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Hossain MA, Roslan HA. Heterologous expression, characterisation and 3D-structural insights of GH18 chitinases derived from sago palm (Metroxylon sagu). Int J Biol Macromol 2024; 279:135533. [PMID: 39265904 DOI: 10.1016/j.ijbiomac.2024.135533] [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: 12/07/2023] [Revised: 07/28/2024] [Accepted: 09/09/2024] [Indexed: 09/14/2024]
Abstract
Although plants don't have chitins, they produce chitinases to protect themselves from biotic and abiotic stressors. There are two forms of chitinases found in organisms: glycosyl hydrolase 18 (GH18) and 19 (GH19) families. Plant GH19 chitinases are well known for their role in protecting against pathogens, but the roles of GH18 chitinases have not been fully elucidated. This study aimed to produce and characterise two recombinant GH18 chitinases from Metroxylon sagu. Two GH18 chitinase genes, MsChi1 and MsChi2, were identified, with nucleotide sequences of 1009 and 1308 bp, respectively. The proteins encoded by MsChi1 and MsChi2 genes were single polypeptide chains of 310 and 300 amino acids with predicted molecular masses of 31.21 and 30.15 kDa, respectively. Both cDNAs were cloned and expressed in the GS115 strain of Pichia pastoris. Recombinant MsChi1 and MsChi2 exhibited optimal activity at 60 °C with acidic pH 4.0 and 5.0, respectively. Both recombinant enzymes could hydrolyze synthetic and natural substrates (colloidal chitin). rMsChi1 preferred 4-nitrophenol N,N'-diacetyl-β-D chitobioside, while rMsChi2 preferred 4-nitrophenol N,N',N″-triacetyl-β-D chitotriose, suggesting they might function as exochitinase and endochitinase, respectively. They also demonstrated antifungal activities against tested fungi. Homology modeling indicated ASP and GLU as essential residues for proton donation and acceptance.
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Affiliation(s)
- Md Anowar Hossain
- Genetic Engineering Laboratory, Faculty of Resource Science and Technology, Universiti Malaysia Sarawak, 94300 Kota Samarahan, Sarawak, Malaysia; Plant Molecular Biotechnology Laboratory, Department of Biochemistry and Molecular Biology, University of Rajshahi, Rajshahi 6205, Bangladesh.
| | - Hairul Azman Roslan
- Genetic Engineering Laboratory, Faculty of Resource Science and Technology, Universiti Malaysia Sarawak, 94300 Kota Samarahan, Sarawak, Malaysia.
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Al-Fakih GOA, Ilyas RA, Huzaifah MRM, El-Shafay AS. Recent advances in sago (Metroxylon sagu) fibres, biopolymers, biocomposites, and their prospective applications in industry: A comprehensive review. Int J Biol Macromol 2024; 269:132045. [PMID: 38710254 DOI: 10.1016/j.ijbiomac.2024.132045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 04/19/2024] [Accepted: 04/30/2024] [Indexed: 05/08/2024]
Abstract
Escalating petroleum depletion and environmental crises linked to conventional plastics have fueled interest in eco-friendly alternatives. Natural fibres and biopolymers are garnering increasing attention due to their sustainability. The sago palm (Metroxylon sagu), a tropical tree, holds potential for such materials, with cellulose-rich fibres (42.4-44.12 %) showcasing strong mechanics. Extracted sago palm starch can be blended, reinforced, or plasticised for improved traits. However, a comprehensive review of sago palm fibres, starch, and biocomposites is notably absent. This paper fills this void, meticulously assessing recent advancements in sago palm fibre, cellulose and starch properties, and their eco-friendly composite fabrication. Moreover, it uncovers the latent prospects of sago palm fibres and biopolymers across industries like automotive, packaging, and bioenergy. This review presents a crucial resource for envisaging and realising sustainable materials.
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Affiliation(s)
- Ghassan O A Al-Fakih
- Faculty of Chemical and Energy Engineering, Universiti Teknologi Malaysia, 81310 UTM Skudai, Johor, Malaysia.
| | - R A Ilyas
- Faculty of Chemical and Energy Engineering, Universiti Teknologi Malaysia, 81310 UTM Skudai, Johor, Malaysia; Centre for Advance Composite Materials (CACM), Faculty of Engineering, Universiti Teknologi Malaysia, Johor Bahru 81310, Malaysia; Institute of Tropical Forest and Forest Products (INTROP), Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia; Centre of Excellence for Biomass Utilization, Universiti Malaysia Perlis, 02600 Arau, Perlis.
| | - M R M Huzaifah
- Institute of Tropical Forest and Forest Products (INTROP), Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia; Department of Crop Science, Faculty of Agricultural and Forestry Sciences, Universiti Putra Malaysia Bintulu Campus, Bintulu 97008, Sarawak, Malaysia.
| | - A S El-Shafay
- Department of Mechanical Engineering, College of Engineering in Al-Kharj, Prince Sattam bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia; Mechanical Power Engineering Department, Faculty of Engineering, Mansoura University, Mansoura 35516, Egypt.
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Purwoko D, Zulaeha S, Tajuddin T, Mira FR, Solikhah MD, Rahmadara G, Hanifah NF, Rusmanto. In silico EST-SSR Identification and Development through EST Sequences from Metroxylon sagu Rottb. for Genetic Diversity Analysis. Trop Life Sci Res 2024; 35:13-32. [PMID: 39262857 PMCID: PMC11383630 DOI: 10.21315/tlsr2024.35.1.2] [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: 01/28/2023] [Accepted: 11/24/2023] [Indexed: 09/13/2024] Open
Abstract
Sago plant (Metroxylon sagu Rottb.) is one of the most carbohydrate-producing plants in the world. Microsatellites or simple sequence repeats (SSRs) play an important role in the genome and are used extensively compared to other molecular markers. For the first time, we are exploiting data expressed sequence tags (EST) of sago plants to identify and characterise markers in this species. EST data about sago plants are obtained through the EST database on the National Center for Biotechnology Information (NCBI) website. We obtained data of 458 Kb (412 contig) with a maximum and minimum length of 1,138 and 124 nucleotides, respectively. We successfully identified 820 perfectly patterned SSR using Phobos 3.3.12 software. The type characterisation of EST-SSR was dominated by tri-nucleotides 36% (294), followed by hexa-nucleotides 24% (202), tetra-nucleotides 15% (120), penta-nucleotides 13% (108) and di-nucleotides 12% (96). The most frequency of SSR motifs in each type is AG, AAG and AAAG. Analysis of synteny on the EST sequence with the online application Phytozome found that sequences were distributed on 12 Oryza sativa chromosomes with a likeness percentage between 63% to 100% and e-value between 0 to 0.094. We developed the primer and generated 19 primers. Furthermore, we validated 7 primers that all generated polymorphic alleles. To our knowledge, this report is the first identification and characterisation of EST-SSR for sago species and these markers can be used for genetic diversity analysis, marker assisted selection (MAS), cultivar identification, kinship analysis and genetic mapping analysis.
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Affiliation(s)
- Devit Purwoko
- Research Centre for Applied Botany, Research Organization for Life Sciences and Environment, National Research and Innovation Agency, Science and Technology Park of Soekarno, Cibinong, Bogor West Java 16911, Indonesia
| | - Siti Zulaeha
- Research Centre for Applied Botany, Research Organization for Life Sciences and Environment, National Research and Innovation Agency, Science and Technology Park of Soekarno, Cibinong, Bogor West Java 16911, Indonesia
| | - Teuku Tajuddin
- Research Centre for Applied Botany, Research Organization for Life Sciences and Environment, National Research and Innovation Agency, Science and Technology Park of Soekarno, Cibinong, Bogor West Java 16911, Indonesia
| | - Farida Rosana Mira
- Directorate of Laboratory Management, Building 630, Science and Technology Park of B. J. Habibie, Serpong, South Tangerang 15314, Indonesia
| | - Maharani Dewi Solikhah
- Research Centre for Energy Convention and Conservation, National Research and Innovation Agency, Science and Technology Park of B.J. Habibie, Serpong, South Tangerang 15314, Indonesia
| | - Gemilang Rahmadara
- Research Centre for Applied Botany, Research Organization for Life Sciences and Environment, National Research and Innovation Agency, Science and Technology Park of Soekarno, Cibinong, Bogor West Java 16911, Indonesia
| | - Nurul Fitri Hanifah
- Research Centre for Applied Botany, Research Organization for Life Sciences and Environment, National Research and Innovation Agency, Science and Technology Park of Soekarno, Cibinong, Bogor West Java 16911, Indonesia
| | - Rusmanto
- Research Centre for Energy Convention and Conservation, National Research and Innovation Agency, Science and Technology Park of B.J. Habibie, Serpong, South Tangerang 15314, Indonesia
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Tan C, Zhang H, Chen H, Guan M, Zhu Z, Cao X, Ge X, Zhu B, Chen D. First Report on Development of Genome-Wide Microsatellite Markers for Stock ( Matthiola incana L.). PLANTS (BASEL, SWITZERLAND) 2023; 12:748. [PMID: 36840095 PMCID: PMC9965543 DOI: 10.3390/plants12040748] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/30/2023] [Accepted: 02/02/2023] [Indexed: 06/18/2023]
Abstract
Stock (Matthiola incana (L.) R. Br.) is a famous annual ornamental plant with important ornamental and economic value. The lack of DNA molecular markers has limited genetic analysis, genome evolution, and marker-assisted selective breeding studies of M. incana. Therefore, more DNA markers are needed to support the further elucidation of the biology and genetics of M. incana. In this study, a high-quality genome of M. incana was initially assembled and a set of effective SSR primers was developed at the whole-genome level using genome data. A total of 45,612 loci of SSRs were identified; the di-nucleotide motifs were the most abundant (77.35%). In total, 43,540 primer pairs were designed, of which 300 were randomly selected for PCR validation, and as the success rate for amplification. In addition, 22 polymorphic SSR markers were used to analyze the genetic diversity of 40 stock varieties. Clustering analysis showed that all varieties could be divided into two clusters with a genetic distance of 0.68, which were highly consistent with their flower shape (potted or cut type). Moreover, we have verified that these SSR markers are effective and transferable within the Brassicaceae family. In this study, potential SSR molecular markers were successfully developed for 40 M. incana varieties using whole genome analysis, providing an important genetic tool for theoretical and applied research on M. incana.
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Affiliation(s)
- Chen Tan
- College of Life Sciences, Gannan Normal University, Ganzhou 341000, China
| | - Haimei Zhang
- College of Life Sciences, Gannan Normal University, Ganzhou 341000, China
| | - Haidong Chen
- College of Life Sciences, Gannan Normal University, Ganzhou 341000, China
| | - Miaotian Guan
- College of Life Sciences, Gannan Normal University, Ganzhou 341000, China
| | - Zhenzhi Zhu
- College of Life Sciences, Gannan Normal University, Ganzhou 341000, China
| | - Xueying Cao
- College of Life Sciences, Gannan Normal University, Ganzhou 341000, China
| | - Xianhong Ge
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 431700, China
| | - Bo Zhu
- College of Life Sciences, Gannan Normal University, Ganzhou 341000, China
| | - Daozong Chen
- College of Life Sciences, Gannan Normal University, Ganzhou 341000, China
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Varga F, Liber Z, Jakše J, Turudić A, Šatović Z, Radosavljević I, Jeran N, Grdiša M. Development of Microsatellite Markers for Tanacetum cinerariifolium (Trevis.) Sch. Bip., a Plant with a Large and Highly Repetitive Genome. PLANTS 2022; 11:plants11131778. [PMID: 35807729 PMCID: PMC9269103 DOI: 10.3390/plants11131778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 06/30/2022] [Accepted: 07/02/2022] [Indexed: 11/16/2022]
Abstract
Dalmatian pyrethrum (Tanacetum cinerariifolium (Trevis.) Sch. Bip.) is an outcrossing plant species (2n = 18) endemic to the eastern Adriatic coast and source of the natural insecticide pyrethrin. Due to the high repeatability and large genome (1C-value = 9.58 pg) our previous attempts to develop microsatellite markers using the traditional method were unsuccessful. Now we have used Illumina paired-end whole genome sequencing and developed a specific procedure to obtain useful microsatellite markers. A total of 796,130,142 high-quality reads (approx. 12.5× coverage) were assembled into 6,909,675 contigs using two approaches (de novo assembly and joining of overlapped pair-end reads). A total of 31,380 contigs contained one or more microsatellite sequences, of which di-(59.7%) and trinucleotide (25.9%) repeats were the most abundant. Contigs containing microsatellites were filtered according to various criteria to achieve better yield of functional markers. After two rounds of testing, 17 microsatellite markers were developed and characterized in one natural population. Twelve loci were selected for preliminary genetic diversity analysis of three natural populations. Neighbor-joining tree, based on the proportion of shared alleles distances, grouped individuals into clusters according to population affiliation. The availability of codominant SSR markers will allow analysis of genetic diversity and structure of natural Dalmatian pyrethrum populations as well as identification of breeding lines and cultivars.
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Affiliation(s)
- Filip Varga
- Department of Seed Science and Technology, Faculty of Agriculture, University of Zagreb, Svetošimunska c. 25, 10000 Zagreb, Croatia; (F.V.); (Z.Š.); (N.J.); (M.G.)
- Centre of Excellence for Biodiversity and Molecular Plant Breeding (CoE CroP-BioDiv), Svetošimunska c. 25, 10000 Zagreb, Croatia; (A.T.); (I.R.)
| | - Zlatko Liber
- Centre of Excellence for Biodiversity and Molecular Plant Breeding (CoE CroP-BioDiv), Svetošimunska c. 25, 10000 Zagreb, Croatia; (A.T.); (I.R.)
- Department of Biology, Faculty of Science, University of Zagreb, Marulićev trg 9a, 10000 Zagreb, Croatia
- Correspondence: ; Tel.: +385-1-4898-092
| | - Jernej Jakše
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000 Ljubljana, Slovenia;
| | - Ante Turudić
- Centre of Excellence for Biodiversity and Molecular Plant Breeding (CoE CroP-BioDiv), Svetošimunska c. 25, 10000 Zagreb, Croatia; (A.T.); (I.R.)
| | - Zlatko Šatović
- Department of Seed Science and Technology, Faculty of Agriculture, University of Zagreb, Svetošimunska c. 25, 10000 Zagreb, Croatia; (F.V.); (Z.Š.); (N.J.); (M.G.)
- Centre of Excellence for Biodiversity and Molecular Plant Breeding (CoE CroP-BioDiv), Svetošimunska c. 25, 10000 Zagreb, Croatia; (A.T.); (I.R.)
| | - Ivan Radosavljević
- Centre of Excellence for Biodiversity and Molecular Plant Breeding (CoE CroP-BioDiv), Svetošimunska c. 25, 10000 Zagreb, Croatia; (A.T.); (I.R.)
- Department of Biology, Faculty of Science, University of Zagreb, Marulićev trg 9a, 10000 Zagreb, Croatia
| | - Nina Jeran
- Department of Seed Science and Technology, Faculty of Agriculture, University of Zagreb, Svetošimunska c. 25, 10000 Zagreb, Croatia; (F.V.); (Z.Š.); (N.J.); (M.G.)
| | - Martina Grdiša
- Department of Seed Science and Technology, Faculty of Agriculture, University of Zagreb, Svetošimunska c. 25, 10000 Zagreb, Croatia; (F.V.); (Z.Š.); (N.J.); (M.G.)
- Centre of Excellence for Biodiversity and Molecular Plant Breeding (CoE CroP-BioDiv), Svetošimunska c. 25, 10000 Zagreb, Croatia; (A.T.); (I.R.)
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Su S, Zhu T, Su J, Li J, Zhao Q, Kang X, Zheng R. Transcriptome analysis of gibberellins and abscisic acid during the flooding response in Fokienia hodginsii. PLoS One 2022; 17:e0263530. [PMID: 35148337 PMCID: PMC8836328 DOI: 10.1371/journal.pone.0263530] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 01/21/2022] [Indexed: 11/19/2022] Open
Abstract
Flooding is one of the main abiotic stresses suffered by plants. Plants respond to flooding stress through regulating their morphological structure, endogenous hormone biosynthesis, and genetic signaling transduction. We previously found that Fokienia hodginsii varieties originating from Gutian exhibited typical flooding tolerance traits compared to three other provenances (Yongzhou, Sanming, Nanping), expressed as increased height, longer diameter at breast height (DBH), and smaller branch angle. Herein, the changes in endogenous gibberellins (GA) and abscisic acid (ABA) contents were measured under flooding stress in F. hodginsii, and ABA was found to decrease, whereas GA increased with time. Furthermore, the GA and ABA contents of the varieties originating from Gutian and the three other provenances were measured, and the results indicated that F. hodginsii from Gutian could respond more rapidly to flooding stress. The transcriptomes of the varieties originating from Gutian and the other three provenances were compared using RNA sequencing to explore the underlying genetic mechanisms of the flood-resistant phenotypes in F. hodginsii. The results indicated that two flood-stress response genes (TRINITY_DN142_c0_g2 and TRINITY_DN7657_c0_g1) were highly related to both the ABA and GA response in F. hodginsii.
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Affiliation(s)
- Shunde Su
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Timber Forest Breeding and Cultivation for Mountainous Areas in Southern China Key Laboratory of Forest Culture and Forest Product Processing Utilization of Fujian Province, Fuzhou, China
| | - Tengfei Zhu
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jun Su
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jian Li
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Qing Zhao
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xiangyang Kang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Renhua Zheng
- Key Laboratory of Timber Forest Breeding and Cultivation for Mountainous Areas in Southern China Key Laboratory of Forest Culture and Forest Product Processing Utilization of Fujian Province, Fuzhou, China
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Sarimana U, Herrero J, Erika P, Indarto N, Wendra F, Santika B, Ritter E, Sembiring Z, Asmono D. Analysis of genetic diversity and discrimination of Oil Palm DxP populations based on the origins of pisifera elite parents. BREEDING SCIENCE 2021; 71:134-143. [PMID: 34377061 PMCID: PMC8329876 DOI: 10.1270/jsbbs.20043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 09/29/2020] [Indexed: 06/13/2023]
Abstract
A total of 251 Dura cross Pisifera (DxP) hybrid palms from six populations descending from six parental African Pisifera origins and involving 12 progenies were analyzed with 19 selected Simple Sequence Repeats (SSR) markers. A total of 110 alleles were produced, ranging from three to eight per SSR, with a mean of 5.8 alleles per SSR locus. Of these, 68.5% were considered shared alleles by more than one population and the remaining 31.5% were population specific alleles. They generated between six and 21 haplotypes in all populations, and depending on the SSR marker, between one and 10 haplotypes within populations. Various parameters for analyzing genetic variability, differentiation and genetic structure were computed using GenAlEx, Structure and Darwin software. The obtained results confirmed microsatellites as a robust, feasible and trustful method for obtaining DNA fingerprints, tracing the source of oil palm samples. With respect to the authenticity of materials or for solving legitimacy issues, accession belonging to each population by SSR markers could be distinguished, but additional SSR should be screened for improving this process.
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Affiliation(s)
- Upit Sarimana
- Department Research and Development, PT Sampoerna Agro Tbk, Jln. Basuki Rahmat no. 788 Palembang 30127, Indonesia
| | - Javier Herrero
- NEIKER - Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Campus Agroalimentario de Arkaute s/n, 01192 Arkaute, Spain
| | - Pratiwi Erika
- Department Research and Development, PT Sampoerna Agro Tbk, Jln. Basuki Rahmat no. 788 Palembang 30127, Indonesia
| | - Nurcahyono Indarto
- Department Research and Development, PT Sampoerna Agro Tbk, Jln. Basuki Rahmat no. 788 Palembang 30127, Indonesia
| | - Fahmi Wendra
- Department Research and Development, PT Sampoerna Agro Tbk, Jln. Basuki Rahmat no. 788 Palembang 30127, Indonesia
| | - Baitha Santika
- Department Research and Development, PT Sampoerna Agro Tbk, Jln. Basuki Rahmat no. 788 Palembang 30127, Indonesia
| | - Enrique Ritter
- NEIKER - Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Campus Agroalimentario de Arkaute s/n, 01192 Arkaute, Spain
| | - Zulhermana Sembiring
- Department Research and Development, PT Sampoerna Agro Tbk, Jln. Basuki Rahmat no. 788 Palembang 30127, Indonesia
| | - Dwi Asmono
- Department Research and Development, PT Sampoerna Agro Tbk, Jln. Basuki Rahmat no. 788 Palembang 30127, Indonesia
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Kpatènon MJ, Salako KV, Santoni S, Zekraoui L, Latreille M, Tollon-Cordet C, Mariac C, Jaligot E, Beulé T, Adéoti K. Transferability, development of simple sequence repeat (SSR) markers and application to the analysis of genetic diversity and population structure of the African fan palm (Borassus aethiopum Mart.) in Benin. BMC Genet 2020; 21:145. [PMID: 33272218 PMCID: PMC7713368 DOI: 10.1186/s12863-020-00955-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 11/17/2020] [Indexed: 02/08/2023] Open
Abstract
Background In Sub-Saharan Africa, Borassus aethiopum Mart. (African fan palm) is an important non-timber forest product-providing palm that faces multiple anthropogenic threats to its genetic diversity. However, this species is so far under-studied, which prevents its sustainable development as a resource. The present work is a first attempt at characterizing the genetic diversity and population structure of B. aethiopum across nine collection sites spanning the three climatic regions of Benin, West Africa, through the use of microsatellite markers. Results During a first phase we relied on the reported transferability of primers developed in other palm species. We find that, in disagreement with previously published results, only 22.5% of the markers tested enable amplification of B. aethiopum DNA and polymorphism detection is very low. In a second phase, we generated a B. aethiopum-specific genomic dataset through high-throughput sequencing and used it for the de novo detection of microsatellite loci. Among the primer pairs targeting these, 11 detected polymorphisms and were further used for analyzing genetic diversity. Across the nine sites, expected heterozygosity (He) ranges from 0.263 to 0.451 with an overall average of 0.354, showing a low genetic diversity. Analysis of molecular variance (AMOVA) shows that within-site variation accounts for 53% of the genetic variation. Accordingly, the low number of migrants and positive values of the fixation index (F) in sites from both the Central (Sudano-Guinean) and the Southern (Guinean) climatic regions suggest limited gene flow between sites. The global correlation between genetic and geographic distances is weak; however, our clustering analyses indicate that B. aethiopum palms from Savè (Center) are genetically more similar to those from the North than to samples from other Central sites. Conclusions In the light of our results, we discuss the use of inter-species transfer vs. de novo development of microsatellite markers in genetic diversity analyses targeting under-studied species, and suggest future applications for our molecular resources. We propose that, while prominent short-range pollen and seed dispersal in Benin explain most of our results, gene flux between the Central and Northern regions, as a result of animal and/or human migrations, might underlie the Savè discrepancy. Supplementary Information The online version contains supplementary material available at 10.1186/s12863-020-00955-y.
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Affiliation(s)
- Mariano Joly Kpatènon
- Laboratoire de Microbiologie et de Technologie Alimentaire (LAMITA), Faculté des Sciences et Techniques, Université d'Abomey-Calavi, Cotonou, Bénin.,Biodiversité et Ecologie des Plantes (BDEP), Faculté des Sciences et Techniques, Université d'Abomey-Calavi, Cotonou, Bénin.,DIADE, Univ Montpellier, IRD, Montpellier, France
| | - Kolawolé Valère Salako
- Biodiversité et Ecologie des Plantes (BDEP), Faculté des Sciences et Techniques, Université d'Abomey-Calavi, Cotonou, Bénin.,Laboratoire de Biomathématiques et d'Estimations Forestières (LABEF), Faculté des Sciences Agronomiques, Université d'Abomey-Calavi, Cotonou, Bénin
| | - Sylvain Santoni
- AGAP, Univ Montpellier, CIRAD, INRAE, Montpellier SupAgro, Montpellier, France
| | | | - Muriel Latreille
- AGAP, Univ Montpellier, CIRAD, INRAE, Montpellier SupAgro, Montpellier, France
| | | | | | - Estelle Jaligot
- DIADE, Univ Montpellier, IRD, Montpellier, France.,CIRAD, UMR DIADE, Montpellier, France
| | - Thierry Beulé
- DIADE, Univ Montpellier, IRD, Montpellier, France.,CIRAD, UMR DIADE, Montpellier, France
| | - Kifouli Adéoti
- Laboratoire de Microbiologie et de Technologie Alimentaire (LAMITA), Faculté des Sciences et Techniques, Université d'Abomey-Calavi, Cotonou, Bénin. .,Biodiversité et Ecologie des Plantes (BDEP), Faculté des Sciences et Techniques, Université d'Abomey-Calavi, Cotonou, Bénin.
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