Fine-mapping and cross-validation of QTLs linked to fatty acid composition in multiple independent interspecific crosses of oil palm

Abstract

BackgroundThe commercial oil palm (Elaeis guineensis Jacq.) produces a mesocarp oil (commonly called ‘palm oil’) with approximately equal proportions of saturated and unsaturated fatty acids (FAs). An increase in unsaturated FAs content or iodine value (IV) as a measure of the degree of unsaturation would help to open up new markets for the oil. One way to manipulate the fatty acid composition (FAC) in palm oil is through introgression of favourable alleles from the American oil palm, E. oleifera, which has a more unsaturated oil.ResultsIn this study, a segregating E. oleifera x E. guineensis (OxG) hybrid population for FAC is used to identify quantitative trait loci (QTLs) linked to IV and various FAs. QTL analysis revealed 10 major and two putative QTLs for IV and six FAs, C14:0, C16:0, C16:1, C18:0, C18:1 and C18:2 distributed across six linkage groups (LGs), OT1, T2, T3, OT4, OT6 and T9. The major QTLs for IV and C16:0 on LGOT1 explained 60.0 – 69.0 % of the phenotypic trait variation and were validated in two independent BC2 populations. The genomic interval contains several key structural genes in the FA and oil biosynthesis pathways such as PATE/FATB, HIBCH, BASS2, LACS4 and DGAT1 and also a relevant transcription factor (TF), WRI1. The literature suggests that some of these genes can exhibit pleiotropic effects in the regulatory networks of these traits. Using the whole genome sequence data, markers tightly linked to the candidate genes were also developed. Clustering trait values according to the allelic forms of these candidate markers revealed significant differences in the IV and FAs of the palms in the mapping and validation crosses.ConclusionsThe candidate gene approach described and exploited here is useful to identify the potential causal genes linked to FAC and can be adopted for marker-assisted selection (MAS) in oil palm.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2607-4) contains supplementary material, which is available to authorized users.

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).…”

Chemical Characteristics and Nutritional Properties of Hybrid Palm Oils

“…The differences in FA composition between oils from African and hybrid palms should be related to the expression of genes encoding β-ketoacyl-ACP synthase (KAS) II, which is specifically used for chain lengthening of C16:0 to C18:0, and stearoyl/palmitoyl-ACP Δ 9 -desaturase. Hereditariness and expression of genes linked to FAs and TAGs biosynthesis were explored by several authors [1,6,[39][40][41]. Different quantitative trait loci (QTLs) for iodine value (index of total unsaturation) and FAs (C14:0, C16:0, C16:1, C18:0, C18:1, C18:2) have been identified, and a few structural genes encoding the enzymes involved in the de novo synthesis of FAs and in the TAG assembly (e.g., acyl-ACP thioesterases, acyl-CoA synthetase, diacylglycerol acyltransferase) have been localized in those genomic intervals.…”

“…The wide range of applications for mesocarp oil is due to its fatty acid (FA) composition. Palm oil has approximately equal amounts of saturated (SFA) and unsaturated fatty acids (UFA), while the mesocarp oil from EO is much more unsaturated [3][4][5][6].…”

Review: Omics and Strategic Yield Improvement in Oil Crops

“…These cumulative effects increase together with the number of QTL markers and their corresponding alleles. Ting et al [121] suggested introgressing favourable genes into Elaeis oleifera in order to manipulate fatty acid composition. Their QTL analysis of a segregating E. oleifera × Elaeis guineensis hybrid population revealed six fatty acids related QTLs located across several linkage groups that were validated in two independent populations.…”