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

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

Origins of temperate adaptation in maize

Four thousand years ago, maize began migrating out of Mexico and into the geographically diverse Southwestern US (1, 2). Maize spread quickly through the lowland deserts, but full maize agriculture in the uplands lagged for another 2,000 years (1, 3). Why did maize agriculture fail to fully develop, despite the persistent presence of maize in the uplands? I tested the hypothesis that early maize in the Southwest US was not adapted to the uplands, specifically testing archaeological maize from the uplands at the beginning of agricultural intensification for early flowering. To better understand temperate adaptation in maize, I led a project to generate tools for accurate imputation and projection of maize inbred haplotypes onto related individuals. We then projected whole genome sequence onto five diverse modern inbred maize populations to further elucidate the genetic architecture of maize flowering through mapping, machine learning and cross population predictions. We find that the genetic architecture of flowering is tightly linked to the temperate-tropical differentiation in American germplasm for four of the five populations, and suggest an independent temperate adaptation occurred in China after 1500. We also find that populations with individuals across the North American temperate adaptation predict others well. We further test that good cross population prediction extends to modern Southwestern landraces by developing a mapping population for flowering time, and show that modern inbred populations can predict divergent modern landraces with high prediction accuracy for days to flowering. We extend flowering predictions to archaeological maize samples dating to the early period of agricultural adoption, and find that this population was already adapted. Using SNPs with the greatest population differentiation over the extremes of temperate-tropical adaptation, we find that temperate adaptation happened in situ in the Southwest, and early southwestern peoples selected on primarily standing variation. 1. J. B. Mabry, ed. Las Capas: Early Irrigation and Sedentism in a Southwestern Floodplain (Center for Desert Archaeology, Tucson, 2008), Anthropological Papers. 2. E. K. Huber, in Fence Lake Project (Statistical Research Inc., Tempe, 2005), vol. 1: Introduction and Site Descriptions of Technical Series. 3. R. G. Matson, B. Chisholm, Basketmaker II Subsistence: Carbon Isotopes and Other Dietary Indicators from Cedar Mesa, Utah. Am. Antiq. 56, 444–459 (1991)

An in situ and morphometric study of maize (Zea mays L.) cob rondel phytoliths from Southwestern North American landraces

We present the first comprehensive computer-assisted morphometric analysis of microscopic rondel1 phytoliths (plant opal microfossils) produced in the cobs of 24 historic Southwestern North American landraces of maize (Zea mays L.) after all were grown in a well-documented agronomic field study. We also present an in situ study of the location of rondel phytolith production within the maize cob and provide a detailed review of previous maize phytolith studies. We found that glumes contained abundant rondel phytoliths throughout the tissue; however, lemma/palea tissue contained no phytoliths. In contrast, cupule tissue had some areas with abundant phytoliths, some with fewer scattered phytoliths, and vast areas that contained no rondel phytoliths. The rondel-rich areas appear to be where the glumes had once attached to the cupule and may be remnants of glume tissue adhering to the cupule. From the morphometric study, we found there were significant differences in the size morphometries of glume rondels depending on their cob location (top, middle, base) but no significant differences in shape morphometries. Using shape morphometries, we could not discriminate reliably among maize cob rondel phytoliths produced by the diverse landraces considered. The inclusion of morphometrics from areas in addition to or in combination with the outer periclinal surface may allow for some discrimination of maize landraces and is an avenue that should be explored further. Although our approach was not successful at identifying differences between essentially modern landraces, there may be significant rondel phytolith morphometric differences between wild, progenitor, and domesticated Zea.Brigham Young University24 month embargo; available online 24 December 2020This item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]

Comprehensive genotyping of the USA national maize inbred seed bank

Background: Genotyping by sequencing, a new low-cost, high-throughput sequencing technology was used to genotype 2,815 maize inbred accessions, preserved mostly at the National Plant Germplasm System in the USA. The collection includes inbred lines from breeding programs all over the world. Results: The method produced 681,257 single-nucleotide polymorphism (SNP) markers distributed across the entire genome, with the ability to detect rare alleles at high confidence levels. More than half of the SNPs in the collection are rare. Although most rare alleles have been incorporated into public temperate breeding programs, only a modest amount of the available diversity is present in the commercial germplasm. Analysis of genetic distances shows population stratification, including a small number of large clusters centered on key lines. Nevertheless, an average fixation index of 0.06 indicates moderate differentiation between the three major maize subpopulations. Linkage disequilibrium (LD) decays very rapidly, but the extent of LD is highly dependent on the particular group of germplasm and region of the genome. The utility of these data for performing genome-wide association studies was tested with two simply inherited traits and one complex trait. We identified trait associations at SNPs very close to known candidate genes for kernel color, sweet corn, and flowering time; however, results suggest that more SNPs are needed to better explore the genetic architecture of complex traits. Conclusions: The genotypic information described here allows this publicly available panel to be exploited by researchers facing the challenges of sustainable agriculture through better knowledge of the nature of genetic diversity