Genome-wide SNP discovery and identification of QTL associated with agronomic traits in oil palm using genotyping-by-sequencing (GBS)

Wirulda Pootakham; Nukoon Jomchai; Panthita Ruang-Areerate; Jeremy R Shearman; Chutima Sonthirod; Duangjai Sangsrakru; Somvong Tragoonrung; Sithichoke Tangphatsornruang

doi:10.1016/j.ygeno.2015.02.002

Genome-wide SNP discovery and identification of QTL associated with agronomic traits in oil palm using genotyping-by-sequencing (GBS)

Genomics. 2015 May;105(5-6):288-95. doi: 10.1016/j.ygeno.2015.02.002. Epub 2015 Feb 20.

Authors

Wirulda Pootakham¹, Nukoon Jomchai², Panthita Ruang-Areerate³, Jeremy R Shearman⁴, Chutima Sonthirod⁵, Duangjai Sangsrakru⁶, Somvong Tragoonrung⁷, Sithichoke Tangphatsornruang⁸

Affiliations

¹ National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Pathum Thani 12120, Thailand. Electronic address: wirulda@alumni.stanford.edu.
² National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Pathum Thani 12120, Thailand. Electronic address: nukoon.jom@biotec.or.th.
³ National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Pathum Thani 12120, Thailand. Electronic address: juntima.cha@biotec.or.th.
⁴ National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Pathum Thani 12120, Thailand. Electronic address: jeremy.she@biotec.or.th.
⁵ National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Pathum Thani 12120, Thailand. Electronic address: chutima.son@biotec.or.th.
⁶ National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Pathum Thani 12120, Thailand. Electronic address: duangjai@biotec.or.th.
⁷ National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Pathum Thani 12120, Thailand. Electronic address: somvong.tra@gmail.com.
⁸ National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Pathum Thani 12120, Thailand. Electronic address: sithichoke.tan@biotec.or.th.

PMID: 25702931
DOI: 10.1016/j.ygeno.2015.02.002

Abstract

Oil palm has become one of the most important oil crops in the world. Marker-assisted selections have played a pivotal role in oil palm breeding programs. Here, we report the use of genotyping-by-sequencing (GBS) approach for a large-scale SNP discovery and genotyping of a mapping population. Reduced representation libraries of 108 F2 progeny were sequenced and a total of 524 million reads were obtained. We detected 21,471 single nucleotide substitutions, most of which (62.6%) represented transition events. Of 3417 fully informative SNP markers, we were able to place 1085 on a linkage map, which spanned 1429.6 cM and had an average of one marker every 1.26 cM. Three QTL affecting trunk height were detected on LG 10, 14 and 15, whereas a single QTL associated with fruit bunch weight was identified on LG 3. The use of GBS approach proved to be rapid, cost-effective and highly reproducible in this species.

Keywords: Genetic linkage mapping; Genotyping-by-sequencing; Oil palm; Quantitative trait loci; Single nucleotide polymorphisms.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Genome, Plant*
Genotype*
Molecular Sequence Data
Palm Oil
Plant Oils / economics*
Polymorphism, Single Nucleotide*
Quantitative Trait Loci*
Trees / genetics*

Substances

Plant Oils
Palm Oil