Genetic control of kernel compositional variation in a maize diversity panel

Authors: RENK, JONATHAN - University Of Minnesota; GILBERT, AMANDA - University Of Minnesota; HATTERY, TRAVIS - Iowa State University; O'CONNOR, CHRISTINE - University Of Minnesota; MONNAHAN, PATRICK - University Of Minnesota; ANDERSON, NICKOLAS - Pepsico; WATERS, AMANDA - Pepsico; EICKHOLT, DAVID - Pepsico; Flint-Garcia, Sherry; YANDEAU-NELSON, MARNA - Iowa State University; HIRSCH, CANDICE - University Of Minnesota

Submitted to: The Plant Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/7/2021
Publication Date: 12/5/2021
Citation: Renk, J.S., Gilbert, A.M., Hattery, T.J., O'Connor, C.H., Monnahan, P.J., Anderson, N., Waters, A.J., Eickholt, D., Flint Garcia, S.A., Yandeau-Nelson, M.D., Hirsch, C.N. 2021. Genetic control of kernel compositional variation in a maize diversity panel. The Plant Genome. 14(3). Article e20115. https://doi.org/10.1002/tpg2.20115.
DOI: https://doi.org/10.1002/tpg2.20115

Interpretive Summary: Corn is used for many agricultural and industrial purposes, including human consumption. Understanding the extent of variation for grain composition traits and the genes controlling these traits is critical to making improved corn varieties for food-grade applications. In this study, we evaluated 16 grain composition traits using a method based on near-infrared spectroscopy for 501 corn lines that were grown in five Midwestern environments. We found that some traits such as protein, fiber, and fat (oil) have a strong genetic component which suggests that breeders can more easily modify these traits when making new corn varieties. Other traits, such as the sugars sucrose, fructose, and glucose have a lower genetic component indicating that they may be more difficult to modify using the near-infrared spectroscopy methods we employed. We also found that the 16 traits are interrelated, but these relationships depend on the type of corn (dent vs popcorn and sweet corn), all of which makes simultaneous modification of multiple traits more challenging. Finally, we conducted an analysis to identify the genes that control each of these 16 traits and found that these traits are mostly controlled by a large number of genes. The results of this study will help breeders in implementing strategies for improving food quality characteristics that have been largely neglected to date.

Technical Abstract: Maize (Zea mays L.) is a multi-purpose row crop grown worldwide, which overtime has often been bred for increased yield at the detriment of lower composition grain quality. Some knowledge of the genetic factors that affect quality traits has been discovered through the study of classical maize mutants. However, much of the underlying genetic architecture controlling these traits and the interaction between these traits remains unknown. To better understand variation that exists for grain compositional traits in maize, we evaluated 501 diverse temperate maize inbred lines in five unique environments and predicted 16 compositional traits (e.g. carbohydrates, protein, and starch) based on the output of near-infrared (NIR) spectroscopy. Phenotypic analysis found substantial variation for compositional traits and the majority of variation was explained by genetic and environmental factors. Correlations and trade-offs among traits in different maize types (e.g. dent, sweetcorn, and popcorn) were explored and significant differences and meaningful correlations were detected. In total, 22.90-71.09 percent of the phenotypic variation across these traits could be explained using 2,386,666 single nucleotide polymorphism (SNP) markers generated from whole-genome resequencing data. A genome-wide association study (GWAS) was conducted using these same markers and found 72 statistically significant SNPs for 11 compositional traits. This study provides valuable insights in the phenotypic variation and genetic control underlying compositional traits that can be used in breeding programs for improving maize grain quality.