Maize HapMap2 identifies extant variation from a genome in flux

Jer Ming Chia; Chi Song; Peter J. Bradbury; Denise Costich; Natalia De Leon; John Doebley; Robert J. Elshire; Brandon Gaut; Laura Geller; Jeffrey C. Glaubitz; Michael Gore; Kate E. Guill; Jim Holland; Matthew B. Hufford; Jinsheng Lai; Meng Li; Xin Liu; Yanli Lu; Richard McCombie; Rebecca Nelson; Jesse Poland; Boddupalli M. Prasanna; Tanja Pyhäjärvi; Tingzhao Rong; Rajandeep S. Sekhon; Qi Sun; Maud I. Tenaillon; Feng Tian; Jun Wang; Xun Xu; Zhiwu Zhang; Shawn M. Kaeppler; Jeffrey Ross-Ibarra; Michael D. McMullen; Edward S. Buckler; Gengyun Zhang; Yunbi Xu; Doreen Ware

doi:10.1038/ng.2313

Maize HapMap2 identifies extant variation from a genome in flux

Jer Ming Chia, Chi Song, Peter J. Bradbury, Denise Costich, Natalia De Leon, John Doebley, Robert J. Elshire, Brandon Gaut, Laura Geller, Jeffrey C. Glaubitz, Michael Gore, Kate E. Guill, Jim Holland, Matthew B. Hufford, Jinsheng Lai, Meng Li, Xin Liu, Yanli Lu, Richard McCombie, Rebecca NelsonJesse Poland, Boddupalli M. Prasanna, Tanja Pyhäjärvi, Tingzhao Rong, Rajandeep S. Sekhon, Qi Sun, Maud I. Tenaillon, Feng Tian, Jun Wang, Xun Xu, Zhiwu Zhang, Shawn M. Kaeppler, Jeffrey Ross-Ibarra, Michael D. McMullen, Edward S. Buckler, Gengyun Zhang, Yunbi Xu, Doreen Ware

Research output: Contribution to journal › Article › peer-review

475 Scopus citations

Abstract

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.

Original language	English (US)
Pages (from-to)	803-807
Number of pages	5
Journal	Nature Genetics
Volume	44
Issue number	7
DOIs	https://doi.org/10.1038/ng.2313
State	Published - Jul 1 2012
Externally published	Yes

Bibliographical note

Generated from Scopus record by KAUST IRTS on 2022-09-13

ASJC Scopus subject areas

Genetics

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10.1038/ng.2313

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Chia, J. M., Song, C., Bradbury, P. J., Costich, D., De Leon, N., Doebley, J., Elshire, R. J., Gaut, B., Geller, L., Glaubitz, J. C., Gore, M., Guill, K. E., Holland, J., Hufford, M. B., Lai, J., Li, M., Liu, X., Lu, Y., McCombie, R., ... Ware, D. (2012). Maize HapMap2 identifies extant variation from a genome in flux. Nature Genetics, 44(7), 803-807. https://doi.org/10.1038/ng.2313

@article{5cf1b96dac3244118d998d291029448e,

title = "Maize HapMap2 identifies extant variation from a genome in flux",

abstract = "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. {\textcopyright} 2012 Nature America, Inc. All rights reserved.",

author = "Chia, {Jer Ming} and Chi Song and Bradbury, {Peter J.} and Denise Costich and {De Leon}, Natalia and John Doebley and Elshire, {Robert J.} and Brandon Gaut and Laura Geller and Glaubitz, {Jeffrey C.} and Michael Gore and Guill, {Kate E.} and Jim Holland and Hufford, {Matthew B.} and Jinsheng Lai and Meng Li and Xin Liu and Yanli Lu and Richard McCombie and Rebecca Nelson and Jesse Poland and Prasanna, {Boddupalli M.} and Tanja Pyh{\"a}j{\"a}rvi and Tingzhao Rong and Sekhon, {Rajandeep S.} and Qi Sun and Tenaillon, {Maud I.} and Feng Tian and Jun Wang and Xun Xu and Zhiwu Zhang and Kaeppler, {Shawn M.} and Jeffrey Ross-Ibarra and McMullen, {Michael D.} and Buckler, {Edward S.} and Gengyun Zhang and Yunbi Xu and Doreen Ware",

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Chia, JM, Song, C, Bradbury, PJ, Costich, D, De Leon, N, Doebley, J, Elshire, RJ, Gaut, B, Geller, L, Glaubitz, JC, Gore, M, Guill, KE, Holland, J, Hufford, MB, Lai, J, Li, M, Liu, X, Lu, Y, McCombie, R, Nelson, R, Poland, J, Prasanna, BM, Pyhäjärvi, T, Rong, T, Sekhon, RS, Sun, Q, Tenaillon, MI, Tian, F, Wang, J, Xu, X, Zhang, Z, Kaeppler, SM, Ross-Ibarra, J, McMullen, MD, Buckler, ES, Zhang, G, Xu, Y & Ware, D 2012, 'Maize HapMap2 identifies extant variation from a genome in flux', Nature Genetics, vol. 44, no. 7, pp. 803-807. https://doi.org/10.1038/ng.2313

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AU - Chia, Jer Ming

AU - Song, Chi

AU - Bradbury, Peter J.

AU - Costich, Denise

AU - De Leon, Natalia

AU - Doebley, John

AU - Elshire, Robert J.

AU - Gaut, Brandon

AU - Geller, Laura

AU - Glaubitz, Jeffrey C.

AU - Gore, Michael

AU - Guill, Kate E.

AU - Holland, Jim

AU - Hufford, Matthew B.

AU - Lai, Jinsheng

AU - Li, Meng

AU - Liu, Xin

AU - Lu, Yanli

AU - McCombie, Richard

AU - Nelson, Rebecca

AU - Poland, Jesse

AU - Prasanna, Boddupalli M.

AU - Pyhäjärvi, Tanja

AU - Rong, Tingzhao

AU - Sekhon, Rajandeep S.

AU - Sun, Qi

AU - Tenaillon, Maud I.

AU - Tian, Feng

AU - Wang, Jun

AU - Xu, Xun

AU - Zhang, Zhiwu

AU - Kaeppler, Shawn M.

AU - Ross-Ibarra, Jeffrey

AU - McMullen, Michael D.

AU - Buckler, Edward S.

AU - Zhang, Gengyun

AU - Xu, Yunbi

AU - Ware, Doreen

N1 - Generated from Scopus record by KAUST IRTS on 2022-09-13

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N2 - 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.

AB - 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.

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U2 - 10.1038/ng.2313

DO - 10.1038/ng.2313

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JO - Nature Genetics

JF - Nature Genetics

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ER -

Maize HapMap2 identifies extant variation from a genome in flux

Abstract

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