title: Genome-wide prediction methods for detecting genetic effects of donor chromosome segments in introgression populations.
abstract: BACKGROUND
  Introgression populations are used to make the genetic variation of unadapted germplasm or wild relatives of crops available for plant breeding. They consist of introgression lines that carry small chromosome segments from an exotic donor in the genetic background of an elite line. The goal of our study was to investigate the detection of favorable donor chromosome segments in introgression lines with statistical methods developed for genome-wide prediction.
  
  
  RESULTS
  Computer simulations showed that genome-wide prediction employing heteroscedastic marker variances had a greater power and a lower false positive rate compared with homoscedastic marker variances when the phenotypic difference between the donor and recipient lines was controlled by few genes. The simulations helped to interpret the analyses of glycosinolate and linolenic acid content in a rapeseed introgression population and plant height in a rye introgression population. These analyses support the superiority of genome-wide prediction approaches that use heteroscedastic marker variances.
  
  
  CONCLUSIONS
  We conclude that genome-wide prediction methods in combination with permutation tests can be employed for analysis of introgression populations. They are particularly useful when introgression lines carry several donor segments or when the donor segments of different introgression lines are overlapping.
authors.affiliation: Institute of Agronomy and Plant Breeding II, Justus Liebig University, 35392 Giessen, Germany. k.christin.falke@wwu.de.
authors.forename: Karen Christin
authors.initials: KC
authors.lastname: Falke
authors.forename: Gregory S
authors.initials: GS
authors.lastname: Mahone
authors.forename: Eva
authors.initials: E
authors.lastname: Bauer
authors.forename: Grit
authors.initials: G
authors.lastname: Haseneyer
authors.forename: Thomas
authors.initials: T
authors.lastname: Miedaner
authors.forename: Frank
authors.initials: F
authors.lastname: Breuer
authors.forename: Matthias
authors.initials: M
authors.lastname: Frisch
mesh_terms: D001947:Breeding; D002875:Chromosomes; D018556:Crops, Agricultural; D055106:Genome-Wide Association Study; D006801:Humans; D008957:Models, Genetic