Date Palm (Phoenix dactylifera L.) Microsatellites: Genome-Wide Resource for Diversity Analysis and Cross-Transferability in Arecaceae

Date palm (Phoenix dactylifera L.) being cultivated in arid and semi-arid regions of the world is an economically important crop in food, sugar, and other industries. To enhance the accuracy and efficiency of breeding and conservation programs in date palm and other related crops, molecular markers, such as microsatellites/simple sequence repeat (SSR), are very important. Molecular markers as genomic resources in date palm are not well explored. Hence, the present study aimed to develop and characterize genome-wide microsatellite markers for date palm and prove their applicability in genetic diversity analysis and cross-genera transferability within the Arecaceae. A total of 215,013 perfect microsatellite motifs were identified across the genome. The most abundant SSR motifs were di-nucleotide repeats (DNR) and mono-nucleotide repeats (MNR) with 37.94% and 37.84% abundance. The motifs were scanned to design primer pairs (169,200), and of them, 71 high polymorphism potential (HPP) markers were validated across three date palm genotypes with an 87.04% amplification success rate. Genetic diversity analysis using 22 polymorphic markers in 48 date palm genotypes revealed high allelic variation and three major genetic clusters. The population structure analysis showed two major clusters (K = 2), indicating two sources of origin for the allelic pools. The polymorphism information content (PIC) of markers ranged from 0.06 to 0.67 with ten markers with high PIC (> 0.5), emphasizing the high informativeness of these markers in genetic studies. Additionally, cross-genera transferability was evaluated in ten species of Arecaceae, with areca nut showing the highest transferability (80.33%) and areca palm the lowest (9.84%). A total of six species showed more than 50% transferability of markers, indicating their potential for comparative genomics in Arecaceae. The novel microsatellite markers developed in the present study will provide valuable tools for genetic diversity analysis, conservation, and marker-assisted breeding (MAB) in date palm and related species of Arecaceae.