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Huo Q, Song R, Ma Z. Recent advances in exploring transcriptional regulatory landscape of crops. FRONTIERS IN PLANT SCIENCE 2024; 15:1421503. [PMID: 38903438 PMCID: PMC11188431 DOI: 10.3389/fpls.2024.1421503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Accepted: 05/23/2024] [Indexed: 06/22/2024]
Abstract
Crop breeding entails developing and selecting plant varieties with improved agronomic traits. Modern molecular techniques, such as genome editing, enable more efficient manipulation of plant phenotype by altering the expression of particular regulatory or functional genes. Hence, it is essential to thoroughly comprehend the transcriptional regulatory mechanisms that underpin these traits. In the multi-omics era, a large amount of omics data has been generated for diverse crop species, including genomics, epigenomics, transcriptomics, proteomics, and single-cell omics. The abundant data resources and the emergence of advanced computational tools offer unprecedented opportunities for obtaining a holistic view and profound understanding of the regulatory processes linked to desirable traits. This review focuses on integrated network approaches that utilize multi-omics data to investigate gene expression regulation. Various types of regulatory networks and their inference methods are discussed, focusing on recent advancements in crop plants. The integration of multi-omics data has been proven to be crucial for the construction of high-confidence regulatory networks. With the refinement of these methodologies, they will significantly enhance crop breeding efforts and contribute to global food security.
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Affiliation(s)
| | | | - Zeyang Ma
- State Key Laboratory of Maize Bio-breeding, Frontiers Science Center for Molecular Design Breeding, Joint International Research Laboratory of Crop Molecular Breeding, National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
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2
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Bhatt V, Muthusamy V, Panda KK, Katral A, Chhabra R, Mishra SJ, Gopinath I, Zunjare RU, Neeraja CN, Rakshit S, Yadava DK, Hossain F. Expression Dynamics of lpa1 Gene and Accumulation Pattern of Phytate in Maize Genotypes Possessing opaque2 and crtRB1 Genes at Different Stages of Kernel Development. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12091745. [PMID: 37176803 PMCID: PMC10180721 DOI: 10.3390/plants12091745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 04/21/2023] [Accepted: 04/21/2023] [Indexed: 05/15/2023]
Abstract
Phytic acid (PA) acts as a storehouse for the majority of the mineral phosphorous (P) in maize; ~80% of the total P stored as phytate P is not available to monogastric animals and thereby causes eutrophication. In addition, phytic acid chelates positively charged minerals making them unavailable in the diet. The mutant lpa1-1 allele reduces PA more than the wild-type LPA1 allele. Further, mutant gene opaque2 (o2) enhances lysine and tryptophan and crtRB1 enhances provitamin-A (proA) more than wild-type O2 and CRTRB1 alleles, respectively. So far, the expression pattern of the mutant lpa1-1 allele has not been analysed in maize genotypes rich in lysine, tryptophan and proA. Here, we analysed the expression pattern of wild and mutant alleles of LPA1, O2 and CRTRB1 genes in inbreds with (i) mutant lpa1-1, o2 and crtRB1 alleles, (ii) wild-type LPA1 allele and mutant o2 and crtRB1 alleles and (iii) wild-type LPA1, O2 and CRTRB1 alleles at 15, 30 and 45 days after pollination (DAP). The average reduction of PA/total phosphorous (TP) in lpa1-1 mutant inbreds was 29.30% over wild-type LPA1 allele. The o2 and crtRB1-based inbreds possessed ~two-fold higher amounts of lysine and tryptophan, and four-fold higher amounts of proA compared to wild-type alleles. The transcript levels of lpa1-1, o2 and crtRB1 genes in lpa1-1-based inbreds were significantly lower than their wild-type versions across kernel development. The lpa1-1, o2 and crtRB1 genes reached their highest peak at 15 DAP. The correlation of transcript levels of lpa1-1 was positive for PA/TP (r = 0.980), whereas it was negative with inorganic phosphorous (iP) (r = -0.950). The o2 and crtRB1 transcripts showed negative correlations with lysine (r = -0.887) and tryptophan (r = -0.893), and proA (r = -0.940), respectively. This is the first comprehensive study on lpa1-1 expression in the maize inbreds during different kernel development stages. The information generated here offers great potential for comprehending the dynamics of phytic acid regulation in maize.
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Affiliation(s)
- Vinay Bhatt
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
- AMITY Institute of Biotechnology, AMITY University, Noida 201313, Uttar Pradesh, India
| | - Vignesh Muthusamy
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Kusuma Kumari Panda
- AMITY Institute of Biotechnology, AMITY University, Noida 201313, Uttar Pradesh, India
| | - Ashvinkumar Katral
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Rashmi Chhabra
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Subhra J Mishra
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Ikkurti Gopinath
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Rajkumar U Zunjare
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | | | - Sujay Rakshit
- ICAR-Indian Institute of Maize Research, Ludhiana 141004, India
- ICAR-Indian Institute of Agricultural Biotechnology, Ranchi 834010, India
| | - Devendra K Yadava
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Firoz Hossain
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
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Advances of Apetala2/Ethylene Response Factors in Regulating Development and Stress Response in Maize. Int J Mol Sci 2023; 24:ijms24065416. [PMID: 36982510 PMCID: PMC10049130 DOI: 10.3390/ijms24065416] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 02/28/2023] [Accepted: 03/10/2023] [Indexed: 03/18/2023] Open
Abstract
Apetala2/ethylene response factor (AP2/ERF) is one of the largest families of transcription factors, regulating growth, development, and stress response in plants. Several studies have been conducted to clarify their roles in Arabidopsis and rice. However, less research has been carried out on maize. In this review, we systematically identified the AP2/ERFs in the maize genome and summarized the research progress related to AP2/ERF genes. The potential roles were predicted from rice homologs based on phylogenetic and collinear analysis. The putative regulatory interactions mediated by maize AP2/ERFs were discovered according to integrated data sources, implying that they involved complex networks in biological activities. This will facilitate the functional assignment of AP2/ERFs and their applications in breeding strategy.
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Wang J, Zou A, Xiang S, Liu C, Peng H, Wen Y, Ma X, Chen H, Ran M, Sun X. Transcriptome analysis reveals the mechanism of zinc ion-mediated plant resistance to TMV in Nicotiana benthamiana. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2022; 184:105100. [PMID: 35715039 DOI: 10.1016/j.pestbp.2022.105100] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 04/08/2022] [Accepted: 04/12/2022] [Indexed: 05/12/2023]
Abstract
Zinc ions (Zn2+) are used to promote plant growth and treat multiple diseases. However, it is still unclear which pathways in plants respond to Zn2+. In this study, we found that supplying (CH3COO)2Zn can effectively delay tobacco mosaic virus (TMV) replication and movement in Nicotiana benthamiana. To further understand the regulatory mechanism of antiviral activity mediated by Zn2+, we examined the transcriptomic changes of leaves treated with Zn2+. Three days after treatment, 7575 differential expression genes (DEGs) were enriched in the Zn2+ treatment group compared with the control group. Through GO and KEGG analysis, the pathway of phosphatidylinositol signaling system and inositol phosphate metabolism were significantly enriched after treated with Zn2+, and a large number of ethylene-responsive transcription factors (ERFs) involved in inositol phosphate metabolism were found to be enriched. We identified ERF5 performed a positive effect on plant immunity. Our findings demonstrated that Zn2+-mediated resistance in N. benthamiana activated signal transduction and regulated the expression of resistance-related genes. The results of the study uncover a global view of mRNA changes in Zn2+-mediated cellular processes involved in the competition between plants and viruses.
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Affiliation(s)
- Jing Wang
- Chongqing Key Laboratory of Plant Disease Biology, College of Plant Protection, Southwest University, Chongqing 400716, China; Chongqing Key Laboratory of Soft-Matter Material Chemistry and Function Manufacturing, Southwest University, Chongqing 400715, China
| | - Aihong Zou
- Chongqing Key Laboratory of Plant Disease Biology, College of Plant Protection, Southwest University, Chongqing 400716, China; Chongqing Key Laboratory of Soft-Matter Material Chemistry and Function Manufacturing, Southwest University, Chongqing 400715, China
| | - Shunyu Xiang
- Chongqing Key Laboratory of Plant Disease Biology, College of Plant Protection, Southwest University, Chongqing 400716, China; Chongqing Key Laboratory of Soft-Matter Material Chemistry and Function Manufacturing, Southwest University, Chongqing 400715, China
| | - Changyun Liu
- Chongqing Key Laboratory of Plant Disease Biology, College of Plant Protection, Southwest University, Chongqing 400716, China; Chongqing Key Laboratory of Soft-Matter Material Chemistry and Function Manufacturing, Southwest University, Chongqing 400715, China
| | - Haoran Peng
- Chongqing Key Laboratory of Plant Disease Biology, College of Plant Protection, Southwest University, Chongqing 400716, China
| | - Yuxia Wen
- Chongqing Key Laboratory of Plant Disease Biology, College of Plant Protection, Southwest University, Chongqing 400716, China; Chongqing Key Laboratory of Soft-Matter Material Chemistry and Function Manufacturing, Southwest University, Chongqing 400715, China
| | - Xiaozhou Ma
- Chongqing Key Laboratory of Plant Disease Biology, College of Plant Protection, Southwest University, Chongqing 400716, China; Chongqing Key Laboratory of Soft-Matter Material Chemistry and Function Manufacturing, Southwest University, Chongqing 400715, China
| | - Haitao Chen
- Chongqing Tobacco Science Research Institute, Chongqing 400715, China
| | - Mao Ran
- Chongqing Tobacco Science Research Institute, Chongqing 400715, China
| | - Xianchao Sun
- Chongqing Key Laboratory of Plant Disease Biology, College of Plant Protection, Southwest University, Chongqing 400716, China; Chongqing Key Laboratory of Soft-Matter Material Chemistry and Function Manufacturing, Southwest University, Chongqing 400715, China.
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Wang W, Xie Y, Liu L, King GJ, White P, Ding G, Wang S, Cai H, Wang C, Xu F, Shi L. Genetic Control of Seed Phytate Accumulation and the Development of Low-Phytate Crops: A Review and Perspective. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:3375-3390. [PMID: 35275483 DOI: 10.1021/acs.jafc.1c06831] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Breeding low phytic acid (lpa) crops is a strategy that has potential to both improve the nutritional quality of food and feed and contribute to the sustainability of agriculture. Here, we review the lipid-independent and -dependent pathways of phytate synthesis and their regulatory mechanisms in plants. We compare the genetic variation of the phytate concentration and distribution in seeds between dicot and monocot species as well as the associated temporal and spatial expression patterns of the genes involved in phytate synthesis and transport. Quantitative trait loci or significant single nucleotide polymorphisms for the seed phytate concentration have been identified in different plant species by linkage and association mapping, and some genes have been cloned from lpa mutants. We summarize the effects of various lpa mutations on important agronomic traits in crop plants and propose SULTR3;3 and SULTR3;4 as optimal target genes for lpa crop breeding.
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Affiliation(s)
- Wei Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, People's Republic of China
- Microelement Research Center, Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, Hubei 430070, People's Republic of China
| | - Yiwen Xie
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, People's Republic of China
- Microelement Research Center, Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, Hubei 430070, People's Republic of China
| | - Lei Liu
- Southern Cross Plant Science, Southern Cross University, Lismore New South Wales 2480, Australia
| | - Graham J King
- Southern Cross Plant Science, Southern Cross University, Lismore New South Wales 2480, Australia
| | - Philip White
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, People's Republic of China
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom
| | - Guangda Ding
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, People's Republic of China
- Microelement Research Center, Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, Hubei 430070, People's Republic of China
| | - Sheliang Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, People's Republic of China
- Microelement Research Center, Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, Hubei 430070, People's Republic of China
| | - Hongmei Cai
- Microelement Research Center, Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, Hubei 430070, People's Republic of China
| | - Chuang Wang
- Microelement Research Center, Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, Hubei 430070, People's Republic of China
| | - Fangsen Xu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, People's Republic of China
- Microelement Research Center, Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, Hubei 430070, People's Republic of China
| | - Lei Shi
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, People's Republic of China
- Microelement Research Center, Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, Hubei 430070, People's Republic of China
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6
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Feng Y, Gu D, Wang Z, Lu C, Fan J, Zhou J, Wang R, Su X. Comprehensive evaluation and analysis of the salinity stress response mechanisms based on transcriptome and metabolome of Staphylococcus aureus. Arch Microbiol 2021; 204:28. [PMID: 34921629 DOI: 10.1007/s00203-021-02624-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 10/03/2021] [Accepted: 10/07/2021] [Indexed: 10/19/2022]
Abstract
Staphylococcus aureus possesses an extraordinary ability to deal with a wide range of osmotic pressure. This study performed transcriptomic and metabolomic analyses on the potential mechanism of gradient salinity stress adaptation in S. aureus ZS01. The results revealed that CPS biosynthetic protein genes were candidate target genes for directly regulating the phenotypic changes of biofilm. Inositol phosphate metabolism was downregulated to reduce the conversion of functional molecules. The gluconeogenesis pathway and histidine synthesis were downregulated to reduce the production of endogenous glucose. The pyruvate metabolism pathway was upregulated to promote the accumulation of succinate. TCA cycle metabolism pathway was downregulated to reduce unnecessary energy loss. L-Proline was accumulated to regulate osmotic pressure. Therefore, these self-protection mechanisms can protect cells from hypertonic environments and help them focus on survival. In addition, we identified ten hub genes. The findings will aid in the prevention and treatment strategies of S. aureus infections.
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Affiliation(s)
- Ying Feng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo, China.,College of Life Sciences, Tonghua Normal University, Tonghua, China.,School of Marine Sciences, Ningbo University, 169 Qixing South Road, Ningbo City, 315211, Zhejiang Province, China
| | - Dizhou Gu
- College of Life Sciences, Tonghua Normal University, Tonghua, China
| | - Ziyan Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo, China.,School of Marine Sciences, Ningbo University, 169 Qixing South Road, Ningbo City, 315211, Zhejiang Province, China
| | - Chenyang Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo, China.,School of Marine Sciences, Ningbo University, 169 Qixing South Road, Ningbo City, 315211, Zhejiang Province, China
| | - Jingfeng Fan
- National Marine Environmental Monitoring Center, Dalian, China
| | - Jun Zhou
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo, China.,School of Marine Sciences, Ningbo University, 169 Qixing South Road, Ningbo City, 315211, Zhejiang Province, China
| | - Rixin Wang
- School of Marine Sciences, Ningbo University, 169 Qixing South Road, Ningbo City, 315211, Zhejiang Province, China.
| | - Xiurong Su
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo, China. .,School of Marine Sciences, Ningbo University, 169 Qixing South Road, Ningbo City, 315211, Zhejiang Province, China.
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El-Sappah AH, Elbaiomy RG, Elrys AS, Wang Y, Zhu Y, Huang Q, Yan K, Xianming Z, Abbas M, El-Tarabily KA, Li J. Genome-Wide Identification and Expression Analysis of Metal Tolerance Protein Gene Family in Medicago truncatula Under a Broad Range of Heavy Metal Stress. Front Genet 2021; 12:713224. [PMID: 34603378 PMCID: PMC8482800 DOI: 10.3389/fgene.2021.713224] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 06/30/2021] [Indexed: 01/02/2023] Open
Abstract
Metal tolerance proteins (MTPs) encompass plant membrane divalent cation transporters to specifically participate in heavy metal stress resistance and mineral acquisition. However, the molecular behaviors and biological functions of this family in Medicago truncatula are scarcely known. A total of 12 potential MTP candidate genes in the M. truncatula genome were successfully identified and analyzed for a phylogenetic relationship, chromosomal distributions, gene structures, docking analysis, gene ontology, and previous gene expression. M. truncatula MTPs (MtMTPs) were further classified into three major cation diffusion facilitator (CDFs) groups: Mn-CDFs, Zn-CDFs, and Fe/Zn-CDFs. The structural analysis of MtMTPs displayed high gene similarity within the same group where all of them have cation_efflux domain or ZT_dimer. Cis-acting element analysis suggested that various abiotic stresses and phytohormones could induce the most MtMTP gene transcripts. Among all MTPs, PF16916 is the specific domain, whereas GLY, ILE, LEU, MET, ALA, SER, THR, VAL, ASN, and PHE amino acids were predicted to be the binding residues in the ligand-binding site of all these proteins. RNA-seq and gene ontology analysis revealed the significant role of MTP genes in the growth and development of M. truncatula. MtMTP genes displayed differential responses in plant leaves, stems, and roots under five divalent heavy metals (Cd2+, Co2+, Mn2+, Zn2+, and Fe2+). Ten, seven, and nine MtMTPs responded to at least one metal ion treatment in the leaves, stems, and roots, respectively. Additionally, MtMTP1.1, MtMTP1.2, and MtMTP4 exhibited the highest expression responses in most heavy metal treatments. Our results presented a standpoint on the evolution of MTPs in M. truncatula. Overall, our study provides a novel insight into the evolution of the MTP gene family in M. truncatula and paves the way for additional functional characterization of this gene family.
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Affiliation(s)
- Ahmed H El-Sappah
- School of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China.,Genetics Department, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
| | | | - Ahmed S Elrys
- Soil Science Department, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
| | - Yu Wang
- School of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
| | - Yumin Zhu
- School of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
| | - Qiulan Huang
- College of Tea Science, Yibin University, Yibin, China
| | - Kuan Yan
- School of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
| | - Zhao Xianming
- School of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
| | - Manzar Abbas
- School of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
| | - Khaled A El-Tarabily
- Department of Biology, College of Science, United Arab Emirates University, Al Ain, United Arab Emirates.,Harry Butler Institute, Murdoch University, Murdoch, WA, Australia
| | - Jia Li
- School of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
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Development of SNP Set for the Marker-Assisted Selection of Guar ( Cyamopsis tetragonoloba (L.) Taub.) Based on a Custom Reference Genome Assembly. PLANTS 2021; 10:plants10102063. [PMID: 34685872 PMCID: PMC8539970 DOI: 10.3390/plants10102063] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 09/20/2021] [Accepted: 09/27/2021] [Indexed: 12/11/2022]
Abstract
Guar gum, a polysaccharide derived from guar seeds, is widely used in a variety of industrial applications, including oil and gas production. Although guar is mostly propagated in India, interest in guar as a new industrial legume crop is increasing worldwide, demanding the development of effective tools for marker-assisted selection. In this paper, we report a wide-ranging set of 4907 common SNPs and 327 InDels generated from RADseq genotyping data of 166 guar plants of different geographical origin. A custom guar reference genome was assembled and used for variant calling. A consensus set of variants was built using three bioinformatic pipelines for short variant discovery. The developed molecular markers were used for genome-wide association study, resulting in the discovery of six markers linked to the variation of an important agronomic trait—percentage of pods matured to the harvest date under long light day conditions. One of the associated variants was found inside the putative transcript sequence homologous to an ABC transporter in Arabidopsis, which has been shown to play an important role in D-myo-inositol phosphates metabolism. Earlier, we suggested that genes involved in myo-inositol phosphate metabolism have significant impact on the early flowering of guar plants. Hence, we believe that the developed SNP set allows for the identification of confident molecular markers of important agrobiological traits.
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Musavizadeh Z, Najafi-Zarrini H, Kazemitabar SK, Hashemi SH, Faraji S, Barcaccia G, Heidari P. Genome-Wide Analysis of Potassium Channel Genes in Rice: Expression of the OsAKT and OsKAT Genes under Salt Stress. Genes (Basel) 2021; 12:784. [PMID: 34065373 PMCID: PMC8160896 DOI: 10.3390/genes12050784] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 05/09/2021] [Accepted: 05/18/2021] [Indexed: 12/21/2022] Open
Abstract
Potassium (K+), as a vital element, is involved in regulating important cellular processes such as enzyme activity, cell turgor, and nutrient movement in plant cells, which affects plant growth and production. Potassium channels are involved in the transport and release of potassium in plant cells. In the current study, three OsKAT genes and two OsAKT genes, along with 11 nonredundant putative potassium channel genes in the rice genome, were characterized based on their physiochemical properties, protein structure, evolution, duplication, in silico gene expression, and protein-protein interactions. In addition, the expression patterns of OsAKTs and OsKATs were studied in root and shoot tissues under salt stress using real-time PCR in three rice cultivars. K+ channel genes were found to have diverse functions and structures, and OsKATs showed high genetic divergence from other K+ channel genes. Furthermore, the Ka/Ks ratios of duplicated gene pairs from the K+ channel gene family in rice suggested that these genes underwent purifying selection. Among the studied K+ channel proteins, OsKAT1 and OsAKT1 were identified as proteins with high potential N-glycosylation and phosphorylation sites, and LEU, VAL, SER, PRO, HIS, GLY, LYS, TYR, CYC, and ARG amino acids were predicted as the binding residues in the ligand-binding sites of K+ channel proteins. Regarding the coexpression network and KEGG ontology results, several metabolic pathways, including sugar metabolism, purine metabolism, carbon metabolism, glycerophospholipid metabolism, monoterpenoid biosynthesis, and folate biosynthesis, were recognized in the coexpression network of K+ channel proteins. Based on the available RNA-seq data, the K+ channel genes showed differential expression levels in rice tissues in response to biotic and abiotic stresses. In addition, the real-time PCR results revealed that OsAKTs and OsKATs are induced by salt stress in root and shoot tissues of rice cultivars, and OsKAT1 was identified as a key gene involved in the rice response to salt stress. In the present study, we found that the repression of OsAKTs, OsKAT2, and OsKAT2 in roots was related to salinity tolerance in rice. Our findings provide valuable insights for further structural and functional assays of K+ channel genes in rice.
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Affiliation(s)
- Zahra Musavizadeh
- Department of Biochemical Sciences, Sapienza University of Rome, 00185 Rome, Italy;
| | - Hamid Najafi-Zarrini
- Department of Plant Breeding, Sari Agricultural Sciences and Natural Resources University (SANRU), Sari 4818166996, Iran; (H.N.-Z.); (S.K.K.); (S.F.)
| | - Seyed Kamal Kazemitabar
- Department of Plant Breeding, Sari Agricultural Sciences and Natural Resources University (SANRU), Sari 4818166996, Iran; (H.N.-Z.); (S.K.K.); (S.F.)
| | - Seyed Hamidreza Hashemi
- Genetics and Agricultural Biotechnology Institute of Tabarestan, Sari Agricultural Sciences and Natural Resources University, Sari 4818166996, Iran;
| | - Sahar Faraji
- Department of Plant Breeding, Sari Agricultural Sciences and Natural Resources University (SANRU), Sari 4818166996, Iran; (H.N.-Z.); (S.K.K.); (S.F.)
| | - Gianni Barcaccia
- Laboratory of Genomics for Breeding, DAFNAE, Campus of Agripolis, University of Padova, Legnaro, 35020 Padova, Italy;
| | - Parviz Heidari
- Faculty of Agriculture, Shahrood University of Technology, Shahrood 3619995161, Iran
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10
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Jin H, Yu X, Yang Q, Fu X, Yuan F. Transcriptome analysis identifies differentially expressed genes in the progenies of a cross between two low phytic acid soybean mutants. Sci Rep 2021; 11:8740. [PMID: 33888781 PMCID: PMC8062490 DOI: 10.1038/s41598-021-88055-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 04/08/2021] [Indexed: 12/13/2022] Open
Abstract
Phytic acid (PA) is a major antinutrient that cannot be digested by monogastric animals, but it can decrease the bioavailability of micronutrients (e.g., Zn and Fe). Lowering the PA content of crop seeds will lead to enhanced nutritional traits. Low-PA mutant crop lines carrying more than one mutated gene (lpa) have lower PA contents than mutants with a single lpa mutant gene. However, little is known about the link between PA pathway intermediates and downstream regulatory activities following the mutation of these genes in soybean. Consequently, we performed a comparative transcriptome analysis using an advanced generation recombinant inbred line with low PA levels [2mlpa (mips1/ipk1)] and a sibling line with homozygous non-mutant alleles and normal PA contents [2MWT (MIPS1/IPK1)]. An RNA sequencing analysis of five seed developmental stages revealed 7945 differentially expressed genes (DEGs) between the 2mlpa and 2MWT seeds. Moreover, 3316 DEGs were associated with 128 metabolic and signal transduction pathways and 4980 DEGs were annotated with 345 Gene Ontology terms related to biological processes. Genes associated with PA metabolism, photosynthesis, starch and sucrose metabolism, and defense mechanisms were among the DEGs in 2mlpa. Of these genes, 36 contributed to PA metabolism, including 22 genes possibly mediating the low-PA phenotype of 2mlpa. The expression of most of the genes associated with photosynthesis (81 of 117) was down-regulated in 2mlpa at the late seed developmental stage. In contrast, the expression of three genes involved in sucrose metabolism was up-regulated at the late seed developmental stage, which might explain the high sucrose content of 2mlpa soybeans. Furthermore, 604 genes related to defense mechanisms were differentially expressed between 2mlpa and 2MWT. In this study, we detected a low PA content as well as changes to multiple metabolites in the 2mlpa mutant. These results may help elucidate the regulation of metabolic events in 2mlpa. Many genes involved in PA metabolism may contribute to the substantial decrease in the PA content and the moderate accumulation of InsP3-InsP5 in the 2mlpa mutant. The other regulated genes related to photosynthesis, starch and sucrose metabolism, and defense mechanisms may provide additional insights into the nutritional and agronomic performance of 2mlpa seeds.
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Affiliation(s)
- Hangxia Jin
- Institute of Crop Science and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Xiaomin Yu
- Institute of Crop Science and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Qinghua Yang
- Institute of Crop Science and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Xujun Fu
- Institute of Crop Science and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Fengjie Yuan
- Institute of Crop Science and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China.
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11
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Perera I, Fukushima A, Akabane T, Horiguchi G, Seneweera S, Hirotsu N. Expression regulation of myo-inositol 3-phosphate synthase 1 (INO1) in determination of phytic acid accumulation in rice grain. Sci Rep 2019; 9:14866. [PMID: 31619750 PMCID: PMC6795888 DOI: 10.1038/s41598-019-51485-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 10/02/2019] [Indexed: 01/07/2023] Open
Abstract
Phytic acid (PA) is the primary phosphorus (P) storage compound in the seeds of cereals and legumes. Low PA crops, which are considered an effective way to improve grain nutrient availability and combat environmental issues relating to seed P have been developed using mutational and reverse genetics approaches. Here, we identify molecular mechanism regulating PA content among natural rice variants. First, we performed genome-wide association (GWA) mapping of world rice core collection (WRC) accessions to understand the genetic determinants underlying PA trait in rice. Further, a comparative study was undertaken to identify the differences in PA accumulation, protein profiles, and gene expression in low (WRC 5) and high PA (WRC 6) accessions. GWA results identified myo-inositol 3-phosphate synthase 1 (INO1) as being closely localized to a significant single nucleotide polymorphism. We found high rates of PA accumulation 10 days after flowering, and our results indicate that INO1 expression was significantly higher in WRC 6 than in WRC 5. Seed proteome assays found that the expression of INO1 was significantly higher in WRC 6. These results suggest that not only the gene itself but regulation of INO1 gene expression at early developmental stages is important in determining PA content in rice.
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Affiliation(s)
- Ishara Perera
- Graduate School of Life Sciences, Toyo University, 1-1-1 Izumino, Itakura-machi, Oura-gun, Gunma, 374-0193, Japan
- Grain Legumes and Oil Crops Research and Development Centre, Department of Agriculture, Angunakolapelessa, Sri Lanka
| | - Ayaka Fukushima
- Graduate School of Life Sciences, Toyo University, 1-1-1 Izumino, Itakura-machi, Oura-gun, Gunma, 374-0193, Japan
| | - Tatsuki Akabane
- Faculty of Life Sciences, Toyo University, 1-1-1 Izumino, Itakura-machi, Oura-gun, Gunma, 374-0193, Japan
| | - Genki Horiguchi
- Graduate School of Life Sciences, Toyo University, 1-1-1 Izumino, Itakura-machi, Oura-gun, Gunma, 374-0193, Japan
| | - Saman Seneweera
- National Institute of Fundamental Studies, Hantana Road, Kandy, Sri Lanka
- Centre for Crop Health, University of Southern Queensland, Toowoomba, QLD, 4350, Australia
| | - Naoki Hirotsu
- Graduate School of Life Sciences, Toyo University, 1-1-1 Izumino, Itakura-machi, Oura-gun, Gunma, 374-0193, Japan.
- Faculty of Life Sciences, Toyo University, 1-1-1 Izumino, Itakura-machi, Oura-gun, Gunma, 374-0193, Japan.
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12
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Faraji S, Rasouli SH, Kazemitabar SK. Genome-wide exploration of C2H2 zinc finger family in durum wheat (Triticum turgidum ssp. Durum): insights into the roles in biological processes especially stress response. Biometals 2018; 31:1019-1042. [PMID: 30288657 DOI: 10.1007/s10534-018-0146-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 09/22/2018] [Indexed: 11/30/2022]
Abstract
C2H2 type of zinc finger transcription factors (C2H2-ZFP TFs) play crucial roles in plant developments and stress response. Regarding its importance, genome-wide study of C2H2-ZFs were performed in multiple important plant species, but any such investigation was not fulfilled in Triticum turgidum ssp. Durum (durum wheat) as an important nutritional crop. The present study identified 122 C2H2-ZFs in durum wheat and physically mapped them onto the genome. The phylogenetic analysis classified these TFs into six major groups. Genes structure and conserved motifs assay showed TtC2H2-ZF involvement in the important cellular functions. Comparative phylogeny between durum wheat TtC2H2-ZF genes and the orthologs in rice revealed the evolutionary relationships of C2H2-ZF proteins. The gene ontology and promoter cis-element analysis indicated that most of TtC2H2-ZF genes are involved in multiple molecular functions including metal ion-binding and various stimuli responses. Further, the miRNAs targeting TtC2H2-ZF transcripts, homology modeling and proteins interaction network were also demonstrated, suggesting the vital cellular functions of TtC2H2-ZFs during various circumstances. The expression heatmap demonstrated differential and tissue-specific expression patterns of these genes. Expression profiling of this gene family members in response to dehydration and heat stresses showed differential expression pattern of these genes at multiple time points of stresses. This study can prepare a comprehensive overview of the durum wheat C2H2-ZF gene family and may provide a new perspective on the evolution of them, which will form the basis for further investigation of the roles of this family members and future genetic engineering studies in crops.
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Affiliation(s)
- Sahar Faraji
- Department of Plant Breeding, Faculty of Crop Science, Sari Agricultural Sciences and Natural Resources University (SANRU), Sari, Iran.
| | - Seyyed Hamidreza Rasouli
- Department of Entrepreneurship Technology, Faculty of Management, Payame Noor University (PNU), Babol, Iran
| | - Seyyed Kamal Kazemitabar
- Department of Plant Breeding, Faculty of Crop Science, Sari Agricultural Sciences and Natural Resources University (SANRU), Sari, Iran
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13
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Aggarwal S, Kumar A, Bhati KK, Kaur G, Shukla V, Tiwari S, Pandey AK. RNAi-Mediated Downregulation of Inositol Pentakisphosphate Kinase ( IPK1) in Wheat Grains Decreases Phytic Acid Levels and Increases Fe and Zn Accumulation. FRONTIERS IN PLANT SCIENCE 2018; 9:259. [PMID: 29559984 PMCID: PMC5845732 DOI: 10.3389/fpls.2018.00259] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 02/14/2018] [Indexed: 05/18/2023]
Abstract
Enhancement of micronutrient bioavailability is crucial to address the malnutrition in the developing countries. Various approaches employed to address the micronutrient bioavailability are showing promising signs, especially in cereal crops. Phytic acid (PA) is considered as a major antinutrient due to its ability to chelate important micronutrients and thereby restricting their bioavailability. Therefore, manipulating PA biosynthesis pathway has largely been explored to overcome the pleiotropic effect in different crop species. Recently, we reported that functional wheat inositol pentakisphosphate kinase (TaIPK1) is involved in PA biosynthesis, however, the functional roles of the IPK1 gene in wheat remains elusive. In this study, RNAi-mediated gene silencing was performed for IPK1 transcripts in hexaploid wheat. Four non-segregating RNAi lines of wheat were selected for detailed study (S3-D-6-1; S6-K-3-3; S6-K-6-10 and S16-D-9-5). Homozygous transgenic RNAi lines at T4 seeds with a decreased transcript of TaIPK1 showed 28-56% reduction of the PA. Silencing of IPK1 also resulted in increased free phosphate in mature grains. Although, no phenotypic changes in the spike was observed but, lowering of grain PA resulted in the reduced number of seeds per spikelet. The lowering of grain PA was also accompanied by a significant increase in iron (Fe) and zinc (Zn) content, thereby enhancing their molar ratios (Zn:PA and Fe:PA). Overall, this work suggests that IPK1 is a promising candidate for employing genome editing tools to address the mineral accumulation in wheat grains.
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Affiliation(s)
- Sipla Aggarwal
- Department of Biotechnology, National Agri-Food Biotechnology Institute, Mohali, India
- Department of Biotechnology, Panjab University, Chandigarh, India
| | - Anil Kumar
- Department of Biotechnology, National Agri-Food Biotechnology Institute, Mohali, India
| | - Kaushal K. Bhati
- Department of Biotechnology, National Agri-Food Biotechnology Institute, Mohali, India
- Copenhagen Plant Science Centre, PLEN, University of Copenhagen, Copenhagen, Denmark
| | - Gazaldeep Kaur
- Department of Biotechnology, National Agri-Food Biotechnology Institute, Mohali, India
| | - Vishnu Shukla
- Department of Biotechnology, National Agri-Food Biotechnology Institute, Mohali, India
| | - Siddharth Tiwari
- Department of Biotechnology, National Agri-Food Biotechnology Institute, Mohali, India
| | - Ajay K. Pandey
- Department of Biotechnology, National Agri-Food Biotechnology Institute, Mohali, India
- *Correspondence: Ajay K. Pandey, ;
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14
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Cominelli E, Orozco-Arroyo G, Sparvoli F. Phytic Acid Biosynthesis and Transport in Phaseolus vulgaris: Exploitation of New Genomic Resources. ACTA ACUST UNITED AC 2017. [DOI: 10.1007/978-3-319-63526-2_8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
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15
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Redekar N, Pilot G, Raboy V, Li S, Saghai Maroof MA. Inference of Transcription Regulatory Network in Low Phytic Acid Soybean Seeds. FRONTIERS IN PLANT SCIENCE 2017; 8:2029. [PMID: 29250090 PMCID: PMC5714895 DOI: 10.3389/fpls.2017.02029] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 11/14/2017] [Indexed: 05/26/2023]
Abstract
A dominant loss of function mutation in myo-inositol phosphate synthase (MIPS) gene and recessive loss of function mutations in two multidrug resistant protein type-ABC transporter genes not only reduce the seed phytic acid levels in soybean, but also affect the pathways associated with seed development, ultimately resulting in low emergence. To understand the regulatory mechanisms and identify key genes that intervene in the seed development process in low phytic acid crops, we performed computational inference of gene regulatory networks in low and normal phytic acid soybeans using a time course transcriptomic data and multiple network inference algorithms. We identified a set of putative candidate transcription factors and their regulatory interactions with genes that have functions in myo-inositol biosynthesis, auxin-ABA signaling, and seed dormancy. We evaluated the performance of our unsupervised network inference method by comparing the predicted regulatory network with published regulatory interactions in Arabidopsis. Some contrasting regulatory interactions were observed in low phytic acid mutants compared to non-mutant lines. These findings provide important hypotheses on expression regulation of myo-inositol metabolism and phytohormone signaling in developing low phytic acid soybeans. The computational pipeline used for unsupervised network learning in this study is provided as open source software and is freely available at https://lilabatvt.github.io/LPANetwork/.
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Affiliation(s)
- Neelam Redekar
- Department of Crop and Soil Environmental Sciences, Virginia Tech, Blacksburg, VA, United States
| | - Guillaume Pilot
- Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Blacksburg, VA, United States
| | - Victor Raboy
- National Small Grains Germplasm Research Center, Agricultural Research Service (USDA), Aberdeen, ID, United States
| | - Song Li
- Department of Crop and Soil Environmental Sciences, Virginia Tech, Blacksburg, VA, United States
| | - M. A. Saghai Maroof
- Department of Crop and Soil Environmental Sciences, Virginia Tech, Blacksburg, VA, United States
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16
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Tan M, Cheng D, Yang Y, Zhang G, Qin M, Chen J, Chen Y, Jiang M. Co-expression network analysis of the transcriptomes of rice roots exposed to various cadmium stresses reveals universal cadmium-responsive genes. BMC PLANT BIOLOGY 2017; 17:194. [PMID: 29115926 PMCID: PMC5678563 DOI: 10.1186/s12870-017-1143-y] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2017] [Accepted: 10/30/2017] [Indexed: 05/18/2023]
Abstract
BACKGROUND The migration of cadmium (Cd) from contaminated soil to rice is a cause for concern. However, the molecular mechanism underlying the response of rice roots to various Cd stresses remains to be clarified from the viewpoint of the co-expression network at a system-wide scale. RESULTS We employed a comparative RNAseq-based approach to identify early Cd-responsive differentially expressed genes (DEGs) in rice 'Nipponbare' seedling roots after 1 h of high-Cd treatment. A multiplicity of the identified 1772 DEGs were implicated in hormone signaling and transcriptional regulation, particularly NACs and WRKYs were all upregulated under Cd stress. All of the 6 Cd-upregulated ABC transporters were pleiotropic drug resistance proteins (PDRs), whereas all of the 6 ZRT/IRT-like proteins (ZIPs) were consistently downregulated by Cd treatment. To further confirm our results of this early transcriptomic response to Cd exposure, we then conducted weighted gene co-expression network analysis (WGCNA) to re-analyze our RNAseq data in combination with other 11 previously published RNAseq datasets for rice roots exposed to diverse concentrations of Cd for extended treatment periods. This integrative approach identified 271 transcripts as universal Cd-regulated DEGs that are key components of the Cd treatment coupled co-expression module. A global view of the 164 transcripts with annotated functions in pathway networks revealed several Cd-upregulated key functional genes, including transporter ABCG36/OsPDR9, 12-oxo-phytodienoic acid reductases (OPRs) for JA synthesis, and ZIM domain proteins JAZs in JA signaling, as well as OsWRKY10, NAC, and ZFP transcription factors. More importantly, 104 of these, including ABCG36/OsPDR9, OsNAC3, as well as several orthologs in group metalloendoproteinase, plastocyanin-like domain containing proteins and pectin methylesterase inhibitor, may respond specifically to various Cd pressures, after subtracting the 60 general stress-responsive genes reported to be commonly upregulated following multiple stresses. CONCLUSION An integrative approach was implemented to identify DEGs and co-expression network modules in response to various Cd pressures, and 104 of the 164 annotatable universal Cd-responsive DEGs may specifically respond to various Cd pressures. These results provide insight into the universal molecular mechanisms beneath the Cd response in rice roots, and suggest many promising targets for improving the rice acclimation process against Cd toxicity.
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Affiliation(s)
- Mingpu Tan
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Dan Cheng
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Yuening Yang
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Guoqiang Zhang
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Mengjie Qin
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Jun Chen
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Yahua Chen
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Mingyi Jiang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
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17
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Chen L, Liao H. Engineering crop nutrient efficiency for sustainable agriculture. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2017; 59:710-735. [PMID: 28600834 DOI: 10.1111/jipb.12559] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 06/06/2017] [Indexed: 05/21/2023]
Abstract
Increasing crop yields can provide food, animal feed, bioenergy feedstocks and biomaterials to meet increasing global demand; however, the methods used to increase yield can negatively affect sustainability. For example, application of excess fertilizer can generate and maintain high yields but also increases input costs and contributes to environmental damage through eutrophication, soil acidification and air pollution. Improving crop nutrient efficiency can improve agricultural sustainability by increasing yield while decreasing input costs and harmful environmental effects. Here, we review the mechanisms of nutrient efficiency (primarily for nitrogen, phosphorus, potassium and iron) and breeding strategies for improving this trait, along with the role of regulation of gene expression in enhancing crop nutrient efficiency to increase yields. We focus on the importance of root system architecture to improve nutrient acquisition efficiency, as well as the contributions of mineral translocation, remobilization and metabolic efficiency to nutrient utilization efficiency.
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Affiliation(s)
- Liyu Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou 510642, China
- Root Biology Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Hong Liao
- Root Biology Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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18
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Haak DC, Fukao T, Grene R, Hua Z, Ivanov R, Perrella G, Li S. Multilevel Regulation of Abiotic Stress Responses in Plants. FRONTIERS IN PLANT SCIENCE 2017; 8:1564. [PMID: 29033955 PMCID: PMC5627039 DOI: 10.3389/fpls.2017.01564] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 08/28/2017] [Indexed: 05/18/2023]
Abstract
The sessile lifestyle of plants requires them to cope with stresses in situ. Plants overcome abiotic stresses by altering structure/morphology, and in some extreme conditions, by compressing the life cycle to survive the stresses in the form of seeds. Genetic and molecular studies have uncovered complex regulatory processes that coordinate stress adaptation and tolerance in plants, which are integrated at various levels. Investigating natural variation in stress responses has provided important insights into the evolutionary processes that shape the integrated regulation of adaptation and tolerance. This review primarily focuses on the current understanding of how transcriptional, post-transcriptional, post-translational, and epigenetic processes along with genetic variation orchestrate stress responses in plants. We also discuss the current and future development of computational tools to identify biologically meaningful factors from high dimensional, genome-scale data and construct the signaling networks consisting of these components.
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Affiliation(s)
- David C. Haak
- Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, BlacksburgVA, United States
| | - Takeshi Fukao
- Department of Crop and Soil Environmental Sciences, Virginia Tech, BlacksburgVA, United States
| | - Ruth Grene
- Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, BlacksburgVA, United States
| | - Zhihua Hua
- Department of Environmental and Plant Biology, Interdisciplinary Program in Molecular and Cellular Biology, Ohio University, AthensOH, United States
| | - Rumen Ivanov
- Institut für Botanik, Heinrich-Heine-Universität DüsseldorfDüsseldorf, Germany
| | - Giorgio Perrella
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of GlasgowGlasgow, United Kingdom
| | - Song Li
- Department of Crop and Soil Environmental Sciences, Virginia Tech, BlacksburgVA, United States
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19
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Wu FY, Tang CY, Guo YM, Bian ZW, Fu JY, Lu GH, Qi JL, Pang YJ, Yang YH. Transcriptome analysis explores genes related to shikonin biosynthesis in Lithospermeae plants and provides insights into Boraginales' evolutionary history. Sci Rep 2017; 7:4477. [PMID: 28667265 PMCID: PMC5493674 DOI: 10.1038/s41598-017-04750-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 05/22/2017] [Indexed: 11/09/2022] Open
Abstract
Shikonin and its derivatives extracted from Lithospermeae plants' red roots have current applications in food and pharmaceutical industries. Previous studies have cloned some genes related to shikonin biosynthesis. However, most genes related to shikonin biosynthesis remain unclear, because the lack of the genome/transcriptome of the Lithospermeae plants. Therefore, in order to provide a new understanding of shikonin biosynthesis, we obtained transcriptome data and unigenes expression profiles in three shikonin-producing Lithospermeae plants, i.e., Lithospermum erythrorhizon, Arnebia euchroma and Echium plantagineum. As a result, two unigenes (i.e., G10H and 12OPR) that are involved in "shikonin downstream biosynthesis" and "methyl jasmonate biosynthesis" were deemed to relate to shikonin biosynthesis in this study. Furthermore, we conducted a Lamiids phylogenetic model and identified orthologous unigenes under positive selection in above three Lithospermeae plants. The results indicated Boraginales was more relative to Solanales/Gentianales than to Lamiales.
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Affiliation(s)
- Feng-Yao Wu
- State Key Laboratory of Pharmaceutical Biotechnology, NJU-NJFU Joint Institute of Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing, 210093, China
| | - Cheng-Yi Tang
- State Key Laboratory of Pharmaceutical Biotechnology, NJU-NJFU Joint Institute of Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing, 210093, China.
| | - Yu-Min Guo
- State Key Laboratory of Pharmaceutical Biotechnology, NJU-NJFU Joint Institute of Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing, 210093, China
| | - Zhuo-Wu Bian
- State Key Laboratory of Pharmaceutical Biotechnology, NJU-NJFU Joint Institute of Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing, 210093, China
| | - Jiang-Yan Fu
- State Key Laboratory of Pharmaceutical Biotechnology, NJU-NJFU Joint Institute of Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing, 210093, China
| | - Gui-Hua Lu
- State Key Laboratory of Pharmaceutical Biotechnology, NJU-NJFU Joint Institute of Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing, 210093, China
| | - Jin-Liang Qi
- State Key Laboratory of Pharmaceutical Biotechnology, NJU-NJFU Joint Institute of Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing, 210093, China
| | - Yan-Jun Pang
- State Key Laboratory of Pharmaceutical Biotechnology, NJU-NJFU Joint Institute of Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing, 210093, China.
| | - Yong-Hua Yang
- State Key Laboratory of Pharmaceutical Biotechnology, NJU-NJFU Joint Institute of Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing, 210093, China.
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20
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Zhang S, Yang W, Zhao Q, Zhou X, Fan Y, Chen R. Rapid Method for Simultaneous Determination of Inositol Phosphates by IPC-ESI–MS/MS and Its Application in Nutrition and Genetic Research. Chromatographia 2017. [DOI: 10.1007/s10337-017-3238-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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