Malus niedzwetzkyana (Dieck) Langenf transcriptome comparison and phylogenetic analysis with Malus sieversii (Ledeb) Roem

Malus niedzwetzkyana (Dieck) Langenf is a special germplasm in which all tissues are rich in anthocyanins. In recent years, M. niedzwetzkyana has gained popularity among consumers because of its healthy pulp composition and beautiful fruit color. Despite its valuable features, many functionally transcribed genes involved in anthocyanin biosynthesis have not been comprehensively explored. In addition, the genetic similarity research of M. niedzwetzkyana was also inconclusive. Over many years, our group has collected 153 Malus samples at home and abroad; therefore, we carried anthocyanin synthesis research using -omics and genetic similarity analysis with simple sequence repeat (SSR) markers. Transcriptome sequencing provided more specific sequences for SSR analysis. The results showed that M. niedzwetzkyana had higher similarity to M. sieversii (Ledeb) Roem in China than in other countries. In addition, we identified 83 unigenes involved in anthocyanin synthesis, which could be used in the early identification of red apple breeding seedlings, and to speed up the breeding of cultivated red apples.