GWAS and genomic prediction: Breeding strategies for maize stover digestibility

Authors: GESTEIRO, NOEMI - Biological Mission Of Galicia Spain; MALVAR, ROSA ANA - Biological Mission Of Galicia Spain; BUTRON, ANA - Biological Mission Of Galicia Spain; Holland, James; LOPEZ-MALVAR, ANA - Universidad De Vigo; PEREIRA-CRESPO, SONIA - Biological Mission Of Galicia Spain; REVILLA, PEDRO - Biological Mission Of Galicia Spain; SANTIAGO, ROGELIO - Biological Mission Of Galicia Spain

Submitted to: Journal of Agriculture and Food Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/21/2025
Publication Date: 8/21/2025
Citation: Gesteiro, N., Malvar, R., Butron, A., Holland, J.B., Lopez-Malvar, A., Pereira-Crespo, S., Revilla, P., Santiago, R. 2025. GWAS and genomic prediction: Breeding strategies for maize stover digestibility. Journal of Agriculture and Food Research. 23. https://doi.org/10.1016/j.jafr.2025.102296.
DOI: https://doi.org/10.1016/j.jafr.2025.102296

Interpretive Summary: Corn (maize) silage is an important component of the diet of dairy cows in many regions of the USA and the world. Milk production is impacted by the digestibility of maize forage, which in turn is affected by cell wall fibers. Here we searched for genes affecting the composition of maize cell wall fibers. Several genes were identified, but their effects were relatively small. Nevertheless, we found that overall genetics had a large impact on these traits. Therefore, we demonstrated that 'genomic selection' methods that model the combined effects of many genes on these traits could be effective ways to breed improved maize for silage, even without using information on individual specific genes.

Technical Abstract: In the European Atlantic coast, maize silage is an important component of the diet of dairy cows. However, the digestibility of maize forage is limited by the resistance of the cell wall fibers, which directly impacts milk production. The optimization of maize for forage aims to increase both the quantity and quality of lignocellulosic biomass, although the complex relationship between cell wall components and digestibility poses diverse challenges. The objectives of this study embrace both the identification of candidate genes and the development of genomic prediction models in order to enhance maize stover digestibility. A genome wide association study was conducted to identify specific genomic regions containing potential candidate genes related to cell wall composition and its impact on digestibility; these noted genes involved in lignin biosynthesis, modification of cell wall polysaccharides and delignifying enzymes. However, QTLs associated represented low phenotypic variation, suggesting that integrating genomic selection into stover digestibility breeding programs could be a more powerful strategy. In this sense, genomic results indicate the necessity to complement the training group with more related individuals within the training population and to integrate more complete genotypic data to maximize progress in maize stover genetic improvement.