Developing genome-wide SNPs and constructing an ultrahigh-density linkage map in oil palm

Abstract

Oil palm (Elaeis guineensis Jacq.) is the leading oil-producing crops and the most important edible oil resource worldwide. DNA markers and genetic linkage maps are essential resources for marker-assisted selection to accelerate genetic improvement. We conducted RAD-seq on an Illumina NextSeq500 to discover genome-wide SNPs, and used the SNPs to construct a linkage map for an oil palm (Tenera) population derived from a cross between a Deli Dura and an AVROS Pisifera. The RAD-seq produced 1,076 million single-end reads across the breeding population containing 155 trees. Mining this dataset detected 510,251 loci. After filtering out loci with low accuracy and more than 20% missing data, 11,394 SNPs were retained. Using these SNPs, in combination with 188 anchor SNPs and 123 microsatellites, we constructed a linkage map containing 10,023 markers covering 16 chromosomes. The map length is 2,938.2 cM with an average marker space of 0.29 cM. The large number of SNPs will supply ample choices of DNA markers in analysing the genetic diversity, population structure and evolution of oil palm. This high-density linkage map will contribute to mapping quantitative trait loci (QTL) for important traits, thus accelerating oil palm genetic improvement.

OIL PALM ECONOMIC PERFORMANCE IN MALAYSIA AND R&D PROGRESS IN 2018

“…The bacterial culture produced three families of ACL namely iturin, surfactin and fengycin with strong anti-fungal activity against Ganoderma (Pramudito et al, 2018). Similarly, Lee et al (2018a) characterised phenazine and phenazine-1-carboxylic acid isolated from Pseudomonas aeuruginosa with anti-microbial activity against G. boninense. Another interesting study conducted by Surendran et al (2018a, b) reported that naturally occurring phenolics acids such as benzoic acid and salicylic acids were able to suppress the enzymatic secretion of Ganoderma spp.…”

“…In this respect, the earlier publications of the genome (Singh et al, 2013a, b) and epigenome (Ong-Abdullah et al, 2015) have continued to fuel further research in oil palm. Bai et al (2018a) developed genome-wide single nucleotide polymorphisms (SNP) and constructed an ultrahigh-density linkage map using the revolutionary restriction-site associated DNA sequencing (RAD-seq) technology. This technology allowed higher frequency of SNP discovery of at least more than 10 000 as compared to the 2000 to 3500 SNP from previous studies (Pootakham et al, 2015;Bai et al, 2017), was modified for use on a highly heterogenous oil palm breeding population.…”

“…In an unrelated study, transcriptome profiling of pollens from dura, pisifera and tenera of E. guineensis was performed to understand the molecular mechanism related to pollen germination. It was found that tenera and pisifera share rather significant similarities between them which could infer that the regulation of pollen germination in tenera and pisifera may be genetically identical (Wang et al, 2018a, b).…”

Experimental validation of in silico predicted RAD locus frequencies using genomic resources and short read data from a model marine mammal

“…The resulting sequence reads are then aligned either de novo or to a reference genome, to generate RAD loci that are interrogated for single nucleotide polymorphisms (SNPs). These in turn provide the basis for diverse applications from linkage and association mapping [3, 4], through elucidating population structure and patterns of introgression [5, 6] to quantifying inbreeding depression [7].…”

Deciphering key proteins of oil palm (Elaeis guineensis Jacq.) fruit mesocarp development by proteomics and chemometrics

“…Oil palm ( E. guineensis ) is the most valuable vegetable oil crop that contributes significantly to the food requirements of the world's growing population which is expected to reach 240 million tons by 2050 . Fruit mesocarp can produce palm oil up to 90% of dry weight, thus representing the highest lipid content compared with other oilseeds .…”