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Reda GK, Ndunguru SF, Csernus B, Knop R, Lugata JK, Szabó C, Czeglédi L, Lendvai ÁZ. Dietary restriction reveals sex-specific expression of the mTOR pathway genes in Japanese quails. Sci Rep 2024; 14:8314. [PMID: 38594358 PMCID: PMC11004124 DOI: 10.1038/s41598-024-58487-9] [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: 09/20/2023] [Accepted: 03/29/2024] [Indexed: 04/11/2024] Open
Abstract
Limited resources affect an organism's physiology through the conserved metabolic pathway, the mechanistic target of rapamycin (mTOR). Males and females often react differently to nutritional limitation, but whether it leads to differential mTOR pathway expression remains unknown. Recently, we found that dietary restriction (DR) induced significant changes in the expression of mTOR pathway genes in female Japanese quails (Coturnix japonica). We simultaneously exposed 32 male and female Japanese quails to either 20%, 30%, 40% restriction or ad libitum feeding for 14 days and determined the expression of six key genes of the mTOR pathway in the liver to investigate sex differences in the expression patterns. We found that DR significantly reduced body mass, albeit the effect was milder in males compared to females. We observed sex-specific liver gene expression. DR downregulated mTOR expression more in females than in males. Under moderate DR, ATG9A and RPS6K1 expressions were increased more in males than in females. Like females, body mass in males was correlated positively with mTOR and IGF1, but negatively with ATG9A and RS6K1 expressions. Our findings highlight that sexes may cope with nutritional deficits differently and emphasise the importance of considering sexual differences in studies of dietary restriction.
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Affiliation(s)
- Gebrehaweria K Reda
- Department of Animal Science, Faculty of Agricultural and Food Sciences and Environmental Management, Institute of Animal Science, Biotechnology and Nature Conservation, University of Debrecen, 4032, Debrecen, Hungary.
- Doctoral School of Animal Science, University of Debrecen, 4032, Debrecen, Hungary.
- Department of Evolutionary Zoology and Human Biology, University of Debrecen, 4032, Debrecen, Hungary.
| | - Sawadi F Ndunguru
- Department of Animal Science, Faculty of Agricultural and Food Sciences and Environmental Management, Institute of Animal Science, Biotechnology and Nature Conservation, University of Debrecen, 4032, Debrecen, Hungary
- Doctoral School of Animal Science, University of Debrecen, 4032, Debrecen, Hungary
- Department of Evolutionary Zoology and Human Biology, University of Debrecen, 4032, Debrecen, Hungary
| | - Brigitta Csernus
- Department of Evolutionary Zoology and Human Biology, University of Debrecen, 4032, Debrecen, Hungary
| | - Renáta Knop
- Department of Animal Science, Faculty of Agricultural and Food Sciences and Environmental Management, Institute of Animal Science, Biotechnology and Nature Conservation, University of Debrecen, 4032, Debrecen, Hungary
| | - James K Lugata
- Doctoral School of Animal Science, University of Debrecen, 4032, Debrecen, Hungary
- Department of Animal Nutrition and Physiology, Faculty of Agriculture and Food Sciences and Environmental Management, University of Debrecen, 4032, Debrecen, Hungary
| | - Csaba Szabó
- Department of Animal Nutrition and Physiology, Faculty of Agriculture and Food Sciences and Environmental Management, University of Debrecen, 4032, Debrecen, Hungary
| | - Levente Czeglédi
- Department of Animal Science, Faculty of Agricultural and Food Sciences and Environmental Management, Institute of Animal Science, Biotechnology and Nature Conservation, University of Debrecen, 4032, Debrecen, Hungary
| | - Ádám Z Lendvai
- Department of Evolutionary Zoology and Human Biology, University of Debrecen, 4032, Debrecen, Hungary
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Ma R, Luo J, Wang W, Fu Y. Changes in the physiological activity of parenchyma cells in Dalbergia odorifera xylem and its relationship with heartwood formation. BMC PLANT BIOLOGY 2023; 23:559. [PMID: 37957552 PMCID: PMC10644609 DOI: 10.1186/s12870-023-04592-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 11/08/2023] [Indexed: 11/15/2023]
Abstract
BACKGROUND The formation of a tree's heartwood gives the wood properties such as natural decay resistance and aesthetic color, and often directly determines the value of wood products. Regulating the quantity and quality of heartwood is of great importance to the use of wood. However, the mechanism of heartwood formation has been poorly understood. RESULTS Using Dalbergia odorifera as the study species, the number of starch grains, the morphology of the nuclei, the changes in the content of water and secondary metabolites were observed continuously in the radial direction of the xylem. The results show that from the outer toward inner sapwood, the starch grains are abundant, the length to diameter ratio of the nuclei is decreasing, and the morphology changes from elongated elliptical and then to round. In the outer transition zone, the starch grains begin to decrease abruptly and the nuclei shrink at a slower rate, with a radial width of approximately 2 mm. In the inner transition zone, the heartwood color begins to appear, the starch grains disappear and a few nuclei with reduced fluorescence are present, with a radial width of approximately 1 mm. Heartwood formation after complete disappearance of the nuclei. The moisture content of the heartwood is higher than that of the sapwood, and the inner transition zone is where the content rises. The secondary metabolites of the heartwood begin to accumulate in large quantities in the inner transition zone. CONCLUSION Based on the physiological changes of parenchyma cells in the xylem, the radial width of the transition zone of Dalbergia odorifera is clearly defined as approximately 3 mm. Both the water and secondary metabolite abrupt changes occur at the final stage of programmed cell death, and neither is a direct cause of programmed cell death in parenchyma cells.
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Affiliation(s)
- Ruoke Ma
- Key Laboratory of National Forestry and Grassland Administration for Fast‑Growing Tree Breeding and Cultivation in Central and Southern China, College of Forestry, Guangxi University, Nanning, 530004, China
| | - Jia Luo
- Key Laboratory of National Forestry and Grassland Administration for Fast‑Growing Tree Breeding and Cultivation in Central and Southern China, College of Forestry, Guangxi University, Nanning, 530004, China
| | - Weijie Wang
- Key Laboratory of National Forestry and Grassland Administration for Fast‑Growing Tree Breeding and Cultivation in Central and Southern China, College of Forestry, Guangxi University, Nanning, 530004, China
| | - Yunlin Fu
- Key Laboratory of National Forestry and Grassland Administration for Fast‑Growing Tree Breeding and Cultivation in Central and Southern China, College of Forestry, Guangxi University, Nanning, 530004, China.
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Ma R, Luo J, Wang W, Song T, Fu Y. Function of the R2R3-MYB Transcription Factors in Dalbergia odorifera and Their Relationship with Heartwood Formation. Int J Mol Sci 2023; 24:12430. [PMID: 37569814 PMCID: PMC10419101 DOI: 10.3390/ijms241512430] [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: 06/21/2023] [Revised: 07/30/2023] [Accepted: 07/31/2023] [Indexed: 08/13/2023] Open
Abstract
R2R3-MYB transcription factors (TFs) form one of the most important TF families involved in regulating various physiological functions in plants. The heartwood of Dalbergia odorifera is a kind of high-grade mahogany and valuable herbal medicine with wide application. However, the role of R2R3-MYB genes in the growth and development of D. odorifera, especially their relevance to heartwood formation, has not been revealed. A total of 126 R2R3-MYBs were screened from the D. odorifera genome and named DodMYB1-126 based on their location on 10 chromosomes. The collinearity results showed that purification selection was the main driving force for the evolution of the R2R3-MYB TFs family, and whole genome/fragment replication event was the main form for expanding the R2R3-MYB family, generating a divergence of gene structure and function. Comparative phylogenetic analysis classified the R2R3-MYB TFs into 33 subfamilies. S3-7,10,12-13,21 and N4-7 were extensively involved in the metabolic process; S9,13,16-19,24-25 and N1-3,8 were associated with the growth and development of D. odorifera. Based on the differential transcriptional expression levels of R2R3-MYBs in different tissues, DodMYB32, DodMYB55, and DodMYB89 were tentatively screened for involvement in the regulatory process of heartwood. Further studies have shown that the DodMYB89, localized in the nucleus, has transcriptional activation activity and is involved in regulating the biosynthesis of the secondary metabolites of heartwood by activating the promoters of the structural genes DodI2'H and DodCOMT. This study aimed to comprehensively analyze the functions of the R2R3-MYB TFs and screen for candidate genes that might be involved in heartwood formation of D. odorifera.
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Affiliation(s)
- Ruoke Ma
- Key Laboratory of National Forestry and Grassland Administration for Fast-Growing Tree Breeding and Cultivation in Central and Southern China, College of Forestry, Guangxi University, Nanning 530004, China; (R.M.); (J.L.); (W.W.)
| | - Jia Luo
- Key Laboratory of National Forestry and Grassland Administration for Fast-Growing Tree Breeding and Cultivation in Central and Southern China, College of Forestry, Guangxi University, Nanning 530004, China; (R.M.); (J.L.); (W.W.)
| | - Weijie Wang
- Key Laboratory of National Forestry and Grassland Administration for Fast-Growing Tree Breeding and Cultivation in Central and Southern China, College of Forestry, Guangxi University, Nanning 530004, China; (R.M.); (J.L.); (W.W.)
| | - Tianqi Song
- College of Agronomy, Northwest A&F University, Xianyang 712000, China;
| | - Yunlin Fu
- Key Laboratory of National Forestry and Grassland Administration for Fast-Growing Tree Breeding and Cultivation in Central and Southern China, College of Forestry, Guangxi University, Nanning 530004, China; (R.M.); (J.L.); (W.W.)
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Lu L, Tang Y, Xu H, Qian Y, Tao J, Zhao D. Selection and verification of reliable internal reference genes in stem development of herbaceous peony ( Paeonia lactiflora Pall.). PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2023; 29:773-782. [PMID: 37520813 PMCID: PMC10382430 DOI: 10.1007/s12298-023-01325-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 05/30/2023] [Accepted: 05/31/2023] [Indexed: 08/01/2023]
Abstract
Herbaceous peony (Paeonia lactiflora Pall.) has emerged in the cut flower market due to its beautiful appearance. The bending flower stems caused by a lack of mechanical strength is the main problem restricting the development of the cut P. lactiflora industry. So it is of great worth to reveal the basis of stem development changes in P. lactiflora to improve its cut flower quality. Quantitative research on gene expression characteristics can provide clues for understanding their biological functions, and the screening of relatively stable expression genes is a prerequisite for the quantitative study of gene expression characteristics. Thus, it is necessary to find appropriate genes during stem development so as to analyze the qRT‒PCR results. In this study, 10 genes were screened, and these genes expressed stably in stems of different stem strengths at three different developmental stages. Then, their expressions were evaluated by RefFinder, BestKeeper, NormFinder, and GeNorm programs. The results demonstrated that γ-tubulin (γ-TUB) was the most suitable gene, followed by α-tubulin (α-TUB) and β-D-glucosidase (β-GUS), whereas histone H3 (His) was the least suitable gene. Besides, the temporal and spatial expression characteristics of PlCOMT1, the key gene concerned with the synthesis of cell wall fillers in P. lactiflora, were also used to evaluate the suitability of genes. Consequently, γ-TUB and α-TUB are the two best combinations during stem development, and their combination can be used for the stem development of P. lactiflora. These findings will provide a reference for the selection of genes related to stem development and the study of molecular mechanisms related to stem development in P. lactiflora. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-023-01325-5.
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Affiliation(s)
- Lili Lu
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, 225009 Jiangsu China
| | - Yuhan Tang
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, 225009 Jiangsu China
| | - Huajie Xu
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, 225009 Jiangsu China
| | - Yi Qian
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, 225009 Jiangsu China
| | - Jun Tao
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, 225009 Jiangsu China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, 225009 Jiangsu China
| | - Daqiu Zhao
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, 225009 Jiangsu China
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Wang Y, Xu J, Zhao W, Li J, Chen J. Genome-wide identification, characterization, and genetic diversity of CCR gene family in Dalbergia odorifera. FRONTIERS IN PLANT SCIENCE 2022; 13:1064262. [PMID: 36600926 PMCID: PMC9806228 DOI: 10.3389/fpls.2022.1064262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 11/28/2022] [Indexed: 06/17/2023]
Abstract
INTRODUCTION Lignin is a complex aromatic polymer plays major biological roles in maintaining the structure of plants and in defending them against biotic and abiotic stresses. Cinnamoyl-CoA reductase (CCR) is the first enzyme in the lignin-specific biosynthetic pathway, catalyzing the conversion of hydroxycinnamoyl-CoA into hydroxy cinnamaldehyde. Dalbergia odorifera T. Chen is a rare rosewood species for furniture, crafts and medicine. However, the CCR family genes in D. odorifera have not been identified, and their function in lignin biosynthesis remain uncertain. METHODS AND RESULTS Here, a total of 24 genes, with their complete domains were identified. Detailed sequence characterization and multiple sequence alignment revealed that the DoCCR protein sequences were relatively conserved. They were divided into three subfamilies and were unevenly distributed on 10 chromosomes. Phylogenetic analysis showed that seven DoCCRs were grouped together with functionally characterized CCRs of dicotyledons involved in developmental lignification. Synteny analysis showed that segmental and tandem duplications were crucial in the expansion of CCR family in D. odorifera, and purifying selection emerged as the main force driving these genes evolution. Cis-acting elements in the putative promoter regions of DoCCRs were mainly associated with stress, light, hormones, and growth/development. Further, analysis of expression profiles from the RNA-seq data showed distinct expression patterns of DoCCRs among different tissues and organs, as well as in response to stem wounding. Additionally, 74 simple sequence repeats (SSRs) were identified within 19 DoCCRs, located in the intron or untranslated regions (UTRs), and mononucleotide predominated. A pair of primers with high polymorphism and good interspecific generality was successfully developed from these SSRs, and 7 alleles were amplified in 105 wild D. odorifera trees from 17 areas covering its whole native distribution. DISCUSSION Overall, this study provides a basis for further functional dissection of CCR gene families, as well as breeding improvement for wood properties and stress resistance in D. odorifera.
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Affiliation(s)
- Yue Wang
- Hainan Yazhou Bay Seed Laboratory, School of Forestry, Sanya Nanfan Research Institute of Hainan University, Sanya, China
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, School of Forestry, Hainan University, Haikou, China
| | - Jieru Xu
- Hainan Yazhou Bay Seed Laboratory, School of Forestry, Sanya Nanfan Research Institute of Hainan University, Sanya, China
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, School of Forestry, Hainan University, Haikou, China
| | - Wenxiu Zhao
- Hainan Yazhou Bay Seed Laboratory, School of Forestry, Sanya Nanfan Research Institute of Hainan University, Sanya, China
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, School of Forestry, Hainan University, Haikou, China
| | - Jia Li
- Hainan Yazhou Bay Seed Laboratory, School of Forestry, Sanya Nanfan Research Institute of Hainan University, Sanya, China
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, School of Forestry, Hainan University, Haikou, China
| | - Jinhui Chen
- Hainan Yazhou Bay Seed Laboratory, School of Forestry, Sanya Nanfan Research Institute of Hainan University, Sanya, China
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, School of Forestry, Hainan University, Haikou, China
- Research Institute of Forestry, Hainan Academy of Forestry (Hainan Academy of Mangrove), Haikou, China
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Li X, Yang S, Liu X, Xia H, Chen Q, Liu Y, Hong Z, Wang J. Iso-Seq and RNA-Seq analyses uncover the molecular response of Dalbergia odorifera T. Chen to low temperature. Gene X 2022; 847:146844. [PMID: 36041593 DOI: 10.1016/j.gene.2022.146844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 08/21/2022] [Accepted: 08/23/2022] [Indexed: 11/29/2022] Open
Abstract
In previous studies, we found young plants propagated from acclimated D. odorifera T. Chen trees displayed increased cold tolerance. To understand the molecular and physiological mechanisms underlying this phenomenon, we prepared acclimated and non-acclimated young D. odorifera T. Chen trees for physiological, RNA-Seq, and Iso-Seq analyses. First, both the acclimated and non-acclimated young trees were grown in 10 ℃ condition, then treated at -3 ℃ for one day, and finally recovered at 10 ℃. The measurement of physiological parameters, including superoxide dismutase, peroxidase, malondialdehyde, thiobarbituric acid, and soluble sugar, showed that the physiological change of acclimated plants is smoother than non-acclimated plants. The RNA-Seq analyses pointed out that cold acclimation already fixed the different gene expression patterns of D. odorifera T. Chen trees. The hormone-related, secondary metabolic, and signal transduction related biological genes tend to show different expressions between the acclimated and non-acclimated D. odorifera T. Chen trees. Moreover, the change of gene expression for some biological processes, such as alpha-Linolenic acid metabolism and its response to hydrogen peroxide, seems to occur earlier in non-acclimated than acclimated plants. The ISO-Seq analyses pointed out that alternative splicing (AS) of some genes was also found, and these AS events were predicted to play important roles in regulating different expression patterns between non-acclimated and acclimated plants. Therefore, according to the performance of this study, we are able to provide some novel understanding of cold tolerance enhanced by cold acclimation in perennial trees.
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Affiliation(s)
- Xiaowen Li
- Zhejiang Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, Wenzhou 325005, China.
| | - Sheng Yang
- Zhejiang Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, Wenzhou 325005, China.
| | - Xing Liu
- Zhejiang Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, Wenzhou 325005, China.
| | - Haitao Xia
- Zhejiang Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, Wenzhou 325005, China.
| | - Qiuxia Chen
- Zhejiang Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, Wenzhou 325005, China.
| | - Yu Liu
- Zhejiang Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, Wenzhou 325005, China.
| | - Zhou Hong
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520, China
| | - Jinwang Wang
- Zhejiang Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, Wenzhou 325005, China.
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Zhao W, Meng X, Xu J, Liu Z, Hu Y, Li B, Chen J, Cao B. Integrated mRNA and Small RNA Sequencing Reveals microRNAs Associated With Xylem Development in Dalbergia odorifera. Front Genet 2022; 13:883422. [PMID: 35547261 PMCID: PMC9081728 DOI: 10.3389/fgene.2022.883422] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 03/23/2022] [Indexed: 11/13/2022] Open
Abstract
Dalbergia odorifera is a rare and precious rosewood specie, whose wood is a very high-quality material for valuable furniture and carving crafts. However, limited information is available about the process of wood formation in D. odorifera. To determine genes that might be closely associated with the xylem differentiation process, we analyzed the differentially expressed genes (DEGs) and microRNAs (miRNAs) from specific xylem tissues of D. odorifera by RNA sequencing (RNA-seq) and small RNA sequencing (small RNA-seq). In total, we obtained 134,221,955 clean reads from RNA-seq and 90,940,761 clean reads from small RNA-seq. By comparing the transition zone (Dotz) and sapwood (Dosw) samples, a total of 395 DEGs were identified. Further analysis revealed that DEGs encoded for WRKY transcription factors (eight genes), lignin synthesis (PER47, COMT, CCR2), cell wall composition (UXS2), gibberellin synthesis (KAO2, GA20OX1), jasmonic acid synthesis (OPR2, CYP74A), and synthesis of flavonoids (PAL2) and terpenoids (CYP71A1). Subsequently, a preliminary analysis by small RNA-seq showed that the expressions of 14 miRNAs (such as miR168a-5p, miR167f-5p, miR167h-5p, miR167e, miR390a, miR156g, novel_52, and novel_9) were significantly different between Dotz and Dosw. Further analysis revealed that the target genes of these differentially expressed miRNAs were enriched in the GO terms "amino acid binding," "cellulase activity," and "DNA beta-glucosyltransferase activity". Further, KEGG pathway annotation showed significant enrichment in "fatty acid elongation" and "biosynthesis of unsaturated fatty acids". These processes might be participating in the xylem differentiation of D. odorifera. Next, expression correlation analysis showed that nine differentially expressed miRNAs were significantly negatively associated with 21 target genes, which encoded for proteins such as pyrH, SPL6, SPL12, GCS1, and ARF8. Overall, this is the first study on miRNAs and their potential functions in the xylem development of D. odorifera, which provides a stepping stone for a detailed functional investigation of D. odorifera miRNAs.
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Affiliation(s)
- Wenxiu Zhao
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, School of Forestry, Hainan University, Haikou, China
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, China
| | - Xiangxu Meng
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, School of Forestry, Hainan University, Haikou, China
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, China
| | - Jiahong Xu
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, School of Forestry, Hainan University, Haikou, China
| | - Zijia Liu
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, China
| | - Yangyang Hu
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, School of Forestry, Hainan University, Haikou, China
| | - Bingyu Li
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, School of Forestry, Hainan University, Haikou, China
| | - Jinhui Chen
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, School of Forestry, Hainan University, Haikou, China
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, China
| | - Bing Cao
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, China
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Liu YP, Zhang Y, Liu F, Liu T, Chen JY, Fu G, Zheng CY, Su DD, Wang YN, Zhou HK, Su X, Aj H, Wang XM. Establishment of reference (housekeeping) genes via quantitative real-time PCR for investigation of the genomic basis of abiotic stress resistance in Psammochloa villosa (Poaceae). JOURNAL OF PLANT PHYSIOLOGY 2022; 268:153575. [PMID: 34837885 DOI: 10.1016/j.jplph.2021.153575] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 11/18/2021] [Accepted: 11/18/2021] [Indexed: 06/13/2023]
Abstract
Psammochloa villosa is a desert plant growing in Northwest China with considerable resistance to abiotic stress, including drought, cold, and salt. To facilitate future studies of stress resistance in Psammochloa villosa, we sought to establish a suite of reference (or housekeeping) genes for utilization within future gene expression studies. Specifically, we selected nine candidate genes based on prior studies and new transcriptomic data for P. villosa, and we evaluated their expression stability in three different tissues of P. villosa under different treatments simulating abiotic stress conditions using four different bioinformatics assessments. Our results showed that TIP41 (TIP41-like family protein) was the most stable reference gene in drought- and salt-stressed leaves and salt-stressed stems, ELF-1α (elongation factor 1-α) was the most stable in cold-stressed leaves and drought- and salt-stressed roots, ACT (actin) was the most stable in drought-stressed stems, TUA (α-tubulin) was the most stable in cold-stressed stems, and 18S rRNA (18S ribosomal RNA) was the most stable in cold-stressed roots. Additionally, we tested the utility of these candidate reference genes to detect the expression pattern of P5CS (Δ1-pyrroline-5-carboxylate synthetase), which is a drought-related gene. This study is the first report on selecting and validating reference genes of P. villosa under various stress conditions and will benefit future investigations of the genomic mechanisms of stress resistance in this ecologically important species.
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Affiliation(s)
- Yu Ping Liu
- School of Life Sciences, Qinghai Normal University, Xining, 810008, China; Academy of Plateau Science and Sustainability, Qinghai Normal University, Xining, 810016, China; Key Laboratory of Medicinal Animal and Plant Resources of the Qinghai-Tibet Plateau in Qinghai Province, Qinghai Normal University, Xining, 810008, China.
| | - Yu Zhang
- School of Life Sciences, Qinghai Normal University, Xining, 810008, China
| | - Feng Liu
- School of Life Sciences, Qinghai Normal University, Xining, 810008, China
| | - Tao Liu
- School of Geography, Qinghai Normal University, Xining, 810008, China; Key Laboratory of Land Surface Processes and Ecological Conservation of the Qinghai-Tibet Plateau, The Ministry of Education, Qinghai Normal University, Xining, 810008, China
| | - Jin Yuan Chen
- School of Life Sciences, Qinghai Normal University, Xining, 810008, China
| | - Gui Fu
- School of Geography, Qinghai Normal University, Xining, 810008, China
| | - Chang Yuan Zheng
- School of Life Sciences, Qinghai Normal University, Xining, 810008, China
| | - Dan Dan Su
- School of Life Sciences, Qinghai Normal University, Xining, 810008, China
| | - Ya Nan Wang
- School of Life Sciences, Qinghai Normal University, Xining, 810008, China
| | - Hua Kun Zhou
- Key Laboratory of Cold Regions Restoration Ecology in Qinghai Province, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, China
| | - Xu Su
- School of Life Sciences, Qinghai Normal University, Xining, 810008, China; Academy of Plateau Science and Sustainability, Qinghai Normal University, Xining, 810016, China; Key Laboratory of Medicinal Animal and Plant Resources of the Qinghai-Tibet Plateau in Qinghai Province, Qinghai Normal University, Xining, 810008, China; Key Laboratory of Land Surface Processes and Ecological Conservation of the Qinghai-Tibet Plateau, The Ministry of Education, Qinghai Normal University, Xining, 810008, China
| | - Harris Aj
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Xiu Mei Wang
- School of Life Sciences, Qinghai Normal University, Xining, 810008, China
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Fernández MB, Lukaszewicz G, Lamattina L, Cassia R. Selection and optimization of reference genes for RT-qPCR normalization: A case study in Solanum lycopersicum exposed to UV-B. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 160:269-280. [PMID: 33529802 DOI: 10.1016/j.plaphy.2021.01.026] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 01/18/2021] [Indexed: 05/11/2023]
Abstract
Quantitative RT- PCR is one of the most common methods to study gene expression in response to stress. Therefore, it is crucial to have suitable reference genes (RGs) for result normalization. Although several reports describe UV-B-modulated gene expression in Solanum lycopersicum, there are no suitable RGs identified until now. The aim of this work was to evaluate the suitability of seven traditional genes: actin (ACT), tubulin (TUB), ubiquitin (UBI), glyceraldehyde- 3 phosphate dehydrogenase (GAPDH), elongation factor 1α (EF1α), phosphatase 2A catalytic subunit (PP2A) and GAGA binding transcriptional activator (GAGA); and two non-traditional genes: thioredoxin h1 (TRX h1) and UV-B RESISTANCE LOCUS 8 (UVR8), as candidate RGs for their potential use as reliable internal controls in leaves, stems and roots of tomato seedlings exposed to acute and chronic UV-B. The stability of these genes expression was evaluated using five statistical algorithms: geNorm, NormFinder, BestKeeper, Delta Ct and ANOVA. Considering the comprehensive stability ranking, we recommend ACT+TUB as the best pair of RGs for leaves, PP2A+GAPDH+TRX h1 for stems and TUB+UVR8 for roots. The reliability of the selected RGs for each tissue was verified amplifying tomato chalcone synthase 1 (CHS1) and cyclobutane pyrimidine dimer (CPD) photolyase (PHR1-LIKE). Under UV-B treatment, CHS1 was upregulated in leaves, stems and roots whereas PHR1-LIKE was only upregulated in leaves and stems. This interpretation differs when the most and least stable RGs are chosen. This is the first report regarding suitable RGs selection for accurate normalization of gene expression in tomato seedlings exposed to UV-B irradiation.
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Affiliation(s)
- María Belén Fernández
- Instituto de Investigaciones Biológicas- Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar Del Plata- Consejo Nacional de Investigaciones Científicas y Técnicas, CC1245 7600, Mar Del Plata, Buenos Aires, Argentina.
| | - Germán Lukaszewicz
- Instituto de Investigaciones Biológicas- Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar Del Plata- Consejo Nacional de Investigaciones Científicas y Técnicas, CC1245 7600, Mar Del Plata, Buenos Aires, Argentina
| | - Lorenzo Lamattina
- Instituto de Investigaciones Biológicas- Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar Del Plata- Consejo Nacional de Investigaciones Científicas y Técnicas, CC1245 7600, Mar Del Plata, Buenos Aires, Argentina
| | - Raúl Cassia
- Instituto de Investigaciones Biológicas- Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar Del Plata- Consejo Nacional de Investigaciones Científicas y Técnicas, CC1245 7600, Mar Del Plata, Buenos Aires, Argentina
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Xing G, Liu K, Li W, Li J, Xing C, Yuan H, Yang J. Evaluation of internal reference genes in Auxenochlorella protothecoides under continuous heterotrophic culture conditions at normal, low and high temperatures. ALGAL RES 2020. [DOI: 10.1016/j.algal.2020.101941] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Sun Y, Gao M, Kang S, Yang C, Meng H, Yang Y, Zhao X, Gao Z, Xu Y, Jin Y, Zhao X, Zhang Z, Han J. Molecular Mechanism Underlying Mechanical Wounding-Induced Flavonoid Accumulation in Dalbergia odorifera T. Chen, an Endangered Tree That Produces Chinese Rosewood. Genes (Basel) 2020; 11:genes11050478. [PMID: 32353985 PMCID: PMC7291145 DOI: 10.3390/genes11050478] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 04/13/2020] [Accepted: 04/24/2020] [Indexed: 01/27/2023] Open
Abstract
Dalbergia odorifera, a critically endangered tree species, produces heartwood containing a vast variety of flavonoids. This heartwood, also known as Chinese rosewood, has high economic and medicinal value, but its formation takes several decades. In this study, we showed that discolored wood induced by pruning displays similar color, structure, and flavonoids content to those of natural heartwood, suggesting that wounding is an efficient method for inducing flavonoid production in D. odorifera. Transcriptome analysis was performed to investigate the mechanism underlying wounding-induced flavonoids production in D. odorifera heartwood. Wounding upregulated the expression of 90 unigenes, which covered 19 gene families of the phenylpropanoid and flavonoid pathways, including PAL, C4H, 4CL, CHS, CHI, 6DCS, F3’5’H, F3H, FMO, GT, PMAT, CHOMT, IFS, HI4’OMT, HID, IOMT, I2’H, IFR, and I3’H. Furthermore, 47 upregulated unigenes were mapped to the biosynthesis pathways for five signal molecules (ET, JA, ABA, ROS, and SA). Exogenous application of these signal molecules resulted in the accumulation of flavonoids in cell suspensions of D. odorifera, supporting their role in wounding-induced flavonoid production. Insights from this study will help develop new methods for rapidly inducing the formation of heartwood with enhanced medicinal value.
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Affiliation(s)
- Ying Sun
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Chinese Peking Union Medical College, Beijing 100193, China; (Y.S.); (M.G.); (C.Y.); (Z.G.); (Y.X.); (Y.J.); (X.Z.)
| | - Mei Gao
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Chinese Peking Union Medical College, Beijing 100193, China; (Y.S.); (M.G.); (C.Y.); (Z.G.); (Y.X.); (Y.J.); (X.Z.)
| | - Seogchan Kang
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA 16802, USA;
| | - Chengmin Yang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Chinese Peking Union Medical College, Beijing 100193, China; (Y.S.); (M.G.); (C.Y.); (Z.G.); (Y.X.); (Y.J.); (X.Z.)
| | - Hui Meng
- Hainan Branch Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Haikou 570311, China; (H.M.); (Y.Y.); (X.Z.)
| | - Yun Yang
- Hainan Branch Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Haikou 570311, China; (H.M.); (Y.Y.); (X.Z.)
| | - Xiangsheng Zhao
- Hainan Branch Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Haikou 570311, China; (H.M.); (Y.Y.); (X.Z.)
| | - Zhihui Gao
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Chinese Peking Union Medical College, Beijing 100193, China; (Y.S.); (M.G.); (C.Y.); (Z.G.); (Y.X.); (Y.J.); (X.Z.)
| | - Yanhong Xu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Chinese Peking Union Medical College, Beijing 100193, China; (Y.S.); (M.G.); (C.Y.); (Z.G.); (Y.X.); (Y.J.); (X.Z.)
| | - Yue Jin
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Chinese Peking Union Medical College, Beijing 100193, China; (Y.S.); (M.G.); (C.Y.); (Z.G.); (Y.X.); (Y.J.); (X.Z.)
| | - Xiaohong Zhao
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Chinese Peking Union Medical College, Beijing 100193, China; (Y.S.); (M.G.); (C.Y.); (Z.G.); (Y.X.); (Y.J.); (X.Z.)
| | - Zheng Zhang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Chinese Peking Union Medical College, Beijing 100193, China; (Y.S.); (M.G.); (C.Y.); (Z.G.); (Y.X.); (Y.J.); (X.Z.)
- Hainan Branch Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Haikou 570311, China; (H.M.); (Y.Y.); (X.Z.)
- Correspondence: (Z.Z.); (J.H.); Tel.: +86-10-57833363 (Z.Z.); +86-10-57833198 (J.H.)
| | - Jianping Han
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Chinese Peking Union Medical College, Beijing 100193, China; (Y.S.); (M.G.); (C.Y.); (Z.G.); (Y.X.); (Y.J.); (X.Z.)
- Correspondence: (Z.Z.); (J.H.); Tel.: +86-10-57833363 (Z.Z.); +86-10-57833198 (J.H.)
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