Gene-Indexed Mutations in Maize
Xiaoduo Lu,Jisheng Liu,Wen Ren,Qun Yang,Zhenguang Chai,Rumei Chen,Lei Wang,Jun Zhao,Zhihong Lang,Haiyang Wang,Yunliu Fan,Jiuran Zhao,Chunyi Zhang +12 more
TLDR
A gene-indexed genome-wide mutation collection is generated through ethyl methanesulfonate mutagenesis andApplication of this mutant collection is exemplified by the identification of the ent-kaurene synthase gene, which encodes a key enzyme in the gibberellin biosynthesis pathway.About:
This article is published in Molecular Plant.The article was published on 2017-12-01 and is currently open access. It has received 114 citations till now. The article focuses on the topics: Ethyl methanesulfonate & Mutation.read more
Citations
More filters
Journal ArticleDOI
High-Throughput CRISPR/Cas9 Mutagenesis Streamlines Trait Gene Identification in Maize
Haijun Liu,Liumei Jian,Xu Jieting,Qinghua Zhang,Zhang Maolin,Minliang Jin,Yong Peng,Jiali Yan,Han Baozhu,Jie Liu,Fan Gao,Liu Xiangguo,Huang Lei,Wenjie Wei,Yunxiu Ding,Yang Xiaofeng,Zhenxian Li,Mingliang Zhang,Jiamin Sun,Minji Bai,Wenhao Song,Hanmo Chen,Xi’ang Sun,Wenqiang Li,Yuming Lu,Ya Liu,Jiuran Zhao,Yangwen Qian,David A. Jackson,David A. Jackson,Alisdair R. Fernie,Jianbing Yan +31 more
TL;DR: This study integrated multiplexed CRISPR/Cas9-based high-throughput targeted mutagenesis with genetic mapping and genomic approaches to successfully target 743 candidate genes corresponding to traits relevant for agronomy and nutrition.
Journal ArticleDOI
The Past, Present, and Future of Maize Improvement: Domestication, Genomics, and Functional Genomic Routes toward Crop Enhancement
TL;DR: An overview of the history of maize domestication and key genes controlling major domestication-related traits is provided, the currently available resources for functional genomics studies in maize are reviewed, and the functions of most of the maize genes that have been positionally cloned and can be used for crop improvement are discussed.
Journal ArticleDOI
Plant Genome Editing and the Relevance of Off-Target Changes
Nathaniel D. Graham,Nathaniel D. Graham,Gunvant Patil,David M. Bubeck,Raymond C. Dobert,Kevin C. Glenn,Annie T. Gutsche,Sandeep Kumar,John A. Lindbo,Luis Maas,Gregory D. May,Miguel E. Vega-Sanchez,Robert M. Stupar,Peter L. Morrell +13 more
TL;DR: Off-target edits in crops present no new safety concerns compared to other breeding practices, and genome editing will likely undergo improved editing specificity along with new developments in SDN delivery and increasing genomic characterization, further improving reagent design and application.
Journal ArticleDOI
CRISPR screens in plants: approaches, guidelines, and future prospects
TL;DR: The general concepts, tools and workflows for establishing CRISPR screens in plants are discussed and the handful of recent reports using this strategy to generate mutant knockout collections or diversify DNA sequences are analyzed.
Journal ArticleDOI
Maize transcription factor ZmBES1/BZR1-5 positively regulates kernel size.
Sun Fu'ai,Sun Fu'ai,Lei Ding,Wenqi Feng,Yang Cao,Fengzhong Lu,Qingqing Yang,Wanchen Li,Yanli Lu,Nitzan Shabek,Fengling Fu,Haoqiang Yu +11 more
TL;DR: The study suggests that ZmBES1/BZR1-5 positively regulates kernel size and provides new insights into understanding the mechanism of kernel development in maize.
References
More filters
Journal ArticleDOI
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.
Journal ArticleDOI
Fast and accurate short read alignment with Burrows–Wheeler transform
Heng Li,Richard Durbin +1 more
TL;DR: Burrows-Wheeler Alignment tool (BWA) is implemented, a new read alignment package that is based on backward search with Burrows–Wheeler Transform (BWT), to efficiently align short sequencing reads against a large reference sequence such as the human genome, allowing mismatches and gaps.
Journal ArticleDOI
The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
Aaron McKenna,Matthew Hanna,Eric Banks,Andrey Sivachenko,Kristian Cibulskis,Andrew Kernytsky,Kiran V. Garimella,David Altshuler,Stacey Gabriel,Mark J. Daly,Mark A. DePristo +10 more
TL;DR: The GATK programming framework enables developers and analysts to quickly and easily write efficient and robust NGS tools, many of which have already been incorporated into large-scale sequencing projects like the 1000 Genomes Project and The Cancer Genome Atlas.
Journal ArticleDOI
A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3
Pablo Cingolani,Adrian E. Platts,Le Lily Wang,M. Coon,Tung T. Nguyen,Luan Wang,Susan Land,Xiangyi Lu,Douglas M. Ruden +8 more
TL;DR: It appears that the 5′ and 3′ UTRs are reservoirs for genetic variations that changes the termini of proteins during evolution of the Drosophila genus.
Journal ArticleDOI
Genome-Wide Insertional Mutagenesis of Arabidopsis thaliana
Jose M. Alonso,Anna Stepanova,Thomas J. Leisse,Christopher J. Kim,Huaming Chen,Paul Shinn,Denise K. Stevenson,Justin Zimmerman,Pascual Barajas,Rosa Cheuk,Carmelita Gadrinab,Collen Heller,Albert Jeske,Eric Koesema,Cristina C. Meyers,Holly Parker,Lance Prednis,Yasser Ansari,Nathan Choy,Hashim Deen,Michael Geralt,Nisha Hazari,Emily Hom,Meagan Karnes,Celene Mulholland,Ral Ndubaku,Ian Thomas Schmidt,Plinio Guzmán,Laura Aguilar-Henonin,Markus Schmid,Detlef Weigel,David E. Carter,Trudy Marchand,Eddy Risseeuw,Debra Brogden,Albana Zeko,William L. Crosby,Charles C. Berry,Joseph R. Ecker +38 more
TL;DR: Genome-wide analysis of the distribution of integration events revealed the existence of a large integration site bias at both the chromosome and gene levels, and insertion mutations were identified in genes that are regulated in response to the plant hormone ethylene.
Related Papers (5)
Improved maize reference genome with single-molecule technologies
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
The B73 Maize Genome: Complexity, Diversity, and Dynamics
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