Genomic exploration of Iranian almond (Prunus dulcis) germplasm: decoding diversity, population structure, and linkage disequilibrium through genotyping-by-sequencing analysis

This study focuses on the genetic diversity and population structure of Prunus dulcis (almond tree), a crucial agricultural component with widespread cultivation and commercial importance, particularly in Iran, a region with a longstanding tradition of almond cultivation. The diverse almond collection in Iran encompasses many local varieties, breeding selections, rootstocks, and international cultivars. This diversity necessitates advanced genotyping techniques to gain insights into genetic diversity, population structure, and linkage disequilibrium (LD). In this paper, genotyping-by-sequencing (GBS) was employed to analyze 62 almond germplasm samples, identifying approximately 63,537 high-quality single nucleotide polymorphisms (SNPs) distributed across the eight chromosomes of the almond genome. On average, there were 30,225 SNPs per chromosome. The analysis yielded an average polymorphism information content (PIC) of 0.315 and an expected heterozygosity (He) rate of 0.28, indicating a significant level of genetic diversity within the studied almond germplasm. The LD analysis demonstrated a rapid decline, with an average LD decay spanning approximately 300 kb for an r2 value of 0.2. This suggests substantial hybridization among the sampled almond varieties. Principal Component Analysis (PCA) and structure analysis could not differentiate genotypes based on geographical origin, providing further evidence of genetic mixing among the studied almond populations. An Analysis of Molecular Variance (AMOVA) highlighted significant genetic diversity within populations but revealed minimal differences. This comprehensive study of Iran's almond genotypes offers valuable insights for future breeding and conservation efforts, emphasizing this agriculturally significant species abundant genetic diversity and intricate population structure.