High-resolution melting (HRM) analysis with SNP or SSR markers related to apple skin color or rootstock identification

Abstract

Anthocyanin biosynthesis is reported to be controlled by one of the transcription factors, called MdMYB1 in apple fruit skin. MdMYB1-1, one allele of MdMYB1 gene, is the only allele associated with the red skin color and other alleles produce yellow or green skin apples. In this study, five single-nucleotide polymorphism (SNP) markers were developed to distinguish which is red-skinned or non-red apples based on the sequences of MdMYB1 alleles. The SNP markers were assessed by high-resolution melting (HRM) analysis according to the melting curves patterns. The “M.9” and “M.26” are the widely used dwarfing rootstocks in South Korea. The discrimination of rootstocks using morphological traits is almost impossible as apple trees get older. HRM analysis has been used to identify “M.9” and “M.26” with simple sequence repeat (SSR) markers. Two SSR markers were highly informative and generated distinguishable curve profiles from HRM analysis. These markers would be efficiently and accurately utilized in breeding program targeting fruit skin color and cultivar identification with HRM analysis.