No abstract

Oil palm is continually being improved via controlled crossing of selected palms to ensure sustainable yields and productivity. As such, correct parental assignment is important as the presence of illegitimates will compromise the progress of improvement. In the present study, we determined the optimal number of microsatellite (SSR) markers for detection of illegitimates in selected oil palm crosses with high confidence. Determining the optimal number of markers to assign parentage will ensure that the DNA fingerprinting will be cost effective for routine use as a quality control tool in oil palm improvement programs. Here, we evaluated a wide range of crosses that included a cross derived from wild germplasm palm. The results revealed that markers with high PIC are informative and detect most of the alleles present in a cross, including those exhibited by the illegitimates. A larger number of optimum sets of markers are needed to detect all illegitimates for crosses with higher levels of genetic diversity. The optimal number of polymorphic SSR markers determined in the present study can ensure that appropriate quality control is implemented for oil palm improvement programs.

The high yielding tenera is the commercial oil palm planting material of choice in Southeast Asia. Notwithstanding this, there is continuous effort to further improve the yield and one way to do this is by addressing the yield components (YCs ). Using 4,451 SNP and over 600 SSR markers , this study revealed quantitative trait loci (QTL) associated with YCs in two breeding populations, a Deli dura x Yangambi pisifera (P2) and a Deli dura x AVROS pisifera (KULIM DxP). Thirteen and 29 QTLs were identified in P2 and KULIM DxP, respectively . They were compared to other YC-linked QTLs reported previously for different genetic backgrounds by mapping the QTL-linked markers to the oil palm genome . The comparison revealed four common chromosomes containing QTLs influencing various YCs . The results reveal the possible presence of closely linked loci or pleiotropic genes influencing YCsPowered by Editorial Manager® and ProduXion Manager® from Aries Systems Corporation in oil palm. Exploiting the genome data has also facilitated the discovery of candidate genes within or near the QTL regions including those related to glycosylation, fatty acid and oil biosynthesis, and development of flower, seed and fruit . Response to Reviewers:Authors responses to Reviewer's comments:Reviewer #1: The manuscript has lot of scientific lacuna. Following major points need to clarified 1. The parents used in the mapping population are have high variation for the traits under study? I don't think the parents have variation for all the traits. In linkage mapping the parents used to generate mapping should vary for the traits. How authors can do GWAS without following the simple logic in linkage mapping studies. It is a very important criteria for mapping QTLsResponse: We thank the reviewer for this very important observation. The parent palms used to generate the two mapping families are the maternal Deli dura (in both cases) and AVROS and Yangambi pisifera (paternal parent). It is widely acknowledged by oil palm breeders that these parental palms, namely the Deli dura as well as the AVROS and Yangambi pisifera have significant variation in yield components (YCs). In fact, pisifera is female sterile and does not produce fruits that develop to maturity and hence, has no YCs associated with it. For crossing programmes, the pisifera palm is often selected based on the performance of its siblings (tenera that has fruit bunches), to indicate its yield potential. In a nutshell, the pisifera palms have no YCs directly associated with them, while the dura palms are selected for having favourable YCs. Thus, the pisifera and dura palms do vary in all aspects of YCs such as bunch weight, fruit-to-bunch ratio, kernel size and shell thickness. This has been well documented in literature e.g. . We have added a sentence in the Materials and methods section on this (under Mapping families, lines 187 -192, page 5). As such, in this study, the phenotypic variance observed in the 16 YCs (presented in Supplementary Table S1) does reflect segregation of the parent...