Genome-wide association and genomic prediction for iron and zinc concentration and iron bioavailability in a collection of yellow dry beans

Authors: IZQUIERDO, PAULO - Michigan State University; SADOHARA, RIE - Michigan State University; Wiesinger, Jason; Glahn, Raymond; URREA, CARLOS - University Of Nebraska; Cichy, Karen

Submitted to: Frontiers in Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/3/2024
Publication Date: 2/5/2024
Citation: Izquierdo, P., Sadohara, R., Wiesinger, J.A., Glahn, R.P., Urrea, C., Cichy, K.A. 2024. Genome-wide association and genomic prediction for iron and zinc concentration and iron bioavailability in a collection of yellow dry beans. Frontiers in Genetics. 15:13303361. https://doi.org/10.3389/fgene.2024.1330361.
DOI: https://doi.org/10.3389/fgene.2024.1330361

Interpretive Summary: Dry bean is the most important legume for human consumption worldwide, providing high levels of protein, dietary fiber, and micronutrients such as Fe and Zn. Biofortification initiatives have focused on increasing dry bean Fe and Zn concentrations through breeding, to improve the nutritional status of humans suffering from Fe and Zn deficiencies. While there has been a push towards breeding for increased seed micronutrient concentrations, multiple studies have also underscored the significance of breeding for enhanced Fe bioavailability. Large genetic variability for Fe and Zn concentration, as well as Fe bioavailability, exists both among and within market class. However, lighter seed types, such as pale-yellow beans, have shown high levels of bioavailable Fe. The objectives of this research were to assess the Fe and Zn concentration and Fe bioavailability of a yellow bean diversity collection, identify genomic regions associated with Fe and Zn concentrations and Fe bioavailability, and test genomic prediction accuracies for these traits. Large phenotypic variability was identified in all traits evaluated. Genomic prediction accuracies ranged from a low of 0.12 for Fe concentration and a high of 0.72 for Fe bioavailability. While the nutritional importance of Fe bioavailability is undeniable, its measurement might be out of reach for many breeding programs. Fortunately, this research suggests that genomic prediction offers high accuracy for Fe bioavailability, presenting a potential solution to mitigate the expenses and extensive duration associated with its measurement.

Technical Abstract: Dry bean is a nutrient-dense food targeted in biofortification programs to increase seed iron and zinc levels. The underlying assumption of breeding for higher mineral content is that enhanced iron and zinc levels will benefit the consumers of these biofortified foods. However, the bioavailability of these minerals is influenced not just by the mineral content but also by their interactions with other seed compounds, such as polyphenols and phytates. This study characterized a diversity panel of 295 genotypes comprising the Yellow Bean Collection (YBC) for seed Fe and Zn concentration, Fe bioavailability (FeBio), and seed yield across two years in two field locations. The genetic architecture of each trait was elucidated via genome-wide association (GWA) and the efficacy of genomic prediction (GP) was assessed. Moreover, 82 yellow breeding lines were evaluated for seed Fe and Zn concentrations as well as seed yield, serving as a prediction set for GP models. Large phenotypic variability was identified in all traits evaluated, and variations of up to 2.8 and 13.7-fold were observed for Fe concentration and FeBio, respectively. Prediction accuracies in the YBC ranged from a low of 0.12 for Fe concentration and a high of 0.72 for FeBio, and an accuracy improvement of 0.03 was observed when a QTL, identified through GWA, was used as fixed effect for FeBio. This study provides evidence of the lack of correlation between FeBio estimated in vitro and Fe concentration and highlights the potential of GP in accurately predicting FeBio, offering a cost-effective alternative to traditional assessment methods.