Genome-wide association study for root morphology and phosphorus acquisition efficiency in diverse maize panels

Authors: RIBEIRO, CARLOS ALEXANDR - Universidade Federal De Vicosa; TINOCO, SYLVIA MORAIS D - Embrapa; DE SOOUZA, VANDER FILLIPE - Universidade Federal De São João Del-Rei; NEGRI, BARBARA FRANCA - Universidade Federal De São João Del-Rei; GAULT, CHRISTINE MARIE - Universidade Federal De São João Del-Rei; PASTINA, MARIA MARTA - Embrapa; MAGALHAES, JURANDIR VIEIRA - Embrapa; GUIMARAES, LAURO JOSE MORE - Embrapa; DE BARROS, EVERALDO GONCAL - Universidade Federal De Vicosa; Buckler, Edward - Ed; GUIMARAES, CLAUDIA TEIXEIR - Universidade Federal De São João Del-Rei

Submitted to: International Journal of Molecular Sciences
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/15/2023
Publication Date: 3/25/2023
Citation: Ribeiro, C.R., Tinoco, S.E., De Soouza, V., Negri, B., Gault, C., Pastina, M., Magalhaes, J., Guimaraes, L.I., De Barros, E.V., Buckler IV, E.S., Guimaraes, C.A. 2023. Genome-wide association study for root morphology and phosphorus acquisition efficiency in diverse maize panels. International Journal of Molecular Sciences. 24(7). Article 6233. https://doi.org/10.3390/ijms24076233.
DOI: https://doi.org/10.3390/ijms24076233

Interpretive Summary: Plants cope with phosphorus deficiency by modifying their root systems to explore the soil more effectively. Here, researchers studied 561 tropical maize inbred lines to understand how the root traits and phosphorus acquisition change under low and high phosphorus conditions. They examined genetic markers (SNPs) in the maize genome to identify associations between specific genes and traits related to root morphology and phosphorus uptake. The study found that phosphorus availability affects root traits, biomass, and phosphorus content differently in different maize panels (Embrapa and DTMA). This indicates that maize uses various root plasticity mechanisms to adapt to low-phosphorus conditions. Among the identified SNPs, two were particularly noteworthy: S9_137746077, linked to a gene encoding a MAPKKK protein kinase, which increased root length and surface area under phosphorus deficiency, and S8_88600375, located within a gene encoding an AGC kinase, which positively affected root length, surface area, and seedling weight under low-phosphorus conditions. The researchers suggest that by leveraging the genetic diversity in maize, it may be possible to exploit candidate genes and favorable alleles to improve phosphorus efficiency in maize breeding programs in Africa and Latin America.

Technical Abstract: Maximizing soil exploration through modifications of the root system is a strategy for plants to overcome phosphorus (P) deficiency. Genome-wide association with 561 tropical maize inbred lines from Embrapa and DTMA panels was undertaken for root morphology and P acquisition traits under low- and high-P concentrations, with 353,540 SNPs. P supply modified root morphology traits, biomass and P content in the global maize panel, but root length and root surface area changed differentially in Embrapa and DTMA panels. This suggests that different root plasticity mechanisms exist for maize adaptation to low-P conditions. A total of 87 SNPs were associated to phenotypic traits in both P conditions at -log10(p-value) = 5, whereas only seven SNPs reached the Bonferroni significance. Among these SNPs, S9_137746077, which is located upstream of the gene GRMZM2G378852 that encodes a MAPKKK protein kinase, was significantly associated with total seedling dry weight, with the same allele increasing root length and root surface area under P deficiency. The C allele of S8_88600375, mapped within GRMZM2G044531 that encodes an AGC kinase, significantly enhanced root length under low P, positively affecting root surface area and seedling weight. The broad genetic diversity evaluated in this panel suggests that candidate genes and favorable alleles could be exploited to improve P efficiency in maize breeding programs of Africa and Latin America.