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Quantitative trait loci mapping in hybrids between Dent and Flint maize multiparental populations reveals group-specific QTL for silage quality traits with variable pleiotropic effects on yield

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Key message

Silage quality traits of maize hybrids between the Dent and Flint heterotic groups mostly involved QTL specific of each parental group, some of them showing unfavorable pleiotropic effects on yield.


Maize (Zea mays L.) is commonly used as silage for cattle feeding in Northern Europe. In addition to biomass production, improving whole-plant digestibility is a major breeding objective. To identify loci involved in the general (GCA, parental values) and specific combining ability (SCA, cross-specific value) components of hybrid value, we analyzed an incomplete factorial design of 951 hybrids obtained by crossing inbred lines issued from two multiparental connected populations, each specific to one of the heterotic groups used for silage in Europe (“Dent” and “Flint”). Inbred lines were genotyped for approximately 20K single nucleotide polymorphisms, and hybrids were phenotyped in eight environments for seven silage quality traits measured by near-infrared spectroscopy, biomass yield and precocity (partly analyzed in a previous study). We estimated variance components for GCA and SCA and their interaction with environment. We performed QTL detection using different models adapted to this hybrid population. Strong family effects and a predominance of GCA components compared to SCA were found for all traits. In total, 230 QTL were detected, with only two showing SCA effects significant at the whole-genome level. More than 80% of GCA QTL were specific of one heterotic group. QTL explained individually less than 5% of the phenotypic variance. QTL co-localizations and correlation between QTL effects of quality and productivity traits suggest at least partial pleiotropic effects. This work opens new prospects for improving maize hybrid performances for both biomass productivity and quality accounting for complementarities between heterotic groups.

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A. I. Seye’s Ph.D. was funded by the Senegalese Institute of Agricultural Research (ISRA) through a Scholarship from the West Africa Agricultural Productivity Program (WAAPP) given by the National Institute of Higher Education in Agricultural Sciences—Montpellier SupAgro. We are grateful to Caussade Semences, Euralis Semences, Limagrain Europe, Maïsadour Semences, Pioneer Genetics, R2n, Syngenta Seeds and KWS grouped in the frame of the ProMais “SAM-MCR” program for the funding, inbred lines development, hybrid production and phenotyping. We also thank scientists from these companies for helpful discussions on the results. We thank Magali Joannin of the INRA station of GQE Le Moulon for seed management and D. Madur and V. Combes for DNA extraction and genotyping analyses. We thank C. Palaffre and the INRA experimental unit of Saint-Martin-de-Hinx for seed production and seed management. We thank Dominique Kermarrec and the INRA station of Ploudaniel for their support to ProMaïs in phenotyping. We thank Pierre Dardenne from CRA-Wallonie for the NIRS prediction equations of silage quality traits.

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Correspondence to Laurence Moreau.

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Seye, A.I., Bauland, C., Giraud, H. et al. Quantitative trait loci mapping in hybrids between Dent and Flint maize multiparental populations reveals group-specific QTL for silage quality traits with variable pleiotropic effects on yield. Theor Appl Genet 132, 1523–1542 (2019). https://doi.org/10.1007/s00122-019-03296-2

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