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 Gouesnard
  • 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

Abstract

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.

Abstract

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.

Abbreviations

GBS

Genotyping-by-sequencing

GWAS

Genome-wide association study

SNP

Single-nucleotide polymorphism

MAF

Minor allele frequency

IBS

Identity by state

PCoA

Principal coordinates analysis

PO

Posterior odds

ASI

Anthesis-silking interval

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
  • 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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