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Liu JJ, Sniezko RA, Houston S, Krakowski J, Alger G, Benowicz A, Sissons R, Zamany A, Williams H, Kegley A, Rancourt B. Genome-Wide Association Study Reveals Polygenic Architecture for Limber Pine Quantitative Disease Resistance to White Pine Blister Rust. PHYTOPATHOLOGY 2024; 114:1626-1636. [PMID: 38489164 DOI: 10.1094/phyto-09-23-0338-r] [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: 03/17/2024]
Abstract
Development of durable resistance effective against a broad range of pathotypes is crucial for restoration of pathogen-damaged ecosystems. This study dissected the complex genetic architecture for limber pine quantitative disease resistance (QDR) to Cronartium ribicola using a genome-wide association study. Eighteen-month-old seedlings were inoculated for resistance screening under controlled conditions. Disease development was quantitatively assessed for QDR-related traits over 4 years postinoculation. To reveal the genomic architecture contributing to QDR-related traits, a set of genes related to disease resistance with genome-wide distribution was selected for targeted sequencing for genotyping of single-nucleotide polymorphisms (SNPs). The genome-wide association study revealed a set of SNPs significantly associated with quantitative traits for limber pine QDR to white pine blister rust, including number of needle spots and stem cankers, as well as survival 4 years postinoculation. The peaks of marker-trait associations displayed a polygenic pattern, with genomic regions as potential resistant quantitative trait loci, distributed over 10 of the 12 linkage groups (LGs) of Pinus. None of them was linked to the Cr4-controlled major gene resistance previously mapped on LG08. Both normal canker and bole infection were mapped on LG05, and the associated SNPs explained their phenotypic variance up to 52%, tagging a major resistant quantitative trait locus. Candidate genes containing phenotypically associated SNPs encoded putative nucleotide-binding site leucine-rich repeat proteins, leucine-rich repeat-receptor-like kinase, cytochrome P450 superfamily protein, heat shock cognate protein 70, glutamate receptor, RNA-binding family protein, and unknown protein. The confirmation of resistant quantitative trait loci broadens the genetic pool of limber pine resistance germplasm for resistance breeding.
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Affiliation(s)
- Jun-Jun Liu
- Natural Resources Canada, Canadian Forest Service, Pacific Forestry Centre, 506 West Burnside Road, Victoria, BC V8Z 1M5, Canada
| | - Richard A Sniezko
- U.S. Department of Agriculture Forest Service, Dorena Genetic Resource Center, 34963 Shoreview Drive, Cottage Grove, OR 97424, U.S.A
| | - Sydney Houston
- Natural Resources Canada, Canadian Forest Service, Pacific Forestry Centre, 506 West Burnside Road, Victoria, BC V8Z 1M5, Canada
| | - Jodie Krakowski
- Independent Consultant, Box 774, Coleman, AB, T0K 0M0, Canada
| | - Genoa Alger
- Parks Canada, Waterton Lakes National Park, Alberta, T0K 2M0, Canada
| | - Andy Benowicz
- Alberta Forestry and Parks, Government of Alberta, Edmonton, T6H 5T6, Canada
| | - Robert Sissons
- Parks Canada, Waterton Lakes National Park, Alberta, T0K 2M0, Canada
| | - Arezoo Zamany
- Natural Resources Canada, Canadian Forest Service, Pacific Forestry Centre, 506 West Burnside Road, Victoria, BC V8Z 1M5, Canada
| | - Holly Williams
- Natural Resources Canada, Canadian Forest Service, Pacific Forestry Centre, 506 West Burnside Road, Victoria, BC V8Z 1M5, Canada
| | - Angelia Kegley
- U.S. Department of Agriculture Forest Service, Dorena Genetic Resource Center, 34963 Shoreview Drive, Cottage Grove, OR 97424, U.S.A
| | - Benjamin Rancourt
- Natural Resources Canada, Canadian Forest Service, Pacific Forestry Centre, 506 West Burnside Road, Victoria, BC V8Z 1M5, Canada
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Ackah M, Boateng NAS, Dhanasekaran S, Zhang H, Yang Q. Genome wide and comprehensive analysis of the cytochrome P450 (CYPs) gene family in Pyrus bretschneideri: Expression patterns during Sporidiobolus pararoseus Y16 enhanced with ascorbic acid (VC) treatment. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 206:108303. [PMID: 38154299 DOI: 10.1016/j.plaphy.2023.108303] [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: 09/08/2023] [Revised: 11/02/2023] [Accepted: 12/21/2023] [Indexed: 12/30/2023]
Abstract
Cytochrome P450s (CYPs) constitute the largest group of enzymes in plants and are involved in a variety of processes related to growth and protection. However, the CYP gene superfamily in pear (Pyrus bretschneideri) and their characteristics is unclear. Through a comprehensive genome-wide analysis, this article identified a total of 74 CYP genes in the P. bretschneideri genome, which were categorized into fourteen families. Motif analysis reveals that most of the ten motifs predicted were with the p450 conserved domain. The majority of the CYP genes have exon arrangements. Furthermore, promoter analysis unveiled a multitude of cis-acting elements associated with diverse responsiveness including hormones, light responsive, anoxic specific inducibility and anaerobic induction. Analysis of the transcriptome data reveal that about 80% of the pear CYPs genes were upregulated and they were positively correlated with the antioxidant's parameters such as total flavonoids and total phenol content as well as ABTS and DPPH radicals. RT-qPCR analysis confirmed that the CYP genes could be regulated in pear. Collectively, our results reveal comprehensive insights into the CYP superfamily in pear and make a valuable contribution to the ongoing process of functional validation.
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Affiliation(s)
- Michael Ackah
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, 212013, Jiangsu, People's Republic of China
| | - Nana Adwoa Serwah Boateng
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, 212013, Jiangsu, People's Republic of China; Ho Technical University, P.O.BOX HP 217, Ho, Volta Region, Ghana
| | - Solairaj Dhanasekaran
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, 212013, Jiangsu, People's Republic of China
| | - Hongyin Zhang
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, 212013, Jiangsu, People's Republic of China
| | - Qiya Yang
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, 212013, Jiangsu, People's Republic of China.
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3
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Chen S, Liu H, Yangzong Z, Gardea-Torresdey JL, White JC, Zhao L. Seed Priming with Reactive Oxygen Species-Generating Nanoparticles Enhanced Maize Tolerance to Multiple Abiotic Stresses. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:19932-19941. [PMID: 37975618 DOI: 10.1021/acs.est.3c07339] [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: 11/19/2023]
Abstract
Climate change-induced extreme weather events (heat, cold, drought, and flooding) will severely affect crop production. Increasing the resilience of crops to fluctuating environmental conditions is critically important. Here, we report that nanomaterials (NMs) with reactive oxygen species (ROS)-generating properties can be used as seed priming agents to simultaneously enhance the tolerance of maize seeds and seedlings to diverse and even multiple stresses. Maize seeds primed with 40 mg/L silver nanoparticles (AgNPs) exhibited accelerated seed germination and an increased germination rate, greater seedling vigor, and better seedling growth under drought (10% and 20% PEG), saline (50 and 100 mM NaCl), and cold (15 °C) stress conditions, indicating enhanced resilience to diverse stresses. Importantly, maize resistance to simultaneous multiple stresses (drought and cold, drought and salt, and salt and cold) was markedly enhanced. Under drought conditions, seed priming significantly boosted root hair density and length (17.3-82.7%), which enabled greater tolerance to water deficiency. RNA-seq analysis reveals that AgNPs seed priming induced a transcriptomic shift in maize seeds. Plant hormone signal transduction and MAPK signaling pathways were activated upon seed priming. Importantly, low-cost and environmentally friendly ROS-generating Fe-based NMs (Fe2O3 and Fe3O4 NPs) were also demonstrated to enhance the resistance of seeds and seedlings to drought, salt, and cold stresses. These findings demonstrate that a simple seed priming strategy can be used to significantly enhance the climate resilience of crops through modulated ROS homeostasis and that this approach could be a powerful nanoenabled tool for addressing worsening food insecurity.
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Affiliation(s)
- Si Chen
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, China
| | - Haolin Liu
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, China
| | - Zhaxi Yangzong
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, China
| | - Jorge L Gardea-Torresdey
- Chemistry and Biochemistry Department, The University of Texas at El Paso, 500 West University Avenue, El Paso, Texas 79968, United States
| | - Jason C White
- The Connecticut Agricultural Experiment Station (CAES), New Haven, Connecticut 06511, United States
| | - Lijuan Zhao
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, China
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Pei T, Zhu S, Liao W, Fang Y, Liu J, Kong Y, Yan M, Cui M, Zhao Q. Gap-free genome assembly and CYP450 gene family analysis reveal the biosynthesis of anthocyanins in Scutellaria baicalensis. HORTICULTURE RESEARCH 2023; 10:uhad235. [PMID: 38156283 PMCID: PMC10753160 DOI: 10.1093/hr/uhad235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 11/01/2023] [Indexed: 12/30/2023]
Abstract
Scutellaria baicalensis Georgi, a member of the Lamiaceae family, is a widely utilized medicinal plant. The flavones extracted from S. baicalensis contribute to numerous health benefits, including anti-inflammatory, antiviral, and anti-tumor activities. However, the incomplete genome assembly hinders biological studies on S. baicalensis. This study presents the first telomere-to-telomere (T2T) gap-free genome assembly of S. baicalensis through the integration of Pacbio HiFi, Nanopore ultra-long and Hi-C technologies. A total of 384.59 Mb of genome size with a contig N50 of 42.44 Mb was obtained, and all sequences were anchored into nine pseudochromosomes without any gap or mismatch. In addition, we analysed the major cyanidin- and delphinidin-based anthocyanins involved in the determination of blue-purple flower using a widely-targeted metabolome approach. Based on the genome-wide identification of Cytochrome P450 (CYP450) gene family, three genes (SbFBH1, 2, and 5) encoding flavonoid 3'-hydroxylases (F3'Hs) and one gene (SbFBH7) encoding flavonoid 3'5'-hydroxylase (F3'5'H) were found to hydroxylate the B-ring of flavonoids. Our studies enrich the genomic information available for the Lamiaceae family and provide a toolkit for discovering CYP450 genes involved in the flavonoid decoration.
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Affiliation(s)
- Tianlin Pei
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, CAS Center for Excellence in Molecular Plant Sciences Chenshan Plant Science Research Center, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
- State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Sanming Zhu
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, CAS Center for Excellence in Molecular Plant Sciences Chenshan Plant Science Research Center, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Taian, 271018, China
| | - Weizhi Liao
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, CAS Center for Excellence in Molecular Plant Sciences Chenshan Plant Science Research Center, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Yumin Fang
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, CAS Center for Excellence in Molecular Plant Sciences Chenshan Plant Science Research Center, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
| | - Jie Liu
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, CAS Center for Excellence in Molecular Plant Sciences Chenshan Plant Science Research Center, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
| | - Yu Kong
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, CAS Center for Excellence in Molecular Plant Sciences Chenshan Plant Science Research Center, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
| | - Mengxiao Yan
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, CAS Center for Excellence in Molecular Plant Sciences Chenshan Plant Science Research Center, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
| | - Mengying Cui
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, CAS Center for Excellence in Molecular Plant Sciences Chenshan Plant Science Research Center, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
| | - Qing Zhao
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, CAS Center for Excellence in Molecular Plant Sciences Chenshan Plant Science Research Center, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
- State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
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Yadav M, Panwar R, Rustagi A, Chakraborty A, Roy A, Singh IK, Singh A. Comprehensive and evolutionary analysis of Spodoptera litura-inducible Cytochrome P450 monooxygenase gene family in Glycine max elucidate their role in defense. FRONTIERS IN PLANT SCIENCE 2023; 14:1221526. [PMID: 38023937 PMCID: PMC10654349 DOI: 10.3389/fpls.2023.1221526] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 09/12/2023] [Indexed: 12/01/2023]
Abstract
Plants being sessile organisms and lacking both circulating phagocytic cells and somatic adaptive immune response, have thrived on various defense mechanisms to fend off insect pests and invasion of pathogens. CYP450s are the versatile enzymes, which thwart plants against insect pests by ubiquitous biosynthesis of phytohormones, antioxidants, and secondary metabolites, utilizing them as feeding deterrents and direct toxins. Therefore, a comprehensive analysis of biotic stress-responsive CYPs from Glycine max was performed to ascertain their function against S. litura-infestation. Phylogenetic analysis and evolutionary studies on conserved domains and motifs disclosed the evolutionary correspondence of these GmCYPs with already characterized members of the CYP450 superfamily and close relatedness to Medicago truncatula. These GmCYPs were mapped on 13 chromosomes; they possess 1-8 exons; they have evolved due to duplication and are localized in endoplasmic reticulumn. Further, identification of methyl-jasmonate, salicylic acid, defense responsive and flavonoid biosynthesis regulating cis-acting elements, their interaction with biotic stress regulating proteins and their differential expression in diverse types of tissues, and during herbivory, depicted their responsiveness to biotic stress. Three-dimensional homology modelling of GmCYPs, docking with heme cofactor required for their catalytic activity and enzyme-substrate interactions were performed to understand the functional mechanism of their action. Moreover, to gain insight into their involvement in plant defense, gene expression analysis was evaluated, which revealed differential expression of 11 GmCYPs upon S. litura-infestation, 12 GmCYPs on wounding while foliar spray of ethylene, methyl-jasmonate and salicylic acid differentially regulated 11 GmCYPs, 6 GmCYPs, and 10 GmCYPs respectively. Our study comprehensively analysed the underlying mechanism of GmCYPs function during S. litura-infestation, which can be further utilized for functional characterization to develop new strategies for enhancing soybean resistance to insect pests.
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Affiliation(s)
- Manisha Yadav
- Department of Botany, Hansraj College, University of Delhi, Delhi, India
- J C Bose Center for Plant Genomics, Hansraj College, University of Delhi, Delhi, India
| | - Ruby Panwar
- Department of Botany, Hansraj College, University of Delhi, Delhi, India
- Department of Botany, Gargi College, University of Delhi, Delhi, India
| | - Anjana Rustagi
- Department of Botany, Gargi College, University of Delhi, Delhi, India
| | - Amrita Chakraborty
- EVA 4.0 Unit, Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Prague, Czechia
| | - Amit Roy
- Forest Molecular Entomology Lab, EXTEMIT-K, EVA 4.0, Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Prague, Czechia
| | - Indrakant K. Singh
- Molecular Biology Research Lab, Department of Zoology, Deshbandhu College, University of Delhi, New Delhi, India
| | - Archana Singh
- Department of Botany, Hansraj College, University of Delhi, Delhi, India
- J C Bose Center for Plant Genomics, Hansraj College, University of Delhi, Delhi, India
- Department of Botany, Gargi College, University of Delhi, Delhi, India
- Department of Plant Molecular Biology, University of Delhi, New Delhi, India
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Sahoo B, Nayak I, Parameswaran C, Kesawat MS, Sahoo KK, Subudhi HN, Balasubramaniasai C, Prabhukarthikeyan SR, Katara JL, Dash SK, Chung SM, Siddiqui MH, Alamri S, Samantaray S. A Comprehensive Genome-Wide Investigation of the Cytochrome 71 ( OsCYP71) Gene Family: Revealing the Impact of Promoter and Gene Variants (Ser33Leu) of OsCYP71P6 on Yield-Related Traits in Indica Rice ( Oryza sativa L.). PLANTS (BASEL, SWITZERLAND) 2023; 12:3035. [PMID: 37687282 PMCID: PMC10490456 DOI: 10.3390/plants12173035] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 08/17/2023] [Accepted: 08/21/2023] [Indexed: 09/10/2023]
Abstract
The cytochrome P450 (CYP450) gene family plays a critical role in plant growth and developmental processes, nutrition, and detoxification of xenobiotics in plants. In the present research, a comprehensive set of 105 OsCYP71 family genes was pinpointed within the genome of indica rice. These genes were categorized into twelve distinct subfamilies, where members within the same subgroup exhibited comparable gene structures and conserved motifs. In addition, 105 OsCYP71 genes were distributed across 11 chromosomes, and 36 pairs of OsCYP71 involved in gene duplication events. Within the promoter region of OsCYP71, there exists an extensive array of cis-elements that are associated with light responsiveness, hormonal regulation, and stress-related signaling. Further, transcriptome profiling revealed that a majority of the genes exhibited responsiveness to hormones and were activated across diverse tissues and developmental stages in rice. The OsCYP71P6 gene is involved in insect resistance, senescence, and yield-related traits in rice. Hence, understanding the association between OsCYP71P6 genetic variants and yield-related traits in rice varieties could provide novel insights for rice improvement. Through the utilization of linear regression models, a total of eight promoters were identified, and a specific gene variant (Ser33Leu) within OsCYP71P6 was found to be linked to spikelet fertility. Additionally, different alleles of the OsCYP71P6 gene identified through in/dels polymorphism in 131 rice varieties were validated for their allelic effects on yield-related traits. Furthermore, the single-plant yield, spikelet number, panicle length, panicle weight, and unfilled grain per panicle for the OsCYP71P6-1 promoter insertion variant were found to contribute 20.19%, 13.65%, 5.637%, 8.79%, and 36.86% more than the deletion variant, respectively. These findings establish a robust groundwork for delving deeper into the functions of OsCYP71-family genes across a range of biological processes. Moreover, these findings provide evidence that allelic variation in the promoter and amino acid substitution of Ser33Leu in the OsCYP71P6 gene could potentially impact traits related to rice yield. Therefore, the identified promoter variants in the OsCYP71P6 gene could be harnessed to amplify rice yields.
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Affiliation(s)
- Bijayalaxmi Sahoo
- Crop Improvement Division, ICAR-National Rice Research Institute, Cuttack 753006, India; (B.S.); (I.N.); (H.N.S.); (C.B.); (J.L.K.); (S.K.D.); (S.S.)
- Department of Botany, Ravenshaw University, Cuttack 753006, India;
| | - Itishree Nayak
- Crop Improvement Division, ICAR-National Rice Research Institute, Cuttack 753006, India; (B.S.); (I.N.); (H.N.S.); (C.B.); (J.L.K.); (S.K.D.); (S.S.)
- Department of Botany, Utkal University, Bhubaneswar 751004, India
| | - C. Parameswaran
- Crop Improvement Division, ICAR-National Rice Research Institute, Cuttack 753006, India; (B.S.); (I.N.); (H.N.S.); (C.B.); (J.L.K.); (S.K.D.); (S.S.)
| | - Mahipal Singh Kesawat
- Department of Genetics and Plant Breeding, Faculty of Agriculture, Sri University, Cuttack 754006, India
| | | | - H. N. Subudhi
- Crop Improvement Division, ICAR-National Rice Research Institute, Cuttack 753006, India; (B.S.); (I.N.); (H.N.S.); (C.B.); (J.L.K.); (S.K.D.); (S.S.)
| | - Cayalvizhi Balasubramaniasai
- Crop Improvement Division, ICAR-National Rice Research Institute, Cuttack 753006, India; (B.S.); (I.N.); (H.N.S.); (C.B.); (J.L.K.); (S.K.D.); (S.S.)
| | | | - Jawahar Lal Katara
- Crop Improvement Division, ICAR-National Rice Research Institute, Cuttack 753006, India; (B.S.); (I.N.); (H.N.S.); (C.B.); (J.L.K.); (S.K.D.); (S.S.)
| | - Sushanta Kumar Dash
- Crop Improvement Division, ICAR-National Rice Research Institute, Cuttack 753006, India; (B.S.); (I.N.); (H.N.S.); (C.B.); (J.L.K.); (S.K.D.); (S.S.)
| | - Sang-Min Chung
- Department of Life Science, Dongguk University-Seoul, Ilsandong-gu, Goyang-si 10326, Gyeonggi-do, Republic of Korea;
| | - Manzer H. Siddiqui
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia; (M.H.S.); (S.A.)
| | - Saud Alamri
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia; (M.H.S.); (S.A.)
| | - Sanghamitra Samantaray
- Crop Improvement Division, ICAR-National Rice Research Institute, Cuttack 753006, India; (B.S.); (I.N.); (H.N.S.); (C.B.); (J.L.K.); (S.K.D.); (S.S.)
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Jiu S, Chen B, Dong X, Lv Z, Wang Y, Yin C, Xu Y, Zhang S, Zhu J, Wang J, Liu X, Sun W, Yang G, Li M, Li S, Zhang Z, Liu R, Wang L, Manzoor MA, José QG, Wang S, Lei Y, Yang L, Dirlewanger E, Dong Y, Zhang C. Chromosome-scale genome assembly of Prunus pusilliflora provides novel insights into genome evolution, disease resistance, and dormancy release in Cerasus L. HORTICULTURE RESEARCH 2023; 10:uhad062. [PMID: 37220556 PMCID: PMC10200261 DOI: 10.1093/hr/uhad062] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 04/02/2023] [Indexed: 05/25/2023]
Abstract
Prunus pusilliflora is a wild cherry germplasm resource distributed mainly in Southwest China. Despite its ornamental and economic value, a high-quality assembled P. pusilliflora genome is unavailable, hindering our understanding of its genetic background, population diversity, and evolutionary processes. Here, we de novo assembled a chromosome-scale P. pusilliflora genome using Oxford Nanopore, Illumina, and chromosome conformation capture sequencing. The assembled genome size was 309.62 Mb, with 76 scaffolds anchored to eight pseudochromosomes. We predicted 33 035 protein-coding genes, functionally annotated 98.27% of them, and identified repetitive sequences covering 49.08% of the genome. We found that P. pusilliflora is closely related to Prunus serrulata and Prunus yedoensis, having diverged from them ~41.8 million years ago. A comparative genomic analysis revealed that P. pusilliflora has 643 expanded and 1128 contracted gene families. Furthermore, we found that P. pusilliflora is more resistant to Colletotrichum viniferum, Phytophthora capsici, and Pseudomonas syringae pv. tomato (Pst) DC3000 infections than cultivated Prunus avium. P. pusilliflora also has considerably more nucleotide-binding site-type resistance gene analogs than P. avium, which explains its stronger disease resistance. The cytochrome P450 and WRKY families of 263 and 61 proteins were divided into 42 and 8 subfamilies respectively in P. pusilliflora. Furthermore, 81 MADS-box genes were identified in P. pusilliflora, accompanying expansions of the SVP and AGL15 subfamilies and loss of the TM3 subfamily. Our assembly of a high-quality P. pusilliflora genome will be valuable for further research on cherries and molecular breeding.
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Affiliation(s)
| | | | - Xiao Dong
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, Yunnan Province, 650201, P. R. China
| | - Zhengxin Lv
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Yuxuan Wang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Chunjin Yin
- Dali Bai Autonomous Prefecture Academy of Agricultural Sciences and Extension, Dali, Yunnan Province, 671600, P. R. China
| | - Yan Xu
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Sen Zhang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Jijun Zhu
- Shanghai Botanical Garden, Shanghai, 200231, P. R. China
| | - Jiyuan Wang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Xunju Liu
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Wanxia Sun
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Guoqian Yang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Meng Li
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu Province, 200037, P. R. China
| | - Shufeng Li
- Dali Bai Autonomous Prefecture Academy of Agricultural Sciences and Extension, Dali, Yunnan Province, 671600, P. R. China
| | - Zhuo Zhang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Ruie Liu
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Lei Wang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Muhammad Aamir Manzoor
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Quero-García José
- INRAe, UMR 1332 de Biologie du Fruit et Pathologie, 33140 Villenave d'Ornon, France
| | - Shiping Wang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Yahui Lei
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, Yunnan Province, 650201, P. R. China
| | - Ling Yang
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, Yunnan Province, 650201, P. R. China
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Liu X, Gong Q, Zhao C, Wang D, Ye X, Zheng G, Wang Y, Cao J, Sun C. Genome-wide analysis of cytochrome P450 genes in Citrus clementina and characterization of a CYP gene encoding flavonoid 3'-hydroxylase. HORTICULTURE RESEARCH 2023; 10:uhac283. [PMID: 36818367 PMCID: PMC9930397 DOI: 10.1093/hr/uhac283] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 12/07/2022] [Indexed: 06/18/2023]
Abstract
Cytochrome P450s (CYPs) are the largest family of enzymes in plant and play multifarious roles in development and defense but the available information about the CYP superfamily in citrus is very limited. Here we provide a comprehensive genome-wide analysis of the CYP superfamily in Citrus clementina genome, identifying 301 CYP genes grouped into ten clans and 49 families. The characteristics of both gene structures and motif compositions strongly supported the reliability of the phylogenetic relationship. Duplication analysis indicated that tandem duplication was the major driving force of expansion for this superfamily. Promoter analysis revealed numerous cis-acting elements related to various responsiveness. RNA-seq data elucidated their expression patterns in citrus fruit peel both during development and in response to UV-B. Furthermore, we characterize a UV-B-induced CYP gene (Ciclev10019637m, designated CitF3'H) as a flavonoid 3'-hydroxylase for the first time. CitF3'H catalyzed numerous flavonoids and favored naringenin in yeast assays. Virus-induced silencing of CitF3'H in citrus seedlings significantly reduced the levels of 3'-hydroxylated flavonoids and their derivatives. These results together with the endoplasmic reticulum-localization of CitF3'H in plant suggest that this enzyme is responsible for the biosynthesis of 3'-hydroxylated flavonoids in citrus. Taken together, our findings provide extensive information about the CYP superfamily in citrus and contribute to further functional verification.
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Affiliation(s)
- Xiaojuan Liu
- Laboratory of Fruit Quality Biology, The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang Provincial Key Laboratory of Integrative Biology of Horticultural Plants, Zhejiang University, Hangzhou, China
| | - Qin Gong
- Laboratory of Fruit Quality Biology, The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang Provincial Key Laboratory of Integrative Biology of Horticultural Plants, Zhejiang University, Hangzhou, China
| | - Chenning Zhao
- Laboratory of Fruit Quality Biology, The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang Provincial Key Laboratory of Integrative Biology of Horticultural Plants, Zhejiang University, Hangzhou, China
| | - Dengliang Wang
- Institute of Fruit Tree Research, Quzhou Academy of Agriculture and Forestry Acience, Quzhou, China
| | - Xianming Ye
- Research and Development Department, Zhejiang Jianong Fruit &Vegetable Co., Ltd, Quzhou, China
| | - Guixia Zheng
- Research and Development Department, Zhejiang Jianong Fruit &Vegetable Co., Ltd, Quzhou, China
| | - Yue Wang
- Laboratory of Fruit Quality Biology, The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang Provincial Key Laboratory of Integrative Biology of Horticultural Plants, Zhejiang University, Hangzhou, China
| | - Jinping Cao
- Laboratory of Fruit Quality Biology, The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang Provincial Key Laboratory of Integrative Biology of Horticultural Plants, Zhejiang University, Hangzhou, China
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9
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Han SA, Xie H, Wang M, Zhang JG, Xu YH, Zhu XH, Caikasimu A, Zhou XW, Mai SL, Pan MQ, Zhang W. Transcriptome and metabolome reveal the effects of three canopy types on the flavonoids and phenolic acids in 'Merlot' (Vitis vinifera L.) berry pericarp. Food Res Int 2023; 163:112196. [PMID: 36596135 DOI: 10.1016/j.foodres.2022.112196] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 11/14/2022] [Accepted: 11/15/2022] [Indexed: 11/21/2022]
Abstract
The flavonoids and phenolic acids in grape berries greatly influence the quality of wine. Various methods are used to shape and prune grapevines, but their effects on the flavonoids and phenolic acids remain unclear. The flavonoids and phenolic acids in the berry pericarps from grapevines pruned using three types of leaf canopy, namely, V-shaped, T-shaped, and vertical shoot-positioned (VSP) canopies, were compared in this study. Results showed that the V-shaped canopy was more favorable for the accumulation of flavonoids and phenolic acids. Transcriptome and metabolome analyses revealed that the differentially expressed genes (DEGs) and differentially regulated metabolites (DRMs) were significantly enriched in the flavonoid and phenylpropanoid biosynthesis pathways. A total of 96 flavonoids and 32 phenolic acids were detected among the DRMs. Their contents were higher in the V-shaped canopy than in the T-shaped and VSP canopies. Conjoint analysis of transcriptome and metabolome showed that nine DEGs (e.g., cytochrome P450 98A9 and 98A2) were significantly correlated to nine phenolic acids (e.g., gentisic acid and neochlorogenic acid) and three genes (i.e., chalcone isomerase, UDP-glycosyltransferase 88A1, and caffeoyl-CoA O-methyltransferase) significantly correlated to 15 flavonoids (e.g., baimaside and tricin-7-O-rutinoside). These genes may be involved in the regulation of various flavonoids and phenolic acids in grape berries, but their functions need validation. This study provides novel insights into the effects of leaf canopy on flavonoids and phenolic acids in the skin of grape berries and reveals the potential regulatory networks involved in this phenomenon.
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Affiliation(s)
- Shou-An Han
- Institute of Horticultural Crops, Xinjiang Academy of Agricultural Science, Urumqi 830001, Xinjiang, China; Scientific Observing and Experimental Station of Pomology (Xinjiang), Ministry of Agriculture and Rural Affairs, Urumqi 830000, Xinjiang, China; Xinjiang Crop Chemical Regulation Engineering Technology Research Center, Urumqi 830091, Xinjiang, China; Key Laboratory of Horticulture Crop Genomics Research and Genetic Improvement in Xinjiang
| | - Hui Xie
- Institute of Horticultural Crops, Xinjiang Academy of Agricultural Science, Urumqi 830001, Xinjiang, China; Scientific Observing and Experimental Station of Pomology (Xinjiang), Ministry of Agriculture and Rural Affairs, Urumqi 830000, Xinjiang, China; Xinjiang Crop Chemical Regulation Engineering Technology Research Center, Urumqi 830091, Xinjiang, China; Key Laboratory of Horticulture Crop Genomics Research and Genetic Improvement in Xinjiang
| | - Min Wang
- Institute of Horticultural Crops, Xinjiang Academy of Agricultural Science, Urumqi 830001, Xinjiang, China; Scientific Observing and Experimental Station of Pomology (Xinjiang), Ministry of Agriculture and Rural Affairs, Urumqi 830000, Xinjiang, China; Xinjiang Crop Chemical Regulation Engineering Technology Research Center, Urumqi 830091, Xinjiang, China; Key Laboratory of Horticulture Crop Genomics Research and Genetic Improvement in Xinjiang
| | - Jun-Gao Zhang
- Xinjiang Crop Chemical Regulation Engineering Technology Research Center, Urumqi 830091, Xinjiang, China; Institute of Nuclear Technology and Biotechnology of Xinjiang Academy of Agricultural Sciences, Urumqi 830001, Xinjiang, China
| | - Yu-Hui Xu
- Adsen Biotechnology Co, Ltd, Urumqi 830000, Xinjiang, China
| | - Xue-Hui Zhu
- Institute of Horticultural Crops, Xinjiang Academy of Agricultural Science, Urumqi 830001, Xinjiang, China
| | - Aiermaike Caikasimu
- Institute of Horticultural Crops, Xinjiang Academy of Agricultural Science, Urumqi 830001, Xinjiang, China; Scientific Observing and Experimental Station of Pomology (Xinjiang), Ministry of Agriculture and Rural Affairs, Urumqi 830000, Xinjiang, China
| | - Xue-Wei Zhou
- Institute of Horticultural Crops, Xinjiang Academy of Agricultural Science, Urumqi 830001, Xinjiang, China
| | - Si-Le Mai
- Institute of Horticultural Crops, Xinjiang Academy of Agricultural Science, Urumqi 830001, Xinjiang, China
| | - Ming-Qi Pan
- Institute of Horticultural Crops, Xinjiang Academy of Agricultural Science, Urumqi 830001, Xinjiang, China; Scientific Observing and Experimental Station of Pomology (Xinjiang), Ministry of Agriculture and Rural Affairs, Urumqi 830000, Xinjiang, China; Xinjiang Crop Chemical Regulation Engineering Technology Research Center, Urumqi 830091, Xinjiang, China
| | - Wen Zhang
- Institute of Horticultural Crops, Xinjiang Academy of Agricultural Science, Urumqi 830001, Xinjiang, China; Scientific Observing and Experimental Station of Pomology (Xinjiang), Ministry of Agriculture and Rural Affairs, Urumqi 830000, Xinjiang, China; Xinjiang Crop Chemical Regulation Engineering Technology Research Center, Urumqi 830091, Xinjiang, China; Key Laboratory of Horticulture Crop Genomics Research and Genetic Improvement in Xinjiang.
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