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Title: Developing genome-wide SNPs and constructing an ultrahigh-density linkage map in oil palm
Authors: Bai, B
Wang, L 
Zhang, Y.J
Lee, M
Rahmadsyah, R
Alfiko, Y
Ye, B.Q
Purwantomo, S
Suwanto, A
Chua, N.-H 
Yue, G.H 
Keywords: article
dura mater
genetic improvement
genetic linkage
genetic marker
genetic variability
population structure
quantitative trait locus
Issue Date: 2018
Publisher: Nature Publishing Group
Citation: Bai, B, Wang, L, Zhang, Y.J, Lee, M, Rahmadsyah, R, Alfiko, Y, Ye, B.Q, Purwantomo, S, Suwanto, A, Chua, N.-H, Yue, G.H (2018). Developing genome-wide SNPs and constructing an ultrahigh-density linkage map in oil palm. Scientific Reports 8 (1) : 691. ScholarBank@NUS Repository.
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. © 2018 The Author(s).
Source Title: Scientific Reports
ISSN: 2045-2322
DOI: 10.1038/s41598-017-18613-2
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