Articles written in Journal of Genetics

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

      Ngoot-Chin Ting Noorhariza Mohd Zaki Rozana Rosli Eng-Ti Leslie Low Maizura Ithnin Suan-Choo Cheah Soon-Guan Tan Rajinder Singh

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      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.

    • Anchoring a genetic map of an interspecific backcross two family to the genome builds of Elaeis


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      The present study evaluated an interspecific backcross two (BC$_{2} $) population of oil palm, which was segregating for fatty acidcomposition (FAC). The purpose of this study was to construct a high-density genetic map for the population, which could be used toanchor the Elaeis guineensis (EG5) and E. oleifera (O7) genome builds and determine the physical positions of the quantitative trait loci(QTLs) associated with FAC. A high-density SNP-based and SSR-based linkage map was successfully constructed for an E. guineensis$\times$ E. oleifera BC2 population. The genetic map had 16 linkage groups spanning 1618.4 cM with 1252 markers (1152 SNPs and 100SSRs). The physical location of the markers were determined through sequence similarity search against EG5 and O7. The majority ofmarkers (81.2%) showed map order consistent with their corresponding position on EG5. In total, 1218 markers were also anchored to 683scaffolds in O7. This study for the first time compared the genetic map of the BC$_{2} $ population with that of a published E. oleifera $\times$ E.guineensis (O$\times$G) interspecific F$_{2} $ hybrid, which revealed 433 common markers (34.6%). More importantly marker order was generallyconsistent in both maps. The published EG5 facilitated orientating the mapped markers in the present BC2 map as well as in the O7scaffolds. Major QTLs associated with iodine value (IV) and palmitic acid (C16:0) content, localized on chromosome 3 and linoleic acid(C18:2) content localized on chromosome 2 of EG5 were also for the first time positioned on the O7 build, revealing the correspondingposition in the E. oleifera genome likely influencing FAC in hybrids and backcrosses.

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