Natural variation for carotenoids in fresh kernels is controlled by uncommon variants in sweet corn

Authors: BASEGGIO, MATHEUS - Cornell University; MURRAY, MATTHEW - University Of Wisconsin; MAGALLANES-LUNDBACK, MARIA - Michigan State University; KACZMAR, NICHOLAS - Cornell University; CHAMNESS, JAMES - Cornell University; Buckler, Edward - Ed; SMITH, MARGARET - Cornell University; DELLAPENNA, DEAN - Michigan State University; TRACY, WILLIAM - University Of Wisconsin; GORE, MICHAEL - Cornell University

Submitted to: The Plant Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/30/2019
Publication Date: 4/24/2020
Citation: Baseggio, M., Murray, M., Magallanes-Lundback, M., Kaczmar, N., Chamness, J., Buckler IV, E.S., Smith, M.E., Dellapenna, D., Tracy, W.F., Gore, M.A. 2020. Natural variation for carotenoids in fresh kernels is controlled by uncommon variants in sweet corn. The Plant Genome. https://doi.org/10.1002/tpg2.20008.
DOI: https://doi.org/10.1002/tpg2.20008

Interpretive Summary: Sweet corn is a popular vegetable in the United States, but contributes little carotenoids (made up of provitamin A carotenoids, lutein and zeaxanthin) to the diet of the consumer. Increasing carotenoids in sweet corn could improve human health and nutrition. This study identified the genes associated with the variation of levels of carotenoids in fresh kernels. Genomic prediction models with moderate to high predictive abilities enabled us to identify the best performing lines for higher vitamin content and the genes identified are now available for use in genomics-assisted selection breeding programs. Through this quantitative genetic analysis, we have established a key step for increasing carotenoids in fresh sweet corn kernels, thus paving the way for the breeding of more nutritious sweet corn that can benefit human consumers.

Technical Abstract: Sweet corn (Zea mays L.) is highly consumed in the United States, but does not make major contributions to the daily intake of carotenoids (provitamin A carotenoids, lutein and zeaxanthin) that would help in the prevention of health complications. A genome-wide association study of seven kernel carotenoids and twelve derivative traits was conducted in a sweet corn inbred line association panel ranging from light to dark yellow in endosperm color to elucidate the genetic basis of carotenoid levels in fresh kernels. In agreement with earlier studies of maize kernels at maturity, we detected an association of B-carotene hydroxylase (crtRB1) with B-carotene concentration and lycopene epsilon cyclase (lcyE) with the ratio of flux between the a- and B-carotene branches in the carotenoid biosynthetic pathway. Additionally, we found that 5% or less of the evaluated inbred lines possessing the shrunken2 (sh2) endosperm mutation had the most favorable lycE allele or crtRB1 haplotype for elevating -Branch carotenoids (B-carotene and zeaxanthin) or B-carotene, respectively. Genomic prediction models with genome-wide markers obtained moderately high predictive abilities for the carotenoid traits, especially lutein, and outperformed models with less markers that targeted candidate genes implicated in the synthesis, retention, and/or genetic control of kernel carotenoids. Taken together, our results constitute an important step toward increasing carotenoids in fresh sweet corn kernels.