Integrating genomic-enabled prediction and high-throughput phenotyping in breeding for climate-resilient bread wheat

Philomin Juliana, Osval A. Montesinos-López, José Crossa, Suchismita Mondal, Lorena González Pérez, Jesse Poland, Julio Huerta-Espino, Leonardo Crespo-Herrera, Velu Govindan, Susanne Dreisigacker, Sandesh Shrestha, Paulino Pérez-Rodríguez, Francisco Pinto Espinosa, Ravi P. Singh

Research output: Contribution to journalArticlepeer-review

48 Scopus citations

Abstract

Genomic selection and high-throughput phenotyping (HTP) are promising tools to accelerate breeding gains for high-yielding and climate-resilient wheat varieties. Hence, our objective was to evaluate them for predicting grain yield (GY) in drought-stressed (DS) and late-sown heat-stressed (HS) environments of the International maize and wheat improvement center’s elite yield trial nurseries. We observed that the average genomic prediction accuracies using fivefold cross-validations were 0.50 and 0.51 in the DS and HS environments, respectively. However, when a different nursery/year was used to predict another nursery/year, the average genomic prediction accuracies in the DS and HS environments decreased to 0.18 and 0.23, respectively. While genomic predictions clearly outperformed pedigree-based predictions across nurseries, they were similar to pedigree-based predictions within nurseries due to small family sizes. In populations with some full-sibs in the training population, the genomic and pedigree-based prediction accuracies were on average 0.27 and 0.35 higher than the accuracies in populations with only one progeny per cross, indicating the importance of genetic relatedness between the training and validation populations for good predictions. We also evaluated the item-based collaborative filtering approach for multivariate prediction of GY using the green normalized difference vegetation index from HTP. This approach proved to be the best strategy for across-nursery predictions, with average accuracies of 0.56 and 0.62 in the DS and HS environments, respectively. We conclude that GY is a challenging trait for across-year predictions, but GS and HTP can be integrated in increasing the size of populations screened and evaluating unphenotyped large nurseries for stress–resilience within years.
Original languageEnglish (US)
Pages (from-to)177-194
Number of pages18
JournalTheoretical and Applied Genetics
Volume132
Issue number1
DOIs
StatePublished - Jan 1 2019
Externally publishedYes

ASJC Scopus subject areas

  • Genetics
  • Agronomy and Crop Science
  • Biotechnology

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