Genetic architecture of palm oil fatty acid composition in cultivated oil palm (Elaeis guineensis Jacq.) compared to its wild relative E. oleifera (H.B.K) Cortés

Abstract

We searched for quantitative trait loci (QTL) associated with the palm oil fatty acid composition of mature fruits of the oil palm E. guineensis Jacq. in comparison with its wild relative E. oleifera (H.B.K) Cortés. The oil palm cross LM2T x DA10D between two heterozygous parents was considered in our experiment as an intraspecific representative of E. guineensis. Its QTLs were compared to QTLs published for the same traits in an interspecific Elaeis pseudo-backcross used as an indirect representative of E. oleifera. Few correlations were found in E. guineensis between pulp fatty acid proportions and yield traits, allowing for the rather independent selection of both types of traits. Sixteen QTLs affecting palm oil fatty acid proportions and iodine value were identified in oil palm. The phenotypic variation explained by the detected QTLs was low to medium in E. guineensis, ranging between 10% and 36%. The explained cumulative variation was 29% for palmitic acid C16:0 (one QTL), 68% for stearic acid C18:0 (two QTLs), 50% for oleic acid C18:1 (three QTLs), 25% for linoleic acid C18:2 (one QTL), and 40% (two QTLs) for the iodine value. Good marker co-linearity was observed between the intraspecific and interspecific Simple Sequence Repeat (SSR) linkage maps. Specific QTL regions for several traits were found in each mapping population. Our comparative QTL results in both E. guineensis and interspecific materials strongly suggest that, apart from two common QTL zones, there are two specific QTL regions with major effects, which might be one in E. guineensis, the other in E. oleifera, which are independent of each other and harbor QTLs for several traits, indicating either pleiotropic effects or linkage. Using QTL maps connected by highly transferable SSR markers, our study established a good basis to decipher in the future such hypothesis at the Elaeis genus level.

Conflict of interest statement

Competing Interests: Indra Syaputra has an affiliation to the commercial funder of this research (SOCFIN Group). This does not alter the authors' adherence to all the PLOS ONE policies on sharing data and materials.

Figures

Figure 1. Principal component analysis (PCA) of palm oil fatty acid proportions of C14:0, C16:0, C18:0, C18:1 and C18:2 in the intraspecific cross LM2T x DA10D and in the interspecific pseudo-backcross SA569.

Note: the figure show projections on the two first axes of the PCA.

Figure 2. Sixteen QTLs of palm oil fatty acid proportions and iodine value identified in the E. guineensis cross LM2T x DA10D, located on the consensus linkage map in oil palm (Eg_Map) of Billotte et al. and compared to the QTL map for same traits published by Montoya et al. in the interspecific Elaeis pseudo-backcross SA569.

Note: Each microsatellite linkage map has 16 linkage groups corresponding to the 16 homologous pairs of chromosomes of the Elaeis genome. The E. guineensis Eg_Map (253 loci) is sharing 156 marker loci in common and good co-linearity with the linkage map of the pseudo-backcross SA569 (362 loci). The QTLs were identified by the Kruskal-Wallis, IM and MQM methods. One star (*) or two stars (**): QTL detected by the MQM method at the genome-wide α threshold value of 5% or 1% respectively. No star: putative QTL as only detected by the Kruskall-Wallis test at p<0.005. The names and the positions (cM) of the markers are given on the right side of the linkage groups. mEgCIRxxxx and mEgESTxxxx: E. guineensis SSR loci. sEgOPGPxxxx: E. guineensis gene SNP loci. mCnCIRxxxx: Cocos nucifera SSR loci. Marker loci common to both maps are indicated by an extension “_R”. The names, positions and confidence regions of the QTLs are given on the left side of the linkage groups. In red: are figured the QTLs of saturated fatty acid proportion; in blue: the QTLs of unsaturated fatty acid proportion and of iodine value.

Figure 3. Effects of E. guineensis versus E. oleifera QTL alleles on the palm oil fatty acid composition, estimated by Montoya et al. from the interspecific pseudo-backross SA569.

Note: the QTL marker loci were used to perform an ANOVA test (type III, post hoc test of Tukey at α = 0.05) to estimate the mean effects of the parent QTL marker alleles on the mean of each phenotypic trait. For the hybrid parent SA65T, the species origin of the QTL marker alleles were identified, and the allelic effects at the QTL were therefore estimated by contrast of E. oleifera (grand-parent SA49D) against E. guineensis (grand-parent LM2466P).