Contributions of Zea mays subspecies mexicana haplotypes to modern maize

Ning Yang, Xi-Wen Xu, Rui-Ru Wang, Wen-Lei Peng, Lichun Cai, Jia-Ming Song, Wenqiang Li, Xin Luo, Luyao Niu, Yuebin Wang, Min Jin, Lu Chen, Jingyun Luo, Min Deng, Long Wang, Qingchun Pan, Feng Liu, David Jackson, Xiaohong Yang, Ling-Ling Chen () and Jianbing Yan ()
Additional contact information
Ning Yang: Huazhong Agricultural University
Xi-Wen Xu: Huazhong Agricultural University
Rui-Ru Wang: Huazhong Agricultural University
Wen-Lei Peng: Huazhong Agricultural University
Lichun Cai: China Agricultural University
Jia-Ming Song: Huazhong Agricultural University
Wenqiang Li: Huazhong Agricultural University
Xin Luo: Huazhong Agricultural University
Luyao Niu: Huazhong Agricultural University
Yuebin Wang: Huazhong Agricultural University
Min Jin: Huazhong Agricultural University
Lu Chen: Huazhong Agricultural University
Jingyun Luo: Huazhong Agricultural University
Min Deng: Huazhong Agricultural University
Long Wang: Huazhong Agricultural University
Qingchun Pan: Huazhong Agricultural University
Feng Liu: Huazhong Agricultural University
David Jackson: Huazhong Agricultural University
Xiaohong Yang: China Agricultural University
Ling-Ling Chen: Huazhong Agricultural University
Jianbing Yan: Huazhong Agricultural University

Nature Communications, 2017, vol. 8, issue 1, 1-10

Abstract: Abstract Maize was domesticated from lowland teosinte (Zea mays ssp. parviglumis), but the contribution of highland teosinte (Zea mays ssp. mexicana, hereafter mexicana) to modern maize is not clear. Here, two genomes for Mo17 (a modern maize inbred) and mexicana are assembled using a meta-assembly strategy after sequencing of 10 lines derived from a maize-teosinte cross. Comparative analyses reveal a high level of diversity between Mo17, B73, and mexicana, including three Mb-size structural rearrangements. The maize spontaneous mutation rate is estimated to be 2.17 × 10−8 ~3.87 × 10−8 per site per generation with a nonrandom distribution across the genome. A higher deleterious mutation rate is observed in the pericentromeric regions, and might be caused by differences in recombination frequency. Over 10% of the maize genome shows evidence of introgression from the mexicana genome, suggesting that mexicana contributed to maize adaptation and improvement. Our data offer a rich resource for constructing the pan-genome of Zea mays and genetic improvement of modern maize varieties.

Date: 2017
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DOI: 10.1038/s41467-017-02063-5

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