Association mapping and genomic prediction for ear rot disease caused by Fusarium verticillioides in a tropical maize germplasm

Authors: KUKI, MAURICIO - University Of Maringa; PINTO, RONALD JOSE - University Of Maringa; BERTAGNA, FILIPE AUGUSTO - University Of Maringa; TESSMANN, DAURI JOSE - University Of Maringa; TEIXEIRA DO AMARAL, ANTONIO - University Of Maringa; SCAPIM, CARLOS ALBERTO - University Of Maringa; Holland, Jim - Jim

Submitted to: Crop Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/14/2020
Publication Date: 7/20/2020
Citation: Kuki, M., Pinto, R.B., Bertagna, F.B., Tessmann, D., Teixeira Do Amaral, A.J., Scapim, C., Holland, J.B. 2020. Association mapping and genomic prediction for ear rot disease caused by Fusarium verticillioides in a tropical maize germplasm. Crop Science. 60:2867-2881.

Interpretive Summary: Fusarium ear rot caused by Fusarium verticillioides is one of the major ear diseases that affects both yield and grain quality in corn. This is a major disease both in the USA and in other parts of the world, including Brazil. We evaluated 320 maize inbreds for resistance to Fusarium ear rot in Brazil and genotyped them with almost 300,000 DNA markers. With these data, we searched for markers associated with ear rot resistance and identified three SNPs associated with symptoms of ear rot, none of which had large effects. Given this evidence that most of the genetic variation for this trait is due to many small effect genes, we then tried an approach called genomic prediction, which uses information from thousands of genetic markers to predict quantitative trait values. Genomic prediction methods had accuracy similar to field evaluations with limited replication, suggesting that this method could be used to augment selection for resistance to ear rot.

Technical Abstract: Fusarium ear rot (FER) caused by Fusarium verticillioides is one of the major ear diseases that affects both yield and grain quality in maize (Zea mays L.), especially in tropical environments. Fusarium genetic resistance is a complex trait, controlled by several small-effect genes and strongly influenced by the environment. We applied a comprehensive genome-wide association study and genomic prediction for ear rot and starburst symptoms, using 291,633 high-quality single nucleotide polymorphism (SNPs) markers in 320 tropical maize inbred lines, in two distinct locations at Brazil southern region. Three SNPs were significantly associated with starburst symptoms, each associated with 6% to 8% of the phenotypic variance, and with gene models that have expression levels in ears, pericarp and kernels, suggesting some influence over FER resistance. No significant SNP was associated with FER, which is an indication that the genetic architecture for this trait is highly polygenic, with potentially many variants having small effects that are not detectable in the association mapping analysis. We observed genomic prediction accuracies ranging from 0.34 to 0.4 for FER and starburst, respectively. Further research is required to validate these significant SNPs and their relationship to genes affecting FER resistance, and also to improve genomic prediction accuracies across different genetic backgrounds.