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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. Additionally, 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.

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.

Although it is possible that warming while temperature maxima decreased (1) contributed to increasing yields, a much more careful analysis is warranted before making potentially harmful statements such as “better weather experienced by US maize accounts for 28% of yield trends since 1981,” as Butler et al. (2) state in PNAS. To effectively measure contributions of climate changes to yield, two alternatives are possible (but unequal in strength of results): ( i ) a dataset containing the same varieties grown from 1981 to 2017 with minimal changes to management practices (empirical approach) or ( ii ) including periods when shifts in temperature trends were not following those in the period studied, along with many more variables to explicitly account for changes in cultural practices and … [↵][1]2To whom correspondence should be addressed. Email: ap874{at}cornell.edu. [1]: #xref-corresp-1-1

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.

Cultivar Tifton 85 bermudagrass ( Cynodon spp.) is often propagated using stolons, but the planting rate required for success ful establishment varies under different soil conditions and on-farm irrigation management. In the sandy soils of the U.S. Gulf Coast, desiccation of planting material can occur rapidly even under irrigated conditions due to variable on-farm irrigation management, and few studies have evaluated stolon planting rate effects under these conditions. The objective was to assess the effect of stolon planting densities on establishment of Tifton 85. Treatments in this 2-yr field study were five planting rates including 1120, 1570, 2020, 2470, and 2920 kg ha –1 arranged in four replicates of a randomized complete block design. Increasing planting rates increased bermudagrass frequency, ground cover, and dry matter harvested and decreased weed cover. All treatments had >80% bermudagrass frequency of occurrence and ground cover 3 mo after planting in 2011, but the three greatest planting rates achieved 80% frequency at 40 days after planting (DAP) compared with 68 DAP for the other treatments. In 2012, no treatment reached 80% frequency or ground cover until 118 DAP. The lowest stolon-planting rate had 38% weed cover in April the year following planting compared with

Use of Tifton 85 bermudagrass [Cynodon dactylon (L.) Pers. X C. transvaalensis Burtt Davy] has increased in pasture-based dairies in the southeastern United States relative to other warm-season grasses. A 2-yr study was conducted to evaluate rotational stocking for two grazing rest periods (RP; 14 and 21 d) and two supplementation rates (SUP; 0.64% [low] and 0.96% [high] of heifer [Bos taurus] body weight) on pasture characteristics and animal performance. Across all treatments, pastures with 14-d RP had greater (P < 0.05) crude protein (CP) concentration and in vitro organic matter digestibility (IVOMD) than pastures with 21-d RP (174 vs. 161 g kg–¹ and 624 vs. 602 g. kg–¹, for CP and IVOMD, respectively). Herbage allowance was less in high than low SUP pastures (0.59 vs. 0.67 kg dry matter (DM) kg live weight (LW)–¹, respectively). In 2010, average daily gain (ADG) was not affected by SUP (0.62 vs. 0.63 kg d–¹ for heifers fed low and high amounts of SUP, respectively) or by RP. However, in 2011 ADG was greater (P = 0.07) for heifers fed high compared to low amounts of SUP (0.61 vs. 0.51 kg d–¹, respectively). Although heifer ADG approached the industry target of 0.7 kg, results suggest forage allowance of < 1 kg DM kg–¹ animal LW limited daily gains. The nutritive value data support the conclusion that Tifton 85 possesses high nutritive value and is suitable for use in pasture-based systems for raising replacement dairy heifers if adequate forage allowance is maintained.

On the Ground Smutgrass (Sporobolus indicus) is an invasive plant in Florida sandy soils, prevalent in central and south Florida where temperatures seldom drop below freezing and hard frost events are infrequent. Smutgrass becomes nonpalatable to cattle as it matures and cattle avoid grazing it after the emergence of seed stalks and when leaves become tough. However, young smutgrass growth is palatable to cattle. High stocking densities in combination with severe defoliation have proven deleterious for this grass. This study evaluated the use of increased stock density and rotational grazing management for 3 years following a one-time defoliation by mowing or burning smutgrass infested pastures.

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% 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% 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.

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.