Literature DB >> 33958781

Advancing crop genomics from lab to field.

Michael D Purugganan1,2, Scott A Jackson3.   

Abstract

Crop genomics remains a key element in ensuring scientific progress to secure global food security. It has been two decades since the sequence of the first plant genome, that of Arabidopsis thaliana, was released, and soon after that the draft sequencing of the rice genome was completed. Since then, the genomes of more than 100 crops have been sequenced, plant genome research has expanded across multiple fronts and the next few years promise to bring further advances spurred by the advent of new technologies and approaches. We are likely to see continued innovations in crop genome sequencing, genetic mapping and the acquisition of multiple levels of biological data. There will be exciting opportunities to integrate genome-scale information across multiple scales of biological organization, leading to advances in our mechanistic understanding of crop biological processes, which will, in turn, provide greater impetus for translation of laboratory results to the field.

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Mesh:

Year:  2021        PMID: 33958781     DOI: 10.1038/s41588-021-00866-3

Source DB:  PubMed          Journal:  Nat Genet        ISSN: 1061-4036            Impact factor:   38.330


  103 in total

1.  Solutions for a cultivated planet.

Authors:  Jonathan A Foley; Navin Ramankutty; Kate A Brauman; Emily S Cassidy; James S Gerber; Matt Johnston; Nathaniel D Mueller; Christine O'Connell; Deepak K Ray; Paul C West; Christian Balzer; Elena M Bennett; Stephen R Carpenter; Jason Hill; Chad Monfreda; Stephen Polasky; Johan Rockström; John Sheehan; Stefan Siebert; David Tilman; David P M Zaks
Journal:  Nature       Date:  2011-10-12       Impact factor: 49.962

2.  Plant genomics: more than food for thought.

Authors:  S P Briggs
Journal:  Proc Natl Acad Sci U S A       Date:  1998-03-03       Impact factor: 11.205

Review 3.  Coming of age: ten years of next-generation sequencing technologies.

Authors:  Sara Goodwin; John D McPherson; W Richard McCombie
Journal:  Nat Rev Genet       Date:  2016-05-17       Impact factor: 53.242

Review 4.  Long-read human genome sequencing and its applications.

Authors:  Glennis A Logsdon; Mitchell R Vollger; Evan E Eichler
Journal:  Nat Rev Genet       Date:  2020-06-05       Impact factor: 53.242

5.  Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism.

Authors:  Wei Chen; Yanqiang Gao; Weibo Xie; Liang Gong; Kai Lu; Wensheng Wang; Yang Li; Xianqing Liu; Hongyan Zhang; Huaxia Dong; Wan Zhang; Lejing Zhang; Sibin Yu; Gongwei Wang; Xingming Lian; Jie Luo
Journal:  Nat Genet       Date:  2014-06-08       Impact factor: 38.330

6.  The transcriptional landscape of polyploid wheat.

Authors:  R H Ramírez-González; P Borrill; D Lang; S A Harrington; J Brinton; L Venturini; M Davey; J Jacobs; F van Ex; A Pasha; Y Khedikar; S J Robinson; A T Cory; T Florio; L Concia; C Juery; H Schoonbeek; B Steuernagel; D Xiang; C J Ridout; B Chalhoub; K F X Mayer; M Benhamed; D Latrasse; A Bendahmane; B B H Wulff; R Appels; V Tiwari; R Datla; F Choulet; C J Pozniak; N J Provart; A G Sharpe; E Paux; M Spannagl; A Bräutigam; C Uauy
Journal:  Science       Date:  2018-08-17       Impact factor: 47.728

7.  A draft sequence of the rice genome (Oryza sativa L. ssp. indica).

Authors:  Jun Yu; Songnian Hu; Jun Wang; Gane Ka-Shu Wong; Songgang Li; Bin Liu; Yajun Deng; Li Dai; Yan Zhou; Xiuqing Zhang; Mengliang Cao; Jing Liu; Jiandong Sun; Jiabin Tang; Yanjiong Chen; Xiaobing Huang; Wei Lin; Chen Ye; Wei Tong; Lijuan Cong; Jianing Geng; Yujun Han; Lin Li; Wei Li; Guangqiang Hu; Xiangang Huang; Wenjie Li; Jian Li; Zhanwei Liu; Long Li; Jianping Liu; Qiuhui Qi; Jinsong Liu; Li Li; Tao Li; Xuegang Wang; Hong Lu; Tingting Wu; Miao Zhu; Peixiang Ni; Hua Han; Wei Dong; Xiaoyu Ren; Xiaoli Feng; Peng Cui; Xianran Li; Hao Wang; Xin Xu; Wenxue Zhai; Zhao Xu; Jinsong Zhang; Sijie He; Jianguo Zhang; Jichen Xu; Kunlin Zhang; Xianwu Zheng; Jianhai Dong; Wanyong Zeng; Lin Tao; Jia Ye; Jun Tan; Xide Ren; Xuewei Chen; Jun He; Daofeng Liu; Wei Tian; Chaoguang Tian; Hongai Xia; Qiyu Bao; Gang Li; Hui Gao; Ting Cao; Juan Wang; Wenming Zhao; Ping Li; Wei Chen; Xudong Wang; Yong Zhang; Jianfei Hu; Jing Wang; Song Liu; Jian Yang; Guangyu Zhang; Yuqing Xiong; Zhijie Li; Long Mao; Chengshu Zhou; Zhen Zhu; Runsheng Chen; Bailin Hao; Weimou Zheng; Shouyi Chen; Wei Guo; Guojie Li; Siqi Liu; Ming Tao; Jian Wang; Lihuang Zhu; Longping Yuan; Huanming Yang
Journal:  Science       Date:  2002-04-05       Impact factor: 47.728

8.  A draft sequence of the rice genome (Oryza sativa L. ssp. japonica).

Authors:  Stephen A Goff; Darrell Ricke; Tien-Hung Lan; Gernot Presting; Ronglin Wang; Molly Dunn; Jane Glazebrook; Allen Sessions; Paul Oeller; Hemant Varma; David Hadley; Don Hutchison; Chris Martin; Fumiaki Katagiri; B Markus Lange; Todd Moughamer; Yu Xia; Paul Budworth; Jingping Zhong; Trini Miguel; Uta Paszkowski; Shiping Zhang; Michelle Colbert; Wei-lin Sun; Lili Chen; Bret Cooper; Sylvia Park; Todd Charles Wood; Long Mao; Peter Quail; Rod Wing; Ralph Dean; Yeisoo Yu; Andrey Zharkikh; Richard Shen; Sudhir Sahasrabudhe; Alun Thomas; Rob Cannings; Alexander Gutin; Dmitry Pruss; Julia Reid; Sean Tavtigian; Jeff Mitchell; Glenn Eldredge; Terri Scholl; Rose Mary Miller; Satish Bhatnagar; Nils Adey; Todd Rubano; Nadeem Tusneem; Rosann Robinson; Jane Feldhaus; Teresita Macalma; Arnold Oliphant; Steven Briggs
Journal:  Science       Date:  2002-04-05       Impact factor: 47.728

9.  Highly integrated single-base resolution maps of the epigenome in Arabidopsis.

Authors:  Ryan Lister; Ronan C O'Malley; Julian Tonti-Filippini; Brian D Gregory; Charles C Berry; A Harvey Millar; Joseph R Ecker
Journal:  Cell       Date:  2008-05-02       Impact factor: 41.582

10.  Widespread long-range cis-regulatory elements in the maize genome.

Authors:  William A Ricci; Zefu Lu; Lexiang Ji; Alexandre P Marand; Christina L Ethridge; Nathalie G Murphy; Jaclyn M Noshay; Mary Galli; María Katherine Mejía-Guerra; Maria Colomé-Tatché; Frank Johannes; M Jordan Rowley; Victor G Corces; Jixian Zhai; Michael J Scanlon; Edward S Buckler; Andrea Gallavotti; Nathan M Springer; Robert J Schmitz; Xiaoyu Zhang
Journal:  Nat Plants       Date:  2019-11-18       Impact factor: 15.793

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  8 in total

1.  Pathways to de novo domestication of crop wild relatives.

Authors:  Shaun Curtin; Yiping Qi; Lázaro E P Peres; Alisdair R Fernie; Agustin Zsögön
Journal:  Plant Physiol       Date:  2022-03-28       Impact factor: 8.340

Review 2.  Omics-Facilitated Crop Improvement for Climate Resilience and Superior Nutritive Value.

Authors:  Tinashe Zenda; Songtao Liu; Anyi Dong; Jiao Li; Yafei Wang; Xinyue Liu; Nan Wang; Huijun Duan
Journal:  Front Plant Sci       Date:  2021-12-01       Impact factor: 5.753

Review 3.  Indian Wheat Genomics Initiative for Harnessing the Potential of Wheat Germplasm Resources for Breeding Disease-Resistant, Nutrient-Dense, and Climate-Resilient Cultivars.

Authors:  Sundeep Kumar; Sherry R Jacob; Reyazul Rouf Mir; V K Vikas; Pawan Kulwal; Tilak Chandra; Satinder Kaur; Uttam Kumar; Suneel Kumar; Shailendra Sharma; Ravinder Singh; Sai Prasad; Anju Mahendru Singh; Amit Kumar Singh; Jyoti Kumari; M S Saharan; Subhash Chander Bhardwaj; Manoj Prasad; Sanjay Kalia; Kuldeep Singh
Journal:  Front Genet       Date:  2022-06-29       Impact factor: 4.772

Review 4.  Machine Learning for Plant Stress Modeling: A Perspective towards Hormesis Management.

Authors:  Amanda Kim Rico-Chávez; Jesus Alejandro Franco; Arturo Alfonso Fernandez-Jaramillo; Luis Miguel Contreras-Medina; Ramón Gerardo Guevara-González; Quetzalcoatl Hernandez-Escobedo
Journal:  Plants (Basel)       Date:  2022-04-02

5.  Genome-wide association study identifies a gene responsible for temperature-dependent rice germination.

Authors:  Hideki Yoshida; Ko Hirano; Kenji Yano; Fanmiao Wang; Masaki Mori; Mayuko Kawamura; Eriko Koketsu; Masako Hattori; Reynante Lacsamana Ordonio; Peng Huang; Eiji Yamamoto; Makoto Matsuoka
Journal:  Nat Commun       Date:  2022-09-29       Impact factor: 17.694

Review 6.  Entailing the Next-Generation Sequencing and Metabolome for Sustainable Agriculture by Improving Plant Tolerance.

Authors:  Muhammad Furqan Ashraf; Dan Hou; Quaid Hussain; Muhammad Imran; Jialong Pei; Mohsin Ali; Aamar Shehzad; Muhammad Anwar; Ali Noman; Muhammad Waseem; Xinchun Lin
Journal:  Int J Mol Sci       Date:  2022-01-07       Impact factor: 5.923

7.  Evolutionary Genetics of Crop-Wild Complexes.

Authors:  Andrés J Cortés; Amandine Cornille; Roxana Yockteng
Journal:  Genes (Basel)       Date:  2021-12-21       Impact factor: 4.096

8.  Comprehensive annotation of the Chinese tree shrew genome by large-scale RNA sequencing and long-read isoform sequencing.

Authors:  Mao-Sen Ye; Jin-Yan Zhang; Dan-Dan Yu; Min Xu; Ling Xu; Long-Bao Lv; Qi-Yun Zhu; Yu Fan; Yong-Gang Yao
Journal:  Zool Res       Date:  2021-11-18
  8 in total

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