Theoretical and Applied Genetics

, Volume 125, Issue 4, pp 731–747

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

  • M. Truntzler
  • N. Ranc
  • M. C. Sawkins
  • S. Nicolas
  • D. Manicacci
  • D. Lespinasse
  • V. Ribière
  • P. Galaup
  • F. Servant
  • C. Muller
  • D. Madur
  • J. Betran
  • A. Charcosset
  • L. Moreau
Original Paper

DOI: 10.1007/s00122-012-1866-y

Cite this article as:
Truntzler, M., Ranc, N., Sawkins, M.C. et al. Theor Appl Genet (2012) 125: 731. doi:10.1007/s00122-012-1866-y

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.

Supplementary material

122_2012_1866_MOESM1_ESM.doc (597 kb)
Supplementary material 1 (DOC 597 kb)

Copyright information

© Springer-Verlag 2012

Authors and Affiliations

  • M. Truntzler
    • 1
  • N. Ranc
    • 2
  • M. C. Sawkins
    • 2
  • S. Nicolas
    • 1
  • D. Manicacci
    • 3
  • D. Lespinasse
    • 2
  • V. Ribière
    • 4
  • P. Galaup
    • 4
  • F. Servant
    • 5
  • C. Muller
    • 5
  • D. Madur
    • 1
  • J. Betran
    • 2
  • A. Charcosset
    • 1
  • L. Moreau
    • 1
  1. 1.INRA, UMR de Genetique Vegetale INRA/Université Paris-Sud/CNRSGif-sur-YvetteFrance
  2. 2.Molecular BreedingSyngenta SeedsSaint-SauveurFrance
  3. 3.Université d’Orsay, UMR de Genetique Vegetale INRA/Université Paris-Sud/CNRSGif-sur-YvetteFrance
  4. 4.Markers laboratorySyngenta SeedsSaint-SauveurFrance
  5. 5.BioinformaticsSyngenta SeedsSaint-SauveurFrance