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ARS Home » Midwest Area » Ames, Iowa » Corn Insects and Crop Genetics Research » Research » Publications at this Location » Publication #422503
Research Project: MaizeGDB - Database and Computational Resources for Maize Genetics, Genomics, and Breeding Research

Location: Corn Insects and Crop Genetics Research

Title: Extensive genome evolution distinguishes maize within a stable tribe of grasses

Author
item STITZER, MICHELLE - Cornell University
item SEETHARAM, ARUN - Iowa State University
item SCHEBEN, A. - Cold Spring Harbor Laboratory
item HSU, S.K. - Cornell University
item SCHULTZ, AIMEE - Cornell University
item AUBUCHON-ELDER, T.M. - Donald Danforth Plant Science Center
item HALE, C. - Cornell University
item SYRING, MICHAEL - Iowa State University
item MINX, P. - Donald Danforth Plant Science Center
item PASQUET, REMY - University Of Montpellier
item MCALLISTER, CHRISTINE - Principia College
item MALCOMBER, SIMON - National Science Foundation (NSF)
item TRAIPERM, PAWEENA - Mahidol University
item LAYTON, DANIEL - Indiana University
item ZHONG, JINSHUN - South China Agricultural Univerisity
item COSTICH, DENISE - Cornell University
item FENGLER, KEVIN - Corteva Agriscience
item HARRIS, CHARLOTTE - Corteva Agriscience
item IRELAN, ZACH - Corteva Agriscience
item LLACA, VICTOR - Corteva Agriscience
item PARAKKA, PRAVEENA - Corteva Agriscience
item ZASTROW-HAYES, GINA - Corteva Agriscience
item DAWE, R. KELLY - University Of Georgia
item Woodhouse, Margaret
item Cannon, Ethalinda
item Portwood Ii, John
item Andorf, Carson
item EL-WALID, M. - Cornell University
item MCMORROW, S. - Cornell University
item FEREBEE, T.H. - Cornell University
item WRIGHTSMAN, T. - Cornell University
item LIU, Z.Y. - Cornell University
item PHILLIPS, A.R. - University Of California, Davis
item ZHAI, J. - Cornell University
item ALBERT, P. - University Of Missouri
item BIRCHLER, JAMES - University Of Missouri
item SIEPEL, A. - Cold Spring Harbor Laboratory
item ROSS-IBARRA, JEFFREY - University Of California, Davis
item ROMAY, M. CINTA - Cornell University
item KELLOGG, ELIZABETH - Danforth Plant Science Center
item Buckler Iv, Edward
item HUFFORD, MATTHEW - Iowa State University

Submitted to: bioRxiv
Publication Type: Pre-print Publication
Publication Acceptance Date: 1/24/2025
Publication Date: 1/24/2025
Citation: Stitzer, M., Seetharam, A., Scheben, A., Hsu, S., Schultz, A., Aubuchon-Elder, T., Hale, C., Syring, M., Minx, P., Pasquet, R., Mcallister, C., Malcomber, S., Traiperm, P., Layton, D., Zhong, J., Costich, D., Fengler, K., Harris, C., Irelan, Z., Llaca, V., Parakka, P., Zastrow-Hayes, G., Dawe, R., Woodhouse, M.H., Cannon, E.K., Portwood II, J.L., Andorf, C.M., El-Walid, M., Mcmorrow, S., Ferebee, T., Wrightsman, T., Liu, Z., Phillips, A., Zhai, J., Albert, P., Birchler, J., Siepel, A., Ross-Ibarra, J., Romay, M., Kellogg, E., Buckler IV, E.S., Hufford, M. 2025. Extensive genome evolution distinguishes maize within a stable tribe of grasses. bioRxiv. Article 2025.01.22.633974. https://doi.org/10.1101/2025.01.22.633974.
DOI: https://doi.org/10.1101/2025.01.22.633974

Interpretive Summary: The Andropogoneae tribe of grasses has evolved to dominate 17% of global land area. Domestication of these grasses in the last 10,000 years has yielded our most productive crops, including maize, sugarcane, and sorghum. The majority of Andropogoneae species have duplicated genomes, and multiple genome copies have been considered a benefit for plants, since they have a tendency to improve the plant's fitness. Pinpointing the benefits of genome duplication has been challenging due to the limited number of available plant genomes. Here, we present genome assemblies of 33 grass genomes, including chromosome-scale assemblies of Zea and Tripsacum, and show that in 12 of 14 independent genome duplication events, genome duplication appears to increase fitness. However, the maize lineage undergoes major chromosome rearrangements, gene loss, and transposable element (TE) amplification compared to the other grasses studies. These genomes provide a comparative baseline for understanding grass evolution, especially important with growing roles in carbon economies.

Technical Abstract: Over the last 20 million years, the Andropogoneae tribe of grasses has evolved to dominate 17% of global land area. Domestication of these grasses in the last 10,000 years has yielded our most productive crops, including maize, sugarcane, and sorghum. The majority of Andropogoneae species are polyploid, and multiple genome copies have been considered an adaptive benefit from either heterosis via fixed heterozygosity, or genetic redundancy masking genetic load. Separating these benefits of polyploidy has been challenging, due to limited genomic sampling of groups of taxa with multiple sampled polyploidy events. Here, we present genome assemblies of 33 taxa, including chromosome-scale assemblies of Zea and Tripsacum, and show that in 12 of 14 independent polyploid formation events polyploidization predominately reconciles genetic load. However, rediploidization occurs in the maize lineage via major chromosome rearrangements, gene loss, and transposable element (TE) amplification. These genomes provide a comparative baseline for understanding C4 grass evolution, especially important with growing roles in carbon economies.