Genomic prediction of maize microphenotypes provides insights for optimizing selection and mining diversity

Xiaoqing Yu, Samuel Leiboff, Xianran Li, Tingting Guo, Natalie Ronning, Xiaoyu Zhang, Gary J. Muehlbauer, Marja C.P. Timmermans, Patrick S. Schnable, Michael J. Scanlon, Jianming Yu

Research output: Contribution to journalArticlepeer-review

2 Scopus citations

Abstract

Effective evaluation of millions of crop genetic stocks is an essential component of exploiting genetic diversity to achieve global food security. By leveraging genomics and data analytics, genomic prediction is a promising strategy to efficiently explore the potential of these gene banks by starting with phenotyping a small designed subset. Reliable genomic predictions have enhanced selection of many macroscopic phenotypes in plants and animals. However, the use of genomicprediction strategies for analysis of microscopic phenotypes is limited. Here, we exploited the power of genomic prediction for eight maize traits related to the shoot apical meristem (SAM), the microscopic stem cell niche that generates all the above-ground organs of the plant. With 435 713 genomewide single-nucleotide polymorphisms (SNPs), we predicted SAM morphology traits for 2687 diverse maize inbreds based on a model trained from 369 inbreds. An empirical validation experiment with 488 inbreds obtained a prediction accuracy of 0.37–0.57 across eight traits. In addition, we show that a significantly higher prediction accuracy was achieved by leveraging the U value (upper bound for reliability) that quantifies the genomic relationships of the validation set with the training set. Our findings suggest that double selection considering both prediction and reliability can be implemented in choosing selection candidates for phenotyping when exploring new diversity is desired. In this case, individuals with less extreme predicted values and moderate reliability values can be considered. Our study expands the turbocharging gene banks via genomic prediction from the macrophenotypes into the microphenotypic space.

Original languageEnglish (US)
Pages (from-to)2456-2465
Number of pages10
JournalPlant Biotechnology Journal
Volume18
Issue number12
DOIs
StatePublished - Dec 2020

Bibliographical note

Funding Information:
This work was supported by the National Science Foundation Grant IOS-1238142, the Iowa State University Plant Sciences Institute and the Iowa State University Raymond F. Baker Center for Plant Breeding. We thank the Iowa State University Crop Bioengineering Center for publication subvention.

Funding Information:
This work was supported by the National Science Foundation Grant IOS‐1238142, the Iowa State University Plant Sciences Institute and the Iowa State University Raymond F. Baker Center for Plant Breeding. We thank the Iowa State University Crop Bioengineering Center for publication subvention.

Publisher Copyright:
© 2020 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd

Keywords

  • genetic diversity
  • genomic selection
  • genomics
  • maize
  • plant breeding
  • shoot apical meristem

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