Genome-wide association study suggests an independent genetic basis of zinc and cadmium concentrations in fresh sweet corn kernels.

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.

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.

Natural variation for carotenoids in fresh kernels is controlled by uncommon variants in sweet corn.

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 ß-carotene hydroxylase (crtRB1) with ß-carotene concentration and lycopene epsilon cyclase (lcyE) with the ratio of flux between the α- and ß-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 ß-branch carotenoids (ß-carotene and zeaxanthin) or ß-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.

Genome-Wide Association Study for Maize Leaf Cuticular Conductance Identifies Candidate Genes Involved in the Regulation of Cuticle Development.

The cuticle, a hydrophobic layer of cutin and waxes synthesized by plant epidermal cells, is the major barrier to water loss when stomata are closed at night and under water-limited conditions. Elucidating the genetic architecture of natural variation for leaf cuticular conductance (gc) is important for identifying genes relevant to improving crop productivity in drought-prone environments. To this end, we conducted a genome-wide association study of gc of adult leaves in a maize inbred association panel that was evaluated in four environments (Maricopa, AZ, and San Diego, CA, in 2016 and 2017). Five genomic regions significantly associated with gc were resolved to seven plausible candidate genes (ISTL1, two SEC14 homologs, cyclase-associated protein, a CER7 homolog, GDSL lipase, and ß-D-XYLOSIDASE 4). These candidates are potentially involved in cuticle biosynthesis, trafficking and deposition of cuticle lipids, cutin polymerization, and cell wall modification. Laser microdissection RNA sequencing revealed that all these candidate genes, with the exception of the CER7 homolog, were expressed in the zone of the expanding adult maize leaf where cuticle maturation occurs. With direct application to genetic improvement, moderately high average predictive abilities were observed for whole-genome prediction of gc in locations (0.46 and 0.45) and across all environments (0.52). The findings of this study provide novel insights into the genetic control of gc and have the potential to help breeders more effectively develop drought-tolerant maize for target environments.

Machine Learning Enables High-Throughput Phenotyping for Analyses of the Genetic Architecture of Bulliform Cell Patterning in Maize.

Bulliform cells comprise specialized cell types that develop on the adaxial (upper) surface of grass leaves, and are patterned to form linear rows along the proximodistal axis of the adult leaf blade. Bulliform cell patterning affects leaf angle and is presumed to function during leaf rolling, thereby reducing water loss during temperature extremes and drought. In this study, epidermal leaf impressions were collected from a genetically and anatomically diverse population of maize inbred lines. Subsequently, convolutional neural networks were employed to measure microscopic, bulliform cell-patterning phenotypes in high-throughput. A genome-wide association study, combined with RNAseq analyses of the bulliform cell ontogenic zone, identified candidate regulatory genes affecting bulliform cell column number and cell width. This study is the first to combine machine learning approaches, transcriptomics, and genomics to study bulliform cell patterning, and the first to utilize natural variation to investigate the genetic architecture of this microscopic trait. In addition, this study provides insight toward the improvement of macroscopic traits such as drought resistance and plant architecture in an agronomically important crop plant.

Multivariate Genome-Wide Association Analyses Reveal the Genetic Basis of Seed Fatty Acid Composition in Oat (Avena sativa L.).

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.

Genome-Wide Association and Genomic Prediction Models of Tocochromanols in Fresh Sweet Corn Kernels.

Sweet corn ( L.), a highly consumed fresh vegetable in the United States, varies for tocochromanol (tocopherol and tocotrienol) levels but makes only a limited contribution to daily intake of vitamin E and antioxidants. We performed a genome-wide association study of six tocochromanol compounds and 14 derivative traits across a sweet corn inbred line association panel to identify genes associated with natural variation for tocochromanols and vitamin E in fresh kernels. Concordant with prior studies in mature maize kernels, an association was detected between γ-tocopherol methyltransferase (vte4) and α-tocopherol content, along with () and () for tocotrienol variation. Additionally, two kernel starch synthesis genes, () and (), were associated with tocotrienols, with the strongest evidence for in combination with fixed, strong and alleles, accounting for the greater amount of tocotrienols in and lines. In prediction models with genome-wide markers, predictive abilities were higher for tocotrienols than tocopherols, and these models were superior to those that used marker sets targeting a priori genes involved in the biosynthesis and/or genetic control of tocochromanols. Through this quantitative genetic analysis, we have established a key step for increasing tocochromanols in fresh kernels of sweet corn for human health and nutrition.

Textura do solo e a estimativa do teor de água no ponto de murcha permanente com psicrômetro / Soil texture and the estimation by Dewpoint Potential Meter of water retention at wilting point

A determinação do volume de água disponível às plantas é fundamental para o correto manejo da irrigação e definição quanto ao uso dos solos agrícolas. Os principais fatores que exercem influência na retenção e disponibilidade de água às plantas são a textura e a estrutura do solo. O objetivo deste trabalho foi quantificar a influência da textura na retenção da água, na condição de ponto de murcha permanente (PMP) das plantas (-1,5MPa), sendo utilizado um psicrômetro modelo WP4-T. Determinaram-se a textura de 100 amostras de solo e o teor de água no PMP. Os resultados indicaram que, em potenciais maiores que -1,0MPa, o psicrômetro mostrou-se pouco preciso, não se recomendando a sua utilização nessa condição. O PMP aumentou de 0,059 para 0,29g g-1, quando o teor de argila aumentou de 120 para 779g kg-1. Obteve-se um bom ajuste dos resultados do teor de água no PMP em função do teor de argila do solo, e 91 por cento da variação do teor de água no PMP puderam ser atribuídos à variação no teor de argila. Conclui-se que o psicrômetro é um equipamento que pode ser utilizado para determinar o PMP, e a equação PMP (g g-1)=0,0003*Argila (g kg-1)+0,0118 pode ser utilizada para estimar o PMP.

The determination of the available water to plants is essential to right irrigation management and definition regarding the use in agricultural soils. The main factors that exert influence on retention and availability of water to plants are texture and soil structure. The aim of this study was to quantify the influence of the texture on water retention in the condition of permanent wilting point (PWP) of plants (-1,5MPa) using a WP4-T Dewpoint Potentia Meter. The texture of 100 soil sample and soil moisture at PWP was determined. Results indicated that, in potentials higher than -1,0MPa, WP4-T seemed not very precise, therefore its use is not recommended in this condition. PWP increased from 0,059 to 0,29g g-1, while the clay content increased from 120 to 779g kg-1. It was obtained a good adjustment of the results of water content at PWP based on clay content of soil, being that 91 percent of variation in water content at PWP could be attributed to variation in clay content. It was concluded that WP4-T is an equipment that can be used to determine PWP and the equation PWP (g g-1)=0,0003 * Clay(g kg-1)+0,0118 can be used to estimate PWP.

Indicadores da qualidade física de um Latossolo Vermelho distrófico típico sob plantio direto escarificado / Physical quality indicators in Latosol under no tillage chiseled

A avaliação da qualidade física dos solos agrícolas tem assumido importância cada vez maior, principalmente em áreas sob sistema plantio direto, uma vez que nesse sistema de manejo ocorrem importantes alterações na estrutura do solo. A resistência mecânica do solo à penetração (RP), o intervalo hídrico ótimo (IHO) e a densidade relativa (DR) têm sido apresentados como opções para essa avaliação. Os objetivos deste trabalho foram avaliar e modelar a RP em função da umidade e densidade do solo e determinar o IHO em função da DR em dois sistemas de manejo. Amostras de solo com estrutura preservada foram coletadas na camada de 0-5cm, em solo sob plantio direto (PD) e plantio direto escarificado (PDE) há seis meses. Em laboratório, determinou-se a RP utilizando penetrômetro eletrônico e efetuou-se um ajuste estatístico individual para cada manejo à equação de Busscher. No PDE, para uma mesma densidade e umidade do solo, a RP foi menor que no PD, e a diferença na RP foi maior entre os dois manejos quando a umidade do solo no campo foi menor. O IHO foi maior no PDE até a DR 0,9. Os resultados permitem concluir que a RP é um parâmetro sensível para determinar a qualidade estrutural do solo e que o PDE reduziu significativamente a RP e aumentou o IHO, o que proporcionará melhores condições para o desenvolvimento radicular das plantas por um período de tempo maior.

The assessment of the physical quality of agricultural soils has taken on added importance, especially in areas under no tillage, as important changes to soil structure occur as a result of this type of management. Soil resistance to penetration (RP), the least limit water range (LLWR) and relative density (RD) have been used as evaluation parameters. The aim of this study was to assess and model RP as a function of soil moisture and density and to determine the LLWR as a function of RD under two management systems. Samples of soils under no tillage (NT) and chiseled no tillage (CNT) for six months and whose structure had been preserved were collected at a depth of 0 to 5cm. In the laboratory, RP was assessed using an electronic penetrometer and each management system was statistically adjusted to Busscher's equation. In CNT soils, RP was lower for the same density and moisture, and lower than the PD, whereas the difference in RP was larger between the two management systems when soil moisture in the field was lower. The LLWR was higher under CNT up to an RD of 0.9. Results allow us to conclude that RP is a sensitive parameter for determining the physical quality of the soil and that CNT significantly reduced RP and increased the LLWR, providing favorable conditions for root growth for a longer time period.