scholarly journals EVALUATION OF MITOCHONDRIAL DNA ISOLATION METHODS FOR OIL PALM (Elaeis guineensis) LEAF

2021 ◽  
Author(s):  
NURAZIYAN AZIMI
Keyword(s):  
Mitochondrial Dna ◽  
Oil Palm ◽  
Dna Isolation ◽  
Elaeis Guineensis ◽  
Isolation Methods

scholarly journals Biased nicking of mitochondrial DNA during extraction can be avoided by choice of isolation method

2021 ◽  
Author(s):  
Bruno Marçal Repolês ◽  
Choco Michael Gorospe ◽  
Phong Tran ◽  
Anna Karin Nilsson ◽  
Paulina H. Wanrooij
Keyword(s):  
Skeletal Muscle ◽  
Mitochondrial Dna ◽  
Dna Isolation ◽  
Isolation Procedure ◽  
Isolation Method ◽  
Strand Breaks ◽  
Careful Choice ◽  
Isolation Methods ◽  
Solid Tissues ◽  
Long Range Pcr

AbstractThe integrity of mitochondrial DNA (mtDNA) isolated from solid tissues is critical for analyses such as long-range PCR. We show that a commonly-used DNA isolation procedure preferentially introduces strand breaks into the mtDNA extracted from the skeletal muscle of aged mice, while mtDNA from adult animals is less affected. We present a comparison of mtDNA isolation methods and identify one that avoids this biased loss of muscle mtDNA integrity. Our results highlight the importance of a careful choice of mtDNA isolation method and serve as a resource to researchers planning analysis of mtDNA isolated from solid tissues.

GENETIC MAP CONSTRUCTION OF IOPRI'S OIL PALM (Elaeis guineensis JACQ.) MAPPING POPULATION DERIVED FROM SP540T BY USING RESTRICTION SITE ASSOCIATED DNA (RAD) MARKERS

2018 ◽  
Vol 25 (1) ◽  
pp. 11-20
Author(s):  
Retno Diah Setiowati ◽  
Enrique Ritter ◽  
Sri Wening ◽  
Yurna Yenni ◽  
Edy Suprianto
Keyword(s):  
Genetic Map ◽  
Oil Palm ◽  
Dna Isolation ◽  
Restriction Site ◽  
Elaeis Guineensis ◽  
Breeding Strategy ◽  
Phenotypic Data ◽  
Map Construction ◽  
Functional Map ◽  
Biology Laboratory

Construction of genetic linkage on oil palm derived SP540T was established in 2012-2015 in colaboration with PPKS, Indonesia with Neiker, Spain. DNA isolation was conducted in Molecular Biology Laboratory in PPKS Marihat meanwhile RAD analysis was performed in Laboratorio Biotecnologia Vegetal, Neiker, Spain. Genetic map construction was carried out using Restriction Site Associated DNA. A total 532 RAD fragments were applied to configure 16 Linkage Groups (LGs) which represented 16 chromosomes of oil palm. The map spans in 1269.9 map unit (mU) or 79.37 mU per chromosome in average and consists of RAD fragments which could be blasted to the DNA data base to identify candidate genes. Genenic map which had been formed is a fondation of constructing an IOPRI functional map (IOPRImap) when it is integrated with phenotypic data. The IOPRImap is expected to facilitate shortening oil palm selection cycle and defining a precise oil palm breeding strategy.

GENETIC MAP CONSTRUCTION OF IOPRI'S OIL PALM (Elaeis guineensis JACQ.) MAPPING POPULATION DERIVED FROM SP540T BY USING RESTRICTION SITE ASSOCIATED DNA (RAD) MARKERS

2017 ◽  
Vol 25 (1) ◽  
pp. 11-20
Author(s):  
Retno Diah Setiowati ◽  
Enrique Ritter ◽  
Sri Wening ◽  
Yurna Yenni ◽  
Edy Suprianto
Keyword(s):  
Genetic Map ◽  
Oil Palm ◽  
Dna Isolation ◽  
Restriction Site ◽  
Elaeis Guineensis ◽  
Breeding Strategy ◽  
Phenotypic Data ◽  
Map Construction ◽  
Functional Map ◽  
Biology Laboratory

Construction of genetic linkage on oil palm derived SP540T was established in 2012-2015 in colaboration with PPKS, Indonesia with Neiker, Spain. DNA isolation was conducted in Molecular Biology Laboratory in PPKS Marihat meanwhile RAD analysis was performed in Laboratorio Biotecnologia Vegetal, Neiker, Spain. Genetic map construction was carried out using Restriction Site Associated DNA. A total 532 RAD fragments were applied to configure 16 Linkage Groups (LGs) which represented 16 chromosomes of oil palm. The map spans in 1269.9 map unit (mU) or 79.37 mU per chromosome in average and consists of RAD fragments which could be blasted to the DNA data base to identify candidate genes. Genenic map which had been formed is a fondation of constructing an IOPRI functional map (IOPRImap) when it is integrated with phenotypic data. The IOPRImap is expected to facilitate shortening oil palm selection cycle and defining a precise oil palm breeding strategy.

Effect of chemicals on disintegration of the operculum in oil palm (Elaeis guineensis) seeds for early germination

2016 ◽  
Vol 44 (3) ◽  
pp. 475-485
Author(s):  
G. Ravichandran ◽  
P. Murugesan ◽  
P. Naveen Kumar ◽  
R.K. Mathur ◽  
D. Ramajayam
Keyword(s):  
Oil Palm ◽  
Elaeis Guineensis ◽  
Early Germination

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

Plant Omics ◽  
2017 ◽  
Vol 10 (05) ◽  
pp. 247-251 ◽  
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

LEGITIMACY OF PROGENIES USING SSR MARKERS AS CONTROLLING SYSTEM AND EARLIER SELECTION IN THE OIL PALM NURSERY (Elaeis guineensis JACQ.)

2018 ◽  
Vol 25 (1) ◽  
pp. 21-30
Author(s):  
Rokhana Faizah ◽  
Sri Wening ◽  
Abdul Razak Purba
Keyword(s):  
Dna Fingerprinting ◽  
Ssr Markers ◽  
Oil Palm ◽  
Dna Markers ◽  
Elaeis Guineensis ◽  
Gene Marker ◽  
Controlling System ◽  
Crossing Probability ◽  
Simple Sequence

Information of legitimacy of oil palm progenies is important to guaranty the quality and to control commercial seeds procedures. A true and legitimate cross will produce progeny which has a combination of their parent's allele. The information could be obtained early in the nursery stage through DNA fingerprinting analysis. Simple Sequence Repeats (SSR) is one of DNA markers used for DNA fingerprinting, since the marker system has advantages to acquire information of allele per individual in population and efficiency diverse allele of progeny and their parents. The aim of the research is to obtain legitimacy of 12 progenies analyzing in the oil palm nursery stage. Thirteen SSR markers were used to analyze 12 crossings number of oil palm. The genotypes data by alleles of SSR inferred and quantified using Gene Marker® Software version 2.4.0 Soft Genetics® LLC and analyzed based on Mendel's Law of Segregation. The result showed based on heredity pattern of progeny and their parent's allele that progenies H were indicated genetically derived from their known parents while progenies from A and G indicated as illegitimate crossing. Probability value for legitimacy of progenies of 9 other crosses has 0.031 and 0.5. Legitimacy analysis of progeny using SSR markers could be used to control the quality of crossing material and earlier selection in the oil palm nursery.

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

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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