1
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Wang ZY, Hu Y, Lv YW, Xiao Y, He ZH, Wu C, Hu XS. Population Structure and Genetic Diversity of the Toona ciliata (Meliaceae) Complex Assayed with Chloroplast DNA Markers. Genes (Basel) 2024; 15:320. [PMID: 38540379 PMCID: PMC10970150 DOI: 10.3390/genes15030320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 02/13/2024] [Accepted: 02/26/2024] [Indexed: 06/14/2024] Open
Abstract
Toona ciliata is a deciduous or semi-deciduous tree species and belongs to the Toona genus of the Meliaceae family. Owing to low natural regeneration and over-exploitation, the species is listed as an endangered species at level II in China and its conservation has received increasing concern. Here, we sampled 447 individuals from 29 populations across the range-wide distribution of the T. ciliata complex in China and assessed their genetic variation using two chloroplast DNA markers. The results showed that the overall haplotype diversity and nucleotide diversity per site were high at h = 0.9767 and π = 0.0303 for the psbA-trnH fragment and h= 0.8999 and π = 0.0189 for the trnL-trnL fragment. Phylogenetic analysis supported the division of the natural distribution of T. ciliata complex into western and eastern regions. The genetic diversity was higher in the western region than in the eastern region, showing significant phylogeographic structure. Genetic differentiation among populations was moderate (Φst=42.87%), and the effects of isolation by distance (IBD) were significant. A neutrality test and mismatch distribution analysis indicated that the distribution of the T. ciliata complex generally did not expand, although a few local populations could likely expand after bottleneck effects. The overall results were complementary to and consolidated previous studies using mitochondrial and nuclear DNA markers. We finally discussed strategies for the genetic conservation of the T. ciliata complex.
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Affiliation(s)
- Zi-Yun Wang
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (Z.-Y.W.); (Y.H.); (Y.-W.L.); (Y.X.); (Z.-H.H.); (C.W.)
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, Guangzhou 510642, China
| | - Ying Hu
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (Z.-Y.W.); (Y.H.); (Y.-W.L.); (Y.X.); (Z.-H.H.); (C.W.)
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, Guangzhou 510642, China
| | - Yan-Wen Lv
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (Z.-Y.W.); (Y.H.); (Y.-W.L.); (Y.X.); (Z.-H.H.); (C.W.)
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, Guangzhou 510642, China
| | - Yu Xiao
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (Z.-Y.W.); (Y.H.); (Y.-W.L.); (Y.X.); (Z.-H.H.); (C.W.)
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, Guangzhou 510642, China
| | - Zi-Han He
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (Z.-Y.W.); (Y.H.); (Y.-W.L.); (Y.X.); (Z.-H.H.); (C.W.)
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, Guangzhou 510642, China
| | - Chao Wu
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (Z.-Y.W.); (Y.H.); (Y.-W.L.); (Y.X.); (Z.-H.H.); (C.W.)
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, Guangzhou 510642, China
| | - Xin-Sheng Hu
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (Z.-Y.W.); (Y.H.); (Y.-W.L.); (Y.X.); (Z.-H.H.); (C.W.)
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, Guangzhou 510642, China
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2
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Xiao Y, Wang X, He Z, Lv Y, Zhang C, Hu X. Assessing the phylogenetic relationship among varieties of Toona ciliata (Meliaceae) in sympatry with chloroplast genomes. Ecol Evol 2023; 13:e10828. [PMID: 38094154 PMCID: PMC10716671 DOI: 10.1002/ece3.10828] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 10/19/2023] [Accepted: 11/28/2023] [Indexed: 07/03/2024] Open
Abstract
Toona ciliata is an endangered species due to over-cutting and low natural regeneration in China. Its genetic conservation is of an increasing concern. However, several varieties are recognized according to the leaf and flower traits, which complicates genetic conservation of T. ciliata. Here, we sequenced the whole chloroplast genome sequences of three samples for each of four varieties (T. ciliata var. ciliata, T. ciliata var. yunnanensis, T. ciliata var. pubescens, and T. ciliata var. henryi) in sympatry and assessed their phylogenetic relationship at a fine spatial scale. The four varieties had genome sizes ranged from 159,546 to 159,617 bp and had small variations in genome structure. Phylogenomic analysis indicated that the four varieties were genetically well-mixed in branch groups. Genetic diversity from the whole chloroplast genome sequences of 12 samples was low among varieties (average π = 0.0003). Besides, we investigated genetic variation of 58 samples of the four varieties in sympatry using two markers (psaA and trnL-trnF) and showed that genetic differentiation was generally insignificant among varieties (Ф st = 0%-5%). Purifying selection occurred in all protein-coding genes except for the ycf2 gene that was under weak positive selection. Most amino acid sites in all protein-coding genes were under purifying selection except for a few sites that were under positive selection. The chloroplast genome-based phylogeny did not support the morphology-based classification. The overall results implicated that a conservation strategy based on the T. ciliata complex rather than on intraspecific taxon was more appropriate.
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Affiliation(s)
- Yu Xiao
- College of Forestry and Landscape ArchitectureSouth China Agricultural UniversityGuangzhouChina
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant GermplasmGuangzhouChina
| | - Xi Wang
- College of Forestry and Landscape ArchitectureSouth China Agricultural UniversityGuangzhouChina
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant GermplasmGuangzhouChina
| | - Zi‐Han He
- College of Forestry and Landscape ArchitectureSouth China Agricultural UniversityGuangzhouChina
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant GermplasmGuangzhouChina
| | - Yan‐Wen Lv
- College of Forestry and Landscape ArchitectureSouth China Agricultural UniversityGuangzhouChina
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant GermplasmGuangzhouChina
| | - Chun‐Hua Zhang
- Institute of Highland Forest Science, Chinese Academy of ForestryKunmingChina
| | - Xin‐Sheng Hu
- College of Forestry and Landscape ArchitectureSouth China Agricultural UniversityGuangzhouChina
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant GermplasmGuangzhouChina
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3
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Li Y, Gu M, Liu X, Lin J, Jiang H, Song H, Xiao X, Zhou W. Sequencing and analysis of the complete mitochondrial genomes of Toona sinensis and Toona ciliata reveal evolutionary features of Toona. BMC Genomics 2023; 24:58. [PMID: 36726084 PMCID: PMC9893635 DOI: 10.1186/s12864-023-09150-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 01/24/2023] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND Toona is a critical genus in the Meliaceae, and the plants of this group are an asset for both restorative and restorative purposes, the most flexible of which are Toona sinensis and Toona ciliata. To concentrate on the advancement of mitochondrial(Mt) genome variety in T.sinensis and T.ciliata, the Mt genomes of the two species were sequenced in high throughput independently, after de novo assembly and annotation to construct a Mt genome map for comparison in genome structure. Find their repetitive sequences and analyze them in comparison with the chloroplast genome, along with Maximum-likelihood(ML) phylogenetic analysis with 16 other relatives. RESULTS (1) T. sinensis and T.ciliata are both circular structures with lengths of 683482 bp and 68300 bp, respectively. They share a high degree of similarity in encoding genes and have AT preferences. All of them have the largest Phe concentration and are the most frequently used codons. (2) Both of their Mt genome are highly preserved in terms of structural and functional genes, while the main variability is reflected in the length of tRNA, the number of genes, and the value of RSCU. (3) T. siniensis and T. ciliata were detected to have 94 and 87 SSRs, respectively, of which mononucleotides accounted for the absolute proportion. Besides, the vast majority of their SSRs were found to be poly-A or poly-T. (4)10 and 11 migrating fragments were identified in the comparison with the chloroplast genome, respectively. (5) In the ML evolutionary tree, T.sinensis and T.ciliata clustered individually into a small branch with 100% support, reflecting two species of Toona are very similarly related to each other. CONCLUSIONS This research provides a basis for the exploitation of T.sinensis and T.ciliata in terms of medicinal, edible, and timber resources to avoid confusion; at the same time, it can explore the evolutionary relationship between the Toona and related species, which does not only have an important practical value, but also provides a theoretical basis for future hybrid breeding of forest trees, molecular markers, and evolutionary aspects of plants, which has great scientific significance.
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Affiliation(s)
- Youli Li
- grid.20561.300000 0000 9546 5767College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 51000 Guangdong China
| | - Min Gu
- grid.20561.300000 0000 9546 5767College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 51000 Guangdong China
| | - Xuanzhe Liu
- grid.20561.300000 0000 9546 5767College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 51000 Guangdong China
| | - Jianna Lin
- grid.20561.300000 0000 9546 5767College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 51000 Guangdong China
| | - Huier Jiang
- grid.20561.300000 0000 9546 5767College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 51000 Guangdong China
| | - Huiyun Song
- grid.20561.300000 0000 9546 5767College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 51000 Guangdong China
| | - Xingcui Xiao
- grid.464457.00000 0004 0445 3867Sichuan Academy of Forestry Sciences, Chengdu, 61008 Sichuan China
| | - Wei Zhou
- grid.20561.300000 0000 9546 5767College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 51000 Guangdong China
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Xiao Y, Zhang XX, Hu Y, Wang X, Li P, He ZH, Lv YW, Chen XY, Hu XS. Phylogeography of Toona ciliata (Meliaceae) Complex in China Inferred from Cytonuclear Markers. Genes (Basel) 2022; 14:116. [PMID: 36672857 PMCID: PMC9858616 DOI: 10.3390/genes14010116] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/23/2022] [Accepted: 12/27/2022] [Indexed: 01/03/2023] Open
Abstract
Toona ciliata is an important timber species but is recognized as an endangered species at level II in China. Its genetic conservation is of increasing concern. Provenance trials and other breeding programs were conducted to develop seed transfer rules and multiplications. Here, we investigated twenty-nine populations sampled across the natural distribution of the T. ciliata complex using mtDNA and nrDNA ITS (ribosomal internal transcribed spacer) markers. Haplotype diversity was h = 0.190 ± 0.202 and nucleotide diversity was π = 0.000383 ± 0.000536 for mtDNA marker. Nucleotide diversity for ITS sequences was 0.00837 ± 0.000783. Haplotypes exhibited phylogeographic structure in spatial distribution. The extent of genetic differentiation was significant (Fst = 0.6994 ± 0.0079 for ITS and 0.8870 ± 0.0077 for mtDNA marker). Isolation by distance (IBD) and by elevation (IBE) occurred among populations. Phylogenetic relationships from mtDNA marker indicated three genetically distinct regions, each without IBD effects. Compared with pollen flow, seed flow was strongly impeded in the western region, but extensive in the central region, and less impeded in the eastern region. Most populations did not exhibit expansion, with only a few populations showing expansion after bottleneck effects. We discussed a strategy of region-based genetic conservation and proposed to conserve multiple populations in the western and eastern regions and a few populations in the central region.
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Affiliation(s)
- Yu Xiao
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangzhou 510642, China
| | - Xin-Xin Zhang
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangzhou 510642, China
| | - Ying Hu
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangzhou 510642, China
| | - Xi Wang
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangzhou 510642, China
| | - Pei Li
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangzhou 510642, China
| | - Zi-Han He
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangzhou 510642, China
| | - Yan-Wen Lv
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangzhou 510642, China
| | - Xiao-Yang Chen
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangzhou 510642, China
| | - Xin-Sheng Hu
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangzhou 510642, China
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5
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Wang X, Xiao Y, He ZH, Li LL, Song HY, Zhang JJ, Cheng X, Chen XY, Li P, Hu XS. A Chromosome-Level Genome Assembly of Toona ciliata (Meliaceae). Genome Biol Evol 2022; 14:6650022. [PMID: 35880739 PMCID: PMC9348625 DOI: 10.1093/gbe/evac121] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/21/2022] [Indexed: 11/13/2022] Open
Abstract
Toona ciliata Roem is an important timber species in the Toona genus of the Meliaceae family and an endangered species due to over-cutting and a low rate of natural regeneration in China. Although molecular markers have been applied to studying population genetic diversity, the absence of a reliable reference genome limits in-depth genetic conservation and evolutionary studies of this species. Here, we reported a high-quality assembly of the whole genome sequence of T. ciliata. The total assembled genome has 520.64 Mb in length anchored on 28 chromosomes (contig N50 = 4.48 Mb). A total of 42,159 genes were predicted after the ab initio, homology-based, and transcriptome analyses. A total of 41,284 protein-encoding genes (97.92%) were functionally annotated and 1,246 non-coding RNAs were identified in the T. ciliata genome. Phylogenomic analysis showed that T. ciliata was divergent at 15.06 (6–25) Ma from T. sinensis of the same genus Toona. This whole genome sequence provides a valuable resource to study the genetic conservation and molecular evolution of T. ciliata in the future.
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Affiliation(s)
- Xi Wang
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangdong, China.,Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, Guangdong, 510642 Guangdong, China
| | - Yu Xiao
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangdong, China.,Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, Guangdong, 510642 Guangdong, China
| | - Zi Han He
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangdong, China.,Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, Guangdong, 510642 Guangdong, China
| | - Ling Ling Li
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangdong, China.,Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, Guangdong, 510642 Guangdong, China
| | - Hui Yun Song
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangdong, China.,Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, Guangdong, 510642 Guangdong, China
| | - Jun Jie Zhang
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangdong, China.,Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, Guangdong, 510642 Guangdong, China
| | - Xiang Cheng
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangdong, China.,Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, Guangdong, 510642 Guangdong, China
| | - Xiao Yang Chen
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangdong, China.,Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, Guangdong, 510642 Guangdong, China
| | - Pei Li
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangdong, China.,Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, Guangdong, 510642 Guangdong, China
| | - Xin Sheng Hu
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangdong, China.,Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, Guangdong, 510642 Guangdong, China
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6
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Gavilan NH, de Freitas Morel LJ, da Silva Coppede J, Taleb-Contini SH, de Castro França S, Bertoni BW, Pereira AMS. Genetic diversity and verbascoside content in natural populations of Pyrostegia venusta (Ker Gawl.) Miers. Mol Biol Rep 2022; 49:8617-8625. [PMID: 35867291 DOI: 10.1007/s11033-022-07697-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 06/09/2022] [Indexed: 10/17/2022]
Abstract
BACKGROUND Pyrostegia venusta (Ker Gawl.) Miers occurs in threatened biodiversity hotspots of Cerrado and Atlantic forest biomes in Brazil and is used in traditional medicine to treat various respiratory and skin diseases. METHODS AND RESULTS This study (i) examined the genetic diversity and structure of six natural populations of P. venusta from different Brazilian regions using sequence-related amplified polymorphism (SRAP) markers; and (ii) compared the intra- and inter-populational levels of the bioactive component verbascoside using high-performance liquid chromatography. The population from Nova Mutum, Mato Grosso, presented the highest genetic variability (Nei index H = 0.2759; Shannon index I = 0.4170; 85.14% polymorphic loci), whereas the population from Araxá, Minas Gerais, presented the lowest genetic variability (H = 0.1811; I = 0.2820; 70.27% polymorphic loci). The intra-populational variability (79%) was significantly higher (p = 0.001) than the inter-populational variability (21%). The populations were clustered into two groups but their genetic differentiation was not associated with geographical origin (Mantel test, r = 0.328; p > 0.05). The verbascoside content significantly differed (p > 0.05) among the six populations and between the individuals from each population. The highest verbascoside levels (> 200 µg/mg extract) were detected in populations from Araxá and Serrana, while the lowest verbacoside levels were detected in populations from Paranaíta and Sinop. CONCLUSIONS This is the first report on the use of SRAP markers to analyze genetic variability in the family Bignoniaceae. Our findings shall help to better understand the genetic and chemical diversity of P. venusta populations, as well as provide useful information to select the most appropriate individuals to prepare phytomedicines.
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Affiliation(s)
- Natália Helena Gavilan
- Departamento de Horticultura, Universidade Estadual Paulista "Júlio de Mesquita Filho", Botucatu, São Paulo, 18618-970, Brazil
| | - Lucas Junqueira de Freitas Morel
- Departamento de Biotecnologia em Plantas Medicinais, Universidade de Ribeirão Preto-UNAERP, Ribeirão Preto, São Paulo, 14096-900, Brazil
| | - Juliana da Silva Coppede
- Departamento de Biotecnologia em Plantas Medicinais, Universidade de Ribeirão Preto-UNAERP, Ribeirão Preto, São Paulo, 14096-900, Brazil
| | - Silvia Helena Taleb-Contini
- Departamento de Biotecnologia em Plantas Medicinais, Universidade de Ribeirão Preto-UNAERP, Ribeirão Preto, São Paulo, 14096-900, Brazil
| | - Suzelei de Castro França
- Departamento de Biotecnologia em Plantas Medicinais, Universidade de Ribeirão Preto-UNAERP, Ribeirão Preto, São Paulo, 14096-900, Brazil
| | - Bianca Waléria Bertoni
- Departamento de Biotecnologia em Plantas Medicinais, Universidade de Ribeirão Preto-UNAERP, Ribeirão Preto, São Paulo, 14096-900, Brazil.,Jardim Botânico de Plantas Medicinais Ordem e Progresso, Jardinópolis, São Paulo, 14680-000, Brazil
| | - Ana Maria Soares Pereira
- Departamento de Biotecnologia em Plantas Medicinais, Universidade de Ribeirão Preto-UNAERP, Ribeirão Preto, São Paulo, 14096-900, Brazil. .,Jardim Botânico de Plantas Medicinais Ordem e Progresso, Jardinópolis, São Paulo, 14680-000, Brazil.
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7
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Estimation of Plant Height and Aboveground Biomass of Toona sinensis under Drought Stress Using RGB-D Imaging. FORESTS 2021. [DOI: 10.3390/f12121747] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Rapid and accurate plant growth and biomass estimation is essential for formulating and implementing targeted forest cultivation measures. In this study, RGB-D imaging technology was used to obtain the RGB and depth imaging data for a Toona sinensis seedling canopy to estimate plant growth and aboveground biomass (AGB). Three hundred T. sinensis seedlings from 20 varieties were planted under five different drought stress treatments. The U-Net model was applied first to achieve highly accurate segmentation of plants from complex backgrounds. Simple linear regression (SLR) was used for plant height prediction, and the other three models, including multivariate linear (ML), random forest (RF) and multilayer perceptron (MLP) regression, were applied to predict the AGB and compared for optimal model selection. The results showed that the SLR model yields promising and reliable results for the prediction of plant height, with R2 and RMSE values of 0.72 and 1.89 cm, respectively. All three regression methods perform well in the prediction of AGB estimation. MLP yields the highest accuracy in predicting dry and fresh aboveground biomass compared to the other two regression models, with R2 values of 0.77 and 0.83, respectively. The combination of Gray, Green minus red (GMR) and Excess green index (ExG) was identified as the key predictor by RReliefF for predicting dry AGB. GMR was the most important in predicting fresh AGB. This study demonstrated that the merits of RGB-D and machine learning models are effective phenotyping techniques for plant height and AGB prediction, and can be used to assist dynamic responses to drought stress for breeding selection.
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8
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Zhou W, Zhang XX, Ren Y, Li P, Chen XY, Hu XS. Mating system and population structure in the natural distribution of Toona ciliata (Meliaceae) in South China. Sci Rep 2020; 10:16998. [PMID: 33046785 PMCID: PMC7550595 DOI: 10.1038/s41598-020-74123-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2019] [Accepted: 09/23/2020] [Indexed: 11/15/2022] Open
Abstract
Most initially perfect flowers of Toona ciliata Roem subsequently develop into functionally unisexual flowers and their relative positions in the same inflorescence could enhance the outcrossing system in this species. Here we investigated the mating system of this species. We used eight nuclear microsatellite markers and investigated the progeny of 125 mother trees from six populations naturally distributed in South China, with sample sizes ranging from 64 to 300 seeds. The multilocus outcrossing rate was 0.970 ± 0.063, and the single locus outcrossing rate was 0.859 ± 0.106, indicating the pattern of predominant outcrossing. Selfing was present in one population, but biparental inbreeding occurred in five populations. Inbreeding was absent in maternal parents, and correlations of selfing among families or among loci were generally insignificant. Positive correlation of paternity at multiple loci was significant in four populations, but was not consistent with the results at single loci. Population substructure occurred in male similarity between outcrosses only in one population. Population genetic differentaitaion was significant (Fst = 34.5%) and the effects of isolation-by-distance at the eight loci were significant among the six populations. These results provide evidence that self-comptability and inbreeding naturally occur in T. ciliata and indicate that inbreeding avoidance is necessary during genetic improvement and breeding of this endangered tree species.
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Affiliation(s)
- Wei Zhou
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangdong, 510642, China.,Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangdong, 510642, China
| | - Xin-Xin Zhang
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangdong, 510642, China.,Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangdong, 510642, China
| | - Ying Ren
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangdong, 510642, China.,Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangdong, 510642, China
| | - Pei Li
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangdong, 510642, China.,Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangdong, 510642, China
| | - Xiao-Yang Chen
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangdong, 510642, China. .,Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangdong, 510642, China.
| | - Xin-Sheng Hu
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangdong, 510642, China. .,Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangdong, 510642, China.
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9
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Song H, Mao W, Duan Z, Que Q, Zhou W, Chen X, Li P. Selection and validation of reference genes for measuring gene expression in Toona ciliata under different experimental conditions by quantitative real-time PCR analysis. BMC PLANT BIOLOGY 2020; 20:450. [PMID: 33003996 PMCID: PMC7528382 DOI: 10.1186/s12870-020-02670-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 09/23/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Before studying gene expression of different organisms, it is important to determine the best reference gene. At present, the most accurate method of detecting gene expression is quantitative real-time PCR (RT-qPCR). With this method, reference genes that are stable in different biological systems and under different conditions can be obtained. Toona ciliata Roem (T. ciliata). is a valuable and fast-growing timber specie. In this study, 20 reference genes were identified using RT-qPCR, as a primary prerequisite for future gene expression analysis. Four different methods, geNorm, NormFinder, BestKeeper, and RankAggreg were used to evaluate the expression stability of the 20 candidate reference genes in various tissues under different conditions. RESULTS The experimental results showed that TUB-α was the most stably expressed reference gene across all samples and UBC17 was the most stable in leaves and young stems under Hypsipyla robusta (H. robusta) and methyl jasmonate (MeJA) treatments. In addition, PP2C59 and UBC5B were the best-performing genes in leaves under H. robusta treatment, while HIS1 and ACT7 were the best reference genes in young stems. The two best reference genes were 60S-18 and TUB-α after treatment at 4 °C. The expression of HIS6 and MUB1 was the most stable under PEG6000 treatment. The accuracy of the selected reference genes was verified using the transcription factor MYB3 (TcMYB3) gene. CONCLUSIONS This is the first report to verify the best reference genes for normalizing gene expression in T. ciliata under different conditions, which will facilitate future elucidation of gene regulations in this species.
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Affiliation(s)
- Huiyun Song
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, Guangzhou, 510642, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangzhou, 510642, China
- South China Agricultural University, College of Forestry and Landscape Architecture, Guangzhou, 510642, China
| | - Wenmai Mao
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, Guangzhou, 510642, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangzhou, 510642, China
- South China Agricultural University, College of Forestry and Landscape Architecture, Guangzhou, 510642, China
| | - Zhihao Duan
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, Guangzhou, 510642, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangzhou, 510642, China
- South China Agricultural University, College of Forestry and Landscape Architecture, Guangzhou, 510642, China
| | - Qingmin Que
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, Guangzhou, 510642, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangzhou, 510642, China
- South China Agricultural University, College of Forestry and Landscape Architecture, Guangzhou, 510642, China
| | - Wei Zhou
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, Guangzhou, 510642, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangzhou, 510642, China
- South China Agricultural University, College of Forestry and Landscape Architecture, Guangzhou, 510642, China
| | - Xiaoyang Chen
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, Guangzhou, 510642, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangzhou, 510642, China
- South China Agricultural University, College of Forestry and Landscape Architecture, Guangzhou, 510642, China
| | - Pei Li
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, Guangzhou, 510642, China.
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangzhou, 510642, China.
- South China Agricultural University, College of Forestry and Landscape Architecture, Guangzhou, 510642, China.
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Zhan X, Li P, Hui W, Deng Y, Gan S, Sun Y, Zhao X, Chen X, Deng X. Genetic diversity and population structure of Toona ciliatarevealed by simple sequence repeat markers. BIOTECHNOL BIOTEC EQ 2019. [DOI: 10.1080/13102818.2018.1561210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Affiliation(s)
- Xin Zhan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, PR China
| | - Pei Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, PR China
| | - Wenkai Hui
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, Sichuan, PR China
| | - Yanwen Deng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, PR China
| | - Siming Gan
- Key Laboratory of State Forestry Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, PR China
| | - Ye Sun
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, PR China
| | - Xianhai Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, PR China
| | - Xiaoyang Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, PR China
| | - Xiaomei Deng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, PR China
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Li P, Shang Y, Zhou W, Hu X, Mao W, Li J, Li J, Chen X. Development of an efficient regeneration system for the precious and fast-growing timber tree Toona ciliata. PLANT BIOTECHNOLOGY (TOKYO, JAPAN) 2018; 35:51-58. [PMID: 31275037 PMCID: PMC6543735 DOI: 10.5511/plantbiotechnology.18.0130a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 01/30/2018] [Indexed: 05/12/2023]
Abstract
Toona ciliata (Chinese mahogany) is an important timber species and secondary protected plant due to excessive exploitation in China. Here we developed a robust and efficient regeneration system for adventitious shoot induction using hypocotyl explants of T. ciliata. To facilitate plant growth, different regulators were added to Murashige-Skoog (MS) medium (0.5 mg/l 6-BA, 1.0 mg/l KT and 0.1 mg/l IBA). A regeneration frequency of 58.67% with four shoots per explant was achieved by horizontal setting of hypocotyls on MS medium and following a 20-day seeding period. MS medium supplemented with 0.3 mg/l 6-BA and 0.2 mg/l NAA was optimal for shoot multiplication and elongation, with a multiplication coefficient of 3.06. A rooting frequency of 93.33% was achieved using the half-strength MS containing 0.1 mg/l NAA. After acclimatization, plantlets were transplanted to sterilized nutrient soil containing a 2 : 1 ratio of vermiculate with 90% survival frequency. Thus, the regeneration system developed in this study would be useful for genetic transformation and other biotechnology endeavours in T. ciliata.
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Affiliation(s)
- Pei Li
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, Guangzhou 510642, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangzhou 510642, China
- South China Agricultural University, College of Forestry and Landscape Architecture, Guangzhou 510642, China
| | - Yuanyuan Shang
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, Guangzhou 510642, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangzhou 510642, China
- South China Agricultural University, College of Forestry and Landscape Architecture, Guangzhou 510642, China
| | - Wei Zhou
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, Guangzhou 510642, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangzhou 510642, China
- South China Agricultural University, College of Forestry and Landscape Architecture, Guangzhou 510642, China
| | - Xinsheng Hu
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, Guangzhou 510642, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangzhou 510642, China
- South China Agricultural University, College of Forestry and Landscape Architecture, Guangzhou 510642, China
| | - Wenmai Mao
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, Guangzhou 510642, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangzhou 510642, China
- South China Agricultural University, College of Forestry and Landscape Architecture, Guangzhou 510642, China
| | - Jingjian Li
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, Guangzhou 510642, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangzhou 510642, China
- South China Agricultural University, College of Forestry and Landscape Architecture, Guangzhou 510642, China
| | - Juncheng Li
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, Guangzhou 510642, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangzhou 510642, China
- South China Agricultural University, College of Forestry and Landscape Architecture, Guangzhou 510642, China
| | - Xiaoyang Chen
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, Guangzhou 510642, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangzhou 510642, China
- South China Agricultural University, College of Forestry and Landscape Architecture, Guangzhou 510642, China
- E-mail: , Tel: +86-20-8528-0001 Fax: +86-20-8528-2693
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Population Structure and Genetic Relationships of Melia Taxa in China Assayed with Sequence-Related Amplified Polymorphism (SRAP) Markers. FORESTS 2016. [DOI: 10.3390/f7040081] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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