Hyperspectral reflectance-derived relationship matrices for genomic prediction of grain yield in wheat

Margaret R. Krause, Lorena González-Pérez, José Crossa, Paulino Pérez-Rodríguez, Osval Montesinos-López, Ravi P. Singh, Susanne Dreisigacker, Jesse Poland, Jessica Rutkoski, Mark Sorrells, Michael A. Gore, Suchismita Mondal

Research output: Contribution to journalArticle

Abstract

Hyperspectral reflectance phenotyping and genomic selection are two emerging technologies that have the potential to increase plant breeding efficiency by improving prediction accuracy for grain yield. Hyperspectral cameras quantify canopy reflectance across a wide range of wavelengths that are associated with numerous biophysical and biochemical processes in plants. Genomic selection models utilize genome-wide marker or pedigree information to predict the genetic values of breeding lines. In this study, we propose a multi-kernel GBLUP approach to genomic selection that uses genomic marker-, pedigree-, and hyperspectral reflectance-derived relationship matrices to model the genetic main effects and genotype x environment (G · E) interactions across environments within a bread wheat (Triticum aestivum L.) breeding program. We utilized an airplane equipped with a hyperspectral camera to phenotype five differentially managed treatments of the yield trials conducted by the Bread Wheat Improvement Program of the International Maize and Wheat Improvement Center (CIMMYT) at Ciudad Obregón, México over four breeding cycles. We observed that single-kernel models using hyperspectral reflectance-derived relationship matrices performed similarly or superior to marker- and pedigree-based genomic selection models when predicting within and across environments. Multi-kernel models combining marker/pedigree information with hyperspectral reflectance phentoypes had the highest prediction accuracies; however, improvements in accuracy over marker- and pedigree-based models were marginal when correcting for days to heading. Our results demonstrate the potential of using hyperspectral imaging to predict grain yield within a multi-environment context and also support further studies on the integration of hyperspectral reflectance phenotyping into breeding programs.

Original languageEnglish (US)
Pages (from-to)1231-1247
Number of pages17
JournalG3: Genes, Genomes, Genetics
Volume9
Issue number4
DOIs
StatePublished - Jan 1 2019
Externally publishedYes

Fingerprint

Pedigree
Triticum
Breeding
Bread
Biophysical Phenomena
Biochemical Phenomena
Aircraft
Genetic Models
Zea mays
Genotype
Genome
Technology
Phenotype
Therapeutics

Keywords

  • GBLUP
  • Genomic prediction
  • Genotype-by-environment interaction
  • GenPred
  • High throughput phenotyping
  • Hyperspectral
  • Reflectance
  • Resources
  • Shared data
  • Wheat breeding

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics
  • Genetics(clinical)

Cite this

Krause, M. R., González-Pérez, L., Crossa, J., Pérez-Rodríguez, P., Montesinos-López, O., Singh, R. P., ... Mondal, S. (2019). Hyperspectral reflectance-derived relationship matrices for genomic prediction of grain yield in wheat. G3: Genes, Genomes, Genetics, 9(4), 1231-1247. https://doi.org/10.1534/g3.118.200856

Hyperspectral reflectance-derived relationship matrices for genomic prediction of grain yield in wheat. / Krause, Margaret R.; González-Pérez, Lorena; Crossa, José; Pérez-Rodríguez, Paulino; Montesinos-López, Osval; Singh, Ravi P.; Dreisigacker, Susanne; Poland, Jesse; Rutkoski, Jessica; Sorrells, Mark; Gore, Michael A.; Mondal, Suchismita.

In: G3: Genes, Genomes, Genetics, Vol. 9, No. 4, 01.01.2019, p. 1231-1247.

Research output: Contribution to journalArticle

Krause, MR, González-Pérez, L, Crossa, J, Pérez-Rodríguez, P, Montesinos-López, O, Singh, RP, Dreisigacker, S, Poland, J, Rutkoski, J, Sorrells, M, Gore, MA & Mondal, S 2019, 'Hyperspectral reflectance-derived relationship matrices for genomic prediction of grain yield in wheat', G3: Genes, Genomes, Genetics, vol. 9, no. 4, pp. 1231-1247. https://doi.org/10.1534/g3.118.200856
Krause MR, González-Pérez L, Crossa J, Pérez-Rodríguez P, Montesinos-López O, Singh RP et al. Hyperspectral reflectance-derived relationship matrices for genomic prediction of grain yield in wheat. G3: Genes, Genomes, Genetics. 2019 Jan 1;9(4):1231-1247. https://doi.org/10.1534/g3.118.200856
Krause, Margaret R. ; González-Pérez, Lorena ; Crossa, José ; Pérez-Rodríguez, Paulino ; Montesinos-López, Osval ; Singh, Ravi P. ; Dreisigacker, Susanne ; Poland, Jesse ; Rutkoski, Jessica ; Sorrells, Mark ; Gore, Michael A. ; Mondal, Suchismita. / Hyperspectral reflectance-derived relationship matrices for genomic prediction of grain yield in wheat. In: G3: Genes, Genomes, Genetics. 2019 ; Vol. 9, No. 4. pp. 1231-1247.
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