Exploiting an oil palm EST database for the development of gene-derived SSR markers and their exploitation for assessment of genetic diversity

Abstract

A total of 5,521 expressed sequence tags (ESTs) from oil palm were used to search for type and frequency of simple sequence repeat (SSR) markers. Dimeric repeat motifs appeared to be the most abundant, followed by tri-nucleotide repeats. Redundancy was eliminated in the original EST set, resulting in 145 SSRs in 136 unique ESTs (114 singletons and 22 clusters). Primers were designed for 94 (69.1%) of the unique ESTs (consisting of 14 consensus and 80 singletons). Primers for 10 EST-SSRs were developed and used to evaluate the genetic diversity of 76 accessions of oil palm originating from seven countries in Africa, and the standard Deli dura population. The average number of observed and effective alleles was 2.56 and 1.84, respectively. The EST-SSR markers were found to be polymorphic with a mean polymorphic information content value of 0.53. Genetic differentiation (FST) among the populations studied was 0.2492 indicating high level of genetic divergence. Moreover, the UPGMA (unweighted pair-group method with arithmetic mean) analysis revealed a strong association between genetic distance and geographic location of the populations studied. The germplasm materials exhibited higher diversity than Deli dura, indicating their potential usefulness in oil palm improvement programmes. The study also revealed that the populations from Nigeria, Congo and Cameroon showed the highest diversity among the germplasm evaluated in this study. The EST-SSRs further demonstrated their worth as a new source of polymorphic markers for phylogenetic analysis, since a high percentage of the markers showed transferability across species and palm taxa.

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

“…Arias et al [40] also reported a maximum PIC value of 0.822 in a comparative study of 189 oil palm materials produced by different commercial companies using 17 SSR markers. The result of the present study is in agreement with earlier reports from Billotte et al [52] and Singh et al [39] on the high polymorphism of CIRAD and MPOB oil palm microsatellite markers used in this study. These highly polymorphic set of microsatellite marker pairs has been used for genetic fingerprinting in breeding programmes.…”

“…The number of alleles per locus is affected by the number of markers and sample size analyzed. Singh et al [39] previously reported lower number of alleles per locus (2.2 -3.2) in E. guineensis germplasm using a smaller set of SSRs and the number of alleles increased (2.8 -3.9) when Ting et al [51] employed a larger set of SSRs to evaluate a wider pool of oil palm germplasm. In fact, Augustina et al [73] reported a total of 163 alleles (mean = 8.2) among the 85 pisifera accessions from germplasm collections of different origins at Sampoerna Agro Tbk (SA) in Indonesia.…”

“…Nine of the sixteen microsatellite markers were developed at the Genomics Unit of ABBC-MPOB [39] [51] and seven at the French Centre de Coopération en Recherche Agronomique pour le Développement (CIRAD; Table 2) [52]. Every forward microsatellite marker was M13-tailed for labeling with one of the four florescent dyes i.e.…”

Analysis of genetic diversity and population structure of oil palm (Elaeis guineensis) from China and Malaysia based on species-specific simple sequence repeat markers

“…Especially, they are easily assayed using polymerase chain reaction (PCR; Powell et al, 1996;Qin et al, 2014). Currently, SSR markers are one of the most promising molecular marker systems for understanding the genetic diversity and structure of oil palm (Singh et al, 2008).…”

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.…”