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Apple is one of the important fruit tree in the world, but traditional genetics and breeding costs more time,labor and money due to apple,s long juvenile period and life cycle,the large plant and self-incompatibility so on. DNA molecular markers were widely developed and applied to various aspects of research in apple with molecular biology booming in recent years,so it was possible to identify apple cultivars quickly. Especially SSR marker is highly polymorphic, codominant, well-repeated and convenient. Fuji and qinguan comprehensive superior traits of venturia inaequalis varieties, not only in our country’s existing varieties and occupies an important position, also is very important hybrid breeding parent material.With the material of apple cultivar Qinguan as the maternal parent, Fuji as male parent and their F1 158 progenies, an optimized PCR reaction system for SSR were obtained:in a 20μL total volume, Taq DNA polymerase 0.5 U, primer 0.1μmol /L, dNTPs 0.3 mmol /L, template DNA 15 ng/μL and Mg2+ 1.8 mmol/L were used. A consensus genetic map from Qinguan×Fuji was constructed by JoinMap 3.0 with SSR markers. Out of 340 SSR primer pairs, 49 were proved having polymorphism between father and mother parents, and 75 SSR markers were acquired by the polymorphic primer pairs. Among these SSR markers, 17 were distorted from the Mendelin ratio, 27 were located on the genetic linkage map composed by 10 linkage groups. Compared with formerly published frame genetic maps, our SSR marker on the linkage group were consistent to the reference map respectively. The result implied that the optimized SSR system is efficient and stable for SSR marker selection and genetic mapping.The disease-resistant performance of apple cultivars Qinguan, Fuji and its F1 progenies were assessed and investigated for apple early deciduous disease in field. The chi-square test showed that the segregation ratio of desease index of F1 progenies was 1:1, and early deciduous disease resistance gene was located on the tenth linkage groups. Compared to the published apple genetic map, our early deciduous disease resistant gene could be placed on the eighth linkage groups of published reference map.
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