title: Genome-wide SNP discovery and identification of QTL associated with agronomic traits in oil palm using genotyping-by-sequencing (GBS).
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.
authors.affiliation: National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Pathum Thani 12120, Thailand. Electronic address: wirulda@alumni.stanford.edu.
authors.forename: Wirulda
authors.initials: W
authors.lastname: Pootakham
authors.affiliation: National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Pathum Thani 12120, Thailand. Electronic address: nukoon.jom@biotec.or.th.
authors.forename: Nukoon
authors.initials: N
authors.lastname: Jomchai
authors.affiliation: National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Pathum Thani 12120, Thailand. Electronic address: juntima.cha@biotec.or.th.
authors.forename: Panthita
authors.initials: P
authors.lastname: Ruang-Areerate
authors.affiliation: National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Pathum Thani 12120, Thailand. Electronic address: jeremy.she@biotec.or.th.
authors.forename: Jeremy R
authors.initials: JR
authors.lastname: Shearman
authors.affiliation: National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Pathum Thani 12120, Thailand. Electronic address: chutima.son@biotec.or.th.
authors.forename: Chutima
authors.initials: C
authors.lastname: Sonthirod
authors.affiliation: National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Pathum Thani 12120, Thailand. Electronic address: duangjai@biotec.or.th.
authors.forename: Duangjai
authors.initials: D
authors.lastname: Sangsrakru
authors.affiliation: National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Pathum Thani 12120, Thailand. Electronic address: somvong.tra@gmail.com.
authors.forename: Somvong
authors.initials: S
authors.lastname: Tragoonrung
authors.affiliation: National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Pathum Thani 12120, Thailand. Electronic address: sithichoke.tan@biotec.or.th.
authors.forename: Sithichoke
authors.initials: S
authors.lastname: Tangphatsornruang
mesh_terms: D018745:Genome, Plant; D005838:Genotype; D008969:Molecular Sequence Data; D000073878:Palm Oil; D010938:Plant Oils / Q000191:economics*; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D014197:Trees / Q000235:genetics*
chemical_list: D010938:Plant Oils; D000073878:Palm Oil
keywords: Genetic linkage mapping; Genotyping-by-sequencing; Oil palm; Quantitative trait loci; Single nucleotide polymorphisms