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Title: The interaction of genotype and environment determines variation in the maize kernal ionome

item ASARO, ALEXANDRA - Danforth Plant Science Center
item Ziegler, Gregory
item ZIYOMO, CATHRINE - Danforth Plant Science Center
item HOEKENGA, OWEN - Consultant
item DILKES, BRIAN - Purdue University
item Baxter, Ivan

Submitted to: G3, Genes/Genomes/Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/17/2016
Publication Date: 12/7/2016
Citation: Asaro, A., Ziegler, G.R., Ziyomo, C., Hoekenga, O., Dilkes, B.P., Baxter, I.R. 2016. The interaction of genotype and environment determines variation in the maize kernal ionome. G3, Genes/Genomes/Genetics. 6(12):4175-4183. doi: 10.1534/g3.116.034827.

Interpretive Summary: Plants take up elements from the soil, a process that is highly regulated by the plant’s genome. In order to look at how maize alters its elemental uptake in response to different environments, we analyzed the kernel elemental content of a population derived from a cross grown 10 different times in six locations. We found that environment had a profound effect on which genetic loci were important for elemental accumulation in the kernel. We also found that the elements are not regulated independently and that mathematical combinations of elements will identify different genetic loci than single element approaches. The mathematical combinations of elements are correlated with environmental variables, suggesting that underlying the observed variation are interactions between genetically controlled factors and environmental variables. Our results suggest that to have a full understanding of elemental accumulation in maize kernels and other food crops, we will need to understand the interactions identified here at the level of the genes and the environmental variables that contribute to loading essential nutrients into seeds.

Technical Abstract: Plants obtain soil-resident elements that support growth and metabolism via water-mediated flow due to transpiration and active transport processes. The availability of elements in the environment can interact with the genetic capacity of the organism to modulate element uptake through plastic adaptive responses, such as homeostasis. In addition, polymorphisms with no or limited adaptive consequence in one environment can dramatically alter element accumulation in another. The complex nature of these interactions suggests that the elemental profile of the plant will vary with the genetic factors influencing accumulation depending on which environment the plant is grown in. In order to investigate genotype by environment interactions underlying elemental accumulation, we analyzed levels of elements in maize kernels of the Intermated B73 x Mo17 (IBM) recombinant inbred population grown in 10 different environments spanning a total of six locations and five different years. We looked for quantitative trait loci controlling elemental accumulation both as independent elemental traits and as co-regulated multi-elemental traits identified using principle components analysis. These two approaches detected two overlapping sets of loci linked to elemental accumulation, many of which were found only in a single growout. By extending our multi-element phenotypes across all of the growouts, we were able to demonstrate that the growth environment has a profound effect on the elemental profile and that some multi-element phenotypes correlate with specific environmental variables. We identified QTL by environment interactions (QEIs) through three methods: linear modeling with environmental covariates, QTL analysis on trait differences between growouts, and QTL analysis on factors obtained from a principle component derived model of ionome variation across environments. Overall, we were able to map 79 elemental QTL, 101 principal component QTL, and several instances of QEI, indicating that elemental profiles are highly heritable, interrelated, and responsive to the environment.