Genome-wide SNP-discovery and analysis of genetic diversity in oil palm using double digest restriction site associated DNA sequencing

2nd International Conference on Natural Resources and Life Sciences

生态环境科学

Nugroho, Y.A.^1 ; Tanjung, Z.A.^2 ; Yono, D.^1 ; Mulyana, A.S.^1 ; Simbolon, H.M.^3 ; Ardi, A.S.^4 ; Yong, Y.Y.^4 ; Utomo, C.^5 ; Liwang, T.^5

Section of Molecular Breeding, Plant Production and Biotechnology Division, PT SMART, Tbk, Bogor

16810, Indonesia^1

Section of Bioinformatics, Plant Production and Biotechnology Division, PT SMART, Tbk, Bogor

16810, Indonesia^2

Dami Mas Sejahtera, Plant Production and Biotechnology Division, PT SMART, Tbk, Riau

28464, Indonesia^3

SMART Research Institute, Jalan Teuku Umar 19, Pekanbaru, Riau

28141, Indonesia^4

Plant Production and Biotechnology Division, PT SMART Tbk, Bogor

16810, Indonesia^5

关键词: EcoRI;    Elaeis guineensis;    MseI;    Oil palm;    SnpEff;   

Others  :  https://iopscience.iop.org/article/10.1088/1755-1315/293/1/012041/pdf
DOI  :  10.1088/1755-1315/293/1/012041

学科分类：环境科学（综合）

来源: IOP

【 摘 要 】

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.