Genome sequencing reveals evidence of adaptive variation in the genus Zea

Authors: CHEN, LU - Huazhong Agricultural University; LUO, JINGYUN - Huazhong Agricultural University; JIN, MINLIANG - Huazhong Agricultural University; YANG, NING - Huazhong Agricultural University; LIU, XIANGGUO - Jilin Agricultural University; PENG, YONG - Huazhong Agricultural University; LI, WENQIANG - Huazhong Agricultural University; PHILLIPS, ALYSSA - University Of California, Davis; CAMERON, BRENDA - University Of California, Davis; BERNAL, JULIO - Texas A&M University; RELLÁN-ÁLVAREZ, RUBÉN - North Carolina State University; SAWERS, RUAIRIDH J. - Pennsylvania State University; QING, LIU - Jilin Agricultural University; YIN, YUEJIA - Jilin Agricultural University; YE, XINNAN - Jilin Academy Of Agricultural Sciences; YAN, JIALI - Huazhong Agricultural University; ZHANG, QINGHUA - Huazhong Agricultural University; ZHANG, XIAOTING - Huazhong Agricultural University; WU, SHENSHEN - Huazhong Agricultural University; GUI, SONGTAO - Huazhong Agricultural University; WEI, WENIJE - Huazhong Agricultural University; WANG, YUEBIN - Huazhong Agricultural University; LUO, YUN - Huazhong Agricultural University; JIANG, CHENGLING - Huazhong Agricultural University; DENG, MIN - Huazhong Agricultural University; JIN, MIN - Huazhong Agricultural University; JIAN, LIUMEI - Huazhong Agricultural University; YU, YANHUI - Huazhong Agricultural University; ZHANG, MAOLIN - Huazhong Agricultural University; YANG, XIAOHONG - China Agricultural University; HUFFORD, MATTHEW - Iowa State University; FERNIE, ALISDAIR - Max-Planck-institut Für Meteorologie; Warburton, Marilyn; ROSS-IBARRA, JEFFREY - University Of California, Davis; YAN, JIANBING - Huazhong Agricultural University

Submitted to: Nature Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/10/2022
Publication Date: 10/22/2022
Citation: Chen, L., Luo, J., Jin, M., Yang, N., Liu, X., Peng, Y., Li, W., Phillips, A., Cameron, B., Bernal, J.S., Rellán-Álvarez, R., Sawers, R.H., Qing, L., Yin, Y., Ye, X., Yan, J., Zhang, Q., Zhang, X., Wu, S., Gui, S., Wei, W., Wang, Y., Luo, Y., Jiang, C., Deng, M., Jin, M., Jian, L., Yu, Y., Zhang, M., Yang, X., Hufford, M.B., Fernie, A.R., Warburton, M.L., Ross-Ibarra, J., Yan, J. 2022. Genome sequencing reveals evidence of adaptive variation in the genus Zea. Nature Genetics. 54:1736-1745. https://doi.org/10.1038/s41588-022-01184-y.
DOI: https://doi.org/10.1038/s41588-022-01184-y

Interpretive Summary: This study is the newest and one of the most comprehensive catalogs of the genetic sequence variation that exists in maize and several of its wild relatives. These relatives can be used to improve maize for traits that maize does not currently possess, so the relatives, and this study, represent a valuable resource to maize breeders. Examples of traits that the wild relatives contain useful sequence diversity for, but that maize does not, are presented. In addition, the evolution of the entire Zea genus is explored with this very extensive data set.

Technical Abstract: Maize is a globally valuable commodity and one of the most extensively studied genetic model organisms. However, we know surprisingly little about the extent and potential utility of the genetic variation contained by the wild relatives of maize. Here, we characterize genomic variation in maize and all wild taxa of the genus Zea, identifying over 65 million SNPs and 8 million Insertion/Deletion (InDel) polymorphisms, and over one thousand novel inversions. Our analysis of nearly 700 genomes of maize and teosinte provides the most comprehensive evolutionary history of the genus to date. It reveals evidence of selection within taxa displaying novel adaptations such as perenniality and tolerance to waterlogging. We focus in detail on evidence of convergent adaptation in highland teosinte and temperate maize. Both display a key role for hormone related pathways in flowering time and high latitude adaptation, and there is significant overlap in selection of the genes underlying these adaptations in both maize groups. To show how this data can identify useful genetic variants, we generated and characterized novel mutant alleles for two flowering time candidate genes. This work provides the most extensive sampling to date of the genetic diversity inherent in the genus Zea, resolving questions on evolution and identifying adaptive variants for direct use in modern breeding.