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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 #358235

Research Project: Improving Crop Efficiency Using Genomic Diversity and Computational Modeling

Location: Plant, Soil and Nutrition Research

Title: Construction of the third generation Zea mays haplotype map

Author
item Bukowski, Robert - Cornell University - New York
item Guo, Xiaosen - Bgi Shenzhen
item Lu, Yanli - Sichuan Agricultural University
item Zou, Cheng - Chinese Academy Of Agricultural Sciences
item He, Bing - Bgi Shenzhen
item Rong, Zhengqin - Bgi Shenzhen
item Yang, Bicheng - Bgi Shenzhen
item Wang, Bo - Bgi Shenzhen
item Xu, Dawen - Bgi Shenzhen
item Xie, Chuanxiao - Chinese Academy Of Agricultural Sciences
item Fan, Longjiang - Zheijiang University
item Gao, Shibin - Sichuan Agricultural University
item Xy, Xun - Bgi Shenzhen
item Zhang, Gengyun - Bgi Shenzhen
item Li, Yingrui - Bgi Shenzhen
item Jiao, Yinping - Cold Spring Harbor Laboratory
item Doebley, John - University Of Wisconsin
item Ross-ibarra, Jeffrey - University Of California
item Buffalo, Vince - University Of California
item Romay, Cinta - Cornell University - New York
item Buckler, Edward - Ed
item Wu, Yunbi - Chinese Academy Of Agricultural Sciences
item Lai, Jinsheng - China Agricultural University
item Ware, Doreen
item Sun, Qi - Cornell University - New York

Submitted to: Gigascience
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/30/2018
Publication Date: 4/1/2018
Citation: Bukowski, R., Guo, X., Lu, Y., Zou, C., He, B., Rong, Z., Yang, B., Wang, B., Xu, D., Xie, C., Fan, L., Gao, S., Xy, X., Zhang, G., Li, Y., Jiao, Y., Doebley, J., Ross-Ibarra, J., Buffalo, V., Romay, C., Buckler IV, E.S., Wu, Y., Lai, J., Ware, D., Sun, Q. 2018. Construction of the third generation Zea mays haplotype map. Gigascience. 7(4):1-12.

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 and novel bioinformatic approaches, this consortium of scientists from around the globe have whole genome characterized over 1200 varieties of maize and identified over 80 million genetic variants. This provides an important global resource for the analysis of natural variation in maize that can be used to advance genetics and breeding.

Technical Abstract: Characterization of genetic variations in maize has been challenging, mainly due to deterioration of collinearity between individual genomes in the species. An international consortium of maize research groups combined resources to develop the maize haplotype version 3 (HapMap 3), built from whole genome sequencing data from 1,218 maize lines, covering pre-domestication and domesticated Zea mays varieties across the world. A new computational pipeline was set up to process over 12 trillion bp of sequencing data, and a set of population genetics filters were applied to identify over 83 million variant sites. We identified polymorphisms in regions where collinearity is largely preserved in the maize species. However, the fact that the B73 genome used as the reference only represents a fraction of all haplotypes is still an important limiting factor.