Frontiers in Plant Science (May 2023)

Improved multi-trait prediction of wheat end-product quality traits by integrating NIR-predicted phenotypes

  • Shiva Azizinia,
  • Daniel Mullan,
  • Allan Rattey,
  • Jayfred Godoy,
  • Hannah Robinson,
  • David Moody,
  • Kerrie Forrest,
  • Gabriel Keeble-Gagnere,
  • Matthew J. Hayden,
  • Matthew J. Hayden,
  • Josquin FG. Tibbits,
  • Hans D. Daetwyler,
  • Hans D. Daetwyler

DOI
https://doi.org/10.3389/fpls.2023.1167221
Journal volume & issue
Vol. 14

Abstract

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Historically, end-product quality testing has been costly and required large flour samples; therefore, it was generally implemented in the late phases of variety development, imposing a huge cost on the breeding effort and effectiveness. High genetic correlations of end-product quality traits with higher throughput and nondestructive testing technologies, such as near-infrared (NIR), could enable early-stage testing and effective selection of these highly valuable traits in a multi-trait genomic prediction model. We studied the impact on prediction accuracy in genomic best linear unbiased prediction (GBLUP) of adding NIR-predicted secondary traits for six end-product quality traits (crumb yellowness, water absorption, texture hardness, flour yield, grain protein, flour swelling volume). Bread wheat lines (1,400–1,900) were measured across 8 years (2012–2019) for six end-product quality traits with standard laboratory assays and with NIR, which were combined to generate predicted data for approximately 27,000 lines. All lines were genotyped with the Infinium™ Wheat Barley 40K BeadChip and imputed using exome sequence data. End-product and NIR phenotypes were genetically correlated (0.5–0.83, except for flour swelling volume 0.19). Prediction accuracies of end-product traits ranged between 0.28 and 0.64 and increased by 30% through the inclusion of NIR-predicted data compared to single-trait analysis. There was a high correlation between the multi-trait prediction accuracy and genetic correlations between end-product and NIR-predicted data (0.69–0.77). Our forward prediction validation revealed a gradual increase in prediction accuracy when adding more years to the multi-trait model. Overall, we achieved genomic prediction accuracy at a level that enables selection for end-product quality traits early in the breeding cycle.

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