Development of EST-SSR markers and population genetic structure and genetic diversity of the Malus transitoria (Batalin) C. K. Schneider in Qinghai-Tibetan Plateau

Malus transitoria (Batalin) C. K. Schneider is a shrub or small tree species native to in and around the Qinghai-Tibetan Plateau (QTP). Using 18 pairs of EST-SSR markers, we examined 142 samples from 8 wild populations of M. transitoria obtained from the QTP. Genetic diversity had been high at the species level and showed the mean expected heterozygosity (He) and Shannon's information index (I) per population were 0.573 and 0.921, as well as the genetic diversity of the WD population (He = 0.595, I = 0.974) had been the greatest, whereas that of the BS population (He = 0.541, I = 0.870) was the lowest. The MKH population had the lowest genetic diversity (Nm = 5.034), while the mean Gene Flow (Nm) was 6.076. Molecular variance analysis (AMOVA) demonstrated moderate genetic differentiation among populations, that Within Populations variation (95%) had been significantly higher than Among Populations variation (5%), which complies to the genetic differentiation coefficient (Fst = 0.057). Two clusters grouped similar to the Unweighted Pair Group Method with Arithmetic (UPGMA) clustering and principal coordinates analysis (PCoA) as per the STRUCTURE analysis. We speculate that long-term orogeny prevents gene exchange across populations, leading to limited gene flow and loss of genetic resources. This research investigated the genetic diversity as well as structure of natural populations of M. transitoria in order to provide a scientific basis of the conservation, breeding, and rational utilization of this tree species germplasm resources in QTP. The lowest Gene Flow population may be preserved by a combination of in-situ conservation and ex-situ conservation (MKH population). Expanding the number of populations and ex-site conservation could preserve the smallest population (XQ population). The other population s could in-situ conserved in order to protect genetic resources.