Evaluation of the simple sequence repeat (SSR) genotyping of Elaeis oleifera germplasm / Wan Nurhayati Wan Hanafi

Special attention has been given to the second species of oil palm, Elaeis oleifera as it possess several interesting agronomic traits such as slow growth, higher oil unsaturation and disease resistance. Studying the variability of E. oleifera germplasm is therefore very important as it serves as a tool to select source of genetic diversity for the oil palm conservation programme. The objectives of this study were 1) to identify the polymorphic E. oleifera gSSRs for E. oleifera, 2) to measure the information content of E. oleifera gSSRs, 3) to unravel the genetic diversity of E. oleifera germplasm, 4) to determine the genetic differentiation of E. oleifera germplasm and 5) to assess the genetic structure of E. oleifera germplasm. MPOB has developed a collection of simple sequence repeats (SSRs) from E. oleifera genome. Initially, optimization of PCR conditions for analysis of the oleifera samples using E. oleifera gSSRs was carried out. A total of 316 E. oleifera gSSRs were tested to evaluate their usefulness to assess the genetic diversity and population structure of E. oleifera populations. The PCR conditions were optimized while keeping the original DNA concentration, annealing temperature (Ta) and other reagent constant. Out of 316 E. oleifera gSSRs screened, 270 produced amplicons and of these numbers, 140 were polymorphic and potentially useful for diversity analysis. The modified PCR condition increases the success of amplifying E. oleifera gSSRs in the E. oleifera DNA samples analyzed. The PCR methods together with the polymorphic E. oleifera gSSRs were applied in genotyping the entire E. oleifera populations. A set of 21 polymorphic E. oleifera gSSRs was analyzed on a total of 214 E. oleifera genomic DNA belonging to eight germplasm originated from four countries in Central and South America (Columbia, Panama, Costa Rica and Honduras). The analysis covered on genetic diversity and genetic structure of eight E. oleifera populations, inferences from 21 polymorphic E. oleifera gSSRs. The average observed heterozygosity across population (Ho=0.249) was less than the expected heterozygosity (He=0.363). The highest population diversity was obtained in population 08 from Columbia (He=0.460±0.055, I=0.870±0.121. Eight of 21 polymorphic E. oleifera gSSRs were informative with PIC>0.5, where sMo00131 is the most informative (PIC=0.853). The populations analysed showed great genetic differentiation (Fsr=0.223). The Nei genetic distance showed the highest genetic distance was between population 01 from Columbia and population 02 from Costa Rica (0.555) while the lowest was between population 02 and population 03 from Honduras (0.019). The eigenvalues of PCoA plot showed that the first two components explained 38.70% of the total variation, which roughly ordinated the E. oleifera individuals into three major groups. Construction of neighbour-joining (NJ) tree separated E. oleifera individuals into two clusters. Model based clustering revealed that E. oleifera population has the highest AK when K was set to 7. The present study provides a diverse pattern of genetic diversity and the existence of genetic differentiation among E. oleifera germplasm. This study highlights the potential contribution of genetic variation of the E. oleifera collection analyzed using E. oleifera gSSRs for germplasm conservation and for utilization in breeding programs. Further conservation should focus on more populations with less number of palms per population development of core collection

Evaluation of the simple sequence repeat (SSR) genotyping of Elaeis oleifera germplasm / Wan Nurhayati Wan Hanafi

Special attention has been given to the second species of oil palm, Elaeis oleifera as it possess several interesting agronomic traits such as slow growth, higher oil unsaturation and disease resistance. Studying the variability of E. oleifera germplasm is therefore very important as it serves as a tool to select source of genetic diversity for the oil palm conservation programme. The objectives of this study were 1) to identify the polymorphic E. oleifera gSSRs for E. oleifera, 2) to measure the information content of E. oleifera gSSRs, 3) to unravel the genetic diversity of E. oleifera germplasm, 4) to determine the genetic differentiation of E. oleifera germplasm and 5) to assess the genetic structure of E. oleifera germplasm. MPOB has developed a collection of simple sequence repeats (SSRs) from E. oleifera genome. Initially, optimization of PCR conditions for analysis of the oleifera samples using E. oleifera gSSRs was carried out. A total of 316 E. oleifera gSSRs were tested to evaluate their usefulness to assess the genetic diversity and population structure of E. oleifera populations. The PCR conditions were optimized while keeping the original DNA concentration, annealing temperature (TA) and other reagent constant. Out of 316 E. oleifera gSSRs screened, 270 produced amplicons and of these numbers, 140 were polymorphic and potentially useful for diversity analysis. The modified PCR condition increases the success of amplifying E. oleifera gSSRs in the E. oleifera DNA samples analyzed. The PCR methods together with the polymorphic E. oleifera gSSRs were applied in genotyping the entire E. oleifera populations. A set of 21 polymorphic E. oleifera gSSRs was analyzed on a total of 214 E. oleifera genomic DNA belonging to eight germplasm originated from four countries in Central and South America (Columbia, Panama, Costa Rica and Honduras)

Application of Whatman FTA card method in oil palm DNA extraction and PCR analysis / Wan Nurhayati Wan Hanafi and Nur Syahirah Abu Bakar

Polymerase Chain Reaction (PCR) analysis in the study of oil palm DNA generally carried out by using DNA template obtained from grinding of leaf samples in liquid nitrogen followed by hexadecyltrimethylammonium bromide (CTAB) protocol. The present study explores the FTA card as a method to retrieve PCR-amplifiable oil palm DNA. Oil palm leaves were cut and crushed before deposited onto the FTA card. An attempt was made by amplifying the EgSHP gene using a punch of FTA card as a DNA template. The successful outcome of PCR was measured by the presence of PCR amplicons on 1% agarose gel electrophoresis, indicate the genotype of oil palm fruit form. This present study demonstrates that the FTA card provides a versatile alternative to the study of oil palm genetics

Analysing population structure of Elaeis Oleifera germplasm using model-based approach programme STRUCTURE / Wan Nurhayati Wan Hanafi …[et al.]

Elaeis oleifera serves as a source of genetic foundation in oil palm improvement programme, as it possess several interesting agronomic traits such as slow growth, higher oil unsaturation and disease resistance. Malaysian Palm Oil Board (MPOB) has developed a collection of simple sequence repeats (SSRs) from Elaeis oleifera genome (E. oleifera-gSSRs). A total of 21 polymoprhic SSR markers were evaluated in the attempt to assess the population structure of E. oleifera populations. The appropriate common ancestry (K) value was determined to be seven from the likelihood scores. The profile from STRUCTURE analysis indicates considerable sharing of genetic components among E. oleifera population with an exception for Population 01 from Columbia and Population 02 from Costa Rica. The present study provides information on population structure of MPOB E. oleifera collection via model-based method for germplasm conservation and utilisation in breeding programmes