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

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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.

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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

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Acknowledgements

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.

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Authors and Affiliations

  1. INRA, UMR AGAP 1334, 2 Place Viala, 34060, Montpellier, France

    Brigitte Gouesnard & Christine Tollon-Cordet

  2. INRA, UMR 0320 Génétique Quantitative et Évolution, le Moulon, Ferme du Moulon, 91190, Gif/Yvette, France

    Sandra Negro, Amélie Laffray, Delphine Madur, Valérie Combes, Cyril Bauland, Laurence Moreau, Alain Charcosset & Stéphane Nicolas

  3. Cornell University, 135 Biotechnology Bldg, Ithaca, NY, 14853, USA

    Jeff Glaubitz

  4. University of Hohenheim, 350 Institute of Plant Breeding, Seed Science, and Population Genetics, 70593, Stuttgart, Germany

    Albrecht Melchinger

  5. CSIC, Misión Biológica de Galicia, Apartado 28, 36080, Pontevedra, Spain

    Pedro Revilla

  6. CIAM-INGACAL, Mabegondo Agricultural Research Centre, Xunta de Galicia, Carretera AC-542 de Betanzos a Mesón do Vento, km 7, Abegondo, 15318, A Coruña, Spain

    Jesus Moreno-Gonzalez

  7. INRA, Unité Expérimentale du Maïs, 40390, St Martin de Hinx, France

    Jacques Laborde

  8. INRA, Unité Expérimentale Ressources Génétiques Végétales en Conditions Océaniques (UERGCO), Kéraïber, 29260, Ploudaniel, France

    Dominique Kermarrec

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  1. Brigitte Gouesnard
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Correspondence to Brigitte Gouesnard.

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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.

Additional information

Communicated by Thomas Lubberstedt.

Electronic supplementary material

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122_2017_2949_MOESM1_ESM.xlsx

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)

Suppl. Table 2: IBS matrix among the 1191 inbred lines of the Flint collection (XLSX 14847 kb)

Supplementary figures 3 (DOCX 1937 kb)

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Gouesnard, B., Negro, S., Laffray, A. et al. Genotyping-by-sequencing highlights original diversity patterns within a European collection of 1191 maize flint lines, as compared to the maize USDA genebank. Theor Appl Genet 130, 2165–2189 (2017). https://doi.org/10.1007/s00122-017-2949-6

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