The oil palm conventional breeding is faced with many challenges, including the long breeding cycle and limited genetic variations available from the existing breeding populations. Recent genomic research revealed the genetic properties of various oil palm populations and could be exploited by recombining favorable alleles through molecular breeding and selection. In aimed to discover high quality single nucleotide polymorphisms (SNPs) sampled from 236 diverse genetic backgrounds palms, a paired-end ddRAD-sequencing was employed to discover allelic variations. Whole 195.62 Gb clean data were generated using ddRAD-seq. After stringent filtering, 8 189 SNPs in the annotated genes were discovered based on the oil palm EG05 reference genome. The high polymorphism rate was observed across the assayed populations, whereby 29 % of loci showed moderate to high putative impact on amino acid changes in silico as predicted by SnpEff software. The Angola and Deli origins seemed to have undergone inbreeding as reflected by the fixation index and the lower observed heterozygosity compared to expected heterozygosity. Assessment of genetic stratification and structure was not strong enough to differentiate the core breeding materials according to their prior genetic backgrounds. The results demonstrated the robustness and high-throuputness of ddRAD sequencing method for SNP discovery.
Increasing of dry areas for Oil Palm plantation due to climate change led the breeders to develop drought stress, tolerant palm. Characterization of genetic materials for their physiological and genetic properties is required. Two distinct progenies derived from Tanzanian origin used for more adaptive to unwatered stress, and Nigerian origin used for more sensitive, were subjected for analysis. Physiological related variables were observed for sap flow, water potential, soil water content, greenhouse temperature and relative humidity, stomatal density, stomatal pore width, and proline content. The Tanzanian origin has more stable in sap flow, longer water potential detected, more adaptive in stomatal closure, and a lower in proline content than Nigerian origins. The genome comparison of both materials was performed by double digest Restriction Associated DNA and captured 299 294 SNPs. It found 9.3 % of those SNPs that were having a different allele with a minor frequency between progenies. And, 0.7 % from filtered SNPs were located and distributed in 167 genes. Two SNP markers were located in aquaporin NIP1-1 gene that related to water translocation between cells. One SNP marker was located in glutamate receptor 2.7-like gene that related to glutamate release and proline biosynthesis. The remaining SNPs will be in further analyzed.
Oil palm is a perennial oil crop that is the most important source of vegetable oil in the world. Oil palm breeding cycle takes a long period of time, therefore molecular marker-assisted selection (MAS) is required to shorten the selection time. This MAS requires the associated marker to desired trait, particularly for yield and yield components as a complex trait and depend on genetic background. The aim of this study was to obtain SSR marker associated with average of bunch weight (ABW). Planting material used in this study was Tenera population derived from Deli Dura x AVROS Pisifera. Seven SSR markers associated to ABW trait from public database were studied. Molecular data were analyzed for SSR markers profile which consisted of allelic diversity, heterozygosity level, and polymorphism information content (PIC). Association between SSR markers to ABW traits was performed with single marker analysis using one way analysis of variance. The results showed that
Abstract. Yono D, Nugroho YA, Tanjung ZA, Utomo C, Liwang T. 2021. Genomewide SNP marker identification associated with drought tolerance in oil palm. Biodiversitas 22: 3138-3144. Drought stress is one of the abiotic stresses that frequently occurred in the oil palm plantation and has a negative impact on fresh fruit bunch (FFB) production. Therefore, drought-tolerant palms are essential to be selected to mitigate this challenge. In Indonesia, several oil palm plantation areas have a dry climate, such as Lampung province. Distinct yield performance palms were identified from well-recorded agronomic trials in these areas, where the palms are frequently exposed to drought stresses every year and lead them to suffer from water deficit response. Group of high and low-yielding palms was selected based on FFB production of each palm for at least ten constitutive years. The double digest restriction amplified DNA (ddRAD) genotyping methods were used to capture the Single Nucleotide Polymorph (SNP) variant from pools of sample association datasets. At least, 538k SNPs were identified from these pooled datasets. A bulked segregant analysis with a Case-Control approach was implemented to screen the contrast SNP profiles between both pools. A total of 56 association signals was selected from sequential filtering. These SNP sites are located in 21 genes. Further SNP validation and phenotypic verification are necessary to obtain SNPs marker for drought-tolerant palm selections.
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