Original Paper

Tree Genetics & Genomes

, Volume 5, Issue 1, pp 93-107

Construction of a dense genetic linkage map for apple rootstocks using SSRs developed from Malus ESTs and Pyrus genomic sequences

  • J.-M. CeltonAffiliated withHorticulture and Food Research Institute of New Zealand Ltd, Palmerston North Research Center
  • , D. S. TustinAffiliated withHorticulture and Food Research Institute of New Zealand Ltd, Hawkes Bay Research Center
  • , D. ChagnéAffiliated withHorticulture and Food Research Institute of New Zealand Ltd, Palmerston North Research Center
  • , S. E. GardinerAffiliated withHorticulture and Food Research Institute of New Zealand Ltd, Palmerston North Research Center Email author 

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Abstract

Marker-assisted selection (MAS) offers quick and reliable prediction of the phenotypes of seedlings in large populations and thus opens new approaches for selection to breeders of apple (Malus x domestica Borkh.). The development of framework maps enables the discovery of genetic markers linked to desired traits. Although genetic maps have been reported for apple scion cultivars, none has previously been constructed for apple rootstocks. We report the construction of framework genetic maps in a cross between ‘M.9’ (‘Malling 9’) and ‘R.5’ (‘Robusta 5’) apple rootstocks. The maps comprise 224 simple sequence repeat (SSR) markers, 18 sequence-characterised amplified regions, 14 single nucleotide polymorphisms and 42 random amplified polymorphic DNAs. A new set of 47 polymorphic SSRs was developed from apple EST sequences and used for construction of this rootstock map. All 17 linkage groups have been identified and aligned to existing apple genetic maps. The maps span 1,175.7 cM (‘M.9’) and 1,086.7 cM (‘R.5’). To improve the efficiency of mapping markers to this framework map, we developed a bin mapping set. Applications of these new genetic maps include the elucidation of the genetic basis of the dwarfing effect of the apple rootstock ‘M.9’ and the analysis of disease and insect resistance traits such as fire blight (Erwinia amylovora), apple scab (Venturia inaequalis) and woolly apple aphid (Eriosoma lanigerum). Markers for traits mapped in this population will be of direct use to apple breeders for MAS and for identification of causative genes by map-based cloning.

Keywords

Apple Genetic map SSR Molecular markers EST