Development and Validation of a High-Density SNP Genotyping Array for African Oil Palm

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• 作者：Qi Bin Kwong¹ ; ^{kwong.qi.bin@simedarby.com" class="auth_mail" title="E-mail the corresponding author} ; Chee Keng Teh¹ ; Ai Ling Ong¹ ; Huey Ying Heng¹ ; Heng Leng Lee¹ ; Mohaimi Mohamed¹ ; Joel Zi-Bin Low¹ ; Sukganah Apparow¹ ; Fook Tim Chew² ; Sean Mayes³ ; Harikrishna Kulaveerasingam¹ ; Martti Tammi¹ ; David Ross Appleton¹
• 关键词：oil palm ; whole-genome SNP array ; genome-wide association study ; genomic selection ; genetic fixation ; genome-wide linkage disequilibrium
• 刊名：Molecular Plant
• 出版年：2016
• 出版时间：1 August 2016
• 年：2016
• 卷：9
• 期：8
• 页码：1132-1141
• 全文大小：1026 K

文摘

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.