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

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.

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Restriction site-associated DNA sequencing for SNP discovery and high-density genetic map construction in southern catfish ( Silurus meridionalis )

Royal Society Open Science ◽

10.1098/rsos.172054 ◽

2018 ◽

Vol 5 (5) ◽

pp. 172054 ◽

Cited By ~ 5

Author(s):

Mimi Xie ◽

Yao Ming ◽

Feng Shao ◽

Jianbo Jian ◽

Yaoguang Zhang ◽

...

Keyword(s):

Linkage Map ◽

Genetic Map ◽

Restriction Site ◽

Genome Structure ◽

High Density ◽

Genetic Maps ◽

High Quality ◽

Silurus Meridionalis ◽

Map Construction ◽

High Density Linkage Map

Single-nucleotide polymorphism (SNP) markers and high-density genetic maps are important resources for marker-assisted selection, mapping of quantitative trait loci (QTLs) and genome structure analysis. Although linkage maps in certain catfish species have been obtained, high-density maps remain unavailable in the economically important southern catfish ( Silurus meridionalis ). Recently developed restriction site-associated DNA (RAD) markers have proved to be a promising tool for SNP detection and genetic map construction. The objective of the present study was to construct a high-density linkage map using SNPs generated by next-generation RAD sequencing in S. meridionalis for future genetic and genomic studies. An F1 population of 100 individuals was obtained by intraspecific crossing of two wild heterozygous individuals. In total, 77 634 putative high-quality bi-allelic SNPs between the parents were discovered by mapping the parents' paired-end RAD reads onto the reference contigs from both parents, of which 54.7% were transitions and 45.3% were transversions (transition/transversion ratio of 1.2). Finally, 26 714 high-quality RAD markers were grouped into 29 linkage groups by using de novo clustering methods (Stacks). Among these markers, 4514 were linked to the female genetic map, 23 718 to the male map and 6715 effective loci were linked to the integrated map spanning 5918.31 centimorgans (cM), with an average marker interval of 0.89 cM. High-resolution genetic maps are a useful tool for both marker-assisted breeding and various genome investigations in catfish, such as sequence assembly, gene localization, QTL detection and genome structure comparison. Hence, such a high-density linkage map will serve as a valuable resource for comparative genomics and fine-scale QTL mapping in catfish species.

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High-density genetic map construction and quantitative trait loci analysis of the stony hard phenotype in peach based on restriction-site associated DNA sequencing

BMC Genomics ◽

10.1186/s12864-018-4952-y ◽

2018 ◽

Vol 19 (1) ◽

Cited By ~ 7

Author(s):

Shaolei Guo ◽

Shahid Iqbal ◽

Ruijuan Ma ◽

Juan Song ◽

Mingliang Yu ◽

...

Keyword(s):

Quantitative Trait Loci ◽

Dna Sequencing ◽

Genetic Map ◽

Quantitative Trait ◽

Restriction Site ◽

High Density ◽

Map Construction ◽

Trait Loci ◽

Stony Hard

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

Journal of Oil Palm Research ◽

10.21894/jopr.2021.0009 ◽

2021 ◽

Author(s):

NURAZIYAN AZIMI

Keyword(s):

Mitochondrial Dna ◽

Oil Palm ◽

Dna Isolation ◽

Elaeis Guineensis ◽

Isolation Methods

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Genome-Wide Association Study (GWAS) for Bunch Components of The Interspecific Population of Elaeis oleifera and Elaeis guineensis

Jurnal Penelitian Kelapa Sawit ◽

10.22302/iopri.jur.jpks.v29i2.144 ◽

2021 ◽

Vol 29 (2) ◽

pp. 97-114

Author(s):

Heri Adriwan Siregar ◽

Edy Suprianto ◽

Sujadi Sujadi ◽

Hernawan Y Rahmadi ◽

Mohamad Arif ◽

...

Keyword(s):

Oil Palm ◽

Genome Wide Association Study ◽

Elaeis Guineensis ◽

Genotyping By Sequencing ◽

Breeding Program ◽

Phenotypic Data ◽

Single Nucleotide ◽

Elaeis Oleifera ◽

Genome Wide ◽

Alternative Approach

The oil palm breeding program for the species Elaeis guineensis and the backcross Elaeis oleifera is running slowly because oil palm is an annual plant. Therefore, it is necessary to have an alternative approach that can accelerate the oil palm breeding program. The SNP (single nucleotide polymorphism) genome-wide approach was then used to study the association between 18 phenotypes of bunch component in oil palm germplasm of E. oleifera from Suriname and Brazil Coari, some interspecific hybrids and some elite progeny of E. guineensis. The genotyping by sequencing (GBS) analysis produced a total of 459 million or approximately 798 thousand reads per sample and 3,252 SNPs were eligible for 456 genotypes. Using various association models, eleven normalized phenotypic data showed significant associations with 29 SNPs. Based on the annotations, 17 SNPs were related to genes wtih certain biological functions. Three SNPs were found to be at the exon of a gene, namely SNP4416, SNP349 and SNP3865, while the other 15 SNPs were at the intragenic to a gene. Four SNPs are common SNPs in phenotypes C16:0 and C18:1 as weel as in C20 0 and C20:1. This research shows the potential of SNPs that can be used as an alternative approach to E. oleifera backcross breeding, although further research is needed for validation purposes.

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

Seed Science and Technology ◽

10.15258/sst.2016.44.3.16 ◽

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

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

Jurnal Penelitian Kelapa Sawit ◽

10.22302/10.22302/iopri.jur.jpks.v25i1.22 ◽

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.

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Impact of oil palm (Elaeis guineensis Jacq.) cultivation on some chemical and microbiological properties of an ultisol

Biology and Fertility of Soils ◽

10.1007/bf00256992 ◽

1987 ◽

Vol 4 (3) ◽

Author(s):

N.O. Aisueni

Keyword(s):

Oil Palm ◽

Elaeis Guineensis ◽

Elaeis Guineensis Jacq ◽

Microbiological Properties

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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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