Multiplexed inter-simple sequence repeat genotyping by sequencing (mig-seq) of nut producing Rubroshorea and Shorea species

Abstract

Engkabang nuts from two Dipterocarpaceae genera, Rubroshorea and Shorea, are collected from semi-managed or wild trees in Borneo to produce oil (tengkawang and terendek oils) and vegetable fat (illipe butter) for own consumption or to be sold locally. Although the nuts of these species display similar fatty acid profiles, the species exhibit diverse morphological and physiological features which are influenced by DNA polymorphisms responsible for the differences in traits among these species. In this study, we determined genome-wide single-nucleotide polymorphisms (SNPs) among geographically diverse Engkabang accessions using the Multiplexed Inter-Simple Sequence Repeat Genotyping by Sequencing (MIG-seq) method. A total of 1,160 SNPs was identified in a collection of ninety-six Engkabang accessions of Rubroshorea macrophylla, R. splendida, and Shorea seminis from Sarawak. Genetic diversity analyses, based on the common SNP sites, divided R. macrophylla accessions into two main groups, Central Sarawak and West Sarawak (R. splendida and S. seminis embedded within). Single-nucleotide polymorphisms data generated in this work will facilitate further genetic studies on Engkabang breeding and production of DNA markers.