The traits analyzed in this study - HI, RL, PCS, C16:0, C18:0, C18:1, C18:2, IV and carotene content - are generally highly heritable in oil palm [14,28,29], indicating that they are amenable to selection either via conventional or molecular breeding. This makes the traits attractive for QTL analysis. Four of them (RL, HI, IV and C18:1) in the 2.6–1 mapping family did not follow a normal distribution, but, as reported by [30], deviation from normal distribution did not appear to greatly affect QTL detection. As expected, all the trait values were intermediate between the means for E. oleifera and E. guineensis, similar to the observations by other studies [16,31]. The wide distribution for all traits measured, suggests that both BC2 populations are ideal for QTL mapping and so for selection and improvement in oil palm. RL and HI in both populations are considerably lower than in commercial DxP as reported by [32], suggesting that these populations can be used for the development of compact palms.
The genetic linkage maps for the two BC2 populations was successfully integrated, improving the resolution of the combined map. The number of palms in the individual populations used in this study was relatively small compared to in other crops. However, such small family sizes are common in oil palm trials with >64 palms being rare. Although the study focused on highly heritable traits, the small population size could have led to an underestimation of the QTL numbers and restricted the QTL analysis to only the most prominent effects. [33] found that the number of QTLs detected increased with population size. To obviate this limitation, the map resolution and hence QTL detection power, were improved by integrating the two BC2 maps. Other factors, such as the phenotypic measurement accuracy and marker density, also contributed to the QTL detection and localization [34].
Development of an ordered set of markers along the oil palm chromosome allows the genome to be screened systematically for linkages to complex traits. SNP markers employed in this study resulted in better genome coverage, increasing the potential for realization of effective marker-assisted selection (MAS). A total of 1,963 polymorphic loci (1,814 SNPs and 149 SSRs) generated 16 LGs, which is consistent with the 16 chromosome-pairs in oil palm [35]. The genome length observed (1,793 cM) was close to that reported by [14,17] of 1,815—1,867 cM for E. guineensis. The average length of the LGs is 112 cM, which is in the range of most agricultural crops [36]. Resolution of the two individual genetic maps was good with an average gap of 0.86 cM (2.6–1) and 1.32 cM (2.6–5). An average interval of 0.91 cM was observed on the BC2 integrated map. This gap was much smaller than those previously reported on oil palm interspecific hybrids of 1.2 - 7.2 cM [14,16,17]. The density of both BC2 genetic maps allowed the genomic segments associated with compactness and FAC traits to be identified. Consistency of the QTLs detected in the independent and integrated maps [see Additional file 3] adds confidence to their detection.
The interspecific hybrid breeding programme in Malaysia aims to develop palms with higher unsaturated oil and compact characteristics, without sacrificing yield. Applying MAS can accelerate the programme as markers can be linked to selected traits to enable early detection. A high logarithm of the odds ratio (LOD) score will provide confidence for integrating the markers in breeding lines, at least in palms of similar genetic backgrounds. In the QTL analysis of vegetative traits, interestingly, the QTLs associated with RL, PCS and HI were located at the same genomic region on LG4, likely representing a major locus influencing compactness in oil palm. Similarly, QTLs for RL and PCS were also located in close proximity on LG8, revealing another major locus for compactness. To date, there are no QTL analysis of vegetative traits in interspecific hybrids. The QTLs detected in this study were compared to those described previously [15], for a segregating E. guineensis population. However, most of the QTLs detected in the current BC2 populations were located on different chromosomes compared with those reported by [15], with the exception of those associated with RL which was on LG11. This suggests that separate genomic regions influence compactness in E. guineensis and the interspecific hybrids. A previous study [18] reported two QTLs related to RL and PCS in E. guineensis. However, a comparison between similarity of the linkage groups could not be made as the sequence information for restriction fragment length polymorphism (RFLP) markers linked to the traits in the study were not publicly available for further analysis. More specifically on the HI, recent reports revealed QTLs and candidate genes influencing it in E. guineensis [10,11]. However, the genomic region linked to HI in this study was different from these two reports.
A total of 13 QTLs were detected for IV, C16:0, C18:0, C18:1 and C18:2 in seven LGs. The results are similar to those of [16,20] on interspecific hybrids, with 19 and 12 QTLs found, respectively. Five of the identified QTLs in this study were similar to those in both reports. The QTL on LG4 for IV on LG15 is in agreement with that by [16]. The major QTLs for IV, C18:1 and C16:0 on LG1 were previously reported for an interspecific hybrid family [20] which shows their potential to be used for making informed decisions in breeding. The results support a previous postulation that the same genomic region has a major influence on the unsaturation (IV) and saturation (C16:0) of palm oil. The QTLs for IV, C18:0 and C18:2, were also located around the same region on LG4, revealing another major locus influencing fatty acid composition. IV was not significantly correlated with C18:0 (at P<0.05) in both mapping families, but its QTL overlapped that for C18:0 in LG4. The QTL for C18:0 on LG4 is similar to that reported by [20]. Overlapping of the QTLs map position for unrelated traits could be due to pleiotropic effects [37]. Since similar work for carotene content in oil palm has not been reported, comparison with other research could not be made.
Availability of the oil palm genome sequence [27] has allowed the underlying QTL interval to be positioned on the EG5 physical map to identify potential candidate genes influencing the traits of interest. The auxin transport protein, BIG, related to HI, is required for auxin efflux and polar auxin transport (PAT) and could influence auxin-mediated developmental responses (e.g. cell elongation, apical dominance, lateral root production, inflorescence architecture, general growth and development) [38]. BIG controls elongation of the pedicel and stem internodes through auxin action. In Arabidopsis, BIG also plays a role in the regulation of responses to phytohormones, such as auxin, cytokinins, ethylene and gibberellic acid (GA), particularly during light-mediated stimuli (e.g. shade avoidance and etiolation) [39,40]. BAM1, in association with RL, encodes a leucine-rich repeat receptor-like serine/threonine-protein kinase which is involved in cell-cell communication during early anther development, and regulates cell division and differentiation, such as in the formation of shape, size and symmetry of leaves [41]. ERECTA, linked to PCS on LG4, regulates aerial architecture (including inflorescence), e.g. shoot apical meristem-originating organ shape, elongation of internodes and pedicels, and adaxial-abaxial polarity, and stomatal patterning, probably by tuning cell division and expansion [42].
In terms of FAC, the CUT1and KCS11 genesare associated with the QTLs for IV, C16:0 and C18:2 on LG1. CUT1 is required for elongation of C24 fatty acid, an essential step in cuticular wax production [43]. This wax is composed of long-chain, aliphatic hydrocarbons derived from very-long-chain fatty acids (VLCFAs). For KCS11, this gene is active on both saturated and mono-unsaturated acyl chains C16 to C20 [44]. It is involved in the pathway of fatty acid biosynthesis, which is part of lipid metabolism. The magnesium-dependent phosphatidate phosphatase gene, PAH2,related to C18:1, is involved in catalyzing the dephosphorylation of phosphatidate to yield diacylglycerol and may function indirectly as a repressor of multiple enzymes involved in phospholipid biosynthesis. However, at this stage, their involvement and influences in controlling compactness and FAC of oil palm are still speculative. Further studies are necessary to characterize these genes to determine their functions in regulating the traits in oil palm.