Genetic diversity and population structure of Indonesia’s mandarin citrus genotypes using simple sequence repeat and start codon targeted markers

Citrus is one of the prominent horticultural crops that is highly consumed by people around the world. Being located near the equator, Indonesia has several mandarin citrus genotypes, including siam and keprok citrus, which remain poorly characterized. Hence, assessing of their genetic diversity will help us identify genotypes that possess important traits suitable for breeding programs. The objective of this study were to analyze the genetic diversity of Indonesia’s local mandarin citrus genotypes using Simple Sequence Repeat (SSR) and Start Codon Targeted (SCoT) markers and compare the robustness of those markers in genetic diversity analysis. Thirty-seven mandarin genotypes consisting of 7 siam cultivars, 28 keprok cultivars, and 2 cultivars derived from their hybridization, were subjected to genetic diversity analysis using 20 SSR and SCoT markers. The number of alleles detected by SCoT markers was higher than by SSR markers. SCoT markers accounted for 119 alleles, while SSR markers accounted for 99 alleles. The number of alleles at each locus detected by SCoT and SSR markers varied from 4 to 9 and 2 to 7, respectively. In addition, 15 SCoT and 13 SSR markers with Polymorphic Information Content (PIC) values greater than 0.5 were identified, which indicated their potential as highly informative markers in citrus breeding programs. The phylogenetic tree and principal coordinate analysis (PCoA) plot constructed from SSR and SCoT markers revealed differentiation between the siam and keprok cultivars. The analysis of molecular variance (AMOVA) results indicated that there was greater genetic variation within populations than among populations, thus suggesting extensive cross-pollination in the citrus genotypes studied. The population structure, as indicated by the highest delta K value of K = 2 in SSR markers and K = 3 in SCoT markers, showed evidence of gene flow occurred among citrus populations. The findings have implication for future citrus breeding.