De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes-Reference-Cited by-同舟云学术

De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes

Published:2021-08-06 Issue:6555 Volume:373 Page:655-662
ISSN:0036-8075
Container-title:Science
language:en
Short-container-title:Science

Author:

Hufford Matthew B.¹^ORCID,Seetharam Arun S.¹²^ORCID,Woodhouse Margaret R.³^ORCID,Chougule Kapeel M.⁴,Ou Shujun¹^ORCID,Liu Jianing⁵^ORCID,Ricci William A.⁶^ORCID,Guo Tingting⁷^ORCID,Olson Andrew⁴^ORCID,Qiu Yinjie⁸^ORCID,Della Coletta Rafael⁸^ORCID,Tittes Silas⁹¹⁰^ORCID,Hudson Asher I.⁹¹⁰,Marand Alexandre P.⁵^ORCID,Wei Sharon⁴,Lu Zhenyuan⁴^ORCID,Wang Bo⁴,Tello-Ruiz Marcela K.⁴^ORCID,Piri Rebecca D.¹¹,Wang Na⁶^ORCID,Kim Dong won⁶,Zeng Yibing⁵,O’Connor Christine H.⁸¹²,Li Xianran⁷^ORCID,Gilbert Amanda M.⁸,Baggs Erin¹³^ORCID,Krasileva Ksenia V.¹³^ORCID,Portwood John L.³^ORCID,Cannon Ethalinda K. S.³^ORCID,Andorf Carson M.³^ORCID,Manchanda Nancy¹,Snodgrass Samantha J.¹^ORCID,Hufnagel David E.¹¹⁴^ORCID,Jiang Qiuhan¹^ORCID,Pedersen Sarah¹,Syring Michael L.¹^ORCID,Kudrna David A.¹⁵^ORCID,Llaca Victor¹⁶^ORCID,Fengler Kevin¹⁶,Schmitz Robert J.⁵^ORCID,Ross-Ibarra Jeffrey⁹¹⁰¹⁷^ORCID,Yu Jianming⁷^ORCID,Gent Jonathan I.⁶^ORCID,Hirsch Candice N.⁸^ORCID,Ware Doreen⁴¹⁸^ORCID,Dawe R. Kelly⁵⁶¹¹^ORCID

Affiliation:

1. Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA.

2. Genome Informatics Facility, Iowa State University, Ames, IA 50011, USA.

3. USDA-ARS Corn Insects and Crop Genetics Research Unit, Iowa State University, Ames, IA 50011, USA.

4. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.

5. Department of Genetics, University of Georgia, Athens, GA 30602, USA.

6. Department of Plant Biology, University of Georgia, Athens, GA 30602, USA.

7. Department of Agronomy, Iowa State University, Ames, IA 50011, USA.

8. Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA.

9. Center for Population Biology, University of California, Davis, CA 95616, USA.

10. Department of Evolution and Ecology, University of California, Davis, CA 95616, USA.

11. Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA.

12. Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, MN 55108, USA.

13. Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA.

14. Virus and Prion Research Unit, National Animal Disease Center, USDA-ARS, Ames, IA, 50010, USA.

15. Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA.

16. Corteva Agriscience, Johnston, IA 50131, USA.

17. Genome Center, University of California, Davis, CA 95616, USA.

18. USDA-ARS NAA Robert W. Holley Center for Agriculture and Health, Agricultural Research Service, Ithaca, NY 14853, USA.

Abstract

An a-maize-ing set of genomes Maize is an important crop cultivated worldwide. As maize spread across the world, selection for local environments resulted in variation, but the impact on differences between the genome has not been quantified. By producing high-quality genomic sequences of the 26 lines used in the maize nested association mapping panel, Hufford et al . map important traits and demonstrate the diversity of maize. Examining RNA and methylation of genes across accessions, the authors identified a core set of maize genes. Beyond this core set, comparative analysis across lines identified high levels of variation in the total set of genes, the maize pan-genome. The value of this resource was further exemplified by mapping quantitative traits of interest, including those related to pathogen resistance. —LMZ

Funder

National Science Foundation

U.S. Department of Agriculture

Additional

Iowa State University Trainee SJS

Publisher

American Association for the Advancement of Science (AAAS)

Subject

Multidisciplinary

Reference175 articles.

1. Insights into the Maize Pan-Genome and Pan-Transcriptome

2. Draft Assembly of Elite Inbred Line PH207 Provides Insights into Genomic and Transcriptome Diversity in Maize