Diversity Assessment with SNP, SSR, AFLP, and RAPD Markers in Plants: A Systematic Review and Meta-Analysis

BackgroundDNA-based molecular markers underpin plant genetic diversity assessment, germplasm characterisation, and conservation prioritisation. Four marker systems dominate the field: Amplified Fragment Length polymorphisms (AFLPs), simple sequence repeats (SSRs), single nucleotide polymorphisms (SNPs), and random amplified polymorphic DNA (RAPDs). No quantitative meta-analysis had pooled their performance on the canonical diversity metrics: polymorphism information content (PIC), expected heterozygosity (He), and resolution power, across plants. Existing reviews are narrative, marker-restricted, or qualitatively conclusive of infeasibility. MethodsA PRISMA 2020-compliant systematic review (registered at the Open Science Framework) was executed. Eligible studies were within-study paired comparisons genotyping the same accession panel with at least two of {SNP, SSR, AFLP, RAPD} and reporting at least one diversity metric. Effect sizes were paired standardised mean differences (Hedges g) computed under the Bernoulli-variance approximation. Random-effects REML meta-analysis used metafor 5.0.1 with Knapp-Hartung adjustment, leave-one-out, and r-sensitivity. ResultsFifteen within-study paired contrasts were eligible, distributed across three pools. Pool 2 (SSR vs SNP, He, k = 5) yielded a pooled Hedges g of 0.494 (95% CI: -0.078 to 1.066, p = 0.075; I{superscript 2} = 90.2%; 95% PI [-0.82, 1.81]). SSRs exceeded SNPs on He in 4 of 5 studies; leave-one-out removal of the panel-size-asymmetric outlier raised the estimate to g = 0.644 (p = 0.025). Pool 3a (dominant-marker stratum, k = 6) yielded g = 0.419 (95% CI: -0.121 to 0.960, p = 0.103; I{superscript 2} = 56.5%); five of six contrasts showed SSR or AFLP exceeding RAPD on per-locus PIC. Pool 1 (PIC, k = 3, exploratory) gave a consistent direction (g = 0.453). All three pools point in the same direction: codominant or AFLP markers carry more per-locus information than the alternative being compared. ConclusionsSSR markers reported higher per-locus diversity than SNP and RAPD markers in plant within-study paired comparisons, mechanistically grounded in the SNP biallelic ceiling and the multi-allelic richness of SSRs. The effect attenuated or reversed in selfing/low-diversity panels and at the per-panel level when SNP panels exceeded approximately 1 000 loci. RAPDs show the lowest per-locus information content of the four classes.