Development and Validation of a High-Density SNP Genotyping Array for African Oil Palm
| Autor: | Mohaimi Mohamed, Chee Keng Teh, Ai Ling Ong, David Ross Appleton, Heng Leng Lee, Harikrishna Kulaveerasingam, Qi Bin Kwong, Sean Mayes, Huey Ying Heng, Fook Tim Chew, Sukganah Apparow, Martti T. Tammi, Joel Zi-Bin Low |
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| Rok vydání: | 2016 |
| Předmět: |
0301 basic medicine
Genotype Quantitative Trait Loci Population Single-nucleotide polymorphism Genome-wide association study Plant Science Arecaceae Biology Polymorphism Single Nucleotide Linkage Disequilibrium 03 medical and health sciences Elaeis oleifera education Molecular Biology Genotyping Genetics education.field_of_study Chromosome Mapping Tag SNP biology.organism_classification SNP genotyping 030104 developmental biology oil palm whole-genome SNP array genome-wide association study genomic selection genetic fixation genome-wide linkage disequilibrium Genome Plant Genome-Wide Association Study SNP array |
| Zdroj: | Molecular Plant. 9:1132-1141 |
| ISSN: | 1674-2052 1752-9867 |
| Popis: | 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 of3 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 r(2) = 0.43 to 146 kb at r(2) = 0.50) when compared with the semi-wild populations (19.5 kb at r(2) = 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. |
| Databáze: | OpenAIRE |
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