Development of DNA molecular ID card in hog millet germplasm based on high motif SSR

Abstract

<p id="C3">In order to identify hog millet (<italic>Panicum miliaceum</italic>) germplasm rapidly, to establish a big data management platform, to provide a theoretical basis for germplasm identification and traceability management, 130 germplasms from four ecological cultivation areas were used as materials to construct a molecular ID based on 35 high-motif SSRs (21, 10, and 4 with four-, five-, and six-nucleotide repeats, respectively). The results showed that 30 out of the 35 SSRs could be used as core markers for the construction of molecular ID cards. Ninety allelic variants were detected; effective allelic variants (<italic>Ne</italic>) ranged from 2.3186 to 2.9982 with an average of 2.7607; Shannon diversity index (<italic>I</italic>) ranged from 0.9158 to 1.0873 with an average of 1.0472. The observed heterozygosity (<italic>Ho</italic>) was 0.5000-0.8678 with a mean of 0.7168; the expected observed heterozygosity (<italic>He</italic>) was 0.5710-0.6691 with a mean of 0.6386; the Nei’s gene diversity index (<italic>Nei</italic>) was 0.5687-0.6665 with a mean of 0.6360; the polymorphism information content (PIC) was 0.5151-0.7898, with a mean of 0.6966. All accessions were divided into three groups (Group I, II, and III) according to UPGMA analysis. In terms of Shanxi accessions, landraces and breeding varieties were classified into Group I and III, respectively, and farmers materials were distributed into three groups. Based on PCA analysis, all accessions were classified into four clusters, which were related to their geographical origin. As for the rule that the most germplasms were determined using the least markers, 3 markers were excluded due to their high similarity coefficient with others, namely RYW23, RYW49, and RYW51. Screening the remaining 27 markers, the combinations of 17 SSR (RYW35, RYW40, RYW37, RYW18, RYW30, RYW16, RYW20, RYW19, RYW8, RYW5, RYW3, RYW7, RYW1, RYW14, RYW9, RYW6, and RYW10) could identify all hog millet accessions. The DNA molecular identifications of character strings, bar code, and quick response (QR) codes were constructed via ID analysis 4.0, software online of bar code and QR codes technique (<uri>http://barcode.cnaidc.com/app/html/bcgcode128.php</uri> and <uri>https://cli.im/</uri>).