ARS | Publication request: Maize HapMap2 identifies extant variation from a genome in flux

Submitted to: Nature Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: March 22, 2012
Publication Date: June 3, 2012
Citation: Chia, J., Song, C., Bradbury, P., Costich, D., De Leon, N., Doebley, J., Elshire, R., Gaut, B., Geller, L., Glaubitz, J., Gore, M.A., Guill, K., Holland, J., Hufford, M., Lai, J., Li, M., Liu, X., Lu, Y., McCombie, R., Nelson, R., Poland, J.A., Prasanna, B., Phyajarvi, T., Rong, T., Sekhon, R., Sun, Q., Tenaillon, M., Tian, F., Wang, J., Xu, X., Zhang, Z., Kaeppler, S.M., Ross-Ibarra, J., McMullen, M.D., Buckler IV, E.S., Zhang, G., Xu, Y., Ware, D. 2012. Maize HapMap2 identifies extant variation from a genome in flux. Nature Genetics. 40:803-807. DOI: 10.1038/ng.2313.

Interpretive Summary: Maize is the world’s largest production crop in the world, and its diversity has allowed it in a few thousand years to adapt to the tropics, mountains, temperate locations. Using next generation sequencing technology, we characterize this diversity to an unprecedented level in the world’s key breeding lines and its wild relatives. Surprisingly, nearly 90% of the genome is associated with structural variation, and this variation is responsible for a substantial portion of trait variation in maize. Despite this incredible structural variation, there is tremendous unity in key gene content even with the sister genus, which suggests that adaptations (perennialism, frost and drought tolerance, etc.) amongst all of maize’s relatives are likely integratable in maize.

Technical Abstract: The maize genome is the largest, most diverse and complex plant genome sequenced to date. Using high-throughput sequencing to access genetic variation and a population genetics model to score the polymorphisms, we characterize and unite the diversity of the world’s key breeding germplasm, wild relatives, and its sister genus. With the discovery of more than 55M SNP/indel variants, this permits for the first time true genome-wide association studies (GWAS) in a complex plant genome. Analysis of structural variation (SV) suggests 90% of the genome is segregating for SV, and GWAS indicates SVs are highly enriched for functional associations. This survey provides the foundation to unite genetic dissection and breeding of germplasm resources across maize and its relatives.