Single Nucleotide Polymorphism (SNP) Analysis of the Endopolygalacturonase Gene in Chinese Bayberry (Myrica rubra)

Endo-PG plays an important role in the ripening of Chinese Bayberry (Myrica rubra) fruit by causing its softening and inducing textural changes. 45 Chinese Bayberry accessions were tested to detect single nucleotide polymorphisms (SNPs) in the endo-PG gene by PCR-based sequencing of a 1866 bp long DNA fragment. A total of 178 SNPs were identified, of which 60 were singleton variable sites and another 118 were parsimony informative sites. The nucleotide diversity value (Pi) was 0.27. A total of 12 haplotypes were identified and a dendrogram was constructed for endo-PG using the neighbor-joining (NJ) clustering method. The results indicated that the 45 accessions were clustered into four groups and that the clustering correlated with fruit hardness. Additionally, some cultivars (e.g. Biqi) were found to have two alleles, conferring pronounced phenotypic differences between allelic combinations and could thus be divided into different groups, while some other cultivars (e.g. Dongkui) had relatively high homozygosity.