Analisis Genomik Terintegrasi Aksesi Kelapa Sawit Afrika dan Indonesia: Wawasan Komparatif dari Genom Kloroplas dan Nukleus serta Pengembangan Penanda in-silico.

This thesis presents an integrated genomic investigation of African oil palm (Elaeis guineensis) aimed at improving understanding of maternal lineage diversity, nuclear genome variation, and genome evolution using complementary organellar and nuclear genome approaches. By combining comparative chloroplast genomics, in-silico genome-wide SSR marker development, and whole-genome sequencing of Tanzanian Dura oil palm, the study addresses major gaps in genomic resources for underrepresented East-African germplasm and provides insights relevant to oil palm domestication, conservation, and breeding. Comparative analysis of complete chloroplast genomes from Tanzania, Cameroonian, and Indonesian accessions revealed a highly conserved plastome structure,gene content, and synteny, consistent with the evolutionary stability of angiosperm chloroplast genomes. Despite this conservation, subtle variations in inverted repeat-single-copy boundary regions, intergenic spacers, and chloroplast SSR distribution enabled the resolution of distinct maternal lineages. Phylogenetic and haplotype network analyses identified multiple chloroplast haplotypes and lineage-specific clustering, indicating that global oil palm germplasm derives from more than one maternal origin and reflects a complex domestication and dispersal history. To completement plastome-based maternal insights, genome-wide SSR loci were mined from three aligned nuclear genomes (EG11, Dura-Tz, and Dura-BBG) using a comparative genomics network. Twenty polymorphic SSR markers with broad chromosomal distribution and favorable primer characteristics were successfully designed and validated in-silico. These markers provide practical and cost-effective tools for genetic diversity, population structure assessment, linkage mapping, and marker-assisted breeding, bridging high-resolution genomic data with applied breeding needs. In addition, this thesis reports the first chromosome-level genome assembly of Tanzanian Dura oil palm, representing a valuable genomic reference for Est-African germplasm. Comparative synteny analyses demonstrated extensive macro syntenic conservation across E.guineensis genomes, while localized structural variations and transposable element dynamics reveled lineage-specific genome diversification. Together, the findings highlight strong genomic conservation coupled with repeat-driven divergence within the species. Keywords: chloroplast genomics, Elaeis guineensis, maternal lineage diversity, SSR markers, whole-genome sequencing