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.
read more
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.
read more
Chat with Paper
AI Agents for this Paper
Find similar papers on Google Scholar, PubMed and Arxiv
Write a critical review of this paper
Analyze citations of this paper to find unaddressed research gaps
Citations
Hybrid allele-specific ChIP-seq analysis identifies variation in brassinosteroid-responsive transcription factor binding linked to traits in maize
Thomas Hartwig,Michael Banf,Gisele Prietsch,Jiachen Zhu,Isabel Mora-Ramirez,Jos H. M. Schippers,Samantha J. Snodgrass,Arun S. Seetharam,Bruno Huettel,Judith M. Kolkman,Jinliang Yang,Julia Engelhorn,Zhi Yong Wang +12 more
TL;DR: In this paper , a hybrid allele-specific chromatin binding sequencing (HASCh-seq) approach was used to identify variations in target binding of the brassinosteroid-responsive TF ZmBZR1 in maize.
Brown midrib mutant and genome‐wide association analysis uncover lignin genes for disease resistance in maize
TL;DR: The role of lignin in plant defense was explored using high-resolution, genome-wide association analysis for resistance to Northern Leaf Blight (NLB) in the Goodman diversity panel as discussed by the authors .
7
Functionally, structurally, and evolutionarily distinct set of genes linked to phenome wide variation in maize
TL;DR: Genome-Phenome Wide Association Study and future similar analytical approaches that leverage data from multiple correlated and uncorrelated traits across the same population may provide a method to prioritize those genes most involved in regulation phenotypic variation across diverse species.
Identifying QTL and candidate genes for prolificacy in maize
TL;DR: In maize, prolificacy, the number of ears per plant, is a trait of interest to maize breeders for breeding high grain-yielding cultivars or specialty corn, as well as being a model trait for decoding the molecular mechanism of maize evolution as mentioned in this paper .
7
Prediction of evolutionary constraint by genomic annotations improves functional prioritization of genomic variants in maize
TL;DR: In this paper , the authors use genomic annotations to accurately predict nucleotide conservation across angiosperms, as a proxy for fitness effect of mutations, and use this approach to select polymorphisms for accurate genomic prediction, and candidate mutations for efficient base editing.
References
The Sequence Alignment/Map format and SAMtools
Heng Li,Bob Handsaker,Alec Wysoker,T. J. Fennell,Jue Ruan,Nils Homer,Gabor T. Marth,Gonçalo R. Abecasis,Richard Durbin +8 more
TL;DR: SAMtools as discussed by the authors implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments.
Trimmomatic: a flexible trimmer for Illumina sequence data
TL;DR: Timmomatic is developed as a more flexible and efficient preprocessing tool, which could correctly handle paired-end data and is shown to produce output that is at least competitive with, and in many cases superior to, that produced by other tools, in all scenarios tested.
57.9K
The variant call format and VCFtools
Petr Danecek,Adam Auton,Gonçalo R. Abecasis,Cornelis A. Albers,Eric Banks,Mark A. DePristo,Robert E. Handsaker,Gerton Lunter,Gabor T. Marth,Stephen T. Sherry,Gilean McVean,Richard Durbin +11 more
TL;DR: VCFtools is a software suite that implements various utilities for processing VCF files, including validation, merging, comparing and also provides a general Perl API.
A framework for variation discovery and genotyping using next-generation DNA sequencing data
Mark A. DePristo,Eric Banks,Ryan Poplin,Kiran V. Garimella,Jared Maguire,Christopher Hartl,Anthony A. Philippakis,Anthony A. Philippakis,Anthony A. Philippakis,Guillermo del Angel,Manuel A. Rivas,Manuel A. Rivas,Matt Hanna,Aaron McKenna,Timothy Fennell,Andrew Kernytsky,Andrey Sivachenko,Kristian Cibulskis,Stacey Gabriel,David Altshuler,David Altshuler,Mark J. Daly,Mark J. Daly +22 more
TL;DR: A unified analytic framework to discover and genotype variation among multiple samples simultaneously that achieves sensitive and specific results across five sequencing technologies and three distinct, canonical experimental designs is presented.
An integrated map of genetic variation from 1,092 human genomes
Gonçalo R. Abecasis,Adam Auton,Lisa D. Brooks,Mark A. DePristo,Richard Durbin,Robert E. Handsaker,Robert E. Handsaker,Hyun Min Kang,Gabor T. Marth,Gil McVean +9 more
TL;DR: It is shown that evolutionary conservation and coding consequence are key determinants of the strength of purifying selection, that rare-variant load varies substantially across biological pathways, and that each individual contains hundreds of rare non-coding variants at conserved sites, such as motif-disrupting changes in transcription-factor-binding sites.
Related Papers (5)
Patrick S. Schnable,Doreen Ware,Robert S. Fulton,Joshua C. Stein,Fusheng Wei,Shiran Pasternak,Chengzhi Liang,Jianwei Zhang,Lucinda Fulton,Tina Graves,Patrick Minx,Amy Denise Reily,Laura Courtney,Scott Kruchowski,Chad Tomlinson,Cindy Strong,Kim D. Delehaunty,Catrina Fronick,Bill Courtney,Susan M. Rock,Eddie Belter,Feiyu Du,Kyung Kim,Rachel Abbott,Marc Cotton,Andrew Levy,Pamela Marchetto,Kerri Ochoa,Stephanie M. Jackson,Barbara Gillam,Weizu Chen,Le Yan,Jamey Higginbotham,Marco Cardenas,Jason Waligorski,Elizabeth Applebaum,Lindsey Phelps,Jason Falcone,Krishna L. Kanchi,T. K. Thane,Adam Scimone,Nay Thane,Jessica Henke,Thomas J. Wang,Jessica Ruppert,Neha Shah,Kelsi Rotter,Jennifer S. Hodges,Elizabeth Ingenthron,Matt Cordes,Sara Kohlberg,Jennifer Sgro,Brandon Delgado,Kelly Mead,Asif T. Chinwalla,Shawn Leonard,Kevin Crouse,Kristi Collura,Dave Kudrna,Jennifer Currie,Ruifeng He,Angelina Angelova,Shanmugam Rajasekar,Teri Mueller,Rene Lomeli,Gabriel Scara,Ara Ko,Krista Delaney,Marina Wissotski,Georgina Lopez,David Campos,Michele Braidotti,Elizabeth Ashley,Wolfgang Golser,Hyeran Kim,Seunghee Lee,Jinke Lin,Zeljko Dujmic,Woojin Kim,Jayson Talag,Andrea Zuccolo,Chuanzhu Fan,Aswathy Sebastian,Melissa Kramer,Lori Spiegel,Lidia Nascimento,Theresa Zutavern,Beth Miller,Claude Ambroise,Stephanie Muller,William Spooner,Apurva Narechania,Liya Ren,Sharon Wei,Sunita Kumari,Ben Faga,Michael J. Levy,Linda McMahan,Peter Van Buren,Matthew W. Vaughn,Kai Ying,Cheng Ting Yeh,Scott J. Emrich,Scott J. Emrich,Yi Jia,Ananth Kalyanaraman,Ananth Kalyanaraman,An-Ping Hsia,W. Brad Barbazuk,Regina S. Baucom,Thomas P. Brutnell,Nicholas C. Carpita,Cristian Chaparro,Jer Ming Chia,Jean-Marc Deragon,James C. Estill,Yan Fu,Jeffrey A. Jeddeloh,Yujun Han,Hye-Ran Lee,Pinghua Li,Damon Lisch,Sanzhen Liu,Zhijie Liu,Dawn H. Nagel,Maureen C. McCann,Phillip SanMiguel,Alan M. Myers,Dan Nettleton,John D. Nguyen,Bryan W. Penning,Lalit Ponnala,Kevin L. Schneider,David C. Schwartz,Anupma Sharma,Carol Soderlund,Nathan M. Springer,Qi Sun,Hao Wang,Michael S. Waterman,Richard P. Westerman,Thomas K. Wolfgruber,Lixing Yang,Yeisoo Yu,Lifang Zhang,Shiguo Zhou,Qihui Zhu,Jeffrey L. Bennetzen,R. Kelly Dawe,Jiming Jiang,Ning Jiang,Gernot G. Presting,Susan R. Wessler,Srinivas Aluru,Srinivas Aluru,Robert A. Martienssen,Sandra W. Clifton,W. Richard McCombie,Rod A. Wing,Richard K. Wilson +159 more
[...]
Yinping Jiao,Paul Peluso,Jinghua Shi,Tiffany Y. Liang,Michelle C. Stitzer,Bo Wang,Michael S. Campbell,Joshua C. Stein,Xuehong Wei,Chen-Shan Chin,Katherine E. Guill,Michael Regulski,Sunita Kumari,Andrew Olson,Jonathan I. Gent,Kevin L. Schneider,Thomas K. Wolfgruber,Michael R. May,Nathan M. Springer,Eric Antoniou,W. Richard McCombie,Gernot G. Presting,Michael D. McMullen,Jeffrey Ross-Ibarra,R. Kelly Dawe,Alex Hastie,David R. Rank,Doreen Ware,Doreen Ware +28 more