Identification of QTLs Associated with Callogenesis and Embryogenesis in Oil Palm Using Genetic Linkage Maps Improved with SSR Markers

Abstract

Clonal reproduction of oil palm by means of tissue culture is a very inefficient process. Tissue culturability is known to be genotype dependent with some genotypes being more amenable to tissue culture than others. In this study, genetic linkage maps enriched with simple sequence repeat (SSR) markers were developed for dura (ENL48) and pisifera (ML161), the two fruit forms of oil palm, Elaeis guineensis. The SSR markers were mapped onto earlier reported parental maps based on amplified fragment length polymorphism (AFLP) and restriction fragment length polymorphism (RFLP) markers. The new linkage map of ENL48 contains 148 markers (33 AFLPs, 38 RFLPs and 77 SSRs) in 23 linkage groups (LGs), covering a total map length of 798.0 cM. The ML161 map contains 240 markers (50 AFLPs, 71 RFLPs and 119 SSRs) in 24 LGs covering a total of 1,328.1 cM. Using the improved maps, two quantitative trait loci (QTLs) associated with tissue culturability were identified each for callusing rate and embryogenesis rate. A QTL for callogenesis was identified in LGD4b of ENL48 and explained 17.5% of the phenotypic variation. For embryogenesis rate, a QTL was detected on LGP16b in ML161 and explained 20.1% of the variation. This study is the first attempt to identify QTL associated with tissue culture amenity in oil palm which is an important step towards understanding the molecular processes underlying clonal regeneration of oil palm.

Assessment of Genetic Diversity of NIFOR Oil Palm Main Breeding Parent Genotypes Using Microsatellite Markers

“…Furthermore, multiplexing PCR products on single gels also reduces the workload for studies requiring a large number of samples [35]. SSR markers are useful in oil palm population genetics and breeding studies [36]- [41], varietal identification [42]- [46], pedigree analysis, genome mapping, and QTL detection for molecular marker-assisted selection [47]- [49]. But to date, studies on the diversity of the current NIFOR oil palm breeding populations have not been carried out using molecular markers.…”

Genetic Relationships between Elite Oil Palms from Nigeria and Selected Breeding and Germplasm Materials from Malaysia via Simple Sequence Repeat (SSR) Markers

“…SSRs have proven their advantage and suitability in oil palm population genetics studies (Billotte et al, 2001;Singh et al, 2008;Arias et al, 2012;Taeprayoon et al, 2015;Bakoumé et al, 2015), varietal identification (Rajinder et al, 2007;Norziha et al, 2008;Thawaro & Te-Chato, 2010;Bakoumé et al, 2011;Hama-Ali et al, 2014), pedigree analysis, genome mapping and QTL detection for molecular marker-assisted selection (Billotte et al, 2010;Ting et al, 2013). Considerable amount of molecular markers studies on oil palm have already been conducted by many oil palm research centres in Malaysia (Malaysian Palm Oil Board, MPOB), France (Centre de Coopération en Recherche Agronomique pour le Développemen, CIRAD), Indonesia (Indonesian Oil Palm Research Institute, IOPRI), and Brazil (Empresa Brasileira de Pesquisa Agropecuária, EMBRAPA), to name a few.…”

AN SNP MARKER POTENTIALLY LINKED TO SOMATIC EMBRYOGENESIS OF OIL PALM (Elaeis guineensis)

“…Identification of Quantitative Trait Loci (QTLs) associated with callogenesis and embryogenesis in oil palm with broad range of markers from AFRLPs, RFLPs, and SSRs has been done (Ting et al 2013), but studies to determine the process of de-differentiation and embryogenesis with specific SNP markers in plant genomes are limited. In this study, the identification of candidate SNP associated with somatic embryogenesis in oil palm were done in silico, which was continued to the validation process based on the phenotype data of oil palm tissue culture.…”