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ARS Home » Northeast Area » Ithaca, New York » Robert W. Holley Center for Agriculture & Health » Plant, Soil and Nutrition Research » Research » Publications at this Location » Publication #270704

Title: Maize HapMap2 identifies extant variation from a genome in flux

Author
item CHIA, JER-MING - COLD SPRING HARBOR LABORATORY
item SONG, CHI - BEIJING GENOME INSTITUTE
item Bradbury, Peter
item COSTICH, DENISE
item DE LEON, NATALIA - UNIVERSITY OF WISCONSIN
item DOEBLEY, JOHN - UNIVERSITY OF WISCONSIN
item ELSHIRE, ROBERT - CORNELL UNIVERSITY - NEW YORK
item GAUT, BRANDON - UNIVERSITY OF CALIFORNIA
item GELLER, LAURA - COLD SPRING HARBOR LABORATORY
item GLAUBITZ, JEFFREY - CORNELL UNIVERSITY - NEW YORK
item GORE, MICHAEL
item GUILL, KATE - UNIVERSITY OF MISSOURI
item HOLLAND, JAMES - NORTH CAROLINA STATE UNIVERSITY
item HUFFORD, MATTHEW - UNIVERSITY OF CALIFORNIA
item LAI, JINSHENG - CHINA AGRICULTURAL UNIVERSITY
item LI, MENG - CORNELL UNIVERSITY - NEW YORK
item LIU, XIN - BEIJING GENOME INSTITUTE
item LU, YANLI - SICHUAN UNIVERSITY
item MCCOMBIE, RICHARD - COLD SPRING HARBOR LABORATORY
item NELSON, REBECCA - CORNELL UNIVERSITY - NEW YORK
item POLAND, JESSE
item PRASANNA, BODDUPALLI - INTERNATIONAL MAIZE & WHEAT IMPROVEMENT CENTER (CIMMYT)
item PHYAJARVI, TANJA - UNIVERSITY OF CALIFORNIA
item RONG, TINGZHAO - SICHUAN UNIVERSITY
item SEKHON, RAJANDEEP - UNIVERSITY OF WISCONSIN
item SUN, QI - CORNELL UNIVERSITY - NEW YORK
item TENAILLON, MAUD - AGRO PARIS TECH
item TIAN, FENG - CORNELL UNIVERSITY - NEW YORK
item WANG, JUN - BEIJING GENOME INSTITUTE
item XU, XUN - BEIJING GENOME INSTITUTE
item ZHANG, ZHIWU - CORNELL UNIVERSITY - NEW YORK
item KAEPPLER, SHAWN - UNIVERSITY OF WISCONSIN
item ROSS-IBARRA, JEFFREY - UNIVERSITY OF CALIFORNIA
item MCMULLEN, MICHAEL
item Buckler, Edward - Ed
item ZHANG, GENYUN - BEIJING GENOME INSTITUTE
item XU, YUNBI - CHINESE ACADEMY OF AGRICULTURAL SCIENCES
item Ware, Doreen

Submitted to: Nature Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/22/2012
Publication Date: 6/3/2012
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.