Genetic identity based on simple sequence repeat (SSR) markers for Quinoa (Chenopodium quinoa Willd.)

Abstract

Molecular markers based on simple sequence repeats (SSRs) constitute a highly effective instrument in the identification of quinoa genotypes (Chenopodium quinoa), and they are very useful in the management and conservation of germplasm banks. The present study was carried out in the Molecular Biology Laboratories of the Megalaboratory of the National University of the Altiplano and the National Agrarian University la Molina. With the objective of determining a minimum group of highly informative initiators for the cultivation of quinoa to study and identify the obtained alleles and implementing and incorporating this technology into research of genetic identity, the molecular analysis of nine loci located by microsatellite markers (SSRs) was performed on a sample of 26 varieties of quinoa: Ayrampo, Amarilla de Marangani, Choclito, Chullpi, Huariponcho, Pandela, Sajama, Witulla, Kcancolla, Negra Collana, Salcedo, Pasankalla, Blanca de Juli, and Chenopodium petiolare from the CIP-Camacani and Blanca de Juli, Kcancolla, Negra Collana, Pasankalla, Altiplano, Illpa INIA, Salcedo, Ayara Blanca de Juli, Ayara Blanca de Arequipa, Ayara Cancolla, Ayara Pasankalla, and Ayara Salcedo from the INIA. Genomic DNA was extracted by PCR (GeneJET Plant Genomic DNA Purification), and 20 microsatellite regions were amplified. The amplified fragments were loaded on polyacrylamide gels to determine their size in base pairs, of which only nine showed products with reading quality (QCA012, QCA015, QCA021, QCA029, QCA034, QCA040, QCA053, QCA055 and QCA067). The fragments were evaluated for their allelic richness, heterozygosity (H) and polymorphic information content (PIC). The data were processed with Gen Alex software ver. 3.5 A total of 67 alleles were detected among the different regions analyzed, with an average of 7 alleles for loci ranging from 142 to 240 bp and an effective number of alleles (ENA) of 5.36. The mean heterozygosity was 0.80, and the mean Polymorphic Information Content (PIC) was 0.81. The markers were highly polymorphic; therefore, the most informative SSR primers in the present study would be made up of three markers with PIC, QCA053 (0.87), QCA015 (0.86) and QCA034 (0.86), for determining the genetic identity of Chenopodium quinoa Willd. These markers can be easily interpreted and are useful for the molecular characterization of quinoa varieties. Analysis of the hierarchical clusters using UPGMA (Unweighted Pair Group Method) clustering identified 5 groups at a similarity coefficient of 0.77 among the quinoa varieties studied in this research.