Construction of SNP-PARMS Fingerprints and Analysis of Genetic Diversity in Taro (Colocasia esculenta)

Taro (Colocasia esculenta) is the fifth most cultivated root crop in the world. During the asexual reproduction of taro, the frequent mutation of somatic cells leads to high genetic diversity. With the continuous increase in the amount of taro germplasm resources collected, efficiently and accurately genotyping taro has become a major problem. The identification of taro resources using penta-primer amplification refractory mutation system single-nucleotide polymorphisms (SNP-PARMS) is a relatively efficient method. After resequencing 29 taro resources in this study, approximately 86.95 million SNPs were obtained. Then, 252 specific SNP loci were screened. Based on these 252 specific SNP loci, 36 pairs of PARMS-SNP markers were formed. Among them, 9 pairs of PARMS-SNP markers with a sample loss rate > 15% were eliminated, and finally 27 pairs of PARMS-SNP markers were determined. The average values of minimal allele frequency (MAF), polymorphic information content (PIC), gene diversity (GD), and heterozygosity of these markers are 0.63, 0.34, 0.49, and 0.45, respectively. We analyzed the population structure and the evolutionary group, and the results showed that the 72 taro resources could be divided into 6 groups. The clustering result of the 72 taro resources based on phenotypic traits showed a potential congruence with the result of grouping in the evolutionary tree, with only a few differences detected between the two classifications. Using these markers, DNA fingerprint maps of 72 taro resources were constructed, and all taro resources were differentiated. Some resources show potential similarities in DNA fingerprint maps, as well is in their phenotypic traits, confirming the validity of the fingerprint. The study’s findings serve as a reference for the analysis of the genetic diversity of taro resources.