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

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 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.

Development and Evaluation of a High Density Genotyping ‘Axiom_Arachis’ Array with 58 K SNPs for Accelerating Genetics and Breeding in Groundnut

“…Also this array achieved high density genome coverage of 1 SNP per 42 Kb in tetraploid genome while 1 SNP per 36 Kb in A subgenome and 1 SNP per 48 Kb in B subgenome. The above density is comparable to other recently developed SNP arrays in maize7, rice6 and oil palm21.…”

Characterizing haploinsufficiency of SHELL gene to improve fruit form prediction in introgressive hybrids of oil palm

“…As the first phase of validation, three fruit forms (120 dura , 305 tenera and 162 pisifera ) belonging to four paternal stocks were selected (Table 1). The genetic stratification of the 587 palms was determined through principal component analysis (PCA) based on our OP200K genotyping array 7 . Four main clusters i.e.…”

Breeding the oil palm (Elaeis guineensisJacq.) for climate change

“…In recent years, there has been an exponential increase in molecular resources and methods to identify polymorphisms controlling the characteristics of interest and to explore the mechanisms linking these polymorphisms to phenotypes. This is particularly the case for the oil palm (Rival and Jaligot, 2010): a sequence of the genome of both E. guineensis and E. oleifera species has been made public (Singh et al, 2013a) and two SNP chips have been recently developed (Kwong et al, 2016;Ting et al, 2016). The genetic determinism of several characters of agronomic interest has been elucidated, such as oil quality (Morcillo et al, 2013), shell thickness (Singh et al, 2013b), fruit colour (Singh et al, 2014) or the mantled somaclonal variation (Jaligot et al, 2014;Ong-Abdullah et al, 2015) together with gene networks at work for oil biosynthesis (Guerin et al, 2016).…”