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

Ying Hu,Bárbara S F Müller,Christina Finegan,Alan M Myers,Carter J Newton,Tracie A Hennen‐Bierwagen ,Esteban F Rios,Bo Wang,Vincent Colantonio,Alexander Settles ,Adalena V Nanni ,Michael A Gore,Kristen A Leach,L Curtis Hannah,Matheus Baseggio,Lillian Hislop,Kelly Swarts,William F Tracy,Emily M Juhl,Juan M González ,M D V De Resende

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.

Highlights

Sweet corn is one of the most important vegetables in the United States and Canada
To further anchor and orient the super scaffolds and unscaffolded contigs into pseudochromosomes, Dovetail Hi–C mapping was used for scaffolding through a hierarchical clustering strategy[14]
We identified an average of 22,322 core genes belonging to gene families that were shared by all seven corn genomes, 16,667 dispensable genes missing orthologous counterparts in at least one of the tested genomes, and 5545 singleton genes assigned to families which were unique to only one line (Supplementary Fig. 4)

Summary

Introduction

We present a de novo assembly of a sweet corn inbred line Ia453 with the mutated shrunken2reference allele (Ia453-sh[2]) This mutation accumulates more sugar and is present in most commercial hybrids developed for the processing and fresh markets. Sweet corn is the result of mutations in genes involved in the starch biosynthesis pathway, which modify the carbohydrate composition by increasing sugar content in the endosperm while reducing starch content. Commercial sweet corn hybrids increased sugar content by exploiting mutations in the sugary[1] (su1) gene, a starch debranching enzyme. Due to this defective enzyme, the endosperm of a mature kernel will appear wrinkled and translucent (Fig. 1a). Ia453-sh[2] is an important public inbred line which contributed to the establishment of sh[2] sweet corn and is one of the parents of Illini Chief and Illini Xtra Sweet, two of the first commercial sh[2] sweet corn hybrids

Methods

Results

Conclusion