Genome-wide association study suggests an independent genetic basis of zinc and cadmium concentrations in fresh sweet corn kernels

Authors: BASEGGIO, MATHEUS - Cornell University; MURRAY, MATTHEW - University Of Wisconsin; WU, DI - Cornell University; ZIEGLER, GREGORY - Danforth Plant Science Center; KACZMAR, NICHOLAS - Cornell University; CHAMNESS, JAMES - Cornell University; HAMILTON, JOHN - Michigan State University; BUELL, ROBIN - Michigan State University; VATAMANIUK, OLENA - Cornell University; Buckler, Edward - Ed; SMITH, MARGARET - Cornell University; BAXTER, IVAN - Danforth Plant Science Center; TRACY, WILLIAM - University Of Wisconsin; GORE, MICHEAL - Cornell University

Submitted to: G3, Genes/Genomes/Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/25/2021
Publication Date: 5/28/2021
Citation: Baseggio, M., Murray, M., Wu, D., Ziegler, G., Kaczmar, N., Chamness, J., Hamilton, J.P., Buell, R.C., Vatamaniuk, O.K., Buckler IV, E.S., Smith, M.E., Baxter, I., Tracy, W.F., Gore, M.A. 2021. Genome-wide association study suggests an independent genetic basis of zinc and cadmium concentrations in fresh sweet corn kernels. G3, Genes/Genomes/Genetics. 11(8). https://doi.org/10.1093/g3journal/jkab186.
DOI: https://doi.org/10.1093/g3journal/jkab186

Interpretive Summary: Despite being one of the most consumed vegetables in the United States, the elemental or trace mineral profile of sweet corn is limited in its dietary contributions. This study evaluated how natural genetic variation in sweet corn can control these nutritional contributors. For all fifteen elements, there was significant genetic variation controlling these traits and and these traits could be selectively bred in genomics-assisted breeding programs. While most of the elemental profiles were controlled by numerous genes, cadmium concentration was substantially controlled by a likely known gene (hma3). Overall, there are substantial opportunities to breed for enhanced elemental nutritional profiles in fresh sweet corn.

Technical Abstract: Despite being one of the most consumed vegetables in the United States, the elemental profile of sweet corn (Zea mays L.) is limited in its dietary contributions. To address this through genetic improvement, a genome-wide association study was conducted for the concentrations of 15 elements in fresh kernels of a sweet corn association panel. In concordance with mapping results from mature maize kernels, we detected a probable pleiotropic association of zinc and iron concentrations with nicotianamine synthase5 (nas5), which purportedly encodes an enzyme involved in synthesis of the metal chelator nicotianamine. In addition, a pervasive association signal was identified for cadmium concentration within a recombination suppressed region on chromosome 2. The likely causal gene underlying this signal was heavy metal ATPase3 (hma3), whose counterpart in rice, OsHMA3, mediates vacuolar sequestration of cadmium and zinc in roots, whereby regulating zinc homeostasis and cadmium accumulation in grains. In our association panel, hma3 associated with cadmium but not zinc accumulation in fresh kernels. This finding implies that selection for low cadmium will not affect zinc levels in fresh kernels. Although less resolved association signals were detected for boron, nickel, and calcium, all 15 elements were shown to have moderate predictive abilities via whole-genome prediction. Collectively, these results help enhance our genomics-assisted breeding efforts centered on improving the elemental profile of fresh sweet corn kernels.