Theoretical and Applied Genetics

, Volume 130, Issue 10, pp 2165–2189 | Cite as

Genotyping-by-sequencing highlights original diversity patterns within a European collection of 1191 maize flint lines, as compared to the maize USDA genebank

  • Brigitte GouesnardEmail author
  • Sandra Negro
  • Amélie Laffray
  • Jeff Glaubitz
  • Albrecht Melchinger
  • Pedro Revilla
  • Jesus Moreno-Gonzalez
  • Delphine Madur
  • Valérie Combes
  • Christine Tollon-Cordet
  • Jacques Laborde
  • Dominique Kermarrec
  • Cyril Bauland
  • Laurence Moreau
  • Alain Charcosset
  • Stéphane Nicolas
Original Article


Key message

Genotyping by sequencing is suitable for analysis of global diversity in maize. We showed the distinctiveness of flint maize inbred lines of interest to enrich the diversity of breeding programs.


Genotyping-by-sequencing (GBS) is a highly cost-effective procedure that permits the analysis of large collections of inbred lines. We used it to characterize diversity in 1191 maize flint inbred lines from the INRA collection, the European Cornfed association panel, and lines recently derived from landraces. We analyzed the properties of GBS data obtained with different imputation methods, through comparison with a 50 K SNP array. We identified seven ancestral groups within the Flint collection (dent, Northern flint, Italy, Pyrenees–Galicia, Argentina, Lacaune, Popcorn) in agreement with breeding knowledge. Analysis highlighted many crosses between different origins and the improvement of flint germplasm with dent germplasm. We performed association studies on different agronomic traits, revealing SNPs associated with cob color, kernel color, and male flowering time variation. We compared the diversity of both our collection and the USDA collection which has been previously analyzed by GBS. The population structure of the 4001 inbred lines confirmed the influence of the historical inbred lines (B73, A632, Oh43, Mo17, W182E, PH207, and Wf9) within the dent group. It showed distinctly different tropical and popcorn groups, a sweet-Northern flint group and a flint group sub-structured in Italian and European flint (Pyrenees–Galicia and Lacaune) groups. Interestingly, we identified several selective sweeps between dent, flint, and tropical inbred lines that co-localized with SNPs associated with flowering time variation. The joint analysis of collections by GBS offers opportunities for a global diversity analysis of maize inbred lines.





Genome-wide association study


Single-nucleotide polymorphism


Minor allele frequency


Identity by state


Principal coordinates analysis


Posterior odds


Anthesis-silking interval



This research was supported by Project Amaizing ANR-10-BTBR-01. We are grateful to Geert Kleijer from Agroscope Changins-Wädenswil of Nyon (ETH Zurich) Switzerland; Wolfgang Schipprack from Universität Hohenheim (UH) of Eckartsweier, Germany; Rita Redaelli from Unita Di Ricerca per la Maiscoltura of Bergamo (ISC), Italy; Amando Ordás from Misión Biológica de Galicia of Pontevedra (CSIC), Spain; Ángel Álvarez from Estacion Experimental de Aula Dei of Zaragoza, Spain; José Ignacio Ruiz de Galarreta from Centro Neiker de Arkaute of Vitoria, Spain; colleagues from Centro de Investigaciones Agrarias de Mabegondo (CIAM), Spain; Guillermo Eyhérabide and colleagues from Instituto National de Tecnologia Agropecuaria (INTA), Argentina; colleagues from Instytut Hodowli Aklimatyzacji Roslin (IHAR), Poland; the “Association pour l’étude et l’amélioration du maïs” (PROMAIS), France who contributed genetic material included in this study. We are grateful to Marie-Christine Le Paslier, Aurélie Bérard from Etude du Polymorphisme des Génomes Végétaux (INRA-EPGV), Anne Boland from Institut de Génomique, Centre National de Génotypage (CEA-IG/CNG), and their staff for quality control of DNA normalisation and DNA plate composition. We are grateful to Ed Buckler and colleagues for GBS data production at Cornell.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical standards

The experiments reported in this study comply with the current laws of France.

Supplementary material

122_2017_2949_MOESM1_ESM.xlsx (236 kb)
Suppl. Table 1: list of the inbred lines of the Flint collection, with the origin of the collection, the country of the breeder, the pedigree, the heterozygosity rate, the admixture coefficients to the 7 clusters, the cluster membership at 50%, the coordinates on the four axis of PCoA, the variety, and the seed provider (XLSX 235 kb)
122_2017_2949_MOESM2_ESM.xlsx (14.5 mb)
Suppl. Table 2: IBS matrix among the 1191 inbred lines of the Flint collection (XLSX 14847 kb)
122_2017_2949_MOESM3_ESM.docx (1.9 mb)
Supplementary figures 3 (DOCX 1937 kb)


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Copyright information

© Springer-Verlag GmbH Germany 2017

Authors and Affiliations

  • Brigitte Gouesnard
    • 1
    Email author
  • Sandra Negro
    • 2
  • Amélie Laffray
    • 2
  • Jeff Glaubitz
    • 3
  • Albrecht Melchinger
    • 4
  • Pedro Revilla
    • 5
  • Jesus Moreno-Gonzalez
    • 6
  • Delphine Madur
    • 2
  • Valérie Combes
    • 2
  • Christine Tollon-Cordet
    • 1
  • Jacques Laborde
    • 7
  • Dominique Kermarrec
    • 8
  • Cyril Bauland
    • 2
  • Laurence Moreau
    • 2
  • Alain Charcosset
    • 2
  • Stéphane Nicolas
    • 2
  1. 1.INRA, UMR AGAP 1334MontpellierFrance
  2. 2.INRA, UMR 0320 Génétique Quantitative et Évolution, le Moulon, Ferme du MoulonGif/YvetteFrance
  3. 3.Cornell UniversityIthacaUSA
  4. 4.University of Hohenheim350 Institute of Plant Breeding, Seed Science, and Population GeneticsStuttgartGermany
  5. 5.CSICPontevedraSpain
  6. 6.CIAM-INGACALMabegondo Agricultural Research Centre, Xunta de GaliciaA CoruñaSpain
  7. 7.INRAUnité Expérimentale du MaïsSt Martin de HinxFrance
  8. 8.INRAUnité Expérimentale Ressources Génétiques Végétales en Conditions Océaniques (UERGCO)PloudanielFrance

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