Genome assembly and population genomic analysis provide insights into the evolution of modern sweet corn

Ying Hu, Vincent Colantonio, Bárbara S. F. Müller, Kristen A. Leach, Adalena Nanni, Christina Finegan, Bo Wang, Matheus Baseggio, Carter J. Newton, Emily M. Juhl, Lillian Hislop, Juan M. Gonzalez, Esteban F. Rios, L. Curtis Hannah, Kelly Swarts, Michael A. Gore, Tracie A. Hennen-Bierwagen, Alan M. Myers, A. Mark Settles, William F. Tracy and Marcio F. R. Resende ()
Additional contact information
Ying Hu: University of Florida
Vincent Colantonio: University of Florida
Bárbara S. F. Müller: University of Florida
Kristen A. Leach: University of Florida
Adalena Nanni: University of Florida
Christina Finegan: University of Florida
Bo Wang: Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor
Matheus Baseggio: Cornell University
Carter J. Newton: Iowa State University
Emily M. Juhl: Iowa State University
Lillian Hislop: University of Wisconsin-Madison
Juan M. Gonzalez: University of Florida
Esteban F. Rios: University of Florida
L. Curtis Hannah: University of Florida
Kelly Swarts: Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter
Michael A. Gore: Cornell University
Tracie A. Hennen-Bierwagen: Iowa State University
Alan M. Myers: Iowa State University
A. Mark Settles: University of Florida
William F. Tracy: University of Wisconsin-Madison
Marcio F. R. Resende: University of Florida

Nature Communications, 2021, vol. 12, issue 1, 1-13

Abstract: Abstract Sweet corn is one of the most important vegetables in the United States and Canada. Here, we present a de novo assembly of a sweet corn inbred line Ia453 with the mutated shrunken2-reference allele (Ia453-sh2). This mutation accumulates more sugar and is present in most commercial hybrids developed for the processing and fresh markets. The ten pseudochromosomes cover 92% of the total assembly and 99% of the estimated genome size, with a scaffold N50 of 222.2 Mb. This reference genome completely assembles the large structural variation that created the mutant sh2-R allele. Furthermore, comparative genomics analysis with six field corn genomes highlights differences in single-nucleotide polymorphisms, structural variations, and transposon composition. Phylogenetic analysis of 5,381 diverse maize and teosinte accessions reveals genetic relationships between sweet corn and other types of maize. Our results show evidence for a common origin in northern Mexico for modern sweet corn in the U.S. Finally, population genomic analysis identifies regions of the genome under selection and candidate genes associated with sweet corn traits, such as early flowering, endosperm composition, plant and tassel architecture, and kernel row number. Our study provides a high-quality reference-genome sequence to facilitate comparative genomics, functional studies, and genomic-assisted breeding for sweet corn.

Date: 2021
References: Add references at CitEc
Citations:

Downloads: (external link)
https://www.nature.com/articles/s41467-021-21380-4 Abstract (text/html)

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-021-21380-4

Ordering information: This journal article can be ordered from
https://www.nature.com/ncomms/

DOI: 10.1038/s41467-021-21380-4

Access Statistics for this article

Nature Communications is currently edited by Nathalie Le Bot, Enda Bergin and Fiona Gillespie

More articles in Nature Communications from Nature
Bibliographic data for series maintained by Sonal Shukla () and Springer Nature Abstracting and Indexing ().