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Htwe YM, Shi P, Zhang D, Li Z, Yu Q, Wang Y. GWAS determined genetic loci associated with callus induction in oil palm tissue culture. Plant Cell Rep 2024; 43:128. [PMID: 38652306 DOI: 10.1007/s00299-024-03221-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 04/14/2024] [Indexed: 04/25/2024]
Abstract
KEY MESSAGE GWAS identified six loci at 25 kb downstream of WAK2, a crucial gene for cell wall and callus formation, enabling development of a SNP marker for enhanced callus induction potential. Efficient callus induction is vital for successful oil palm tissue culture, yet identifying genomic loci and markers for early detection of genotypes with high potential of callus induction remains unclear. In this study, immature male inflorescences from 198 oil palm accessions (dura, tenera and pisifera) were used as explants for tissue culture. Callus induction rates were collected at one-, two- and three-months after inoculation (C1, C2 and C3) as phenotypes. Resequencing generated 11,475,258 high quality single nucleotide polymorphisms (SNPs) as genotypes. GWAS was then performed, and correlation analysis revealed a positive association of C1 with both C2 (R = 0.81) and C3 (R = 0.50), indicating that C1 could be used as the major phenotype for callus induction rate. Therefore, only significant SNPs (P ≤ 0.05) in C1 were identified to develop markers for screening individuals with high potential of callus induction. Among 21 significant SNPs in C1, LD block analysis revealed six SNPs on chromosome 12 (Chr12) potentially linked to callus formation. Subsequently, 13 SNP markers were identified from these loci and electrophoresis results showed that marker C-12 at locus Chr12_12704856 can be used effectively to distinguish the GG allele, which showed the highest probability (69%) of callus induction. Furthermore, a rapid SNP variant detection method without electrophoresis was established via qPCR-based melting curve analysis. Our findings facilitated marker-assisted selection for specific palms with high potential of callus induction using immature male inflorescence as explant, aiding ortet palm selection in oil palm tissue culture.
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Affiliation(s)
- Yin Min Htwe
- National Key Laboratory for Tropical Crop Breeding, Coconut Research Institute of Chinese Academy of Tropical Agricultural Sciences, Wenchang, Hainan, China
- Hainan Yazhou Bay Seed Laboratory, Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, China
| | - Peng Shi
- National Key Laboratory for Tropical Crop Breeding, Coconut Research Institute of Chinese Academy of Tropical Agricultural Sciences, Wenchang, Hainan, China
- Hainan Yazhou Bay Seed Laboratory, Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, China
| | - Dapeng Zhang
- National Key Laboratory for Tropical Crop Breeding, Coconut Research Institute of Chinese Academy of Tropical Agricultural Sciences, Wenchang, Hainan, China
- Hainan Yazhou Bay Seed Laboratory, Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, China
| | - Zhiying Li
- National Key Laboratory for Tropical Crop Breeding, Coconut Research Institute of Chinese Academy of Tropical Agricultural Sciences, Wenchang, Hainan, China
- Hainan Yazhou Bay Seed Laboratory, Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, China
| | - Qun Yu
- National Key Laboratory for Tropical Crop Breeding, Coconut Research Institute of Chinese Academy of Tropical Agricultural Sciences, Wenchang, Hainan, China
- Hainan Yazhou Bay Seed Laboratory, Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, China
| | - Yong Wang
- National Key Laboratory for Tropical Crop Breeding, Coconut Research Institute of Chinese Academy of Tropical Agricultural Sciences, Wenchang, Hainan, China.
- Hainan Yazhou Bay Seed Laboratory, Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, China.
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Wu W, Feng X, Wang N, Shao S, Liu M, Si F, Chen L, Jin C, Xu S, Guo Z, Zhong C, Shi S, He Z. Genomic analysis of Nypa fruticans elucidates its intertidal adaptations and early palm evolution. J Integr Plant Biol 2024; 66:824-843. [PMID: 38372488 DOI: 10.1111/jipb.13625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 01/28/2024] [Indexed: 02/20/2024]
Abstract
Nypa fruticans (Wurmb), a mangrove palm species with origins dating back to the Late Cretaceous period, is a unique species for investigating long-term adaptation strategies to intertidal environments and the early evolution of palms. Here, we present a chromosome-level genome sequence and assembly for N. fruticans. We integrated the genomes of N. fruticans and other palm family members for a comparative genomic analysis, which confirmed that the common ancestor of all palms experienced a whole-genome duplication event around 89 million years ago, shaping the distinctive characteristics observed in this clade. We also inferred a low mutation rate for the N. fruticans genome, which underwent strong purifying selection and evolved slowly, thus contributing to its stability over a long evolutionary period. Moreover, ancient duplicates were preferentially retained, with critical genes having experienced positive selection, enhancing waterlogging tolerance in N. fruticans. Furthermore, we discovered that the pseudogenization of Early Methionine-labelled 1 (EM1) and EM6 in N. fruticans underly its crypto-vivipary characteristics, reflecting its intertidal adaptation. Our study provides valuable genomic insights into the evolutionary history, genome stability, and adaptive evolution of the mangrove palm. Our results also shed light on the long-term adaptation of this species and contribute to our understanding of the evolutionary dynamics in the palm family.
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Affiliation(s)
- Weihong Wu
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Xiao Feng
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
- Greater Bay Area Institute of Precision Medicine, School of Life Sciences, Fudan University, Guangzhou, 511462, China
| | - Nan Wang
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Shao Shao
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Min Liu
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Fa Si
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Linhao Chen
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Chuanfeng Jin
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Shaohua Xu
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Zixiao Guo
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Cairong Zhong
- Hainan Academy of Forestry (Hainan Academy of Mangrove), Haikou, 571100, China
| | - Suhua Shi
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Ziwen He
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
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Carvalho-Madrigal S, Sanín MJ. The role of introgressive hybridization in shaping the geographically isolated gene pools of wax palm populations (genus Ceroxylon). Mol Phylogenet Evol 2024; 193:108013. [PMID: 38195012 DOI: 10.1016/j.ympev.2024.108013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 12/22/2023] [Accepted: 01/06/2024] [Indexed: 01/11/2024]
Abstract
The speciation continuum is the process by which genetic groups diverge until they reach reproductive isolation. It has become common in the literature to show that this process is gradual and flickering, with possibly many instances of secondary contact and introgression after divergence has started. The level of divergence might vary among genomic regions due to, among others, the different forces and roles of selection played by the shared regions. Through hybrid capture, we sequenced ca. 4,000 nuclear regions in populations of six species of wax palms, five of which form a monophyletic group (genus Ceroxylon, Arecaceae: Ceroxyloideae). We show that in this group, the different populations show varying degrees of introgressive hybridization, and two of them are backcrosses of the other three 'pure' species. This is particularly interesting because these three species are dioecious, have a shared main pollinator, and have slightly overlapping reproductive seasons but highly divergent morphologies. Our work supports shows wax palms diverge under positive and background selection in allopatry, and hybridize due to secondary contact and inefficient reproductive barriers, which sustain genetic diversity. Introgressed regions are generally not under positive selection. Peripheral populations are backcrosses of other species; thus, introgressive hybridization is likely modulated by demographic effects rather than selective pressures. In general, these species might function as an 'evolutionary syngameon' where expanding, peripheral, small, and isolated populations maintain diversity by crossing with available individuals of other wax palms. In the Andean context, species can benefit from gained variation from a second taxon or the enhancement of population sizes by recreating a common genetic pool.
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Affiliation(s)
| | - María José Sanín
- School of Mathematical and Natural Sciences, Arizona State University, West Valley Campus, Glendale, United States.
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Wang Y, Yan J, Yang M, Zou J, Zheng Y, Li D. EgMADS3 directly regulates EgLPAAT to mediate medium-chain fatty acids (MCFA) anabolism in the mesocarp of oil palm. Plant Cell Rep 2024; 43:107. [PMID: 38558250 DOI: 10.1007/s00299-024-03200-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 03/19/2024] [Indexed: 04/04/2024]
Abstract
KEY MESSAGE EgMADS3, a pivotal transcription factor, positively regulates MCFA accumulation via binding to the EgLPAAT promoter, advancing lipid content in mesocarp of oil palm. Lipids function as the structural components of cell membranes, which serve as permeable barriers to the external environment of cells. The medium-chain fatty acid in the stored lipids of plants is an important renewable energy. Most research on MCFA production in plant lipid synthesis is based on biochemical methods, and the importance of transcriptional regulation in MCFA synthesis and its incorporation into TAGs needs further research. Oil palm is the most productive oil crop in the world and has the highest productivity among the main oil crops. In this study, the MADS transcription factor (EgMADS3) in the mesocarp of oil palm was characterized. Through the VIGS-virus induced gene silencing, it was determined that the potential target gene of EgMADS3 was related to the biosynthesis of medium-chain fatty acid (MCFA). Transient transformation in protoplasts and qRT-PCR analysis showed that EgMADS3 positively regulated the expression of EgLPAAT. The results of the yeast one-hybrid assays and EMSA indicated the interaction between EgMADS3 and EgLPAAT promoter. Through genetic transformation and fatty acid analysis, it is concluded that EgMADS3 directly regulates the mid-chain fatty acid synthesis pathway of the potential target gene EgLPAAT, thus promotes the accumulation of MCFA and improves the total lipid content. This study is innovative in the functional analysis of the MADS family transcription factor in the metabolism of medium-chain fatty acids (MCFA) of oil palm, provides a certain research basis for improving the metabolic pathway of chain fatty acids in oil palm, and improves the synthesis of MCFA in plants. Our results will provide a reference direction for further research on improving the oil quality through biotechnology of oil palm.
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Affiliation(s)
- Yaning Wang
- Sanya Nanfan Research Institute, College of Tropical Crops, Hainan University, Hainan, 570228, China
| | - Jinqi Yan
- Sanya Nanfan Research Institute, College of Tropical Crops, Hainan University, Hainan, 570228, China
| | | | - Jixin Zou
- Rubber Research Institute of Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou, 571101, China
| | - Yusheng Zheng
- Sanya Nanfan Research Institute, College of Tropical Crops, Hainan University, Hainan, 570228, China
| | - Dongdong Li
- Sanya Nanfan Research Institute, College of Tropical Crops, Hainan University, Hainan, 570228, China.
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Wei L, Yang C, John Martin JJ, Li R, Zhou L, Cheng S, Cao H, Liu X. Metabonomics and Transcriptomic Analysis of Free Fatty Acid Synthesis in Seedless and Tenera Oil Palm. Int J Mol Sci 2024; 25:1686. [PMID: 38338979 PMCID: PMC10855455 DOI: 10.3390/ijms25031686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 01/26/2024] [Accepted: 01/28/2024] [Indexed: 02/12/2024] Open
Abstract
Oil palm, a tropical woody oil crop, is widely used in food, cosmetics, and pharmaceuticals due to its high production efficiency and economic value. Palm oil is rich in free fatty acids, polyphenols, vitamin E, and other nutrients, which are beneficial for human health when consumed appropriately. Therefore, investigating the dynamic changes in free fatty acid content at different stages of development and hypothesizing the influence of regulatory genes on free fatty acid metabolism is crucial for improving palm oil quality and accelerating industry growth. LC-MS/MS is used to analyze the composition and content of free fatty acids in the flesh after 95 days (MS1 and MT1), 125 days (MS2 and MT2), and 185 days (MS3 and MT3) of Seedless (MS) and Tenera (MT) oil palm species fruit pollination. RNA-Seq was used to analyze the expression of genes regulating free fatty acid synthesis and accumulation, with differences in genes and metabolites mapped to the KEGG pathway map using the KEGG (Kyoto encyclopedia of genes and genomes) enrichment analysis method. A metabolomics study identified 17 types of saturated and 13 types of unsaturated free fatty acids during the development of MS and MT. Transcriptomic research revealed that 10,804 significantly different expression genes were acquired in the set differential gene threshold between MS and MT. The results showed that FabB was positively correlated with the contents of three main free fatty acids (stearic acid, myristate acid, and palmitic acid) and negatively correlated with the contents of free palmitic acid in the flesh of MS and MT. ACSL and FATB were positively correlated with the contents of three main free fatty acids and negatively correlated with free myristate acid. The study reveals that the expression of key enzyme genes, FabB and FabF, may improve the synthesis of free myristate in oil palm flesh, while FabF, ACSL, and FATB genes may facilitate the production of free palmitoleic acid. These genes may also promote the synthesis of free stearic acid and palmitoleic acid in oil palm flesh. However, the FabB gene may inhibit stearic acid synthesis, while ACSL and FATB genes may hinder myristate acid production. This study provides a theoretical basis for improving palm oil quality.
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Affiliation(s)
- Lu Wei
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang 571339, China; (L.W.); (C.Y.); (J.J.J.M.); (R.L.); (L.Z.)
- National Key Laboratory for Tropical Crop Breeding, Haikou 571101, China
- School of Horticulture, Hainan University, Haikou 570228, China
| | - Cheng Yang
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang 571339, China; (L.W.); (C.Y.); (J.J.J.M.); (R.L.); (L.Z.)
- National Key Laboratory for Tropical Crop Breeding, Haikou 571101, China
| | - Jerome Jeyakumar John Martin
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang 571339, China; (L.W.); (C.Y.); (J.J.J.M.); (R.L.); (L.Z.)
- National Key Laboratory for Tropical Crop Breeding, Haikou 571101, China
| | - Rui Li
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang 571339, China; (L.W.); (C.Y.); (J.J.J.M.); (R.L.); (L.Z.)
- National Key Laboratory for Tropical Crop Breeding, Haikou 571101, China
| | - Lixia Zhou
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang 571339, China; (L.W.); (C.Y.); (J.J.J.M.); (R.L.); (L.Z.)
- National Key Laboratory for Tropical Crop Breeding, Haikou 571101, China
| | - Shuanghong Cheng
- College of Tropical Crops, Yunnan Agricultural University, Pu’er 665000, China;
| | - Hongxing Cao
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang 571339, China; (L.W.); (C.Y.); (J.J.J.M.); (R.L.); (L.Z.)
- National Key Laboratory for Tropical Crop Breeding, Haikou 571101, China
| | - Xiaoyu Liu
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang 571339, China; (L.W.); (C.Y.); (J.J.J.M.); (R.L.); (L.Z.)
- National Key Laboratory for Tropical Crop Breeding, Haikou 571101, China
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Zhou L, John Martin JJ, Li R, Zeng X, Wu Q, Li Q, Fu D, Li X, Liu X, Ye J, Cao H. Catalase (CAT) Gene Family in Oil Palm ( Elaeis guineensis Jacq.): Genome-Wide Identification, Analysis, and Expression Profile in Response to Abiotic Stress. Int J Mol Sci 2024; 25:1480. [PMID: 38338758 PMCID: PMC10855858 DOI: 10.3390/ijms25031480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 01/11/2024] [Accepted: 01/23/2024] [Indexed: 02/12/2024] Open
Abstract
Catalases (CATs) play crucial roles in scavenging H2O2 from reactive oxygen species, controlling the growth and development of plants. So far, genome-wide identification and characterization of CAT genes in oil palm have not been reported. In the present study, five EgCAT genes were obtained through a genome-wide identification approach. Phylogenetic analysis divided them into two subfamilies, with closer genes sharing similar structures. Gene structure and conserved motif analysis demonstrated the conserved nature of intron/exon organization and motifs among the EgCAT genes. Several cis-acting elements related to hormone, stress, and defense responses were identified in the promoter regions of EgCATs. Tissue-specific expression of EgCAT genes in five different tissues of oil palm was also revealed by heatmap analysis using the available transcriptome data. Stress-responsive expression analysis showed that five EgCAT genes were significantly expressed under cold, drought, and salinity stress conditions. Collectively, this study provided valuable information on the oil palm CAT gene family and the validated EgCAT genes can be used as potential candidates for improving abiotic stress tolerance in oil palm and other related crops.
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Affiliation(s)
- Lixia Zhou
- National Key Laboratory for Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (L.Z.); (J.J.J.M.); (R.L.); (X.Z.); (Q.W.); (Q.L.); (D.F.); (X.L.); (X.L.)
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang 571339, China
| | - Jerome Jeyakumar John Martin
- National Key Laboratory for Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (L.Z.); (J.J.J.M.); (R.L.); (X.Z.); (Q.W.); (Q.L.); (D.F.); (X.L.); (X.L.)
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang 571339, China
| | - Rui Li
- National Key Laboratory for Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (L.Z.); (J.J.J.M.); (R.L.); (X.Z.); (Q.W.); (Q.L.); (D.F.); (X.L.); (X.L.)
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang 571339, China
| | - Xianhai Zeng
- National Key Laboratory for Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (L.Z.); (J.J.J.M.); (R.L.); (X.Z.); (Q.W.); (Q.L.); (D.F.); (X.L.); (X.L.)
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang 571339, China
| | - Qiufei Wu
- National Key Laboratory for Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (L.Z.); (J.J.J.M.); (R.L.); (X.Z.); (Q.W.); (Q.L.); (D.F.); (X.L.); (X.L.)
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang 571339, China
| | - Qihong Li
- National Key Laboratory for Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (L.Z.); (J.J.J.M.); (R.L.); (X.Z.); (Q.W.); (Q.L.); (D.F.); (X.L.); (X.L.)
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang 571339, China
| | - Dengqiang Fu
- National Key Laboratory for Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (L.Z.); (J.J.J.M.); (R.L.); (X.Z.); (Q.W.); (Q.L.); (D.F.); (X.L.); (X.L.)
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang 571339, China
| | - Xinyu Li
- National Key Laboratory for Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (L.Z.); (J.J.J.M.); (R.L.); (X.Z.); (Q.W.); (Q.L.); (D.F.); (X.L.); (X.L.)
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang 571339, China
| | - Xiaoyu Liu
- National Key Laboratory for Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (L.Z.); (J.J.J.M.); (R.L.); (X.Z.); (Q.W.); (Q.L.); (D.F.); (X.L.); (X.L.)
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang 571339, China
| | - Jianqiu Ye
- National Key Laboratory for Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (L.Z.); (J.J.J.M.); (R.L.); (X.Z.); (Q.W.); (Q.L.); (D.F.); (X.L.); (X.L.)
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang 571339, China
| | - Hongxing Cao
- National Key Laboratory for Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (L.Z.); (J.J.J.M.); (R.L.); (X.Z.); (Q.W.); (Q.L.); (D.F.); (X.L.); (X.L.)
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang 571339, China
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Nagappan J, Ooi SE, Chan KL, Kadri F, Nurazah Z, Halim MAA, Angel LPL, Sundram S, Chin CF, May ST, Low ETL. Transcriptional effects of carbon and nitrogen starvation on Ganoderma boninense, an oil palm phytopathogen. Mol Biol Rep 2024; 51:212. [PMID: 38273212 DOI: 10.1007/s11033-023-09054-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 10/24/2023] [Indexed: 01/27/2024]
Abstract
BACKGROUND Ganoderma boninense is a phytopathogen of oil palm, causing basal and upper stem rot diseases. METHODS The genome sequence was used as a reference to study gene expression during growth in a starved carbon (C) and nitrogen (N) environment with minimal sugar and sawdust as initial energy sources. This study was conducted to mimic possible limitations of the C-N nutrient sources during the growth of G. boninense in oil palm plantations. RESULTS Genome sequencing of an isolate collected from a palm tree in West Malaysia generated an assembly of 67.12 Mb encoding 19,851 predicted genes. Transcriptomic analysis from a time course experiment during growth in this starvation media identified differentially expressed genes (DEGs) that were found to be associated with 29 metabolic pathways. During the active growth phase, 26 DEGs were related to four pathways, including secondary metabolite biosynthesis, carbohydrate metabolism, glycan metabolism and mycotoxin biosynthesis. G. boninense genes involved in the carbohydrate metabolism pathway that contribute to the degradation of plant cell walls were up-regulated. Interestingly, several genes associated with the mycotoxin biosynthesis pathway were identified as playing a possible role in pathogen-host interaction. In addition, metabolomics analysis revealed six metabolites, maltose, xylobiose, glucooligosaccharide, glycylproline, dimethylfumaric acid and arabitol that were up-regulated on Day2 of the time course experiment. CONCLUSIONS This study provides information on genes expressed by G. boninense in metabolic pathways that may play a role in the initial infection of the host.
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Affiliation(s)
- Jayanthi Nagappan
- Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia
- School of Biosciences, University of Nottingham Malaysia, Jalan Broga, 43500, Semenyih, Selangor, Malaysia
| | - Siew-Eng Ooi
- Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia
| | - Kuang-Lim Chan
- Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia
| | - Faizun Kadri
- Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia
| | - Zain Nurazah
- Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia
| | - Mohd Amin Ab Halim
- Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia
| | - Lee Pei Lee Angel
- Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia
| | - Shamala Sundram
- Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia
| | - Chiew-Foan Chin
- School of Biosciences, University of Nottingham Malaysia, Jalan Broga, 43500, Semenyih, Selangor, Malaysia
| | - Sean T May
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Nr Loughborough, LE12 5RD, UK
| | - Eng Ti Leslie Low
- Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia.
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Meira FS, Ribeiro DG, de Campos SS, Falcão LL, Gomes ACMM, de Alencar Dusi DM, Marcellino LH, Mehta A, Scherwinski-Pereira JE. Differential expression of genes potentially related to the callogenesis and in situ hybridization of SERK gene in macaw palm (Acrocomia aculeata Jacq.) Lodd. ex Mart. Protoplasma 2024; 261:89-101. [PMID: 37482557 DOI: 10.1007/s00709-023-01881-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 07/03/2023] [Indexed: 07/25/2023]
Abstract
For the purpose of understanding the molecular processes triggered during callus formation in macaw palm, the expression of seven genes potentially involved in this process, identified in previous studies and from the literature, was investigated by RT-qPCR. In addition, in situ hybridization of the SERK gene was performed. Leaf tissues from adult plants from two macaw palm accession were inoculated in a medium combined with Picloram at a concentration of 450 μM to induce callus. The expression analysis was performed from leaf samples from two accessions of different origins (Municipalities of Tiros, MG, and Buriti Vermelho, DF, Brazil), which are characterized as non-responsive (NR) and responsive (R), respectively. The material was collected before callus induction (0 DAI, initial day) and 120 days after callus induction (120 DAI). Genes related to development (SERK, OASA, EF1, ANN1) and stress (LEA, CAT2, and MDAR5) were evaluated. The results obtained showed that all the genes involved with the development had their expressions downregulated at 0 DAI when the accession R was compared with the accession NR. On the other hand, it was possible to observe that these genes were upregulated at 120 DAI. The LEA stress gene showed a tendency to increase expression in the NR accession, while the R accession showed decreased expression and the CAT2 and MDAR5 genes showed upregulation in both accessions. In situ hybridization showed SERK transcripts in the vascular bundles, indicating the expression of SERK in this region, in addition to its expression in calluses. The results obtained in this study support our hypothesis that the regulation of genes involved in the control of oxidative stress and development is crucial for the formation of calluses in macaw palm.
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Affiliation(s)
- Filipe Sathler Meira
- Universidade de Brasília, Instituto de Ciências Biológicas, Campus Universitário Darcy Ribeiro, Brasília, DF, 70910-900, Brazil
| | - Daiane Gonzaga Ribeiro
- Universidade de Brasília, Instituto de Ciências Biológicas, Campus Universitário Darcy Ribeiro, Brasília, DF, 70910-900, Brazil
| | - Samanta Siqueira de Campos
- Universidade Federal do Rio Grande do Sul, Departamento de Horticultura e Silvicultura, Porto Alegre, RS, 91540-000, Brazil
| | - Loeni Ludke Falcão
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, PqEB, Brasília, 70770-917, Brazil
| | | | | | - Lucilia Helena Marcellino
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, PqEB, Brasília, 70770-917, Brazil
| | - Angela Mehta
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, PqEB, Brasília, 70770-917, Brazil
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9
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Jousson A, Naciri Y, Christe C, Marazzi B, Stauffer F. Not just females and males: Unravelling the complex sex determinism of the hemp palm, Trachycarpus fortunei. Am J Bot 2023; 110:e16257. [PMID: 38014995 DOI: 10.1002/ajb2.16257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 10/18/2023] [Accepted: 10/18/2023] [Indexed: 11/29/2023]
Abstract
PREMISE The ornamental Asian palm Trachycarpus fortunei (Arecaceae: Coryphoideae) is widely planted in temperate regions. In Europe, it has spread outside of gardens, particularly on the southern side of the Alps. Sexual expression in the species is complex, varying from dioecy to polygamy. This study investigated (1) sexual floral development and (2) genetic markers implicated in sex determinism. METHODS The morphology and anatomy of floral organs at different developmental stages were studied using SEM observations and anatomical section. Sex determinism was explored using a genome-wide association study approach, searching for correlations between 31,000 single-nucleotide polymorphisms and sex affiliation of 122 palms from 21 wild populations. RESULTS We observed that sexual differentiation appears late in floral development of T. fortunei. Morpho-anatomical characters of flowers conducive to panmixia were observed, such as well-differentiated septal nectaries that are thought to promote cross-pollination. At the molecular level, homozygous and heterozygous allelic systems with closely linked regions were found for sex determinism in individuals with female and "dominant-male" phenotypes, respectively. Through our wide sampling in the southern Alps, the closely linked genetic regions in males suggest that at least fifteen percent of wild palms are the direct offspring of "males" that can also produce fertile pistillate flowers. CONCLUSIONS Trachycarpus fortunei is a further example of unstable sexual expression found in the family Arecaceae and represents an evolutionary path towards an XY genetic system. Our structural and genetic results may explain the high species dispersal ability in the southern Alps.
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Affiliation(s)
- Antoine Jousson
- PhyloLab and MorphoLab, Conservatoire et Jardin Botaniques de Genève, Chemin de l'Impératrice 1, 1292, Chambésy, Geneva, Switzerland
- Departement of Plant Sciences, Université de Genève, Chemin de l'Impératrice 1, 1292, Chambésy, Geneva, Switzerland
| | - Yamama Naciri
- PhyloLab and MorphoLab, Conservatoire et Jardin Botaniques de Genève, Chemin de l'Impératrice 1, 1292, Chambésy, Geneva, Switzerland
- Departement of Plant Sciences, Université de Genève, Chemin de l'Impératrice 1, 1292, Chambésy, Geneva, Switzerland
| | - Camille Christe
- PhyloLab and MorphoLab, Conservatoire et Jardin Botaniques de Genève, Chemin de l'Impératrice 1, 1292, Chambésy, Geneva, Switzerland
- Departement of Plant Sciences, Université de Genève, Chemin de l'Impératrice 1, 1292, Chambésy, Geneva, Switzerland
| | - Brigitte Marazzi
- Natural History Museum of Canton Ticino, Viale C. Cattaneo 4, 6900, Lugano, Switzerland
- InfoFlora C/O Natural History Museum of Canton Ticino, Viale C. Cattaneo 4, Lugano, 6900, Switzerland
| | - Fred Stauffer
- PhyloLab and MorphoLab, Conservatoire et Jardin Botaniques de Genève, Chemin de l'Impératrice 1, 1292, Chambésy, Geneva, Switzerland
- Departement of Plant Sciences, Université de Genève, Chemin de l'Impératrice 1, 1292, Chambésy, Geneva, Switzerland
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10
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Cao J, Wang W, Xu X, Li SY, Zheng Y, Li DD. Identification and Analysis of MADS-Box Genes Expressed in the Mesocarp of Oil Palm Fruit (Elaeis guineensis Jacq.). Biochem Genet 2023; 61:2382-2400. [PMID: 37060482 DOI: 10.1007/s10528-023-10376-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Accepted: 03/14/2023] [Indexed: 04/16/2023]
Abstract
Oil palm (Elaeis guineensis) is the most important tropical oil-bearing crop species worldwide. MADS-box proteins, which play crucial roles in plant growth and development and are involved in various physiological and biochemical processes, compose one of the largest families of plant transcription factors. In this study, 42 MADS-box genes were screened from the mesocarp transcriptome database of oil palm fruit, and their phylogenetic relationships with Arabidopsis thaliana MADS-box genes were analyzed. Based on the results, MADS-box genes from oil palm mesocarp were classified into four groups: MIKCc-type, MIKC*-type, Mα-type, and Mγ-type MADS-box genes. Members of the subfamilies were classified according to the presence of three specific protein motifs. To explore the differential expression of the MADS-box genes, the dynamic expression of all selected MADS-box genes in oil palm was measured by RNA-seq. The high expression of specific MADS-box genes in the mesocarp of oil palm during different developmental stages indicates that those genes may play important roles in the cell division of and metabolite accumulation in the fruit and could become important targets for fruit development and oil accumulation research in oil palm.
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Affiliation(s)
- Jiaqi Cao
- Sanya Nanfan Research Institute, College of Tropical Crops, Hainan University, Hainan, 570228, China
| | - Wei Wang
- Sanya Nanfan Research Institute, College of Tropical Crops, Hainan University, Hainan, 570228, China
| | - Xin Xu
- Sanya Nanfan Research Institute, College of Tropical Crops, Hainan University, Hainan, 570228, China
| | - Si-Yu Li
- Sanya Nanfan Research Institute, College of Tropical Crops, Hainan University, Hainan, 570228, China
| | - Yusheng Zheng
- Sanya Nanfan Research Institute, College of Tropical Crops, Hainan University, Hainan, 570228, China
| | - Dong-Dong Li
- Sanya Nanfan Research Institute, College of Tropical Crops, Hainan University, Hainan, 570228, China.
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11
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Francisconi AF, Marroquín JAM, Cauz-Santos LA, van den Berg C, Martins KKM, Costa MF, Picanço-Rodrigues D, de Alencar LD, Zanello CA, Colombo CA, Hernández BGD, Amaral DT, Lopes MTG, Veasey EA, Zucchi MI. Complete chloroplast genomes of six neotropical palm species, structural comparison, and evolutionary dynamic patterns. Sci Rep 2023; 13:20635. [PMID: 37996522 PMCID: PMC10667357 DOI: 10.1038/s41598-023-44631-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 10/10/2023] [Indexed: 11/25/2023] Open
Abstract
The Arecaceae family has a worldwide distribution, especially in tropical and subtropical regions. We sequenced the chloroplast genomes of Acrocomia intumescens and A. totai, widely used in the food and energy industries; Bactris gasipaes, important for palm heart; Copernicia alba and C. prunifera, worldwide known for wax utilization; and Syagrus romanzoffiana, of great ornamental potential. Copernicia spp. showed the largest chloroplast genomes (C. prunifera: 157,323 bp and C. alba: 157,192 bp), while S. romanzoffiana and B. gasipaes var. gasipaes presented the smallest (155,078 bp and 155,604 bp). Structurally, great synteny was detected among palms. Conservation was also observed in the distribution of single sequence repeats (SSR). Copernicia spp. presented less dispersed repeats, without occurrence in the small single copy (SSC). All RNA editing sites were C (cytidine) to U (uridine) conversions. Overall, closely phylogenetically related species shared more sites. Almost all nodes of the phylogenetic analysis showed a posterior probability (PP) of 1.0, reaffirming the close relationship between Acrocomia species. These results elucidate the conservation among palm chloroplast genomes, but point to subtle structural changes, providing support for the evolutionary dynamics of the Arecaceae family.
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Affiliation(s)
- Ana Flávia Francisconi
- Programa de Pós-Gradução em Genética e Biologia Molecular, Universidade Estadual de Campinas, R. Monteiro Lobato, 255-Barão Geraldo, Campinas, São Paulo, CEP 13083-862, Brazil
| | - Jonathan Andre Morales Marroquín
- Programa de Pós-Gradução em Genética e Biologia Molecular, Universidade Estadual de Campinas, R. Monteiro Lobato, 255-Barão Geraldo, Campinas, São Paulo, CEP 13083-862, Brazil
| | - Luiz Augusto Cauz-Santos
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, 1030, Wien, Austria
| | - Cássio van den Berg
- Departamento de Ciências Biológicas, Universidade Estadual de Feira de Santana, Av. Transnordestina S/N-Novo Horizonte, Feira de SantanaFeira de Santana, Bahia, CEP 44036-900, Brazil
| | - Kauanne Karolline Moreno Martins
- Programa de Pós-Gradução em Genética e Biologia Molecular, Universidade Estadual de Campinas, R. Monteiro Lobato, 255-Barão Geraldo, Campinas, São Paulo, CEP 13083-862, Brazil
| | - Marcones Ferreira Costa
- Programa de Pós-Gradução em Genética e Biologia Molecular, Universidade Estadual de Campinas, R. Monteiro Lobato, 255-Barão Geraldo, Campinas, São Paulo, CEP 13083-862, Brazil
- Universidade Federal do Piauí, BR-343 Km 3.5, Floriano, Piauí, CEP 64808-605, Brazil
| | - Doriane Picanço-Rodrigues
- Departamento de Biologia, Universidade Federal do Amazonas, Avenida Gen. Rodrigo Octávio Jordão Ramos, 3000-Coroado I-Campus Universitário-Senador Arthur Virgílio Filho-Setor Sul, Bloco H, Manaus, Amazonas, CEP 69077-000, Brazil
| | - Luciano Delmodes de Alencar
- Programa de Pós-Gradução em Genética e Biologia Molecular, Universidade Estadual de Campinas, R. Monteiro Lobato, 255-Barão Geraldo, Campinas, São Paulo, CEP 13083-862, Brazil
| | - Cesar Augusto Zanello
- Programa de Pós-Gradução em Genética e Biologia Molecular, Universidade Estadual de Campinas, R. Monteiro Lobato, 255-Barão Geraldo, Campinas, São Paulo, CEP 13083-862, Brazil
| | - Carlos Augusto Colombo
- Instituto Agronômico, Av. Theodureto de Almeida Camargo, 1500, Campinas, São Paulo, CEP 13075-630, Brazil
| | | | - Danilo Trabuco Amaral
- Departamento de Biologia, Centro de Ciências Humanas e Biológicas, Universidade Federal do ABC, Avenida dos Estados, 5001, Santo André, São Paulo, CEP 09040-040, Brazil
| | - Maria Teresa Gomes Lopes
- Faculdade de Ciências Agrárias, Universidade Federal do Amazonas, Avenida Rodrigo Otávio Ramos, 3000-Bairro Coroado, Manaus, Amazonas, CEP 69077-000, Brazil
| | - Elizabeth Ann Veasey
- Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Avenida Pádua Dias, 11-Bairro São Dimas, Piracicaba, São Paulo, CEP 13418-900, Brazil
| | - Maria Imaculada Zucchi
- Agência Paulista de Tecnologia dos Agronegócios (APTA), Polo Centro Sul, Rodovia SP 127 Km 30, CP 28, Piracicaba, São Paulo, CEP 13400-970, Brazil.
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12
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Xiao F, Zhao Y, Wang X, Mao Y, Jian X. Comparative transcriptome analysis of dioecious floral development in Trachycarpus fortunei using Illumina and PacBio SMRT sequencing. BMC Plant Biol 2023; 23:536. [PMID: 37919651 PMCID: PMC10623883 DOI: 10.1186/s12870-023-04551-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 10/22/2023] [Indexed: 11/04/2023]
Abstract
BACKGROUND Trachycarpus fortunei is a plant with significant economic and ornamental value. Both male and female flowers of T. fortunei originate as bisexual flowers, and selective abortion occurs during floral development. However, the regulatory mechanisms underlying this process remain unclear in T. fortunei. In this study, transcriptome sequencing with Illumina and Pacific BioSciences (PacBio) single-molecule real-time (SMRT) platforms were used to investigate gene expression differences between male and female T. fortunei plants. RESULTS A total of 833,137 full-length non-chimeric (FLNC) reads were obtained, and 726,846 high-quality full-length transcripts were identified. A total of 159 genes were differentially expressed between male and female flowers at all development stages. Some of the differentially expressed genes (DEGs) showed male bias, including serine/threonine-protein kinase (STPK), THUMP1 homolog and other genes. Through single-nucleotide polymorphisms(SNPs) identification, 28 genes were considered as potential sex-associated SNPs. Time-Ordered Gene Co-expression Network (TO-GCN) analysis revealed that MADS2 and MADS26 may play important roles in the development of female and male flowers T. fortune plants, respectively. CONCLUSIONS These findings provide a genetic basis for flower development and differentiation in T. fortunei, and improve our understanding of the mechanisms underlying sexual differentiation in T. fortunei.
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Affiliation(s)
- Feng Xiao
- Institute for Forest Resources and Environment of Guizhou, Key Laboratory of Forest Cultivation in Plateau Mountain of Guizhou Province, College of Forestry, Guizhou University, Guiyang, 550025, Guizhou, China
| | - Yang Zhao
- Institute for Forest Resources and Environment of Guizhou, Key Laboratory of Forest Cultivation in Plateau Mountain of Guizhou Province, College of Forestry, Guizhou University, Guiyang, 550025, Guizhou, China.
| | - Xiurong Wang
- Institute for Forest Resources and Environment of Guizhou, Key Laboratory of Forest Cultivation in Plateau Mountain of Guizhou Province, College of Forestry, Guizhou University, Guiyang, 550025, Guizhou, China
| | - Yuexiong Mao
- Institute for Forest Resources and Environment of Guizhou, Key Laboratory of Forest Cultivation in Plateau Mountain of Guizhou Province, College of Forestry, Guizhou University, Guiyang, 550025, Guizhou, China
| | - Xueyan Jian
- School of Continuing Education, Yanbian University, Yanji, 133002, Jilin, China
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13
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Roslan ND, Sundram S, Hong LW, Ling KL, Vadamalai G. Analysis of Coconut cadang-cadang viroid variants on field samples exhibiting variation in orange spotting symptom expression and severity. Mol Biol Rep 2023; 50:9699-9705. [PMID: 37676433 DOI: 10.1007/s11033-023-08771-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 08/18/2023] [Indexed: 09/08/2023]
Abstract
BACKGROUND Sequence variation has been attributed to symptom variations but has not been investigated in Orange Spotting-Coconut cadang-cadang viroid (OS-CCCVd) infected palms. Likewise, the relationship between Coconut cadang-cadang viroid (CCCVd) variants, Orange Spotting (OS) severity and the accumulation of the viroid in the palms have not been elucidated. This paper describes the characterization of CCCVd variants by cloning and sequencing, followed by correlation with symptom expression. METHODS AND RESULTS Total nucleic acids were extracted from leaf samples harvested from frond 20 of seven Dura × Pisifera (D × P) African oil palm (Elaeis guineensis Jacq.) aged between 13 and 21 years old collected from local plantations. The nucleic acids were fractionated using 5% non-denaturing polyacrylamide gel electrophoresis (PAGE) before being subjected to detection by reverse transcribed polymerase chain reaction (RT-PCR). The PCR products were cloned into a plasmid vector and the sequence of the clones was analyzed. CCCVd variants were quantified using real-time qPCR assay with CCCVd specific primers. Sixteen randomly selected clones of (OP246) had an arbitrary 100% identity with CCCVdOP246 (GeneBank Accession No: HQ608513). Meanwhile, four clones had >93% similarity with several minor sequence variations forming variants of OP234, OP235, OP251 and OP279. CONCLUSION The OS symptoms observed in the field were characterized into three categories based on the size and morphology of the orange spots on the affected fronds. In addition, there was no direct correlation between disease severity and the accumulation of CCCVd variants in oil palm. This finding is the first report describing the sequence variation of the CCCVd RNA and symptom variation in OS oil palm field samples.
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Affiliation(s)
- Nur Diyana Roslan
- Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia
| | - Shamala Sundram
- Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia
| | - Lau Wei Hong
- Department of Plant Protection, Faculty of Agriculture, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Kong Lih Ling
- Institute of Plantation Studies, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Ganesan Vadamalai
- Department of Plant Protection, Faculty of Agriculture, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia.
- Institute of Plantation Studies, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia.
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14
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Yu J, Khomenko I, Biasioli F, Li M, Varotto C. A Novel Isoprene Synthase from the Monocot Tree Copernicia prunifera (Arecaceae) Confers Enhanced Drought Tolerance in Transgenic Arabidopsis. Int J Mol Sci 2023; 24:15329. [PMID: 37895009 PMCID: PMC10607627 DOI: 10.3390/ijms242015329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 09/18/2023] [Accepted: 10/17/2023] [Indexed: 10/29/2023] Open
Abstract
The capacity to emit isoprene, among other stresses, protects plants from drought, but the molecular mechanisms underlying this trait are only partly understood. The Arecaceae (palms) constitute a very interesting model system to test the involvement of isoprene in enhancing drought tolerance, as their high isoprene emissions may have contributed to make them hyperdominant in neotropical dry forests, characterized by recurrent and extended periods of drought stress. In this study we isolated and functionally characterized a novel isoprene synthase, the gene responsible for isoprene biosynthesis, from Copernicia prunifera, a palm from seasonally dry tropical forests. When overexpressed in the non-emitter Arabidopsis thaliana, CprISPS conferred significant levels of isoprene emission, together with enhanced tolerance to water limitation throughout plant growth and development, from germination to maturity. CprISPS overexpressors displayed higher germination, cotyledon/leaf greening, water usage efficiency, and survival than WT Arabidopsis under various types of water limitation. This increased drought tolerance was accompanied by a marked transcriptional up-regulation of both ABA-dependent and ABA-independent key drought response genes. Taken together, these results demonstrate the capacity of CprISPS to enhance drought tolerance in Arabidopsis and suggest that isoprene emission could have evolved in Arecaceae as an adaptive mechanism against drought.
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Affiliation(s)
- Jiamei Yu
- Biodiversity, Ecology and Environment Area, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all’Adige, 38098 Trento, Italy;
- Department of Biology, University of Padova, 35121 Padova, Italy
| | - Iuliia Khomenko
- Food and Nutrition Area, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all’Adige, 38098 Trento, Italy; (I.K.); (F.B.)
| | - Franco Biasioli
- Food and Nutrition Area, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all’Adige, 38098 Trento, Italy; (I.K.); (F.B.)
| | - Mingai Li
- Biodiversity, Ecology and Environment Area, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all’Adige, 38098 Trento, Italy;
- National Biodiversity Future Center (NBFC), 90133 Palermo, Italy
| | - Claudio Varotto
- Biodiversity, Ecology and Environment Area, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all’Adige, 38098 Trento, Italy;
- National Biodiversity Future Center (NBFC), 90133 Palermo, Italy
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15
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Anggraini E, Vadamalai G, Kong LL, Mat M, Lau WH. Variants in the mitochondrial genome sequence of Oryctes rhinoceros (Coleoptera: Scarabaeidae) infected with Oryctes rhinoceros nudivirus in oil palm and coconut plantations. Sci Rep 2023; 13:16850. [PMID: 37803044 PMCID: PMC10558481 DOI: 10.1038/s41598-023-43691-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 09/27/2023] [Indexed: 10/08/2023] Open
Abstract
The CRB (coconut rhinoceros beetle) haplotype was classified into CRB-S and CRB-G, based on the presence of single nucleotide polymorphisms (SNPs) in the mitochondrial cox1 gene. Mitochondrial genomes (mitogenomes) are the most widely used genetic resources for molecular evolution, phylogenetics, and population genetics in relation to insects. This study presents the mitogenome CRB-G and CRB-S which were collected in Johor, Malaysia. The mitogenome of CRB-G collected from oil palm plantations in 2020 and 2021, and wild coconut palms in 2021 was 15,315 bp, 15,475 bp, and 17,275 bp, respectively. The CRB-S was discovered in coconut and oil palms in 2021, and its mitogenome was 15,484 bp and 17,142 bp, respectively. All the mitogenomes have 37 genes with more than 99% nucleotide sequence homology, except the CRB-G haplotype collected from oil palm in 2021 with 89.24% nucleotide sequence homology. The mitogenome of Johor CRBs was variable in the natural population due to its elevated mutation rate. Substitutions and indels in cox1, cox2, nad2 and atp6 genes were able to distinguish the Johor CRBs into two haplotypes. The mitogenome data generated in the present study may provide baseline information to study the infection and relationship between the two haplotypes of Johor CRB and OrNV in the field. This study is the first report on the mitogenomes of mixed haplotypes of CRB in the field.
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Affiliation(s)
- Erise Anggraini
- Department of Plant Protection, Faculty of Agriculture, Universiti Putra Malaysia, 43400, UPM Serdang, Selangor, Malaysia
- Department of Plant Pests and Diseases, Faculty of Agriculture, Universitas Sriwijaya, Indralaya, Ogan Ilir, 30662, South Sumatra, Indonesia
| | - Ganesan Vadamalai
- Department of Plant Protection, Faculty of Agriculture, Universiti Putra Malaysia, 43400, UPM Serdang, Selangor, Malaysia
| | - Lih Ling Kong
- Institute of Plantation Studies, Universiti Putra Malaysia, 43400, UPM Serdang, Selangor, Malaysia
| | - Mazidah Mat
- Malaysian Agricultural Research and Development Institute, Persiaran MARDI-UPM, 43400, Serdang, Selangor, Malaysia
| | - Wei Hong Lau
- Department of Plant Protection, Faculty of Agriculture, Universiti Putra Malaysia, 43400, UPM Serdang, Selangor, Malaysia.
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16
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Aditama R, Tanjung ZA, Aprilyanto V, Sudania WM, Utomo C, Liwang T. Identification of oil palm cis-regulatory elements based on DNA free energy and single nucleotide polymorphism density. Comput Biol Chem 2023; 106:107931. [PMID: 37481844 DOI: 10.1016/j.compbiolchem.2023.107931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 06/29/2023] [Accepted: 07/17/2023] [Indexed: 07/25/2023]
Abstract
Transcription control through cis-regulatory elements (CREs) is one of important regulators of gene expression. This study aimed to identify the location of CREs in oil palm (Elaeis guineensis Jacq.) using the combination of DNA free energy and single nucleotide polymorphism (SNP) density approaches. Promoter region sequences were extracted oil palm genome spanning from 1500 nucleotides (nt) upstream to 1000 nt downstream of every annotated transcription start sites (TSS). Free energy profiles of each promoter region were calculated using PromPredict software. Raw reads from the deep sequencing of 59 oil palm origins were used to calculate SNP density of each promoter region. The result showed that the average free energy (AFE) on the upstream region of TSS is about 1.5 kcal/mol higher compared to the downstream region. Using DNA free energy method, 16,281 regions of CREs were predicted. Most of predicted CREs was located between 1 and 500 nt upstream of TSS. Anti-correlation pattern between free energy and SNP density was observed on the predicted regions of CREs. This anti-correlated pattern was also observed on an experimentally determined promoter of the oil palm metallothionein gene, EgMSP1. Considering the increasing use of promoter information on plant biotechnology, an easy and accurate promoter prediction using the combination of free energy and SNP density method could be recommended.
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Affiliation(s)
- Redi Aditama
- Biotechnology Department, Plant Production and Biotechnology Division, PT SMART Tbk., Bogor 16810, Indonesia
| | - Zulfikar Achmad Tanjung
- Biotechnology Department, Plant Production and Biotechnology Division, PT SMART Tbk., Bogor 16810, Indonesia
| | - Victor Aprilyanto
- Biotechnology Department, Plant Production and Biotechnology Division, PT SMART Tbk., Bogor 16810, Indonesia
| | - Widyartini Made Sudania
- Biotechnology Department, Plant Production and Biotechnology Division, PT SMART Tbk., Bogor 16810, Indonesia
| | - Condro Utomo
- Biotechnology Department, Plant Production and Biotechnology Division, PT SMART Tbk., Bogor 16810, Indonesia.
| | - Tony Liwang
- Biotechnology Department, Plant Production and Biotechnology Division, PT SMART Tbk., Bogor 16810, Indonesia
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17
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Echavarria MAZ, Barrantes EAB, Helmic EE, Bartlett CR, Bahder BW. A new species of planthopper in the genus Cobacella (Hemiptera: Auchenorrhyncha: Derbidae) from oil palm (Elaeis guineensis) in Costa Rica. Zootaxa 2023; 5351:107-121. [PMID: 38221496 DOI: 10.11646/zootaxa.5351.1.4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Indexed: 01/16/2024]
Abstract
Recent survey work in Costa Rica has revealed a high diversity of planthoppers in the family Derbidae on palms (Arecaceae). During an expedition to Costa Rica in 2021, specimens were collected from African oil palm (Elaeis guineensis) along the pacific coast and determined to represent a new species of derbid in the genus Cobacella. Herein, the novel taxon, Cobacella palmensis sp. n., is described and compared with the two other species in the genus. Supplemental molecular data for the cytochrome c oxidase subunit I (COI) barcoding region, 18S rRNA gene and D9-D10 expansion region of the 28S rRNA gene are provided to test the placement of the novel taxon relative to available otiocerine planthoppers. We also present a preliminary key to the species of Cobacella and review all available specimen records of the genus.
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Affiliation(s)
- Marco A Zumbado Echavarria
- Universidad de Costa RicaSede San Ramn; Departamento de Ciencias Naturales; de la Iglesia el Tremedal 400 mts al Oeste carretera hacia San Pedro; San Ramn; Alajuela; Costa Rica.
| | - Edwin A Barrantes Barrantes
- Universidad de Costa RicaSede San Ramn; Departamento de Ciencias Naturales; de la Iglesia el Tremedal 400 mts al Oeste carretera hacia San Pedro; San Ramn; Alajuela; Costa Rica.
| | - Ericka E Helmic
- University of Florida; Department of Entomology and Nematology - Fort Lauderdale Research and Education Center; 3205 College Ave.; Davie; FL 33314-7719; USA.
| | - Charles R Bartlett
- University of Delaware; Department of Entomology and Wildlife Ecology; 250 Townsend Hall; Newark; DE 19716-2160; USA.
| | - Brian W Bahder
- University of Florida; Department of Entomology and Nematology - Fort Lauderdale Research and Education Center; 3205 College Ave.; Davie; FL 33314-7719; USA.
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18
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Zhou L, Yarra R. Genome-Wide Analysis of SPL/miR156 Module and Its Expression Analysis in Vegetative and Reproductive Organs of Oil Palm ( Elaeis guineensis). Int J Mol Sci 2023; 24:13658. [PMID: 37686464 PMCID: PMC10488160 DOI: 10.3390/ijms241713658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 08/25/2023] [Accepted: 09/02/2023] [Indexed: 09/10/2023] Open
Abstract
The SPL (SQUAMOSA-promoter binding protein-like) gene family is one of the largest plant transcription factors and is known to be involved in the regulation of plant growth, development, and stress responses. The genome-wide analysis of SPL gene members in a diverse range of crops has been elucidated. However, none of the genome-wide studies on the SPL gene family have been carried out for oil palm, an important oil-yielding plant. In this research, a total of 24 EgSPL genes were identified via a genome-wide approach. Phylogenetic analysis revealed that most of the EgSPLs are closely related to the Arabidopsis and rice SPL gene members. EgSPL genes were mapped onto the only nine chromosomes of the oil palm genome. Motif analysis revealed conservation of the SBP domain and the occurrence of 1-10 motifs in EgSPL gene members. Gene duplication analysis demonstrated the tandem duplication of SPL members in the oil palm genome. Heatmap analysis indicated the significant expression of SPL genes in shoot and flower organs of oil palm plants. Among the identified EgSPL genes, a total 14 EgSPLs were shown to be targets of miR156. Real-time PCR analysis of 14 SPL genes showed that most of the EgSPL genes were more highly expressed in female and male inflorescences of oil palm plants than in vegetative tissues. Altogether, the present study revealed the significant role of EgSPL genes in inflorescence development.
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Affiliation(s)
- Lixia Zhou
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang 571339, China
| | - Rajesh Yarra
- Department of Plant and Agroecosytem Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA;
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19
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Bittencourt CB, Carvalho da Silva TL, Rodrigues Neto JC, Leão AP, de Aquino Ribeiro JA, Maia ADHN, de Sousa CAF, Quirino BF, Souza Júnior MT. Molecular Interplay between Non-Host Resistance, Pathogens and Basal Immunity as a Background for Fatal Yellowing in Oil Palm ( Elaeis guineensis Jacq.) Plants. Int J Mol Sci 2023; 24:12918. [PMID: 37629099 PMCID: PMC10454536 DOI: 10.3390/ijms241612918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 08/08/2023] [Accepted: 08/13/2023] [Indexed: 08/27/2023] Open
Abstract
An oil palm (Elaeis guineensis Jacq.) bud rod disorder of unknown etiology, named Fatal Yellowing (FY) disease, is regarded as one of the top constraints with respect to the growth of the palm oil industry in Brazil. FY etiology has been a challenge embraced by several research groups in plant pathology throughout the last 50 years in Brazil, with no success in completing Koch's postulates. Most recently, the hypothesis of having an abiotic stressor as the initial cause of FY has gained ground, and oxygen deficiency (hypoxia) damaging the root system has become a candidate for stress. Here, a comprehensive, large-scale, single- and multi-omics integration analysis of the metabolome and transcriptome profiles on the leaves of oil palm plants contrasting in terms of FY symptomatology-asymptomatic and symptomatic-and collected in two distinct seasons-dry and rainy-is reported. The changes observed in the physicochemical attributes of the soil and the chemical attributes and metabolome profiles of the leaves did not allow the discrimination of plants which were asymptomatic or symptomatic for this disease, not even in the rainy season, when the soil became waterlogged. However, the multi-omics integration analysis of enzymes and metabolites differentially expressed in asymptomatic and/or symptomatic plants in the rainy season compared to the dry season allowed the identification of the metabolic pathways most affected by the changes in the environment, opening an opportunity for additional characterization of the role of hypoxia in FY symptom intensification. Finally, the initial analysis of a set of 56 proteins/genes differentially expressed in symptomatic plants compared to the asymptomatic ones, independent of the season, has presented pieces of evidence suggesting that breaks in the non-host resistance to non-adapted pathogens and the basal immunity to adapted pathogens, caused by the anaerobic conditions experienced by the plants, might be linked to the onset of this disease. This set of genes might offer the opportunity to develop biomarkers for selecting oil palm plants resistant to this disease and to help pave the way to employing strategies to keep the safety barriers raised and strong.
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Affiliation(s)
- Cleiton Barroso Bittencourt
- Graduate Program of Plant Biotechnology, Federal University of Lavras, Lavras 37203-202, MG, Brazil; (C.B.B.); (T.L.C.d.S.)
| | | | - Jorge Cândido Rodrigues Neto
- The Brazilian Agricultural Research Corporation, Embrapa Agroenergy, Brasília 70770-901, DF, Brazil; (J.C.R.N.); (A.P.L.); (J.A.d.A.R.); (B.F.Q.)
| | - André Pereira Leão
- The Brazilian Agricultural Research Corporation, Embrapa Agroenergy, Brasília 70770-901, DF, Brazil; (J.C.R.N.); (A.P.L.); (J.A.d.A.R.); (B.F.Q.)
| | - José Antônio de Aquino Ribeiro
- The Brazilian Agricultural Research Corporation, Embrapa Agroenergy, Brasília 70770-901, DF, Brazil; (J.C.R.N.); (A.P.L.); (J.A.d.A.R.); (B.F.Q.)
| | | | | | - Betania Ferraz Quirino
- The Brazilian Agricultural Research Corporation, Embrapa Agroenergy, Brasília 70770-901, DF, Brazil; (J.C.R.N.); (A.P.L.); (J.A.d.A.R.); (B.F.Q.)
| | - Manoel Teixeira Souza Júnior
- Graduate Program of Plant Biotechnology, Federal University of Lavras, Lavras 37203-202, MG, Brazil; (C.B.B.); (T.L.C.d.S.)
- The Brazilian Agricultural Research Corporation, Embrapa Agroenergy, Brasília 70770-901, DF, Brazil; (J.C.R.N.); (A.P.L.); (J.A.d.A.R.); (B.F.Q.)
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20
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Wang L, Lee M, Yi Wan Z, Bai B, Ye B, Alfiko Y, Rahmadsyah R, Purwantomo S, Song Z, Suwanto A, Hua Yue G. A Chromosome-level Reference Genome of African Oil Palm Provides Insights into Its Divergence and Stress Adaptation. Genomics Proteomics Bioinformatics 2023; 21:440-454. [PMID: 36435453 PMCID: PMC10787024 DOI: 10.1016/j.gpb.2022.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 10/02/2022] [Accepted: 11/17/2022] [Indexed: 11/27/2022]
Abstract
The palm family (Arecaceae), consisting of ∼ 2600 species, is the third most economically important family of plants. The African oil palm (Elaeis guineensis) is one of the most important palms. However, the genome sequences of palms that are currently available are still limited and fragmented. Here, we report a high-quality chromosome-level reference genome of an oil palm, Dura, assembled by integrating long reads with ∼ 150× genome coverage. The assembled genome was 1.7 Gb in size, covering 94.5% of the estimated genome, of which 91.6% was assigned into 16 pseudochromosomes and 73.7% was repetitive sequences. Relying on the conserved synteny with oil palm, the existing draft genome sequences of both date palm and coconut were further assembled into chromosomal level. Transposon burst, particularly long terminal repeat retrotransposons, following the last whole-genome duplication, likely explains the genome size variation across palms. Sequence analysis of the VIRESCENS gene in palms suggests that DNA variations in this gene are related to fruit colors. Recent duplications of highly tandemly repeated pathogenesis-related proteins from the same tandem arrays play an important role in defense responses to Ganoderma. Whole-genome resequencing of both ancestral African and introduced oil palms in Southeast Asia reveals that genes under putative selection are notably associated with stress responses, suggesting adaptation to stresses in the new habitat. The genomic resources and insights gained in this study could be exploited for accelerating genetic improvement and understanding the evolution of palms.
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Affiliation(s)
- Le Wang
- Temasek Life Sciences Laboratory, Singapore 117604, Singapore
| | - May Lee
- Temasek Life Sciences Laboratory, Singapore 117604, Singapore
| | - Zi Yi Wan
- Temasek Life Sciences Laboratory, Singapore 117604, Singapore
| | - Bin Bai
- Temasek Life Sciences Laboratory, Singapore 117604, Singapore; Wheat Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou 730070, China
| | - Baoqing Ye
- Temasek Life Sciences Laboratory, Singapore 117604, Singapore
| | - Yuzer Alfiko
- Biotech Lab, Wilmar International, Bekasi 17530, Indonesia
| | | | | | - Zhuojun Song
- Temasek Life Sciences Laboratory, Singapore 117604, Singapore
| | | | - Gen Hua Yue
- Temasek Life Sciences Laboratory, Singapore 117604, Singapore; Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore.
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21
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Ooi SE, Sarpan N, Taranenko E, Feshah I, Nuraziyan A, Roowi SH, Burhan MN, Jayanthi N, Rahmah ARS, Teh OK, Ong-Abdullah M, Tatarinova TV. Small RNAs and Karma methylation in Elaeis guineensis mother palms are linked to high clonal mantling. Plant Mol Biol 2023; 111:345-363. [PMID: 36609897 DOI: 10.1007/s11103-022-01330-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Accepted: 12/08/2022] [Indexed: 06/17/2023]
Abstract
The mantled phenotype is an abnormal somaclonal variant arising from the oil palm cloning process and severe phenotypes lead to oil yield losses. Hypomethylation of the Karma retrotransposon within the B-type MADS-box EgDEF1 gene has been associated with this phenotype. While abnormal Karma-EgDEF1 hypomethylation was detected in mantled clones, we examined the methylation state of Karma in ortets that gave rise to high mantling rates in their clones. Small RNAs (sRNAs) were proposed to play a role in Karma hypomethylation as part of the RNA-directed DNA methylation process, hence differential expression analysis of sRNAs between the ortet groups was conducted. While no sRNA was differentially expressed at the Karma-EgDEF1 region, three sRNA clusters were differentially regulated in high-mantling ortets. The first two down-regulated clusters were possibly derived from long non-coding RNAs while the third up-regulated cluster was derived from the intron of a DnaJ chaperone gene. Several predicted mRNA targets for the first two sRNA clusters conversely displayed increased expression in high-mantling relative to low-mantling ortets. These predicted mRNA targets may be associated with defense or pathogenesis response. In addition, several differentially methylated regions (DMRs) were identified in Karma and its surrounding regions, mainly comprising subtle CHH hypomethylation in high-mantling ortets. Four of the 12 DMRs were located in a region corresponding to hypomethylated areas at the 3'end of Karma previously reported in mantled clones. Further investigations on these sRNAs and DMRs may indicate the predisposition of certain ortets towards mantled somaclonal variation.
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Affiliation(s)
- Siew-Eng Ooi
- Malaysian Palm Oil Board, 6 Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia.
| | - Norashikin Sarpan
- Malaysian Palm Oil Board, 6 Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia
| | - Elizaveta Taranenko
- Department of Biology, University of La Verne, La Verne, CA, USA
- Laboratory of Forest Genomics, Genome Research and Education Center, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, Krasnoyarsk, Russia, 660036
| | - Ishak Feshah
- Malaysian Palm Oil Board, 6 Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia
| | - Azimi Nuraziyan
- Malaysian Palm Oil Board, 6 Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia
| | | | | | - Nagappan Jayanthi
- Malaysian Palm Oil Board, 6 Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia
| | - Abdul Rahman Siti Rahmah
- Malaysian Palm Oil Board, 6 Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia
| | - Ooi-Kock Teh
- Institute of Plant and Microbial Biology, Academia Sinica, 128 Sec. 2, Academia Rd., Nankang, Taipei, Taiwan, R.O.C
| | - Meilina Ong-Abdullah
- Malaysian Palm Oil Board, 6 Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia.
| | - Tatiana V Tatarinova
- Department of Biology, University of La Verne, La Verne, CA, USA.
- Laboratory of Forest Genomics, Genome Research and Education Center, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, Krasnoyarsk, Russia, 660036.
- Vavilov Institute for General Genetics, Moscow, Russia.
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia.
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22
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Diaz-Martin Z, Browne L, Cabrera D, Olivo J, Karubian J. Impacts of Flowering Density on Pollen Dispersal and Gametic Diversity Are Scale Dependent. Am Nat 2023; 201:52-64. [PMID: 36524929 DOI: 10.1086/721918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
AbstractPollen dispersal is a key evolutionary and ecological process, but the degree to which variation in the density of concurrently flowering conspecific plants (i.e., coflowering density) shapes pollination patterns remains understudied. We monitored coflowering density and corresponding pollination patterns of the insect-pollinated palm Oenocarpus bataua in northwestern Ecuador and found that the influence of coflowering density on these patterns was scale dependent: high neighborhood densities were associated with reductions in pollen dispersal distance and gametic diversity of progeny arrays, whereas we observed the opposite pattern at the landscape scale. In addition, neighborhood coflowering density also impacted forward pollen dispersal kernel parameters, suggesting that low neighborhood densities encourage pollen movement and may promote gene flow and genetic diversity. Our work reveals how coflowering density at different spatial scales influences pollen movement, which in turn informs our broader understanding of the mechanisms underlying patterns of genetic diversity and gene flow within populations of plants.
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23
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Sinsirimongkol K, Buasong A, Teppabut Y, Pholmanee N, Chen Y, Miller AJ, Punyasuk N. EgNRT2.3 and EgNAR2 expression are controlled by nitrogen deprivation and encode proteins that function as a two-component nitrate uptake system in oil palm. J Plant Physiol 2022; 279:153833. [PMID: 36257088 DOI: 10.1016/j.jplph.2022.153833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 09/29/2022] [Accepted: 10/02/2022] [Indexed: 06/16/2023]
Abstract
Oil palm (Elaeis guineensis Jacq.) is an important crop for oil and biodiesel production. Oil palm plantations require extensive fertilizer additions to achieve a high yield. Fertilizer application decisions and management for oil palm farming rely on leaf tissue and soil nutrient analyses with little information available to describe the key players for nutrient uptake. A molecular understanding of how nutrients, especially nitrogen (N), are taken up in oil palm is very important to improve fertilizer use and formulation practice in oil palm plantations. In this work, two nitrate uptake genes in oil palm, EgNRT2.3 and EgNAR2, were cloned and characterized. Spatial expression analysis showed high expression of these two genes was mainly found in un-lignified young roots. Interestingly, EgNRT2.3 and EgNAR2 were up-regulated by N deprivation, but their expression pattern depended on the form of N source. Promoter analysis of these two genes confirmed the presence of regulatory elements that support these expression patterns. The Xenopus oocyte assay showed that EgNRT2.3 and EgNAR2 had to act together to take up nitrate. The results suggest that EgNRT2.3 and EgNAR2 act as a two-component nitrate uptake system in oil palm.
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Affiliation(s)
| | - Atcharaporn Buasong
- Department of Biotechnology, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | - Yada Teppabut
- Department of Biotechnology, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | - Nutthida Pholmanee
- Department of Biotechnology, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | - Yi Chen
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Anthony J Miller
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Napassorn Punyasuk
- Department of Biotechnology, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand.
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24
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Schley RJ, Pellicer J, Ge X, Barrett C, Bellot S, Guignard MS, Novák P, Suda J, Fraser D, Baker WJ, Dodsworth S, Macas J, Leitch AR, Leitch IJ. The ecology of palm genomes: repeat-associated genome size expansion is constrained by aridity. New Phytol 2022; 236:433-446. [PMID: 35717562 PMCID: PMC9796251 DOI: 10.1111/nph.18323] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 05/18/2022] [Indexed: 06/15/2023]
Abstract
Genome size varies 2400-fold across plants, influencing their evolution through changes in cell size and cell division rates which impact plants' environmental stress tolerance. Repetitive element expansion explains much genome size diversity, and the processes structuring repeat 'communities' are analogous to those structuring ecological communities. However, which environmental stressors influence repeat community dynamics has not yet been examined from an ecological perspective. We measured genome size and leveraged climatic data for 91% of genera within the ecologically diverse palm family (Arecaceae). We then generated genomic repeat profiles for 141 palm species, and analysed repeats using phylogenetically informed linear models to explore relationships between repeat dynamics and environmental factors. We show that palm genome size and repeat 'community' composition are best explained by aridity. Specifically, Ty3-gypsy and TIR elements were more abundant in palm species from wetter environments, which generally had larger genomes, suggesting amplification. By contrast, Ty1-copia and LINE elements were more abundant in drier environments. Our results suggest that water stress inhibits repeat expansion through selection on upper genome size limits. However, elements that may associate with stress-response genes (e.g. Ty1-copia) have amplified in arid-adapted palm species. Overall, we provide novel evidence of climate influencing the assembly of repeat 'communities'.
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Affiliation(s)
- Rowan J. Schley
- University of ExeterLaver Building, North Park RoadExeterDevonEX4 4QEUK
- Royal Botanic GardensKewSurreyTW9 3ABUK
| | - Jaume Pellicer
- Royal Botanic GardensKewSurreyTW9 3ABUK
- Institut Botànic de Barcelona (IBB, CSIC‐Ajuntament de Barcelona)Passeig del Migdia sn08038BarcelonaSpain
| | - Xue‐Jun Ge
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical GardenChinese Academy of SciencesGuangzhou510650China
| | - Craig Barrett
- Department of BiologyWest Virginia UniversityMorgantownWV26506USA
| | | | | | - Petr Novák
- Biology Centre, Institute of Plant Molecular BiologyCzech Academy of Sciences370 05České BudějoviceCzech Republic
| | | | | | | | - Steven Dodsworth
- School of Biological SciencesUniversity of PortsmouthPortsmouthHampshirePO1 2DYUK
| | - Jiří Macas
- Biology Centre, Institute of Plant Molecular BiologyCzech Academy of Sciences370 05České BudějoviceCzech Republic
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25
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Pereira AG, da Silva Ferreira MF, da Silveira TC, Soler-Guilhen JH, Canal GB, Alves LB, de Almeida FAN, Gaiotto FA, Ferreira A. Patterns of genetic diversity and structure of a threatened palm species (Euterpe edulis Arecaceae) from the Brazilian Atlantic Forest. Heredity (Edinb) 2022; 129:161-168. [PMID: 35697755 PMCID: PMC9411632 DOI: 10.1038/s41437-022-00549-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 05/25/2022] [Accepted: 06/01/2022] [Indexed: 11/08/2022] Open
Abstract
The detection of distribution patterns of genetic diversity of plant and animal species has contributed to the understanding of biodiversity and evolutionary history of the Atlantic Forest. We used microsatellite markers to access the genetic diversity and structure of 26 populations and 527 adult individuals of Euterpe edulis, a native palm which is an important food resource for fauna and is intensively exploited due to economic reasons. We found high genetic diversity and inbreeding in all populations analyzed. We report highest rates of inbreeding for this species, which could reflect the anthropic impacts of selective cutting, fragmentation, and change in foraging behavior from pollinators and less availability and mobility of large dispersers. We detected by STRUCTURE, two genetic groups, Northern and Southern, which divide the Brazilian Atlantic Forest geographically. These groups have low genetic admixtures, but we found a region of lineage hybridization in the contact zone with low recent gene flow. Distribution pattern of this species corroborates results from previous studies reporting the Last Glacial Maximum (LGM) have shaped the structuring of the species through movements of forests' expansion and contraction. The STRUCTURE analysis of each group revealed the presence of genetic subgroups with low rates of recurrent gene flow. Southern subgroups have higher rates of admixtures than the Northern subgroups, revealing greater historical connectivity of forests in this region.
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Affiliation(s)
| | | | | | | | | | | | | | - Fernanda Amato Gaiotto
- Department of Biological Sciences, Universidade Estadual de Santa Cruz, Ilhéus, Bahia, Brazil
| | - Adésio Ferreira
- Department of Agronomy, Universidade Federal do Espírito Santo, Alegre, Brazil
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26
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Francisconi AF, Cauz-Santos LA, Morales Marroquín JA, van den Berg C, Alves-Pereira A, Delmondes de Alencar L, Picanço-Rodrigues D, Zanello CA, Ferreira Costa M, Gomes Lopes MT, Veasey EA, Zucchi MI. Complete chloroplast genomes and phylogeny in three Euterpe palms (E. edulis, E. oleracea and E. precatoria) from different Brazilian biomes. PLoS One 2022; 17:e0266304. [PMID: 35901127 PMCID: PMC9333295 DOI: 10.1371/journal.pone.0266304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 06/28/2022] [Indexed: 11/29/2022] Open
Abstract
The Brazilian palm fruits and hearts-of-palm of Euterpe edulis, E. oleracea and E. precatoria are an important source for agro-industrial production, due to overexploitation, conservation strategies are required to maintain genetic diversity. Chloroplast genomes have conserved sequences, which are useful to explore evolutionary questions. Besides the plastid DNA, genome skimming allows the identification of other genomic resources, such as single nucleotide polymorphisms (SNPs), providing information about the genetic diversity of species. We sequenced the chloroplast genome and identified gene content in the three Euterpe species. We performed comparative analyses, described the polymorphisms among the chloroplast genome sequences (repeats, indels and SNPs) and performed a phylogenomic inference based on 55 palm species chloroplast genomes. Finally, using the remaining data from genome skimming, the nuclear and mitochondrial reads, we identified SNPs and estimated the genetic diversity among these Euterpe species. The Euterpe chloroplast genomes varied from 159,232 to 159,275 bp and presented a conserved quadripartite structure with high synteny with other palms. In a pairwise comparison, we found a greater number of insertions/deletions (indels = 93 and 103) and SNPs (284 and 254) between E. edulis/E. oleracea and E. edulis/E. precatoria when compared to E. oleracea/E. precatoria (58 indels and 114 SNPs). Also, the phylogeny indicated a closer relationship between E. oleracea/E. precatoria. The nuclear and mitochondrial genome analyses identified 1,077 SNPs and high divergence among species (FST = 0.77), especially between E. edulis and E. precatoria (FST = 0.86). These results showed that, despite the few structural differences among the chloroplast genomes of these Euterpe palms, a differentiation between E. edulis and the other Euterpe species can be identified by point mutations. This study not only brings new knowledge about the evolution of Euterpe chloroplast genomes, but also these new resources open the way for future phylogenomic inferences and comparative analyses within Arecaceae.
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Affiliation(s)
- Ana Flávia Francisconi
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Estadual de Campinas, Campinas, São Paulo, Brasil
- * E-mail: (MIZ); (AFF)
| | | | | | - Cássio van den Berg
- Departamento de Ciências Biológicas, Universidade Estadual de Feira de Santana, Feira de Santana, Bahia, Brasil
- Departamento de Genética, Universidade de São Paulo, Piracicaba, São Paulo, Brasil
| | - Alessandro Alves-Pereira
- Departamento de Biologia Vegetal, Universidade Estadual de Campinas, Campinas, São Paulo, Brasil
| | - Luciano Delmondes de Alencar
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Estadual de Campinas, Campinas, São Paulo, Brasil
| | | | - Cesar Augusto Zanello
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Estadual de Campinas, Campinas, São Paulo, Brasil
| | - Marcones Ferreira Costa
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Estadual de Campinas, Campinas, São Paulo, Brasil
- Campus Amílcar Ferreira Sobral, Universidade Federal do Piauí, Floriano, Piauí, Brasil
| | - Maria Teresa Gomes Lopes
- Departamento de Produção Animal e Vegetal, Universidade Federal do Amazonas, Manaus, Amazonas, Brasil
| | - Elizabeth Ann Veasey
- Departamento de Genética, Universidade de São Paulo, Piracicaba, São Paulo, Brasil
| | - Maria Imaculada Zucchi
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Estadual de Campinas, Campinas, São Paulo, Brasil
- Agência Paulista de Tecnologia dos Agronegócios, Piracicaba, São Paulo, Brasil
- * E-mail: (MIZ); (AFF)
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Seyum EG, Bille NH, Abtew WG, Rastas P, Arifianto D, Domonhédo H, Cochard B, Jacob F, Riou V, Pomiès V, Lopez D, Bell JM, Cros D. Genome properties of key oil palm (Elaeis guineensis Jacq.) breeding populations. J Appl Genet 2022; 63:633-650. [PMID: 35691996 DOI: 10.1007/s13353-022-00708-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 05/26/2022] [Accepted: 06/04/2022] [Indexed: 11/29/2022]
Abstract
A good knowledge of the genome properties of the populations makes it possible to optimize breeding methods, in particular genomic selection (GS). In oil palm (Elaeis guineensis Jacq), the world's main source of vegetable oil, this would provide insight into the promising GS results obtained so far. The present study considered two complex breeding populations, Deli and La Mé, with 943 individuals and 7324 single-nucleotide polymorphisms (SNPs) from genotyping-by-sequencing. Linkage disequilibrium (LD), haplotype sharing, effective size (Ne), and fixation index (Fst) were investigated. A genetic linkage map spanning 1778.52 cM and with a recombination rate of 2.85 cM/Mbp was constructed. The LD at r2=0.3, considered the minimum to get reliable GS results, spanned over 1.05 cM/0.22 Mbp in Deli and 0.9 cM/0.21 Mbp in La Mé. The significant degree of differentiation existing between Deli and La Mé was confirmed by the high Fst value (0.53), the pattern of correlation of SNP heterozygosity and allele frequency among populations, and the decrease of persistence of LD and of haplotype sharing among populations with increasing SNP distance. However, the level of resemblance between the two populations over short genomic distances (correlation of r values between populations >0.6 for SNPs separated by <0.5 cM/1 kbp and percentage of common haplotypes >40% for haplotypes <3600 bp/0.20 cM) likely explains the superiority of GS models ignoring the parental origin of marker alleles over models taking this information into account. The two populations had low Ne (<5). Population-specific genetic maps and reference genomes are recommended for future studies.
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Affiliation(s)
- Essubalew Getachew Seyum
- Department of Plant Biology and Physiology, Faculty of Sciences, University of Yaoundé I, Yaoundé, Cameroon
- CETIC (African Center of Excellence in Information and Communication Technologies), University of Yaoundé I, Yaoundé, Cameroon
- Department of Horticulture and Plant Sciences, Jimma University College of Agriculture and Veterinary Medicine, P.O. Box 307, Jimma, Ethiopia
| | - Ngalle Hermine Bille
- Department of Plant Biology and Physiology, Faculty of Sciences, University of Yaoundé I, Yaoundé, Cameroon
| | - Wosene Gebreselassie Abtew
- Department of Horticulture and Plant Sciences, Jimma University College of Agriculture and Veterinary Medicine, P.O. Box 307, Jimma, Ethiopia
| | - Pasi Rastas
- Institute of Biotechnology, Helsinki Institute of Life Science (HiLIFE), University of Helsinki, 00014, Helsinki, Finland
| | | | | | | | | | - Virginie Riou
- CIRAD (Centre de coopération Internationale en Recherche Agronomique pour le Développement), UMR AGAP Institut, F-34398, Montpellier, France
- UMR AGAP Institut, University of Montpellier, CIRAD, INRAE, Institut Agro, F-34398, Montpellier, France
| | - Virginie Pomiès
- CIRAD (Centre de coopération Internationale en Recherche Agronomique pour le Développement), UMR AGAP Institut, F-34398, Montpellier, France
- UMR AGAP Institut, University of Montpellier, CIRAD, INRAE, Institut Agro, F-34398, Montpellier, France
| | - David Lopez
- CIRAD (Centre de coopération Internationale en Recherche Agronomique pour le Développement), UMR AGAP Institut, F-34398, Montpellier, France
- UMR AGAP Institut, University of Montpellier, CIRAD, INRAE, Institut Agro, F-34398, Montpellier, France
| | - Joseph Martin Bell
- Department of Plant Biology and Physiology, Faculty of Sciences, University of Yaoundé I, Yaoundé, Cameroon
| | - David Cros
- CIRAD (Centre de coopération Internationale en Recherche Agronomique pour le Développement), UMR AGAP Institut, F-34398, Montpellier, France.
- UMR AGAP Institut, University of Montpellier, CIRAD, INRAE, Institut Agro, F-34398, Montpellier, France.
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Xu X, Li M, Zou JX, Zheng YS, Li DD. EgMYB108 regulates very long-chain fatty acid (VLCFA) anabolism in the mesocarp of oil palm. Plant Cell Rep 2022; 41:1449-1460. [PMID: 35362736 DOI: 10.1007/s00299-022-02868-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Accepted: 03/18/2022] [Indexed: 06/14/2023]
Abstract
EgMYB108 regulates VLCFA anabolism in oil palm. Very long-chain fatty acids (VLCFAs), which are fatty acids with more than 18 C, can not only be used as a form of triglyceride (TAG) but also provide precursors for the biosynthesis of cuticle wax, and they exist in plant epidermal cells in the form of wax in higher plants. However, which and how transcriptional factors (TFs) regulate this process is largely unknown in oil palm. In this study, a MYB transcription factor (EgMYB108) with high expression in the mesocarp of oil palm fruit was characterized. Overexpression of EgMYB108 promoted not only total lipid content but also VLCFA accumulation in oil palm embryoids. Subsequently, transient transformation in protoplasts and qRT-PCR analysis indicated that the EgKCS5 and EgLACS4 genes were significantly increased with the overexpression of EgMYB108. Furthermore, yeast one‑hybrid assays, dual-luciferase assays and EMSAs demonstrated that EgMYB108 binds to the promoters of EgKCS5 and EgLACS4 and regulates their transcription. Finally, EgMYB108 interacts with the promoters of EgLACS and EgKCS simultaneously and finally improves the VLCFA and total lipid contents; a pathway summarizing this interaction was depicted.. The results provide new insight into the mechanism by which EgMYB108 regulates lipid and VLCFA accumulation in oil palm.
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Affiliation(s)
- Xin Xu
- Sanya Nanfan Research Institute, College of Tropical Crops, Hainan University, Sanya, 572025, Hainan, China
| | - Menghan Li
- Sanya Nanfan Research Institute, College of Tropical Crops, Hainan University, Sanya, 572025, Hainan, China
| | - Ji-Xin Zou
- Sanya Nanfan Research Institute, College of Tropical Crops, Hainan University, Sanya, 572025, Hainan, China
- Rubber Research Institute of Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou, 571101, China
| | - Yu-Sheng Zheng
- Sanya Nanfan Research Institute, College of Tropical Crops, Hainan University, Sanya, 572025, Hainan, China
| | - Dong-Dong Li
- Sanya Nanfan Research Institute, College of Tropical Crops, Hainan University, Sanya, 572025, Hainan, China.
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Faizah R, Putranto RA, Raharti VR, Supena N, Sukma D, Budiani A, Wening S, Sudarsono S. Defense response changes in roots of oil palm (Elaeis guineensis Jacq.) seedlings after internal symptoms of Ganoderma boninense Pat. infection. BMC Plant Biol 2022; 22:139. [PMID: 35331141 PMCID: PMC8944027 DOI: 10.1186/s12870-022-03493-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Accepted: 02/25/2022] [Indexed: 05/14/2023]
Abstract
BACKGROUND The development of basal stem rot (BSR) disease in oil palm is associated with lignin during vegetative growth and salicylic acid (SA) biosynthesis. The increase in the lignin content, SA accumulation, growth, and root biomass could indicate the resistance of oil palm seedlings to BSR disease. Therefore, although there are many studies on the interactions between the Ganoderma boninense and oil palm, research on evaluation of physiological processes, biochemistry, and molecules occurring during early internal symptoms of BSR in roots of oil palm (Elaeis guineensis Jacq.) are essential. RESULTS Ganoderma boninense inoculation indicated that C01, C02, and C05 seedlings were susceptible, while the other three seedlings, C03, C07, and C08, were resistant based on Ganoderma Disease Index (GDI). Infection by G. boninense in the most susceptible seedlings C05 reduced fresh weight of roots (FW) by 9.0%, and lignin content by 10.9%. The most resistant seedlings C08 were reduced by only 8.4%, and 0.2% regarding their fresh weight and lignin content, respectively. BSR disease induced SA accumulation in the most susceptible C08 and decreased peroxidase (PRX) enzyme (EC 1.11.1.7) activities in root tissues of oil palm seedlings except C07 and C08 where PRX activities remained high in the 4 months after planting. Infection with G. boninense also increased glutathione S-transferase U19-like (EgGSTU19) gene expression in the root tissues of susceptible seedlings, while laccase-24 (EgLCC24) gene expression was associated with resistance against BSR disease. Based on the relative expression of twelve genes, two genes are categorized as receptors (EgWAKL5, EgMIK1), two genes as biosynthesis signal transduction compound (EgOPR5, EgACO1), five genes as defense responses (EgROMT, EgSOT12, EgLCC24, EgGLT3, EgGSTU19), and one gene as trans-resveratrol di-O-methyltransferase-like (EgRNaseIII) predicted related to BSR infection. While two other genes remain unknown (EgUnk1, EgUnk2). CONCLUSIONS Ganoderma infection-induced SA accumulation and lignification in resistant accessions promote the seedlings root biomass. Oil palm seedlings have a synergistic physical, biochemical, and molecular defense mechanism to the BSR disease. The utilization of nucleotide-based molecular markers using EgLCC24 gene is able to detect resistant oil palm seedlings to G. boninense.
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Affiliation(s)
- Rokhana Faizah
- Plant Breeding and Biotechnology Study Program, Department of Agronomy and Horticulture, Faculty of Agriculture, Bogor Agricultural University (IPB University), Jl. Meranti, Dramaga Campus, Bogor, 16680, Indonesia.
- Indonesian Oil Palm Research Institute, Jl. Brigjen Katamso No. 51, Medan, North Sumatera, 20158, Indonesia.
| | - Riza Arief Putranto
- Indonesian Research Institute for Biotechnology and Bioindustry, Jl. Taman Kencana No. 1, Bogor, 16128, Indonesia
- PT Riset Perkebunan Nusantara (Nusantara Estate Crops Research), Jl. Salak no. 1A, Bogor, 16128, Indonesia
| | - Vivi Restu Raharti
- Department of Agrotechnology, Agriculture Faculty, Jenderal Soedirman University, Jl. Dr. Soeparno No. 63, Karangwangkal, North Purwokerto, Central Java, 53122, Indonesia
| | - Nanang Supena
- Indonesian Oil Palm Research Institute, Jl. Brigjen Katamso No. 51, Medan, North Sumatera, 20158, Indonesia
| | - Dewi Sukma
- Plant Breeding and Biotechnology Study Program, Department of Agronomy and Horticulture, Faculty of Agriculture, Bogor Agricultural University (IPB University), Jl. Meranti, Dramaga Campus, Bogor, 16680, Indonesia
| | - Asmini Budiani
- Indonesian Research Institute for Biotechnology and Bioindustry, Jl. Taman Kencana No. 1, Bogor, 16128, Indonesia
| | - Sri Wening
- Indonesian Oil Palm Research Institute, Jl. Brigjen Katamso No. 51, Medan, North Sumatera, 20158, Indonesia
| | - Sudarsono Sudarsono
- Plant Breeding and Biotechnology Study Program, Department of Agronomy and Horticulture, Faculty of Agriculture, Bogor Agricultural University (IPB University), Jl. Meranti, Dramaga Campus, Bogor, 16680, Indonesia
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Zhang A, Jin L, Yarra R, Cao H, Chen P, John Martin JJ. Transcriptome analysis reveals key developmental and metabolic regulatory aspects of oil palm (Elaeis guineensis Jacq.) during zygotic embryo development. BMC Plant Biol 2022; 22:112. [PMID: 35279075 PMCID: PMC8917659 DOI: 10.1186/s12870-022-03459-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 02/07/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Oil palm is the most efficient oil-producing crop in the world, and the yield of palm oil is associated with embryonic development. However, a comprehensive understanding of zygotic embryo development at the molecular level remains elusive. In order to address this issue, we report the transcriptomic analysis of zygotic embryo development in oil palm, specifically focusing on regulatory genes involved in important biological pathways. RESULTS In this study, three cDNA libraries were prepared from embryos at S1 (early-stage), S2 (middle-stage), and S3 (late-stage). There were 16,367, 16,500, and 18,012 genes characterized at the S1, S2, and S3 stages of embryonic development, respectively. A total of 1522, 2698, and 142 genes were differentially expressed in S1 vs S2, S1 vs S3, and S2 vs S3, respectively. Using Gene Ontology (GO) term enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis to identify key genes and pathways. In the hormone signaling pathway, genes related to auxin antagonize the output of cytokinin which regulates the development of embryo meristem. The genes related to abscisic acid negatively regulating the synthesis of gibberellin were strongly up-regulated in the mid-late stage of embryonic development. The results were reported the early synthesis and mid-late degradation of sucrose, as well as the activation of the continuous degradation pathway of temporary starch, providing the nutrients needed for differentiation of the embryonic cell. Moreover, the transcripts of genes involved in fatty acid synthesis were also abundantly accumulated in the zygotic embryos. CONCLUSION Taken together, our research provides a new perspective on the developmental and metabolic regulation of zygotic embryo development at the transcriptional level in oil palm.
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Affiliation(s)
- Anni Zhang
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, College of Horticulture, Hainan University, Haikou, 570228, China
| | - Longfei Jin
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences / Hainan Key Laboratory of Tropical Oil Crops Biology, Wenchang, 571339, China
| | - Rajesh Yarra
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences / Hainan Key Laboratory of Tropical Oil Crops Biology, Wenchang, 571339, China
| | - Hongxing Cao
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences / Hainan Key Laboratory of Tropical Oil Crops Biology, Wenchang, 571339, China
| | - Ping Chen
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, College of Horticulture, Hainan University, Haikou, 570228, China.
| | - Jerome Jeyakumar John Martin
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences / Hainan Key Laboratory of Tropical Oil Crops Biology, Wenchang, 571339, China.
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Zhou L, Yarra R. Genome-wide identification and expression analysis of bZIP transcription factors in oil palm (Elaeis guineensis Jacq.) under abiotic stress. Protoplasma 2022; 259:469-483. [PMID: 34212248 DOI: 10.1007/s00709-021-01666-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 05/07/2021] [Indexed: 06/13/2023]
Abstract
The bZIP transcription factors are well-known transcription regulators and play a key role in regulating various developmental, biological processes, and stress responses in plants. However, information on bZIP transcription factors is not yet available in oil palm, an important oil yielding crop. The present study identified the 97 bZIP transcription factor family members in oil palm genome via a genome-wide approach. Phylogenetic analysis clustered all EgbZIPs into 12 clusters with Arabidopsis and rice bZIPs. EgbZIP gene structure analysis showed a distinct variation in the intron-exon organization among all EgbZIPs. Conserved motif analysis demonstrated the occurrence of ten additional conserved motifs besides having a common bZIP domain. All the identified 97 EgbZIPs were unevenly distributed on 16 chromosomes and exhibited tandem duplication in oil palm genome. Our results aslo demonstrated that tissue-specific expression patterns of EgbZIPs based on the available transcriptome data of six different tissue of oil palm. Stress-responsive expression analysis showed that 11EgbZIP transcription factors were highly expressed under cold, salinity, drought stress conditions. Taken together, our findings will provide insightful information on bZIP transcription factors as one of the stress-responsive regulators in oil palm.
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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, People's Republic of China.
| | - Rajesh Yarra
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences/Hainan Key Laboratory of Tropical Oil Crops Biology, Wenchang, Hainan, 571339, People's Republic of China
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Zhou L, Yarra R, Yang Y, Liu Y, Yang M, Cao H. The oil palm R2R3-MYB subfamily genes EgMYB111 and EgMYB157 improve multiple abiotic stress tolerance in transgenic Arabidopsis plants. Plant Cell Rep 2022; 41:377-393. [PMID: 34817657 DOI: 10.1007/s00299-021-02814-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 11/12/2021] [Indexed: 06/13/2023]
Abstract
We found that overexpression of EgMYB111 and EgMYB157 genes positively regulate the abiotic stress tolerance. MYB family genes are well-known regulators in modulating the abiotic stress-responsive mechanisms in plants. However, lesser is known about the functional roles of oil palm MYB genes. Previously, we found that oil palm MYB genes such as EgMYB111 and EgMYB157 were significantly up-regulated under salinity, cold, and drought stress conditions. In this study, we over-expressed EgMYB111 and EgMYB157 genes separately in Arabidopsis plants. The transgenic Arabidopsis plants expressing EgMYB111 have shown improved tolerance to salinity, cold and drought stress conditions, whereas transgenic Arabidopsis plants expressing EgMYB157 dispalyed improved tolerance to cold and drought stress conditions only. Various biochemical analyses also revealed significant improvement of antioxidant enzyme activities, photosynthetic pigments, net photosynthetic rate, stomatal conductance, and intercellular CO2 concentration in transgenic plants compared to wild-type plants under cold, drought, and salinity stress conditions. Significant up-regulation of various known stress marker genes such as RD22, RD29A, RAB18, COR47, ABA1, ABI1, HAB1 was also noticed in EgMYB111 and EgMYB157 expressing transgenic plants compared to wild-type plants under cold, drought, and salinity stress conditions. Taken together, over-expression of EgMYB111 and/or EgMYB157 significantly improve abiotic tolerance in transgenic Arabidopsis plants, indicating that EgMYB111 and EgMYB157 are the potential candidates for developing abiotic stress-tolerant crops in near future.
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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, People's Republic of China.
| | - Rajesh Yarra
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Hainan Key Laboratory of Tropical Oil Crops Biology, Wenchang, Hainan, 571339, People's Republic of China
| | - Yaodong Yang
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Hainan Key Laboratory of Tropical Oil Crops Biology, Wenchang, Hainan, 571339, People's Republic of China
| | - Yanju Liu
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Hainan Key Laboratory of Tropical Oil Crops Biology, Wenchang, Hainan, 571339, People's Republic of China
| | - Mengdi Yang
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Hainan Key Laboratory of Tropical Oil Crops Biology, Wenchang, Hainan, 571339, People's Republic of China
| | - Hongxing Cao
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Hainan Key Laboratory of Tropical Oil Crops Biology, Wenchang, Hainan, 571339, People's Republic of China
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33
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Jin L, Yarra R, Zhou L, Cao H. The auxin response factor (ARF) gene family in Oil palm (Elaeis guineensis Jacq.): Genome-wide identification and their expression profiling under abiotic stresses. Protoplasma 2022; 259:47-60. [PMID: 33792785 DOI: 10.1007/s00709-021-01639-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Accepted: 03/18/2021] [Indexed: 06/12/2023]
Abstract
Auxin response factors (ARFs) play vital role in controlling growth and developmental processes of plants via regulating the auxin signaling pathways. However, the identification and functional roles of ARFs in oil palm plants remain elusive. Here, we identified a total of 23 ARF (EgARF) genes in oil palm through a genome-wide identification approach. The EgARF gene structure analysis revealed the presence of intron-rich ARF gene family in genome of oil palm. Further analysis demonstrated the uneven distribution of 23EgARFs on 16 chromosomes of oil palm. Phylogenetic analysis clustered all the EgARFs into four groups. Twenty-one EgARFs contained BDD, ARF, and CTD domains, whereas EgARF5 and EgARF7 lacked the CTD domain. The evolution of ARF genes in oil palm genome has been expanded by segmental duplication events. The cis-acting regulatory elements of EgARF gene family were predominantly associated with the stress and hormone responses. Expression profiling data demonstrated the constitutive and tissue-specific expression of EgARF genes in various tissues of oil palm. Real-time PCR analysis of 19 EgARF genes expression levels under cold, drought, and salt stress conditions proved their prominent role under abiotic stress responses. Altogether, our study provides a basis for studying the molecular and functional roles of ARF genes in oil palm.
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Affiliation(s)
- Longfei Jin
- Hainan Key Laboratory of Tropical Oil Crops Biology, Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, 571339, Hainan, People's Republic of China.
| | | | - Lixia Zhou
- Hainan Key Laboratory of Tropical Oil Crops Biology, Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, 571339, Hainan, People's Republic of China
| | - Hongxing Cao
- Hainan Key Laboratory of Tropical Oil Crops Biology, Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, 571339, Hainan, People's Republic of China
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Zaki NM, Schwarzacher T, Singh R, Madon M, Wischmeyer C, Hanim Mohd Nor N, Zulkifli MA, Heslop-Harrison JSP. Chromosome identification in oil palm (Elaeis guineensis) using in situ hybridization with massive pools of single copy oligonucleotides and transferability across Arecaceae species. Chromosome Res 2021; 29:373-390. [PMID: 34657216 DOI: 10.1007/s10577-021-09675-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 09/22/2021] [Accepted: 09/23/2021] [Indexed: 11/26/2022]
Abstract
Chromosome identification is essential for linking sequence and chromosomal maps, verifying sequence assemblies, showing structural variations and tracking inheritance or recombination of chromosomes and chromosomal segments during evolution and breeding programs. Unfortunately, identification of individual chromosomes and chromosome arms has been a major challenge for some economically important crop species with a near-continuous chromosome size range and similar morphology. Here, we developed oligonucleotide-based chromosome-specific probes that enabled us to establish a reference chromosome identification system for oil palm (Elaeis guineensis Jacq., 2n = 32). Massive oligonucleotide sequence pools were anchored to individual chromosome arms using dual and triple fluorescent in situ hybridization (EgOligoFISH). Three fluorescently tagged probe libraries were developed to contain, in total 52,506 gene-rich single-copy 47-mer oligonucleotides spanning each 0.2-0.5 Mb across strategically placed chromosome regions. They generated 19 distinct FISH signals and together with rDNA probes enabled identification of all 32 E. guineensis chromosome arms. The probes were able to identify individual homoeologous chromosome regions in the related Arecaceae palm species: American oil palm (Elaeis oleifera), date palm (Phoenix dactylifera) and coconut (Cocos nucifera) showing the comparative organization and concerted evolution of genomes in the Arecaceae. The oligonucleotide probes developed here provide a valuable approach to chromosome arm identification and allow tracking chromosome transfer in hybridization and breeding programs in oil palm, as well as comparative studies within Arecaceae.
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Affiliation(s)
- Noorhariza Mohd Zaki
- MPOB Malaysian Palm Oil Board, 6 Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia.
| | | | - Rajinder Singh
- MPOB Malaysian Palm Oil Board, 6 Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia
| | | | | | - Nordiana Hanim Mohd Nor
- MPOB Malaysian Palm Oil Board, 6 Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia
| | - Muhammad Azwan Zulkifli
- MPOB Malaysian Palm Oil Board, 6 Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia
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Santos da Silva R, Roland Clement C, Balsanelli E, de Baura VA, Maltempi de Souza E, Pacheco de Freitas Fraga H, do Nascimento Vieira L. The plastome sequence of Bactris gasipaes and evolutionary analysis in tribe Cocoseae (Arecaceae). PLoS One 2021; 16:e0256373. [PMID: 34428237 PMCID: PMC8384209 DOI: 10.1371/journal.pone.0256373] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 08/04/2021] [Indexed: 11/18/2022] Open
Abstract
The family Arecaceae is distributed throughout tropical and subtropical regions of the world. Among the five subfamilies, Arecoideae is the most species-rich and still contains some ambiguous inter-generic relationships, such as those within subtribes Attaleinae and Bactridineae. The hypervariable regions of plastid genomes (plastomes) are interesting tools to clarify unresolved phylogenetic relationships. We sequenced and characterized the plastome of Bactris gasipaes (Bactridinae) and compared it with eight species from the three Cocoseae sub-tribes (Attaleinae, Bactridinae, and Elaeidinae) to perform comparative analysis and to identify hypervariable regions. The Bactris gasipaes plastome has 156,646 bp, with 113 unique genes. Among them, four genes have an alternative start codon (cemA, rps19, rpl2, and ndhD). Plastomes are highly conserved within tribe Cocoseae: 97.3% identity, length variation of ~2 kb, and a single ~4.5 kb inversion in Astrocaryum plastomes. The LSC/IR and IR/SSC junctions vary among the subtribes: in Bactridinae and Elaeidinae the rps19 gene is completely contained in the IR region; in the subtribe Attaleinae the rps19 gene is only partially contained in the IRs. The hypervariable regions selected according to sequence variation (SV%) and frequency of parsimony informative sites (PIS%) revealed plastome regions with great potential for molecular analysis. The ten regions with greatest SV% showed higher variation than the plastid molecular markers commonly used for phylogenetic analysis in palms. The phylogenetic trees based on the plastomes and the hypervariable regions (SV%) datasets had well-resolved relationships, with consistent topologies within tribe Cocoseae, and confirm the monophyly of the subtribes Bactridinae and Attaleinae.
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Affiliation(s)
| | - Charles Roland Clement
- Coordenação de Tecnologia e Inovação, Instituto Nacional de Pesquisas da Amazônia, Manaus, AM, Brazil
| | - Eduardo Balsanelli
- Departamento de Bioquímica e Biologia Molecular, Núcleo de Fixação Biológica de Nitrogênio, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
- Departamento de Bioquímica e Biologia Molecular, GoGenetic, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
| | - Valter Antonio de Baura
- Departamento de Bioquímica e Biologia Molecular, Núcleo de Fixação Biológica de Nitrogênio, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
| | - Emanuel Maltempi de Souza
- Departamento de Bioquímica e Biologia Molecular, Núcleo de Fixação Biológica de Nitrogênio, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
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Hosni H, Diallo A, Morcillo F, Vaissayre V, Collin M, Tranchant-Dubreuil C, Dussert S, Joët T, Castaño F, Marquínez X, Stauffer FW, Hodel DR, Castillo Mont JJ, Adam H, Jouannic S, Tregear JW. Redox-related gene expression and sugar accumulation patterns are altered in the edible inflorescence produced by the cultivated form of pacaya palm (Chamaedorea tepejilote). Ann Bot 2021; 128:231-240. [PMID: 33978714 PMCID: PMC8324030 DOI: 10.1093/aob/mcab060] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 05/07/2021] [Indexed: 05/23/2023]
Abstract
BACKGROUND AND AIMS The pacaya palm is a dioecious neotropical palm species that is exploited in Latin America for its male inflorescence, which is edible when immature. It is cultivated, in a non-intensive manner, in Guatemala, where a morphotype occurs that produces much larger, more highly branched inflorescences compared with wild palms. We sought to identify molecular factors underlying this phenotypic divergence, which is likely to be a product of domestication. METHODS We performed RNA-seq-based studies on immature pacaya palm male inflorescences in order to identify genes that might be directly or indirectly affected in their expression in relation to domestication. We also measured the accumulation of a range of soluble sugar molecules to provide information on the biochemical status of the two different types of material. KEY RESULTS A total of 408 genes were found to display significantly different expression levels between the wild and cultivated morphotypes. Three different functional categories were found to be enriched in the gene set that was upregulated in the cultivated morphotype: redox balance; secondary metabolism; and transport. Several sugars were found to accumulate at higher levels in inflorescences of the cultivated morphotype, in particular myo-inositol, fructose and glucose. CONCLUSIONS The observed upregulation of redox-related genes in the cultivated morphotype is corroborated by the observation of higher myo-inositol accumulation, which has been shown to be associated with enhanced scavenging of reactive oxygen species in other plants and which may affect meristem activity.
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Affiliation(s)
- Hanene Hosni
- Institut de Recherche pour le Développement (IRD), UMR DIADE, Université de Montpellier, Montpellier, France
| | - Abdoulaye Diallo
- Institut de Recherche pour le Développement (IRD), UMR DIADE, Université de Montpellier, Montpellier, France
| | - Fabienne Morcillo
- CIRAD, DIADE, Montpellier, France
- DIADE, Université de Montpellier, Institut de Recherche pour le Développement, Montpellier, France
| | - Virginie Vaissayre
- Institut de Recherche pour le Développement (IRD), UMR DIADE, Université de Montpellier, Montpellier, France
| | - Myriam Collin
- Institut de Recherche pour le Développement (IRD), UMR DIADE, Université de Montpellier, Montpellier, France
| | | | - Stéphane Dussert
- Institut de Recherche pour le Développement (IRD), UMR DIADE, Université de Montpellier, Montpellier, France
| | - Thierry Joët
- Institut de Recherche pour le Développement (IRD), UMR DIADE, Université de Montpellier, Montpellier, France
| | - Felipe Castaño
- Universidad Industrial de Santander, Escuela de Biología, Calle, Bucaramanga, Colombia
| | - Xavier Marquínez
- Universidad Nacional de Colombia, Departamento de Biología, Carrera, Bogotá, Colombia
| | - Fred W Stauffer
- Conservatoire et Jardin botaniques de la Ville de Genève, Université de Genève, Laboratoire de Systématique Végétale et Biodiversité, Chambésy, Switzerland
| | - Donald R Hodel
- University of California, Cooperative Extension, Alhambra, CA, USA
| | | | - Hélène Adam
- Institut de Recherche pour le Développement (IRD), UMR DIADE, Université de Montpellier, Montpellier, France
| | - Stefan Jouannic
- Institut de Recherche pour le Développement (IRD), UMR DIADE, Université de Montpellier, Montpellier, France
| | - James W Tregear
- Institut de Recherche pour le Développement (IRD), UMR DIADE, Université de Montpellier, Montpellier, France
- For correspondence. E-mail
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Cássia-Silva C, Freitas CG, Jardim L, Bacon CD, Collevatti RG. In situ radiation explains the frequency of dioecious palms on islands. Ann Bot 2021; 128:205-215. [PMID: 33949659 PMCID: PMC8324027 DOI: 10.1093/aob/mcab056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 04/28/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND AND AIMS Dioecy has evolved up to 5000 times in angiosperms, despite the potentially high intrinsic costs to unisexuality. Dioecy prevents inbreeding, which is especially relevant on isolated islands when gene pools are small. Dioecy is also associated with certain dispersal traits, such as fruit size and type. However, the influence of dioecy on other life history traits and island distribution remains poorly understood. Here, we test the effect of dioecy on palm (Arecaceae) speciation rates, fruit size and frequency on islands. METHODS We used phylogenetic comparative methods to estimate the ancestral state of the sexual system and its impact on speciation rates and fruit size. Frequency of sexual systems, effect of insularity on the probability of being dioecious, and phylogenetic clustering of island dioecious vs. mainland species were inferred. Lastly, we determined the interplay of insularity and sexual system on speciation rates. KEY RESULTS Palms repeatedly evolved different sexual systems (dioecy, monoecy and polygamy) from a hermaphrodite origin. Differences in speciation rates and fruit size among the different sexual systems were not identified. An effect of islands on the probability of the palms being dioecious was also not found. However, we found a high frequency and phylogenetic clustering of dioecious palms on islands, which were not correlated with higher speciation rates. CONCLUSIONS The high frequency and phylogenetic clustering may be the result of in situ radiation and suggest an 'island effect' for dioecious palms, which was not explained by differential speciation rates. This island effect also cannot be attributed to long-distance dispersal due to the lack of fruit size difference among sexual systems, and particularly because palm dispersal to islands is highly constrained by the interaction between the sizes of fruit and frugivores. Taken together, we suggest that trait flexibility in sexual system evolution and the in situ radiation of dioecious lineages are the underlying causes of the outstanding distribution of palms on islands.
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Affiliation(s)
- Cibele Cássia-Silva
- Laboratório de Genética & Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, GO, Brazil
| | - Cíntia G Freitas
- Pós-Graduação em Ecologia e Conservação, Setor de Ciências Biológicas, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Lucas Jardim
- Laboratório de Ecologia Teórica e Síntese, Departamento de Ecologia, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, GO, Brazil
| | - Christine D Bacon
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | - Rosane G Collevatti
- Laboratório de Genética & Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, GO, Brazil
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Díaz BG, Zucchi MI, Alves‐Pereira A, de Almeida CP, Moraes ACL, Vianna SA, Azevedo-Filho J, Colombo CA. Genome-wide SNP analysis to assess the genetic population structure and diversity of Acrocomia species. PLoS One 2021; 16:e0241025. [PMID: 34283830 PMCID: PMC8291712 DOI: 10.1371/journal.pone.0241025] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 07/05/2021] [Indexed: 01/01/2023] Open
Abstract
Acrocomia (Arecaceae) is a genus widely distributed in tropical and subtropical America that has been achieving economic interest due to the great potential of oil production of some of its species. In particular A. aculeata, due to its vocation to supply oil with the same productive capacity as the oil palm (Elaeis guineenses) even in areas with water deficit. Although eight species are recognized in the genus, the taxonomic classification based on morphology and geographic distribution is still controversial. Knowledge about the genetic diversity and population structure of the species is limited, which has limited the understanding of the genetic relationships and the orientation of management, conservation, and genetic improvement activities of species of the genus. In the present study, we analyzed the genomic diversity and population structure of Acrocomia genus, including 172 samples from seven species, with a focus on A. aculeata with 117 samples covering a wide geographical area of occurrence of the species, using Single Nucleotide Polymorphism (SNP) markers originated from Genotyping By Sequencing (GBS).The genetic structure of the Acrocomia species were partially congruent with the current taxonomic classification based on morphological characters, recovering the separation of the species A. aculeata, A. totai, A. crispa and A. intumescens as distinct taxonomic groups. However, the species A. media was attributed to the cluster of A. aculeata while A. hassleri and A. glauscescens were grouped together with A. totai. The species that showed the highest and lowest genetic diversity were A. totai and A. media, respectively. When analyzed separately, the species A. aculeata showed a strong genetic structure, forming two genetic groups, the first represented mainly by genotypes from Brazil and the second by accessions from Central and North American countries. Greater genetic diversity was found in Brazil when compared to the other countries. Our results on the genetic diversity of the genus are unprecedented, as is also establishes new insights on the genomic relationships between Acrocomia species. It is also the first study to provide a more global view of the genomic diversity of A. aculeata. We also highlight the applicability of genomic data as a reference for future studies on genetic diversity, taxonomy, evolution and phylogeny of the Acrocomia genus, as well as to support strategies for the conservation, exploration and breeding of Acrocomia species and in particular A. aculeata.
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Affiliation(s)
| | - Maria Imaculada Zucchi
- Biology Institute, University of Campinas UNICAMP, Campinas-SP, Brazil
- Centro de Pesquisa de Recursos Genéticos Vegetais, Instituto Agronômico-IAC, Campinas-SP, Brazil
| | | | - Caléo Panhoca de Almeida
- Centro de Pesquisa de Recursos Genéticos Vegetais, Instituto Agronômico-IAC, Campinas-SP, Brazil
| | | | - Suelen Alves Vianna
- Centro de Pesquisa de Recursos Genéticos Vegetais, Instituto Agronômico-IAC, Campinas-SP, Brazil
| | - Joaquim Azevedo-Filho
- Centro de Pesquisa de Recursos Genéticos Vegetais, Instituto Agronômico-IAC, Campinas-SP, Brazil
| | - Carlos Augusto Colombo
- Centro de Pesquisa de Recursos Genéticos Vegetais, Instituto Agronômico-IAC, Campinas-SP, Brazil
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Ooi SE, Feshah I, Nuraziyan A, Sarpan N, Ata N, Lim CC, Choo CN, Wong WC, Wong FH, Wong CK, Ong-Abdullah M. Leaf transcriptomic signatures for somatic embryogenesis potential of Elaeis guineensis. Plant Cell Rep 2021; 40:1141-1154. [PMID: 33929599 DOI: 10.1007/s00299-021-02698-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Accepted: 04/13/2021] [Indexed: 06/12/2023]
Abstract
Potentially embryogenic oil palms can be identified through leaf transcriptomic signatures. Differential expression of genes involved in flowering time, and stress and light responses may associate with somatic embryogenesis potential. Clonal propagation is an attractive approach for the mass propagation of high yielding oil palms. A major issue hampering the effectiveness of oil palm tissue culture is the low somatic embryogenesis rate. Previous studies have identified numerous genes involved in oil palm somatic embryogenesis, but their association with embryogenic potential has not been determined. In this study, differential expression analysis of leaf transcriptomes from embryogenic and non-embryogenic mother palms revealed that transcriptome profiles from non- and poor embryogenic mother palms were more similar than highly embryogenic palms. A total of 171 genes exhibiting differential expression in non- and low embryogenesis groups could also discriminate high from poor embryogenesis groups of another tissue culture agency. Genes related to flowering time or transition such as FTIP, FRIGIDA-LIKE, and NF-YA were up-regulated in embryogenic ortets, suggesting that reproduction timing of the plant may associate with somatic embryogenesis potential. Several light response or photosynthesis-related genes were down-regulated in embryogenic ortets, suggesting a link between photosynthesis activity and embryogenic potential. As expression profiles of the differentially expressed genes are very similar between non- and low embryogenic groups, machine learning approaches with several candidate genes may generate a more sensitive model to better discriminate non-embryogenic from embryogenic ortets.
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Affiliation(s)
- Siew-Eng Ooi
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, 6 Persiaran Institusi, 43000, Kajang, Selangor, Malaysia.
| | - Ishak Feshah
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, 6 Persiaran Institusi, 43000, Kajang, Selangor, Malaysia
| | - Azimi Nuraziyan
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, 6 Persiaran Institusi, 43000, Kajang, Selangor, Malaysia
| | - Norashikin Sarpan
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, 6 Persiaran Institusi, 43000, Kajang, Selangor, Malaysia
| | - Nabeel Ata
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, 6 Persiaran Institusi, 43000, Kajang, Selangor, Malaysia
| | - Chin-Ching Lim
- United Plantations Bhd., Jenderata Estate, 36009, Teluk Intan, Perak, Malaysia
| | - Chin-Nee Choo
- Advanced Agriecological Research Sdn. Bhd., 11 Jalan Teknologi 3/6, Taman Sains Selangor 1, Kota Damansara, 47810, Petaling Jaya, Selangor, Malaysia
| | - Wei-Chee Wong
- Advanced Agriecological Research Sdn. Bhd., 11 Jalan Teknologi 3/6, Taman Sains Selangor 1, Kota Damansara, 47810, Petaling Jaya, Selangor, Malaysia
| | - Foo-Hin Wong
- United Plantations Bhd., Jenderata Estate, 36009, Teluk Intan, Perak, Malaysia
| | - Choo-Kien Wong
- Advanced Agriecological Research Sdn. Bhd., 11 Jalan Teknologi 3/6, Taman Sains Selangor 1, Kota Damansara, 47810, Petaling Jaya, Selangor, Malaysia
| | - Meilina Ong-Abdullah
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, 6 Persiaran Institusi, 43000, Kajang, Selangor, Malaysia
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Camacho-Villalobos A, Serna F, Flores J, Flores H, Manrique P, Bendezu J. Morphological and molecular characterization of an Elaeis oleifera (H.B.K) Cortes germplasm collection located in Ucayali, Peru. PLoS One 2021; 16:e0250445. [PMID: 33956829 PMCID: PMC8101761 DOI: 10.1371/journal.pone.0250445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 04/07/2021] [Indexed: 12/05/2022] Open
Abstract
The African oil palm (Elaeis guineensis Jacq) is a crop that is widely distributed in tropical regions around the world; however, this crop is subject to limitations such as rapid trunk growth and susceptibility to bud rot and red ring diseases particularly in South America. To overcome these limitations, national breeding and conservation programs have been established, and there is a need to identify parental palms from natural populations of the American oil palm (E. oleifera H.B.K. Cortes) with desirable yield and morphological traits (i.e., yield production and bunch number) and with high genetic diversity. However, in Peru the morphological and genetic data related to this important crop is limited. In this study, we characterized the morphological and yield and estimated the genetic diversity using 12 neutral microsatellite markers (simple sequence repeats, SSRs) across 72 oil palm individuals belonging to the E. oleifera germplasm collection located in the tropical region of Ucayali, Peru. Our results showed that morphological and yield traits explained approximately 40.39% of the variability within the Peruvian germplasm. Furthermore, Yield Production was highly correlated with two yield traits: Bunch Number (0.67) and Average weight per bunch (0.78). Based on the yield and morphological traits, a clustering analysis was performed and three phenotypic groups were identified (1, 2 and 3) in which groups 1 and 3 showed high scores associated primarily with yield traits. Microsatellite markers revealed 143 alleles, 11.92 ± 4.72 alleles per locus (A) and an expected heterozygosity (He) of 0.69 ± 0.045. A structural analysis identified three populations (k = 3), that were not related to the phenotypic groups. Interestingly, a multiple allele background was identified within the groups using multilocus and phylogenetic relationship analyses. This is the first Peruvian report regarding E. oleifera that shows preliminary data of the morphological and yield traits and genetic data, and highlight the importance of this information to set up future steps to national breeding strategies and improve the conservation of genetic material of E. oleifera. Overall, these novel findings could contribute to the development of the local oil palm industry in Peru.
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Affiliation(s)
- Alina Camacho-Villalobos
- Estación Experimental Agraria Pucallpa, Dirección de Desarrollo Tecnológico Agrario, Instituto Nacional de Innovación Agraria (INIA), Coronel Portillo, Ucayali, Perú
- * E-mail: (ACV); (JB)
| | - Fernando Serna
- Centro Experimental La Molina, Dirección de Recursos Genéticos y Biotecnología, Instituto Nacional de Innovación Agraria (INIA), Lima, Perú
| | - Jhofre Flores
- Facultad de Ciencias Agropecuarias, Universidad Nacional de Ucayali (UNU), Coronel Portillo, Ucayali, Perú
| | - Hector Flores
- Centro Experimental La Molina, Dirección de Recursos Genéticos y Biotecnología, Instituto Nacional de Innovación Agraria (INIA), Lima, Perú
| | | | - Jorge Bendezu
- Estación Experimental Agraria Pucallpa, Dirección de Recursos Genéticos y Biotecnología, Instituto Nacional de Innovación Agraria (INIA), Coronel Portillo, Ucayali, Perú
- * E-mail: (ACV); (JB)
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Myint KA, Yaakub Z, Rafii MY, Oladosu Y, Samad MYA, Ramlee SI, Mustaffa S, Arolu F, Abdullah N, Marjuni M, Amiruddin MD. Genetic Diversity Assessment of MPOB-Senegal Oil Palm Germplasm Using Microsatellite Markers. Biomed Res Int 2021; 2021:6620645. [PMID: 33997027 PMCID: PMC8116142 DOI: 10.1155/2021/6620645] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 04/24/2021] [Indexed: 12/03/2022]
Abstract
Molecular characterization of oil palm germplasm is crucial in utilizing and conserving germplasm with promising traits. This study was conducted to evaluate the genetic diversity structures and relationships among 26 families of MPOB-Senegal oil palm germplasm using thirty-five microsatellite markers. High level of polymorphism (P = 96.26%), number of effective allele (N e = 2.653), observed heterozygosity (H o = 0.584), expected heterozygosity (H e = 0.550), total heterozygosity (H T = 0.666), and rare alleles (54) were observed which indicates that MPOB-Senegal germplasm has a broad genetic variation. Among the SSR markers, sMo00053 and sMg00133 were the most informative markers for discrimination among the MPOB-Senegal oil palm germplasm for having the highest private alleles and the rare alleles. For selection and conservation, oil palm populations with high rare alleles and Nei's gene diversity index should be considered as these populations may possess unique genes for further exploitation.
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Affiliation(s)
- Khin Aye Myint
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Zulkifli Yaakub
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | - Mohd Y. Rafii
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Yusuff Oladosu
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Mohd Yusoff Abd Samad
- Department of Soil Management, Faculty of Agriculture, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Shairul Izan Ramlee
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Suzana Mustaffa
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | - Fatai Arolu
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Norziha Abdullah
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | - Marhalil Marjuni
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | - Mohd Din Amiruddin
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
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Gutbrod P, Reichert S, Gutbrod K, Hamai A, Bréhélin C, Ngando-Ebongue G, Dörmann P. Fatty acid isoprenoid alcohol ester synthesis in fruits of the African Oil Palm (Elaeis guineensis). Phytochemistry 2021; 185:112684. [PMID: 33581596 DOI: 10.1016/j.phytochem.2021.112684] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 01/27/2021] [Accepted: 01/28/2021] [Indexed: 06/12/2023]
Abstract
The African Oil Palm (Elaeis guineensis; family Arecaceae) represents the most important oil crop for food and feed production and for biotechnological applications. Two types of oil can be extracted from palm fruits, the mesocarp oil which is rich in palmitic acid and in carotenoids (provitamin A) and tocochromanols (vitamin E), and the kernel oil with high amounts of lauric and myristic acid. We identified fatty acid phytyl esters (FAPEs) in the mesocarp and kernel tissues of mature fruits, mostly esterified with oleic acid and very long chain fatty acids. In addition, fatty acid geranylgeranyl esters (FAGGEs) accumulated in mesocarp and kernels to even larger amounts. In contrast, FAPEs and FAGGEs amounts and fatty acid composition in leaves were very similar. Analysis of wild accessions of African Oil Palm from Cameroon revealed a considerable variation in the amounts and composition of FAPEs and FAGGEs in mesocarp and kernel tissues. Exogenous supplementation of phytol or geranylgeraniol to mesocarp slices resulted in the incorporation of these alcohols into FAPEs and FAGGEs, respectively, indicating that they are synthesized via enzymatic reactions. Three candidate genes of the esterase/lipase/thioesterase (ELT) family were identified in the Oil Palm genome. The genes are differentially expressed in mesocarp tissue with EgELT1 showing the highest expression. Geranylgeraniol from FAGGE might be recycled and used as a substrate for the synthesis of carotenoids and tocotrienols during fruit development. Thus, FAPEs and FAGGEs in the mesocarp and kernel of Oil Palm provide an additional metabolic source for fatty acids and phytol or geranylgeraniol, respectively.
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Affiliation(s)
- Philipp Gutbrod
- Institute of Molecular Physiology and Biotechnology of Plants (IMBIO), University of Bonn, Karlrobert-Kreiten-Strasse 13, 53115, Bonn, Germany
| | - Sophie Reichert
- Institute of Molecular Physiology and Biotechnology of Plants (IMBIO), University of Bonn, Karlrobert-Kreiten-Strasse 13, 53115, Bonn, Germany
| | - Katharina Gutbrod
- Institute of Molecular Physiology and Biotechnology of Plants (IMBIO), University of Bonn, Karlrobert-Kreiten-Strasse 13, 53115, Bonn, Germany
| | - Amazigh Hamai
- Université de Bordeaux, CNRS, Laboratoire de Biogenèse Membranaire, UMR 5200, F-33140, Villenave d'Ornon, France
| | - Claire Bréhélin
- Université de Bordeaux, CNRS, Laboratoire de Biogenèse Membranaire, UMR 5200, F-33140, Villenave d'Ornon, France
| | - Georges Ngando-Ebongue
- Institute of Agricultural Research for Development, Center for Oil Palm Research (IRAD-CEREPAH) of La Dibamba, P.O. Box 243, Douala, Cameroon
| | - Peter Dörmann
- Institute of Molecular Physiology and Biotechnology of Plants (IMBIO), University of Bonn, Karlrobert-Kreiten-Strasse 13, 53115, Bonn, Germany.
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B KB, Mathur RK, M V B V, Shil S, G R, P A, H P B. Genome-wide association study (GWAS) of major QTLs for bunch and oil yield related traits in Elaeis guineensis L. Plant Sci 2021; 305:110810. [PMID: 33691957 DOI: 10.1016/j.plantsci.2020.110810] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 12/23/2020] [Accepted: 12/29/2020] [Indexed: 06/12/2023]
Abstract
Oil palm (Elaeis guineensis Jacq.) is a long breeding cycle perennial crop with a genome size of 1.8 Gb. This is the first report of GWAS on large number of 310 African germplasm using 400 SSR markers till date. Highly significant correlation was found between leaf area (LA) and rachis length (RL) (0.75) followed by bunch weight (BW) and bunch index (BI) (0.65), whereas negative correlation was observed between bunch number (BN) and average bunch weight (ABW). First two principal component analysis (PCA) together explained maximum amount of variation (84.5 %). The PCA1 revealed that group 2 (Guinea Bissau and Cameroon) and group 4 (Zambia and Cameroon) genotypes are best suitable for BN, BI and BW traits. GWAS of six bunch yield and seven bunch oil yield traits with SSRs resulted in the identification 43 significant quantitative trait loci (QTLs) by mixed linear model (MLM) approach. Seven SSR loci were found to be linked to oil to dry mesocarp (ODM) on chromosomes 1,4,7,10,12 and 15. The SSR locus mEgCIR1753 for ODM was significantly linked at a p of ≤0.05 which explained 34.6 % of phenotypic variance. The important parameters like ODM, OWM and OB were located on 4, 10, 11 and 15 chromosomes. The leaf area and ODM were associated with candidate genes representing of low-temperature-induced 65 kDa proteins. The identified markers can be effectively used for marker assisted selection of high yielding oil palm genotypes.
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Affiliation(s)
- Kalyana Babu B
- ICAR-Indian Institute of Oil Palm Research, Pedavegi, 534 450, West Godavari (Dt), Andhra Pradesh, India.
| | - R K Mathur
- ICAR-Indian Institute of Oil Palm Research, Pedavegi, 534 450, West Godavari (Dt), Andhra Pradesh, India
| | - Venu M V B
- ICAR-Indian Institute of Oil Palm Research, Pedavegi, 534 450, West Godavari (Dt), Andhra Pradesh, India
| | - Sandip Shil
- ICAR-Indian Institute of Oil Palm Research, Pedavegi, 534 450, West Godavari (Dt), Andhra Pradesh, India
| | - Ravichandran G
- ICAR-Indian Institute of Oil Palm Research, Pedavegi, 534 450, West Godavari (Dt), Andhra Pradesh, India
| | - Anita P
- ICAR-Indian Institute of Oil Palm Research, Pedavegi, 534 450, West Godavari (Dt), Andhra Pradesh, India
| | - Bhagya H P
- ICAR-Indian Institute of Oil Palm Research, Pedavegi, 534 450, West Godavari (Dt), Andhra Pradesh, India
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Ithnin M, Vu WT, Shin MG, Suryawanshi V, Sherbina K, Zolkafli SH, Serdari NM, Amiruddin MD, Abdullah N, Mustaffa S, Marjuni M, Nookiah R, Kushairi A, Marjoram P, Nuzhdin SV, Chang PL, Singh R. Genomic diversity and genome-wide association analysis related to yield and fatty acid composition of wild American oil palm. Plant Sci 2021; 304:110731. [PMID: 33568284 DOI: 10.1016/j.plantsci.2020.110731] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 10/13/2020] [Accepted: 10/15/2020] [Indexed: 05/15/2023]
Abstract
Existing Elaeis guineensis cultivars lack sufficient genetic diversity due to extensive breeding. Harnessing variation in wild crop relatives is necessary to expand the breadth of agronomically valuable traits. Using RAD sequencing, we examine the natural diversity of wild American oil palm populations (Elaeis oleifera), a sister species of the cultivated Elaeis guineensis oil palm. We genotyped 192 wild E. oleifera palms collected from seven Latin American countries along with four cultivated E. guineensis palms. Honduras, Costa Rica, Panama and Colombia palms are panmictic and genetically similar. Genomic patterns of diversity suggest that these populations likely originated from the Amazon Basin. Despite evidence of a genetic bottleneck and high inbreeding observed in these populations, there is considerable genetic and phenotypic variation for agronomically valuable traits. Genome-wide association revealed several candidate genes associated with fatty acid composition along with vegetative and yield-related traits. These observations provide valuable insight into the geographic distribution of diversity, phenotypic variation and its genetic architecture that will guide choices of wild genotypes for crop improvement.
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Affiliation(s)
- Maizura Ithnin
- Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, Kajang, Selangor, 43000, Malaysia
| | - Wendy T Vu
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Min-Gyoung Shin
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Vasantika Suryawanshi
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Katrina Sherbina
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Siti Hazirah Zolkafli
- Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, Kajang, Selangor, 43000, Malaysia
| | - Norhalida Mohamed Serdari
- Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, Kajang, Selangor, 43000, Malaysia
| | - Mohd Din Amiruddin
- Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, Kajang, Selangor, 43000, Malaysia
| | - Norziha Abdullah
- Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, Kajang, Selangor, 43000, Malaysia
| | - Suzana Mustaffa
- Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, Kajang, Selangor, 43000, Malaysia
| | - Marhalil Marjuni
- Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, Kajang, Selangor, 43000, Malaysia
| | - Rajanaidu Nookiah
- Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, Kajang, Selangor, 43000, Malaysia
| | - Ahmad Kushairi
- Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, Kajang, Selangor, 43000, Malaysia
| | - Paul Marjoram
- Department of Preventative Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Sergey V Nuzhdin
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Peter L Chang
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA.
| | - Rajinder Singh
- Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, Kajang, Selangor, 43000, Malaysia.
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de Santana Lopes A, Gomes Pacheco T, Nascimento da Silva O, do Nascimento Vieira L, Guerra MP, Pacca Luna Mattar E, de Baura VA, Balsanelli E, Maltempi de Souza E, de Oliveira Pedrosa F, Rogalski M. Plastid genome evolution in Amazonian açaí palm (Euterpe oleracea Mart.) and Atlantic forest açaí palm (Euterpe edulis Mart.). Plant Mol Biol 2021; 105:559-574. [PMID: 33386578 DOI: 10.1007/s11103-020-01109-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Accepted: 12/15/2020] [Indexed: 06/12/2023]
Abstract
The plastomes of E. edulis and E. oleracea revealed several molecular markers useful for genetic studies in natural populations and indicate specific evolutionary features determined by vicariant speciation. Arecaceae is a large and diverse family occurring in tropical and subtropical ecosystems worldwide. E. oleracea is a hyperdominant species of the Amazon forest, while E. edulis is a keystone species of the Atlantic forest. It has reported that E. edulis arose from vicariant speciation after the emergence of the belt barrier of dry environment (Cerrado and Caatinga biomes) between Amazon and Atlantic forests, isolating the E. edulis in the Atlantic forest. We sequenced the complete plastomes of E. edulis and E. oleracea and compared them concerning plastome structure, SSRs, tandem repeats, SNPs, indels, hotspots of nucleotide polymorphism, codon Ka/Ks ratios and RNA editing sites aiming to investigate evolutionary traits possibly affected by distinct environments. Our analyses revealed 303 SNPs, 91 indels, and 82 polymorphic SSRs among both species. Curiously, the narrow correlation among localization of repetitive sequences and indels strongly suggests that replication slippage is involved in plastid DNA mutations in Euterpe. Moreover, most non-synonymous substitutions represent amino acid variants in E. edulis that evolved specifically or in a convergent manner across the palm phylogeny. Amino acid variants observed in several plastid proteins in E. edulis were also identified as positive signatures across palm phylogeny. The higher incidence of specific amino acid changes in plastid genes of E. edulis in comparison with E. oleracea probably configures adaptive genetic variations determined by vicariant speciation. Our data indicate that the environment generates a selective pressure on the plastome making it more adapted to specific conditions.
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Affiliation(s)
- Amanda de Santana Lopes
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Túlio Gomes Pacheco
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Odyone Nascimento da Silva
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Leila do Nascimento Vieira
- Laboratório de Fisiologia do Desenvolvimento e Genética Vegetal, Programa de Pós-graduação em Recursos Genéticos Vegetais, Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil
| | - Miguel Pedro Guerra
- Laboratório de Fisiologia do Desenvolvimento e Genética Vegetal, Programa de Pós-graduação em Recursos Genéticos Vegetais, Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil
| | | | - Valter Antonio de Baura
- Departamento de Bioquímica e Biologia Molecular, Núcleo de Fixação Biológica de Nitrogênio, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Eduardo Balsanelli
- Departamento de Bioquímica e Biologia Molecular, Núcleo de Fixação Biológica de Nitrogênio, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Emanuel Maltempi de Souza
- Departamento de Bioquímica e Biologia Molecular, Núcleo de Fixação Biológica de Nitrogênio, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Fábio de Oliveira Pedrosa
- Departamento de Bioquímica e Biologia Molecular, Núcleo de Fixação Biológica de Nitrogênio, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Marcelo Rogalski
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil.
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Fooyontphanich K, Morcillo F, Joët T, Dussert S, Serret J, Collin M, Amblard P, Tangphatsornruang S, Roongsattham P, Jantasuriyarat C, Verdeil JL, Tranbarger TJ. Multi-scale comparative transcriptome analysis reveals key genes and metabolic reprogramming processes associated with oil palm fruit abscission. BMC Plant Biol 2021; 21:92. [PMID: 33573592 PMCID: PMC7879690 DOI: 10.1186/s12870-021-02874-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 02/01/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Fruit abscission depends on cell separation that occurs within specialized cell layers that constitute an abscission zone (AZ). To determine the mechanisms of fleshy fruit abscission of the monocot oil palm (Elaeis guineensis Jacq.) compared with other abscission systems, we performed multi-scale comparative transcriptome analyses on fruit targeting the developing primary AZ and adjacent tissues. RESULTS Combining between-tissue developmental comparisons with exogenous ethylene treatments, and naturally occurring abscission in the field, RNAseq analysis revealed a robust core set of 168 genes with differentially regulated expression, spatially associated with the ripe fruit AZ, and temporally restricted to the abscission timing. The expression of a set of candidate genes was validated by qRT-PCR in the fruit AZ of a natural oil palm variant with blocked fruit abscission, which provides evidence for their functions during abscission. Our results substantiate the conservation of gene function between dicot dry fruit dehiscence and monocot fleshy fruit abscission. The study also revealed major metabolic transitions occur in the AZ during abscission, including key senescence marker genes and transcriptional regulators, in addition to genes involved in nutrient recycling and reallocation, alternative routes for energy supply and adaptation to oxidative stress. CONCLUSIONS The study provides the first reference transcriptome of a monocot fleshy fruit abscission zone and provides insight into the mechanisms underlying abscission by identifying key genes with functional roles and processes, including metabolic transitions, cell wall modifications, signalling, stress adaptations and transcriptional regulation, that occur during ripe fruit abscission of the monocot oil palm. The transcriptome data comprises an original reference and resource useful towards understanding the evolutionary basis of this fundamental plant process.
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Affiliation(s)
- Kim Fooyontphanich
- UMR DIADE, Institut de Recherche Pour le Développement, Université de Montpellier, IRD Centre de Montpellier, 911 Avenue Agropolis BP 64501, 34394 Cedex 5, Montpellier, France
- Grow A Green Co, Ltd. 556 Maha Chakraphat Rd. Namaung, Chachoengsao, Chachoengsao Province, 24000, Thailand
| | - Fabienne Morcillo
- UMR DIADE, Institut de Recherche Pour le Développement, Université de Montpellier, IRD Centre de Montpellier, 911 Avenue Agropolis BP 64501, 34394 Cedex 5, Montpellier, France
- CIRAD, DIADE, F-34398, Montpellier, France
| | - Thierry Joët
- UMR DIADE, Institut de Recherche Pour le Développement, Université de Montpellier, IRD Centre de Montpellier, 911 Avenue Agropolis BP 64501, 34394 Cedex 5, Montpellier, France
| | - Stéphane Dussert
- UMR DIADE, Institut de Recherche Pour le Développement, Université de Montpellier, IRD Centre de Montpellier, 911 Avenue Agropolis BP 64501, 34394 Cedex 5, Montpellier, France
| | - Julien Serret
- UMR DIADE, Institut de Recherche Pour le Développement, Université de Montpellier, IRD Centre de Montpellier, 911 Avenue Agropolis BP 64501, 34394 Cedex 5, Montpellier, France
| | - Myriam Collin
- UMR DIADE, Institut de Recherche Pour le Développement, Université de Montpellier, IRD Centre de Montpellier, 911 Avenue Agropolis BP 64501, 34394 Cedex 5, Montpellier, France
| | | | - Sithichoke Tangphatsornruang
- National Science and Technology Development Agency, 111 Thailand Science Park, Phahonyothin Road, Pathum Thani, Thailand
| | - Peerapat Roongsattham
- UMR DIADE, Institut de Recherche Pour le Développement, Université de Montpellier, IRD Centre de Montpellier, 911 Avenue Agropolis BP 64501, 34394 Cedex 5, Montpellier, France
- Department of Genetics, Faculty of Science, Kasetsart University Bangkhen Campus, 50 Phahonyothin Road Jatujak, Bangkok, Thailand
| | - Chatchawan Jantasuriyarat
- Department of Genetics, Faculty of Science, Kasetsart University Bangkhen Campus, 50 Phahonyothin Road Jatujak, Bangkok, Thailand
| | - Jean-Luc Verdeil
- CIRAD, UMR AGAP, F-34398, Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Timothy J Tranbarger
- UMR DIADE, Institut de Recherche Pour le Développement, Université de Montpellier, IRD Centre de Montpellier, 911 Avenue Agropolis BP 64501, 34394 Cedex 5, Montpellier, France.
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Ngoot-Chin T, Zulkifli MA, van de Weg E, Zaki NM, Serdari NM, Mustaffa S, Zainol Abidin MI, Sanusi NSNM, Smulders MJM, Low ETL, Ithnin M, Singh R. Detection of ploidy and chromosomal aberrations in commercial oil palm using high-throughput SNP markers. Planta 2021; 253:63. [PMID: 33544231 DOI: 10.1007/s00425-021-03567-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 01/04/2021] [Indexed: 05/14/2023]
Abstract
Karyotyping using high-density genome-wide SNP markers identified various chromosomal aberrations in oil palm (Elaeis guineensis Jacq.) with supporting evidence from the 2C DNA content measurements (determined using FCM) and chromosome counts. Oil palm produces a quarter of the world's total vegetable oil. In line with its global importance, an initiative to sequence the oil palm genome was carried out successfully, producing huge amounts of sequence information, allowing SNP discovery. High-capacity SNP genotyping platforms have been widely used for marker-trait association studies in oil palm. Besides genotyping, a SNP array is also an attractive tool for understanding aberrations in chromosome inheritance. Exploiting this, the present study utilized chromosome-wide SNP allelic distributions to determine the ploidy composition of over 1,000 oil palms from a commercial F1 family, including 197 derived from twin-embryo seeds. Our method consisted of an inspection of the allelic intensity ratio using SNP markers. For palms with a shifted or abnormal distribution ratio, the SNP allelic frequencies were plotted along the pseudo-chromosomes. This method proved to be efficient in identifying whole genome duplication (triploids) and aneuploidy. We also detected several loss of heterozygosity regions which may indicate small chromosomal deletions and/or inheritance of identical by descent regions from both parents. The SNP analysis was validated by flow cytometry and chromosome counts. The triploids were all derived from twin-embryo seeds. This is the first report on the efficiency and reliability of SNP array data for karyotyping oil palm chromosomes, as an alternative to the conventional cytogenetic technique. Information on the ploidy composition and chromosomal structural variation can help to better understand the genetic makeup of samples and lead to a more robust interpretation of the genomic data in marker-trait association analyses.
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Affiliation(s)
- Ting Ngoot-Chin
- Malaysian Palm Oil Board (MPOB), 6, Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia
| | - Muhammad Azwan Zulkifli
- Malaysian Palm Oil Board (MPOB), 6, Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia
| | - Eric van de Weg
- Plant Breeding, Wageningen University and Research, Wageningen, The Netherlands
| | - Noorhariza Mohd Zaki
- Malaysian Palm Oil Board (MPOB), 6, Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia
| | - Norhalida Mohamed Serdari
- Malaysian Palm Oil Board (MPOB), 6, Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia
| | - Suzana Mustaffa
- Malaysian Palm Oil Board (MPOB), 6, Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia
| | - Mohd Isa Zainol Abidin
- Plant Breeding and Services Department, KULIM Plantations Berhad, 81900, Kota Tinggi, Johor, Malaysia
| | - Nik Shazana Nik Mohd Sanusi
- Malaysian Palm Oil Board (MPOB), 6, Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia
| | | | - Eng Ti Leslie Low
- Malaysian Palm Oil Board (MPOB), 6, Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia
| | - Maizura Ithnin
- Malaysian Palm Oil Board (MPOB), 6, Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia
| | - Rajinder Singh
- Malaysian Palm Oil Board (MPOB), 6, Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia.
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Kong SL, Abdullah SNA, Ho CL, Musa MHB, Yeap WC. Comparative transcriptome analysis reveals novel insights into transcriptional responses to phosphorus starvation in oil palm (Elaeis guineensis) root. BMC Genom Data 2021; 22:6. [PMID: 33568046 PMCID: PMC7863428 DOI: 10.1186/s12863-021-00962-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 01/05/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Phosphorus (P), in its orthophosphate form (Pi) is an essential macronutrient for oil palm early growth development in which Pi deficiency could later on be reflected in lower biomass production. Application of phosphate rock, a non-renewable resource has been the common practice to increase Pi accessibility and maintain crop productivity in Malaysia. However, high fixation rate of Pi in the native acidic tropical soils has led to excessive utilization of P fertilizers. This has caused serious environmental pollutions and cost increment. Even so, the Pi deficiency response mechanism in oil palm as one of the basic prerequisites for crop improvement remains largely unknown. RESULTS Using total RNA extracted from young roots as template, we performed a comparative transcriptome analysis on oil palm responding to 14d and 28d of Pi deprivation treatment and under adequate Pi supply. By using Illumina HiSeq4000 platform, RNA-Seq analysis was successfully conducted on 12 paired-end RNA-Seq libraries and generated more than 1.2 billion of clean reads in total. Transcript abundance estimated by fragments per kilobase per million fragments (FPKM) and differential expression analysis revealed 36 and 252 genes that are differentially regulated in Pi-starved roots at 14d and 28d, respectively. Genes possibly involved in regulating Pi homeostasis, nutrient uptake and transport, hormonal signaling and gene transcription were found among the differentially expressed genes. CONCLUSIONS Our results showed that the molecular response mechanism underlying Pi starvation in oil palm is complexed and involved multilevel regulation of various sensing and signaling components. This contribution would generate valuable genomic resources in the effort to develop oil palm planting materials that possess Pi-use efficient trait through molecular manipulation and breeding programs.
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Affiliation(s)
- Sze-Ling Kong
- Laboratory of Sustainable Agronomy and Crop Protection, Institute of Plantation Studies, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Siti Nor Akmar Abdullah
- Laboratory of Sustainable Agronomy and Crop Protection, Institute of Plantation Studies, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia.
- Department of Agriculture Technology, Faculty of Agriculture, University Putra Malaysia, 43400, Serdang, Selangor, Malaysia.
| | - Chai-Ling Ho
- Laboratory of Sustainable Agronomy and Crop Protection, Institute of Plantation Studies, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, University Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Mohamed Hanafi Bin Musa
- Department of Land Management, Faculty of Agriculture, University Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Wan-Chin Yeap
- Sime Darby Technology Centre Sdn. Bhd., Block A, UPM-MTDC Technology Centre III, Lebuh Silikon, University Putra Malaysia, 43400, Serdang, Selangor, Malaysia
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Sakeh NM, Abdullah SNA, Bahari MNA, Azzeme AM, Shaharuddin NA, Idris AS. EgJUB1 and EgERF113 transcription factors as potential master regulators of defense response in Elaeis guineensis against the hemibiotrophic Ganoderma boninense. BMC Plant Biol 2021; 21:59. [PMID: 33482731 PMCID: PMC7825162 DOI: 10.1186/s12870-020-02812-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 12/22/2020] [Indexed: 06/12/2023]
Abstract
BACKGROUND Hemibiotrophic pathogen such as the fungal pathogen Ganoderma boninense that is destructive to oil palm, manipulates host defense mechanism by strategically switching from biotrophic to necrotrophic phase. Our previous study revealed two distinguishable expression profiles of oil palm genes that formed the basis in deducing biotrophic phase at early interaction which switched to necrotrophic phase at a later stage of infection. RESULTS The present report is a continuing study from our previous published transcriptomic profiling of oil palm seedlings against G. boninense. We focused on identifying differentially expressed genes (DEGs) encoding transcription factors (TFs) from the same RNA-seq data; resulting in 106 upregulated and 108 downregulated TFs being identified. The DEGs are involved in four established defense-related pathways responsible for cell wall modification, reactive oxygen species (ROS)-mediated signaling, programmed cell death (PCD) and plant innate immunity. We discovered upregulation of JUNGBRUNNEN 1 (EgJUB1) during the fungal biotrophic phase while Ethylene Responsive Factor 113 (EgERF113) demonstrated prominent upregulation when the palm switches to defense against necrotrophic phase. EgJUB1 was shown to have a binding activity to a 19 bp palindromic SNBE1 element, WNNYBTNNNNNNNAMGNHW found in the promoter region of co-expressing EgHSFC-2b. Further in silico analysis of promoter regions revealed co-expression of EgJUB1 with TFs containing SNBE1 element with single nucleotide change at either the 5th or 18th position. Meanwhile, EgERF113 binds to both GCC and DRE/CRT elements promoting plasticity in upregulating the downstream defense-related genes. Both TFs were proven to be nuclear-localized based on subcellular localization experiment using onion epidermal cells. CONCLUSION Our findings demonstrated unprecedented transcriptional reprogramming of specific TFs potentially to enable regulation of a specific set of genes during different infection phases of this hemibiotrophic fungal pathogen. The results propose the intricacy of oil palm defense response in orchestrating EgJUB1 during biotrophic and EgERF113 during the subsequent transition to the necrotrophic phase. Binding of EgJUB1 to SNBE motif instead of NACBS while EgERF113 to GCC-box and DRE/CRT motifs is unconventional and not normally associated with pathogen infection. Identification of these phase-specific oil palm TFs is important in designing strategies to tackle or attenuate the progress of infection.
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Affiliation(s)
- Nurshafika Mohd Sakeh
- Institute of Plantation Studies, Universiti Putra Malaysia (UPM), 43400, Serdang, Selangor, Malaysia
| | - Siti Nor Akmar Abdullah
- Institute of Plantation Studies, Universiti Putra Malaysia (UPM), 43400, Serdang, Selangor, Malaysia.
- Department of Agriculture Technology, Faculty of Agriculture, Universiti Putra Malaysia (UPM), 43400, Serdang, Selangor, Malaysia.
| | | | - Azzreena Mohamad Azzeme
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia (UPM), 43400, Serdang, Selangor, Malaysia
| | - Noor Azmi Shaharuddin
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia (UPM), 43400, Serdang, Selangor, Malaysia
| | - Abu Seman Idris
- Ganoderma and Diseases Research for Oil Palm Unit, Malaysian Palm Oil Board, No. 6, Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia
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Kamaruddin K, Ithnin M, Ting NC, Yaakub Z, Nik Mohd Sanusi NS, Sritharan K, Singh R. Anchoring a genetic map of an interspecific backcross two family to the genome builds of Elaeis. J Genet 2021; 100:7. [PMID: 33707358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The present study evaluated an interspecific backcross two (BC2) population of oil palm, which was segregating for fatty acid composition (FAC). The purpose of this study was to construct a high-density genetic map for the population, which could be used to anchor the Elaeis guineensis (EG5) and E. oleifera (O7) genome builds and determine the physical positions of the quantitative trait loci (QTLs) associated with FAC. A high-density SNP-based and SSR-based linkage map was successfully constructed for an E. guineensis x E. oleifera BC2 population. The genetic map had 16 linkage groups spanning 1618.4 cM with 1252 markers (1152 SNPs and 100 SSRs). The physical location of the markers were determined through sequence similarity search against EG5 and O7. The majority of markers (81.2%) showed map order consistent with their corresponding position on EG5. In total, 1218 markers were also anchored to 683 scaffolds in O7. This study for the first time compared the genetic map of the BC2 population with that of a published E. oleifera x E. guineensis (O x G) interspecific F1 hybrid, which revealed 433 common markers (34.6%). More importantly marker order was generally consistent in both maps. The published EG5 facilitated orientating the mapped markers in the present BC2 map as well as in the O7 scaffolds. Major QTLs associated with iodine value (IV) and palmitic acid (C16:0) content, localized on chromosome 3 and linoleic acid (C18:2) content localized on chromosome 2 of EG5 were also for the first time positioned on the O7 build, revealing the corresponding position in the E. oleifera genome likely influencing FAC in hybrids and backcrosses.
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Affiliation(s)
- Katialisa Kamaruddin
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, P.O. Box 10620, Kuala Lumpur 50720, Malaysia.
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