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United States Department of Agriculture

Agricultural Research Service

Research Project: IDENTIFICATION OF FUNCTIONAL SEQUENCE IN PLANT GENOMES THROUGH BIOINFORMATIC, GENOMIC, AND GENETIC APPROACHES Title: Maize HapMap2 identifies extant variation from a genome in flux

Authors
item Chia, Jer-Ming -
item Song, Chi -
item Bradbury, Peter
item Costich, Denise
item DE Leon, Natalia -
item Doebley, John -
item Elshire, Robert -
item Gaut, Brandon -
item Geller, Laura -
item Glaubitz, Jeffrey -
item Gore, Michael
item Guill, Kate -
item Holland, James -
item Hufford, Matthew -
item Lai, Jinsheng -
item Li, Meng -
item Liu, Xin -
item Lu, Yanli -
item Mccombie, Richard -
item Nelson, Rebecca -
item Poland, Jesse
item Prasanna, Boddupalli -
item Phyajarvi, Tanja -
item Rong, Tingzhao -
item Sekhon, Rajandeep -
item Sun, Qi -
item Tenaillon, Maud -
item Tian, Feng -
item Wang, Jun -
item Xu, Xun -
item Zhang, Zhiwu -
item Kaeppler, Shawn -
item Ross-Ibarra, Jeffrey -
item McMullen, Michael
item Buckler, Edward
item Zhang, Genyun -
item Xu, Yunbi -
item Ware, Doreen

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.

Last Modified: 12/19/2014