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Background: Additional to total protein content, the amino acid (AA) profile is important to the nutritional value of soybean seed. The AA profile in soybean seed is a complex quantitative trait controlled by multiple interconnected genes and pathways controlling the accumulation of each AA. With a total of 621 soybean germplasm, we used three genome-wide association study (GWAS)-based approaches to investigate the genomic regions controlling the AA content and profile in soybean. Among those approaches, the GWAS network analysis we implemented takes advantage of the relationships between specific AAs to identify the genetic control of AA profile., Results: For Approach I, GWAS were performed for the content of 24 single AAs under all environments combined. Significant SNPs grouping into 16 linkage disequilibrium (LD) blocks from 18 traits were identified. For Approach II, the individual AAs were grouped by five families according to their metabolic pathways and were examined based on the sum, ratios, and interactions of AAs within the same biochemical family. Significant SNPs grouping into 35 LD blocks were identified, with SNPs associated with traits from the same biochemical family often positioned on the same LD blocks. Approach III, a correlation-based network analysis, was performed to assess the empirical relationships among AAs. Two groups were described by the network topology, Group 1: Ala, Gly, Lys, available Lys (Alys), and Thr and Group 2: Ile and Tyr. Significant SNPs associated with a ratio of connected AAs or a ratio of a single AA to its fully or partially connected metabolic groups were identified within 9 LD blocks for Group 1 and 2 LD blocks for Group 2. Among 40 identified QTL for AA or AA-derived traits, three genomic regions were novel in terms of seed composition traits (oil, protein, and AA content). An additional 24 regions had previously not been specifically associated with the AA content., Conclusions: Our results confirmed loci identified from previous studies but also suggested that network approaches for studying AA contents in soybean seed are valuable. Three genomic regions (Chr 5: 41,754,397-41,893,109 bp, Chr 9: 1,537,829-1,806,586 bp, and Chr 20: 31,554,795-33,678,257 bp) were significantly identified by all three approaches. Yet, the majority of associations between a genomic region and an AA trait were approach- and/or environment-specific. Using a combination of approaches provides insights into the genetic control and pleiotropy among AA contents, which can be applied to mechanistic understanding of variation in AA content as well as tailored nutrition in cultivars developed from soybean breeding programs., Competing Interests: Declarations. Ethics approval and consent to participate: Not applicable. Consent for publication: Not applicable. Competing interests: The authors declare no competing interests., (© 2024. The Author(s).)

In some peanut (Arachis hypogaea L.) producing regions, growth and photosynthesis-limiting low and high temperature extremes are common. Heat acclimation potential of photosynthesis and respiration is a coping mechanism that is species-dependent and should be further explored for peanut. The objectives of the current study are (1) to evaluate the response of photosynthesis, its component processes, and respiration to low and high temperatures, and (2) to determine the heat acclimation potential of photosynthesis and respiration during early vegetative growth of peanut. Peanut was exposed to four different growth temperature regimes: (1) optimum temperature (30/20 °C day/night), (2) low temperature (20/15 °C), (3) moderately high temperature (35/25 °C), and (4) a high temperature extreme (40/30 °C). Low temperature and both high temperatures caused substantial reductions in growth and net photosynthetic rate. Mesophyll conductance and RuBP regeneration co-limited net photosynthetic rate under low temperature. Rubisco carboxylation was the most negatively impacted biochemical processes by high temperatures; however, diffusional limitations were not evident under high temperature conditions. Photosynthesis did not acclimate to high temperatures, while respiration and photorespiration exhibited heat acclimation. The inability of photosynthesis to acclimate to high temperature is likely a major constraint to early season growth in peanut., 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 © 2025 Elsevier Masson SAS. All rights reserved.)

In plants, the biosynthetic pathways of some specialized metabolites are partitioned into specialized or rare cell types, as exemplified by the monoterpenoid indole alkaloid (MIA) pathway of Catharanthus roseus (Madagascar Periwinkle), the source of the anticancer compounds vinblastine and vincristine. In the leaf, the C. roseus MIA biosynthetic pathway is partitioned into three cell types with the final known steps of the pathway expressed in the rare cell type termed idioblast. How cell-type specificity of MIA biosynthesis is achieved is poorly understood. We generated single-cell multi-omics data from C. roseus leaves. Integrating gene expression and chromatin accessibility profiles across single cells, as well as transcription factor (TF)-binding site profiles, we constructed a cell-type-aware gene regulatory network for MIA biosynthesis. We showcased cell-type-specific TFs as well as cell-type-specific cis-regulatory elements. Using motif enrichment analysis, co-expression across cell types, and functional validation approaches, we discovered a novel idioblast-specific TF (Idioblast MYB1, CrIDM1) that activates expression of late-stage MIA biosynthetic genes in the idioblast. These analyses not only led to the discovery of the first documented cell-type-specific TF that regulates the expression of two idioblast-specific biosynthetic genes within an idioblast metabolic regulon but also provides insights into cell-type-specific metabolic regulation., (© 2024 The Author(s). New Phytologist © 2024 New Phytologist Foundation.)

Ascochyta blight, caused by the necrotrophic fungus Ascochyta rabiei, is a major threat to chickpea production worldwide. Resistance genes with broad-spectrum protection against virulent A. rabiei strains are required to secure chickpea yield in the US Northern Great Plains. Here, we performed a genome-wide association (GWA) study to discover novel sources of genetic variation for Ascochyta blight resistance using a worldwide germplasm collection of 219 chickpea lines. Ascochyta blight resistance was evaluated at 3, 9, 11, 13, and 14 days post-inoculation. Multiple GWA models revealed eight quantitative trait nucleotides (QTNs) across timepoints mapped to chromosomes 1, 3, 4, 6, and 7. Of these eight QTNs, only CM001767.1_28299946 on Chr 4 had previously been reported. QTN CM001766.1_36967269 on Chr 3 explained up to 33% of the variation in disease severity and was mapped to an exonic region of the pentatricopeptide repeat-containing protein At4g02750-like gene (LOC101506608). This QTN was confirmed across all models and timepoints. A total of 153 candidate genes, including genes with roles in pathogen recognition and signaling, cell wall biosynthesis, oxidative burst, and regulation of DNA transcription, were observed surrounding QTN-targeted regions. Further gene expression analysis on the QTNs identified in this study will provide insights into defense-related genes that can be further incorporated into breeding of new chickpea cultivars to minimize fungicide applications required for successful chickpea production in the US Northern Great Plains., Competing Interests: Declarations. Competing interests: The authors declare no competing interests., (© 2024. The Author(s).)

Background: Phelipanche aegyptiaca is one of the most noxious parasitic weedy broomrapes in Xinjiang, China. Understanding its morphological polymorphism and genetic diversity can support effective control strategies. This study investigated the morphological and genetic diversity among and within populations from different geographical regions and host species across Xinjiang to characterize their relationships., Results: Thirteen ISSR primers were used, resulting in 173 clear bands, 172 of which (99%) were polymorphic. Significant genetic variations were observed within regional and host groups, while variation among groups was relatively low. Gene flow was frequent, with a significant correlation of 1.57 between geographic regions and 5.57 between host species groups. Morphological traits exhibited substantial variability, with diverse coefficients ranging from 16% to 50%. Canonical correspondence analysis indicated that samples primarily clustered by region, not by host species. There was a significant correlation between morphological and genetic diversity across geographical groups., Conclusion: The findings suggest that genetic and morphological diversity are key factors in the expansion of P. aegyptiaca's host-range and its spread. Morphological diversity appears to result from the interaction between genetic variation and environmental factors. This study offers new insights into the adaptation and evolution of P. aegyptiaca in relation to its genetic, morphological diversity and dissemination. © 2024 Society of Chemical Industry., (© 2024 Society of Chemical Industry.)

Potato (Solanum tuberosum L.) is one of the most important food crops globally and is especially vulnerable to heat stress. However, substantial knowledge gaps remain in our understanding of the developmental mechanisms associated with tuber responses to heat stress. This study used whole-plant physiology, transcriptomics, and phytohormone profiling to elucidate how heat stress affects potato tuber development. When plants were grown in projected future elevated temperature conditions, abscisic acid (ABA) levels decreased in leaf and tuber tissues, whereas rates of leaf carbon assimilation and stomatal conductance were not significantly affected compared to those plants grown in historical temperature conditions. While plants grown in projected future elevated temperature conditions initiated more tubers per plant on average, there was a 66% decrease in mature tubers at the final harvest compared to those plants grown in historical temperature conditions. We hypothesize that reduced tuber yields at elevated temperatures are not due to reduced tuber initiation, but due to impaired tuber filling. Transcriptomic analysis detected significant changes in the expression of genes related to ABA response, heat stress, and starch biosynthesis. The tuberization repressor genes SELF-PRUNING 5G (StSP5G) and CONSTANS-LIKE1 (StCOL1) were differentially expressed in tubers grown in elevated temperatures. Two additional known tuberization genes, IDENTITY OF TUBER 1 (StIT1) and TIMING OF CAB EXPRESSION 1 (StTOC1), displayed distinct expression patterns under elevated temperatures compared to historical temperature conditions but were not differentially expressed. This work highlights potential gene targets and key developmental stages associated with tuberization to develop potatoes with greater heat tolerance., Competing Interests: Conflict of interest statement. None declared., (© The Author(s) 2024. Published by Oxford University Press on behalf of American Society of Plant Biologists.)

Soil waterlogging and drought correspond to contrasting water extremes resulting in plant dehydration. Dehydration in response to waterlogging occurs due to impairments to root water transport, but no previous study has addressed whether limitations to water transport occur beyond this organ or whether dehydration alone can explain shoot impairments. Using common bean (Phaseolus vulgaris) as a model species, we report that waterlogging also impairs water transport in leaves and stems. During the very first hours of waterlogging, leaves transiently dehydrated to water potentials close to the turgor loss point, possibly driving rapid stomatal closure and partially explaining the decline in leaf hydraulic conductance. The initial decline in leaf hydraulic conductance (occurring within 24 h), however, surpassed the levels predicted to occur based solely on dehydration. Constraints to leaf water transport resulted in a hydraulic disconnection between leaves and stems, furthering leaf dehydration during waterlogging and after soil drainage. As leaves dehydrated later during waterlogging, leaf embolism initiated and extensive embolism levels amplified leaf damage. The hydraulic disconnection between leaves and stems prevented stem water potentials from declining below the threshold for critical embolism levels in response to waterlogging. This allowed plants to survive waterlogging and soil drainage. In summary, leaf and stem dehydration are central in defining plant impairments in response to waterlogging, thus creating similarities between waterlogging and drought. Yet, our findings point to the existence of additional players (likely chemicals) partially controlling the early declines in leaf hydraulic conductance and contributing to leaf damage during waterlogging., Competing Interests: Conflict of interest statement. None declared., (© The Author(s) 2024. Published by Oxford University Press on behalf of American Society of Plant Biologists.)

Heat stress affects various components of photosynthetic machinery of which Rubisco activation inhibition due to heat sensitive Rubisco activase (RCA) is the most prominent. Detailed comparison of RCA coding genes identified a tandem duplication event in the grass family lineage where the duplicated genes showed very different evolutionary pattern. One of the two genes showed high level of sequence conservation whereas the second copy, although present only 1.5 kb away, was highly variable among various plant species because of loss of introns, alternative splicing and loss of the last exon coding redox regulated C-terminal extension domain. Gene specific expression analysis, both at the transcription as well as the protein level, showed very different expression pattern of the two RCA copies. Expression of the highly conserved copy was higher under normal plant growing conditions that decreased many folds under heat stress with substantial genotypic variation, but the variable copy showed much higher expression under heat stress conditions across all grass species. The cultivated rice has only one functional gene as the second copy became nonfunctional due to multiple deletions but Oryza brachyantha and Oryza australiensis still have two functional Rca genes. Detailed analysis of the promoter region of the two copies among various plant species showed insertion of several transposable elements harboring heat responsive elements in the heat inducible copy of the gene. The conserved RCA copy of wheat didn't have any transposable insertions whereas in that of maize has one heat shock element and sorghum had two. It would be interesting to study if the higher level of heat stress tolerance observed in sorghum and maize is associated with the differences observed for RCA. Key message This manuscript is reporting a grass family-specific tandem duplication event in RCA genes of cereals. The duplicated copies underwent neo-functionalization to evolve novel function to deal with heat stress. One copy of the tandem duplication maintained a high level of conservation whereas the second copy showed tremendous divergence to evolve species specific function of the gene. Specific function to respond to heat stress likely evolved via the insertion of various heat responsive elements carried by transposable elements., Competing Interests: Declarations. Conflict of interest: The authors declare no conflict of interest., (© 2024. The Author(s), under exclusive licence to Springer Nature B.V.)

Background: The genome-wide association study (GWAS) is a powerful method for mapping quantitative trait loci (QTL). However, standard GWAS can detect only QTL that segregate in the mapping population. Crossing populations with different characteristics increases genetic variability but F2 or back-crosses lack mapping resolution due to the limited number of recombination events. This drawback can be overcome with advanced intercross line (AIL) populations, which increase the number recombination events and provide a more accurate mapping resolution. Recent studies in humans have revealed ancestry-dependent genetic architecture and shown the effectiveness of admixture mapping in admixed populations., Results: Through the incorporation of line-of-origin effects and GWAS on an F 9 AIL population, we identified genes that affect body weight at eight weeks of age (BW8) in chickens. The proposed ancestral-haplotype-based GWAS (testing only the origin regardless of the alleles) revealed three new QTLs on GGA12, GGA15, and GGA20. By using the concepts of ancestral homozygotes (individuals that carry two haplotypes of the same origin) and ancestral heterozygotes (carrying one haplotype of each origin), we identified 632 loci that exhibited high-parent (the heterozygote is better than both parents) and mid-parent (the heterozygote is better than the median of the parents) dominance across 12 chromosomes. Out of the 199 genes associated with BW8, EYA1, PDE1C, and MYC were identified as the best candidate genes for further validation., Conclusions: In addition to the candidate genes reported in this study, our research demonstrates the effectiveness of incorporating ancestral information in population genetic analyses, which can be broadly applicable for genetic mapping in populations generated by ancestors with distinct phenotypes and genetic backgrounds. Our methods can benefit both geneticists and biologists interested in the genetic determinism of complex traits., Competing Interests: Declarations. Ethics approval and consent to participate: The animal welfare committee of the State Key Laboratory of Animal Biotech Breeding approved all animal care and experimental procedures with approval number SKLAB-2014-06-07. Consent for publication: Not applicable. Competing interests: The authors declare no competing interests., (© 2024. The Author(s).)

This study examined the growth parameters of both glyphosate-susceptible and glyphosate-resistant biotypes of Amaranthus palmeri , designated as GA2005 and GA2017, respectively. A two-year microplot field study was conducted to assess their growth characteristics. Scheduled destructive harvests on named harvest days (HD) were conducted to collect measurements for further calculation of net assimilation rate (NAR; g m -2  day -1 ), specific leaf area (SLA), leaf weight ratio (LWR), stem-to-leaf ratio (SLR), leaf area index (LAI), leaf area ratio (LAR; cm 2 g -1 ), leaf area duration (LAD; days), relative growth rate (RGR; g.g -1  day -1 ) and plant volume (m 3 ). In addition, stem diameter, number of leaves, and Chlorophyll content (μmol m 2 ) were determined. The main objective was to identify growth parameters that differentiate biotypes along the plant life cycle. While certain growth parameters showed no variation among biotypes, differences in leaf area index (LAI) over HD and chlorophyll content and leaf area duration (LAD) were observed as the main effects. Glyphosate-resistant biotypes exhibited higher LAD and chlorophyll content, potentially conferring a competitive advantage, especially in heavily used glyphosate environments. The study highlights the complexity of intraspecific genetic differentiation, adaptation, and environmental factors affecting A. palmeri. It may offer insights into biotype distinction and resistance spread while advancing our comprehension of species adaptation and growth strategies for enhanced control., Competing Interests: The authors declare no conflicts of interest., (© 2024 The Author(s). Plant‐Environment Interactions published by New Phytologist Foundation and John Wiley & Sons Ltd.)

Chicken production, both in the local and commercial sectors, contributes significantly to human livelihood and food security. Precise use of diverse genetic resources is primary in breeding programs. The study analyzed the genetic diversity and population structure of commercial chickens and indigenous chicken ecotypes from three different agro-ecological zones (Semi-Deciduous Rainforest Zone, Guinea Savannah, and Coastal Savannah) using SilicoDArT and SNP markers, utilizing whole-genome sequencing and phenotypic data. Phenotypic data were collected from 72 indigenous chicken ecotypes across the three AEZs, and 32 commercial birds kept at the Kwame Nkrumah University of Science and Technology (KNUST). DNA samples used for sequencing were obtained from 88 chickens (62 indigenous chicken ecotypes and 26 commercial chickens). A total of 54,995 SilicoDArT and 85,396 SNPs markers were generated from DArTseq genotyping. After filtering, 44,784 SilicoDArT and 58,353 SNP were used for genetic diversity and population structure analysis. Both markers showed high reproducibility and call rate. Polymorphic information content (PIC) values ranged from 0.00 to 0.50, while ≥ 50 % showed PIC values more than the median. Furthermore, we obtained F ST values, Nei's genetic distance, dendrogram analysis, and principal component analysis (PCA) of commercial and indigenous chickens. The F ST and Nei's genetic distance showed that there is high genetic diversity between the commercial chickens and the indigenous chicken ecotypes. However, there was low genetic diversity among the indigenous chicken ecotypes. The PCA analysis indicated a clear separation between the commercial and indigenous chicken ecotypes, while no clear separation was observed between the indigenous chicken ecotypes. The phenotypic data and the dendrogram indicated that naked and frizzle genes do not markedly alter the genetics of indigenous and commercial birds, and their influence on economic traits may be solely determined by the prevailing environmental conditions. The results indicate that there is high genetic differentiation between commercial and indigenous chickens based on SilicoDArT and SNP markers. The indigenous chickens from the agro-ecological zones have low genetic diversity and might have a common origin. Naked neck and frizzle genes do not markedly alter the genetic performance of birds in terms of economic traits. Therefore, the superiority of birds carrying these genes in economic traits may be solely due to environmental variation., 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 © 2024 Elsevier B.V. All rights reserved.)

Similar to cellulose synthases (CESAs), cellulose synthase-like D (CSLD) proteins synthesize β-1,4-glucan in plants. CSLDs are important for tip growth and cytokinesis, but it was unknown whether they form membrane complexes in vivo or produce microfibrillar cellulose. We produced viable CESA-deficient mutants of the moss Physcomitrium patens to investigate CSLD function without interfering CESA activity. Microscopy and spectroscopy showed that CESA-deficient mutants synthesize cellulose microfibrils that are indistinguishable from those in vascular plants. Correspondingly, freeze-fracture electron microscopy revealed rosette-shaped particle assemblies in the plasma membrane that are indistinguishable from CESA-containing rosette cellulose synthesis complexes (CSCs). Our data show that proteins other than CESAs, most likely CSLDs, produce cellulose microfibrils in P. patens protonemal filaments. The data suggest that the specialized roles of CSLDs in cytokinesis and tip growth are based on differential expression and different interactions with microtubules and possibly Ca 2+ , rather than structural differences in the microfibrils they produce.

Potato ( Solanum tuberosum ) is the third most important food crop in the world. Although the potato genome has been fully sequenced, functional genomics research of potato lags relative to other major food crops due primarily to the lack of a model experimental potato line. Here, we present a diploid potato line, 'Jan', which possesses all essential characteristics for facile functional genomics studies. Jan has a high level of homozygosity after seven generations of self-pollination. Jan is vigorous and highly fertile with outstanding tuber traits, high regeneration rates, and excellent transformation efficiencies. We generated a chromosome-scale genome assembly for Jan, annotated genes, and identified syntelogs relative to the potato reference genome assembly DMv6.1 to facilitate functional genomics. To miniaturize plant architecture, we developed two "mini-Jan" lines with compact and dwarf plant stature using CRISPR/Cas9-mediated mutagenesis targeting the Dwarf and Erecta genes related to growth. Mini-Jan mutants are fully fertile and will permit higher-throughput studies in limited growth chamber and greenhouse space. Thus, Jan and mini-Jan provide an outstanding model system that can be leveraged for gene editing and functional genomics research in potato., Competing Interests: Conflict of interest The authors have not declared a conflict of interest.

Here, we examine how radiation impacts the dissolution behavior of boehmite by subjecting dry nanoparticles of different sizes to 60 Co γ radiation and subsequently analyzing their dissolution behavior in caustic solutions as a function of temperature. The measured kinetics show that irradiation with an amount 228.24 Mrad significantly slows the dissolution rate, particularly for smaller sizes at lower temperatures. Specifically, the temperature-dependent dissolution rates of irradiated 20 nm boehmite versus pristine material in 3 M NaOH solutions were several times lower (e.g., rate constant of 0.026 vs 0.075 h -1 at 60 °C), with an apparent activation energy 40 kJ mol -1 higher. Although various imaging techniques and X-ray diffraction measurements consistently revealed no obvious differences between pristine and irradiated samples, after irradiation significant binding energy shifts were detected in the X-ray photoelectron Spectroscopy peaks of Al 2p and O 1s, and a change in their relative intensities indicated a lower O/Al ratio. This suggests that γ-irradiation may stabilize boehmite particle surfaces by driving their chemistry and structure toward more stable aluminum oxide forms. This finding may help explain slower dissolution rates of boehmite in nuclear waste and may be useful for the development of more robust predictive models and effective strategies for waste processing.

Legacy phosphorus (P) is a concept advanced by Dr. Andrew Sharpley and colleagues that was originally applied to the persistence of anthropogenic signatures in watersheds, and it has since been adopted in a diversity of settings to help guide the science and management of P. Following Sharpley's example to develop consensus-based science, we considered contrasting perspectives on legacy P and defined legacy P as those stores within the environment that arise from historic human activity excluding "natural" or "background" geogenic sources. Legacy P is not restricted to one system or setting; it may reside in soils, sediments, biota, and water bodies. Legacy P has been estimated by fluxes (inputs minus outputs of P to a system) or, equivalently, by mass stocks (total minus geogenic). Because the origin of P in the environment cannot currently be directly quantified, we recommend that researchers report "total P" to track wider watershed P stocks and fluxes of P that include legacy P. We recognize that the definition of legacy P will continue to evolve as we continue to work toward consensus. Ultimately, the final definition of legacy P has consequences for the implementation and success of regulatory and voluntary strategies for legacy P management in agricultural systems. We support continued progress toward a consensus-backed, research-grounded definition for legacy P that is widely applicable yet useful for guiding management and policy., (© 2024 The Author(s). Journal of Environmental Quality published by Wiley Periodicals LLC on behalf of American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America. This article has been contributed to by U.S. Government employees and their work is in the public domain in the USA.)

Tall fescue ( Festuca arundinacea ) is a widely adopted forage and turf grass. This is partly due to a fungal endophyte, Epichloë coenophiala, which confers both abiotic and biotic stress tolerance. Although PCR primers exist to test for endophyte presence, these were not designed to quantitatively analyze the amount of fungus in the plant. In this study, we test different primer sets for quantitative biomass analysis of tall fescue and E. coenophiala. We report standard curves, r-squared, and efficiency values for every primer set and identify those most suited for qPCR in this system., Competing Interests: The authors declare that there are no conflicts of interest present., (Copyright: © 2024 by the authors.)

The dry forests of northern Peru are dominated by the legumous tree Neltuma pallida which is adapted to hot arid and semiarid conditions in the tropics. Despite having been successfully introduced in multiple other areas around the world, N. pallida is currently threatened in its native area, where it is invaluable for the dry forest ecosystem and human subsistence. A major tool for enhancing ecosystem conservation and understanding the adaptive properties of N. pallida to dry forest ecosystems is the construction of a reference genome sequence. Here, we report on a high-quality reference genome for N. pallida. The final genome assembly size is 403.7 Mb, consisting of 14 pseudochromosomes and 63 scaffolds with an N50 size of 26.2 Mb and a 34.3% GC content. Use of Benchmarking Universal Single Copy Orthologs revealed 99.2% complete orthologs. Long terminal repeat elements dominated the repetitive sequence content which was 51.2%. Genes were annotated using N. pallida transcripts, plant protein sequences, and ab initio predictions resulting in 22,409 protein-coding genes encoding 24,607 gene models. Comparative genomic analysis showed evidence of rapidly evolving gene families related to disease resistance, transcription factors, and signaling pathways. The chromosome-scale N. pallida reference genome will be a useful resource for understanding plant evolution in extreme and highly variable environments., (© The Author(s) 2024. Published by Oxford University Press on behalf of The Genetics Society of America.)

Dietary intake can be an important exposure route to per- and polyfluoroalkyl substances (PFASs). Little is known about the bioaccumulation of emerging per- and polyfluoroalkyl ether acids (PFEAs) in garden produce from PFAS-impacted communities and the associated dietary exposure risk. In this study, 53 produce samples were collected from five residential gardens near a fluorochemical manufacturer. Summed PFAS concentrations ranged from 0.0026 to 38 ng/g wet weight of produce, and water-rich produce exhibited the highest PFAS levels. The PFAS signature was dominated by PFEAs, and hexafluoropropylene oxide-dimer acid (commonly known as GenX) was detected in 72% of samples. Based on average measured GenX concentrations, chronic-exposure daily limits were as low as 289 g produce/day for children (3-6 yr). This analysis does not consider other PFEAs that were present at higher concentrations, but for which reference doses were not available. This study revealed that consuming residential garden produce grown in PFAS-impacted communities can be an important exposure pathway.

This strategic plan summarizes the major accomplishments achieved in the last quinquennial by the soybean [Glycine max (L.) Merr.] genetics and genomics research community and outlines key priorities for the next 5 years (2024-2028). This work is the result of deliberations among over 50 soybean researchers during a 2-day workshop in St Louis, MO, USA, at the end of 2022. The plan is divided into seven traditional areas/disciplines: Breeding, Biotic Interactions, Physiology and Abiotic Stress, Functional Genomics, Biotechnology, Genomic Resources and Datasets, and Computational Resources. One additional section was added, Training the Next Generation of Soybean Researchers, when it was identified as a pressing issue during the workshop. This installment of the soybean genomics strategic plan provides a snapshot of recent progress while looking at future goals that will improve resources and enable innovation among the community of basic and applied soybean researchers. We hope that this work will inform our community and increase support for soybean research., (© 2024 The Author(s). The Plant Genome published by Wiley Periodicals LLC on behalf of Crop Science Society of America.)

Root systems are uniquely adapted to fluctuations in external nutrient availability. In response to suboptimal nitrogen conditions, plants adopt a root foraging strategy that favors a deeper and more branched root architecture, enabling them to explore and acquire soil resources. This response is gradually suppressed as nitrogen conditions improve. However, the root hairless mutant buzz in Brachypodium distachyon shows a constitutive nitrogen-foraging phenotype with increased root growth and root branching under nitrate-rich conditions. To investigate how this unique root structure and root hair morphology in the buzz mutant affects nitrate metabolism, we measured the expression of nitrate-responsive genes, nitrate uptake and accumulation, nitrate reductase activity, and nitrogen use efficiency. We found that nitrate responses were upregulated by low nitrate conditions in buzz relative to wild type and correlated with increased expression of nitrate transport genes. In addition, buzz mutants showed increased nitrate uptake and a higher accumulation of nitrate in shoots. The buzz mutant also showed increased nitrate reductase activity in the shoots under low nitrate conditions. However, developmentally mature wild-type and buzz plants grown under low nitrate had similar nitrogen use efficiencies. These findings suggest that BUZZ influences nitrate signaling and that enhanced responsiveness to nitrate is required in buzz seedlings to compensate for the lack of root hairs. These data question the importance of root hairs in enhancing nitrate uptake and expand our understanding of how root hairs in grasses affect physiological responses to low nitrate availability., (© 2024 The Author(s). The Plant Journal published by Society for Experimental Biology and John Wiley & Sons Ltd.)

Access to broad genomic resources and closely linked marker-trait associations for common beans (Phaseolus vulgaris L.) can facilitate development of improved varieties with increased yield, improved market quality traits, and enhanced disease resistance. The emergence of virulent races of anthracnose (caused by Colletotrichum lindemuthianum) and bean common mosaic virus (BCMV) highlight the need for improved methods to identify and incorporate pan-genomic variation in breeding for disease resistance. We sequenced the P. vulgaris Andean Diversity Panel (ADP) and performed a genome-wide association study (GWAS) to identify associations for resistance to BCMV and eight races of anthracnose. Historical single nucleotide polymorphism (SNP)-chip and phenotypic data enabled a three-way comparison between SNP-chip, reference-based whole genome shotgun sequence (WGS)-SNP, and reference-free k-mer (short nucleotide subsequence) GWAS. Across all traits, there was excellent concordance between SNP-chip, WGS-SNP, and k-mer GWAS results-albeit at a much higher marker resolution for the WGS data sets. Significant k-mer haplotype variation revealed selection of the linked I-gene and Co-u traits in North American breeding lines and cultivars. Due to structural variation, only 9.1 to 47.3% of the significantly associated k-mers could be mapped to the reference genome. Thus, to determine the genetic context of cis-associated k-mers, we generated draft whole genome assemblies of four ADP accessions and identified an expanded local repertoire of disease resistance genes associated with resistance to anthracnose and BCMV. With access to variant data in the context of a pan-genome, high resolution mapping of agronomic traits for common bean is now feasible., (© 2024 The Author(s). The Plant Genome published by Wiley Periodicals LLC on behalf of Crop Science Society of America.)

With every 1°C rise in temperature, yields are predicted to decrease by 5%-6% for both cool and warm season crops, threatening food production, which should double by 2050 to meet the global demand. While high night-time temperature (HNT) stress is expected to increase due to climate change, limited information is available on the genetic control of the trait, especially in wheat (Triticum aestivum L.). To identify genes controlling the HNT trait, we evaluated a doubled haploid (DH) population developed from a cross between an HNT tolerant line KSG1203 and KSG0057, a selection out of a mega variety PBW343 from South East Asia that turned out to be HNT susceptible. The population, along with the parents, were evaluated under 30°C night-time (HNT stress) keeping the daytime temperature to normal 22°C. The same daytime and 16°C night-time temperature were used as a control. The HNT treatment negatively impacted all agronomic traits under evaluation, with a percentage reduction of 0.5%-35% for the tolerant parent, 8%-75% for the susceptible parent, and 8%-50% for the DH population. Performed using sequencing-based genotyping, quantitative trait locus (QTL) mapping identified 19 QTLs on 13 wheat chromosomes explaining 9.72%-28.81% of cumulative phenotypic variance for HNT stress tolerance, along with 13 that were for traits under normal growing conditions. The size of QTL intervals ranged between 0.021 and 97.48 Mb, with the number of genes ranging between 2 and 867. A candidate gene analysis for the smallest six QTL intervals identified eight putative candidates for night-time heat stress tolerance., (© 2024 The Author(s). The Plant Genome published by Wiley Periodicals LLC on behalf of Crop Science Society of America.)

Exploration of novel alleles from ex situ collection is still limited in modern plant breeding as these alleles exist in genetic backgrounds of landraces that are not adapted to modern production environments. The practice of backcross breeding results in preservation of the adapted background of elite parents but leaves little room for novel alleles from landraces to be incorporated. Selection of adaptation-associated linkage blocks instead of the entire adapted background may allow breeders to incorporate more of the landrace's genetic background and to observe and evaluate novel alleles. Important adaptation-associated linkage blocks would have been selected over multiple cycles of breeding and hence are likely to exhibit signatures of positive selection or selective sweeps. We conducted genome-wide scan for candidate selective sweeps (CSS) using F st , Rsb, and xpEHH in state, regional, spring, winter, and market-class population pairs and reported 446 CSS in 19 population pairs over time and 1033 CSS in 44 population pairs across geography and class. Further validation of these CSS in specific breeding programs may lead to identification of sets of loci that can be selected to restore population-specific adaptation in pre-breeding germplasms., (© 2024 The Author(s). The Plant Genome published by Wiley Periodicals LLC on behalf of Crop Science Society of America.)

Phosphorus (P) is essential for growing crops, but the supply of high-quality phosphate rock reserves used for fertilizer production is finite while losses of P from the food/waste system cause considerable environmental damage. A variety of emerging approaches in biotechnology are reviewed that hold promise for improving the sustainability of P use in the food/water systems. These include improved sensors, cell culture approaches to meat production, bio-based P adsorption and transformation strategies, advancements in understanding of polyphosphate-accumulating organisms, and new approaches involving biomineralization and anaerobic treatment. By advancing these technologies to scale, progress can be made in developing a circular phosphorus economy that improves food security while protecting drinking water and aquatic ecosystems., Competing Interests: Declaration of Competing Interest James Elser reports financial support was provided by National Science Foundation. Douglas F. Call, Jessica A. Deaver, Owen W. Duckworth, Brooke K. Mayer, Eric S. McLamore, Bruce E. Rittmann, Maheen Mahmood, and Paul Westerhoff report financial support was provided by National Science Foundation. If there are other authors, they 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 © 2024 The Authors. Published by Elsevier Ltd.. All rights reserved.)

Adequate micronutrient concentrations in crops are essential for human health and agricultural productivity. However, 30% of plants growing on cultivated soils worldwide are deficient in iron (Fe). Because of low micronutrient bioavailability, graminaceous plants have evolved to exude small molecules, called phytosiderophores, into the soil environment, which strongly complex and promote uptake of trace elements. The development of a synthetic phytosiderophore, proline-2'-deoxymugeneic acid (PDMA), has been shown to promote Fe uptake in rice plants; however, its binding capabilities with other metals, which may impact the ability to promote the uptake of Fe and other trace nutrient metals commonly found in soils, remain unknown. We conducted spectrophotometric titrations to determine the stability constants (logK) of PDMA complexes with Mn(II), Co(II), Cu(II), Ni(II), and Zn(II). We determined that PDMA complex stability constants correlated with: (1) the hydrolysis constants of metal ions (logK OH ) in complexes; (2) the ionic potential of complexed metals; and (3) the corresponding complex stability constants of other mugineic acid type phytosiderophores, as well as the trishydroxamate microbial siderophore DFOB. These correlations demonstrate the potential, and limitations, on our ability to predict the stability of phytosiderophore complexes with metal ions with different physicochemical properties and with potentially different coordination structures., Competing Interests: Declarations. Competing interests: The authors declare no competing interests., (© 2024. The Author(s), under exclusive licence to Springer Nature B.V.)

Background: Considering the nutritional value and adaptability of quinoa, integrating it into African diets could enhance food and nutrition security, contingent on the acceptability of quinoa-based foods. This study therefore determined consumer acceptability of six stiff porridge (nsima) samples, their sensory profiles, and their emotion profiles. The samples comprised controls made from whole corn flour, dehulled corn flour, and soaked, dehulled corn flour and from 1:1 blends of quinoa and each corn flour type., Results: Despite quinoa being unfamiliar, none of the stiff porridge samples prepared using 1:1 blend of quinoa and corn flour was disliked (liking score of ≤4 on a 9-point hedonic scale). Sensory properties and emotions both had significant (P < 0.05) effects on consumer acceptability. When samples were perceived to be bitter, sticky, and thick, there was an overall mean reduction in liking of 2.3, 1.0, and 0.3, respectively. With regard to emotions, the highest positive mean impact of 1.6 was associated with feeling satisfied followed by being happy and nostalgic (1.4). The sensory and emotion profiles of nsima prepared using whole corn flour were like those of quinoa-based nsima samples. However, profiles of nsima samples from dehulled corn, and soaked dehulled corn flour, respectively, were considered ideal., Conclusion: Quinoa-based nsima can be adopted easily by the current consumers of whole corn flour nsima in Malawi and possibly in other African countries with similar dietary inclinations. However, there is a need to find effective and feasible methods of removing saponin from quinoa to maximize acceptability of the resulting quinoa-based nsima. © 2024 Society of Chemical Industry., (© 2024 Society of Chemical Industry.)

Background: We have previously shown that the expression of a constitutively active nitrate reductase variant and the suppression of CLCNt2 gene function (belonging to the chloride channel (CLC) gene family) in field-grown tobacco reduces tobacco-specific nitrosamines (TSNA) accumulation in cured leaves and cigarette smoke. In both cases, TSNA reductions resulted from a strong diminution of free nitrate in the leaf, as nitrate is a precursor of the TSNA-producing nitrosating agents formed during tobacco curing and smoking. These nitrosating agents modify tobacco alkaloids to produce TSNAs, the most problematic of which are NNN (N-nitrosonornicotine) and NNK (4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone). The expression of a deregulated nitrate reductase enzyme (DNR) that is no longer responsive to light regulation is believed to diminish free nitrate pools by immediately channeling incoming nitrate into the nitrate assimilation pathway. The reduction in nitrate observed when the two tobacco gene copies encoding the vacuolar nitrate transporter CLCNt2 were down-regulated by RNAi-mediated suppression or knocked out using the CRISPR-Cas technology was mechanistically distinct; likely attributable to the inability of the tobacco cell to efficiently sequester nitrate into the vacuole where this metabolite is protected from further assimilation. In this study, we used transcriptomic and metabolomic analyses to compare the nitrate assimilation response in tobacco plants either expressing DNR or lacking CLCNt2 function., Results: When grown in a controlled environment, both DNR and CLCNt2-KO (CLCKO) plants exhibited (1) reduced nitrate content in the leaf; (2) increased N-assimilation into the amino acids Gln and Asn; and (3) a similar pattern of differential regulation of several genes controlling stress responses, including water stress, and cell wall metabolism in comparison to wild-type plants. Differences in gene regulation were also observed between DNR and CLCKO plants, including genes encoding nitrite reductase and asparagine synthetase., Conclusions: Our data suggest that even though both DNR and CLCKO plants display common characteristics with respect to nitrate assimilation, cellular responses, water stress, and cell wall remodeling, notable differences in gene regulatory patterns between the two low nitrate plants are also observed. These findings open new avenues in using plants fixing more nitrogen into amino acids for plant improvement or nutrition perspectives., Competing Interests: Declarations. Ethics approval and consent to participate: Not applicable. Consent for publication: Not applicable. Competing interests: LB, JB, NS, and SG are employees of Philip Morris Products S.A. with NS and SG having equity or stocks. JL and RED are employees of North Carolina State University (NCSU). There are two patents relating to the content of this manuscript. Author LB has a patent (WO2014096283A2) and authors LB, JU, and RED have a joint patent (WO2016046288A1). Philip Morris Products S.A. is a tobacco manufacturer and was involved in the review and approval of the manuscript for publication., (© 2024. The Author(s).)

Predicting phenotypes from a combination of genetic and environmental factors is a grand challenge of modern biology. Slight improvements in this area have the potential to save lives, improve food and fuel security, permit better care of the planet, and create other positive outcomes. In 2022 and 2023 the first open-to-the-public Genomes to Fields (G2F) initiative Genotype by Environment (GxE) prediction competition was held using a large dataset including genomic variation, phenotype and weather measurements and field management notes, gathered by the project over nine years. The competition attracted registrants from around the world with representation from academic, government, industry, and non-profit institutions as well as unaffiliated. These participants came from diverse disciplines include plant science, animal science, breeding, statistics, computational biology and others. Some participants had no formal genetics or plant-related training, and some were just beginning their graduate education. The teams applied varied methods and strategies, providing a wealth of modeling knowledge based on a common dataset. The winner's strategy involved two models combining machine learning and traditional breeding tools: one model emphasized environment using features extracted by Random Forest, Ridge Regression and Least-squares, and one focused on genetics. Other high-performing teams' methods included quantitative genetics, machine learning/deep learning, mechanistic models, and model ensembles. The dataset factors used, such as genetics; weather; and management data, were also diverse, demonstrating that no single model or strategy is far superior to all others within the context of this competition., (Published by Oxford University Press on behalf of The Genetics Society of America 2024.)