Development of DNA Fingerprints and Assessment of Genetic Diversity in 54 Chenopodium quinoa Germplasm Accessions using InDel Markers

Abstract To characterize genetic diversity, clarify the relationships between accessions, and build a molecular identification system for quinoa ( Chenopodium quinoa Willd.), 54 accessions from different sources were phenotyped and genotyped with 45 polymorphic InDel primer pairs that gave clear and repeatable amplification. Ninety stable and scorable band loci were obtained. The mean effective number of alleles, Nei’s gene diversity, Shannon’s information index, and polymorphism information content (PIC) were 1.7496, 0.4179, 0.6053, and 0.3271, which indicates that the tested collection has moderate genetic diversity. Phenotypic clustering divided the accessions into three groups at a phenotypic distance of about 0.50, whereas molecular clustering separated them into five groups at a genetic similarity coefficient of about 0.57. The accessions from different geographical origins were interspersed in the clusters. The DNA fingerprint was generated by coding the 90 band loci in a fixed order; each accession had a unique code, so that all accessions tested could be distinguished. These results provide a molecular basis for accession identity verification, assessment of genetic relationships, screening for duplicate material, and the selection of parents for crossing.