Molecular identification of broomcorn millet germplasm resources in Shaanxi based on SSR

To construct the DNA molecular identity card of broomcorn millet (<italic>Panicum miliaceum</italic> L.), we conducted an experiment using 181 core germplasm samples of Shaanxi millets. The core primers were obtained through several rounds of PCR screening and optimization of millet-specific SSR markers developed in the preliminary stage of our research group. Chromosomal localization of the core markers was performed by comparing their sequences with the reference genome information of broomcorn millet using BLAST. FAM/HEX labels were added the 5' end of SSR primers, and the presence or absence of fragments detected by capillary electrophoresis was represented as “0/1”. The differentiation of fragments was carried out using ID Analysis 4.0, and the size of the amplified fragments was recorded in format (0-9) to construct unique material strings. These strings were then subjected to genetic diversity analysis using software tools such as Pop Gene, Power Marker, MEGA, Structure, and NTSYS. Our test results showed that seven combinations of fluorescent SSRs (RYW3, RYW6, RYW37, RYW40, RYW43, RYW125, and RYW146) could distinguish the 181 materials. These markers were unevenly distributed across five chromosomes, and a total of 77 allelic variants were detected, with an average of 11 variants per marker. The observed Shannon's diversity index (I) ranged from 0.8145 (RYW146) to 7.8254 (RYW125), with an average of 5.9076. The observed heterozygosity (Ho) ranged from 0.2627 (RYW146) to 0.9506 (RYW3), while the expected heterozygosity (He) ranged from 0.3329 (RYW146) to 0.8747 (RYW125). Nei’s gene diversity index (Nei) varied from 0.3315 (RYW146) to 0.8722 (RYW125). The Polymorphism Information Content (PIC) ranged from 0.5923 (RYW146) to 0.9445 (RYW125), with an average of 0.8419. Using the UPGMA clustering method, we categorized the 181 resources into three clusters. Principal component analysis resulted in the classification of the materials into ten taxa, which were consistent with their geographic sources. To provide convenient access to the DNA molecular identity cards, we utilized online QR code technology (<uri>https://cli.im/</uri>) for the 181 Shaanxi broomcorn millet core germplasm samples.