SSR mining in oil palm EST database: application in oil palm germplasm diversity studies

Abstract

This study reports on the detection of additional expressed sequence tags (EST) derived simple sequence repeat (SSR) markers for the oil palm. A large collection of 19243 Elaeis guineensis ESTs were assembled to give 10258 unique sequences, of which 629 ESTs were found to contain 722 SSRs with a variety of motifs. Dinucleotide repeats formed the largest group (45.6%) consisting of 66.9% AG/CT, 21.9% AT/AT, 10.9% AC/GT and 0.3% CG/CG motifs. This was followed by trinucleotide repeats, which is the second most abundant repeat types (34.5%) consisting of AAG/CTT (23.3%), AGG/CCT (13.7%), CCG/CGG (11.2%), AAT/ATT (10.8%), AGC/GCT (10.0%), ACT/AGT (8.8%), ACG/CGT (7.6%), ACC/GGT (7.2%), AAC/GTT (3.6%) and AGT/ACT (3.6%) motifs. Primer pairs were designed for 405 unique EST-SSRs and 15 of these were used to genotype 105 E. guineensis and 30 E. oleifera accessions. Fourteen SSRs were polymorphic in at least one germplasm revealing a total of 101 alleles. The high percentage (78.0%) of alleles found to be specific for either E. guineensis or E. oleifera has increased the power for discriminating the two species. The estimates of genetic differentiation detected by EST-SSRs were compared to those reported previously. The transferability across palm taxa to two Cocos nucifera and six exotic palms is also presented. The polymerase chain reaction (PCR) products of three primer-pairs detected in E. guineensis, E. oleifera, C. nucifera and Jessinia bataua were cloned and sequenced. Sequence alignments showed mutations within the SSR site and the flanking regions. Phenetic analysis based on the sequence data revealed that C. nucifera is closer to oil palm compared to J. bataua; consistent with the taxanomic classification.

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

“…The mean H o and H e values in this study was 0.6296 and 0.7616, respectively, higher compared to those reported by Ting et al (2010) (0.400 and 0.437, respectively) using 15 SSR markers and Bakoumé et al (2015) (0.460 and 0.644, respectively) using 16 SSR markers. These high mean values of H o and H e depicted the high genetic variability in the oil palm samples evaluated in this study notwithstanding that the materials have undergone some selection and breeding activities.…”

“…Open pollination that prevails in the natural oil palm groves whereby an oil palm tree receives pollens from many donor trees contributes to increasing allelic diversity. Results of the present study (H e = 0.347) and the previous study by Ting et al (2010; H e = 0.340) revealed the presence of low genetic variation among MPOB Deli dura. The Deli dura has undergone several cycles of selection compared to NIFOR Deli dura.…”

DNA Profiles of MTG (Moderat Tahan Gano) Oil Palm Variety Based on SSR Marker

“…Also, [16] revealed even lower values (He = 0.340) for Deli dura via 15 EST-SSRs. Recently, [15] reported Ho values (0.310 and 0.211) and He values (0.549 and 0.559) for Deli dura MPOB (Malaysia) and Deli dura Dabou (Côte d'Ivoire) with 16 microsatellite markers.…”

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

“…When compared to the previous report of Cochard et al (2009), lower values of expected heterozygosity (H e = 0.373) for Deli NIFOR and (H e = 0.510) for 6 Deli dura populations from different origins using 14 SSR markers. Also, Ting et al [51] revealed even lower values (H e = 0.340) for Deli dura via 15 EST-SSRs. Recently, Bakoume et al [38] reported H o values (0.310 and 0.211) and H e values (0.549 and 0.559) for Deli dura MPOB (Malaysia) and Deli dura Dabou (Côte d'Ivoire) with 16 microsatellite markers.…”

“…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.…”