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This review examines analytical methodology for food flavor analysis. Traditionally, flavor chemistry research has relied on sensory-guided chromatography techniques to identify individual compounds responsible for aroma or taste activity. Among the over 12,000 volatile compounds identified in foods, hundreds have been linked to aroma characteristics, and many taste-active compounds have also been discovered. However analytical methods based on singular compound evaluation are not without limitation and can overlook drivers of flavor perception by ignoring potential stimuli (i.e. antagonists, modulators), interactions among stimuli, and sub-threshold activity. More recently, chemical profiling methods coupled with multivariate analysis, termed flavoromics, have led to advances in flavor research. Utilization of flavoromic methods provides additional opportunities to define chemical stimuli that influence flavor profiles and qualities of food, as well as their contributions to complex perceptions, such as consumer acceptance., Competing Interests: Conflict of interestThe authors declare that they have no conflict of interest., (© The Korean Society of Food Science and Technology 2024. Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.)

Randomized controlled trials (RCT) demonstrate that whole wheat consumption improves glycemia. However, substantial inter-individual variation is often observed, highlighting that dietary whole grain recommendations may not support the health of all persons. The objective of this report is to describe the rationale and design of a planned RCT aimed at establishing the gut microbiota and metabolome signatures that predict whole wheat-mediated improvements in glucose tolerance in adults with prediabetes. It is hypothesized that a controlled diet containing wheat bread (WHEAT; 160 g/day) compared with refined bread (WHITE) will improve glucose tolerance in a gut microbiota-mediated manner. Biospecimens will be collected before and after each 2-week study arm. Testing for oral glucose tolerance and gastrointestinal permeability will be performed post-intervention. Assessments will include oral glucose tolerance (primary outcome) and secondary outcomes including gut microbiota, targeted and untargeted metabolomics of fecal and plasma samples, intestinal and host inflammatory responses, and intestinal permeability. WHEAT is predicted to alleviate glucose intolerance by shifting microbiota composition to increase short-chain fatty acid-producing bacteria while reducing populations implicated in intestinal inflammation, barrier dysfunction, and systemic endotoxemia. Further, benefits from WHEAT are anticipated to correlate with gut-level and systemic metabolomic responses that can help to explain the expected inter-individual variability in glucose tolerance. Thus, knowledge gained from integrating multi-omic responses associating with glucose tolerance could help to establish a precision nutrition-based framework that can alleviate cardiometabolic risk. This framework could inform novel dietary whole grain recommendations by enhancing our understanding of inter-individual responsiveness to whole grain consumption., Competing Interests: Author declarations RSB is the Editor-in-Chief and JZ is a Guest Editor of Nutrition Research. Manuscript handling was performed by a designated staff person from Elsevier to blind RSB and JZ to the peer review process. None of the other authors have any relevant conflicts of interest to disclose., (Copyright © 2024 Elsevier Inc. All rights reserved.)

Island species are highly vulnerable due to habitat destruction and their often small population sizes with reduced genetic diversity. The Hawaiian Islands constitute the most isolated archipelago on the planet, harboring many endemic species. Kokia is an endangered flowering plant genus endemic to these islands, encompassing 3 extant and 1 extinct species. Recent studies provided evidence of unexpected genetic diversity within Kokia. Here, we provide high-quality genome assemblies for all 3 extant Kokia species, including an improved genome for Kokia drynarioides. All 3 Kokia genomes contain 12 chromosomes exhibiting high synteny within and between Kokia and the sister taxon Gossypioides kirkii. Gene content analysis revealed a net loss of genes in K. cookei compared to other species, whereas the gene complement in K. drynarioides remains stable and that of Kokia kauaiensis displays a net gain. A dated phylogeny estimates the divergence time from the last common ancestor for the 3 Kokia species at ∼1.2 million years ago (mya), with the sister taxa (K. cookei + K. drynarioides) diverging ∼0.8 mya. Kokia appears to have followed a stepping-stone pattern of colonization and diversification of the Hawaiian archipelago, likely starting on low or now submerged older islands. The genetic resources provided may benefit conservation efforts of this endangered endemic genus., Competing Interests: Conflicts of interest The author(s) declare no conflict of interest., (© The Author(s) 2024. Published by Oxford University Press on behalf of The Genetics Society of America.)

Avian pathogenic Escherichia coli (APEC) cause avian colibacillosis and accurately distinguishing infectious isolates is critical for controlling its transmission. Multilocus sequence typing (MLST) is an accurate and efficient strain identification method for epidemiological surveillance. This research aimed to develop a fast and high-throughput workflow that simultaneously sequences the Achtman typing scheme's 7 housekeeping genes of multiple E. coli isolates using the Oxford Nanopore Technologies (ONT) platform for large-scale APEC study. E. coli strains were isolated from poultry farms, the housekeeping genes were amplified, and amplicons were sequenced on an R9.4 MinION flow cell using the Nanopore GridION sequencer (ONT, Oxford, UK) following the initial workflow (ONT-MLST). Moreover, the workflow was revised by introducing large-scale DNA extraction and multiplex PCR into the ONT-MLST workflow and applied to 242 new isolates, 18 isolates from the previous workflow, and 5 ATCC reference strains using Flongle flow cell on the Nanopore MinION Mk1C sequencer (ONT, Oxford, UK). Finally, the sequence type (ST) results of the 308 isolates collected from infected chickens and poultry farm environments were reported and analyzed. Data indicated that E. coli belonging to ST159, ST8578, and ST355 have the potential to infect multiple organs in broiler. In addition, zoonotic STs, ST69, ST10, ST38, and ST131, were detected from poultry farms. With the advantages of the high throughput of ONT, this study provides a rapid workflow for large-scale E. coli typing and identified frequently isolated sequence types related to APEC infection in poultry., (Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.)

New interspecific hybrid hazelnut crosses between American ( Corylus americana ) and European ( Corylus avellana ) hazelnuts are being developed to support a commercial industry in the Midwest region of the United States. In this study, volatile compounds that impact consumer aroma liking of roasted hybrid hazelnuts ( C. americana × C. avellana ) were investigated by targeted and nontargeted GC/MS flavoromics. Chemical profiles from 10 roasted hybrid hazelnut samples were modeled with consumer aroma liking scores by orthogonal partial least-squares with good fit and predictive performance ( R 2 ≥ 0.92, Q 2 ≥ 0.82, RMSE CV = 0.2). Top ranked predictors positively correlated with liking included 12 aroma compounds and 4 profiled volatiles for the targeted and nontargeted methods, respectively. Sensory recombination testing of hazelnut samples with addition of the 12 predictive odorants was preferred by consumers ( p < 0.001, Δ aroma liking = 2.2 on 9-point scale) and perceived as more roasty, nutty, and sweet compared to the control ( p < 0.05). Addition of the 4 predictive volatiles at subthreshold levels also was preferred ( p = 0.02) and perceived as less earthy and mushroom like than the control ( p < 0.05).

American-European hybrid hazelnuts ( Corylus americana × Corylus avellana ) are an emerging crop in the Upper Midwest of the United States that have been reported to have unique sensory characteristics compared to traditionally grown European hazelnuts. In this study, key odor-active compounds in a roasted hybrid hazelnut variety ( C. americana × C. avellana ) were identified and profiled across different hybrid hazelnut varietals to understand sensory differences. Gas chromatography/mass spectrometry/olfactometry analysis identified 33 odorants with high flavor dilution factors (FD ≥ 16) in the roasted hybrid hazelnut, including 2-acetylpyrazine and 2-aminoacetophenone as first reported hazelnut odorants. Descriptive sensory analysis profiles of the roasted hazelnut and an aroma recombination model consisting of 27 odorants quantified above their odor detection thresholds were not significantly different for the six evaluated attributes, confirming the aroma contribution of the identified odorants. Variation in all 33 aroma-active compounds across 12 hybrid and two European hazelnut varieties was visualized through principal component analysis and related to aroma profiles previously characterized by consumers.

Premise: A complicating factor in analyzing allopolyploid genomes is the possibility of physical interactions between homoeologous chromosomes during meiosis, resulting in either crossover (homoeologous exchanges) or non-crossover products (homoeologous gene conversion). Homoeologous gene conversion was first described in cotton by comparing SNP patterns in sequences from two diploid progenitors with those from the allopolyploid subgenomes. These analyses, however, did not explicitly consider other evolutionary scenarios that may give rise to similar SNP patterns as homoeologous gene conversion, creating uncertainties about the reality of the inferred gene conversion events., Methods: Here, we use an expanded phylogenetic sampling of high-quality genome assemblies from seven allopolyploid Gossypium species (all derived from the same polyploidy event), four diploid species (two closely related to each subgenome), and a diploid outgroup to derive a robust method for identifying potential genomic regions of gene conversion and homoeologous exchange., Results: We found little evidence for homoeologous gene conversion in allopolyploid cottons, and that only two of the 40 best-supported events were shared by more than one species. We did, however, reveal a single, shared homoeologous exchange event at one end of chromosome 1, which occurred shortly after allopolyploidization but prior to divergence of the descendant species., Conclusions: Overall, our analyses demonstrated that homoeologous gene conversion and homoeologous exchanges are uncommon in Gossypium, affecting between zero and 24 genes per subgenome (0.0-0.065%) across the seven species. More generally, we highlighted the potential problems of using simple four-taxon tests to investigate patterns of homoeologous gene conversion in established allopolyploids., (© 2024 The Author(s). American Journal of Botany published by Wiley Periodicals LLC on behalf of Botanical Society of America.)

Interspecific American-European hazelnut (Corylus americana × C. avellana) hybrids are being developed for the Upper Midwest region of the United States, which have potential economic and ecological benefits. Currently, researchers are working on pre-commercialization initiatives to create a local hazelnut industry. However, a lack of knowledge on the sensory characteristics and consumer acceptability of the hybrid hazelnuts have been identified as potential limitations to production. This study investigated consumer responses to hybrid hazelnuts, employing hedonic ratings and check-all-that-apply (CATA) questions. Twelve roasted hazelnut hybrids were subjected to consumer evaluation for liking (aroma, color, flavor, texture, and overall) and aroma and flavor descriptors. Consumers also evaluated two European hazelnut varieties for comparative purposes. Liking scores were significantly different (p < 0.05) across different hybrid varieties and when comparing specific hybrids with European varieties. CATA sensory profiles specific to different varieties were also observed and discriminating attributes were identified using multiple-response methodologies. Penalty analysis based on CATA further identified the attributes roasty, hazelnut-like, caramel-like, chocolate-like, sweet, and salty as primary drivers of aroma/flavor liking, while earthy, burnt, and bitter were identified as primary drivers of disliking. Overall, unique flavors that impacted liking were found in hybrid hazelnuts and, when compared with European hazelnuts, provided insights for breeding and post-processing strategies to optimize product quality., (© 2024 The Author(s). Journal of Food Science published by Wiley Periodicals LLC on behalf of Institute of Food Technologists.)

Elucidating genetic diversity within wild forms of modern crops is essential for understanding domestication and the possibilities of wild germplasm utilization. Gossypium hirsutum is a predominant source of natural plant fibers and the most widely cultivated cotton species. Wild forms of G. hirsutum are challenging to distinguish from feral derivatives, and truly wild populations are uncommon. Here we characterize a population from Mound Key Archaeological State Park, Florida using genome-wide SNPs extracted from 25 individuals over three sites. Our results reveal that this population is genetically dissimilar from other known wild, landrace, and domesticated cottons, and likely represents a pocket of previously unrecognized wild genetic diversity. The unexpected level of divergence between the Mound Key population and other wild cotton populations suggests that the species may harbor other remnant and genetically distinct populations that are geographically scattered in suitable habitats throughout the Caribbean. Our work thus has broader conservation genetic implications and suggests that further exploration of natural diversity in this species is warranted., (© 2024. The Author(s).)

We report the whole-genome sequences of Escherichia coli strains APEC-O2-MS1266 and APEC-O2-MS1657 isolated from the liver and heart of infected broilers in Mississippi State, US. The genomic information of these two causative strains may provide a valuable reference for comparative studies of avian pathogenic E. coli ., Competing Interests: The authors declare no conflict of interest.

Bitter compounds are common in nature and among drugs. Previously, machine learning tools were developed to predict bitterness from the chemical structure. However, known structures are estimated to represent only 5-10% of the metabolome, and the rest remain unassigned or "dark". We present BitterMasS, a Random Forest classifier that was trained on 5414 experimental mass spectra of bitter and nonbitter compounds, achieving precision = 0.83 and recall = 0.90 for an internal test set. Next, the model was tested against spectra newly extracted from the literature 106 bitter and nonbitter compounds and for additional spectra measured for 26 compounds. For these external test cases, BitterMasS exhibited 67% precision and 93% recall for the first and 58% accuracy and 99% recall for the second. The spectrum-bitterness prediction strategy was more effective than the spectrum-structure-bitterness prediction strategy and covered more compounds. These encouraging results suggest that BitterMasS can be used to predict bitter compounds in the metabolome without the need for structural assignment of individual molecules. This may enable identification of bitter compounds from metabolomics analyses, for comparing potential bitterness levels obtained by different treatments of samples and for monitoring bitterness changes overtime.

American-European ( Corylus americana × Corylus avellana ) hazelnut hybrids are being developed for the Midwest-growing region of the United States. However, an inadequate understanding of the compounds that impact the consumer acceptance of hazelnuts limits breeding programs. Nontargeted liquid chromatography/mass spectrometry (LC/MS) chemical profiles of 12 roasted hybrid hazelnut samples and the corresponding consumer flavor liking scores were modeled by orthogonal partial least squares with good fit and predictive ability ( R 2 Y > 0.9, Q 2 > 0.9) to identify compounds that impact nut liking. The five most predictive compounds ( 1 - 5 ) were negatively correlated to flavor liking, selected as putative markers, purified by multidimensional preparative LC/MS, structurally elucidated (nuclear magnetic resonance, MS), quantified, and validated for sensory relevance. Compound 1 was identified as 1″-O-3'- b -glucofuranosyl-1'-O-1- b -glucofuranosyl-(2,6-dihydroxyphenyl)-ethan-4-one. Compounds 2 and 4 were identified as rotamers of 2-(3-hydroxy-2-oxoindolin-3-yl) acetic acid 3-O-6'-galactopyranosyl-2″-(2″oxoindolin-3″yl) acetate, whereas compounds 3 and 5 were identified as rotamers of 1″-O-1'- b -glucofuranosyl-9-O-6'- b -glucopyranosyl-2″-(2″-oxoindolin-3″yl) acetate. Sensory evaluation determined that all compounds were characterized by bitterness and/or astringency. The sensory threshold values of compounds 1 - 5 were determined to be below the concentrations reported in 91, 83, 41, 25, and 41% of all 12 hybrid hazelnut samples, respectively, indicating they contributed to aversive flavor attributes.

The metritis complex (MC), a group of post-partum uterine diseases, is associated with increased treatment costs and reduced milk yield and fertility. The goal of this study was to identify genetic variants, genes, or genomic regions that modulate MC disease. A genome-wide association study was performed using a single-locus mixed linear model of 1967 genotypes (624,460 SNPs) and metritis complex records. Then, in-silico functional analyses were performed to detect biological mechanisms and pathways associated with the development of MC. The ATP8A2 , COX16 , AMN , and TRAF3 genes, located on chromosomes 12, 10, and 21, were associated with MC at p ≤ 0.0001. These genes are involved in the regulation of cholesterol metabolism in the stromal tissue of the uterus, which can be directly associated with the mode of transmission for pathogens causing the metritis complex. The modulation of cholesterol abundance alters the efficiency of virulence factors and may affect the susceptibility of the host to infection. The SIPA1L1 , DEPDC5 , and RNF122 genes were also significantly associated with MC at p ≤ 0.0001 and are involved in the PI3k-Akt pathway, responsible for activating the autophagic processes. Thus, the dysregulation of these genes allows for unhindered bacterial invasion, replication, and survival within the endometrium.

The umami taste of pea protein ingredients can be desirable or undesirable based on the food application. The compounds contributing to the umami perception of pea protein isolate (PPI) were investigated. Sensory-guided prep-liquid chromatography fractionation of a 10% aqueous PPI solution revealed one well-known compound, monosodium glutamate (MSG), however, it was reported at a subthreshold concentration. Two umami enhancing compounds 5'-adenosine monophosphate (AMP) and 5'-uridine monophosphate (UMP) were subsequently identified after the LC fractions were re-evaluated with MSG. Sensory recombination studies, utilizing the aqueous PPI solution as the base, confirmed AMP and UMP were umami enhancers of MSG and contributed approximately 81% of the perceived umami intensity. However UMP was only reported to enhance umami perception in combination with AMP (not individually) indicating synergistic interactions were observed between the two enhancer compounds. Therefore the presence of all three compounds are important for umami perception and provide an improved basis to tailor the flavor profile in PPI products., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 Elsevier Ltd. All rights reserved.)

Rebaudioside A, a sweet-tasting steviol glycoside, is known to degrade in food products during storage and thought to contribute to flavor instability. The impact of rebaudioside A degradation compounds on flavor perception was investigated. Sensory descriptive analysis indicated rebaudioside A degradation compounds, at concentrations below detection thresholds, modified the perception of taste, somatosensorial, and retronasal aroma attributes of a strawberry-flavored model beverage. Gas chromatography/mass spectrometry analysis and orthonasal sensory tetrad tests further indicated the addition of the degradation compounds did not significantly alter the volatile aroma composition or orthonasal perception, respectively. Altogether, subthreshold unimodal and cross-modal integration of multisensory percepts were supported to impact the flavor performance of rebaudioside A., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 Elsevier Ltd. All rights reserved.)

Coffee "body" is acknowledged by coffee industry professionals to be an attribute which contributes meaningfully to overall coffee quality and is defined as the collective tactile sensation imparted by the beverage. Currently, there is limited knowledge of the chemical compounds that contribute to tactile attributes in coffee. In the present work, coffee body was determined to be comprised of 4 sub-attributes including mouthcoating, astringency, chalkiness, and thickness and the specific constituents contributing to the tactile sensation of mouthcoating were further pursued using sensory-guided fractionation via preparative-scale liquid chromatography. Signal detection-based sensory methodologies were employed to characterize the sensory effects elicited by selected compounds in water and coffee matrices. Two chlorogenic acids, 3-O-caffeoylquinic acid (3-CQA) and 4-O-caffeoylquinic acid (4-CQA), were observed to impart subtle but significantly perceptible mouthcoating effects in water and/or coffee. Counterintuitively, sensory perception was inversely related to compound concentration. Complex receptor-ligand interactions or salivary lubrication dynamics are discussed as two potential mechanisms to explain this inverse relationship. Taken together, the outcomes of the present study (1) provide new targets for coffee tactile sensation optimization and modulation, (2) identify a novel dimension of sensory impact for two compounds of the chlorogenic acid family, and (3) present a need for deeper investigation into 3-CQA and 4-CQA mechanisms of sensation., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 Elsevier Ltd. All rights reserved.)

The bitterness perception of coffee is a key attribute that impacts consumer acceptance. Nontargeted liquid chromatography/mass spectrometry (LC/MS) flavoromics analysis was applied to identify compounds that enhance the bitter perception of roasted coffee brew. Orthogonal partial least squares (OPLS) analysis was used to model the comprehensive chemical profiles and sensory bitter intensity ratings of fourteen coffee brews with good fit and predictivity. Five compounds that were highly predictive and positively correlated to bitter intensity were selected from the OPLS model, further isolated, and purified using preparative LC fractionation. Sensory recombination testing demonstrated that five compounds significantly enhanced the bitter perception of coffee when presented as a mixture, but not when presented individually. In addition, a set of roasting experiments revealed the five compounds were generated during the coffee roasting process., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 Elsevier Ltd. All rights reserved.)

Cotton has been domesticated independently four times for its fiber, but the genomic targets of selection during each domestication event are mostly unknown. Comparative analysis of the transcriptome during cotton fiber development in wild and cultivated materials holds promise for revealing how independent domestications led to the superficially similar modern cotton fiber phenotype in upland ( G. hirsutum ) and Pima ( G. barbadense ) cotton cultivars. Here we examined the fiber transcriptomes of both wild and domesticated G. hirsutum and G. barbadense to compare the effects of speciation versus domestication, performing differential gene expression analysis and coexpression network analysis at four developmental timepoints (5, 10, 15, or 20 days after flowering) spanning primary and secondary wall synthesis. These analyses revealed extensive differential expression between species, timepoints, domestication states, and particularly the intersection of domestication and species. Differential expression was higher when comparing domesticated accessions of the two species than between the wild, indicating that domestication had a greater impact on the transcriptome than speciation. Network analysis showed significant interspecific differences in coexpression network topology, module membership, and connectivity. Despite these differences, some modules or module functions were subject to parallel domestication in both species. Taken together, these results indicate that independent domestication led G. hirsutum and G. barbadense down unique pathways but that it also leveraged similar modules of coexpression to arrive at similar domesticated phenotypes.

The aversive bitter taste of pea protein ingredients limits product acceptability. Compounds contributing to the bitter perception of pea protein isolates were investigated. Off-line multi-dimensional sensory-guided preparative liquid chromatography fractionation of a 10% aqueous PPI solution revealed one main bitter compound that was identified by Fourier transform ion cyclotron resonance mass spectrometry and de novo tandem mass spectrometry (MS/MS) sequencing as the 37 amino acid peptide PA1b from pea albumin and further confirmed by synthesis. Quantitative MS/MS analysis reported that the concentration of the bitter peptide was 129.3 mg/L, which was above the determined bitter sensory threshold value of 3.8 mg/L and in agreement with the perceived bitter taste of the sample.

Labeo rohita (rohu) is a carp important to aquaculture in South Asia, with a production volume close to Atlantic salmon. While genetic improvements to rohu are ongoing, the genomic methods commonly used in other aquaculture improvement programs have historically been precluded in rohu, partially due to the lack of a high-quality reference genome. Here we present a high-quality de novo genome produced using a combination of next-generation sequencing technologies, resulting in a 946 Mb genome consisting of 25 chromosomes and 2,844 unplaced scaffolds. Notably, while approximately half the size of the existing genome sequence, our genome represents 97.9% of the genome size newly estimated here using flow cytometry. Sequencing from 120 individuals was used in conjunction with this genome to predict the population structure, diversity, and divergence in three major rivers (Jamuna, Padma, and Halda), in addition to infer a likely sex determination mechism in rohu. These results demonstrate the utility of the new rohu genome in modernizing some aspects of rohu genetic improvement programs., Competing Interests: Conflicts of interest The authors declare no conflict of interest. Supplemental material available at G3 online., (© The Author(s) 2023. Published by Oxford University Press on behalf of the Genetics Society of America.)

Gossypium herbaceum is a species of cotton native to Africa and Asia that is one of the 2 domesticated diploids. Together with its sister-species G. arboreum, these A-genome taxa represent models of the extinct A-genome donor of modern polyploid cotton, which provide about 95% of cotton grown worldwide. As part of a larger effort to characterize variation and improve resources among diverse diploid and polyploid cotton genomes, we sequenced and assembled the genome of G. herbaceum cultivar (cv.) Wagad, representing the first domesticated accession for this species. This chromosome-level genome was generated using a combination of PacBio long-read technology, HiC, and Bionano optical mapping and compared to existing genome sequences in cotton. We compare the genome of this cultivar to the existing genome of wild G. herbaceum subspecies africanum to elucidate changes in the G. herbaceum genome concomitant with domestication and extend these analyses to gene expression using available RNA-seq. Our results demonstrate the utility of the G. herbaceum cv. Wagad genome in understanding domestication in the diploid species, which could inform modern breeding programs., Competing Interests: Conflicts of interest The authors declare no conflict of interest., (Published by Oxford University Press on behalf of the Genetics Society of America 2022.)

We present an improved ddRAD-Seq protocol for identifying single nucleotide polymorphisms (SNPs). It utilizes selected restriction enzyme digestion fragments, quick acting ligases that are neutral with the restriction enzyme buffer eliminating buffer exchange steps, and adapters designed to be compatible with Illumina index primers. Library amplification and barcoding are completed in one PCR step, and magnetic beads are used to purify the genomic fragments from the ligation and library generation steps. Our protocol increases the efficiency and decreases the time to complete a ddRAD-Seq experiment. To demonstrate its utility, we compared SNPs from our protocol with those from whole genome resequencing data from Gossypium herbaceum and Gossypium arboreum. Principal component analysis demonstrated that the variability of the combined data was explained by the genotype (PC1) and methodology applied (PC2). Phylogenetic analysis showed that the SNPs from our method clustered with SNPs from the resequencing data of the corresponding genotype. Sequence alignments illustrated that for homozygous loci, more than 90% of the SNPs from the resequencing data were discovered by our method. Our analyses suggest that our ddRAD-Seq method is reliable in identifying SNPs suitable for phylogenetic and association genetic studies while reducing cost and time over known methods., Competing Interests: Declaration of competing interest The authors declare no conflict of interest regarding the research, authorship, funding, and publication of this work., (Copyright © 2022 The Authors. Published by Elsevier Inc. All rights reserved.)

Domestication in the cotton genus is remarkable in that it has occurred independently four different times at two different ploidy levels. Relatively little is known about genome evolution and domestication in the cultivated diploid species Gossypium herbaceum and Gossypium arboreum, due to the absence of wild representatives for the latter species, their ancient domestication, and their joint history of human-mediated dispersal and interspecific gene flow. Using in-depth resequencing of a broad sampling from both species, we provide support for their independent domestication, as opposed to a progenitor-derivative relationship, showing that diversity (mean π = 6 × 10-3) within species is similar, and that divergence between species is modest (FST = 0.413). Individual accessions were homozygous for ancestral single-nucleotide polymorphisms at over half of variable sites, while fixed, derived sites were at modest frequencies. Notably, two chromosomes with a paucity of fixed, derived sites (i.e., chromosomes 7 and 10) were also strongly implicated as having experienced high levels of introgression. Collectively, these data demonstrate variable permeability to introgression among chromosomes, which we propose is due to divergent selection under domestication and/or the phenomenon of F2 breakdown in interspecific crosses. Our analyses provide insight into the evolutionary forces that shape diversity and divergence in the diploid cultivated species and establish a foundation for understanding the contribution of introgression and/or strong parallel selection to the extensive morphological similarities shared between species., (© The Author(s) 2022. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution.)

Flavor instability of ready-to-drink (RTD) coffee during storage negatively impacts product quality. Untargeted liquid chromatography/mass spectrometry (LC/MS) analysis was applied to identify chemical compounds that degraded during storage and impacted the flavor attributes of RTD coffee. LC/MS chemical profiles of non-aged and aged coffee samples were modeled against the degree of difference sensory scores by orthogonal partial least squares with good fit (R 2 Y = 0.966) and predictive ability (Q 2  = 0.960). The top five predictive chemical features were subsequently purified by off-line multidimensional Prep-LC, revealing ten coeluting chlorogenic acid lactones (CGLs) compounds that were identified by LC/MS and nuclear magnetic resonance (NMR). The concentrations of eight CGLs significantly decreased in the coffee during the 4-month storage. Sensory recombination testing revealed the degradation of 3-O-caffeoyl-ɣ-quinide and 4-O-caffeoyl-ɣ-quinide significantly impacted the flavor stability of RTD coffee at subthreshold concentrations., (Copyright © 2022 Elsevier Ltd. All rights reserved.)

Malic acid derivatives from camu-camu ( Myrciaria dubia ) fruit exhibited a strong in vitro inhibitory activity toward pancreatic α-amylase and α-glucosidase enzymes. During a bioguided chromatographic fractionation process of the whole fruit (pulp and peelings) polar extract, isomers ( S )-4-butoxy-2-hydroxy-4-oxobutanoic acid ( 1 ) and ( S )-4-butoxy-3-hydroxy-4-oxobutanoic acid ( 2 ) (84:16) were isolated and identified as a potent inhibitor of α-amylase (IC 50 = 11.69 ± 1.75 μg/mL) and α-glucosidase (IC 50 = 102.69 ± 4.16 μg/mL). The chemical structures were confirmed by HPLC-ESIMS and 1 H and 13 C NMR (one- and two-dimensional) analyses. The structure-based virtual screening demonstrated that the aliphatic moiety plays a significant role in the binding mode of the test alkyl malate esters. Compound 1 exhibited the best interaction profile to bind both enzymes, having key structural features to form relevant contacts by involving adequate enzyme-ligand complex stabilization and compactness over time., Competing Interests: The authors declare no competing financial interest., (© 2022 The Authors. Published by American Chemical Society.)

Cytonuclear coevolution is a common feature among plants, which coordinates gene expression and protein products between the nucleus and organelles. Consequently, lineage-specific differences may result in incompatibilities between the nucleus and cytoplasm in hybrid taxa. Allopolyploidy is also a common phenomenon in plant evolution. The hybrid nature of allopolyploids may result in cytonuclear incompatibilities, but the massive nuclear redundancy created during polyploidy affords additional avenues for resolving cytonuclear conflict (i.e. cytonuclear accommodation). Here we evaluate expression changes in organelle-targeted nuclear genes for 6 allopolyploid lineages that represent 4 genera (i.e. Arabidopsis, Arachis, Chenopodium, and Gossypium) and encompass a range in polyploid ages. Because incompatibilities between the nucleus and cytoplasm could potentially result in biases toward the maternal homoeolog and/or maternal expression level, we evaluate patterns of homoeolog usage, expression bias, and expression-level dominance in cytonuclear genes relative to the background of noncytonuclear expression changes and to the diploid parents. Although we find subsets of cytonuclear genes in most lineages that match our expectations of maternal preference, these observations are not consistent among either allopolyploids or categories of organelle-targeted genes. Our results indicate that cytonuclear expression evolution may be subtle and variable among genera and genes, likely reflecting a diversity of mechanisms to resolve nuclear-cytoplasmic incompatibilities in allopolyploid species., (© The Author(s) 2022. Published by Oxford University Press on behalf of Genetics Society of America.)

The cotton chromosome substitution line, CS-B15sh, exhibits 41% lower injury from 2,4-D when applied at the field recommended rate of 1.12 kg ae ha -1 (1×) than does Texas Marker-1 (TM-1). CS-B15sh was developed in the genetic background of Gossypium hirsutum L. cv TM-1 and has chromosome introgression on the short arm of chromosome 15 from Gossypium barbadense L. cv. Pima 379. In a previous experiment, we observed reduced translocation of [ 14 C]2,4-D outside the treated leaf tissue in CS-B15sh, which contrasted with an increased translocation of the herbicide in the tissues above and below the treated leaf in TM-1. Our results indicate a potential 2,4-D tolerance mechanism in CS-B15sh involving altered movement of 2,4-D. Here, we used RNA sequencing (RNA-seq) to determine the differential expression of genes between 2,4-D-challenged and control plants of the tolerant (CS-B15sh) and susceptible lines (TM-1 and Pima 379). Several components of the 2,4-D/auxin-response pathway-including ubiquitin E3 ligase, PB1|AUX/IAA, ARF transcription factors, and F-box proteins of the SCF TIR1/AFB complex-were upregulated with at least threefold higher expression in TM-1 compared with CS-B15sh, while both Pima 379 and TM-1 showed the same fold change expression for PB1|AUX/IAA mRNA. Some genes associated with herbicide metabolism, including flavin monooxygenase (Gohir.A01G174100) and FAD-linked oxidase (Gohir.D06G002600), exhibited at least a twofold increase in CS-B15sh than in TM-1 (the gene was not expressed in Pima 379), suggesting a potential relationship between the gene's expression and 2,4-D tolerance. It is interesting to note that glutathione S-transferase was differentially expressed in both CS-B15sh and Pima 379 but not in TM-1, while cytochrome P450 and other genes involved in the oxidation-reduction process were significantly expressed only in CS-B15sh in response to 2,4-D. Gene set enrichment analysis on the union DEGs of the three cotton genotypes revealed the depletion of transcripts involved in photosynthesis and enrichment of transcripts involved in ABA response and signaling., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Perez, Mauleon, Arick, Magbanua, Peterson, Dean and Tseng.)

Mitochondrial and plastid functions depend on coordinated expression of proteins encoded by genomic compartments that have radical differences in copy number of organellar and nuclear genomes. In polyploids, doubling of the nuclear genome may add challenges to maintaining balanced expression of proteins involved in cytonuclear interactions. Here, we use ribo-depleted RNA sequencing (RNA-seq) to analyze transcript abundance for nuclear and organellar genomes in leaf tissue from four different polyploid angiosperms and their close diploid relatives. We find that even though plastid genomes contain <1% of the number of genes in the nuclear genome, they generate the majority (69.9 to 82.3%) of messenger RNA (mRNA) transcripts in the cell. Mitochondrial genes are responsible for a much smaller percentage (1.3 to 3.7%) of the leaf mRNA pool but still produce much higher transcript abundances per gene compared to nuclear genome. Nuclear genes encoding proteins that functionally interact with mitochondrial or plastid gene products exhibit mRNA expression levels that are consistently more than 10-fold lower than their organellar counterparts, indicating an extreme cytonuclear imbalance at the RNA level despite the predominance of equimolar interactions at the protein level. Nevertheless, interacting nuclear and organellar genes show strongly correlated transcript abundances across functional categories, suggesting that the observed mRNA stoichiometric imbalance does not preclude coordination of cytonuclear expression. Finally, we show that nuclear genome doubling does not alter the cytonuclear expression ratios observed in diploid relatives in consistent or systematic ways, indicating that successful polyploid plants are able to compensate for cytonuclear perturbations associated with nuclear genome doubling.

The complex composition of the follicular fluid (FF), the intimate proximity to the oocyte, and the continual changes in their composition have a major effect on folliculogenesis and oogenesis. To date, the profiling of FF proteomes during follicle selection, development, and ovulation has not been comprehensively investigated. Therefore, a shotgun proteomics approach and bioinformatics analyses were used to profile the proteomes of equine FF harvested in vivo from follicles at the following development stages: predeviation (18-20 mm), deviation (22-25 mm), postdeviation (26-29 mm), preovulatory (30-35 mm), and impending ovulation. A total of 294 proteins were detected in FF (FDR <1%), corresponding to 65 common proteins and 124, 142, 167, 132, and 142 proteins in the predeviation, deviation, postdeviation, preovulatory, and impending ovulation groups, respectively. The higher expression of properdin and several other proteins belonging to the complement system during the deviation time and ovulation suggested their contribution in the selection of the future dominant follicle and ovulation. Apolipoprotein A-1 and antithrombin-III appeared to be important throughout folliculogenesis. The "complement and coagulation cascades" was the major KEGG pathway across all stages of follicle development. The significant expression of several proteins belonging to the serine-type endopeptidase indicated their likely contribution to follicle and oocyte development. Our data provide an extensive description and functional analyses of the equine FF proteome during follicle selection, development, and ovulation. This information will help improve understanding of the ovarian function and ovulatory dysfunctions and might serve as a reference for future biomarker discovery for oocyte quality assessment., (© 2022 Wiley Periodicals LLC.)

Non-volatile compounds that impact the acceptability of strawberry preserves were investigated by untargeted LC-MS flavoromics analysis. Chemical profiles for fifteen strawberry preserves were modeled against consumer liking scores by orthogonal partial least squares (OPLS) with good fit (R 2 Y = 0.995) and predictive ability (Q 2  = 0.918). Four chemical compounds predictive of acceptability were identified, by accurate MS and NMR, as secoisolariciresinol monoglucoside, (+)-isolariciresinol monoglucoside, 1-hexanoyl-phloroglucinol-2-O-β-d-glucoside, and the novel compound decanoic acid-4-O-β-d-glucoside. Sensory recombination testing of preserve samples with added levels of the four predictive LC-MS compounds indicated perceivable sensory changes in the flavor profile. Female consumers significantly preferred the recombination preserve with added levels of both predictive GC-MS and LC-MS compounds as compared to the control preserve, demonstrating the applicability of the approach for understanding product liking., (Copyright © 2022 Elsevier Ltd. All rights reserved.)

Volatile compounds that impact the acceptability of strawberry preserves were investigated by untargeted GC-MS flavoromics analysis. Chemical profiles for fifteen strawberry preserves were modeled against consumer liking scores by orthogonal partial least squares (OPLS) with good fit (R 2 Y = 0.998) and predictive ability (Q 2  = 0.853). Ten highly predictive compounds were selected, nine of which were identified, and eight of which were quantified using tandem mass spectrometry. Sensory recombination difference testing revealed that the addition of predictive compounds to an average-liked preserve at levels found in the most-liked preserve induced a perceptible difference to frequent consumers of strawberry jams. One of the highly predictive compounds was identified (MS and synthesis) as a novel linalool oxide product 2-methyl-2-vinyl-tetrahydrofuran with a fruity, herbal-minty, piney aroma and a low odor threshold value., (Copyright © 2022 Elsevier Ltd. All rights reserved.)

Untargeted LC-MS flavoromics chemical profiling was used to identify compounds predictive of Rebaudioside A (Reb A) flavor instability in an acidified beverage after 6 weeks at 35 °C. High-quality orthogonal partial least squares analysis models were developed from the chemical data and d' values from tetrad sensory panel testing with good predictive ability. The top four highly predictive compounds were selected and identified as Reb A (negatively correlated) and three Reb A degradation compounds (positively correlated), which included a rearrangement, hydration, and an epoxidation/rearrangement of Reb A, termed compounds 1, 2, and 3, respectively. The concentrations of compounds 1-3 in the aged beverages were determined to be below the sensory recognition threshold values. However, sensory recombination testing of compounds 1-3 as a tertiary mixture revealed a perceivably significant flavor change that was aligned with the aged beverage., (Copyright © 2021. Published by Elsevier Ltd.)

Coffee brew flavor is known to degrade during storage. Untargeted and targeted LC/MS flavoromics analysis was applied to identify chemical compounds generated during storage that impacted the flavor stability of ready-to-drink (RTD) coffee. MS chemical profiles for sixteen RTD coffee samples stored for 0, 1, 2, and 4 months at 30 °C were modeled against the sensory degree of difference (DOD) scores by orthogonal partial least squares (OPLS) with good fit and predictive ability. Five highly predictive untargeted chemical features positively correlated to DOD were subsequently identified as 3-caffeoylquinic acid, 4-caffeoylquinic acid, 5-caffeoylquinic acid, 3-O-feruloylquinic acid, and 5-O-feruloylquinic acid. The increase in the six acidic compounds during storage was confirmed by sensory recombination tests to significantly impact the flavor stability of RTD coffee during storage. A decrease in pH, rather than an increase in total acidity, was supported to impact the coffee flavor profile.

The instability of rebaudioside A (Reb A) in food product applications during storage challenges their utilization. The pathways of Reb A degradation in aged acidic beverages were investigated. Three Reb A degradation compounds of known sensory importance were monitored, consisting of ( 1 ) a rearrangement, ( 2 ) a hydration, and ( 3 ) an epoxidation/rearrangement product. Using deuterium-labeled water (D 2 O) experiments, compounds 1 - 2 were reported to be generated by acid-catalyzed mechanisms involving the formation of a carbocation on carbon position 16, followed by either deprotonation via E 1 elimination on C15 to form the more thermodynamically stable trisubstituted alkene (compound 1 ), or by the Markovnikov addition of water via SN 1 substitution to form a tertiary alcohol (compound 2 ). Compound 3 was generated by epoxidation of the exomethylene at the C16-17 positions, followed by the opening and rearrangement of the ring to form a new alkene bond between C15-C16 and a primary alcohol on C17. Further analysis of the effect of beverage ingredients indicated the addition of caramel color significantly increased ( p < 0.0001) the concentrations of compounds 1 - 2 compared to the aged control by 89 and 83%, respectively, whereas a specific coffee flavor and caramel color were reported to significantly reduce ( p < 0.0001) the formation of compound 3 compared to the aged control during storage by 90 and 79%, respectively.

Whole wheat flour has a shorter shelf life than refined wheat flour due to off-flavor development. An untargeted liquid chromatography/mass spectrometry (LC/MS) flavoromics approach was applied to identify compounds that negatively impact the flavor liking in whole wheat bread made from aged flours. The chemical profiles of thirteen breads made from aged flours were obtained using LC/MS and modeled by orthogonal partial least squares (OPLS) to predict flavor liking. Top predictive chemical features (negatively correlated) were identified as pinellic acid (9 S ,12 S ,13 S -trihydroxy-10 E -octadecenoic acid), 12,13-dihydroxy-9 Z -octadecenoic acid, and 1-(9 Z ,12 Z -octadecadienoyl)- sn - glycero -3-phosphocholine. The sensory analysis confirmed the three compounds increased the bitterness intensity of the bread samples. The formation of the trihydroxy fatty acid bitter compound, pinellic acid (9 S ,12 S ,13 S -trihydroxy-10 E -octadecenoic acid), was impacted by the lipoxygenase activity of the flour; however, there was no influence on the formation of 12,13-dihydroxy-9 Z -octadecenoic acid or 1-(9 Z ,12 Z -octadecadienoyl)- sn - glycero -3-phosphocholine. Additionally, the concentrations of all bitter compounds were significantly higher in bread made from aged flour versus non-aged flour.

Untargeted LC-MS flavoromic analysis was utilized to identify chemical compounds that impact consumer liking of whole wheat bread. Chemical fingerprints of thirteen whole wheat breads were modeled against consumer flavor liking scores by orthogonal partial least squares (OPLS) with good fit (R 2 Y = 0.98) and predictive ability (Q 2  = 0.95). The four most predictive features (negatively correlated) were identified as 9S,12S,13S-trihydroxy-octadec-10E-enoic acid (pinellic acid), 9S,12S,13S-trihydroxy-octadeca-10E,15Z-dienoic acid, 8R*,9R*,10S*-trihydroxy-octadec-6Z-enoic acid, and 1-(octadeca-9Z,12Z-dienoyl)-sn-glycero-3-phosphocholine. Sensory validation studies including bitter threshold determination and recombination tests confirmed the contribution of these compounds to the perceived bitterness intensity of the bread samples and the overall negative impact on flavor liking. Lipoxygenase activity of the flour was reported to have a significant impact on the formation of the three bitter compounds (trihydroxy fatty acids) in the bread samples., (Copyright © 2021 Elsevier Ltd. All rights reserved.)

The main objective of this study was to identify compounds that contribute to the bitter taste attributes of American hazelnuts (C. americana) and derived hybrids. Sensory-guided Prep-LC fractionation analysis selected four compounds as bitter that were further identified by MS and NMR as carpinontriol B, 2-(3-hydroxy-2-oxoindolin-3-yl)acetic acid 3-O-6'-galactopyranosyl-2″-(2″oxoindolin-3″yl) acetate, giffonin-2-O-[(α-d-glucopyranosyl)-6'-O-(3-hydroxy-3-methylglutaric acid) and Afzelin, termed compounds 1-4, respectively. The concentrations of compounds 1, 2, 3, and 4 were determined across 88 American hybrid hazelnut genotypes and reported to be present at levels above their bitter threshold values in 94, 75, 25, and 0% of the samples, respectively. Moreover, the concentrations of compounds 1 and 3 were significantly higher for nuts dehusked prior to drying during post-harvest handling, which is expected to result in a higher perceived bitter intensity., (Copyright © 2021 Elsevier Ltd. All rights reserved.)

Cotton is an important crop that has been the beneficiary of multiple genome sequencing efforts, including diverse representatives of wild species for germplasm development. Gossypium anomalum is a wild African diploid species that harbors stress-resistance and fiber-related traits with potential application to modern breeding efforts. In addition, this species is a natural source of cytoplasmic male sterility and a resource for understanding hybrid lethality in the genus. Here, we report a high-quality de novo genome assembly for G. anomalum and characterize this genome relative to existing genome sequences in cotton. In addition, we use the synthetic allopolyploids 2(A2D1) and 2(A2D3) to discover regions in the G. anomalum genome potentially involved in hybrid lethality, a possibility enabled by introgression of regions homologous to the D3 (Gossypium davidsonii) lethality loci into the synthetic 2(A2D3) allopolyploid., (Published by Oxford University Press on behalf of Genetics Society of America 2021.)

Upland cotton (Gossypium hirsutum L.) is susceptible to damage by the root-knot and the reniform nematodes, causing yield losses greater than 4% annually in the United States. In addition, these nematodes are synergistic with seeding disease and root rot pathogens that exacerbate diseases and subsequent yield losses. Production practices to minimize nematode damage include crop rotation and nematicides, but these techniques need to be repeated and are expensive. The use of resistant cultivars is deemed the most effective and economical approach for managing nematodes in cotton. Here, we describe the genomes of two nematode-resistant lines of cotton, BARBREN-713 and BAR 32-30. These genomes may expedite the development of DNA markers that can be used to efficiently introduce nematode resistance into commercially valuable Upland lines., (Published by Oxford University Press 2021.)

Bitterness is a common aversive flavor attribute of foods associated with low consumer acceptance. Untargeted LC-MS flavoromic profiling was utilized to identify endogenous compounds that influence the generation of the bitter compound 9,12,13-trihydroxy-trans-10-octadecenoic acid (pinellic acid) during bread making. A diverse sample set of wheat germplasm was chemically profiled. The corresponding pinellic acid concentrations after dough formation were modeled by orthogonal partial least squares (OPLS) with good fit (R 2 Y = 0.8) and predictive ability (Q 2  = 0.6). The most predictive feature (negatively correlated), postulated to interfere with the biosynthetic pathway, was identified as schaftoside, an apigenin di-C-glycoside. Recombination experiments involving the addition of schaftoside to flour prior to breadmaking resulted in a 26% decrease in pinellic acid formation and significantly lower perceived bitterness intensity in whole wheat bread. This work provides novel understanding of bitter generation pathways in wheat products and new strategies to improve flavor profiles and consumer acceptability., (Copyright © 2021 Elsevier Ltd. All rights reserved.)

Untargeted LC-MS flavoromic profiling was utilized to identify compounds that suppress bitterness perception of coffee brew. The chemical profiles of fourteen brew samples and corresponding perceived bitterness intensities determined by descriptive sensory analysis were modeled by orthogonal partial least squares (OPLS) with good fit (R 2 Y > 0.9) and predictive ability (Q 2  > 0.9). Ten chemical markers that were highly predictive and negatively correlated to bitter intensity were subsequently purified by multi-dimensional preparative LC-MS to conduct sensory recombination testing and/or confirm compound identifications by NMR. Three of the ten compounds evaluated, namely 4-caffeoylquinic acid, 5-caffeoylquinic acid, and 2-O-β-d-glucopyranosyl-atractyligenin were identified as bitter modulators in coffee, and significantly decreased the perceived bitterness intensity of the brew., (Copyright © 2021 Elsevier Ltd. All rights reserved.)

Cotton is an important textile crop whose gains in production over the last century have been challenged by various diseases. Because many modern cultivars are susceptible to several pests and pathogens, breeding efforts have included attempts to introgress wild, naturally resistant germplasm into elite lines. Gossypium stocksii is a wild cotton species native to Africa, which is part of a clade of vastly understudied species. Most of what is known about this species comes from pest resistance surveys and/or breeding efforts, which suggests that G. stocksii could be a valuable reservoir of natural pest resistance. Here, we present a high-quality de novo genome sequence for G. stocksii. We compare the G. stocksii genome with resequencing data from a closely related, understudied species (Gossypium somalense) to generate insight into the relatedness of these cotton species. Finally, we discuss the utility of the G. stocksii genome for understanding pest resistance in cotton, particularly resistance to cotton leaf curl virus., (Published by Oxford University Press on behalf of Genetics Society of America 2021. This work is written by (a) US Government employee(s) and is in the public domain in the US.)

Background: Different taste preferences correlated with genetic variations may lead to food consumption patterns that contribute to nutrient-related health outcomes such as hypertension., Objectives: The aim of this study was to determine whether single nucleotide polymorphisms (SNPs) in the salt taste receptor genes SCNN 1 B and TRPV 1 affect salt taste perception among normotensive and hypertensive people., Materials and Methods: We conducted a cross-sectional case control study by design consisting of a normotensive and hypertensive group. Participants were 253 adults with age range of 20-82 residing in Mississippi, USA. For each of 128 normotensives and 125 hypertensives, the salt taste recognition threshold and salt taste receptor genotype were determined., Results: The hypertensive group had a higher salt taste recognition threshold than the normotensive group ( P < 0.001). The polymorphism of TRPV 1, rs4790522, with the AA genotype was associated with a higher salt recognition threshold (lower salt taste sensitivity) in people with hypertension and obesity. Moreover, the polymorphism of TRPV 1, rs8065080, and SCNN 1 B , rs239345, genes were associated with a risk of hypertension ( P =0.016 and P =0.024)., Conclusion: Correlations between SNPs, salt taste sensitivity, and hypertension risk were observed. People with hypertension had a higher salt taste threshold than those with normotension., Competing Interests: The authors declare no conflicts of interest., (Copyright © 2021 Pradtana Tapanee et al.)

Polyploidy is a widespread phenomenon throughout eukaryotes. Due to the coexistence of duplicated genomes, polyploids offer unique challenges for estimating gene expression levels, which is essential for understanding the massive and various forms of transcriptomic responses accompanying polyploidy. Although previous studies have explored the bioinformatics of polyploid transcriptomic profiling, the causes and consequences of inaccurate quantification of transcripts from duplicated gene copies have not been addressed. Using transcriptomic data from the cotton genus (Gossypium) as an example, we present an analytical workflow to evaluate a variety of bioinformatic method choices at different stages of RNA-seq analysis, from homoeolog expression quantification to downstream analysis used to infer key phenomena of polyploid expression evolution. In general, EAGLE-RC and GSNAP-PolyCat outperform other quantification pipelines tested, and their derived expression dataset best represents the expected homoeolog expression and co-expression divergence. The performance of co-expression network analysis was less affected by homoeolog quantification than by network construction methods, where weighted networks outperformed binary networks. By examining the extent and consequences of homoeolog read ambiguity, we illuminate the potential artifacts that may affect our understanding of duplicate gene expression, including an overestimation of homoeolog co-regulation and the incorrect inference of subgenome asymmetry in network topology. Taken together, our work points to a set of reasonable practices that we hope are broadly applicable to the evolutionary exploration of polyploids., (© The Author(s) 2020. Published by Oxford University Press.)

The genetic basis of general plant vigor is of major interest to food producers, yet the trait is recalcitrant to genetic mapping because of the number of loci involved, their small effects, and linkage. Observations of heterosis in many crops suggests that recessive, malfunctioning versions of genes are a major cause of poor performance, yet we have little information on the mutational spectrum underlying these disruptions. To address this question, we generated a long-read assembly of a tropical japonica rice (Oryza sativa) variety, Carolina Gold, which allowed us to identify structural mutations (>50 bp) and orient them with respect to their ancestral state using the outgroup, Oryza glaberrima. Supporting prior work, we find substantial genome expansion in the sativa branch. While transposable elements (TEs) account for the largest share of size variation, the majority of events are not directly TE-mediated. Tandem duplications are the most common source of insertions and are highly enriched among 50-200bp mutations. To explore the relative impact of various mutational classes on crop fitness, we then track these structural events over the last century of US rice improvement using 101 resequenced varieties. Within this material, a pattern of temporary hybridization between medium and long-grain varieties was followed by recent divergence. During this long-term selection, structural mutations that impact gene exons have been removed at a greater rate than intronic indels and single-nucleotide mutations. These results support the use of ab initio estimates of mutational burden, based on structural data, as an orthogonal predictor in genomic selection., Competing Interests: The authors have declared that no competing interests exist.

The role of small molecules on the somatosensory properties of prunes ( Prunus domestica ) was investigated. Sensory descriptive analysis defined two main somatosensations, "thickness" and "slippery". On the basis of these two attributes, sensory-guided multidimensional fractionation techniques allowed for the isolation of four main compounds, which were identified by mass spectrometry and comparison to authentic standards. Three compounds were identified as monosubstituted isomers of chlorogenic acid, namely, 1- O -caffeoylquinic acid (1-CQA), 3- O -caffeoylquinic acid (3-CQA), and 4- O -caffeoylquinic acid (4-CQA), in addition to a fourth, vanillic acid glucoside (VG). Sensory recombination model analysis of each compound at endogenous concentrations of the prunes indicated that all compounds significantly contributed to slippery sensations, whereas 3-CQA, 4-CQA, and VG contributed to thickness sensations (α = 0.05).

Background: Flooding throughout fall and winter months is an effective practice for rice (Oryza sativa L.) straw decomposition, soil seedbank depletion, and waterfowl habitat in Mississippi. Nevertheless, limited research is available regarding the effects of fall-winter flooding and seed burial depth on Palmer amaranth (Amaranthus palmeri S. Wats.) seed germination. The objective of this study was to evaluate the effect of flooding period and seed burial depth on A. palmeri seed damage and germination in three different soil textures in Mississippi., Results: Amaranthus palmeri seed damage was greater when seeds were buried in sandy loam compared to silt loam soil textures. An interaction between flooding period and seed burial depth was present for A. palmeri seed germination. Flooding periods of 1-month (at 0 and 15 cm burial depth) and 2 months (at 0 cm burial depth) provided similar A. palmeri seed germination compared to no-flooding (at 0 cm burial depth). In addition, flooding periods of 3, 4, and 5 months reduced A. palmeri seed germination by 10, 10 and 14 percentage points at 0 cm burial depth, and 36, 40, and 41 percentage points when seeds were buried at 15 cm, respectively, across all soil textures., Conclusion: This research demonstrates that flooding for 3, 4, and 5-months throughout fall and winter is an effective cultural practice to increase soil seedbank depletion through reduced germination potential to help manage herbicide-resistant A. palmeri populations in sandy loam, silt, and silt loam soil textures. © 2020 Society of Chemical Industry., (© 2020 Society of Chemical Industry.)