Construction of the third-generation Zea mays haplotype map.
Robert Bukowski,Xiaosen Guo,Yanli Lu,Cheng Zou,Bing He,Zhengqin Rong,Bo Wang,Dawen Xu,Bicheng Yang,Chuanxiao Xie,Longjiang Fan,Shibin Gao,Xun Xu,Gengyun Zhang,Yingrui Li,Yinping Jiao,John Doebley,Jeffrey Ross-Ibarra,Anne Lorant,Vince Buffalo,M. Cinta Romay,Edward S. Buckler,Edward S. Buckler,Doreen Ware,Jinsheng Lai,Qi Sun,Yunbi Xu +26 more
TL;DR: The maize haplotype version 3 (HapMap 3) was built from whole-genome sequencing data from 1218 maize lines, covering predomestication and domesticated Zea mays varieties across the world as discussed by the authors.
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Abstract: Author(s): Bukowski, Robert; Guo, Xiaosen; Lu, Yanli; Zou, Cheng; He, Bing; Rong, Zhengqin; Wang, Bo; Xu, Dawen; Yang, Bicheng; Xie, Chuanxiao; Fan, Longjiang; Gao, Shibin; Xu, Xun; Zhang, Gengyun; Li, Yingrui; Jiao, Yinping; Doebley, John F; Ross-Ibarra, Jeffrey; Lorant, Anne; Buffalo, Vince; Romay, M Cinta; Buckler, Edward S; Ware, Doreen; Lai, Jinsheng; Sun, Qi; Xu, Yunbi | Abstract: BackgroundCharacterization 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 1218 maize lines, covering predomestication and domesticated Zea mays varieties across the world.ResultsA new computational pipeline was set up to process more than 12 trillion bp of sequencing data, and a set of population genetics filters was applied to identify more than 83 million variant sites.ConclusionsWe 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.
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Citations
Resistance to Abiotic Stress: Theory and Applications in Maize Breeding
R. N. Gadag,Jayant S. Bhat,Ganapati Mukri,Robin Gogoi,S. B. Suby,Abhijit Das,Sarita Yadav,Pranjal Yadava,M. L. Nithyashree,Gopalakrishna K. Naidu,Sunil Kumar Yadav,K. Shilpa +11 more
- 01 Jan 2021
TL;DR: In this article, the authors used genetic mapping of yield and yield component traits under abiotic stresses opened the new way of marker assisted maize breeding for stress tolerance, which has resulted in effective utilization of cross boundary information across different and /or unrelated species.
Incomplete dominance of deleterious alleles contributes substantially to trait variation and heterosis in maize.
Jinliang Yang,Sofiane Mezmouk,Andy Baumgarten,Edward S. Buckler,Edward S. Buckler,Edward S. Buckler,Katherine E. Guill,Michael D. McMullen,Michael D. McMullen,Rita H. Mumm,Jeffrey Ross-Ibarra +10 more
TL;DR: Results provide empirical support for an important role for incomplete dominance of deleterious alleles in explaining heterosis and demonstrate the utility of incorporating functional annotation in phenotypic prediction and plant breeding.
Kernel size-related genes revealed by an integrated eQTL analysis during early maize kernel development.
Junling Pang,Junjie Fu,Na Zong,Jing Wang,Dandan Song,Xia Zhang,Cheng He,Ting Fang,Hongwei Zhang,Yunliu Fan,Guoying Wang,Jun Zhao +11 more
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Single-cell analysis of cis-regulatory elements.
TL;DR: In this paper, the role of cis-regulatory elements in cell identity maintenance, differentiation, and functional specialization has remained relatively unexplored in plant systems, and single-cell profiling has emerged as a powerful tool to circumvent these past obstacles by enabling unbiased charting of transcriptional and cisregulatory states at the resolution of individual cells.
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