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Molecular Breeding

, 37:80 | Cite as

Multi-trait genomic prediction for nitrogen response indices in tropical maize hybrids

  • Danilo Hottis LyraEmail author
  • Leandro de Freitas Mendonça
  • Giovanni Galli
  • Filipe Couto Alves
  • Ítalo Stefanine Correia Granato
  • Roberto Fritsche-Neto
Article

Abstract

In maize breeding, genomic prediction may be an efficient tool for selecting single-crosses evaluated under abiotic stress conditions. In addition, a promising strategy is applying multiple-trait genomic prediction using selection indices (SIs), increasing genetics gains and reducing time per cycles. In this study, we aimed (i) to compare accuracy of single- and multi-trait genomic prediction (STGP; MTGP) in two maize datasets, (ii) to evaluate prediction of four selection indices that could contribute to the selection of tropical maize hybrids under contrasting nitrogen conditions, and (iii) to compare the use of linear (GBLUP) and nonlinear (RKHS/GK) kernels in STGP and MTGP analyses. For either single-trait GBLUP and RKHS analyses, the highest values obtained for accuracy were 0.40 and 0.41 using harmonic mean (HM), respectively. From multi-trait GBLUP and GK, using the combination of selection indices in MTGP seems to be suitable, increasing the accuracy. Adding grain yield and plant height in MTGP showed a slight improvement in accuracy compared to STGP. In general, there was a modest benefit of using single-trait RKHS and GK multi-trait, rather than GBLUP.

Keywords

Abiotic stress Single-trait genomic prediction Gaussian kernel GBLUP Genomic heritability 

Notes

Acknowledgements

We thank Helix Sementes® (São Paulo, Brazil) for the dataset II, and the Allogamous Plant Breeding Laboratory for the technical and scientific support.

Compliance with ethical standards

Funding

This project was supported by São Paulo Research Foundation-FAPESP (Process: 2013/24135–2; 2014/26326–2; 2015/14376–8) and Coordination for the Improvement of Higher Level Personnel (CAPES).

Supplementary material

11032_2017_681_Fig5_ESM.gif (660 kb)
Supplemental Fig. S1

Population structure analysis of tropical maize inbred lines. (a) First two principal components of 49 inbred lines, and BIC values of k-means clustering. (b) First two principal components of 106 inbred lines, and BIC values of k-means clustering. The dashed black line shows the number of groups inferred in each method. (GIF 660 kb)

11032_2017_681_MOESM1_ESM.tiff (2.6 mb)
High Resolution Image (TIFF 2630 kb)
11032_2017_681_Fig6_ESM.gif (5.7 mb)
Supplemental Fig. S2

Scatterplot between the combinations of four selection indices (a-f). N-agronomic efficiency (NAE, ton ton−1 N ha−1), low-N tolerance index (LNTI, %), low-N agronomy efficiency (LNAE, ton ha−1), and harmonic mean (HM). The solid red line is the regression slope and 95% confidence interval (light gray band). (GIF 5864 kb)

11032_2017_681_MOESM2_ESM.tiff (9.1 mb)
High Resolution Image (TIFF 9363 kb)

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Copyright information

© Springer Science+Business Media Dordrecht 2017

Authors and Affiliations

  • Danilo Hottis Lyra
    • 1
    Email author
  • Leandro de Freitas Mendonça
    • 1
  • Giovanni Galli
    • 1
  • Filipe Couto Alves
    • 1
  • Ítalo Stefanine Correia Granato
    • 1
  • Roberto Fritsche-Neto
    • 1
  1. 1.University of São Paulo, Luiz de Queiroz College of AgricultureDepartment of GeneticsSão PauloBrazil

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