Genome properties of key oil palm (Elaeis guineensis Jacq.) breeding populations

Abstract Good knowledge about genome properties of the populations helps to optimize breeding methods, particularly genomic selection (GS). In oil palm (Elaeis guineensis Jacq.), the first global source of vegetable oil, GS gave promising results. The present study considered two complex oil palm breeding populations, Deli and La Mé, with 943 individuals and 7,324 single-nucleotide polymorphisms (SNPs) from genotyping-by-sequencing. Linkage disequilibrium (LD), haplotype sharing, effective size (Ne), and fixation index (Fst) were investigated. A genetic linkage map was constructed, including 4,252 SNPs and spanning 1,778.52 cM, with an average recombination rate of 2.85 cM/Mbp. The LD at r²=0.3, considered as the minimum to get reliable results for genomic predictions, spanned over 1.05 cM/0.22 Mbp in Deli and 0.9 cM/0.21 Mbp in La Mé. The significant degree of differentiation existing between Deli and La Mé was confirmed by the high Fst value (0.53), the pattern of correlation of SNP heterozygosity and allele frequency among populations, and the decrease of persistence of LD and of haplotype sharing among populations with increasing SNP distance. However, the level of resemblance between the two populations over short genomic distances (correlation of r values between populations >0.6 for SNPs separated by <0.5 cM or <1 kbp and percentage of common haplotypes >40% for haplotypes <3,600 bp or <0.20 cM) likely explains the superiority of GS models ignoring the parental origin of marker alleles over models taking this information into account. The two populations had low Ne (<5). Population-specific genetic maps and reference genomes are needed for future studies.