Empirical comparison of genomic and phenotypic selection for resistance to Fusarium ear rot and fumonisin contamination in maize

Authors: BUTOTO, ERIC - North Carolina State University; Brewer, Jason; Holland, Jim - Jim

Submitted to: Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/7/2022
Publication Date: 7/4/2022
Citation: Butoto, E., Brewer, J.C., Holland, J.B. 2022. Empirical comparison of genomic and phenotypic selection for resistance to Fusarium ear rot and fumonisin contamination in maize. Theoretical and Applied Genetics. https://doi.org/10.1007/s00122-022-04150-8.
DOI: https://doi.org/10.1007/s00122-022-04150-8

Interpretive Summary: Fusarium verticillioides is a common maize (Zea mays L.) pathogen that causes Fusarium ear rot (FER) and produces the mycotoxin fumonisin (FUM). This study empirically compared phenotypic selection (PS) and genomic selection (GS) for improving FER and FUM resistance. Three intermating generations of recurrent GS were conducted in the same time frame and from a common base population as two generations of recurrent PS. Lines sampled from each PS and GS cycle were evaluated in three North Carolina environments in 2020. We observed similar cumulative responses to GS and PS, representing decreases of about 50% of mean FER and FUM compared to the base population. The first cycle of GS was more effective than later cycles. PS and GS both achieved about 70% of predicted total gain from selection for FER, but only about 26% of predicted gains for FUM, suggesting that heritability for FUM was overestimated. We observed a 20% decrease in genetic marker variation from PS and 30% decrease from GS. Our greatest challenge was our inability to quickly obtain dense and consistent set of marker genotypes across generations of GS. Practical implementation of GS in individual small-scale breeding programs will require cheaper and faster genotyping methods, and such technological advances will present opportunities to significantly optimize selection and mating schemes for future GS efforts beyond what we were able to achieve in this study.

Technical Abstract: Fusarium verticillioides is a common fungal pathogen of maize that causes Fusarium ear rot (FER) and produces fumonisin (FUM), a mycotoxin associated with various maladies in humans and animals that consume contaminated grain. Response to phenotypic selection (PS) is hindered by the cost and time required to obtain accurate evaluations of FER and FUM. This study empirically compares genomic and phenotypic selection ability to improve FER and FUM resistance. Three intermating generations of recurrent genomic selection (GS) with optimal contribution methodology were conducted in the same time frame and common base population as two generations of recurrent PS. Lines sampled from each PS and GS cycle were evaluated in three North Carolina environments in 2020. We observed slightly greater linear responses to GS than PS for FER and FUM, but also a noticeable decline in response to the last cycle of GS. The final cycles of PS and GS did not differ significantly for FER and FUM content. We observed a 28% decrease in molecular genetic variation from GS and a 20% decrease from PS; balancing rapid genetic gain and loss of genetic variation will be important in recurrent GS. Both PS and GS indirectly affected other important traits, such as grain yield, test weight, and ear morphology. Our greatest challenge was our inability to quickly obtain dense and consistent set of marker genotypes across generations of GS. Practical implementation of GS in individual public-sector breeding programs will require cheaper and faster dense genotyping methods.