Genome assembly and population genomic analysis provide insights into the evolution of modern sweet corn. Hu, Y., Colantonio, V., Müller, B. S. F., Leach, K. A., Nanni, A., Finegan, C., Wang, B., Baseggio, M., Newton, C. J., Juhl, E. M., Hislop, L., Gonzalez, J. M., Rios, E. F., Hannah, L. C., Swarts, K., Gore, M. A., Hennen-Bierwagen, T. A., Myers, A. M., Settles, A. M., Tracy, W. F., & Resende, M. F. R. Nature Communications, 12(1):1227, February, 2021. Publisher: Nature Publishing Group![Genome assembly and population genomic analysis provide insights into the evolution of modern sweet corn [link]](https://bibbase.org/img/filetypes/link.svg "link")
Paper doi abstract bibtex 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.
@article{hu_genome_2021,
title = {Genome assembly and population genomic analysis provide insights into the evolution of modern sweet corn},
volume = {12},
copyright = {2021 The Author(s)},
issn = {2041-1723},
url = {https://www.nature.com/articles/s41467-021-21380-4},
doi = {10.1038/s41467-021-21380-4},
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.},
language = {en},
number = {1},
urldate = {2024-03-22},
journal = {Nature Communications},
author = {Hu, Ying and Colantonio, Vincent and Müller, Bárbara S. F. and Leach, Kristen A. and Nanni, Adalena and Finegan, Christina and Wang, Bo and Baseggio, Matheus and Newton, Carter J. and Juhl, Emily M. and Hislop, Lillian and Gonzalez, Juan M. and Rios, Esteban F. and Hannah, L. Curtis and Swarts, Kelly and Gore, Michael A. and Hennen-Bierwagen, Tracie A. and Myers, Alan M. and Settles, A. Mark and Tracy, William F. and Resende, Marcio F. R.},
month = feb,
year = {2021},
note = {Publisher: Nature Publishing Group},
keywords = {Agricultural genetics, Evolutionary biology, Plant breeding},
pages = {1227},
}
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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. 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