Genome-Wide SNP Analysis Reveals Distinct Genetic Clusters and Admixture Patterns in Sago Palm (Early view)

Abstract

The sago palm (Metroxylon sagu Rottb.) is an important starch-producing crop in Sarawak, Malaysia, but its genetic improvement and varietal authentication remain limited by the lack of genome-wide molecular markers. This study applied Illumina-based low-depth whole-genome resequencing to identify single nucleotide polymorphisms (SNPs) and assess genetic differentiation among sago palm varieties. Seventy-two accessions representing thorny high-yield, thornless high-yield and thorny low-yield varieties were sequenced using the Illumina NovaSeq platform. Sequencing generated 4.3–9.7 Gb of data per sample, corresponding to 8.4×–19.1× genome coverage, with an average coverage of 11.7×. Variant calling initially identified 4,129,378 SNPs, of which 376,875 high-confidence SNPs were retained after filtering. The selected SNP dataset had 11.79% missing data, 10.38% heterozygous sites and an average minor allele frequency of 0.0706. Population-level diversity estimates showed that expected heterozygosity was highest in KR (H_e = 0.217), followed by TS (H_e = 0.187), MC (H_e = 0.187), MS (H_e = 0.188), AB (H_e = 0.179) and TC (H_e = 0.176). Genome-wide SNP analyses using phylogenetic clustering, genetic distance analysis, principal component analysis and ADMIXTURE revealed genetic structuring among the sampled accessions. PCA separated the major varietal groups, with PC1 and PC2 explaining 20.5% and 9.0% of the genetic variation, respectively. ADMIXTURE analysis supported K = 4 as the best-fitting model, indicating three main varietal lineages and an additional ancestry component consistent with substructure or admixture. Thorny high-yield and thornless high-yield accessions generally formed distinct clusters, whereas the thorny low-yield group showed greater genetic heterogeneity and partial ancestry sharing with other groups. These findings demonstrate the utility of genome-wide SNP markers for resolving genetic relationships among sago palm varieties and provide a foundation for germplasm management, varietal authentication and future breeding strategies.