title: Diversity and linkage disequilibrium features in a composite public/private dent maize panel: consequences for association genetics as evaluated from a case study using flowering time.
abstract: Recent progress in genotyping and resequencing techniques have opened new opportunities for deciphering quantitative trait variation by looking for associations between traits of interest and polymorphisms in panels of diverse inbred lines. Association mapping raises specific issues related to the choice of appropriate (i) panels and marker-densities and (ii) statistical methods to capture associations. In this study, we used a panel of 314 maize inbred lines from the dent pool, composed of inbred material from public institutes (113 inbred lines) and a private company (201 inbred lines). We showed that local LD was higher and genetic diversity lower in the material of private origin than in the public material. We compared the results obtained by different software for identifying population structure and computing relatedness among lines, and ran association tests for earliness related traits. Our results confirmed the importance of the mite polymorphism of Vgt1 on flowering time, but also showed that its effect can be captured by zmRap2.7 polymorphisms located 70 kb apart. We also highlighted associations with polymorphisms within genes putatively involved in lignin biosynthesis pathway, which deserve further investigations.
authors.affiliation: INRA, UMR de Genetique Vegetale INRA/Université Paris-Sud/CNRS, Gif-sur-Yvette, France. marion.truntz@gmail.com
authors.forename: M
authors.initials: M
authors.lastname: Truntzler
authors.forename: N
authors.initials: N
authors.lastname: Ranc
authors.forename: M C
authors.initials: MC
authors.lastname: Sawkins
authors.forename: S
authors.initials: S
authors.lastname: Nicolas
authors.forename: D
authors.initials: D
authors.lastname: Manicacci
authors.forename: D
authors.initials: D
authors.lastname: Lespinasse
authors.forename: V
authors.initials: V
authors.lastname: Ribière
authors.forename: P
authors.initials: P
authors.lastname: Galaup
authors.forename: F
authors.initials: F
authors.lastname: Servant
authors.forename: C
authors.initials: C
authors.lastname: Muller
authors.forename: D
authors.initials: D
authors.lastname: Madur
authors.forename: J
authors.initials: J
authors.lastname: Betran
authors.forename: A
authors.initials: A
authors.lastname: Charcosset
authors.forename: L
authors.initials: L
authors.lastname: Moreau
mesh_terms: D035264:Flowers / Q000235:genetics* / Q000502:physiology*; D056726:Genetic Association Studies; D014644:Genetic Variation; D018745:Genome, Plant / Q000235:genetics; D007178:Inbreeding; D015810:Linkage Disequilibrium / Q000235:genetics*; D010641:Phenotype; D011110:Polymorphism, Genetic; D011157:Population Dynamics; D025341:Principal Component Analysis; D017149:Private Sector; D017150:Public Sector; D013997:Time Factors; D003313:Zea mays / Q000235:genetics*