ProbBreed: a novel tool for calculating the risk of cultivar recommendation in multienvironment trials.

Neglecting genotype-by-environment interactions in multienvironment trials (MET) increases the risk of flawed cultivar recommendations for growers. Recent advancements in probability theory coupled with cutting-edge software offer a more streamlined decision-making process for selecting suitable candidates across diverse environments. Here, we present the user-friendly ProbBreed package in R, which allows breeders to calculate the probability of a given genotype outperforming competitors under a Bayesian framework. This article outlines the package's basic workflow and highlights its key features, ranging from MET model fitting to estimating the per se and pairwise probabilities of superior performance and stability for selection candidates. Remarkably, only the selection intensity is required to compute these probabilities. By democratizing this complex yet efficient methodology, ProbBreed aims to enhance decision-making and ultimately contribute to more accurate cultivar recommendations in breeding programs.

Aniline Derivatives from Lignin under Mild Conditions Enabled by Electrochemistry.

The development of environmentally friendly methods for the valorization of important phenolic platform chemicals originating directly from lignin-first depolymerization into value-added N-chemicals, such as aniline derivatives, is of high industrial interest. In this work, we tackle this challenging transformation by the judicious combination of electrochemical conversion and chemical functionalization steps. In the first step, lignin-derived para-substituted guaiacols and syringols undergo an atom-efficient, room-temperature anodic oxidation using methanol both as solvent and reagent towards the formation of the corresponding cyclohexadienone derivatives, which are subsequently converted to synthetically challenging ortho-methoxy substituted anilines by reaction with ethyl glycinate hydrochloride under mild conditions. The developed method was applied to crude lignin depolymerization bio-oils, derived from reductive catalytic fractionation (RCF) mediated either by copper-doped porous metal oxide (Cu20 PMO) or Ru/C, allowing the selective production of 4-propanol-2-methoxyaniline (1Gb) and 4-propyl-2-methoxyaniline (2Gb), respectively, from pine lignocellulose. Finally, the application of 2Gb was further studied in the synthesis of carbazole 2Gc, a lignin-derived analogue of biologically active alkaloid murrayafoline A.

First Record of Wyeomyia mitchellii in Nuevo León, Mexico.

On October 5, 2021, mosquito collections were conducted in Nuevo León in search of an undescribed species within the genus Wyeomyia reported previously in this state. Species collected included Aedes quadrivittatus, Ae. amabilis, Ae. triseriatus group, Ae. albopictus, and Wy. mitchellii. Although the undescribed species was not found, the occurrence record for Wy. mitchellii in Nuevo León constitutes the 1st record for this species in this state. Additionally, historical records of the presence of Wy. mitchelli in Mexico, available in the literature, were reviewed and updated. Specimens collected during this study were deposited in the Culicidae Collection of the Parasitology Department, Autonomous Agrarian University Antonio Narro, Laguna unit. With the addition of Wy. mitchellii to the mosquito fauna of Nuevo León, there are currently 67 species in the state.

Leveraging probability concepts for cultivar recommendation in multi-environment trials.

KEY MESSAGE: We propose using probability concepts from Bayesian models to leverage a more informed decision-making process toward cultivar recommendation in multi-environment trials. Statistical models that capture the phenotypic plasticity of a genotype across environments are crucial in plant breeding programs to potentially identify parents, generate offspring, and obtain highly productive genotypes for target environments. In this study, our aim is to leverage concepts of Bayesian models and probability methods of stability analysis to untangle genotype-by-environment interaction (GEI). The proposed method employs the posterior distribution obtained with the No-U-Turn sampler algorithm to get Hamiltonian Monte Carlo estimates of adaptation and stability probabilities. We applied the proposed models in two empirical tropical datasets. Our findings provide a basis to enhance our ability to consider the uncertainty of cultivar recommendation for global or specific adaptation. We further demonstrate that probability methods of stability analysis in a Bayesian framework are a powerful tool for unraveling GEI given a defined intensity of selection that results in a more informed decision-making process toward cultivar recommendation in multi-environment trials.

Estimation of Molecular Pairwise Relatedness in Autopolyploid Crops.

A suitable pairwise relatedness estimation is key to genetic studies. Several methods are proposed to compute relatedness in autopolyploids based on molecular data. However, unlike diploids, autopolyploids still need further studies considering scenarios with many linked molecular markers with known dosage. In this study, we provide guidelines for plant geneticists and breeders to access trustworthy pairwise relatedness estimates. To this end, we simulated populations considering different ploidy levels, meiotic pairings patterns, number of loci and alleles, and inbreeding levels. Analysis were performed to access the accuracy of distinct methods and to demonstrate the usefulness of molecular marker in practical situations. Overall, our results suggest that at least 100 effective biallelic molecular markers are required to have good pairwise relatedness estimation if methods based on correlation is used. For this number of loci, current methods based on multiallelic markers show lower performance than biallelic ones. To estimate relatedness in cases of inbreeding or close relationships (as parent-offspring, full-sibs, or half-sibs) is more challenging. Methods to estimate pairwise relatedness based on molecular markers, for different ploidy levels or pedigrees were implemented in the AGHmatrix R package.

High-Resolution Linkage Map With Allele Dosage Allows the Identification of Regions Governing Complex Traits and Apospory in Guinea Grass (Megathyrsus maximus).

Forage grasses are mainly used in animal feed to fatten cattle and dairy herds, and guinea grass (Megathyrsus maximus) is considered one of the most productive of the tropical forage crops that reproduce by seeds. Due to the recent process of domestication, this species has several genomic complexities, such as autotetraploidy and aposporous apomixis. Consequently, approaches that relate phenotypic and genotypic data are incipient. In this context, we built a linkage map with allele dosage and generated novel information of the genetic architecture of traits that are important for the breeding of M. maximus. From a full-sib progeny, a linkage map containing 858 single nucleotide polymorphism (SNP) markers with allele dosage information expected for an autotetraploid was obtained. The high genetic variability of the progeny allowed us to map 10 quantitative trait loci (QTLs) related to agronomic traits, such as regrowth capacity and total dry matter, and 36 QTLs related to nutritional quality, which were distributed among all homology groups (HGs). Various overlapping regions associated with the quantitative traits suggested QTL hotspots. In addition, we were able to map one locus that controls apospory (apo-locus) in HG II. A total of 55 different gene families involved in cellular metabolism and plant growth were identified from markers adjacent to the QTLs and APOSPORY locus using the Panicum virgatum genome as a reference in comparisons with the genomes of Arabidopsis thaliana and Oryza sativa. Our results provide a better understanding of the genetic basis of reproduction by apomixis and traits important for breeding programs that considerably influence animal productivity as well as the quality of meat and milk.

Novel Bayesian Networks for Genomic Prediction of Developmental Traits in Biomass Sorghum.

The ability to connect genetic information between traits over time allow Bayesian networks to offer a powerful probabilistic framework to construct genomic prediction models. In this study, we phenotyped a diversity panel of 869 biomass sorghum (Sorghum bicolor (L.) Moench) lines, which had been genotyped with 100,435 SNP markers, for plant height (PH) with biweekly measurements from 30 to 120 days after planting (DAP) and for end-of-season dry biomass yield (DBY) in four environments. We evaluated five genomic prediction models: Bayesian network (BN), Pleiotropic Bayesian network (PBN), Dynamic Bayesian network (DBN), multi-trait GBLUP (MTr-GBLUP), and multi-time GBLUP (MTi-GBLUP) models. In fivefold cross-validation, prediction accuracies ranged from 0.46 (PBN) to 0.49 (MTr-GBLUP) for DBY and from 0.47 (DBN, DAP120) to 0.75 (MTi-GBLUP, DAP60) for PH. Forward-chaining cross-validation further improved prediction accuracies of the DBN, MTi-GBLUP and MTr-GBLUP models for PH (training slice: 30-45 DAP) by 36.4-52.4% relative to the BN and PBN models. Coincidence indices (target: biomass, secondary: PH) and a coincidence index based on lines (PH time series) showed that the ranking of lines by PH changed minimally after 45 DAP. These results suggest a two-level indirect selection method for PH at harvest (first-level target trait) and DBY (second-level target trait) could be conducted earlier in the season based on ranking of lines by PH at 45 DAP (secondary trait). With the advance of high-throughput phenotyping technologies, our proposed two-level indirect selection framework could be valuable for enhancing genetic gain per unit of time when selecting on developmental traits.

Viscous Fingering of Miscible Liquids in Porous and Swellable Media for Rapid Diagnostic Tests.

In lateral flow and colorimetric test strip diagnostics, the effects of capillary action and diffusion on speed and sensitivity have been well studied. However, another form of fluid motion can be generated due to stresses and instabilities generated in pores when two miscible liquids with different densities and viscosities come into contact. This study explored how a swellable test pad can be deployed for measuring urea in saliva by partially prefilling the pad with a miscible solution of greater viscosity and density. The resultant Korteweg stresses and viscous fingering patterns were analyzed using solutions with added food color through video analysis and image processing. Image analysis was simplified using the saturation channel after converting RGB image sequences to HSB. The kinetics of liquid mixing agreed with capillary displacement results for miscible liquids undergoing movement from Korteweg stresses. After capillary filling, there was significant movement of liquid due to these fluidic effects, which led to mixing of the saliva sample with an enzyme test solution. Owing to the simplicity and speed of this test method, urea can be analyzed with an electronic nose over a useful range for detecting salivary urea concentration for rapid and early detection of dehydration.

High-Resolution Genetic Map and QTL Analysis of Growth-Related Traits of Hevea brasiliensis Cultivated Under Suboptimal Temperature and Humidity Conditions.

Rubber tree (Hevea brasiliensis) cultivation is the main source of natural rubber worldwide and has been extended to areas with suboptimal climates and lengthy drought periods; this transition affects growth and latex production. High-density genetic maps with reliable markers support precise mapping of quantitative trait loci (QTL), which can help reveal the complex genome of the species, provide tools to enhance molecular breeding, and shorten the breeding cycle. In this study, QTL mapping of the stem diameter, tree height, and number of whorls was performed for a full-sibling population derived from a GT1 and RRIM701 cross. A total of 225 simple sequence repeats (SSRs) and 186 single-nucleotide polymorphism (SNP) markers were used to construct a base map with 18 linkage groups and to anchor 671 SNPs from genotyping by sequencing (GBS) to produce a very dense linkage map with small intervals between loci. The final map was composed of 1,079 markers, spanned 3,779.7 cM with an average marker density of 3.5 cM, and showed collinearity between markers from previous studies. Significant variation in phenotypic characteristics was found over a 59-month evaluation period with a total of 38 QTLs being identified through a composite interval mapping method. Linkage group 4 showed the greatest number of QTLs (7), with phenotypic explained values varying from 7.67 to 14.07%. Additionally, we estimated segregation patterns, dominance, and additive effects for each QTL. A total of 53 significant effects for stem diameter were observed, and these effects were mostly related to additivity in the GT1 clone. Associating accurate genome assemblies and genetic maps represents a promising strategy for identifying the genetic basis of phenotypic traits in rubber trees. Then, further research can benefit from the QTLs identified herein, providing a better understanding of the key determinant genes associated with growth of Hevea brasiliensis under limiting water conditions.

Linkage Disequilibrium and Population Structure in Wild and Cultivated Populations of Rubber Tree (Hevea brasiliensis).

Among rubber tree species, which belong to the Hevea genus of the Euphorbiaceae family, Hevea brasiliensis (Willd. ex Adr.de Juss.) Muell. Arg. is the main commercial source of natural rubber production worldwide. Knowledge of the population structure and linkage disequilibrium (LD) of this species is essential for the efficient organization and exploitation of genetic resources. Here, we obtained single-nucleotide polymorphisms (SNPs) using a genotyping-by-sequencing (GBS) approach and then employed the SNPs for the following objectives: (i) to identify the positions of SNPs on a genetic map of a segregating mapping population, (ii) to evaluate the population structure of a germplasm collection, and (iii) to detect patterns of LD decay among chromosomes for future genetic association studies in rubber tree. A total of 626 genotypes, including both germplasm accessions (368) and individuals from a genetic mapping population (254), were genotyped. A total of 77,660 and 21,283 SNPs were detected by GBS in the germplasm and mapping populations, respectively. The mapping population, which was previously mapped, was constructed with 1,062 markers, among which only 576 SNPs came from GBS, reducing the average interval between two adjacent markers to 4.4 cM. SNPs from GBS genotyping were used for the analysis of genetic structure and LD estimation in the germplasm accessions. Two groups, which largely corresponded to the cultivated and wild populations, were detected using STRUCTURE and via principal coordinate analysis. LD analysis, also using the mapped SNPs, revealed that non-random associations varied along chromosomes, with regions of high LD interspersed with regions of low LD. Considering the length of the genetic map (4,693 cM) and the mean LD (0.49 for cultivated and 0.02 for wild populations), a large number of evenly spaced SNPs would be needed to perform genome-wide association studies in rubber tree, and the wilder the genotypes used, the more difficult the mapping saturation.

Ereptiospiration.

Pure coconut oil, lanolin, and acetaminophen were vaporized at rates of 1-50 mg/min, using a porous network exhibiting a temperature gradient from 5000 to 5500 K/mm, without incurring noticeable chemical changes due to combustion, oxidation, or other thermally-induced chemical structural changes. The newly coined term "ereptiospiration" is used here to describe this combination of thermal transpiration at high temperature gradients since the process can force the creation of thermal aerosols by rapid heating in a localized zone. Experimental data were generated for these materials using two different supports for metering the materials to the battery powered coil: namely, a stainless steel fiber bundle and a 3-D printed steel cartridge. Heating coconut oil, lanolin, or acetaminophen in a beaker to lower temperatures than those achieved at the surface of the coil showed noticeable and rapid degradation in the samples, while visual and olfactory observations for ereptiospiration showed no noticeable degradation in lanolin and coconut oil while HPLC chromatograms along with visual observation confirm that within the limit of detection, acetaminophen remains chemically unaltered by ereptiospiration.

Feasibility Study of an Optical Caustic Plasmonic Light Scattering Sensor for Human Serum Anti-Dengue Protein E Antibody Detection.

Antibody detection and accurate diagnosis of tropical diseases is essential to help prevent the spread of disease. However, most detection methods lack cost-effectiveness and field portability, which are essential features for achieving diagnosis in a timely manner. To address this, 3D-printed oblate spheroid sample chambers were fabricated to measure green light scattering of gold nanoparticles using an optical caustic focus to detect antibodies. Scattering signals of 20-200 nm gold nanoparticles using a green laser were compared to green light emitting diode (LED) light source signals and to Mie theory. The change in signal from 60 to 120 nm decreased in the order of Mie Theory > optical caustic scattering > 90° scattering. These results suggested that conjugating 60 nm gold nanoparticles and using an optical caustic system to detect plasmonic light scattering, would result in a sensitive test for detecting human antibodies in serum. Therefore, we studied the light scattering response of conjugated gold nanoparticles exposed to different concentrations of anti-protein E antibody, and a feasibility study of 10 human serum samples using dot blot and a handheld optical caustic-based sensor device. The overall agreement between detection methods suggests that the new sensor concept shows promise to detect gold nanoparticle aggregation in a homogeneous assay. Further testing and protocol optimization is needed to draw conclusions on the positive and negative predictive values for this new testing system.

Linking rhizosphere microbiome composition of wild and domesticated Phaseolus vulgaris to genotypic and root phenotypic traits.

Plant domestication was a pivotal accomplishment in human history, but also led to a reduction in genetic diversity of crop species compared to their wild ancestors. How this reduced genetic diversity affected plant-microbe interactions belowground is largely unknown. Here, we investigated the genetic relatedness, root phenotypic traits and rhizobacterial community composition of modern and wild accessions of common bean (Phaseolus vulgaris) grown in agricultural soil from the highlands of Colombia, one of the centers of common bean diversification. Diversity Array Technology-based genotyping and phenotyping of local common bean accessions showed significant genetic and root architectural differences between wild and modern accessions, with a higher specific root length for the wild accessions. Canonical Correspondence Analysis indicated that the divergence in rhizobacterial community composition between wild and modern bean accessions is associated with differences in specific root length. Along the bean genotypic trajectory, going from wild to modern, we observed a gradual decrease in relative abundance of Bacteroidetes, mainly Chitinophagaceae and Cytophagaceae, and an increase in relative abundance of Actinobacteria and Proteobacteria, in particular Nocardioidaceae and Rhizobiaceae, respectively. Collectively, these results establish a link between common bean domestication, specific root morphological traits and rhizobacterial community assembly.

AGHmatrix: R Package to Construct Relationship Matrices for Autotetraploid and Diploid Species: A Blueberry Example.

Progress in the rate of improvement in autopolyploid species has been limited compared with diploids, mainly because software and methods to apply advanced prediction and selection methodologies in autopolyploids are lacking. The objectives of this research were to (i) develop an R package for autopolyploids to construct the relationship matrix derived from pedigree information that accounts for autopolyploidy and double reduction and (ii) use the package to estimate the level and effect of double reduction in an autotetraploid blueberry breeding population with extensive pedigree information. The package is unique, as it can create A-matrices for different levels of ploidy and double reduction, which can then be used by breeders to fit mixed models in the context of predicting breeding values (BVs). Using the data from this blueberry population, we found for all the traits that tetrasomic inheritance creates a better fit than disomic inheritance. In one of the five traits studied, the level of double reduction was different from zero, decreasing the estimated heritability, but it did not affect the prediction of BVs. We also discovered that different depths of pedigree would have significant implications on the estimation of double reduction using this approach. This freely available R package is available for autopolyploid breeders to estimate the level of double reduction present in their populations and the impact in the estimation of genetic parameters as well as to use advanced methods of prediction and selection.

Evidence of Allopolyploidy in Urochloa humidicola Based on Cytological Analysis and Genetic Linkage Mapping.

The African species Urochloa humidicola (Rendle) Morrone & Zuloaga (syn. Brachiaria humidicola (Rendle) Schweick.) is an important perennial forage grass found throughout the tropics. This species is polyploid, ranging from tetra to nonaploid, and apomictic, which makes genetic studies challenging; therefore, the number of currently available genetic resources is limited. The genomic architecture and evolution of U. humidicola and the molecular markers linked to apomixis were investigated in a full-sib F1 population obtained by crossing the sexual accession H031 and the apomictic cultivar U. humidicola cv. BRS Tupi, both of which are hexaploid. A simple sequence repeat (SSR)-based linkage map was constructed for the species from 102 polymorphic and specific SSR markers based on simplex and double-simplex markers. The map consisted of 49 linkage groups (LGs) and had a total length of 1702.82 cM, with 89 microsatellite loci and an average map density of 10.6 cM. Eight homology groups (HGs) were formed, comprising 22 LGs, and the other LGs remained ungrouped. The locus that controls apospory (apo-locus) was mapped in LG02 and was located 19.4 cM from the locus Bh027.c.D2. In the cytological analyses of some hybrids, bi- to hexavalents at diakinesis were observed, as well as two nucleoli in some meiocytes, smaller chromosomes with preferential allocation within the first metaphase plate and asynchronous chromosome migration to the poles during anaphase. The linkage map and the meiocyte analyses confirm previous reports of hybridization and suggest an allopolyploid origin of the hexaploid U. humidicola. This is the first linkage map of an Urochloa species, and it will be useful for future quantitative trait locus (QTL) analysis after saturation of the map and for genome assembly and evolutionary studies in Urochloa spp. Moreover, the results of the apomixis mapping are consistent with previous reports and confirm the need for additional studies to search for a co-segregating marker.

SNP genotyping allows an in-depth characterisation of the genome of sugarcane and other complex autopolyploids.

Many plant species of great economic value (e.g., potato, wheat, cotton, and sugarcane) are polyploids. Despite the essential roles of autopolyploid plants in human activities, our genetic understanding of these species is still poor. Recent progress in instrumentation and biochemical manipulation has led to the accumulation of an incredible amount of genomic data. In this study, we demonstrate for the first time a successful genetic analysis in a highly polyploid genome (sugarcane) by the quantitative analysis of single-nucleotide polymorphism (SNP) allelic dosage and the application of a new data analysis framework. This study provides a better understanding of autopolyploid genomic structure and is a sound basis for genetic studies. The proposed methods can be employed to analyse the genome of any autopolyploid and will permit the future development of high-quality genetic maps to assist in the assembly of reference genome sequences for polyploid species.

Cutting a drop of water pinned by wire loops using a superhydrophobic surface and knife.

A water drop on a superhydrophobic surface that is pinned by wire loops can be reproducibly cut without formation of satellite droplets. Drops placed on low-density polyethylene surfaces and Teflon-coated glass slides were cut with superhydrophobic knives of low-density polyethylene and treated copper or zinc sheets, respectively. Distortion of drop shape by the superhydrophobic knife enables a clean break. The driving force for droplet formation arises from the lower surface free energy for two separate drops, and it is modeled as a 2-D system. An estimate of the free energy change serves to guide when droplets will form based on the variation of drop volume, loop spacing and knife depth. Combining the cutting process with an electrofocusing driving force could enable a reproducible biomolecular separation without troubling satellite drop formation.

Isoelectric focusing in a drop.

A novel approach to molecular separations is investigated using a technique termed droplet-based isoelectric focusing. Drops are manipulated discretely on a superhydrophobic surface, subjected to low voltages for isoelectric focusing, and split-resulting in a preparative separation. A universal indicator dye demonstrates the generation of stable, reversible pH gradients (3-10) in ampholyte buffers, and these gradients lead to protein focusing within the drop length. Focusing was visually characterized, spectroscopically verified, and assessed quantitatively by noninvasive light scattering measurements. It was found to correlate with a quantitative model based on 1D steady-state theory. This work illustrates that molecular separations can be deployed within a single open drop, and the differential fractions can be separated into new discrete liquid elements.

Anisotropic particle synthesis inside droplet templates on superhydrophobic surfaces.

We demonstrate how droplet templates dispensed on superhydrophobic substrates can be used to fabricate both shape-anisotropic ("doughnut") and composition-anisotropic ("patchy magnetic") supraparticles. The macroscopic shape of the closely-packed particle assemblies is guided by the droplet meniscus. Aqueous droplets of monodisperse microsphere suspensions dispensed on the substrates initially acquire near-spherical shape due to a high contact angle. During the solvent evaporation, however, silica suspension droplets undergo shape transitions (concaving) guiding the structure of the final assemblies into doughnut supraparticles. Composition anisotropy is achieved by drying a droplet containing a mixed suspension of latex and magnetic nanoparticles, while exposing it to magnetic field gradients. Depending on the pattern of the magnetic fields, the magnetic nanoparticles segregate into single, bilateral, or trilateral, patched spherical supraparticles. The physical effects leading to the development of anisotropy are discussed. Unlike the conventional wet self-assembly (WSA) methods where the final structures need to be extracted from the liquid environment, this efficient one-step procedure produces ready to use "dry" supraparticles.

Demonstration of sandwich and competitive modulated supraparticle fluoroimmunoassay applied to cardiac protein biomarker myoglobin.

Modulated supraparticle structures are used to improve sandwich and competitive fluoroimmunoassays. The improved methods are demonstrated on myoglobin, a key diagnostic protein for detection of heart damage. The resulting method uses microliter volumes with bovine serum samples doped with varying concentrations of equine myoglobin. These immunoassays use micron-diameter iron oxide particles as a solid phase for antibody anchoring. Introduction of a magnetic field creates dipole moments on the particles, which attracts them to each other to form rod-like supraparticle structures. These structures can rotate within an alternating magnetic field generating convective flow and a periodic signal that can be analyzed with lock-in amplification enabling more sensitive detection. The system is demonstrated on a target associated with acute myocardial infarction (AMI). This disease causes decreased oxygen delivery to the heart resulting in tissue death and the release of cardiac myoglobin into the bloodstream. Studies have shown that the assessment and monitoring of serum myoglobin concentrations is important when making an early diagnosis of AMI. Early diagnosis is crucial since treatment is most effective when done within the first two hours of symptoms. The modulated assay is rapid, accurate, and sensitive for myoglobin assessment of small-volume serum samples. Using a cut-off value of 5.0 nM (85 ng/mL) for AMI induced myoglobin, the modulated competitive assay was able to diagnose AMI-like conditions in serum doped with myoglobin after an incubation time of only 10 min. The standard curve developed for the modulated sandwich assay was linear over a range of zero to 1 nM (17 ng/mL) with a lower limit of detection at 50 pM (0.85 ng/mL).