.2023.1212135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 06/27/2023] [Indexed: 07/29/2023]
Abstract
Late blight (Phytophthora infestans) is a serious disease of potatoes. The aim of this study was to screen wild potato species and identify differentially expressed genes (DEGs) associated with late blight resistance. Wild potato species such as PIN45 (Solanum pinnatisectum), CPH62 (Solanum cardiophyllum), JAM07 (Solanum jamesii), MCD24 (Solanum microdontum), PLD47 (Solanum polyadenium), and cv. Kufri Bahar (control) were tested by artificial inoculation of P. infestans under controlled conditions. Transcriptomes of the leaf tissues (96 h post-inoculation) were sequenced using the Illumina platform. Statistically significant (p < 0.05) DEGs were analyzed in wild species by comparison with the control, and upregulated (>2 log2 fold change, FC) and downregulated (<-2 log2 FC) genes were identified. DEGs were functionally characterized with Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Selected genes were validated by real-time PCR analysis to confirm RNA-seq results. We identified some upregulated genes associated with late blight resistance in wild species such as cytochrome P450, proline-rich protein, MYB transcription factor MYB139, ankyrin repeat-containing protein, and LRR receptor-like serine/threonine-protein kinase in PIN45; glucosyltransferase, fructose-bisphosphate aldolase, and phytophthora-inhibited protease 1 in CPH62; steroid binding protein and cysteine proteinase 3 in JAM07; glycine-rich cell wall structural protein 1 and RING finger protein in MCD24; and cysteine proteinase 3 and major latex protein in PLD47. On the other hand, downregulated genes in these species were snakin-2 and WRKY transcription factor 3 in PIN45; lichenase and phenylalanine ammonia-lyase 1 in CPH62; metallothionein and LRR receptor-like serine/threonine-protein kinase in JAM07; UDP-glucoronosyl/UDP-glucosyl transferase family protein and steroid binding protein in MCD24; and cytoplasmic small heat shock protein class I and phosphatase PLD47. Our study identified highly resistant wild potato species and underlying genes such as disease resistance, stress response, phytohormones, and transcription factors (e.g., MYB, WRKY, AP2/ERF, and AN1) associated with late blight resistance in wild potato species.
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Affiliation(s)
- Nisha Bhatia
- Division of Crop Improvement, Indian Council of Agricultural Research—Central Potato Research Institute, Shimla, Himachal Pradesh, India
- School of Biotechnology, Shoolini University, Solan, Himachal Pradesh, India
| | - Jagesh Kumar Tiwari
- Division of Crop Improvement, Indian Council of Agricultural Research—Central Potato Research Institute, Shimla, Himachal Pradesh, India
- Division of Vegetable Improvement, Indian Council of Agricultural Research—Indian Institute of Vegetable Research, Varanasi, Uttar Pradesh, India
| | - Chandresh Kumari
- School of Biotechnology, Shoolini University, Solan, Himachal Pradesh, India
| | - Rasna Zinta
- Division of Crop Improvement, Indian Council of Agricultural Research—Central Potato Research Institute, Shimla, Himachal Pradesh, India
- School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, Punjab, India
| | - Sanjeev Sharma
- Division of Crop Improvement, Indian Council of Agricultural Research—Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Ajay Kumar Thakur
- Division of Crop Improvement, Indian Council of Agricultural Research—Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Tanuja Buckseth
- Division of Crop Improvement, Indian Council of Agricultural Research—Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Dalamu Dalamu
- Division of Crop Improvement, Indian Council of Agricultural Research—Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Rajesh Kumar Singh
- Division of Crop Improvement, Indian Council of Agricultural Research—Central Potato Research Institute, Shimla, Himachal Pradesh, India
- Division of Vegetable Improvement, Indian Council of Agricultural Research—Indian Institute of Vegetable Research, Varanasi, Uttar Pradesh, India
| | - Vinod Kumar
- Division of Crop Improvement, Indian Council of Agricultural Research—Central Potato Research Institute, Shimla, Himachal Pradesh, India
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Roychowdhury R, Das SP, Gupta A, Parihar P, Chandrasekhar K, Sarker U, Kumar A, Ramrao DP, Sudhakar C. Multi-Omics Pipeline and Omics-Integration Approach to Decipher Plant's Abiotic Stress Tolerance Responses. Genes (Basel) 2023; 14:1281. [PMID: 37372461 PMCID: PMC10298225 DOI: 10.3390/genes14061281] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 06/03/2023] [Accepted: 06/14/2023] [Indexed: 06/29/2023] Open
Abstract
The present day's ongoing global warming and climate change adversely affect plants through imposing environmental (abiotic) stresses and disease pressure. The major abiotic factors such as drought, heat, cold, salinity, etc., hamper a plant's innate growth and development, resulting in reduced yield and quality, with the possibility of undesired traits. In the 21st century, the advent of high-throughput sequencing tools, state-of-the-art biotechnological techniques and bioinformatic analyzing pipelines led to the easy characterization of plant traits for abiotic stress response and tolerance mechanisms by applying the 'omics' toolbox. Panomics pipeline including genomics, transcriptomics, proteomics, metabolomics, epigenomics, proteogenomics, interactomics, ionomics, phenomics, etc., have become very handy nowadays. This is important to produce climate-smart future crops with a proper understanding of the molecular mechanisms of abiotic stress responses by the plant's genes, transcripts, proteins, epigenome, cellular metabolic circuits and resultant phenotype. Instead of mono-omics, two or more (hence 'multi-omics') integrated-omics approaches can decipher the plant's abiotic stress tolerance response very well. Multi-omics-characterized plants can be used as potent genetic resources to incorporate into the future breeding program. For the practical utility of crop improvement, multi-omics approaches for particular abiotic stress tolerance can be combined with genome-assisted breeding (GAB) by being pyramided with improved crop yield, food quality and associated agronomic traits and can open a new era of omics-assisted breeding. Thus, multi-omics pipelines together are able to decipher molecular processes, biomarkers, targets for genetic engineering, regulatory networks and precision agriculture solutions for a crop's variable abiotic stress tolerance to ensure food security under changing environmental circumstances.
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Affiliation(s)
- Rajib Roychowdhury
- Department of Plant Pathology and Weed Research, Institute of Plant Protection, Agricultural Research Organization (ARO)—The Volcani Institute, Rishon Lezion 7505101, Israel
| | - Soumya Prakash Das
- School of Bioscience, Seacom Skills University, Bolpur 731236, West Bengal, India
| | - Amber Gupta
- Dr. Vikram Sarabhai Institute of Cell and Molecular Biology, Faculty of Science, Maharaja Sayajirao University of Baroda, Vadodara 390002, Gujarat, India
| | - Parul Parihar
- Department of Biotechnology and Bioscience, Banasthali Vidyapith, Banasthali 304022, Rajasthan, India
| | - Kottakota Chandrasekhar
- Department of Plant Biochemistry and Biotechnology, Sri Krishnadevaraya College of Agricultural Sciences (SKCAS), Affiliated to Acharya N.G. Ranga Agricultural University (ANGRAU), Guntur 522034, Andhra Pradesh, India
| | - Umakanta Sarker
- Department of Genetics and Plant Breeding, Faculty of Agriculture, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur 1706, Bangladesh
| | - Ajay Kumar
- Department of Botany, Maharshi Vishwamitra (M.V.) College, Buxar 802102, Bihar, India
| | - Devade Pandurang Ramrao
- Department of Biotechnology, Mizoram University, Pachhunga University College Campus, Aizawl 796001, Mizoram, India
| | - Chinta Sudhakar
- Plant Molecular Biology Laboratory, Department of Botany, Sri Krishnadevaraya University, Anantapur 515003, Andhra Pradesh, India
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Alam I, Zhang H, Du H, Rehman NU, Manghwar H, Lei X, Batool K, Ge L. Bioengineering Techniques to Improve Nitrogen Transformation and Utilization: Implications for Nitrogen Use Efficiency and Future Sustainable Crop Production. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:3921-3938. [PMID: 36842151 DOI: 10.1021/acs.jafc.2c08051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Nitrogen (N) is crucial for plant growth and development, especially in physiological and biochemical processes such as component of different proteins, enzymes, nucleic acids, and plant growth regulators. Six categories, such as transporters, nitrate absorption, signal molecules, amino acid biosynthesis, transcription factors, and miscellaneous genes, broadly encompass the genes regulating NUE in various cereal crops. Herein, we outline detailed research on bioengineering modifications of N metabolism to improve the different crop yields and biomass. We emphasize effective and precise molecular approaches and technologies, including N transporters, transgenics, omics, etc., which are opening up fascinating opportunities for a complete analysis of the molecular elements that contribute to NUE. Moreover, the detection of various types of N compounds and associated signaling pathways within plant organs have been discussed. Finally, we highlight the broader impacts of increasing NUE in crops, crucial for better agricultural yield and in the greater context of global climate change.
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Affiliation(s)
- Intikhab Alam
- College of Forestry and Landscape Architecture, Department of Grassland Science, South China Agricultural University (SCAU), Guangzhou 510642, China
- College of Life Sciences, SCAU, Guangzhou 510642, China
- Guangdong Subcenter of the National Center for Soybean Improvement, SCAU, Guangzhou 510642, China
| | - Hanyin Zhang
- College of Forestry and Landscape Architecture, Department of Grassland Science, South China Agricultural University (SCAU), Guangzhou 510642, China
- Guangdong Subcenter of the National Center for Soybean Improvement, SCAU, Guangzhou 510642, China
| | - Huan Du
- College of Forestry and Landscape Architecture, Department of Grassland Science, South China Agricultural University (SCAU), Guangzhou 510642, China
- College of Life Sciences, SCAU, Guangzhou 510642, China
- Guangdong Subcenter of the National Center for Soybean Improvement, SCAU, Guangzhou 510642, China
| | - Naveed Ur Rehman
- Guangdong Subcenter of the National Center for Soybean Improvement, SCAU, Guangzhou 510642, China
| | - Hakim Manghwar
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry and Landscape Architecture, SCAU, Guangzhou 510642, China
| | - Xiao Lei
- College of Forestry and Landscape Architecture, Department of Grassland Science, South China Agricultural University (SCAU), Guangzhou 510642, China
- Guangdong Subcenter of the National Center for Soybean Improvement, SCAU, Guangzhou 510642, China
| | - Khadija Batool
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Liangfa Ge
- College of Forestry and Landscape Architecture, Department of Grassland Science, South China Agricultural University (SCAU), Guangzhou 510642, China
- Guangdong Subcenter of the National Center for Soybean Improvement, SCAU, Guangzhou 510642, China
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Sunseri F, Aci MM, Mauceri A, Caldiero C, Puccio G, Mercati F, Abenavoli MR. Short-term transcriptomic analysis at organ scale reveals candidate genes involved in low N responses in NUE-contrasting tomato genotypes. FRONTIERS IN PLANT SCIENCE 2023; 14:1125378. [PMID: 36938018 PMCID: PMC10020590 DOI: 10.3389/fpls.2023.1125378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 02/13/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Understanding the complex regulatory network underlying plant nitrogen (N) responses associated with high Nitrogen Use Efficiency (NUE) is one of the main challenges for sustainable cropping systems. Nitrate (NO3 -), acting as both an N source and a signal molecule, provokes very fast transcriptome reprogramming, allowing plants to adapt to its availability. These changes are genotype- and tissue-specific; thus, the comparison between contrasting genotypes is crucial to uncovering high NUE mechanisms. METHODS Here, we compared, for the first time, the spatio-temporal transcriptome changes in both root and shoot of two NUE contrasting tomato genotypes, Regina Ostuni (high-NUE) and UC82 (low-NUE), in response to short-term (within 24 h) low (LN) and high (HN) NO3 - resupply. RESULTS Using time-series transcriptome data (0, 8, and 24 h), we identified 395 and 482 N-responsive genes differentially expressed (DEGs) between RO and UC82 in shoot and root, respectively. Protein kinase signaling plant hormone signal transduction, and phenylpropanoid biosynthesis were the main enriched metabolic pathways in shoot and root, respectively, and were upregulated in RO compared to UC82. Interestingly, several N transporters belonging to NRT and NPF families, such as NRT2.3, NRT2.4, NPF1.2, and NPF8.3, were found differentially expressed between RO and UC82 genotypes, which might explain the contrasting NUE performances. Transcription factors (TFs) belonging to several families, such as ERF, LOB, GLK, NFYB, ARF, Zinc-finger, and MYB, were differentially expressed between genotypes in response to LN. A complementary Weighted Gene Co-expression Network Analysis (WGCNA) allowed the identification of LN-responsive co-expression modules in RO shoot and root. The regulatory network analysis revealed candidate genes that might have key functions in short-term LN regulation. In particular, an asparagine synthetase (ASNS), a CBL-interacting serine/threonine-protein kinase 1 (CIPK1), a cytokinin riboside 5'-monophosphate phosphoribohydrolase (LOG8), a glycosyltransferase (UGT73C4), and an ERF2 were identified in the shoot, while an LRR receptor-like serine/threonine-protein kinase (FEI1) and two TFs NF-YB5 and LOB37 were identified in the root. DISCUSSION Our results revealed potential candidate genes that independently and/or concurrently may regulate short-term low-N response, suggesting a key role played by cytokinin and ROS balancing in early LN regulation mechanisms adopted by the N-use efficient genotype RO.
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Affiliation(s)
- Francesco Sunseri
- Dipartimento Agraria, Università Mediterranea di Reggio Calabria, Reggio Calabria, Italy
- National Research Council of Italy, Institute of Biosciences and Bioresources (CNR-IBBR), Palermo, Italy
| | - Meriem Miyassa Aci
- Dipartimento Agraria, Università Mediterranea di Reggio Calabria, Reggio Calabria, Italy
| | - Antonio Mauceri
- Dipartimento Agraria, Università Mediterranea di Reggio Calabria, Reggio Calabria, Italy
| | - Ciro Caldiero
- Dipartimento Agraria, Università Mediterranea di Reggio Calabria, Reggio Calabria, Italy
| | - Guglielmo Puccio
- National Research Council of Italy, Institute of Biosciences and Bioresources (CNR-IBBR), Palermo, Italy
- Dipartimento di Scienze Agrarie, Alimentari e Forestali, Università degli Studi di Palermo, Viale delle Scienze, Palermo, Italy
| | - Francesco Mercati
- National Research Council of Italy, Institute of Biosciences and Bioresources (CNR-IBBR), Palermo, Italy
| | - Maria Rosa Abenavoli
- Dipartimento Agraria, Università Mediterranea di Reggio Calabria, Reggio Calabria, Italy
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Wellpott K, Jozefowicz AM, Meise P, Schum A, Seddig S, Mock HP, Winkelmann T, Bündig C. Combined nitrogen and drought stress leads to overlapping and unique proteomic responses in potato. PLANTA 2023; 257:58. [PMID: 36795167 PMCID: PMC9935667 DOI: 10.1007/s00425-023-04085-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 01/31/2023] [Indexed: 06/18/2023]
Abstract
Nitrogen deficient and drought-tolerant or sensitive potatoes differ in proteomic responses under combined (NWD) and individual stresses. The sensitive genotype 'Kiebitz' exhibits a higher abundance of proteases under NWD. Abiotic stresses such as N deficiency and drought affect the yield of Solanum tuberosum L. tremendously. Therefore, it is of importance to improve potato genotypes in terms of stress tolerance. In this study, we identified differentially abundant proteins (DAPs) in four starch potato genotypes under N deficiency (ND), drought stress (WD), or combined stress (NWD) in two rain-out shelter experiments. The gel-free LC-MS analysis generated a set of 1177 identified and quantified proteins. The incidence of common DAPs in tolerant and sensitive genotypes under NWD indicates general responses to this stress combination. Most of these proteins were part of the amino acid metabolism (13.9%). Three isoforms of S-adenosyl methionine synthase (SAMS) were found to be lower abundant in all genotypes. As SAMS were found upon application of single stresses as well, these proteins appear to be part of the general stress response in potato. Interestingly, the sensitive genotype 'Kiebitz' showed a higher abundance of three proteases (subtilase, carboxypeptidase, subtilase family protein) and a lower abundance of a protease inhibitor (stigma expressed protein) under NWD stress compared to control plants. The comparably tolerant genotype 'Tomba', however, displayed lower abundances of proteases. This indicates a better coping strategy for the tolerant genotype and a quicker reaction to WD when previously stressed with ND.
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Affiliation(s)
- Katharina Wellpott
- Department of Woody Plant and Propagation Physiology, Institute of Horticultural Production Systems, Leibniz University Hannover, Herrenhäuser Straße 2, 30419, Hannover, Germany
| | - Anna M Jozefowicz
- Applied Biochemistry, Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstr. 3, 06466, Seeland, Germany
| | - Philipp Meise
- Institute for Resistance Research and Stress Tolerance, Julius-Kühn-Institute (JKI), Bundesforschungsinstitut Für Kulturpflanzen, Rudolf-Schick-Platz 3a, 18190, Sanitz, Germany
| | - Annegret Schum
- Institute for Resistance Research and Stress Tolerance, Julius-Kühn-Institute (JKI), Bundesforschungsinstitut Für Kulturpflanzen, Rudolf-Schick-Platz 3a, 18190, Sanitz, Germany
| | - Sylvia Seddig
- Institute for Resistance Research and Stress Tolerance, Julius-Kühn-Institute (JKI), Bundesforschungsinstitut Für Kulturpflanzen, Rudolf-Schick-Platz 3a, 18190, Sanitz, Germany
| | - Hans-Peter Mock
- Applied Biochemistry, Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstr. 3, 06466, Seeland, Germany
- Universidad de Costa Rica, CIGRAS, 11501-2060, San Pedro, Costa Rica
| | - Traud Winkelmann
- Department of Woody Plant and Propagation Physiology, Institute of Horticultural Production Systems, Leibniz University Hannover, Herrenhäuser Straße 2, 30419, Hannover, Germany
| | - Christin Bündig
- Department of Woody Plant and Propagation Physiology, Institute of Horticultural Production Systems, Leibniz University Hannover, Herrenhäuser Straße 2, 30419, Hannover, Germany.
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Naqvi RZ, Siddiqui HA, Mahmood MA, Najeebullah S, Ehsan A, Azhar M, Farooq M, Amin I, Asad S, Mukhtar Z, Mansoor S, Asif M. Smart breeding approaches in post-genomics era for developing climate-resilient food crops. FRONTIERS IN PLANT SCIENCE 2022; 13:972164. [PMID: 36186056 PMCID: PMC9523482 DOI: 10.3389/fpls.2022.972164] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 08/15/2022] [Indexed: 06/16/2023]
Abstract
Improving the crop traits is highly required for the development of superior crop varieties to deal with climate change and the associated abiotic and biotic stress challenges. Climate change-driven global warming can trigger higher insect pest pressures and plant diseases thus affecting crop production sternly. The traits controlling genes for stress or disease tolerance are economically imperative in crop plants. In this scenario, the extensive exploration of available wild, resistant or susceptible germplasms and unraveling the genetic diversity remains vital for breeding programs. The dawn of next-generation sequencing technologies and omics approaches has accelerated plant breeding by providing the genome sequences and transcriptomes of several plants. The availability of decoded plant genomes offers an opportunity at a glance to identify candidate genes, quantitative trait loci (QTLs), molecular markers, and genome-wide association studies that can potentially aid in high throughput marker-assisted breeding. In recent years genomics is coupled with marker-assisted breeding to unravel the mechanisms to harness better better crop yield and quality. In this review, we discuss the aspects of marker-assisted breeding and recent perspectives of breeding approaches in the era of genomics, bioinformatics, high-tech phonemics, genome editing, and new plant breeding technologies for crop improvement. In nutshell, the smart breeding toolkit in the post-genomics era can steadily help in developing climate-smart future food crops.
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Rutkovskaya EA, Gancheva MS, Lebedeva MA, Lutova LA. Identification and Expression Analysis of CEP Genes in Potato. RUSS J GENET+ 2022. [DOI: 10.1134/s1022795422060072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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19
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Kumar P, Eriksen RL, Simko I, Shi A, Mou B. Insights into nitrogen metabolism in the wild and cultivated lettuce as revealed by transcriptome and weighted gene co-expression network analysis. Sci Rep 2022; 12:9852. [PMID: 35701518 PMCID: PMC9197935 DOI: 10.1038/s41598-022-13954-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Accepted: 05/31/2022] [Indexed: 11/08/2022] Open
Abstract
Large amounts of nitrogen fertilizers applied during lettuce (Lactuca sativa L.) production are lost due to leaching or volatilization, causing severe environmental pollution and increased costs of production. Developing lettuce varieties with high nitrogen use efficiency (NUE) is the eco-friendly solution to reduce nitrogen pollution. Hence, in-depth knowledge of nitrogen metabolism and assimilation genes and their regulation is critical for developing high NUE varieties. In this study, we performed comparative transcriptomic analysis of the cultivated lettuce (L. sativa L.) and its wild progenitor (L. serriola) under high and low nitrogen conditions. A total of 2,704 differentially expressed genes were identified. Key enriched biological processes included photosynthesis, oxidation-reduction process, chlorophyll biosynthetic process, and cell redox homeostasis. The transcription factors (TFs) belonging to the ethylene responsive factor family and basic helix-loop-helix family were among the top differentially expressed TFs. Using weighted gene co-expression network analysis we constructed nine co-expression modules. Among these, two modules were further investigated because of their significant association with total nitrogen content and photosynthetic efficiency of photosystem II. Three highly correlated clusters were identified which included hub genes for nitrogen metabolism, secondary metabolites, and carbon assimilation, and were regulated by cluster specific TFs. We found that the expression of nitrogen transportation and assimilation genes varied significantly between the two lettuce species thereby providing the opportunity of introgressing wild alleles into the cultivated germplasm for developing lettuce cultivars with more efficient use of nitrogen.
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Affiliation(s)
- Pawan Kumar
- Crop Improvement and Protection Research Unit, USDA-ARS, 1636 E Alisal St, Salinas, CA, 93905, USA.
| | - Renee L Eriksen
- Forage Seed and Cereal Research Unit, USDA-ARS, 3450 SW Campus Way, Corvallis, OR, 97331, USA
| | - Ivan Simko
- Crop Improvement and Protection Research Unit, USDA-ARS, 1636 E Alisal St, Salinas, CA, 93905, USA
| | - Ainong Shi
- Department of Horticulture, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Beiquan Mou
- Crop Improvement and Protection Research Unit, USDA-ARS, 1636 E Alisal St, Salinas, CA, 93905, USA
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20
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Guo H, Pu X, Jia H, Zhou Y, Ye G, Yang Y, Na T, Wang J. Transcriptome analysis reveals multiple effects of nitrogen accumulation and metabolism in the roots, shoots, and leaves of potato (Solanum tuberosum L.). BMC PLANT BIOLOGY 2022; 22:282. [PMID: 35676629 PMCID: PMC9178895 DOI: 10.1186/s12870-022-03652-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 05/16/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Nitrogen (N) is a major element and fundamental constituent of grain yield. N fertilizer plays an essential role in the roots, shoots, and leaves of crop plants. Here, we obtained two N-sensitive potato cultivars. RESULTS The plants were cultivated in the pots using N-deficient and N-sufficient conditions. Crop height, leaf chlorophyll content, dry matter, and N-accumulation significantly decreased under N-deficient conditions. Furthermore, we performed a comprehensive analysis of the phenotype and transcriptome, GO terms, and KEGG pathways. We used WGCNA of co-expressed genes, and 116 differentially expressed hub genes involved in photosynthesis, nitrogen metabolism, and secondary metabolites to generate 23 modules. Among those modules, six NRT gene families, four pigment genes, two auxin-related genes, and two energy-related genes were selected for qRT-PCR validation. CONCLUSIONS Overall, our study demonstrates the co-expressed genes and potential pathways associated with N transport and accumulation in potato cultivars' roots, shoots, and leaves under N-deficient conditions. Therefore, this study provides new ideas to conduct further research on improving nitrogen use efficiency in potatoes.
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Affiliation(s)
- Heng Guo
- Qinghai University/Qinghai Academy of Agriculture and Forestry Sciences/Northwest potato Engineering Research Center of Ministry of Education/Key Laboratory of Qinghai-Tibetan Plateau Biotechnology of Ministry of Education, Xining, 810016 Qinghai China
| | - Xiuqin Pu
- Qinghai University/Qinghai Academy of Agriculture and Forestry Sciences/Northwest potato Engineering Research Center of Ministry of Education/Key Laboratory of Qinghai-Tibetan Plateau Biotechnology of Ministry of Education, Xining, 810016 Qinghai China
| | - Hao Jia
- Qinghai University/Qinghai Academy of Agriculture and Forestry Sciences/Northwest potato Engineering Research Center of Ministry of Education/Key Laboratory of Qinghai-Tibetan Plateau Biotechnology of Ministry of Education, Xining, 810016 Qinghai China
| | - Yun Zhou
- Qinghai University/Qinghai Academy of Agriculture and Forestry Sciences/Northwest potato Engineering Research Center of Ministry of Education/Key Laboratory of Qinghai-Tibetan Plateau Biotechnology of Ministry of Education, Xining, 810016 Qinghai China
| | - Guangji Ye
- Qinghai University/Qinghai Academy of Agriculture and Forestry Sciences/Northwest potato Engineering Research Center of Ministry of Education/Key Laboratory of Qinghai-Tibetan Plateau Biotechnology of Ministry of Education, Xining, 810016 Qinghai China
| | - Yongzhi Yang
- Qinghai University/Qinghai Academy of Agriculture and Forestry Sciences/Northwest potato Engineering Research Center of Ministry of Education/Key Laboratory of Qinghai-Tibetan Plateau Biotechnology of Ministry of Education, Xining, 810016 Qinghai China
| | - Tiancang Na
- Qinghai University/Qinghai Academy of Agriculture and Forestry Sciences/Northwest potato Engineering Research Center of Ministry of Education/Key Laboratory of Qinghai-Tibetan Plateau Biotechnology of Ministry of Education, Xining, 810016 Qinghai China
| | - Jian Wang
- Qinghai University/Qinghai Academy of Agriculture and Forestry Sciences/Northwest potato Engineering Research Center of Ministry of Education/Key Laboratory of Qinghai-Tibetan Plateau Biotechnology of Ministry of Education, Xining, 810016 Qinghai China
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21
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Rasool F, Khan MR, Schneider M, Uzair M, Aqeel M, Ajmal W, Léon J, Naz AA. Transcriptome unveiled the gene expression patterns of root architecture in drought-tolerant and sensitive wheat genotypes. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 178:20-30. [PMID: 35247694 DOI: 10.1016/j.plaphy.2022.02.025] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 01/26/2022] [Accepted: 02/27/2022] [Indexed: 06/14/2023]
Abstract
Drought is a big challenge for agricultural production. Root attributes are the important target traits for breeding high-yielding sustainable wheat varieties against ever changing climatic conditions. However, the transcriptomic of wheat concerning root architecture remained obscure. Here, we explored RNA-Seq based transcriptome to dissect putative genes involved in root system variations in naturally occurring six genotypes (drought-tolerant and sensitive) of wheat. Global RNA-Seq based root transcriptome analysis revealed single nucleotide polymorphisms (SNPs) variations and differentially expressed genes. Putative 56 SNPs were identified related to 15 genes involved in root architecture. Enrichment of these genes using GO terms demonstrated that differentially expressed genes (DEGs) are divided into sub-categories implicated in molecular functions, cellular components and biological processes. The KEGG analysis of DEGs in each comparison of genotype include metabolic, biosynthesis of secondary metabolites, microbial metabolism in diverse environments and biosynthesis of antibiotics. A deeper insight into DEGs unveiled various pathways involved in drought response and positive gravitropism. These genes belong to various transcription factor families such as DOF, C3H, MYB, and NAC involved in root developmental and stress-related pathways. Local White and UZ-11-CWA-8, which are drought-tolerant genotypes, harbor over-representation of most of DEGs or transcription factors. Notably, a microtubule-associated protein MAPRE1 belonging to RP/EB family recruited in positive gravitropism was enriched. Real-time PCR analysis revealed expression of MAPRE1 and PAL genes is consistent with RNA-seq data. The presented data and genetic resources seem valuable for providing genes involved in the root system architecture of drought-tolerant and susceptible genotypes.
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Affiliation(s)
- Fatima Rasool
- Genome Editing & Sequencing Lab, National Centre for Bioinformatics, Quaid-i-Azam University, Islamabad, 45320, Pakistan; National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre, Park Road, Islamabad, 45500, Pakistan
| | - Muhammad Ramzan Khan
- Genome Editing & Sequencing Lab, National Centre for Bioinformatics, Quaid-i-Azam University, Islamabad, 45320, Pakistan; National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre, Park Road, Islamabad, 45500, Pakistan.
| | - Michael Schneider
- Institute of Crop Science and Resource Conservation (INRES), Department of Crop Genetics and Biotechnology, Rheinische Friedrich-Wilhelms University of Bonn, Germany
| | - Muhammad Uzair
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre, Park Road, Islamabad, 45500, Pakistan
| | - Muhammad Aqeel
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre, Park Road, Islamabad, 45500, Pakistan
| | - Wajya Ajmal
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre, Park Road, Islamabad, 45500, Pakistan
| | - Jens Léon
- Institute of Crop Science and Resource Conservation (INRES), Department of Crop Genetics and Biotechnology, Rheinische Friedrich-Wilhelms University of Bonn, Germany
| | - Ali Ahmed Naz
- Institute of Crop Science and Resource Conservation (INRES), Department of Crop Genetics and Biotechnology, Rheinische Friedrich-Wilhelms University of Bonn, Germany.
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22
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Kaur S, Shamshad M, Jindal S, Kaur A, Singh S, sharma A, Kaur S. RNA-Seq-Based Transcriptomics Study to Investigate the Genes Governing Nitrogen Use Efficiency in Indian Wheat Cultivars. Front Genet 2022; 13:853910. [PMID: 35432475 PMCID: PMC9009086 DOI: 10.3389/fgene.2022.853910] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 02/18/2022] [Indexed: 11/24/2022] Open
Abstract
High NUE (nitrogen use efficiency) has great practical significance for sustainable crop production. Wheat is one of the main cultivated crops worldwide for human food and nutrition. However, wheat grain productivity is dependent upon cultivars with high NUE in addition to the application of nitrogen fertilizers. In order to understand the molecular mechanisms exhibiting a high NUE response, a comparative transcriptomics study was carried out through RNA-seq analysis to investigate the gene expression that regulates NUE, in root and shoot tissue of N-efficient (PBW677) and N-inefficient (703) cultivars under optimum and nitrogen (N) stress. Differentially expressed gene analysis revealed a total of 2,406 differentially expressed genes (DEGs) present in both the contrasting cultivars under N stress. The efficient genotype PBW677 had considerably more abundant DEGs with 1,653 (903 roots +750 shoots) compared to inefficient cultivar PBW703 with 753 (96 roots +657 shoots). Gene ontology enrichment and pathway analysis of these DEGs suggested that the two cultivars differed in terms of adaptive mechanism. Gene enrichment analysis revealed that among the upregulated and downregulated genes the overrepresented and underrepresented gene categories belonged to biological processes like DNA binding, response to abiotic stimulus, photosynthesis, carbon fixation, carbohydrate metabolic process, nitrogen compound metabolic process, nitrate transport, and translation in cultivar PBW677, while the enriched biological processes were nucleosome assembly, chromatin remodeling, DNA packaging, lipid transport, sulfur compound metabolic process, protein modifications, and protein folding and refolding in N inefficient cultivar PBW703. We found several transcription factors (MYB, WRKY, RING finger protein, zinc finger protein, transporters, NRT1, amino acid transporters, sugar), protein kinases, and genes involved in N absorption, transportation, and assimilation to be highly expressed in high NUE cultivar PBW677. In our study, we report 13 potential candidate genes which showed alternate gene expression in the two contrasting cultivars under study. These genes could serve as potential targets for future breeding programs.
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Affiliation(s)
- Sarabjit Kaur
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - M. Shamshad
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Suruchi Jindal
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Amandeep Kaur
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Satinder Singh
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Achla sharma
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
- *Correspondence: Achla sharma, ; Satinder Kaur,
| | - Satinder Kaur
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
- *Correspondence: Achla sharma, ; Satinder Kaur,
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23
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Li Y, Wang M, Teng K, Dong D, Liu Z, Zhang T, Han L. Transcriptome profiling revealed candidate genes, pathways and transcription factors related to nitrogen utilization and excessive nitrogen stress in perennial ryegrass. Sci Rep 2022; 12:3353. [PMID: 35233054 PMCID: PMC8888628 DOI: 10.1038/s41598-022-07329-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 02/10/2022] [Indexed: 11/09/2022] Open
Abstract
Ryegrass (Lolium perenne L.), a high-quality forage grass, is a good nutrient source for herbivorous livestock. However, improving nitrogen use efficiency and avoiding nitrate toxicity caused by excessive nitrogen are continual challenges in ryegrass production. The molecular mechanism underlying the response of ryegrass to nitrogen, especially excessive nitrogen, remains unclear. In this study, the transcriptomic changes under different nitrogen levels were investigated in perennial ryegrass by high-throughput next-generation RNA sequencing. Phenotypic characterization showed that treatment with half of the standard N concentration (N0.5) led to a better growth state than the other three treatments. The treatments with the standard N concentration (N1) and treatments with ten times higher than the standard N concentration (N10) contained excessive nitrogen, which placed stress on plant growth. Analysis of differentially expressed genes indicated that 345 and 104 genes are involved in the regulation of nitrogen utilization and excessive nitrogen stress, respectively. KEGG enrichment analysis suggested that "photosynthesis-antenna proteins" may respond positively to appropriate nitrogen conditions, whereas "steroid biosynthesis", "carotenoid biosynthesis" and "C5-branched dibasic acid metabolism" were identified as the top significantly enriched pathways in response to excessive nitrogen. Additionally, 21 transcription factors (TFs) related to nitrogen utilization were classified into 10 families, especially the AP2-EREBP and MYB TF families. Four TFs related to excessive nitrogen stress were identified, including LOBs, NACs, AP2-EREBPs and HBs. The expression patterns of these selected genes were also analyzed. These results provide new insight into the regulatory mechanism of ryegrass in response to nitrogen utilization and excessive nitrogen stress.
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Affiliation(s)
- Yinruizhi Li
- Turfgrass Research Institute, College of Grassland Science, Beijing Forestry University, Beijing, China
| | - Mengdi Wang
- Turfgrass Research Institute, College of Grassland Science, Beijing Forestry University, Beijing, China
| | - Ke Teng
- Beijing Research and Development Center for Grass and Environment, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Di Dong
- Turfgrass Research Institute, College of Grassland Science, Beijing Forestry University, Beijing, China
| | - Zhuocheng Liu
- Turfgrass Research Institute, College of Grassland Science, Beijing Forestry University, Beijing, China
| | - Tiejun Zhang
- Turfgrass Research Institute, College of Grassland Science, Beijing Forestry University, Beijing, China
| | - Liebao Han
- Turfgrass Research Institute, College of Grassland Science, Beijing Forestry University, Beijing, China.
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24
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Tiwari JK, Buckseth T, Zinta R, Bhatia N, Dalamu D, Naik S, Poonia AK, Kardile HB, Challam C, Singh RK, Luthra SK, Kumar V, Kumar M. Germplasm, Breeding, and Genomics in Potato Improvement of Biotic and Abiotic Stresses Tolerance. FRONTIERS IN PLANT SCIENCE 2022; 13:805671. [PMID: 35197996 PMCID: PMC8859313 DOI: 10.3389/fpls.2022.805671] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 01/17/2022] [Indexed: 05/23/2023]
Abstract
Potato is one of the most important food crops in the world. Late blight, viruses, soil and tuber-borne diseases, insect-pests mainly aphids, whiteflies, and potato tuber moths are the major biotic stresses affecting potato production. Potato is an irrigated and highly fertilizer-responsive crop, and therefore, heat, drought, and nutrient stresses are the key abiotic stresses. The genus Solanum is a reservoir of genetic diversity, however, a little fraction of total diversity has been utilized in potato breeding. The conventional breeding has contributed significantly to the development of potato varieties. In recent years, a tremendous progress has been achieved in the sequencing technologies from short-reads to long-reads sequence data, genomes of Solanum species (i.e., pan-genomics), bioinformatics and multi-omics platforms such as genomics, transcriptomics, proteomics, metabolomics, ionomics, and phenomics. As such, genome editing has been extensively explored as a next-generation breeding tool. With the available high-throughput genotyping facilities and tetraploid allele calling softwares, genomic selection would be a reality in potato in the near future. This mini-review covers an update on germplasm, breeding, and genomics in potato improvement for biotic and abiotic stress tolerance.
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Affiliation(s)
| | | | - Rasna Zinta
- ICAR-Central Potato Research Institute, Shimla, India
| | - Nisha Bhatia
- ICAR-Central Potato Research Institute, Shimla, India
- School of Biotechnology, Shoolini University, Solan, India
| | - Dalamu Dalamu
- ICAR-Central Potato Research Institute, Shimla, India
| | - Sharmistha Naik
- ICAR-Central Potato Research Institute, Shimla, India
- ICAR-National Research Centre for Grapes, Pune, India
| | - Anuj K. Poonia
- School of Biotechnology, Shoolini University, Solan, India
| | - Hemant B. Kardile
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR, United States
| | - Clarissa Challam
- ICAR-Central Potato Research Institute, Regional Station, Shillong, India
| | | | - Satish K. Luthra
- ICAR-Central Potato Research Institute, Regional Station, Meerut, India
| | - Vinod Kumar
- ICAR-Central Potato Research Institute, Shimla, India
| | - Manoj Kumar
- ICAR-Central Potato Research Institute, Regional Station, Meerut, India
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25
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Feng Z, Ji S, Cui D. Integration of the Metabolomic and Transcriptome Analysis Reveals the Remarkable Compounds of G. bicolor Young and Mature Leaves under Different Iron Nutrient Conditions. Int J Mol Sci 2022; 23:ijms23031160. [PMID: 35163082 PMCID: PMC8835294 DOI: 10.3390/ijms23031160] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 01/15/2022] [Accepted: 01/19/2022] [Indexed: 02/04/2023] Open
Abstract
Gynura bicolor (Roxb. ex Willd.) DC. (G. bicolor) is a functional vegetable rich in iron (Fe) and widely grown in Asia (e.g., Japan and China). Because most Fe in the soil exists in the form of insoluble oxides or hydroxides, it is difficult for plants to obtain Fe from the soil. A comparative metabolomic and transcriptome study was carried out to investigate the effect of Fe deficiency on metabolite synthesis and gene expression in young and mature leaves of G. bicolor. Fe deficiency caused chlorosis and decreased the chlorophyll content in young leaves. The metabolomic results for young leaves showed that l-glutamate and 4-hydroxybutanoic acid lactone significantly increased and decreased, respectively. The transcriptome results showed that the expression levels of genes involved in ferric reduction oxidase 7 and 14-kDa proline-rich protein DC2.15-like were significantly upregulated and downregulated, respectively. However, Fe deficiency had little effect on mature leaves.
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Affiliation(s)
- Zhe Feng
- College of Biosystems Engineering and Food Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China; (Z.F.); (S.J.)
- Key Laboratory of on Site Processing Equipment for Agricultural Products, 866 Yuhangtang Road, Hangzhou 310058, China
| | - Shuyu Ji
- College of Biosystems Engineering and Food Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China; (Z.F.); (S.J.)
- Key Laboratory of on Site Processing Equipment for Agricultural Products, 866 Yuhangtang Road, Hangzhou 310058, China
| | - Di Cui
- College of Biosystems Engineering and Food Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China; (Z.F.); (S.J.)
- Key Laboratory of on Site Processing Equipment for Agricultural Products, 866 Yuhangtang Road, Hangzhou 310058, China
- Correspondence: ; Tel.: +86-159-256-006-17
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Sathee L, Krishna GK, Adavi SB, Jha SK, Jain V. Role of protein phosphatases in the regulation of nitrogen nutrition in plants. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:2911-2922. [PMID: 35035144 PMCID: PMC8720119 DOI: 10.1007/s12298-021-01115-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 11/18/2021] [Accepted: 12/07/2021] [Indexed: 05/20/2023]
Abstract
The reversible protein phosphorylation and dephosphorylation mediated by protein kinases and phosphatases regulate different biological processes and their response to environmental cues, including nitrogen (N) availability. Nitrate assimilation is under the strict control of phosphorylation-dephosphorylation mediated post-translational regulation. The protein phosphatase family with approximately 150 members in Arabidopsis and around 130 members in rice is a promising player in N uptake and assimilation pathways. Protein phosphatase 2A (PP2A) enhances the activation of nitrate reductase (NR) by deactivating SnRK1 and reduces the binding of inhibitory 14-3-3 proteins on NR. The functioning of nitrate transporter NPF6.3 is regulated by phosphorylation of CBL9 (Calcineurin B like protein 9) and CIPK23 (CBL interacting protein kinase 23) module. Phosphorylation by CIPK23 inhibits the activity of NPF6.3, whereas protein phosphatases (PP2C) enhance the NPF6.3-dependent nitrate sensing. PP2Cs and CIPK23 also regulate ammonium transporters (AMTs). Under either moderate ammonium supply or high N demand, CIPK23 is bound and inactivated by PP2Cs. Ammonium uptake is mediated by nonphosphorylated and active AMT1s. Whereas, under high ammonium availability, CIPK23 gets activated and phosphorylate AMT1;1 and AMT1;2 rendering them inactive. Recent reports suggest the critical role of protein phosphatases in regulating N use efficiency (NUE). In rice, PP2C9 regulates NUE by improving N uptake and assimilation. Comparative leaf proteome of wild type and PP2C9 over-expressing transgenic rice lines showed 30 differentially expressed proteins under low N level. These proteins are involved in photosynthesis, N metabolism, signalling, and defence.
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Affiliation(s)
- Lekshmy Sathee
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, 110 012 India
| | - G. K. Krishna
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, 110 012 India
- Department of Plant Physiology, College of Agriculture, Kerala Agricultural University, Thrissur, 680 656 India
| | - Sandeep B. Adavi
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, 110 012 India
| | - Shailendra K. Jha
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110 012 India
| | - Vanita Jain
- Agricultural Education Division, ICAR, KAB-II, New Delhi, 110 012 India
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27
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Nguyen TT, Alizadeh H, Leung DW. Response of potato (Solanum tuberosum L., cv. Iwa) nodal explants to low inorganic nitrogen supply in vitro. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2021. [DOI: 10.1016/j.bcab.2021.102215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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28
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Zhang J, Han Z, Lu Y, Zhao Y, Wang Y, Zhang J, Ma H, Han YZ. Genome-wide identification, structural and gene expression analysis of the nitrate transporters (NRTs) family in potato (Solanum tuberosum L.). PLoS One 2021; 16:e0257383. [PMID: 34673820 PMCID: PMC8530285 DOI: 10.1371/journal.pone.0257383] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 09/01/2021] [Indexed: 11/18/2022] Open
Abstract
Nitrogen (N2) is the most important source of mineral N for plant growth, which was mainly transported by nitrate transporters (NRTs). However, little is known about the NRT gene family in potato. In this study, StNRT gene family members were identified in potato. In addition, we performed StNRT subfamily classification, gene structure and distribution analysis, and conserved domain prediction using various bioinformatics tools. Totally, 39 StNRT gene members were identified in potato genome, including 33, 4 and 2 member belong to NRT1, NRT2, and NRT3, respectively. These 39 StNRT genes were randomly distributed on all chromosomes. The collinearity results show that StNRT members in potato are closely related to Solanum lycopersicum and Solanum melongena. For the expression, different members of StNRT play different roles in leaves and roots. Especially under sufficient nitrogen conditions, different members have a clear distribution in different tissues. These results provide valuable information for identifying the members of the StNRT family in potato and could provide functional characterization of StNRT genes in further research.
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Affiliation(s)
- Jingying Zhang
- College of horticulture, Jilin Agricultural University, Changchun City, P.R. China
| | - Zhijun Han
- College of horticulture, Jilin Agricultural University, Changchun City, P.R. China
| | - Yue Lu
- College of horticulture, Jilin Agricultural University, Changchun City, P.R. China
| | - Yanfei Zhao
- College of horticulture, Jilin Agricultural University, Changchun City, P.R. China
| | - Yaping Wang
- College of horticulture, Jilin Agricultural University, Changchun City, P.R. China
| | - Jiayue Zhang
- College of horticulture, Jilin Agricultural University, Changchun City, P.R. China
| | - Haoran Ma
- College of horticulture, Jilin Agricultural University, Changchun City, P.R. China
| | - Yu Zhu Han
- College of horticulture, Jilin Agricultural University, Changchun City, P.R. China
- * E-mail:
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Sun Y, Xu X, Zhang T, Yang Y, Tong H, Yuan H. Comparative transcriptome analysis provides insights into steviol glycoside synthesis in stevia (Stevia rebaudiana Bertoni) leaves under nitrogen deficiency. PLANT CELL REPORTS 2021; 40:1709-1722. [PMID: 34129077 DOI: 10.1007/s00299-021-02733-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 06/08/2021] [Indexed: 06/12/2023]
Abstract
Transcriptome analysis revealed the potential mechanism of nitrogen regulating steviol glycosides synthesis via shifting of leaf carbon metabolic flux or inducing certain transcription factors. Nitrogen (N) plays key regulatory roles in both stevia (Stevia rebaudiana) growth and the synthesis of its functional metabolite steviol glycosides (SGs), but the mechanism by which this nutrient regulates SGs synthesis remains to be elucidated. To address this question, a pot experiment was performed in a greenhouse where stevia plants fertilized with N (the control as CK plants) and compared with plants without the supply of N. Physiological and biochemical analyses were conducted to test the growth and metabolic responses of plants to N regimes. Our results showed that N deficiency significantly inhibited plant growth and leaf photosynthesis, while increased leaf SGs contents in stevia (49.97, 46.64 and 84.80% respectively for rebaudioside A, stevioside, and rebaudioside C), which may be partly due to "concentration effect". Then, transcriptome analysis was conducted to understand the underlying mechanisms. A total of 535 differentially expressed genes were identified, and carbon metabolism-related events were highlighted by Gene Ontology and Kyoto Encyclopedia of Genes and Genomes. Many of these genes were significantly upregulated by N-deficiency, including those involved in "phenylpropanoid biosynthesis", "flavonoid biosynthesis" and "starch and sucrose metabolism". Our study also analyzed the expression patterns of SGs synthesis-related genes under two N regimes and the potential transcription factors linking N nutrition and SG metabolism. N-deficiency may promote SGs synthesis by changing the carbon metabolism flux or inducing certain transcription factors. Our results provide deeper insight into the relationship between N nutrition and SGs synthesis in stevia plants.
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Affiliation(s)
- Yuming Sun
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, No. 1 Qianhuhoucun Village, Zhongshan Gate, Nanjing, 210014, China
- The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, China
| | - Xiaoyang Xu
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, No. 1 Qianhuhoucun Village, Zhongshan Gate, Nanjing, 210014, China
- The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, China
| | - Ting Zhang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, No. 1 Qianhuhoucun Village, Zhongshan Gate, Nanjing, 210014, China
- The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, China
| | - Yongheng Yang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, No. 1 Qianhuhoucun Village, Zhongshan Gate, Nanjing, 210014, China
- The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, China
| | - Haiying Tong
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, No. 1 Qianhuhoucun Village, Zhongshan Gate, Nanjing, 210014, China
- The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, China
| | - Haiyan Yuan
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, No. 1 Qianhuhoucun Village, Zhongshan Gate, Nanjing, 210014, China.
- The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, China.
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Fiaz S, Wang X, Khan SA, Ahmar S, Noor MA, Riaz A, Ali K, Abbas F, Mora-Poblete F, Figueroa CR, Alharthi B. Novel plant breeding techniques to advance nitrogen use efficiency in rice: A review. GM CROPS & FOOD 2021; 12:627-646. [PMID: 34034628 PMCID: PMC9208628 DOI: 10.1080/21645698.2021.1921545] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Recently, there has been a remarkable increase in rice production owing to genetic improvement and increase in application of synthetic fertilizers. For sustainable agriculture, there is dire need to maintain a balance between profitability and input cost. To meet the steady growing demands of the farming community, researchers are utilizing all available resources to identify nutrient use efficient germplasm, but with very little success. Therefore, it is essential to understand the underlying genetic mechanism controlling nutrients efficiency, with the nitrogen use efficiency (NUE) being the most important trait. Information regarding genetic factors controlling nitrogen (N) transporters, assimilators, and remobilizers can help to identify candidate germplasms via high-throughput technologies. Large-scale field trials have provided morphological, physiological, and biochemical trait data for the detection of genomic regions controlling NUE. The functional aspects of these attributes are time-consuming, costly, labor-intensive, and less accurate. Therefore, the application of novel plant breeding techniques (NPBTs) with context to genome engineering has opened new avenues of research for crop improvement programs. Most recently, genome editing technologies (GETs) have undergone enormous development with various versions from Cas9, Cpf1, base, and prime editing. These GETs have been vigorously adapted in plant sciences for novel trait development to insure food quantity and quality. Base editing has been successfully applied to improve NUE in rice, demonstrating the potential of GETs to develop germplasms with improved resource use efficiency. NPBTs continue to face regulatory setbacks in some countries due to genome editing being categorized in the same category as genetically modified (GM) crops. Therefore, it is essential to involve all stakeholders in a detailed discussion on NPBTs and to formulate uniform policies tackling biosafety, social, ethical, and environmental concerns. In the current review, we have discussed the genetic mechanism of NUE and NPBTs for crop improvement programs with proof of concepts, transgenic and GET application for the development of NUE germplasms, and regulatory aspects of genome edited crops with future directions considering NUE.
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Affiliation(s)
- Sajid Fiaz
- Department of Plant Breeding and Genetics, The University of Haripur 22620, Khyber, Pakhtunkhwa, Pakistan
| | - Xiukang Wang
- College of Life Sciences, Yan'an University, Yan'an, Shaanxi, China
| | - Sher Aslam Khan
- Department of Plant Breeding and Genetics, The University of Haripur 22620, Khyber, Pakhtunkhwa, Pakistan
| | - Sunny Ahmar
- Institute of Biological Sciences, Campus Talca, Universidad deTalca, Talca, Chile
| | - Mehmood Ali Noor
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Key Laboratory of Crop Physiology and Ecology, Ministry of Agriculture, Beijing, China
| | - Aamir Riaz
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, Zhejiang, China
| | - Kazim Ali
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre, Islamabad, Pakistan
| | - Farhat Abbas
- Research Center for Ornamental Plants, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Freddy Mora-Poblete
- Institute of Biological Sciences, Campus Talca, Universidad deTalca, Talca, Chile
| | - Carlos R Figueroa
- Institute of Biological Sciences, Campus Talca, Universidad deTalca, Talca, Chile
| | - Badr Alharthi
- College of Khurma, Taif University, Taif, Saudi Arabia.,College of Science and Engineering, Flinders University, Adelaide, South Australia
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Zheng K, Lu J, Li J, Yu Y, Zhang J, He Z, Ismail OM, Wu J, Xie X, Li X, Xu G, Dou D, Wang X. Efficiency of chitosan application against Phytophthora infestans and the activation of defence mechanisms in potato. Int J Biol Macromol 2021; 182:1670-1680. [PMID: 34022316 DOI: 10.1016/j.ijbiomac.2021.05.097] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 05/09/2021] [Accepted: 05/15/2021] [Indexed: 01/23/2023]
Abstract
Late blight, caused by the oomycete Phytophthora infestans, is one of the most devastating diseases that results in huge losses of potato crops worldwide. Chitosan as a defence elicitor can induce plant innate immunity against pathogen infection, but the efficiency and specific defence mechanism of chitosan against late blight in potato have not been elaborated. In this study, we demonstrated that the application of chitosan significantly enhanced potato resistance and reduced P. infestans infection in potted potato and in the field. Large-scale transcriptomic analysis suggested that chitosan preferentially activated several important pathways related to the plant defence response. Notably, we revealed that chitosan triggered pattern-triggered immunity responses in potato. Chitosan could trigger pattern recognition receptors to initiate intracellular signalling, and gradually amplify the immune signal. qRT-PCR verification showed that chitosan induced the expression of defence-related genes in potato. Moreover, treatment with chitosan result in Induced Systemic Resistance (ISR) in potato, including an accumulation of plant hormone salicylic acid, increase in the level of phenylalanine ammonia lyase activity and a content decrease of malondialdehyde. These findings help elucidate chitosan-mediated activation of the immune system in potato and provide a potential ecofriendly strategy to control potato late blight in the field.
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Affiliation(s)
- Kangkai Zheng
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing 100193, PR China
| | - Jie Lu
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing 100193, PR China; Heilongjiang Academy of Agricultural Sciences, Harbin 150086, PR China
| | - Jie Li
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing 100193, PR China
| | - Yin Yu
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing 100193, PR China
| | - Jia Zhang
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing 100193, PR China
| | - Ziwei He
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing 100193, PR China
| | - Omayma M Ismail
- Horticultural Crop Technology, National Research Center (NRC), 12311, Egypt
| | - Jie Wu
- Institute of Plant Protection, Hebei Academy of Agricultural and Forestry Sciences, IPM Center of Hebei Province, Baoding 071000, PR China
| | - Xuejun Xie
- Changzhou Institute of Technology, Changzhou 213032, PR China
| | - Xiaobo Li
- Crops Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Provincial Key Laboratory of Crop Genetic Improvement, Guangdong, Guangzhou 510640, PR China
| | - Guangyuan Xu
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing 100193, PR China
| | - Daolong Dou
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing 100193, PR China
| | - Xiaodan Wang
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing 100193, PR China.
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Wang F, Ge S, Xu X, Xing Y, Du X, Zhang X, Lv M, Liu J, Zhu Z, Jiang Y. Multiomics Analysis Reveals New Insights into the Apple Fruit Quality Decline under High Nitrogen Conditions. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:5559-5572. [PMID: 33945277 DOI: 10.1021/acs.jafc.1c01548] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Excessive application of nitrogen (N) fertilizer is common in Chinese apple production. High N reduced the contents of soluble sugar and total flavonoids by 16.05 and 19.01%, respectively, resulting in poor fruit quality. Moreover, high N increased the total N and decreased the total C and C/N ratio of apple fruits. On the basis of the transcriptomic, proteomic, and metabolomic analyses, the global network was revealed. High N inhibited the accumulation of carbohydrates (sucrose, glucose, and trehalose) and flavonoids (rhamnetin-3-O-rutinoside, rutin, and trihydroxyisoflavone-7-O-galactoside) in fruits, and more C skeletons were used to synthesize amino acids and their derivatives (especially low C/N ratio, e.g., arginine) to be transferred to N metabolism. This study revealed new insights into the decline in soluble sugar and flavonoids caused by high N, and hub genes (MD07G1172700, MD05G1222800, MD16G1227200, MD01G1174400, and MD02G1207200) and hub proteins (PFK, gapN, and HK) were obtained.
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Affiliation(s)
- Fen Wang
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an 271018, Shandong, China
| | - Shunfeng Ge
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an 271018, Shandong, China
| | - Xinxiang Xu
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an 271018, Shandong, China
| | - Yue Xing
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an 271018, Shandong, China
| | - Xin Du
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an 271018, Shandong, China
| | - Xin Zhang
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an 271018, Shandong, China
| | - Mengxue Lv
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an 271018, Shandong, China
| | - Jingquan Liu
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an 271018, Shandong, China
| | - Zhanling Zhu
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an 271018, Shandong, China
| | - Yuanmao Jiang
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an 271018, Shandong, China
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Tiwari JK, Rawat S, Luthra SK, Zinta R, Sahu S, Varshney S, Kumar V, Dalamu D, Mandadi N, Kumar M, Chakrabarti SK, Rao AR, Rai A. Genome sequence analysis provides insights on genomic variation and late blight resistance genes in potato somatic hybrid (parents and progeny). Mol Biol Rep 2021; 48:623-635. [PMID: 33442830 DOI: 10.1007/s11033-020-06106-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 12/18/2020] [Indexed: 11/29/2022]
Abstract
Wild Solanum species are the important resources for potato improvement. With the availability of potato genome and sequencing progress, knowledge about genomic resources is essential for novel genes discovery. Hence, the aim of this study was to decipher draft genome sequences of unique potato genotypes i.e. somatic hybrid P8 (J1), wild species S. pinnatisectum (J2), progeny MSH/14-112 (P8 × cv. Kufri Jyoti) (J3), and S. tuberosum dihaploid C-13 (J4). Draft genome sequencing using Illumina platform and reference-based assemblies with the potato genome yielded genome assembly size of 725.01 Mb (J1), 724.95 Mb (J2), 725.01 Mb (J3), and 809.59 Mb (J4). Further, 39,260 (J1), 25,711 (J2), 39,730 (J3) and 30,241 (J4) genes were identified and 17,411 genes were found common in the genotypes particularly late blight resistance genes (R3a, RGA2, RGA3, R1B-16, Rpi-blb2, Rpi and Rpi-vnt1). Gene ontology (GO) analysis showed that molecular function was predominant and signal transduction was major KEGG pathways. Further, gene enrichment analysis revealed dominance of metabolic process (GO: 0008152) in all the samples. Phylogeny analysis showed relatedness with potato and other plant species. Heterozygous single nucleotide polymorphism (SNP) was more than homozygous, and SNP in genic region was more than inter-genic region. Copy number variation (CNV) analysis indicated greater number of deletions than duplications. Sequence diversity and conserved motifs analysis revealed variation for late blight resistance genes. Quantitative real-time polymerase chain reaction (qRT-PCR) analysis showed differential expression of late blight resistance genes. Our study provides insights on genome sequence, structural variation and late blight resistance genes in potato somatic hybrid (parents and progeny) for future research.
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Affiliation(s)
- Jagesh Kumar Tiwari
- ICAR-Central Potato Research Institute, Shimla, 171001, Himachal Pradesh, India.
| | - Shashi Rawat
- ICAR-Central Potato Research Institute, Shimla, 171001, Himachal Pradesh, India
| | - Satish K Luthra
- ICAR-Central Potato Research Institute, Regional Station, Modipuram, Meerut, 250110, Uttar Pradesh, India
| | - Rasna Zinta
- ICAR-Central Potato Research Institute, Shimla, 171001, Himachal Pradesh, India
| | - Sarika Sahu
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012, India
| | - Shivangi Varshney
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012, India
| | - Vinod Kumar
- ICAR-Central Potato Research Institute, Shimla, 171001, Himachal Pradesh, India
| | - Dalamu Dalamu
- ICAR-Central Potato Research Institute, Regional Station, Kufri, Shimla, 171012, Himachal Pradesh, India
| | - Nagesh Mandadi
- ICAR-Central Potato Research Institute, Shimla, 171001, Himachal Pradesh, India
| | - Manoj Kumar
- ICAR-Central Potato Research Institute, Shimla, 171001, Himachal Pradesh, India
| | | | - Atmakuri R Rao
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012, India
| | - Anil Rai
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012, India
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Zhang J, Han Z, Lu Y, Zhao Y, Wang Y, Zhang J, Ma H, Han YZ. Genome-wide identification, structural and gene expression analysis of the nitrate transporters (NRTs) family in potato (Solanum tuberosum L.). PLoS One 2021. [PMID: 34673820 DOI: 10.1371/journalpone.0257383] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2023] Open
Abstract
Nitrogen (N2) is the most important source of mineral N for plant growth, which was mainly transported by nitrate transporters (NRTs). However, little is known about the NRT gene family in potato. In this study, StNRT gene family members were identified in potato. In addition, we performed StNRT subfamily classification, gene structure and distribution analysis, and conserved domain prediction using various bioinformatics tools. Totally, 39 StNRT gene members were identified in potato genome, including 33, 4 and 2 member belong to NRT1, NRT2, and NRT3, respectively. These 39 StNRT genes were randomly distributed on all chromosomes. The collinearity results show that StNRT members in potato are closely related to Solanum lycopersicum and Solanum melongena. For the expression, different members of StNRT play different roles in leaves and roots. Especially under sufficient nitrogen conditions, different members have a clear distribution in different tissues. These results provide valuable information for identifying the members of the StNRT family in potato and could provide functional characterization of StNRT genes in further research.
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Affiliation(s)
- Jingying Zhang
- College of horticulture, Jilin Agricultural University, Changchun City, P.R. China
| | - Zhijun Han
- College of horticulture, Jilin Agricultural University, Changchun City, P.R. China
| | - Yue Lu
- College of horticulture, Jilin Agricultural University, Changchun City, P.R. China
| | - Yanfei Zhao
- College of horticulture, Jilin Agricultural University, Changchun City, P.R. China
| | - Yaping Wang
- College of horticulture, Jilin Agricultural University, Changchun City, P.R. China
| | - Jiayue Zhang
- College of horticulture, Jilin Agricultural University, Changchun City, P.R. China
| | - Haoran Ma
- College of horticulture, Jilin Agricultural University, Changchun City, P.R. China
| | - Yu Zhu Han
- College of horticulture, Jilin Agricultural University, Changchun City, P.R. China
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Tiong J, Sharma N, Sampath R, MacKenzie N, Watanabe S, Metot C, Lu Z, Skinner W, Lu Y, Kridl J, Baumann U, Heuer S, Kaiser B, Okamoto M. Improving Nitrogen Use Efficiency Through Overexpression of Alanine Aminotransferase in Rice, Wheat, and Barley. FRONTIERS IN PLANT SCIENCE 2021; 12:628521. [PMID: 33584777 PMCID: PMC7875890 DOI: 10.3389/fpls.2021.628521] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 01/06/2021] [Indexed: 05/20/2023]
Abstract
Nitrogen is an essential nutrient for plants, but crop plants are inefficient in the acquisition and utilization of applied nitrogen. This often results in producers over applying nitrogen fertilizers, which can negatively impact the environment. The development of crop plants with more efficient nitrogen usage is, therefore, an important research goal in achieving greater agricultural sustainability. We utilized genetically modified rice lines over-expressing a barley alanine aminotransferase (HvAlaAT) to help characterize pathways which lead to more efficient use of nitrogen. Under the control of a stress-inducible promoter OsAnt1, OsAnt1:HvAlaAT lines have increased above-ground biomass with little change to both nitrate and ammonium uptake rates. Based on metabolic profiles, carbon metabolites, particularly those involved in glycolysis and the tricarboxylic acid (TCA) cycle, were significantly altered in roots of OsAnt1:HvAlaAT lines, suggesting higher metabolic turnover. Moreover, transcriptomic data revealed that genes involved in glycolysis and TCA cycle were upregulated. These observations suggest that higher activity of these two processes could result in higher energy production, driving higher nitrogen assimilation, consequently increasing biomass production. Other potential mechanisms contributing to a nitrogen-use efficient phenotype include involvements of phytohormonal responses and an alteration in secondary metabolism. We also conducted basic growth studies to evaluate the effect of the OsAnt1:HvAlaAT transgene in barley and wheat, which the transgenic crop plants increased seed production under controlled environmental conditions. This study provides comprehensive profiling of genetic and metabolic responses to the over-expression of AlaAT and unravels several components and pathways which contribute to its nitrogen-use efficient phenotype.
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Affiliation(s)
- Jingwen Tiong
- School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, SA, Australia
| | - Niharika Sharma
- School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, SA, Australia
- NSW Department of Primary Industries, Orange, NSW, Australia
| | - Ramya Sampath
- School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, SA, Australia
| | - Nenah MacKenzie
- School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, SA, Australia
| | - Sayuri Watanabe
- School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, SA, Australia
- ARC Industrial Transformation Research Hub for Wheat in a Hot and Dry Climate, Waite Research Institute, University of Adelaide, Glen Osmond, SA, Australia
| | - Claire Metot
- School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, SA, Australia
- ARC Industrial Transformation Research Hub for Wheat in a Hot and Dry Climate, Waite Research Institute, University of Adelaide, Glen Osmond, SA, Australia
| | - Zhongjin Lu
- Arcadia Biosciences, Davis, CA, United States
| | | | - Yingzhi Lu
- Arcadia Biosciences, Davis, CA, United States
| | - Jean Kridl
- Arcadia Biosciences, Davis, CA, United States
| | - Ute Baumann
- School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, SA, Australia
- ARC Industrial Transformation Research Hub for Wheat in a Hot and Dry Climate, Waite Research Institute, University of Adelaide, Glen Osmond, SA, Australia
| | - Sigrid Heuer
- ARC Industrial Transformation Research Hub for Wheat in a Hot and Dry Climate, Waite Research Institute, University of Adelaide, Glen Osmond, SA, Australia
- Rothamsted Research, Harpenden, United Kingdom
| | - Brent Kaiser
- ARC Industrial Transformation Research Hub for Wheat in a Hot and Dry Climate, Waite Research Institute, University of Adelaide, Glen Osmond, SA, Australia
- Centre for Carbon, Water and Food, University of Sydney, Brownlow Hill, NSW, Australia
| | - Mamoru Okamoto
- School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, SA, Australia
- ARC Industrial Transformation Research Hub for Wheat in a Hot and Dry Climate, Waite Research Institute, University of Adelaide, Glen Osmond, SA, Australia
- *Correspondence: Mamoru Okamoto,
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Tiwari JK, Buckseth T, Singh RK, Kumar M, Kant S. Prospects of Improving Nitrogen Use Efficiency in Potato: Lessons From Transgenics to Genome Editing Strategies in Plants. FRONTIERS IN PLANT SCIENCE 2020; 11:597481. [PMID: 33424892 PMCID: PMC7785987 DOI: 10.3389/fpls.2020.597481] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 12/10/2020] [Indexed: 05/27/2023]
Affiliation(s)
- Jagesh Kumar Tiwari
- Indian Council of Agricultural Research (ICAR)-Central Potato Research Institute, Shimla, India
| | - Tanuja Buckseth
- Indian Council of Agricultural Research (ICAR)-Central Potato Research Institute, Shimla, India
| | - Rajesh Kumar Singh
- Indian Council of Agricultural Research (ICAR)-Central Potato Research Institute, Shimla, India
| | - Manoj Kumar
- Indian Council of Agricultural Research (ICAR)-Central Potato Research Institute, Shimla, India
| | - Surya Kant
- Agriculture Victoria, Grains Innovation Park, Horsham, VIC, Australia
- Faculty of Veterinary and Agricultural Sciences, Centre for Agricultural Innovation, School of Agriculture and Food, The University of Melbourne, Melbourne, VIC, Australia
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37
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Zhang J, Wang Y, Zhao Y, Zhang Y, Zhang J, Ma H, Han Y. Transcriptome analysis reveals Nitrogen deficiency induced alterations in leaf and root of three cultivars of potato (Solanum tuberosum L.). PLoS One 2020; 15:e0240662. [PMID: 33119630 PMCID: PMC7595393 DOI: 10.1371/journal.pone.0240662] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 09/30/2020] [Indexed: 11/18/2022] Open
Abstract
Nitrogen (N) is a key element for the production of potato. The N uptake efficiency, N use efficiency and increased N utilization efficiency can be decreased by N deficiency treatment. We performed this study to investigate the association between transcriptomic profiles and the efficiencies of N in potato. Potato cultivars "Yanshu 4" (short for Y), "Xiabodi" (cv. Shepody, short for X) and "Chunshu 4" (short for C) were treated with sufficient N fertilizer and deficient N fertilizer. Then, the growth parameters and tuber yield were recorded; the contents of soluble sugar and protein were measured; and the activities of enzymes were detected. Leaf and root transcriptomes were analyzed and differentially expressed genes (DEGs) in response to N deficiency were identified. The results showed that N deficiency decreased the nitrate reductase (NR), glutamine synthetase (GS) and root activity. Most of the DEGs between N-treated and N-deficiency participate the processes of transport, nitrate transport, nitrogen compound transport and N metabolism in C and Y, not in X, indicating the cultivar-dependent response to N deficiency. DEGs like glutamate dehydrogenase (StGDH), glutamine synthetase (StGS) and carbonic anhydrase (StCA) play key roles in these processes mentioned above. DEGs related to N metabolism showed a close relationship with the N utilization efficiency (UTE), but not with N use efficiency (NUE). The Major Facilitator Superfamily (MFS) members, like nitrate transporter 2.4 (StNRT2.4), 2.5 (StNRT2.5) and 2.7 (StNRT2.7), were mainly enriched in the processes associated with response to stresses and defense, indicating that N deficiency induced stresses in all cultivars.
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Affiliation(s)
- Jingying Zhang
- College of Horticulture, Jilin Agricultural University, Changchun City, P.R. China
| | - Yaping Wang
- College of Horticulture, Jilin Agricultural University, Changchun City, P.R. China
| | - Yanfei Zhao
- College of Horticulture, Jilin Agricultural University, Changchun City, P.R. China
| | - Yun Zhang
- College of Horticulture, Jilin Agricultural University, Changchun City, P.R. China
| | - Jiayue Zhang
- College of Horticulture, Jilin Agricultural University, Changchun City, P.R. China
| | - Haoran Ma
- College of Horticulture, Jilin Agricultural University, Changchun City, P.R. China
| | - Yuzhu Han
- College of Horticulture, Jilin Agricultural University, Changchun City, P.R. China
- * E-mail:
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Zhang Y, Jiao Y, Li Y, Tian Q, Du X, Deng Y. Comprehensive analysis of microRNAs in the mantle central and mantle edge provide insights into shell formation in pearl oyster Pinctada fucata martensii. Comp Biochem Physiol B Biochem Mol Biol 2020; 252:110508. [PMID: 32992005 DOI: 10.1016/j.cbpb.2020.110508] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 08/12/2020] [Accepted: 09/23/2020] [Indexed: 01/15/2023]
Abstract
MicroRNAs (miRNAs) are a class of non-coding RNA molecules with post-transcriptional regulatory activity in various biological processes. Pearl oyster Pinctada fucata martensii is one of the main species cultured for marine pearl production in China and Japan. In this study, we constructed two small RNA libraries of mantle central (MC) and mantle edge (ME) from P. f. martensii and obtained 24,175,537 and 21,593,898 clean reads, respectively. A total of 258 miRNAs of P. f. martensii (Pm-miRNA) were identified, and 93 differentially expressed miRNAs (DEMs) including 49 known Pm-miRNAs and 44 novel Pm-miRNAs were obtained from the MC and ME. The target transcripts of these DEMs were obviously enriched in neuroactive ligand-receptor interaction pathway, and others. After over-expression of Pm-miR-124 and Pm-miR-9a-5p in the MC by mimic injection into the muscle of P. f. martensii, nacre exhibited a disorderly growth as detected by scanning electron microscopy. Pm-nicotinic acetylcholine receptor alpha subunit, Pm-neuropeptide Y and Pm-chitin synthase were investigated as the targets of Pm-miR-124; and Pm-tumor necrosis factor receptor associated factor 2 and Pm-chitin synthase were investigated as the targets of Pm-miR-9a-5p. These predicted target transcripts were down-regulated after the over-expression of Pm-miR-124 and Pm-miR-9a-5p in MC. This study comprehensively analyzed the miRNAs in mantle tissues to enhance our understanding of the regulatory mechanism underlying shell formation.
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Affiliation(s)
- Yuting Zhang
- Fishery College, Guangdong Ocean University, Zhanjiang 524088, China
| | - Yu Jiao
- Fishery College, Guangdong Ocean University, Zhanjiang 524088, China; Guangdong Science and Innovation Center for Pearl Culture, Zhanjiang 524088, China
| | - Yiping Li
- Fishery College, Guangdong Ocean University, Zhanjiang 524088, China
| | - Qunli Tian
- Fishery College, Guangdong Ocean University, Zhanjiang 524088, China
| | - Xiaodong Du
- Fishery College, Guangdong Ocean University, Zhanjiang 524088, China; Guangdong Science and Innovation Center for Pearl Culture, Zhanjiang 524088, China
| | - Yuewen Deng
- Fishery College, Guangdong Ocean University, Zhanjiang 524088, China; Guangdong Science and Innovation Center for Pearl Culture, Zhanjiang 524088, China.
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Tiwari JK, Buckseth T, Zinta R, Saraswati A, Singh RK, Rawat S, Chakrabarti SK. Genome-wide identification and characterization of microRNAs by small RNA sequencing for low nitrogen stress in potato. PLoS One 2020; 15:e0233076. [PMID: 32428011 PMCID: PMC7237020 DOI: 10.1371/journal.pone.0233076] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 04/28/2020] [Indexed: 11/18/2022] Open
Abstract
Nitrogen is an important nutrient for plant growth and tuber quality of potato. Since potato crop requires high dose of N, improving nitrogen use efficiency (NUE) of plant is an inevitable approach to minimize N fertilization. The aim of this study was to identify and characterize microRNAs (miRNAs) by small RNA sequencing in potato plants grown in aeroponic under two contrasting N (high and low) regimes. A total of 119 conserved miRNAs belonging to 41 miRNAs families, and 1002 putative novel miRNAs were identified. From total, 52 and 54 conserved miRNAs, and 404 and 628 putative novel miRNAs were differentially expressed in roots and shoots, respectively under low N stress. Of total 34,135 predicted targets, the gene ontology (GO) analysis indicated that maximum targets belong to biological process followed by molecular function and cellular component. Eexpression levels of the selected miRNAs and targets were validated by real time-quantitative polymerase chain reaction (RT-qPCR) analysis. Two predicted targets of potential miRNAs (miR397 and miR398) were validated by 5' RLM-RACE (RNA ligase mediated rapid amplification of cDNA ends). In general, predicted targets are associated with stress-related, kinase, transporters and transcription factors such as universal stress protein, heat shock protein, salt-tolerance protein, calmodulin binding protein, serine-threonine protein kinsae, Cdk10/11- cyclin dependent kinase, amino acid transporter, nitrate transporter, sugar transporter, transcription factor, F-box family protein, and zinc finger protein etc. Our study highlights that miR397 and miR398 play crucial role in potato during low N stress management. Moreover, study provides insights to modulate miRNAs and their predicted targets to develop N-use efficient potato using transgenic/genome-editing tools in future.
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Affiliation(s)
- Jagesh Kumar Tiwari
- Indian Council of Agricultural Research-Central Potato Research Institute, Shimla, Himachal Pradesh, India
- * E-mail:
| | - Tanuja Buckseth
- Indian Council of Agricultural Research-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Rasna Zinta
- Indian Council of Agricultural Research-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Aastha Saraswati
- Indian Council of Agricultural Research-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Rajesh Kumar Singh
- Indian Council of Agricultural Research-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Shashi Rawat
- Indian Council of Agricultural Research-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Swarup Kumar Chakrabarti
- Indian Council of Agricultural Research-Central Potato Research Institute, Shimla, Himachal Pradesh, India
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