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Title: Developing genome-wide SNPs and constructing an ultrahigh-density linkage map in oil palm
Authors: Suwanto, Antonius
Chua, Nam-Hai
Yue, Gen Hua
Bai, Bin
Wang, Le
Zhang, Ying Jun
Lee, May
Rahmadsyah, Rahmadsyah
Alfiko, Yuzer
Ye, Bao Qing
Purwantomo, Sigit
Keywords: Oil Palm
Genome-wide SNPs
Issue Date: 2018
Source: Bai, B., Wang, L., Zhang, Y. J., Lee, M., Rahmadsyah, R., Alfiko, Y., et al. (2018). Developing genome-wide SNPs and constructing an ultrahigh-density linkage map in oil palm. Scientific Reports, 8(1), 691-.
Series/Report no.: Scientific Reports
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.
ISSN: 2045-2322
DOI: 10.1038/s41598-017-18613-2
Rights: © 2018 The Author(s) (Nature Publishing Group). This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit
Fulltext Permission: open
Fulltext Availability: With Fulltext
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