1
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Sonsungsan P, Nganga ML, Lieberman MC, Amundson KR, Stewart V, Plaimas K, Comai L, Henry IM. A k-mer-based bulked segregant analysis approach to map seed traits in unphased heterozygous potato genomes. G3 (BETHESDA, MD.) 2024; 14:jkae035. [PMID: 38366577 PMCID: PMC10989861 DOI: 10.1093/g3journal/jkae035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 02/06/2024] [Accepted: 02/09/2024] [Indexed: 02/18/2024]
Abstract
High-throughput sequencing-based methods for bulked segregant analysis (BSA) allow for the rapid identification of genetic markers associated with traits of interest. BSA studies have successfully identified qualitative (binary) and quantitative trait loci (QTLs) using QTL mapping. However, most require population structures that fit the models available and a reference genome. Instead, high-throughput short-read sequencing can be combined with BSA of k-mers (BSA-k-mer) to map traits that appear refractory to standard approaches. This method can be applied to any organism and is particularly useful for species with genomes diverged from the closest sequenced genome. It is also instrumental when dealing with highly heterozygous and potentially polyploid genomes without phased haplotype assemblies and for which a single haplotype can control a trait. Finally, it is flexible in terms of population structure. Here, we apply the BSA-k-mer method for the rapid identification of candidate regions related to seed spot and seed size in diploid potato. Using a mixture of F1 and F2 individuals from a cross between 2 highly heterozygous parents, candidate sequences were identified for each trait using the BSA-k-mer approach. Using parental reads, we were able to determine the parental origin of the loci. Finally, we mapped the identified k-mers to a closely related potato genome to validate the method and determine the genomic loci underlying these sequences. The location identified for the seed spot matches with previously identified loci associated with pigmentation in potato. The loci associated with seed size are novel. Both loci are relevant in future breeding toward true seeds in potato.
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Affiliation(s)
- Pajaree Sonsungsan
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok 10330, Thailand
| | - Mwaura Livingstone Nganga
- Department of Plant Biology and Genome Center, University of California, Davis, Davis, CA 95616, USA
| | - Meric C Lieberman
- Department of Plant Biology and Genome Center, University of California, Davis, Davis, CA 95616, USA
| | - Kirk R Amundson
- Department of Plant Biology and Genome Center, University of California, Davis, Davis, CA 95616, USA
| | - Victoria Stewart
- Department of Plant Biology and Genome Center, University of California, Davis, Davis, CA 95616, USA
| | - Kitiporn Plaimas
- Omics Science and Bioinformatics Center, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
- Advanced Virtual and Intelligent Computing (AVIC) Center, Department of Mathematics and Computer Science, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Luca Comai
- Department of Plant Biology and Genome Center, University of California, Davis, Davis, CA 95616, USA
| | - Isabelle M Henry
- Department of Plant Biology and Genome Center, University of California, Davis, Davis, CA 95616, USA
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2
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Chen BC, Wu XJ, Dong QJ, Xiao JP. Screening and functional analysis of StMYB transcription factors in pigmented potato under low-temperature treatment. BMC Genomics 2024; 25:283. [PMID: 38500027 PMCID: PMC10946176 DOI: 10.1186/s12864-024-10059-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Accepted: 01/29/2024] [Indexed: 03/20/2024] Open
Abstract
MYB transcription factors play an extremely important regulatory role in plant responses to stress and anthocyanin synthesis. Cloning of potato StMYB-related genes can provide a theoretical basis for the genetic improvement of pigmented potatoes. In this study, two MYB transcription factors, StMYB113 and StMYB308, possibly related to anthocyanin synthesis, were screened under low-temperature conditions based on the low-temperature-responsive potato StMYB genes family analysis obtained by transcriptome sequencing. By analyzed the protein properties and promoters of StMYB113 and StMYB308 and their relative expression levels at different low-temperature treatment periods, it is speculated that StMYB113 and StMYB308 can be expressed in response to low temperature and can promote anthocyanin synthesis. The overexpression vectors of StMYB113 and StMYB308 were constructed for transient transformation tobacco. Color changes were observed, and the expression levels of the structural genes of tobacco anthocyanin synthesis were determined. The results showed that StMYB113 lacking the complete MYB domain could not promote the accumulation of tobacco anthocyanins, while StMYB308 could significantly promote the accumulation involved in tobacco anthocyanins. This study provides a theoretical reference for further study of the mechanism of StMYB113 and StMYB308 transcription factors in potato anthocyanin synthesis.
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Affiliation(s)
- Bi-Cong Chen
- College of Agronomy and Biotechnology, Yunnan Agricultural University, No.95 Jinhei Road, Panlong District, Kunming City, 650201, Yunnan, China
| | - Xiao-Jie Wu
- College of Agronomy and Biotechnology, Yunnan Agricultural University, No.95 Jinhei Road, Panlong District, Kunming City, 650201, Yunnan, China
| | - Qiu-Ju Dong
- College of Agronomy and Biotechnology, Yunnan Agricultural University, No.95 Jinhei Road, Panlong District, Kunming City, 650201, Yunnan, China
| | - Ji-Ping Xiao
- College of Agronomy and Biotechnology, Yunnan Agricultural University, No.95 Jinhei Road, Panlong District, Kunming City, 650201, Yunnan, China.
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3
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Malankar NN, Kondhare KR, Saha K, Mantri M, Banerjee AK. The phased short-interfering RNA siRD29(-) regulates GIBBERELLIN 3-OXIDASE 3 during stolon-to-tuber transitions in potato. PLANT PHYSIOLOGY 2023; 193:2555-2572. [PMID: 37691396 DOI: 10.1093/plphys/kiad493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 08/10/2023] [Accepted: 08/22/2023] [Indexed: 09/12/2023]
Abstract
Phased short-interfering RNAs (phasiRNAs) fine tune various stages of growth, development, and stress responses in plants. Potato (Solanum tuberosum) tuberization is a complex process, wherein a belowground modified stem (stolon) passes through developmental stages like swollen stolon and minituber before it matures to a potato. Previously, we identified several phasiRNA-producing loci (PHAS) from stolon-to-tuber transition stages. However, whether phasiRNAs mediate tuber development remains unknown. Here, we show that a gene encoding NB-ARC DOMAIN-CONTAINING DISEASE RESISTANCE PROTEIN (StRGA4; a PHAS locus) is targeted by Stu-microRNA482c to generate phasiRNAs. Interestingly, we observed that one of the phasiRNAs, referred as short-interfering RNA D29(-), i.e. siRD29(-), targets the gibberellin (GA) biosynthesis gene GIBBERELLIN 3-OXIDASE 3 (StGA3ox3). Since regulation of bioactive GA levels in stolons controls tuber development, we hypothesized that a gene regulatory module, Stu-miR482c-StRGA4-siRD29(-)-StGA3ox3, could govern tuber development. Through transient expression assays and small RNA sequencing, generation of siRD29(-) and its phase was confirmed in planta. Notably, the expression of StGA3ox3 was higher in swollen stolon compared to stolon, whereas siRD29(-) showed a negative association with StGA3ox3 expression. Antisense (AS) lines of StGA3ox3 produced more tubers compared to wild type. As expected, StRGA4 overexpression (OE) lines had high levels of siRD29(-) and mimicked the phenotypes of StGA3ox3-AS lines, indicating the functionality of this module in potato. In vitro tuberization assays (with or without a GA inhibitor) using StGA3ox3 antisense lines and overexpression lines of StGA3ox3 or StRGA4 revealed that StGA3ox3 controls the tuber stalk development. Taken together, our findings suggest that a phasiRNA, siRD29(-), mediates the regulation of StGA3ox3 during stolon-to-tuber transitions in potato.
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Affiliation(s)
- Nilam N Malankar
- Biology Division, Indian Institute of Science Education and Research (IISER Pune), Pune, 411008 Maharashtra, India
| | - Kirtikumar R Kondhare
- Biology Division, Indian Institute of Science Education and Research (IISER Pune), Pune, 411008 Maharashtra, India
- Biochemical Sciences Division, CSIR - National Chemical Laboratory (CSIR-NCL), Pune, 411008 Maharashtra, India
| | - Kishan Saha
- Biology Division, Indian Institute of Science Education and Research (IISER Pune), Pune, 411008 Maharashtra, India
| | - Mohit Mantri
- Biology Division, Indian Institute of Science Education and Research (IISER Pune), Pune, 411008 Maharashtra, India
| | - Anjan K Banerjee
- Biology Division, Indian Institute of Science Education and Research (IISER Pune), Pune, 411008 Maharashtra, India
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4
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Zhang Z, Zhou D, Li S, Pan J, Liang J, Wu X, Wu XN, Krall L, Zhu G. Multiomics Analysis Reveals the Chemical and Genetic Bases of Pigmented Potato Tuber. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:16402-16416. [PMID: 37856829 DOI: 10.1021/acs.jafc.3c04979] [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: 10/21/2023]
Abstract
Anthocyanins and carotenoids determine the diversity of potato tuber flesh pigmentation; here, the underlying chemical and genetic bases were elucidated by multiomics analyses. A total of 31 anthocyanins and 30 carotenoids were quantified in five differently pigmented tubers. Cyanidin and pelargonidin derivatives determined the redness, while malvidin, petunidin, and delphinidin derivatives contributed to purpleness. Violaxanthin derivatives determined the light-yellow color, while zeaxanthin and antheraxanthin derivatives further enhanced the deep-yellow deposition. Integrated transcriptome and proteome analyses identified that F3'5'H highly enhanced anthocyanin biosynthesis in purple flesh and was responsible for metabolic divergence between red and purple samples. BCH2 significantly enhanced carotenoid biosynthesis in yellow samples and along with ZEP, NCED1, and CCD1 genes determined metabolic divergence between light and deep-yellow samples. The weighted correlation network analysis constructed a regulatory network revealing the central role of AN1 in regulating anthocyanin biosynthesis, and 10 new transcription factors related to anthocyanin and carotenoid metabolism regulation were identified. Our findings provide targeted genes controlling tuber pigmentation, which will be meaningful for the genetic manipulation of tuber quality improvement.
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Affiliation(s)
- Zhong Zhang
- Yunnan key Laboratory of Potato Biology, Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, School of Life Sciences, Yunnan Normal University, Kunming, Yunnan 650500, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Dao Zhou
- Yunnan key Laboratory of Potato Biology, Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, School of Life Sciences, Yunnan Normal University, Kunming, Yunnan 650500, China
| | - Shalan Li
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan and Center for Life Science, School of Life Sciences, Yunnan University, Kunming 650500, China
| | - Jun Pan
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Jun Liang
- Yunnan key Laboratory of Potato Biology, Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, School of Life Sciences, Yunnan Normal University, Kunming, Yunnan 650500, China
| | - Xi Wu
- Yunnan key Laboratory of Potato Biology, Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, School of Life Sciences, Yunnan Normal University, Kunming, Yunnan 650500, China
| | - Xu Na Wu
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan and Center for Life Science, School of Life Sciences, Yunnan University, Kunming 650500, China
| | - Leonard Krall
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan and Center for Life Science, School of Life Sciences, Yunnan University, Kunming 650500, China
| | - Guangtao Zhu
- Yunnan key Laboratory of Potato Biology, Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, School of Life Sciences, Yunnan Normal University, Kunming, Yunnan 650500, China
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5
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Liu F, Zhao P, Chen G, Wang Y, Yang Y. A comparative analysis of small RNA sequencing data in tubers of purple potato and its red mutant reveals small RNA regulation in anthocyanin biosynthesis. PeerJ 2023; 11:e15349. [PMID: 37223121 PMCID: PMC10202107 DOI: 10.7717/peerj.15349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 04/13/2023] [Indexed: 05/25/2023] Open
Abstract
Anthocyanins are a group of natural pigments acting as stress protectants induced by biotic/abiotic stress in plants. Although the metabolic pathway of anthocyanin has been studied in potato, the roles of miRNAs on the metabolic pathway remain unclear. In this study, a purple tetraploid potato of SD92 and its red mutant of SD140 were selected to explore the regulation mechanism of miRNA in anthocyanin biosynthesis. A comparative analysis of small RNAs between SD92 and SD140 revealed that there were 179 differentially expressed miRNAs, including 65 up- and 114 down-regulated miRNAs. Furthermore, 31 differentially expressed miRNAs were predicted to potentially regulate 305 target genes. KEGG pathway enrichment analysis for these target genes showed that plant hormone signal transduction pathway and plant-pathogen interaction pathway were significantly enriched. The correlation analysis of miRNA sequencing data and transcriptome data showed that there were 140 negative regulatory miRNA-mRNA pairs. The miRNAs included miR171 family, miR172 family, miR530b_4 and novel_mir170. The mRNAs encoded transcription factors, hormone response factors and protein kinases. All these results indicated that miRNAs might regulate anthocyanin biosynthesis through transcription factors, hormone response factors and protein kinase.
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Affiliation(s)
- Fang Liu
- Institute of Vegetables, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Peng Zhao
- Institute of Vegetables, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Guangxia Chen
- Institute of Vegetables, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Yongqiang Wang
- Institute of Vegetables, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Yuanjun Yang
- Institute of Vegetables, Shandong Academy of Agricultural Sciences, Jinan, China
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6
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Arora S, Singh AK, Chaudhary B. Coordination of floral and fiber development in cotton (Gossypium) by hormone- and flavonoid-signalling associated regulatory miRNAs. PLANT MOLECULAR BIOLOGY 2023; 112:1-18. [PMID: 37067671 DOI: 10.1007/s11103-023-01341-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 02/16/2023] [Indexed: 05/09/2023]
Abstract
Various plant development activities and stress responses are tightly regulated by various microRNAs (miRNA) and their target genes, or transcription factors in a spatiotemporal manner. Here, to exemplify how flowering-associated regulatory miRNAs synchronize their expression dynamics during floral and fiber development in cotton, constitutive expression diminution transgenic lines of auxin-signaling regulatory Gh-miR167 (35S-MIM167) were developed through target mimicry approach. 'Moderate' (58% to 80%)- and 'high' (> 80%)-Gh-miR167 diminution mimic lines showed dosage-dependent developmental deformities in anther development, pollen maturation, and fruit (= boll) formation. Cross pollination of 'moderate' 35S-MIM167 mimic lines with wild type (WT) plant partially restored boll formation and emergence of fiber initials on the ovule surface. Gh-miR167 diminution favored organ-specific transcription biases in miR159, miR166 as well as miR160, miR164, and miR172 along with their target genes during anther and petal development, respectively. Similarly, accumulative effect of percent Gh-miR167 diminution, cross regulation of its target ARF6/8 genes, and temporal mis-expression of hormone signaling- and flavonoid biosynthesis-associated regulatory miRNAs at early fiber initiation stage caused irregular fiber formation. Spatial and temporal transcription proportions of regulatory miRNAs were also found crucial for the execution of hormone- and flavonoid-dependent progression of floral and fiber development. These observations discover how assorted regulatory genetic circuits get organized in response to Gh-miR167 diminution and converge upon ensuing episodes of floral and fiber development in cotton.
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Affiliation(s)
- Sakshi Arora
- School of Biotechnology, Gautam Buddha University, Greater Noida, 201312, India
| | - Amarjeet Kumar Singh
- Center for Genetic Manipulation of Crop Plants, University of Delhi South Campus, New Delhi, 110021, India
| | - Bhupendra Chaudhary
- School of Biotechnology, Gautam Buddha University, Greater Noida, 201312, India.
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7
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Luo M, Sun X, Xu M, Tian Z. Identification of miRNAs Involving Potato- Phytophthora infestans Interaction. PLANTS (BASEL, SWITZERLAND) 2023; 12:461. [PMID: 36771544 PMCID: PMC9921761 DOI: 10.3390/plants12030461] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 01/03/2023] [Accepted: 01/17/2023] [Indexed: 06/18/2023]
Abstract
sRNAs (small RNAs) play an important role in regulation of plant immunity against a variety of pathogens. In this study, sRNA sequencing analysis was performed to identify miRNAs (microRNAs) during the interaction of potato and Phytophthora infestans. Totally, 171 potato miRNAs were identified, 43 of which were annotated in the miRNA database and 128 were assigned as novel miRNAs in this study. Those potato miRNAs may target 878 potato genes and half of them encode resistance proteins. Fifty-three potato miRNAs may target 194 P. infestans genes. Three potato miRNAs (novel 72, 133, and 140) were predicted to have targets only in the P. infestans genome. miRNAs transient expression and P. infestans inoculation assay showed that miR396, miR166, miR6149-5P, novel133, or novel140 promoted P. infestans colonization, while miR394 inhibited colonization on Nicotiana benthamiana leaves. An artificial miRNA target (amiRNA) degradation experiment demonstrated that miR394 could target both potato gene (PGSC0003DMG400034305) and P. infestans genes. miR396 targets the multicystatin gene (PGSC0003DMG400026899) and miR6149-5p could shear the galactose oxidase F-box protein gene CPR30 (PGSC0003DMG400021641). This study provides new information on the aspect of cross-kingdom immune regulation in potato-P. infestans interaction at the sRNAs regulation level.
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Affiliation(s)
- Ming Luo
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University (HZAU), Wuhan 430070, China
| | - Xinyuan Sun
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University (HZAU), Wuhan 430070, China
- Key Laboratory of Potato Biology and Biotechnology (HZAU), Ministry of Agriculture and Rural Affairs, Wuhan 430070, China
- Potato Engineering and Technology Research Center of Hubei Province (HZAU), Wuhan 430070, China
| | - Meng Xu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University (HZAU), Wuhan 430070, China
- Key Laboratory of Potato Biology and Biotechnology (HZAU), Ministry of Agriculture and Rural Affairs, Wuhan 430070, China
- Potato Engineering and Technology Research Center of Hubei Province (HZAU), Wuhan 430070, China
| | - Zhendong Tian
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University (HZAU), Wuhan 430070, China
- Key Laboratory of Potato Biology and Biotechnology (HZAU), Ministry of Agriculture and Rural Affairs, Wuhan 430070, China
- Potato Engineering and Technology Research Center of Hubei Province (HZAU), Wuhan 430070, China
- Hubei Hongshan Laboratory (HZAU), Wuhan 430070, China
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8
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Liu Y, Li Y, Liu Z, Wang L, Lin-Wang K, Zhu J, Bi Z, Sun C, Zhang J, Bai J. Integrative analysis of metabolome and transcriptome reveals a dynamic regulatory network of potato tuber pigmentation. iScience 2022; 26:105903. [PMID: 36818280 PMCID: PMC9932491 DOI: 10.1016/j.isci.2022.105903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 11/12/2022] [Accepted: 12/26/2022] [Indexed: 12/30/2022] Open
Abstract
Potatoes consist of flavonoids that provide health benefits for human consumers. To learn more about how potato tuber flavonoid accumulation and flesh pigmentation are controlled, we analyzed the transcriptomic and metabolomic profile of potato tubers from three colored potato clones at three developmental phases using an integrated approach. From the 72 flavonoids identified in pigmented flesh, differential abundance was noted for anthocyanins, flavonols, and flavones. Weighted gene co-expression network analysis further allowed modules and candidate genes that positively or negatively regulate flavonoid biosynthesis to be identified. Furthermore, an R2R3-MYB repressor StMYB3 and an R3-MYB repressor StMYBATV involved in the modulation of anthocyanin biosynthesis during tuber development were identified. Both StMYB3 and StMYBATV could interact with the cofactor StbHLH1 and repress anthocyanin biosynthesis. Our results indicate a feedback regulatory mechanism of a coordinated MYB activator-repressor network on fine-tuning of potato tuber pigmentation during tuber development.
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Affiliation(s)
- Yuhui Liu
- State Key Laboratory of Aridland Crop Science/Agronomy College, Gansu Agricultural University, Lanzhou 730070, China
| | - Yuanming Li
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China
| | - Zhen Liu
- State Key Laboratory of Aridland Crop Science/Agronomy College, Gansu Agricultural University, Lanzhou 730070, China
| | - Lei Wang
- Potato Research Center, Hebei North University, Zhangjiakou 075000, China
| | - Kui Lin-Wang
- The New Zealand Institute for Plant and Food Research Limited, Mt Albert, Private Bag 92169, Auckland Mail Centre, Auckland 1142, New Zealand
| | - Jinyong Zhu
- State Key Laboratory of Aridland Crop Science/Agronomy College, Gansu Agricultural University, Lanzhou 730070, China
| | - Zhenzhen Bi
- State Key Laboratory of Aridland Crop Science/Agronomy College, Gansu Agricultural University, Lanzhou 730070, China
| | - Chao Sun
- State Key Laboratory of Aridland Crop Science/Agronomy College, Gansu Agricultural University, Lanzhou 730070, China
| | - Junlian Zhang
- State Key Laboratory of Aridland Crop Science/Agronomy College, Gansu Agricultural University, Lanzhou 730070, China,College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China
| | - Jiangping Bai
- State Key Laboratory of Aridland Crop Science/Agronomy College, Gansu Agricultural University, Lanzhou 730070, China,Corresponding author
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9
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Wang X, Yao S, Htet WPPM, Yue Y, Zhang Z, Sun K, Chen S, Luo K, Fan D. MicroRNA828 negatively regulates lignin biosynthesis in stem of Populus tomentosa through MYB targets. TREE PHYSIOLOGY 2022; 42:1646-1661. [PMID: 35220431 DOI: 10.1093/treephys/tpac023] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 02/17/2022] [Indexed: 06/14/2023]
Abstract
Lignin biosynthesis in the sclerenchyma cells is strictly controlled by a complex network of genetic and environmental signals. In the last decades, the transcriptional regulation of lignin synthesis in woody species has been established. However, the role of microRNA-mediated post-transcriptional modulation in secondary cell wall biosynthesis remains poorly understood. Here, we identified a microRNA, miR828, involved in the regulation specific to lignin biosynthesis during stem development in Populus tomentosa Carr. miR828 is preferentially expressed in the secondary vascular tissues during stem development. Two MYB genes (MYB171 and MYB011) were validated as direct targets of miR828 by degradome analysis and green fluorescent protein signal detection. Overexpression of miR828 in poplar downregulated genes for lignin biosynthesis, resulting in reduced lignin content in cell walls. Conversely, suppression of miR828 in plants by the short tandem target mimics elevated the expression of lignin biosynthetic genes and increased lignin deposition. We further revealed that poplar MYB171, as the most abundant miR828 target in the stem, is a positive regulator for lignin biosynthesis. Transient expression assays showed that both MYB171 and MYB011 activated PAL1 and CCR2 transcription, whereas the introduction of miR828 significantly suppressed their expression that was induced by MYB171 or MYB011. Collectively, our results demonstrate that the miR828-MYBs module precisely regulates lignin biosynthesis during the stem development in P. tomentosa through transcriptional and post-transcriptional manners.
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Affiliation(s)
- Xianqiang Wang
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing 400715, China
| | - Shu Yao
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing 400715, China
| | - Win Pa Pa Myo Htet
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing 400715, China
| | - Yuchen Yue
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing 400715, China
| | - Zhuanzhuan Zhang
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing 400715, China
| | - Kuan Sun
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing 400715, China
| | - Sijie Chen
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing 400715, China
| | - Keming Luo
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing 400715, China
- Key Laboratory of Eco-environments of Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing 400715, China
| | - Di Fan
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing 400715, China
- Key Laboratory of Eco-environments of Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing 400715, China
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10
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Pandey J, Scheuring DC, Koym JW, Vales MI. Genomic regions associated with tuber traits in tetraploid potatoes and identification of superior clones for breeding purposes. FRONTIERS IN PLANT SCIENCE 2022; 13:952263. [PMID: 35937326 PMCID: PMC9354404 DOI: 10.3389/fpls.2022.952263] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 06/29/2022] [Indexed: 05/05/2023]
Abstract
In potato breeding, morphological tuber traits are important selection targets to meet the demands of the fresh and processing markets. Understanding the genetic basis of tuber traits should guide selection and improve breeding efficiencies. However, this is challenging in potato due to the complexity of the traits and the polyploid nature of the potato genome. High-throughput affordable molecular markers and new software specific for polyploid species have the potential to unlock previously unattainable levels of understanding of the genetic basis of tuber traits in tetraploid potato. In this study, we genotyped a diversity panel of 214 advanced clones with the 22 K SNP potato array and phenotyped it in three field environments in Texas. We conducted a genome-wide association study using the GWASpoly software package to identify genomic regions associated with tuber morphological traits. Some of the QTLs discovered confirmed prior studies, whereas others were discovered for the first time. The main QTL for tuber shape was detected on chromosome 10 and explained 5.8% of the phenotypic variance. GWAS analysis of eye depth detected a significant QTL on chromosome 10 and explained 3.9% of the phenotypic variance. Another QTL peak for eye depth on chromosome 5 was located near the CDF1 gene, an important regulator of maturity in potato. Our study found that multiple QTLs govern russeting in potato. A major QTL for flesh color on chromosome 3 that explained 26% of the phenotypic variance likely represents the Y locus responsible for yellow flesh in potato tubers. Several QTLs were detected for purple skin color on chromosome 11. Furthermore, genomic estimated breeding values were obtained, which will aid in the early identification of superior parental clones that should increase the chances of producing progenies with higher frequencies of the desired tuber traits. These findings will contribute to a better understanding of the genetic basis of morphological traits in potato, as well as to identifying parents with the best breeding values to improve selection efficiency in our potato breeding program.
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Affiliation(s)
- Jeewan Pandey
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, United States
| | - Douglas C. Scheuring
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, United States
| | - Jeffrey W. Koym
- Texas A&M University AgriLife Research and Extension Center, Lubbock, TX, United States
| | - M. Isabel Vales
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, United States
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11
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Lin F, Chen SP, Lin KH, Chen C, Yao F, Zhong L, Chen W, Kuo YW. Integrated small RNA profiling and degradome analysis of Anthurium andraeanum cultivars with different-colored spathes. JOURNAL OF PLANT RESEARCH 2022; 135:609-626. [PMID: 35534649 DOI: 10.1007/s10265-022-01394-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 04/24/2022] [Indexed: 06/14/2023]
Abstract
MicroRNAs (miRNAs) are known to play vital roles in coloration of leaves, flowers, and fruits in plants. However, their functions in spathe coloration are poorly known. Anthurium andraeanum is a popular ornamental plant with various spathe colors. In this study, small RNA and degradome libraries from three A. andraeanum cultivars with different-colored spathes were constructed and sequenced. Illumina sequencing resulted in 94 conserved miRNAs, and 34 novel miRNAs in total were then identified based on precursor sequences and hairpin structures. Differential expression analysis showed that 52, 51, and 49 miRNAs were differentially expressed in comparisons of orange- versus white-colored spathe, purple- versus white-colored spathe, and purple- versus orange-colored spathe, respectively. The expression patterns of miRNAs and their corresponding targets involved in spathe coloration were further analyzed, and displayed that miR156b and miR529 were highly abundant in the spathes with higher anthocyanin content. These two miRNAs co-targeted a gene encoding SPL17, which may function as a negative regulator in anthocyanin accumulation. In addition, miR408 was also abundantly expressed in purple- and orange-colored spathes, and its typical targets were also identified. This comprehensive integrated analysis provides insight into the miRNA-mediated genetic regulation in spathe coloration of A. andraeanum.
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Affiliation(s)
- Fazhuang Lin
- Institute of Flowers, Sanming Academy of Agricultural Sciences, Sanming, 365000, Fujian, China
| | - Shi-Peng Chen
- Institute of Dryland Crops, Sanming Academy of Agricultural Sciences, Sanming, 365000, Fujian, China
| | - Kuan-Hung Lin
- Department of Horticulture and Biotechnology, Chinese Culture University, Taipei, 11114, Taiwan
| | - Changming Chen
- Institute of Flowers, Sanming Academy of Agricultural Sciences, Sanming, 365000, Fujian, China
| | - Fengqin Yao
- Institute of Flowers, Sanming Academy of Agricultural Sciences, Sanming, 365000, Fujian, China
| | - Linshan Zhong
- Institute of Flowers, Sanming Academy of Agricultural Sciences, Sanming, 365000, Fujian, China
| | - Weiting Chen
- Institute of Flowers, Sanming Academy of Agricultural Sciences, Sanming, 365000, Fujian, China
| | - Yun-Wei Kuo
- Institute of Flowers, Sanming Academy of Agricultural Sciences, Sanming, 365000, Fujian, China.
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12
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Wu X, Ma Y, Wu J, Wang P, Zhang Z, Xie R, Liu J, Fan B, Wei W, Nie LZ, Liu X. Identification of microRNAs and their target genes related to the accumulation of anthocyanin in purple potato tubers ( Solanum tuberosum). PLANT DIRECT 2022; 6:e418. [PMID: 35865074 PMCID: PMC9289217 DOI: 10.1002/pld3.418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 05/16/2022] [Accepted: 06/04/2022] [Indexed: 06/15/2023]
Abstract
MicroRNAs (miRNAs) are types of endogenous non-coding small RNAs found in eukaryotes that are 18-25 nucleotides long. miRNAs are considered to be key regulatory factors of the expression of target mRNA. The roles of miRNAs involved in the regulation of anthocyanin accumulation in pigmented potatoes have not been systematically reported. In this study, the differentially expressed miRNAs and their target genes involved in the accumulation of anthocyanin during different developmental stages in purple potato (Solanum tuberosum L.) were identified using small RNA (sRNA) and degradome sequencing. A total of 275 differentially expressed miRNAs were identified in the sRNA libraries. A total of 69,387,200 raw reads were obtained from three degradome libraries. The anthocyanin responsive miRNA-mRNA modules were analyzed, and 37 miRNAs and 23 target genes were obtained. Different miRNAs regulate the key enzymes of anthocyanin synthesis in purple potato. The structural genes included phenylalanine ammonia lyase, chalcone isomerase, flavanone 3-hydroxylase, and anthocyanidin 3-O-glucosyltransferase. The regulatory genes included WD40, MYB, and SPL9. stu-miR172e-5p_L-1R-1, stu-miR828a, stu-miR29b-4-5p, stu-miR8019-5p_L-4R-3, stu-miR396b-5p, stu-miR5303f_L-7R + 2, stu-miR7997a_L-3, stu-miR7997b_L-3, stu-miR7997c_L + 3R-5_2ss2TA3AG, stu-miR156f-5p_L + 1, stu-miR156a, stu-miR156a_R-1, stu-miR156e, stu-miR858, stu-miR5021, stu-miR828 and their target genes were validated by qRT-PCR. They play important roles in the coloration and accumulation of purple potatoes. These results provide new insights into the biosynthesis of anthocyanins in pigmented potatoes.
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Affiliation(s)
- Xiaojuan Wu
- Agricultural CollegeInner Mongolia Agricultural UniversityHohhotChina
| | - Yanhong Ma
- Agricultural CollegeInner Mongolia Agricultural UniversityHohhotChina
| | - Juan Wu
- Agricultural CollegeInner Mongolia Agricultural UniversityHohhotChina
| | - Peijie Wang
- Agricultural CollegeInner Mongolia Agricultural UniversityHohhotChina
| | - Zhicheng Zhang
- Agricultural CollegeInner Mongolia Agricultural UniversityHohhotChina
- Wulanchabu Academy of Agricultural and Forest SciencesWulanchabuChina
| | - Rui Xie
- Inner Mongolia Academy of Agricultural & Animal Husbandry SciencesHohhotChina
| | - Jie Liu
- HuaSong Seed Industry (Beijing) co. LTDBeijingChina
| | - Bobo Fan
- Agricultural CollegeInner Mongolia Agricultural UniversityHohhotChina
| | - Wei Wei
- HuaSong Seed Industry (Beijing) co. LTDBeijingChina
| | - Li Zhen Nie
- Inner Mongolia Academy of Agricultural & Animal Husbandry SciencesHohhotChina
| | - Xuting Liu
- Agricultural CollegeInner Mongolia Agricultural UniversityHohhotChina
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13
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Tirumalai V, Narjala A, Swetha C, Sundar GVH, Sujith TN, Shivaprasad PV. Cultivar-specific miRNA-mediated RNA silencing in grapes. PLANTA 2022; 256:17. [PMID: 35737180 DOI: 10.1007/s00425-022-03934-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 05/28/2022] [Indexed: 06/15/2023]
Abstract
In-depth comparative degradome analysis of two domesticated grape cultivars with diverse secondary metabolite accumulation reveals differential miRNA-mediated targeting. Small (s)RNAs such as micro(mi)RNAs and secondary small interfering (si) often work as negative switches of gene expression. In plants, it is well known that miRNAs target and cleave mRNAs that have high sequence complementarity. However, it is not known if there are variations in miRNA-mediated targeting between subspecies and cultivars that have been subjected to vast genetic modifications through breeding and other selections. Here, we have used PAREsnip2 tool for analysis of degradome datasets derived from two contrasting domesticated grape cultivars having varied fruit color, habit and leaf shape. We identified several interesting variations in sRNA targeting using degradome and 5'RACE analysis between two contrasting grape cultivars that was further correlated using RNA-seq analysis. Several of the differences we identified are associated with secondary metabolic pathways. We propose possible means by which sRNAs might contribute to diversity in secondary metabolites and other development pathways between two domesticated cultivars of grapes.
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Affiliation(s)
- Varsha Tirumalai
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore, 560065, India
- SASTRA University, Thirumalaisamudram, Thanjavur, 613401, India
| | - Anushree Narjala
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore, 560065, India
- SASTRA University, Thirumalaisamudram, Thanjavur, 613401, India
| | - Chenna Swetha
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore, 560065, India
- SASTRA University, Thirumalaisamudram, Thanjavur, 613401, India
| | - G Vivek Hari Sundar
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore, 560065, India
| | - T N Sujith
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore, 560065, India
| | - P V Shivaprasad
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore, 560065, India.
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Han G, Li Y, Yang Z, Wang C, Zhang Y, Wang B. Molecular Mechanisms of Plant Trichome Development. FRONTIERS IN PLANT SCIENCE 2022; 13:910228. [PMID: 35720574 PMCID: PMC9198495 DOI: 10.3389/fpls.2022.910228] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 05/13/2022] [Indexed: 05/25/2023]
Abstract
Plant trichomes, protrusions formed from specialized aboveground epidermal cells, provide protection against various biotic and abiotic stresses. Trichomes can be unicellular, bicellular or multicellular, with multiple branches or no branches at all. Unicellular trichomes are generally not secretory, whereas multicellular trichomes include both secretory and non-secretory hairs. The secretory trichomes release secondary metabolites such as artemisinin, which is valuable as an antimalarial agent. Cotton trichomes, also known as cotton fibers, are an important natural product for the textile industry. In recent years, much progress has been made in unraveling the molecular mechanisms of trichome formation in Arabidopsis thaliana, Gossypium hirsutum, Oryza sativa, Cucumis sativus, Solanum lycopersicum, Nicotiana tabacum, and Artemisia annua. Here, we review current knowledge of the molecular mechanisms underlying fate determination and initiation, elongation, and maturation of unicellular, bicellular and multicellular trichomes in several representative plants. We emphasize the regulatory roles of plant hormones, transcription factors, the cell cycle and epigenetic modifications in different stages of trichome development. Finally, we identify the obstacles and key points for future research on plant trichome development, and speculated the development relationship between the salt glands of halophytes and the trichomes of non-halophytes, which provides a reference for future studying the development of plant epidermal cells.
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Affiliation(s)
- Guoliang Han
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Sciences, Shandong Normal University, Jinan, China
- Dongying Institute, Shandong Normal University, Dongying, China
| | - Yuxia Li
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Sciences, Shandong Normal University, Jinan, China
| | - Zongran Yang
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Sciences, Shandong Normal University, Jinan, China
| | - Chengfeng Wang
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Sciences, Shandong Normal University, Jinan, China
| | - Yuanyuan Zhang
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Sciences, Shandong Normal University, Jinan, China
| | - Baoshan Wang
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Sciences, Shandong Normal University, Jinan, China
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15
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Odgerel K, Jose J, Karsai-Rektenwald F, Ficzek G, Simon G, Végvári G, Bánfalvi Z. Effects of the repression of GIGANTEA gene StGI.04 on the potato leaf transcriptome and the anthocyanin content of tuber skin. BMC PLANT BIOLOGY 2022; 22:249. [PMID: 35596149 PMCID: PMC9121593 DOI: 10.1186/s12870-022-03636-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 05/09/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND GIGANTEA (GI) is a plant-specific, circadian clock-regulated, nuclear protein with pleiotropic functions found in many plant species. This protein is involved in flowering, circadian clock control, chloroplast biogenesis, carbohydrate metabolism, stress responses, and volatile compound synthesis. In potato (Solanum tuberosum L.), its only role appears to be tuber initiation; however, based on findings in other plant species, we hypothesised that the function of GI in potatoes is not restricted only to tuberisation. RESULTS To test this hypothesis, the expression of a GI gene in the commercial potato cultivar 'Désirée' was repressed, and the effects of repression at morphological and transcriptome level were investigated. Previously, two copies of GI genes in potato were found. A construct to reduce the mRNA levels of one of these genes (StGI.04) was assembled, and the effects of antisense repression were studied in greenhouse-grown plants. The highest level of repression reached around 50%. However, this level did not influence tuber formation and yield but did cause a reduction in tuber colour. Using high-performance liquid chromatography (HPLC), significant reductions in cyanidin 3,5-di-O-glucoside and pelargonidin 3,5-di-O-glucoside contents of tuber peels were detected. Anthocyanins are synthesized through a branch of the phenylpropanoid pathway. The transcriptome analysis indicated down-regulation in the expression of PHENYLALANINE AMMONIA LYASE (PAL), the LEUCOANTHOCYANIDIN OXIDISING enzyme gene LDOX, and the MYB-RELATED PROTEIN Hv1 (MYB-Hv1), a transcription factor coding gene, which is presumably involved in the regulation of flavonoid biosynthesis, in the leaves of a selected StGI.04-repressed line. Furthermore, alterations in expression of genes affecting the circadian clock, flowering, starch synthesis, and stress responses were detected in the leaves of the selected StGI.04-repressed line. CONCLUSIONS We tested the effects of antisense repression of StGI.04 expression in potatoes and found that as with GI in other plant species, it influences the expression of the key genes of the circadian clock, flowering, starch synthesis, and stress responses. Furthermore, we detected a novel function of a GI gene in influencing the anthocyanin synthesis and potato tuber skin colour.
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Affiliation(s)
- Khongorzul Odgerel
- Genetics and Biotechnology Institute, Hungarian University of Agriculture and Life Sciences, Szent-Györgyi A. u. 4, Gödöllő, H-2100, Hungary
| | - Jeny Jose
- Genetics and Biotechnology Institute, Hungarian University of Agriculture and Life Sciences, Szent-Györgyi A. u. 4, Gödöllő, H-2100, Hungary
- Centre for Agricultural Research, Eötvös Loránd Research Network, Brunszvik u. 2, Martonvásár, H-2462, Hungary
| | - Flóra Karsai-Rektenwald
- Genetics and Biotechnology Institute, Hungarian University of Agriculture and Life Sciences, Szent-Györgyi A. u. 4, Gödöllő, H-2100, Hungary
| | - Gitta Ficzek
- Department of Fruit Growing, Institute of Horticulture, Hungarian University of Agriculture and Life Sciences, Villányi út 29-43, Budapest, H-1118, Hungary
| | - Gergely Simon
- Department of Fruit Growing, Institute of Horticulture, Hungarian University of Agriculture and Life Sciences, Villányi út 29-43, Budapest, H-1118, Hungary
| | - György Végvári
- Institute of Viticulture and Oenology, Faculty of Natural Sciences, Eszterházy Károly Catholic University, Eszterházy tér 1, Eger, H-3300, Hungary
| | - Zsófia Bánfalvi
- Genetics and Biotechnology Institute, Hungarian University of Agriculture and Life Sciences, Szent-Györgyi A. u. 4, Gödöllő, H-2100, Hungary.
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16
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Sun Y, Zhang H, Dong W, He S, Qiao S, Qi X, Hu Q. Integrated analysis of the transcriptome, sRNAome, and degradome reveals the network regulating fruit skin coloration in sponge gourd (Luffa cylindrica). Sci Rep 2022; 12:3338. [PMID: 35228643 PMCID: PMC8885689 DOI: 10.1038/s41598-022-07431-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 02/18/2022] [Indexed: 11/09/2022] Open
Abstract
Sponge gourd fruit skin color is an important quality-related trait because it substantially influences consumer preferences. However, little is known about the miRNAs and genes regulating sponge gourd fruit skin coloration. This study involved an integrated analysis of the transcriptome, sRNAome, and degradome of sponge gourd fruit skins with green skin (GS) and white skin (WS). A total of 4,331 genes were differentially expressed between the GS and WS, with 2,442 down-regulated and 1,889 up-regulated genes in WS. The crucial genes involved in chlorophyll metabolism, chloroplast development, and chloroplast protection were identified (e.g., HEMA, CHLM, CRD1, POR, CAO, CLH, SGR, CAB, BEL1-like, KNAT, ARF, and peroxidase genes). Additionally, 167 differentially expressed miRNAs were identified, with 70 up-regulated and 97 down-regulated miRNAs in WS. Degradome sequencing identified 125 differentially expressed miRNAs and their 521 differentially expressed target genes. The miR156, miR159, miR166, miR167, miR172, and miR393 targeted the genes involved in chlorophyll metabolism, chloroplast development, and chloroplast protection. Moreover, a flavonoid biosynthesis regulatory network was established involving miR159, miR166, miR169, miR319, miR390, miR396, and their targets CHS, 4CL, bHLH, and MYB. The qRT-PCR data for the differentially expressed genes were generally consistent with the transcriptome results. Subcellular localization analysis of selected proteins revealed their locations in different cellular compartments, including nucleus, cytoplasm and endoplasmic reticulum. The study findings revealed the important miRNAs, their target genes, and the regulatory network controlling fruit skin coloration in sponge gourd.
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Yang J, Chen Y, Xiao Z, Shen H, Li Y, Wang Y. Multilevel regulation of anthocyanin-promoting R2R3-MYB transcription factors in plants. FRONTIERS IN PLANT SCIENCE 2022; 13:1008829. [PMID: 36147236 PMCID: PMC9485867 DOI: 10.3389/fpls.2022.1008829] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 08/22/2022] [Indexed: 05/14/2023]
Abstract
Anthocyanins are common secondary metabolites in plants that confer red, blue, and purple colorations in plants and are highly desired by consumers for their visual appearance and nutritional quality. In the last two decades, the anthocyanin biosynthetic pathway and transcriptional regulation of anthocyanin biosynthetic genes (ABGs) have been well characterized in many plants. From numerous studies on model plants and horticultural crops, many signaling regulators have been found to control anthocyanin accumulation via regulation of anthocyanin-promoting R2R3-MYB transcription factors (so-called R2R3-MYB activators). The regulatory mechanism of R2R3-MYB activators is mediated by multiple environmental factors (e.g., light, temperature) and internal signals (e.g., sugar, ethylene, and JA) in complicated interactions at multiple levels. Here, we summarize the transcriptional control of R2R3-MYB activators as a result of natural variations in the promoter of their encoding genes, upstream transcription factors and epigenetics, and posttranslational modifications of R2R3-MYB that determine color variations of horticultural plants. In addition, we focus on progress in elucidating the integrated regulatory network of anthocyanin biosynthesis mediated by R2R3-MYB activators in response to multiple signals. We also highlight a few gene cascade modules involved in the regulation of anthocyanin-related R2R3-MYB to provide insights into anthocyanin production in horticultural plants.
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Affiliation(s)
- Jianfei Yang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- School of Forestry, Northeast Forestry University, Harbin, China
| | - Yunzhu Chen
- State Key Laboratory of Utilization of Woody Oil Resource, Hunan Academy of Forestry, Changsha, China
| | - Zhihong Xiao
- State Key Laboratory of Utilization of Woody Oil Resource, Hunan Academy of Forestry, Changsha, China
| | - Hailong Shen
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- School of Forestry, Northeast Forestry University, Harbin, China
| | - Yuhua Li
- College of Life Sciences, Northeast Forestry University, Harbin, China
- Yuhua Li,
| | - Yu Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- College of Life Sciences, Northeast Forestry University, Harbin, China
- *Correspondence: Yu Wang,
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18
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Kunej U, Jakše J, Radišek S, Štajner N. Identification and Characterization of Verticillium nonalfalfae-Responsive MicroRNAs in the Roots of Resistant and Susceptible Hop Cultivars. PLANTS (BASEL, SWITZERLAND) 2021; 10:1883. [PMID: 34579416 PMCID: PMC8471970 DOI: 10.3390/plants10091883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 08/30/2021] [Accepted: 09/09/2021] [Indexed: 11/27/2022]
Abstract
MicroRNAs are 21- to 24-nucleotide-long, non-coding RNA molecules that regulate gene expression at the post-transcriptional level. They can modulate various biological processes, including plant response and resistance to fungal pathogens. Hops are grown for use in the brewing industry and, recently, also for the pharmaceutical industry. Severe Verticillium wilt caused by the phytopathogenic fungus Verticillium nonalfalfae, is the main factor in yield loss in many crops, including hops (Humulus lupulus L.). In our study, we identified 56 known and 43 novel miRNAs and their expression patterns in the roots of susceptible and resistant hop cultivars after inoculation with V. nonalfalfae. In response to inoculation with V. nonalfalfae, we found five known and two novel miRNAs that are differentially expressed in the susceptible cultivar and six known miRNAs in the resistant cultivar. Differentially expressed miRNAs target 49 transcripts involved in protein localization and pigment synthesis in the susceptible cultivar, whereas they are involved in transcription factor regulation and hormone signalling in the resistant cultivar. The results of our study suggest that the susceptible and resistant hop cultivars respond differently to V. nonalfalfae inoculation at the miRNA level and that miRNAs may contribute to the successful defence of the resistant cultivar.
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Affiliation(s)
- Urban Kunej
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia; (U.K.); (J.J.)
| | - Jernej Jakše
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia; (U.K.); (J.J.)
| | - Sebastjan Radišek
- Plant Protection Department, Slovenian Institute of Hop Research and Brewing, 3310 Žalec, Slovenia;
| | - Nataša Štajner
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia; (U.K.); (J.J.)
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Khusnutdinov E, Sukhareva A, Panfilova M, Mikhaylova E. Anthocyanin Biosynthesis Genes as Model Genes for Genome Editing in Plants. Int J Mol Sci 2021; 22:8752. [PMID: 34445458 PMCID: PMC8395717 DOI: 10.3390/ijms22168752] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 08/09/2021] [Accepted: 08/13/2021] [Indexed: 12/13/2022] Open
Abstract
CRISPR/Cas, one of the most rapidly developing technologies in the world, has been applied successfully in plant science. To test new nucleases, gRNA expression systems and other inventions in this field, several plant genes with visible phenotypic effects have been constantly used as targets. Anthocyanin pigmentation is one of the most easily identified traits, that does not require any additional treatment. It is also associated with stress resistance, therefore plants with edited anthocyanin genes might be of interest for agriculture. Phenotypic effect of CRISPR/Cas editing of PAP1 and its homologs, DFR, F3H and F3'H genes have been confirmed in several distinct plant species. DFR appears to be a key structural gene of anthocyanin biosynthesis, controlled by various transcription factors. There are still many promising potential model genes that have not been edited yet. Some of them, such as Delila, MYB60, HAT1, UGT79B2, UGT79B3 and miR156, have been shown to regulate drought tolerance in addition to anthocyanin biosynthesis. Genes, also involved in trichome development, such as TTG1, GLABRA2, MYBL2 and CPC, can provide increased visibility. In this review successful events of CRISPR/Cas editing of anthocyanin genes are summarized, and new model genes are proposed. It can be useful for molecular biologists and genetic engineers, crop scientists, plant genetics and physiologists.
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Affiliation(s)
| | | | | | - Elena Mikhaylova
- Institute of Biochemistry and Genetics, Ufa Federal Research Center RAS, Prospekt Oktyabrya 71, 450054 Ufa, Russia; (E.K.); (A.S.); (M.P.)
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20
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LaFountain AM, Yuan YW. Repressors of anthocyanin biosynthesis. THE NEW PHYTOLOGIST 2021; 231:933-949. [PMID: 33864686 PMCID: PMC8764531 DOI: 10.1111/nph.17397] [Citation(s) in RCA: 87] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 03/29/2021] [Indexed: 05/07/2023]
Abstract
Anthocyanins play a variety of adaptive roles in both vegetative tissues and reproductive organs of plants. The broad functionality of these compounds requires sophisticated regulation of the anthocyanin biosynthesis pathway to allow proper localization, timing, and optimal intensity of pigment deposition. While it is well-established that the committed steps of anthocyanin biosynthesis are activated by a highly conserved MYB-bHLH-WDR (MBW) protein complex in virtually all flowering plants, anthocyanin repression seems to be achieved by a wide variety of protein and small RNA families that function in different tissue types and in response to different developmental, environmental, and hormonal cues. In this review, we survey recent progress in the identification of anthocyanin repressors and the characterization of their molecular mechanisms. We find that these seemingly very different repression modules act through a remarkably similar logic, the so-called 'double-negative logic'. Much of the double-negative regulation of anthocyanin production involves signal-induced degradation or sequestration of the repressors from the MBW protein complex. We discuss the functional and evolutionary advantages of this logic design compared with simple or sequential positive regulation. These advantages provide a plausible explanation as to why plants have evolved so many anthocyanin repressors.
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Affiliation(s)
- Amy M LaFountain
- Department of Ecology and Evolutionary Biology, University of Connecticut, 75 North Eagleville Road, Storrs, CT, 06269-3043, USA
| | - Yao-Wu Yuan
- Department of Ecology and Evolutionary Biology, University of Connecticut, 75 North Eagleville Road, Storrs, CT, 06269-3043, USA
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21
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Zhang Y, Yang J, Zhu L, Xue J, Hu H, Cui J, Xu J. Identification of microRNAs and their target genes related to needle discoloration of evergreen tree Chinese cedar (Cryptomeria fortunei) in cold winters. PLANTA 2021; 254:31. [PMID: 34283297 DOI: 10.1007/s00425-021-03685-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 07/12/2021] [Indexed: 06/13/2023]
Abstract
Comparative analysis of miRNAs and their gene targets between the evergreen and yellowish-brown Cryptomeria fortunei phenotypes in cold winters suggests a possible role of miRNA-regulated pathways in needle color. Cryptomeria fortunei (Chinese cedar) is a conifer tree of considerable economic, ornamental and ecological importance. Despite the evergreen nature of C. fortunei, most needles turn yellowish- or reddish-brown in winter. The roles of microRNAs (miRNAs) in regulating pigment biosynthesis in color-leafed plants have been widely investigated. However, whether or not an miRNA-mediated staged discoloration mechanism exists in evergreen C. fortunei is currently unknown. In this study, we deciphered the microRNAs landscape in overwintering C. fortunei needles using high-throughput sequencing. A total of 517 known and 212 novel miRNA mature/star sequences, including 233 differentially expressed miRNAs, were identified. Based on integrated transcriptome and miRNA analysis, 2702 target unigenes of the miRNAs were predicted and these targets were significantly enriched in pigment-related biosynthesis pathways. A miRNA-target pigment biosynthesis regulatory network was then constructed, and its module miRNA (ath-miR858b, aly-miR858-3p, cme-miR828 and novel33_mature)-MYBs (v-myb avian myeloblastosis viral oncogene homolog) appeared to be a key factor regulating needle discoloration in C. fortunei. These miRNA-MYBs were further confirmed by degradome sequencing. Overall, these findings provide new insight into the posttranscriptional regulatory mechanism of leaf/needle discoloration in gymnosperms and may contribute to the miRNA-mediated genetic improvement of evergreen C. fortunei needles.
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Affiliation(s)
- Yingting Zhang
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, 210037, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
- College of Forestry, Nanjing Forestry University, Nanjing, 210037, China
| | - Junjie Yang
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, 210037, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
- College of Forestry, Nanjing Forestry University, Nanjing, 210037, China
| | - Lijuan Zhu
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, 210037, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
- College of Forestry, Nanjing Forestry University, Nanjing, 210037, China
| | - Jinyu Xue
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, 210037, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
- College of Forestry, Nanjing Forestry University, Nanjing, 210037, China
| | - Hailiang Hu
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, 210037, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
- College of Forestry, Nanjing Forestry University, Nanjing, 210037, China
| | - Jiebing Cui
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, 210037, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
- College of Forestry, Nanjing Forestry University, Nanjing, 210037, China
| | - Jin Xu
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, 210037, China.
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China.
- College of Forestry, Nanjing Forestry University, Nanjing, 210037, China.
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22
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Li C, Wang M, Qiu X, Zhou H, Lu S. Noncoding RNAs in Medicinal Plants and their Regulatory Roles in Bioactive Compound Production. Curr Pharm Biotechnol 2021; 22:341-359. [PMID: 32469697 DOI: 10.2174/1389201021666200529101942] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 02/14/2020] [Accepted: 03/30/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Noncoding RNAs (ncRNAs), such as microRNAs (miRNAs), small interfering RNAs (siRNAs) and long noncoding RNAs (lncRNAs), play significant regulatory roles in plant development and secondary metabolism and are involved in plant response to biotic and abiotic stresses. They have been intensively studied in model systems and crops for approximately two decades and massive amount of information have been obtained. However, for medicinal plants, ncRNAs, particularly their regulatory roles in bioactive compound biosynthesis, are just emerging as a hot research field. OBJECTIVE This review aims to summarize current knowledge on herbal ncRNAs and their regulatory roles in bioactive compound production. RESULTS So far, scientists have identified thousands of miRNA candidates from over 50 medicinal plant species and 11794 lncRNAs from Salvia miltiorrhiza, Panax ginseng, and Digitalis purpurea. Among them, more than 30 miRNAs and five lncRNAs have been predicted to regulate bioactive compound production. CONCLUSION The regulation may achieve through various regulatory modules and pathways, such as the miR397-LAC module, the miR12112-PPO module, the miR156-SPL module, the miR828-MYB module, the miR858-MYB module, and other siRNA and lncRNA regulatory pathways. Further functional analysis of herbal ncRNAs will provide useful information for quality and quantity improvement of medicinal plants.
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Affiliation(s)
- Caili Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 151 Malianwa North Road, Haidian District, Beijing 100193, China
| | - Meizhen Wang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 151 Malianwa North Road, Haidian District, Beijing 100193, China
| | - Xiaoxiao Qiu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 151 Malianwa North Road, Haidian District, Beijing 100193, China
| | - Hong Zhou
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 151 Malianwa North Road, Haidian District, Beijing 100193, China
| | - Shanfa Lu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 151 Malianwa North Road, Haidian District, Beijing 100193, China
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23
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Lin S, Singh RK, Navarre DA. R2R3-MYB transcription factors, StmiR858 and sucrose mediate potato flavonol biosynthesis. HORTICULTURE RESEARCH 2021; 8:25. [PMID: 33518700 PMCID: PMC7847999 DOI: 10.1038/s41438-021-00463-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 11/20/2020] [Accepted: 11/23/2020] [Indexed: 05/06/2023]
Abstract
Flavonols and other phenylpropanoids protect plants from biotic and abiotic stress and are dietarily desirable because of their health-promoting properties. The ability to develop new potatoes (Solanum tuberosum) with optimal types and amounts of phenylpropanoids is limited by lack of knowledge about the regulatory mechanisms. Exogenous sucrose increased flavonols, whereas overexpression of the MYB StAN1 induced sucrolytic gene expression. Heterologous StAN1 protein bound promoter fragments from sucrolytic genes (SUSY1 and INV1). Two additional MYBs and one microRNA were identified that regulated potato flavonols. Overexpression analysis showed MYB12A and C increased amounts of flavonols and other phenylpropanoids. Endogenous flavonol amounts in light-exposed organs were much higher those in the dark. Expression levels of StMYB12A and C were high in flowers but low in tubers. Transient overexpression of miR858 altered potato flavonol metabolism. Endogenous StmiR858 expression was much lower in flowers than leaves and correlated with flavonol amounts in these organs. Collectively, these findings support the hypothesis that sucrose, MYBs, and miRNA control potato phenylpropanoid metabolism in a finely tuned manner that includes a feedback loop between sucrose and StAN1. These findings will aid in the development of potatoes with phenylpropanoid profiles optimized for crop performance and human health.
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Affiliation(s)
- Sen Lin
- Irrigated Agriculture Research and Extension Center, Washington State University, Prosser, WA, USA
| | - Rajesh K Singh
- Irrigated Agriculture Research and Extension Center, Washington State University, Prosser, WA, USA
- Department of Biotechnology, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India
| | - Duroy A Navarre
- Irrigated Agriculture Research and Extension Center, Washington State University, Prosser, WA, USA.
- USDA-Agricultural Research Service, Prosser, WA, USA.
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24
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Yamagishi M, Sakai M. The MicroRNA828/MYB12 Module Mediates Bicolor Pattern Development in Asiatic Hybrid Lily ( Lilium spp.) Flowers. FRONTIERS IN PLANT SCIENCE 2020; 11:590791. [PMID: 33193545 PMCID: PMC7661471 DOI: 10.3389/fpls.2020.590791] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 10/08/2020] [Indexed: 05/06/2023]
Abstract
Some Asiatic hybrid lily cultivars develop bicolor tepals, which consist of anthocyanin-pigmented upper halves and un-pigmented lower halves. MYB12, a subgroup 6 member of R2R3-MYB that positively regulates anthocyanin biosynthesis, is downregulated in the lower halves. However, MYB12 is usually expressed over entire tepal regions in numerous lily cultivars. Why MYB12 of bicolor cultivars exhibits variable expression spatially in a single tepal remains unclear. Since the lily MYB12 mRNA harbored a binding site for microRNA828 (miR828), the involvement of miR828 in variable spatial accumulation of MYB12 transcripts was evaluated. We analyzed the cleavage of MYB12 mRNA, mature miR828 accumulation, and MYB12 transcript-derived siRNA generation (microRNA-seq). In the bicolor tepals, mature miR828 was more highly accumulated in the lower halves than in the upper halves, and miR828-directed cleavage of MYB12 transcripts was observed predominantly in the lower halves. Moreover, the cleavage triggered the production of secondary siRNA from MYB12 transcripts, and the siRNAs were accumulated predominantly in the lower halves. Consequently, miR828 suppressed MYB12 transcript accumulation in the white region, and the miR828/MYB12 module participated in the development of bicolor patterns in lily flowers. The results present the first example of a microRNA mediating flower color patterns. Finally, we discuss the potential of miR828 creating flower color variations through suppressing the activity of subgroup 6 R2R3-MYB positive regulators in other species.
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Affiliation(s)
- Masumi Yamagishi
- Research Faculty of Agriculture, Graduate School of Agriculture, Hokkaido University, Sapporo, Japan
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25
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Chen C, Xie F, Hua Q, Tel-Zur N, Zhang L, Zhang Z, Zhang R, Zhao J, Hu G, Qin Y. Integrated sRNAome and RNA-Seq analysis reveals miRNA effects on betalain biosynthesis in pitaya. BMC PLANT BIOLOGY 2020; 20:437. [PMID: 32962650 PMCID: PMC7510087 DOI: 10.1186/s12870-020-02622-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 08/25/2020] [Indexed: 05/30/2023]
Abstract
BACKGROUND MicroRNAs (miRNAs) and their regulatory functions in anthocyanin, carotenoid, and chlorophyll accumulation have been extensively characterized in many plant species. However, the miRNA regulatory mechanism in betalain biosynthesis remains mostly unknown. RESULTS In this study, 126 conserved miRNAs and 41 novel miRNAs were first isolated from Hylocereus monacanthus, among which 95 conserved miRNAs belonged to 53 miRNA families. Thirty-four candidate miRNAs related to betalain biosynthesis were differentially expressed. The expression patterns of those differential expressed miRNAs were analyzed in various pitaya tissues by RT-qPCR. A significantly negative correlation was detected between the expression levels of half those miRNAs and corresponding target genes. Target genes of miRNAs i.e. Hmo-miR157b-HmSPL6-like, Hmo-miR160a-Hpcyt P450-like3, Hmo-miR6020-HmCYP71A8-like, Hmo-novel-2-HmCYP83B1-like, Hmo-novel-15-HmTPST-like, Hmo-miR828a-HmTT2-like, Hmo-miR858-HmMYB12-like, Hmo-miR858-HmMYBC1-like and Hmo-miR858-HmMYB2-like were verified by 5'RACE and transient expression system in tobacco. CONCLUSIONS Hmo-miR157b, Hmo-miR160a, Hmo-miR6020 Hmo-novel-2, Hmo-novel-15, Hmo-miR828a and Hmo-miR858 play important roles in pitaya fruit coloration and betalain accumulation. Our findings provide new insights into the roles of miRNAs and their target genes of regulatory functions involved in betalain biosynthesis of pitaya.
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Affiliation(s)
- Canbin Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agrobioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs, College of Horticulture, South China Agricultural University, Guangzhou, Guangdong, 510642, P. R. China
| | - Fangfang Xie
- State Key Laboratory for Conservation and Utilization of Subtropical Agrobioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs, College of Horticulture, South China Agricultural University, Guangzhou, Guangdong, 510642, P. R. China
| | - Qingzhu Hua
- State Key Laboratory for Conservation and Utilization of Subtropical Agrobioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs, College of Horticulture, South China Agricultural University, Guangzhou, Guangdong, 510642, P. R. China
| | - Noemi Tel-Zur
- French Associates Institute for Agriculture and Biotechnology of Drylands, The J. Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, 84990, Beersheba, Israel
| | - Lulu Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agrobioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs, College of Horticulture, South China Agricultural University, Guangzhou, Guangdong, 510642, P. R. China
| | - Zhike Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agrobioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs, College of Horticulture, South China Agricultural University, Guangzhou, Guangdong, 510642, P. R. China
| | - Rong Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agrobioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs, College of Horticulture, South China Agricultural University, Guangzhou, Guangdong, 510642, P. R. China
| | - Jietang Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agrobioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs, College of Horticulture, South China Agricultural University, Guangzhou, Guangdong, 510642, P. R. China
| | - Guibing Hu
- State Key Laboratory for Conservation and Utilization of Subtropical Agrobioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs, College of Horticulture, South China Agricultural University, Guangzhou, Guangdong, 510642, P. R. China
| | - Yonghua Qin
- State Key Laboratory for Conservation and Utilization of Subtropical Agrobioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs, College of Horticulture, South China Agricultural University, Guangzhou, Guangdong, 510642, P. R. China.
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26
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D'Amelia V, Villano C, Batelli G, Çobanoğlu Ö, Carucci F, Melito S, Chessa M, Chiaiese P, Aversano R, Carputo D. Genetic and epigenetic dynamics affecting anthocyanin biosynthesis in potato cell culture. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 298:110597. [PMID: 32771154 DOI: 10.1016/j.plantsci.2020.110597] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 06/30/2020] [Accepted: 07/03/2020] [Indexed: 06/11/2023]
Abstract
Anthocyanins are antioxidant pigments widely used in drugs and food preparations. Flesh-coloured tubers of the cultivated potato Solanum tuberosum are important sources of different anthocyanins. Due to the high degree of decoration achieved by acylation, anthocyanins from potato are very stable and suitable for the food processing industry. The use of cell culture allows to extract anthocyanins on-demand, avoiding seasonality and consequences associated with land-based-tuber production. However, a well-known limit of cell culture is the metabolic instability and loss of anthocyanin production during successive subcultures. To get a general picture of mechanisms responsible for this instability, we explored both genetic and epigenetic regulation that may affect anthocyanin production in cell culture. We selected two clonally related populations of anthocyanin-producing (purple) and non-producing (white) potato cells. Through targeted molecular investigations, we identified and functionally characterized an R3-MYB, here named StMYBATV. This transcription factor can interact with bHLHs belonging to the MBW (R2R3-MYB, bHLH and WD40) anthocyanin activator complex and, potentially, may interfere with its formation. Genome methylation analysis revealed that, for several genomic loci, anthocyanin-producing cells were more methylated than clonally related white cells. In particular, we localized some methylation events in ribosomal protein-coding genes. Overall, our study explores novel molecular aspects associated with loss of anthocyanins in cell culture systems.
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Affiliation(s)
- Vincenzo D'Amelia
- National Research Council of Italy, Institute of Biosciences and Bioresources, Research Division Portici (CNR-IBBR), Portici, 80055, Italy; Department of Agricultural Sciences, University of Naples Federico II, Portici, 80055, Italy
| | - Clizia Villano
- Department of Agricultural Sciences, University of Naples Federico II, Portici, 80055, Italy
| | - Giorgia Batelli
- National Research Council of Italy, Institute of Biosciences and Bioresources, Research Division Portici (CNR-IBBR), Portici, 80055, Italy
| | - Özmen Çobanoğlu
- Department of Agricultural Sciences, University of Naples Federico II, Portici, 80055, Italy
| | - Francesca Carucci
- Department of Agricultural Sciences, University of Naples Federico II, Portici, 80055, Italy
| | - Sara Melito
- Department of Agricultural Sciences, University of Sassari, Sassari, 07100, Italy
| | - Mario Chessa
- Department of Chemistry and Pharmacy, University of Sassari, Sassari, 07100, Italy
| | - Pasquale Chiaiese
- Department of Agricultural Sciences, University of Naples Federico II, Portici, 80055, Italy
| | - Riccardo Aversano
- Department of Agricultural Sciences, University of Naples Federico II, Portici, 80055, Italy.
| | - Domenico Carputo
- Department of Agricultural Sciences, University of Naples Federico II, Portici, 80055, Italy.
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27
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Tirumalai V, Swetha C, Nair A, Pandit A, Shivaprasad PV. miR828 and miR858 regulate VvMYB114 to promote anthocyanin and flavonol accumulation in grapes. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:4775-4792. [PMID: 31145783 PMCID: PMC6760283 DOI: 10.1093/jxb/erz264] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 05/21/2019] [Indexed: 05/20/2023]
Abstract
MicroRNAs are a class of non-coding small RNAs involved in the negative regulation of gene expression, which play critical roles in developmental and metabolic pathways. Studies in several plants have identified a few microRNAs and other small RNAs that target regulators of the phenylpropanoid metabolic pathway called the MYB transcription factors. However, it is not well understood how sRNA-mediated regulation of MYBs influences the accumulation of specific secondary metabolites. Using sRNA sequencing, degradome analysis, mRNA sequencing, and proteomic analysis, we establish that grape lines with high anthocyanin content express two MYB-targeting microRNAs abundantly, resulting in the differential expression of specific MYB proteins. miR828 and miR858 target coding sequences of specific helix motifs in the mRNA sequences of MYB proteins. Targeting by miR828 caused MYB RNA decay and the production of a cascade of secondary siRNAs that depend on RNA-dependent RNA polymerase 6. MYB suppression and cascade silencing was more robust in grape lines with high anthocyanin content than in a flavonol-rich grape line. We establish that microRNA-mediated silencing targeted the repressor class of MYBs to promote anthocyanin biosynthesis in grape lines with high anthocyanins. We propose that this process regulates the expression of appropriate MYBs in grape lines to produce specific secondary metabolites.
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Affiliation(s)
- Varsha Tirumalai
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore, India
- SASTRA University, Thirumalaisamudram, Thanjavur, India
| | - Chenna Swetha
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore, India
- SASTRA University, Thirumalaisamudram, Thanjavur, India
| | - Ashwin Nair
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore, India
- SASTRA University, Thirumalaisamudram, Thanjavur, India
| | - Awadhesh Pandit
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore, India
| | - Padubidri V Shivaprasad
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore, India
- Correspondence:
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28
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Zhao A, Cui Z, Li T, Pei H, Sheng Y, Li X, Zhao Y, Zhou Y, Huang W, Song X, Peng T, Wang J. mRNA and miRNA Expression Analysis Reveal the Regulation for Flower Spot Patterning in Phalaenopsis 'Panda'. Int J Mol Sci 2019; 20:ijms20174250. [PMID: 31480267 PMCID: PMC6747512 DOI: 10.3390/ijms20174250] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Revised: 08/25/2019] [Accepted: 08/26/2019] [Indexed: 12/16/2022] Open
Abstract
Phalaenopsis cultivar ‘Panda’ is a beautiful and valuable ornamental for its big flower and unique big spots on the petals and sepals. Although anthocyanins are known as the main pigments responsible for flower colors in Phalaenopsis, and the anthocyanins biosynthetic pathway in Phalaenopsis is generally well known, the detailed knowledge of anthocynins regulation within the spot and non-spot parts in ‘Panda’ flower is limited. In this study, transcriptome and small RNA libraries analysis from spot and non-spot sepal tissues of ‘Panda’ were performed, and we found PeMYB7, PeMYB11, and miR156g, miR858 is associated with the purple spot patterning in its sepals. Transcriptome analyses showed a total 674 differentially expressed genes (DEGs), with 424 downregulated and 250 upregulated (Non-spot-VS-Spot), and 10 candidate DEGs involved in anthocyanin biosynthetic pathway. The qPCR analysis confirmed that seven candidate structure genes (PeANS, PeF3′H, PeC4H, PeF3H, PeF3H1, Pe4CL2, and PeCHI) have significantly higher expressing levels in spot tissues than non-spot tissues. A total 1552 differentially expressed miRNAs (DEMs) were detected with 676 downregulated and 876 upregulated. However, microRNA data showed no DEMs targeting on anthocyanin biosynthesis structure gene, while a total 40 DEMs target transcription factor (TF) genes, which expressed significantly different level in spot via non-spot sepal, including 2 key MYB regulator genes. These results indicated that the lack of anthocyanidins in non-spot sepal may not directly be caused by microRNA suppressing anthocyanidin synthesis genes rather than the MYB genes. Our findings will help in understanding the role of miRNA molecular mechanisms in the spot formation pattern of Phalaenopsis, and would be useful to provide a reference to similar research in other species.
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Affiliation(s)
- Anjin Zhao
- Key Laboratory of Ministry of Education for Genetics and Germplasm Innovation of Tropical Special Trees and Ornamental Plants, Hainan Key Laboratory for Biology of Tropical Ornamental Plants Germplasm, College of Forestry, Hainan University, Haikou 570228, China
| | - Zheng Cui
- Key Laboratory of Ministry of Education for Genetics and Germplasm Innovation of Tropical Special Trees and Ornamental Plants, Hainan Key Laboratory for Biology of Tropical Ornamental Plants Germplasm, College of Forestry, Hainan University, Haikou 570228, China
| | - Tingge Li
- Key Laboratory of Ministry of Education for Genetics and Germplasm Innovation of Tropical Special Trees and Ornamental Plants, Hainan Key Laboratory for Biology of Tropical Ornamental Plants Germplasm, College of Forestry, Hainan University, Haikou 570228, China
| | - Huiqin Pei
- Key Laboratory of Ministry of Education for Genetics and Germplasm Innovation of Tropical Special Trees and Ornamental Plants, Hainan Key Laboratory for Biology of Tropical Ornamental Plants Germplasm, College of Forestry, Hainan University, Haikou 570228, China
| | - Yuhui Sheng
- Key Laboratory of Ministry of Education for Genetics and Germplasm Innovation of Tropical Special Trees and Ornamental Plants, Hainan Key Laboratory for Biology of Tropical Ornamental Plants Germplasm, College of Forestry, Hainan University, Haikou 570228, China
| | - Xueqing Li
- Key Laboratory of Ministry of Education for Genetics and Germplasm Innovation of Tropical Special Trees and Ornamental Plants, Hainan Key Laboratory for Biology of Tropical Ornamental Plants Germplasm, College of Forestry, Hainan University, Haikou 570228, China
| | - Ying Zhao
- Key Laboratory of Ministry of Education for Genetics and Germplasm Innovation of Tropical Special Trees and Ornamental Plants, Hainan Key Laboratory for Biology of Tropical Ornamental Plants Germplasm, College of Forestry, Hainan University, Haikou 570228, China
- Research Center for Terrestrial Biodiversity of the South China Sea, College of Forestry, Hainan University, Haikou 570228, China
| | - Yang Zhou
- Key Laboratory of Ministry of Education for Genetics and Germplasm Innovation of Tropical Special Trees and Ornamental Plants, Hainan Key Laboratory for Biology of Tropical Ornamental Plants Germplasm, College of Forestry, Hainan University, Haikou 570228, China
- Research Center for Terrestrial Biodiversity of the South China Sea, College of Forestry, Hainan University, Haikou 570228, China
| | - Wenjun Huang
- Department of Development and Design, Hainan University, Haikou 570228, China
| | - Xiqiang Song
- Key Laboratory of Ministry of Education for Genetics and Germplasm Innovation of Tropical Special Trees and Ornamental Plants, Hainan Key Laboratory for Biology of Tropical Ornamental Plants Germplasm, College of Forestry, Hainan University, Haikou 570228, China
- Research Center for Terrestrial Biodiversity of the South China Sea, College of Forestry, Hainan University, Haikou 570228, China
| | - Ting Peng
- Key Laboratory of Germplasm Innovation on Protection and Conservation of Mountain Plant Resources, Ministry of Education/College of Agriculture, Guizhou University, Guiyang 550025, China
| | - Jian Wang
- Key Laboratory of Ministry of Education for Genetics and Germplasm Innovation of Tropical Special Trees and Ornamental Plants, Hainan Key Laboratory for Biology of Tropical Ornamental Plants Germplasm, College of Forestry, Hainan University, Haikou 570228, China.
- Research Center for Terrestrial Biodiversity of the South China Sea, College of Forestry, Hainan University, Haikou 570228, China.
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Liu Y, Lin-Wang K, Espley RV, Wang L, Li Y, Liu Z, Zhou P, Zeng L, Zhang X, Zhang J, Allan AC. StMYB44 negatively regulates anthocyanin biosynthesis at high temperatures in tuber flesh of potato. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:3809-3824. [PMID: 31020330 PMCID: PMC6685667 DOI: 10.1093/jxb/erz194] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Accepted: 04/11/2019] [Indexed: 05/23/2023]
Abstract
High temperatures are known to reduce anthocyanin accumulation in a number of diverse plant species. In potato (Solanum tuberosum L.), high temperature significantly reduces tuber anthocyanin pigment content. However, the mechanism of anthocyanin biosynthesis in potato tuber under heat stress remains unknown. Here we show that high temperature causes reduction of anthocyanin biosynthesis in both potato tuber skin and flesh, with white areas forming between the vasculature and periderm. Heat stress reduced the expression of the R2R3 MYB transcription factors (TFs) StAN1 and StbHLH1, members of the transcriptional complex responsible for coordinated regulation of the skin and flesh pigmentation, as well as anthocyanin biosynthetic pathway genes in white regions. However, the core phenylpropanoid pathway, lignin, and chlorogenic acid (CGA) pathway genes were up-regulated in white areas, suggesting that suppression of the anthocyanin branch may result in re-routing phenylpropanoid flux into the CGA or lignin biosynthesis branches. Two R2R3 MYB TFs, StMYB44-1 and StMYB44-2, were highly expressed in white regions under high temperature. In transient assays, StMYB44 represses anthocyanin accumulation in leaves of Nicotiana tabacum and N. benthamiana by directly suppressing the activity of the dihydroflavonol reductase (DFR) promoter. StMYB44-1 showed stronger repressive capacity than StMYB44-2, with both predicted proteins containing the repression-associated EAR motif with some variation. StMYB44-1 conferred repression without a requirement for a basic helix-loop-helix (bHLH) partner, suggesting a different repression mechanism from that of reported anthocyanin repressors. We propose that temperature-induced reduction of anthocyanin accumulation in potato flesh is caused by down-regulation of the activating anthocyanin regulatory complex, by enhancing the expression of flesh-specific StMYB44 and alteration of phenylpropanoid flux.
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Affiliation(s)
- Yuhui Liu
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
| | - Kui Lin-Wang
- The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research) Mt Albert, Auckland, New Zealand
| | - Richard V Espley
- The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research) Mt Albert, Auckland, New Zealand
| | - Li Wang
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Yuanming Li
- College of Horticulture, Gansu Agricultural University, Lanzhou, China
| | - Zhen Liu
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Horticulture, Gansu Agricultural University, Lanzhou, China
| | - Ping Zhou
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Lihui Zeng
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | | | - Junlian Zhang
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Horticulture, Gansu Agricultural University, Lanzhou, China
| | - Andrew C Allan
- The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research) Mt Albert, Auckland, New Zealand
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
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