title: Mixed model approach for IBD-based QTL mapping in a complex oil palm pedigree.
abstract: BACKGROUND
  Elaeis guineensis is the world's leading source of vegetable oil, and the demand is still increasing. Oil palm breeding would benefit from marker-assisted selection but genetic studies are scarce and inconclusive. This study aims to identify genetic bases of oil palm production using a pedigree-based approach that is innovative in plant genetics.
  
  
  RESULTS
  A quantitative trait locus (QTL) mapping approach involving two-step variance component analysis was employed using phenotypic data on 30852 palms from crosses between more than 300 genotyped parents of two heterotic groups. Genome scans were performed at parental level by modeling QTL effects as random terms in linear mixed models with identity-by-descent (IBD) kinship matrices. Eighteen QTL regions controlling production traits were identified among a large genetically diversified sample from breeding program. QTL patterns depended on the genetic origin, with only one region shared between heterotic groups. Contrasting effects of QTLs on bunch number and weights reflected the close negative correlation between the two traits.
  
  
  CONCLUSIONS
  The pedigree-based approach using data from ongoing breeding programs is a powerful, relevant and economic approach to map QTLs. Genetic determinisms contributing to heterotic effects have been identified and provide valuable information for orienting oil palm breeding strategies.
authors.affiliation: CIRAD, UMR AGAP (Genetic Improvement and Adaptation of Mediterranean and Tropical Plant Research Unit), Campus international de Baillarguet, 34398, Montpellier, France. sebastien.tisne@cirad.fr.
authors.forename: Sébastien
authors.initials: S
authors.lastname: Tisné
authors.affiliation: CIRAD, UMR AGAP (Genetic Improvement and Adaptation of Mediterranean and Tropical Plant Research Unit), Campus international de Baillarguet, 34398, Montpellier, France. marie.denis@cirad.fr.
authors.forename: Marie
authors.initials: M
authors.lastname: Denis
authors.affiliation: CIRAD, UMR AGAP (Genetic Improvement and Adaptation of Mediterranean and Tropical Plant Research Unit), Campus international de Baillarguet, 34398, Montpellier, France. david.cros@cirad.fr.
authors.forename: David
authors.initials: D
authors.lastname: Cros
authors.affiliation: CIRAD, UMR AGAP (Genetic Improvement and Adaptation of Mediterranean and Tropical Plant Research Unit), Campus international de Baillarguet, 34398, Montpellier, France. virginie.pomies@cirad.fr.
authors.forename: Virginie
authors.initials: V
authors.lastname: Pomiès
authors.affiliation: CIRAD, UMR AGAP (Genetic Improvement and Adaptation of Mediterranean and Tropical Plant Research Unit), Campus international de Baillarguet, 34398, Montpellier, France. virginie.riou@cirad.fr.
authors.forename: Virginie
authors.initials: V
authors.lastname: Riou
authors.affiliation: Agriculture Department, SOCFINDO (PT Socfin-Indonesia), Medan, Indonesia. psbb_socfindo@yahoo.co.id.
authors.forename: Indra
authors.initials: I
authors.lastname: Syahputra
authors.affiliation: INRAB, CRAPP, Pobè, Bénin. omores_alphonse@yahoo.fr.
authors.forename: Alphonse
authors.initials: A
authors.lastname: Omoré
authors.affiliation: PalmElit SAS, 34980, Montferrier sur Lez, France. tristan.durand-gasselin@palmelit.com.
authors.forename: Tristan
authors.initials: T
authors.lastname: Durand-Gasselin
authors.affiliation: CIRAD, UMR AGAP (Genetic Improvement and Adaptation of Mediterranean and Tropical Plant Research Unit), Campus international de Baillarguet, 34398, Montpellier, France. jean-marc.bouvet@cirad.fr.
authors.forename: Jean-Marc
authors.initials: JM
authors.lastname: Bouvet
authors.affiliation: CIRAD, UMR AGAP (Genetic Improvement and Adaptation of Mediterranean and Tropical Plant Research Unit), Campus international de Baillarguet, 34398, Montpellier, France. benoit.cochard@palmelit.com.|PalmElit SAS, 34980, Montferrier sur Lez, France. benoit.cochard@palmelit.com.
authors.forename: Benoît
authors.initials: B
authors.lastname: Cochard
mesh_terms: D028023:Arecaceae / Q000235:genetics*; D001947:Breeding; D002874:Chromosome Mapping; D003433:Crosses, Genetic; D008040:Genetic Linkage; D005838:Genotype; D018895:Microsatellite Repeats / Q000235:genetics*; D008957:Models, Genetic; D000073878:Palm Oil; D010375:Pedigree; D010938:Plant Oils; D040641:Quantitative Trait Loci / Q000235:genetics*
chemical_list: D010938:Plant Oils; D000073878:Palm Oil