Genetic diversity and structure of Ganoderma boninense isolates from oil palm and other plantation crops

Abstract. Purba A, Hayati R, Putri LAP, Chalil D, Afandi D, Syahputra I, Basyuni M. 2020. Genetic diversity and structure of Ganoderma boninense isolates from oil palm and other plantation crops. Biodiversitas 21: 451-456. Oil palm is an economically important plant, which one of the most important sources of vegetable oil in the world. However, oil palm plantation and other crops face the treat basal stem rot (BSR) disease by Ganoderma boninense. A study on genetic diversity and structure of G. boninense is therefore needed in order to formulate improved control strategies for this disease. This work aimed to analyze the genetic diversity and structure of the G. boninense isolates derived from different hosts, 131 oil palm (Elaeis guineensis), six rubber (Hevea brasiliensis), three coconuts (Cocos nucifera), and three lontar palm (Borassus flabellifer). Genetic diversity and population structure of G. boninense isolates were investigated using six SSR markers with GenAlex 6.502 software. Results showed that several microsatellite loci indicated specific primary success rates, such as KT124402, KT124399, and KT124394, depicting high polymorphism content (>75%). This result suggested that these markers were equally effective in determining the polymorphisms of G. boninense isolates. A hierarchical analysis of molecular variance (AMOVA) revealed that genetic diversity mostly found among individuals within a population (88%), then among populations (8%), and within individuals (4%).. Phylogeny analysis showed two clusters of Ganoderma isolates. which was considered variation as dissimilar across with origin. The present study indicated that G. boninense from oil palm was predominantly comprised of a genetically distinct individual.

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Genetic diversity and gene flow amongst admixed populations of Ganoderma boninense, causal agent of basal stem rot in African oil palm (Elaeis guineensis Jacq.) in Sarawak (Malaysia), Peninsular Malaysia, and Sumatra (Indonesia)

Mycologia ◽

10.1080/00275514.2021.1884815 ◽

2021 ◽

pp. 1-16

Author(s):

W. C. Wong ◽

H. J. Tung ◽

M. Nurul Fadhilah ◽

F. Midot ◽

S. Y. L. Lau ◽

...

Keyword(s):

Genetic Diversity ◽

Gene Flow ◽

Oil Palm ◽

Elaeis Guineensis ◽

Peninsular Malaysia ◽

Causal Agent ◽

Stem Rot ◽

Ganoderma Boninense ◽

Basal Stem Rot ◽

African Oil Palm

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Genetic Diversity and Population Structure of Field Isolates of Ganoderma Boninense from Oil Palm Plantation in Solomon Islands

Proceedings ◽

10.3390/proceedings2019036056 ◽

2020 ◽

Vol 36 (1) ◽

pp. 56

Author(s):

Mudge ◽

Rama ◽

Pilotti ◽

Godwin

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Oil Palm ◽

Elaeis Guineensis ◽

Solomon Islands ◽

Economic Importance ◽

Ganoderma Boninense ◽

Perennial Crop ◽

Great Economic Importance

Oil palm (Elaeis guineensis Jacq.) is a long-term perennial crop of great economic importance to [...]

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Assessment of genetic diversity and population structure of oil palm (Elaeis guineensis Jacq.) field genebank: A step towards molecular-assisted germplasm conservation

PLoS ONE ◽

10.1371/journal.pone.0255418 ◽

2021 ◽

Vol 16 (7) ◽

pp. e0255418

Author(s):

Siou Ting Gan ◽

Chin Jit Teo ◽

Shobana Manirasa ◽

Wei Chee Wong ◽

Choo Kien Wong

Keyword(s):

Genetic Diversity ◽

Genetic Distance ◽

Oil Palm ◽

Core Collection ◽

Elaeis Guineensis ◽

Germplasm Conservation ◽

Ex Situ ◽

Fixation Index ◽

Core Set ◽

Genetic Diversity And Structure

Oil palm (Elaeis guineensis) germplasm is exclusively maintained as ex situ living collections in the field for genetic conservation and evaluation. However, this is not for long term and the maintenance of field genebanks is expensive and challenging. Large area of land is required and the germplasms are exposed to extreme weather conditions and casualty from pests and diseases. By using 107 SSR markers, this study aimed to examine the genetic diversity and relatedness of 186 palms from a Nigerian-based oil palm germplasm and to identify core collection for conservation. On average, 8.67 alleles per SSR locus were scored with average effective number of alleles per population ranging from 1.96 to 3.34 and private alleles were detected in all populations. Mean expected heterozygosity was 0.576 ranging from 0.437 to 0.661 and the Wright’s fixation index calculated was -0.110. Overall moderate genetic differentiation among populations was detected (mean pairwise population FST = 0.120, gene flow Nm = 1.117 and Nei’s genetic distance = 0.466) and this was further confirmed by AMOVA analysis. UPGMA dendogram and Bayesian structure analysis concomitantly clustered the 12 populations into eight genetic groups. The best core collection assembled by Core Hunter ver. 3.2.1 consisted of 58 palms accounting for 31.2% of the original population, which was a smaller core set than using PowerCore 1.0. This core set attained perfect allelic coverage with good representation, high genetic distance between entries, and maintained genetic diversity and structure of the germplasm. This study reported the first molecular characterization and validation of core collections for oil palm field genebank. The established core collection via molecular approach, which captures maximum genetic diversity with minimum redundancy, would allow effective use of genetic resources for introgression and for sustainable oil palm germplasm conservation. The way forward to efficiently conserve the field genebanks into next generation without losing their diversity was further discussed.

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The chitinase activity of oil palm (Elaeis guineensis Jacq.) roots against fungal endophytes and pathogenic Ganoderma boninense

Plant Omics ◽

10.21475/poj.10.05.17.pne853 ◽

2017 ◽

Vol 10 (05) ◽

pp. 247-251 ◽

Cited By ~ 2

Author(s):

Yurnaliza ◽

◽

Rizkita Rachmi Esyanti ◽

Agus Susanto ◽

I Nyoman Pugeg Aryantha ◽

...

Keyword(s):

Oil Palm ◽

Elaeis Guineensis ◽

Fungal Endophytes ◽

Chitinase Activity ◽

Ganoderma Boninense ◽

Elaeis Guineensis Jacq

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EgJUB1 and EgERF113 transcription factors as potential master regulators of defense response in Elaeis guineensis against the hemibiotrophic Ganoderma boninense

BMC Plant Biology ◽

10.1186/s12870-020-02812-7 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Nurshafika Mohd Sakeh ◽

Siti Nor Akmar Abdullah ◽

Mohammad Nazri Abdul Bahari ◽

Azzreena Mohamad Azzeme ◽

Noor Azmi Shaharuddin ◽

...

Keyword(s):

Transcription Factors ◽

Oil Palm ◽

Defense Response ◽

Fungal Pathogen ◽

Defense Mechanism ◽

Elaeis Guineensis ◽

Expression Profiles ◽

Present Report ◽

Ganoderma Boninense ◽

Cell Wall Modification

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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Genetic diversity and population structure of Plasmodium falciparum in Nigeria: insights from microsatellite loci analysis

Malaria Journal ◽

10.1186/s12936-021-03734-x ◽

2021 ◽

Vol 20 (1) ◽

Author(s):

Fehintola V. Ajogbasile ◽

Adeyemi T. Kayode ◽

Paul E. Oluniyi ◽

Kazeem O. Akano ◽

Jessica N. Uwanibe ◽

...

Keyword(s):

Genetic Diversity ◽

Plasmodium Falciparum ◽

Population Structure ◽

Microsatellite Loci ◽

Control Strategies ◽

Population Diversity ◽

Parasite Population ◽

Nested Polymerase Chain Reaction ◽

Public Health Burden ◽

Genetic Diversity And Structure

Abstract Background Malaria remains a public health burden especially in Nigeria. To develop new malaria control and elimination strategies or refine existing ones, understanding parasite population diversity and transmission patterns is crucial. Methods In this study, characterization of the parasite diversity and structure of Plasmodium falciparum isolates from 633 dried blood spot samples in Nigeria was carried out using 12 microsatellite loci of P. falciparum. These microsatellite loci were amplified via semi-nested polymerase chain reaction (PCR) and fragments were analysed using population genetic tools. Results Estimates of parasite genetic diversity, such as mean number of different alleles (13.52), effective alleles (7.13), allelic richness (11.15) and expected heterozygosity (0.804), were high. Overall linkage disequilibrium was weak (0.006, P < 0.001). Parasite population structure was low (Fst: 0.008–0.105, AMOVA: 0.039). Conclusion The high level of parasite genetic diversity and low population structuring in this study suggests that parasite populations circulating in Nigeria are homogenous. However, higher resolution methods, such as the 24 SNP barcode and whole genome sequencing, may capture more specific parasite genetic signatures circulating in the country. The results obtained can be used as a baseline for parasite genetic diversity and structure, aiding in the formulation of appropriate therapeutic and control strategies in Nigeria.

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