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Mali S, Zinta G. Genome-wide identification and expression analysis reveal the role of histone methyltransferase and demethylase genes in heat stress response in potato (Solanum tuberosum L.). Biochim Biophys Acta Gen Subj 2024; 1868:130507. [PMID: 37925032 DOI: 10.1016/j.bbagen.2023.130507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 10/05/2023] [Accepted: 10/30/2023] [Indexed: 11/06/2023]
Abstract
BACKGROUND Potato (Solanum tuberosum L.), the third most important non-cereal crop, is sensitive to high temperature. Histone modifications have been known to regulate various abiotic stress responses. However, the role of histone methyltransferases and demethylases remain unexplored in potato under heat stress. METHODS Potato genome database was used for genome-wide analysis of StPRMT and StHDMA gene families, which were further characterized by analyzing gene structure, conserved motif, domain organization, sub-cellular localization, promoter region and phylogenetic relationships. Additionally, expression profiling under high-temperature stress in leaf and stolon tissue of heat contrasting potato genotypes was done to study their role in response to high temperature stress. RESULTS The genome-wide analysis led to identification of nine StPRMT and eleven StHDMA genes. Structural analysis, including conserved motifs, exon/intron structure and phylogenetic relationships classified StPRMT and StHDMA gene families into two classes viz. Class I and Class II. A variety of cis-regulatory elements were explored in the promoter region associated with light, developmental, hormonal and stress responses. Prediction of sub-cellular localization of StPRMT proteins revealed their occurrence in nucleus and cytoplasm, whereas StHDMA proteins were observed in different sub-cellular compartments. Furthermore, expression profiling of StPRMT and StHDMA gene family members revealed genes responding to heat stress. Heat-inducible expression of StPRMT1, StPRMT3, StPRMT4 and StPRMT5 in leaf and stolon tissues of HS and HT cultivar indicated them as probable candidates for enhancing thermotolerance in potato. However, StHDMAs responded dynamically in leaf and stolon tissue of heat contrasting genotypes under high temperature. CONCLUSION The current study presents a detailed analysis of histone modifiers in potato and indicates their role as an important epigenetic regulators modulating heat tolerance. GENERAL SIGNIFICANCE Understanding epigenetic mechanisms underlying heat tolerance in potato will contribute towards breeding of thermotolerant potato varieties.
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Affiliation(s)
- Surbhi Mali
- Integrative Plant AdaptOmics Lab (iPAL), Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur, Himachal Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Gaurav Zinta
- Integrative Plant AdaptOmics Lab (iPAL), Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur, Himachal Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India.
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Wang T, Udayabhanu J, Gu X, Wu R, Xin S, Chen Q, Zhang Y, Yang X, Peng S, Chen J, Huang T. Induction of Axillary Bud Swelling of Hevea brasiliensis to Regenerate Plants through Somatic Embryogenesis and Analysis of Genetic Stability. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12091803. [PMID: 37176861 PMCID: PMC10181009 DOI: 10.3390/plants12091803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 04/19/2023] [Accepted: 04/25/2023] [Indexed: 05/15/2023]
Abstract
To overcome rubber tree (RT) tissue culture explant source limitations, the current study aimed to establish a new Hevea brasiliensis somatic embryogenesis (SE) system, laying the technical foundation for the establishment of an axillary-bud-based seedling regeneration system. In this study, in vitro plantlets of Hevea brasiliensis Chinese Academy of Tropical Agricultural Sciences 917 (CATAS 917) were used as the experimental materials. Firstly, the optimum conditions for axillary bud swelling were studied; then, the effects of phenology, the swelling time of axillary buds (ABs), and medium of embryogenic callus induction were studied. Plantlets were obtained through somatic embryogenesis. Flow cytometry, inter-simple sequence repeat (ISSR molecular marker) and chromosome karyotype analysis were used to study the genetic stability of regenerated plants along with budding seedlings (BSs) and secondary somatic embryo seedlings (SSESs) as the control. The results show that the rubber tree's phenology period was mature, and the axillary bud induction rate was the highest in the 2 mg/L 6-benzyladenine (6-BA) medium (up to 85.83%). Later, 3-day-old swelling axillary buds were used as explants for callogenesis and somatic embryogenesis. The callus induction rate was optimum in MH (Medium in Hevea) + 1.5 mg/L 2,4-dichlorophenoxyacetic acid (2,4-D) + 1.5 mg/L 1-naphthalene acetic acid (NAA) + 1.5 mg/L Kinetin (KT) + 70 g/L sucrose (56.55%). The regenerated plants were obtained after the 175-day culture of explants through callus induction, embryogenic callus induction, somatic embryo development, and plant regeneration. Compared with the secondary somatic embryo seedling control, axillary bud regeneration plants (ABRPs) were normal diploid plants at the cellular and molecular level, with a variation rate of 7.74%.
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Affiliation(s)
- Taihua Wang
- Hainan Yazhou Bay Seed Laboratory, Sanya Nanfan Research Institute, Hainan University, Sanya 572025, China
- College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Jinu Udayabhanu
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Science, Haikou 571101, China
- Haikou Key Laboratory of Innovation of Seedlings of Tropical Plants, Haikou 571101, China
| | - Xiaochuan Gu
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Science, Haikou 571101, China
- Haikou Key Laboratory of Innovation of Seedlings of Tropical Plants, Haikou 571101, China
| | - Rizhi Wu
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Science, Haikou 571101, China
- Haikou Key Laboratory of Innovation of Seedlings of Tropical Plants, Haikou 571101, China
| | - Shichao Xin
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Science, Haikou 571101, China
- Haikou Key Laboratory of Innovation of Seedlings of Tropical Plants, Haikou 571101, China
| | - Qiuhui Chen
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Science, Haikou 571101, China
| | - Yuanyuan Zhang
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Science, Haikou 571101, China
| | - Xianfeng Yang
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Science, Haikou 571101, China
- Haikou Key Laboratory of Innovation of Seedlings of Tropical Plants, Haikou 571101, China
| | - Suna Peng
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Science, Haikou 571101, China
- Haikou Key Laboratory of Innovation of Seedlings of Tropical Plants, Haikou 571101, China
| | - Jianmiao Chen
- Hainan Yazhou Bay Seed Laboratory, Sanya Nanfan Research Institute, Hainan University, Sanya 572025, China
- College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Tiandai Huang
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Science, Haikou 571101, China
- Haikou Key Laboratory of Innovation of Seedlings of Tropical Plants, Haikou 571101, China
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Zhou L, Yarra R, Jin L, Yang Y, Cao H, Zhao Z. Identification and expression analysis of histone modification gene (HM) family during somatic embryogenesis of oil palm. BMC Genomics 2022; 23:11. [PMID: 34983381 PMCID: PMC8729141 DOI: 10.1186/s12864-021-08245-2] [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: 08/18/2021] [Accepted: 12/07/2021] [Indexed: 11/23/2022] Open
Abstract
Background Oil palm (Elaeis guineensis, Jacq.) is an important vegetable oil-yielding plant. Somatic embryogenesis is a promising method to produce large-scale elite clones to meet the demand for palm oil. The epigenetic mechanisms such as histone modifications have emerged as critical factors during somatic embryogenesis. These histone modifications are associated with the regulation of various genes controlling somatic embryogenesis. To date, none of the information is available on the histone modification gene (HM) family in oil palm. Results We reported the identification of 109 HM gene family members including 48 HMTs, 27 HDMs, 13 HATs, and 21 HDACs in the oil palm genome. Gene structural and motif analysis of EgHMs showed varied exon–intron organization and with conserved motifs among them. The identified 109 EgHMs were distributed unevenly across 16 chromosomes and displayed tandem duplication in oil palm genome. Furthermore, relative expression analysis showed the differential expressional pattern of 99 candidate EgHM genes at different stages (non-embryogenic, embryogenic, somatic embryo) of somatic embryogenesis process in oil palm, suggesting the EgHMs play vital roles in somatic embryogenesis. Our study laid a foundation to understand the regulatory roles of several EgHM genes during somatic embryogenesis. Conclusions A total of 109 histone modification gene family members were identified in the oil palm genome via genome-wide analysis. The present study provides insightful information regarding HM gene’s structure, their distribution, duplication in oil palm genome, and also their evolutionary relationship with other HM gene family members in Arabidopsis and rice. Finally, our study provided an essential role of oil palm HM genes during somatic embryogenesis process. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08245-2.
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Affiliation(s)
- Lixia Zhou
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences/ Hainan Key Laboratory of Tropical Oil Crops Biology, Wenchang, Hainan, 571339, P. R. China.
| | - Rajesh Yarra
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences/ Hainan Key Laboratory of Tropical Oil Crops Biology, Wenchang, Hainan, 571339, P. R. China
| | - Longfei Jin
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences/ Hainan Key Laboratory of Tropical Oil Crops Biology, Wenchang, Hainan, 571339, P. R. China
| | - Yaodong Yang
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences/ Hainan Key Laboratory of Tropical Oil Crops Biology, Wenchang, Hainan, 571339, P. R. China
| | - Hongxing Cao
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences/ Hainan Key Laboratory of Tropical Oil Crops Biology, Wenchang, Hainan, 571339, P. R. China
| | - Zhihao Zhao
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences/ Hainan Key Laboratory of Tropical Oil Crops Biology, Wenchang, Hainan, 571339, P. R. China
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Li HL, Wang Y, Guo D, Zhu JH, Peng SQ. Differential Expression of lncRNAs and miRNAs Between Self-Rooting Juvenile and Donor Clones Unveils Novel Insight Into the Molecular Regulation of Rubber Biosynthesis in Hevea brasiliensis. FRONTIERS IN PLANT SCIENCE 2022; 12:740597. [PMID: 35069613 PMCID: PMC8767119 DOI: 10.3389/fpls.2021.740597] [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: 07/13/2021] [Accepted: 11/02/2021] [Indexed: 06/14/2023]
Abstract
The rubber tree (Hevea brasiliensis Muell. Arg.) is a tropical tree species that produce natural rubber. Self-rooted juvenile clones (SRJCs) are novel rubber tree planting materials developed through primary somatic embryogenesis. SRJCs have a higher rubber yield compared with donor clones (DCs). The molecular basis underlying increased rubber yield in SRJCs remains largely unknown. Here, the latex from SRJCs and DCs were collected for strand-specific and small RNA-seq methods. A total of 196 differentially expressed long noncoding RNAs (DELs), and 11 differentially expressed microRNAs were identified in latex between SRJCs and DCs. Targeted genes of DELs were markedly enriched for various biological pathways related to plant hormone signal transduction, photosynthesis, glutathione metabolism, and amino acids biosynthesis. DELs probably acted as cis-acting regulation was calculated, and these DELs relevant to potentially regulate rubber biosynthesis, reactive oxygen species metabolism, and epigenetic modification. Furthermore, the DELs acting as microRNA targets were studied. The interaction of microRNA and DELs might involve in the regulation of natural rubber biosynthesis.
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