Apple varieties from Kazakhstan and their relation to foreign cultivars assessed with RosBREED 10K SNP array

Abstract

Apples are one of the most important fruit tree crops in Kazakhstan. However, the local varieties remain poorly studied relative to foreign cultivars. Here we compared 24 well-characterized of Malus domestica specimens and 21 Malus sieversii specimens from Kazakhstan in comparison with foreign collection. A total of 3,119 SNP markers from the RosBREED Apple 10k SNP array were selected for data comparison after quality control. The cultivars from Kazakhstan were found to be closely related to foreign domestic apple varieties and could be classified into two distinguishable clusters. 'Saltanať, 'Zailiyskoe', 'Kazakh Jubilee', 'Talgar', 'Rubin' (KZJ, 'Aport' ('Aport Alexander') together with the German cultivar 'Geheimrat Dr. Oldenburg' form the most distinct group in both admixture and genetic distance analyses. Another distinct group included five cultivars related to 'Golden Delicious'. Malus sieversii samples from Kazakhstan and the New Zealand collection formed a separate mixed cluster. Malus sieversii from Kazakhstan form a distinct compact sub-cluster comprising mostly samples from the Institute of Plant Biology and Biotechnology. Malus sieversii samples from the New Zealand collection formed a more heterogeneous group compared to wild and domestic apple from Kazakhstan.