Development and validation of a high-density SNP genotyping array for African Oil Palm

Kwong, Qi Bin and Teh, Chee Keng and Ong, Ai Ling and Heng, Huey Ying and Lee, Heng Leng and Mohamed, Mohaimi and Low, Joel Zi-Bin and Apparow, Sukganah and Chew, Fook Tim and Mayes, Sean and Kulaveerasingam, Harikrishna and Tammi, Martti and Appleton, David Ross (2016) Development and validation of a high-density SNP genotyping array for African Oil Palm. Molecular Plant, 9 (8). pp. 1132-1141. ISSN 1752-9867

[img]
Preview
PDF - Requires a PDF viewer such as GSview, Xpdf or Adobe Acrobat Reader
Download (2MB) | Preview

Abstract

High-density single nucleotide polymorphism (SNP) genotyping arrays are powerful tools that can measure the level of genetic polymorphism within a population. To develop a whole-genome SNP array for oil palms, SNP discovery was performed using deep resequencing of eight libraries derived from 132 Elaeis guineensis and Elaeis oleifera palms belonging to 59 origins, resulting in the discovery of >3 million putative SNPs. After SNP filtering, the Illumina OP200K custom array was built with 170 860 successful probes. Phenetic clustering analysis revealed that the array could distinguish between palms of different origins in a way consistent with pedigree records. Genome-wide linkage disequilibrium declined more slowly for the commercial populations (ranging from 120 kb at r2 = 0.43 to 146 kb at r2 = 0.50) when compared with the semi-wild populations (19.5 kb at r2 = 0.22). Genetic fixation mapping comparing the semi-wild and commercial population identified 321 selective sweeps. A genome-wide association study (GWAS) detected a significant peak on chromosome 2 associated with the polygenic component of the shell thickness trait (based on the trait shell-to-fruit; S/F %) in tenera palms. Testing of a genomic selection model on the same trait resulted in good prediction accuracy (r = 0.65) with 42% of the S/F%variation explained. The first high-density SNP genotyping array for oil palm has been developed and shown to be robust for use in genetic studies and with potential for developing early trait prediction to shorten the oil palm breeding cycle.

Item Type: Article
Keywords: oil palm, whole-genome SNP array, genome-wide association study, genomic selection, genetic fixation, genome-wide linkage disequilibrium
Schools/Departments: University of Nottingham, UK > Faculty of Science > School of Biosciences > Division of Plant and Crop Sciences
Identification Number: 10.1016/j.molp.2016.04.010
Depositing User: Mayes, Sean
Date Deposited: 04 Sep 2017 09:41
Last Modified: 05 Sep 2017 08:48
URI: http://eprints.nottingham.ac.uk/id/eprint/45372

Actions (Archive Staff Only)

Edit View Edit View