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Publication Details
AFRICAN RESEARCH NEXUS
SHINING A SPOTLIGHT ON AFRICAN RESEARCH
biochemistry, genetics and molecular biology
Maize HapMap2 identifies extant variation from a genome in flux
Nature Genetics, Volume 44, No. 7, Year 2012
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Description
Whereas breeders have exploited diversity in maize for yield improvements, there has been limited progress in using beneficial alleles in undomesticated varieties. Characterizing standing variation in this complex genome has been challenging, with only a small fraction of it described to date. Using a population genetics scoring model, we identified 55 million SNPs in 103 lines across pre-domestication and domesticated Zea mays varieties, including a representative from the sister genus Tripsacum. We find that structural variations are pervasive in the Z. mays genome and are enriched at loci associated with important traits. By investigating the drivers of genome size variation, we find that the larger Tripsacum genome can be explained by transposable element abundance rather than an allopolyploid origin. In contrast, intraspecies genome size variation seems to be controlled by chromosomal knob content. There is tremendous overlap in key gene content in maize and Tripsacum, suggesting that adaptations from Tripsacum (for example, perennialism and frost and drought tolerance) can likely be integrated into maize. © 2012 Nature America, Inc. All rights reserved.
Authors & Co-Authors
Chia, Jer Ming
United States, Cold Spring Harbor
Cold Spring Harbor Laboratory
Song, Chi
China, Shenzhen
Bgi-shenzhen
Bradbury, Peter J.
United States, Ithaca
Cornell University
United States, Washington, D.c.
United States Department of Agriculture
Costich, Denise Elston
United States, Ithaca
Cornell University
United States, Washington, D.c.
United States Department of Agriculture
De Leon, Natalia
United States, Madison
University of Wisconsin-madison
Doebley, John
United States, Madison
University of Wisconsin-madison
Elshire, R.
United States, Ithaca
Cornell University
Gaut, Brandon S.
United States, Irvine
University of California, Irvine
Geller, Laura
United States, Cold Spring Harbor
Cold Spring Harbor Laboratory
Glaubitz, Jeffrey C.
United States, Ithaca
Cornell University
Gore, Michael Allen
United States, Washington, D.c.
United States Department of Agriculture
United States, Maricopa
Usda Ars U.s. Arid-land Agricultural Research Center
Guill, Kate E.
United States, Washington, D.c.
United States Department of Agriculture
United States, Columbia
University of Missouri
Holland, Jim
United States, Washington, D.c.
United States Department of Agriculture
United States, Raleigh
Nc State University
Hufford, Matthew B.
United States, Davis
University of California, Davis
Lai, Jinsheng
China, Beijing
China Agricultural University
Li, Meng
United States, Ithaca
Cornell University
Liu, Xin
China, Shenzhen
Bgi-shenzhen
Lu, Yanli
China, Ya'an
Sichuan Agricultural University
McCombie, W. Richard
United States, Cold Spring Harbor
Cold Spring Harbor Laboratory
Nelson, Rebecca J.
United States, Ithaca
Cornell University
Poland, Jesse A.
United States, Washington, D.c.
United States Department of Agriculture
United States, Manhattan
Kansas State University
Boddupalli, Prasanna M.
Kenya, Nairobi
International Maize and Wheat Improvement Center Cimmyt
Pyhäjärvi, Tanja
United States, Davis
University of California, Davis
Rong, Tingzhao
China, Ya'an
Sichuan Agricultural University
Sekhon, Rajandeep S.
United States, Madison
University of Wisconsin-madison
Sun, Qi
United States, Ithaca
Cornell University
Tenaillon, Maud Irne
United States, Irvine
University of California, Irvine
France, Gif-sur-yvette
Génétique Quantitative et Évolution le Moulon
Tian, Feng
United States, Ithaca
Cornell University
Wang, Jun
China, Shenzhen
Bgi-shenzhen
Xu, Xun
China, Shenzhen
Bgi-shenzhen
Zhang, Zhiwu
United States, Ithaca
Cornell University
Kaeppler, Shawn M.
United States, Madison
University of Wisconsin-madison
Ross-Ibarra, Jeffrey
United States, Davis
University of California, Davis
McMullen, Michael D.
United States, Washington, D.c.
United States Department of Agriculture
United States, Columbia
University of Missouri
Buckler, Ed S.
United States, Ithaca
Cornell University
United States, Washington, D.c.
United States Department of Agriculture
Zhang, Gengyun
China, Shenzhen
Bgi-shenzhen
Xu, Yunbi
China, Beijing
Chinese Academy of Agricultural Sciences
Mexico, Texcoco
Centro Internacional de Mejoramiento de Maiz y Trigo
Ware, Doreen H.
United States, Cold Spring Harbor
Cold Spring Harbor Laboratory
United States, Washington, D.c.
United States Department of Agriculture
Statistics
Citations: 560
Authors: 38
Affiliations: 17
Identifiers
Doi:
10.1038/ng.2313
ISSN:
10614036
e-ISSN:
15461718
Research Areas
Genetics And Genomics
Study Design
Cross Sectional Study