Investigating genomic prediction strategies for grain carotenoid traits in a tropical/subtropical maize panel

Abstract

Vitamin A deficiency remains prevalent on a global scale, including in regions where maize constitutes a high percentage of human diets. One solution for alleviating this deficiency has been to increase grain concentrations of provitamin A carotenoids in maize (Zea maysssp.maysL.)—an example of biofortification. The International Maize and Wheat Improvement Center (CIMMYT) developed a Carotenoid Association Mapping panel of 380 inbred lines adapted to tropical and subtropical environments that have varying grain concentrations of provitamin A and other health-beneficial carotenoids. This project assesses the accuracy of several genomic prediction (GP) strategies for these traits (β-carotene, β-cryptoxanthin, provitamin A, lutein, and zeaxanthin) within and between four environments in Mexico. Methods employing Ridge Regression-Best Linear Unbiased Prediction, Elastic Net, or Reproducing Kernel Hilbert Spaces had high accuracy in predicting all tested provitamin A carotenoid traits and outperformed Least Absolute Shrinkage and Selection Operator. Furthermore, prediction accuracies were higher when using genome-wide markers rather than only the markers proximal to two previously identified carotenoid-related genes that have been used in marker-assisted selection, suggesting that GP is worthwhile for these traits, even though key genes have already been identified. Prediction accuracy was maintained for all traits (except lutein) in between-environment prediction. The TASSEL (Trait Analysis by aSSociation, Evolution, and Linkage) Genomic Selection plugin performed as well as other more computationally intensive methods for within-environment prediction. The findings observed herein indicate the utility of GP methods for these traits and could inform their resource-efficient implementation in biofortification breeding programs.

SNP analysis of Ukrainian maize inbreds with alternative state of molecular carotenogenesis marker crtRB1-3’TE

“…It was found that some single nucleotide replacements, revealed in genome-wide genotyping, have a statistical association with the allelic state of carotenoid pathway genes and the content of carotenoids in maize grain (Diepenbrock et al, 2021). In some studies, along with classic markers of the allelic state of the β-carotene hydroxylase 1 and lycopene-ε-cyclase genes, namely crtRB1-3´TE, crtRB1-5´TE, crtRB1-InDel14, lcyE-3´INDL, lcyE-5´INDL, lcyE-SNP216, single nucleotide substitutionsin these genes were signifi cant for the same plant (Maazou et al, 2023;Sserumaga et al, 2019;Kondwakwenda et al, 2020;LaPorte et al, 2023;Azmach et al, 2018;Kebede et al, 2021). LaPorte et al ( 2023) concluded that when genome-wide markers were used, the accuracy of genomic prediction for the carotenoid content in maize grain was higher than when only the markers proximal to two carotenoid-related genes were used.…”