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Sugarcane mosaic virus [SCMV (Potyvirus sugarcane mosaic virus)] is an ssRNA virus that negatively affects yield in maize (Zea mays) worldwide. Resistance to SCMV is controlled primarily by a single dominant gene (Scm1). The goal of this study was to identify sweet corn (Z. mays) inbreds that demonstrate resistance to SCMV, confirm the presence of genomic regions previously identified in maize associated with resistance, and identify other resistant loci in sweet corn. Eight plants from each of 563 primarily sweet corn inbred lines were tested for SCMV resistance. Plants were inoculated 14 d after planting and observed for signs of infection 24 d after planting. A subset of 420 inbred lines were genotyped using 7504 high-quality genotyping-by-sequencing single-nucleotide polymorphism markers. Population structure of the panel was observed, and a genome-wide association study was conducted to identify loci associated with SCMV resistance. Forty-six of the inbreds were found to be resistant to SCMV 10 d after inoculation. The Scm1 locus was confirmed with the presence of two significant loci on chromosome 6 (P = 2.5 × 10−8 and 1.6 × 10−8), 5 Mb downstream of the Scm1 gene previously located at Chr6: 14194429.14198587 and the surrounding 2.7-Mb presence–absence variation. We did not identify other loci associated with resistance. This research has increased information on publicly available SCMV-resistant germplasm useful to future breeding projects and demonstrated that SCMV resistance in this sweet corn panel is driven by the Scm1 gene.

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., Sweet corn is one of the most important vegetables in North America and has undergone different selection pressures than non-sweet cultivars. Here, the authors report its genome assembly and reveal the evolutionary history of modern sweet corn through population genomic analyses.

Common bean (Phaseolus vulgaris L.) is one of the most important legume crops for human consumption. The Native Seeds/SEARCH common bean collection consists of locally-adapted accessions collected from the southwestern US and northwestern Mexico. In this study, a representative panel of nearly 300 accessions from this collection was genotyped with more than 10,000 high-quality SNP markers and phenotyped for seed coat patterns. The collection consists primarily of accessions from the Mesoamerican gene pool, and they separate into three distinct subpopulations, with strong population differentiation (FST > 0.4) observed between them. Through a genome-wide association study with the Mesoamerican accessions, we identified several SNPs on chromosome 8 that are associated with seed coat pattern traits and reside proximal to the putative location of the C locus, a locus previously shown to control the pattern of the seed coat. Five myb transcription factors linked to these SNPs were identified as candidate causal genes for seed coat patterns controlled by the C locus. Furthermore, we identified a potentially novel locus on chromosome 10 that appears to control the Anasazi seed coat phenotype. Our work is the first to characterize the genetic diversity of the Native Seeds/SEARCH common bean collection, providing valuable genetic information for germplasm conservation efforts.

Despite being one of the most consumed vegetables in the United States, the elemental profile of sweet corn (Zea mays L.) is limited in its dietary contributions. To address this through genetic improvement, a genome-wide association study was conducted for the concentrations of 15 elements in fresh kernels of a sweet corn association panel. In concordance with mapping results from mature maize kernels, we detected a probable pleiotropic association of zinc and iron concentrations with nicotianamine synthase5 (nas5), which purportedly encodes an enzyme involved in synthesis of the metal chelator nicotianamine. In addition, a pervasive association signal was identified for cadmium concentration within a recombination suppressed region on chromosome 2. The likely causal gene underlying this signal was heavy metal ATPase3 (hma3), whose counterpart in rice, OsHMA3, mediates vacuolar sequestration of cadmium and zinc in roots, whereby regulating zinc homeostasis and cadmium accumulation in grains. In our association panel, hma3 associated with cadmium but not zinc accumulation in fresh kernels. This finding implies that selection for low cadmium will not affect zinc levels in fresh kernels. Although less resolved association signals were detected for boron, nickel, and calcium, all 15 elements were shown to have moderate predictive abilities via whole-genome prediction. Collectively, these results help enhance our genomics-assisted breeding efforts centered on improving the elemental profile of fresh sweet corn kernels.

Sweet corn (Zea mays L.) is highly consumed in the United States, but does not make major contributions to the daily intake of carotenoids (provitamin A carotenoids, lutein and zeaxanthin) that would help in the prevention of health complications. A genome-wide association study of seven kernel carotenoids and twelve derivative traits was conducted in a sweet corn inbred line association panel ranging from light to dark yellow in endosperm color to elucidate the genetic basis of carotenoid levels in fresh kernels. In agreement with earlier studies of maize kernels at maturity, we detected an association of β-carotene hydroxylase (crtRB1) with β-carotene concentration and lycopene epsilon cyclase (lcyE) with the ratio of flux between the α- and β-carotene branches in the carotenoid biosynthetic pathway. Additionally, we found that 5% or less of the evaluated inbred lines possessing the shrunken2 (sh2) endosperm mutation had the most favorable lycE allele or crtRB1 haplotype for elevating β-branch carotenoids (β-carotene and zeaxanthin) or β-carotene, respectively. Genomic prediction models with genome-wide markers obtained moderately high predictive abilities for the carotenoid traits, especially lutein, and outperformed models with less markers that targeted candidate genes implicated in the synthesis, retention, and/or genetic control of kernel carotenoids. Taken together, our results constitute an important step toward increasing carotenoids in fresh sweet corn kernels.

Oat (Avena sativa L.) has a high concentration of oils, comprised primarily of healthful unsaturated oleic and linoleic fatty acids. To accelerate oat plant breeding efforts, we sought to identify loci associated with variation in fatty acid composition, defined as the types and quantities of fatty acids. We genotyped a panel of 500 oat cultivars with genotyping-by-sequencing and measured the concentrations of ten fatty acids in these oat cultivars grown in two environments. Measurements of individual fatty acids were highly correlated across samples, consistent with fatty acids participating in shared biosynthetic pathways. We leveraged these phenotypic correlations in two multivariate genome-wide association study (GWAS) approaches. In the first analysis, we fitted a multivariate linear mixed model for all ten fatty acids simultaneously while accounting for population structure and relatedness among cultivars. In the second, we performed a univariate association test for each principal component (PC) derived from a singular value decomposition of the phenotypic data matrix. To aid interpretation of results from the multivariate analyses, we also conducted univariate association tests for each trait. The multivariate mixed model approach yielded 148 genome-wide significant single-nucleotide polymorphisms (SNPs) at a 10% false-discovery rate, compared to 129 and 73 significant SNPs in the PC and univariate analyses, respectively. Thus, explicit modeling of the correlation structure between fatty acids in a multivariate framework enabled identification of loci associated with variation in seed fatty acid concentration that were not detected in the univariate analyses. Ultimately, a detailed characterization of the loci underlying fatty acid variation can be used to enhance the nutritional profile of oats through breeding., This research was supported by PepsiCo Global R&D, the USDA–ARS, USDA-NIFA-AFRI 2011-68002-30029 (Triticeae-CAP), USDA-NIFA-AFRI 2017-67007-25939 (Wheat-CAP), USDA-NIFA-AFRI 2017-67007-26502, and Hatch Project 149-447.

Brassica napus L. represents a potential plant feedstock for the sustainable production of hydrotreated renewable fuels needed to support carbon-based energy production. However, to increase the use of plant-derived oils for energy needs, breeding efforts are required to optimize the amount and profile of fatty acids (FAs) contained in the oil extracted from B. napus seed to meet demands of the various market categories. To this end, we analyzed the genetic basis of FA content and composition of seed from a diverse panel of spring-type B. napus accessions evaluated at four US locations across multiple years. The extent of phenotypic variations for total oil content, nine FA compounds, and 14 derivative traits were found, in general, to be highly heritable. A genome-wide association study (GWAS) was conducted that detected 53 SNPs significantly associated with one or more of the 24 FA seed traits, resulting in the implicated genetic role of 12 candidate genes, four of which had two homologs each, from the acyl-lipid pathway. To our knowledge, the two detected homologs of 3-Ketoacyl-CoA thiolase (KAT), have never been associated with seed oil traits in B. napus. Through the application of whole-genome prediction, the 24 FA seed traits were generally found to have moderately high predictive abilities (70% of traits with abilities > 0.70), suggesting that these traits are highly amenable to genomic selection. Overall, our results contribute to the expanding body of knowledge regarding key enzymes in the acyl-lipid pathway at the quantitative genetic level and illustrate how genomics-assisted breeding could be leveraged to genetically improve FA seed traits in B. napus.