Apple Structural Genomics

  • Schuyler S. Korban
  • Stefano Tartarini
Part of the Plant Genetics and Genomics: Crops and Models book series (PGG, volume 6)

A primary focus of apple genetics is the elucidation of genes influencing diverse phenotypes of economically important horticultural traits. Most of these phenotypes are genetically complex; i.e., controlled by multiple genes occupying chromosomal positions referred to as quantitative trait loci (QTL). Mapping of QTLs has become a common first step toward understanding the molecular basis of complex genetic traits, and it has provided the impetus for developing detailed genome maps. These genome maps are built with the aid of various biochemical and molecular markers such as isozymes, restriction fragment length polymorphisms (RFLPs), random amplified polymorphic DNAs (RAPDs), amplified fragment length polymorphisms (AFLPs), and simple sequence repeats (SSRs), among others. Dominant markers, such as RAPDs, can be used for map alignment if these markers are heterozygous in both parents, but their transferability to other maps is limited. While, co-dominant markers such as SSRs are also useful in map alignment, but they are also transferable between mapping populations. More recently, single nucleotide polymorphisms (SNPs) have taken hold as SNPs can occur in both coding (gene) and noncoding regions of the genome. Those SNPs found within a coding sequence are of particular interest as they are more likely to alter the biological function of a protein. SNPs are major contributors to genetic variation, comprising approximately 80% of all know polymorphisms, and their density in plants is variable depending on the species, while in the human genome it is estimated to be on average of 1 per 1000 base pairs. Although SNPs are mostly biallelic (less informative than short tandem repeats), they are more frequent and mutationally stable, making them suitable for association studies in which linkage disequilibrium (LD) between markers and an unknown variant is used to map mutations in complex traits. SNP maps will help in identifying multiple genes associated with such complex traits influencing tree architecture, fruit quality, and disease resistance. These associations are difficult to establish with conventional gene-hunting methods because a single altered gene may only be a small contributor to such a trait.


Quantitative Trait Locus RAPD Marker Scar Marker Apple Cultivar Scab Resistance 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


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© Springer Science+Business Media, LLC 2009

Authors and Affiliations

  1. 1.Department of Natural Resources and Environmental SciencesUniversity of IllinoisUrbanaUSA 61801
  2. 2.Department of Fruit and Woody Plant SciencesAlma Mater Studiorum – Bologna University40127 BolognaItaly

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