Combining GWAS and TWAS to identify candidate causal genes for tocochromanol levels in maize grain

Authors: WU, D - Cornell University; LI, XIAOWEI - Cornell University; TANAKA, RYOKEI - Cornell University; WOOD, JOSHUA - University Of Georgia; TIBBS-CORTES, LAURA - Iowa State University; MAGALLANES-LUNDBACK, MARIA - Michigan State University; BORNOWSKI, NOLAN - Michigan State University; HAMILTON, JOHN - University Of Georgia; VAILLANCOURT, B - University Of Georgia; DIEPENBROCK, CHRISTINE - University Of California, Davis; Li, Xianran; DEASON, NICHOLAS - Michigan State University; SCHOENBAUM, GREGORY - Iowa State University; YU, JIANMING - Iowa State University; BUELL, ROBIN - University Of Georgia; DELLAPENNA, DEAN - Michigan State University; GORE, MICHAEL - Cornell University

Submitted to: Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/1/2022
Publication Date: 8/1/2022
Citation: Wu, D., Li, X., Tanaka, R., Wood, J., Tibbs-Cortes, L., Magallanes-Lundback, M., Bornowski, N., Hamilton, J., Vaillancourt, B., Diepenbrock, C., Li, X., Deason, N., Schoenbaum, G., Yu, J., Buell, R., Dellapenna, D., Gore, M. 2022. Combining GWAS and TWAS to identify candidate causal genes for tocochromanol levels in maize grain. Genetics. 221(4). Article iyac091. https://doi.org/10.1093/genetics/iyac091.
DOI: https://doi.org/10.1093/genetics/iyac091

Interpretive Summary: Understanding how genetics, environment factors, and development process contribute to varied crop performances among natural fields is a long-standing question. Because plant height can be easily traced, it is an idea trait to explore the interactions among these three key factors. This study characterized plant height dynamics of a sorghum genetic population across 9 environments (4 environments have multiple measurements spanning the entire growing season). A combination of genetic mapping, crop growth modelling, and explicit environment factors identifying depicted how plant genes dynamically responded to environmental cue and adjusted the growth rate to reach varied final plant heights. This study illustrated the interactions of three factors: gene, environment, and development lead to the varied performances in natural condition.

Technical Abstract: •Phenotypic plasticity is observed widely in plants and often studied with reaction norms for adult plant or end-of-season traits. Uncovering genetic, environmental, and developmental patterns behind the observed phenotypic variation under natural field conditions is needed. • With a sorghum (Sorghum bicolor) genetic population evaluated for plant height in seven natural field conditions, we investigated the major pattern that differentiated these environments. We then examined the physiological relevance of the identified environmental index by investigating the developmental trajectory of the population with multi-stage height measurements in four additional environments and conducting crop growth modeling. • We found that diurnal temperature range (DTR) during the rapid growth period of sorghum development was an effective environmental index. Three genetic loci (Dw1, Dw3, and qHT7.1) were consistently detected for individual environments, reaction-norm parameters across environments, and growth-curve parameters through the season. Their genetic effects changed dynamically along the environmental gradient and the developmental stage. A conceptual model with three-dimensional reaction norms was proposed to showcase the interconnecting components: gene and genetics, environment, and development. • Beyond genomic and environmental analyses, further integration of development and physiology at the whole-plant and molecular levels into complex trait dissection would enhance our understanding of mechanisms underlying phenotypic variation.