Promoter deletion in the soybean Compact mutant leads to overexpression of a gene with homology to the C20-gibberellin 2-oxidase family.

Height is a critical component of plant architecture, significantly affecting crop yield. The genetic basis of this trait in soybean remains unclear. In this study, we report the characterization of the Compact mutant of soybean, which has short internodes. The candidate gene was mapped to chromosome 17, and the interval containing the causative mutation was further delineated using biparental mapping. Whole-genome sequencing of the mutant revealed an 8.7 kb deletion in the promoter of the Glyma.17g145200 gene, which encodes a member of the class III gibberellin (GA) 2-oxidases. The mutation has a dominant effect, likely via increased expression of the GA 2-oxidase transcript observed in green tissue, as a result of the deletion in the promoter of Glyma.17g145200. We further demonstrate that levels of GA precursors are altered in the Compact mutant, supporting a role in GA metabolism, and that the mutant phenotype can be rescued with exogenous GA3. We also determined that overexpression of Glyma.17g145200 in Arabidopsis results in dwarfed plants. Thus, gain of promoter activity in the Compact mutant leads to a short internode phenotype in soybean through altered metabolism of gibberellin precursors. These results provide an example of how structural variation can control an important crop trait and a role for Glyma.17g145200 in soybean architecture, with potential implications for increasing crop yield.

Adolescent: provider connectedness and STI risk reduction following a brief alcohol intervention: findings from a randomized controlled trial.

Objective: Given the frequent co-occurrence between alcohol use and sexual behavior among adolescents, alcohol interventions may play a role in helping prevent sexually transmitted infections (STIs) in this age group. Psychotherapy "common factors" are one potential active ingredient in intervention efficacy. Thus, the purpose of this study was to evaluate the influence of a critical common factor, adolescent: provider connectedness, on STI risk reduction at 3 months post-intervention. Methods: Community-based youth (N = 168) were randomized to two 60-min individual sessions of either motivational interviewing (MI) or brief adolescent mindfulness (BAM). Logistic regressions predicted post-intervention positive STI from adolescent: provider connectedness, intervention condition, and their interaction. Path analytic models tested post-intervention hazardous drinking as a mediator of the association between adolescent: provider connectedness and reduction in STI risk at 3-month follow-up. Results: Stronger adolescent: provider connectedness reduced risk of STI at 3 months post-intervention, with no differences by treatment condition. A mediational relationship between adolescent: provider connectedness and STI risk via hazardous drinking was not observed. Conclusion: Psychotherapeutic common factors, including adolescent: provider connectedness, may be important in mitigating adolescent health risk in behavioral interventions, above and beyond intervention condition and beyond the target behavior of the intervention.

Twin study of caffeine use, ADHD, and disrupted sleep in ABCD youth.

OBJECTIVE: Evidence suggests that caffeine use disproportionately impacts sleep functioning among youth with attention-deficit/hyperactivity disorder (ADHD). The present study aimed to examine the association of caffeine use with disrupted sleep, and to test moderating effects of ADHD, by leveraging differences within twin pairs to explore potential quasi-causal (i.e., within-pair) effects. METHOD: N = 765 complete same-sex twin pairs (mean age at baseline = 10.14 [SD = .5]; 49% girls; 73% white) from the ABCD study reported caffeine use and frequency of disrupted sleep; parents reported youth ADHD symptoms. Cotwin control analyses predicted disrupted sleep from caffeine use, ADHD, and their interaction at ages 10 and 12. RESULTS: Neither quasi-causal within-pair effects of caffeine use on disrupted sleep, nor a moderating role of ADHD were identified. Posthoc biometric models indicated that genetic and environmental influences on these phenotypes may change over time, such that genetic influences on disrupted sleep began to emerge more robustly around early adolescence. Additionally, caffeine use and disrupted sleep, but not ADHD, displayed overlapping genetic influences (12-13% of total phenotypic variance) at age 10. CONCLUSIONS: In a sample of preadolescent twin pairs from the ABCD Study, we did not observe evidence that caffeine use was quasi-causally associated with disrupted sleep at this early developmental stage. However, caffeine use and disrupted sleep emerged with shared etiologic influences. In sum, this study sets the stage for examining these dynamic patterns in future examinations of this critical and timely ABCD study sample, as genetic and environmental influences on behavior are known to change throughout development. (PsycInfo Database Record (c) 2023 APA, all rights reserved).

Examining the influence of adolescent:provider alliance on youth hazardous drinking: Findings from a randomized controlled trial.

PURPOSE: Behavioral interventions to reduce hazardous drinking are only moderately successful in promoting sustained behavior change and post-intervention effect sizes among adolescents remain modest. This study aimed to explore a relevant therapeutic active ingredient, adolescent:provider alliance, as a moderator of short-term (3 month) adolescent intervention outcomes within the course of a larger parent randomized control trial (RCT). METHODS: Participants were community-based youth engaged in hazardous drinking (N = 168) who were randomized to 2 sessions of either motivational interviewing (MI) or mindfulness (brief adolescent mindfulness; BAM). Youth reported pre-intervention hazardous drinking at baseline and rated therapeutic alliance (a metric of adolescent:provider "connectedness" that helps facilitate working relationships during interventions) immediately post-intervention; they reported hazardous drinking again at 3 months post-intervention. Negative binomial regressions predicted post-intervention hazardous drinking score from adolescent:provider alliance, intervention condition, and their interaction. RESULTS: Mean hazardous drinking was reduced by 34-40 % across both intervention conditions, with no significant between-condition differences. Stronger adolescent:provider alliance was associated with lower hazardous drinking scores at 3 months, but this effect was attenuated after controlling for baseline hazardous drinking. Contrary to predictions, adolescent:provider alliance did not appear to moderate the effect of intervention condition in this sample of young people engaged in hazardous drinking. CONCLUSIONS: Consistent with prior literature, baseline hazardous drinking was a robust predictor of treatment outcomes. At the same time, these results suggest that future work may benefit from continuing to examine and disaggregate the nature of adolescent:provider alliance across the spectrum of empirically supported brief interventions for adolescent hazardous drinking. CLINICAL TRIALS REGISTRATION NUMBER: ClinicalTrials.gov identifier: NCT03367858. Data Sharing Statement: Requests for deidentified individual participant data can be made to the first author.

Detection of vaping, cannabis use, and hazardous prescription opioid use among adolescents.

There has been a global surge in adolescents' use of electronic nicotine delivery systems (vaping), cannabis (vaped and edible), and prescription opioids, collectively termed ECPO. The nature of ECPO use can make it difficult to detect due to few obvious immediate physical and behavioural signs, as well as subtle long-term effects that allow adolescents to transition from initial exploration into hazardous ECPO use without easy detection by care providers. Here, we address the nature of the presentation of ECPO use in adolescents (roughly age 13-18 years), including challenges in detecting use and related complications, which affect screening, prevention, and intervention. We begin by reviewing empirical data on these difficult to detect effects in adolescents, including acute effects at cellular and neural levels and long-term neurocognitive and developmental changes that precede outwardly detectable physical signs. We then provide concrete approaches for providers to screen for ECPO use in adolescents even in the absence of overt physical and behavioural symptoms. Finally, we conclude with direct practice recommendations for prevention and intervention.

Intersection between social inequality and emotion regulation on emerging adult cannabis use.

Emerging adulthood (EA; ages 18-25) is characterized by socioemotional and neurodevelopmental challenges. Cannabis is a widely used substance among EAs, and hazardous use may increase risk for sustained use patterns and related health consequences. Research shows differential increases in hazardous use by objective as well as subjective measures of social inequality, with more concerning trajectories for youth with greater experiences of social inequality. Learning how to flexibly monitor and modify emotions in proactive ways (i.e., emotion regulation) is a central developmental task navigated during the EA window. Challenges to and with emotion regulation processes can contribute to the emergence of mental health symptoms during EA, including hazardous cannabis use. In this perspective, we highlight emotion dysregulation and social inequality as two critical factors that interact to either buffer against or exacerbate cannabis use during the EA period, noting critical gaps in the literature that merit additional research. We recommend novel methods and longitudinal designs to help clarify how dynamic cognition-emotion interplay predicts trajectories of negative emotional experiences and cannabis use in EA.

Evaluating Providers' Prescription Opioid Instructions to Pediatric Patients.

Receiving an opioid prescription during childhood increases the risk of hazardous prescription opioid (PO) use during emerging adulthood. Instruction on how to safely use POs plays an essential role in pediatric patients' capacity to utilize as well as to discontinue POs appropriately. This study aimed to evaluate pediatric PO label instructions provided to a large sample of pediatric outpatients. Data were extracted from the electronic healthcare records system identifying pediatric patients who received a PO between 2016 and 2019 from pediatric outpatient medical clinics were affiliated with a northwestern United States medical center and children's hospital. Pediatric patients (n = 12,613) between 0−17 years old who received a PO during outpatient care were included. Patients with chronic health conditions (e.g., cancer) or who received their PO from an inpatient medical setting were excluded. Patient demographics, medication instructions, associated diagnoses, and other prescription information (e.g., name of medication, dose, and quantity dispensed) were examined using automated text classification. Many label instructions did not include any indication/reason for use (20.8%). Virtually none of the POs (>99%) included instructions for how to reduce/wean off POs, contact information for questions about the POs, and/or instructions around how to dispose of the POs. Efforts are needed to ensure that pediatric PO instructions contain essential elements to improve comprehension of when and how to use POs for pediatric patients.

Joint risk prediction for hazardous use of alcohol, cannabis, and tobacco among adolescents: A preliminary study using statistical and machine learning.

For some, substance use during adolescence may be a stepping stone on the way to substance use disorders in adulthood. Risk prediction models may help identify adolescent users at elevated risk for hazardous substance use. This preliminary analysis used cross-sectional data (n = 270, ages 13-18) from the baseline dataset of a randomized controlled trial intervening with adolescent alcohol and/or cannabis use. Models were developed for jointly predicting quantitative scores on three measures of hazardous substance use (Rutgers Alcohol Problems Index, Adolescent Cannabis Problem Questionnaire, and Hooked on Nicotine Checklist) based on personal risk factors using two statistical and machine learning methods: multivariate covariance generalized linear models (MCGLM) and penalized multivariate regression with a lasso penalty. The predictive accuracy of a model was evaluated using root mean squared error computed via leave-one-out cross-validation. The final proposed model was an MCGLM model. It has eleven risk factors: age, early life stress, age of first tobacco use, age of first cannabis use, lifetime use of other substances, age of first use of other substances, maternal education, parental attachment, family cigarette use, family history of hazardous alcohol use, and family history of hazardous cannabis use. Different subsets of these risk factors feature in the three outcome-specific components of this joint model. The quantitative risk estimate provided by the proposed model may help identify adolescent substance users of cannabis, alcohol, and tobacco who may be at an elevated risk of developing hazardous substance use.

Time for a paradigm shift: The adolescent brain in addiction treatment.

OBJECTIVE: One route to improve adolescent addiction treatment outcomes is to use translational approaches to help identify developmental neuroscience mechanisms that undergird active treatment ingredients and advance adolescent behavior change. METHODS: This sample included 163 adolescents (ages 15-19) randomized to motivational interviewing (MI) vs. brief adolescent mindfulness (BAM). Youth completed an fMRI paradigm assessing adolescent brain response to therapist language (complex reflection vs. mindful; complex reflection vs. confront; mindful vs. confront) at pre- (prior to the completion of the full intervention) and post-treatment (at 3-month follow-up) and behavioral measures at 3, 6 and 12 months. RESULTS: Youth in both treatment groups showed significant problem drinking reductions at 3 and 6 months, but MI youth demonstrated significantly better treatment outcomes than BAM youth at 12 months. We observed several significant treatment group differences (MI > BAM) in neural response to therapist language, including at pre-treatment when examining complex reflection vs. mindful, and complex reflection vs. confront (e.g., superior temporal gyrus, lingual gyrus); and at post-treatment when examining mindful vs. confront (e.g., supplementary motor area; middle frontal gyrus). When collapsed across treatment groups (MI + BAM), we observed significant differences by time, with youth showing a pattern of brain change in response to complex reflection vs. mindful, and complex reflection vs. confront (e.g., precuneus; postcentral gyrus). There was no evidence of a significant group × time interaction. However, brain change in response to therapist language (complex reflection vs. confront) in regions such as middle frontal gyrus, was associated with reductions in problem drinking at 12 months. Yet, few treatment group differences were observed. CONCLUSIONS: These data underscore the need to better understand therapist language and it's impact on the developing brain, in order to inform and aggregate the most impactful elements of addiction treatment for future treatment development for adolescents.

Molecular-assisted breeding for improved carbohydrate profiles in soybean seed.

KEY MESSAGE: Two independent variant raffinose synthase 3 (RS3) alleles produced an equivalent phenotype and implicated the gene as a key contributor to soybean seed carbohydrate phenotype. Soybean is an important crop because the processed seed is utilized as a vegetable oil and a high protein meal typically used in livestock feeds. Raffinose and stachyose, the raffinose family of oligosaccharides (RFO) carbohydrate components of the seed, are synthesized in developing soybean seeds from sucrose and galactinol. Sucrose is considered positive for metabolizable energy, while RFO are anti-nutritional factors in diets of monogastric animals such as humans, poultry, and swine. To increase metabolizable energy available in soybean seed meal, prior research has been successful in deploying variant alleles of key soybean raffinose synthase (RS) genes leading to reductions or near elimination of seed RFO, with significant increases in seed sucrose. The objective of this research was to investigate the specific role of variants of the RS3 gene in a genomic context and improve molecular marker-assisted selection for the ultra-low (UL) RFO phenotype in soybean seeds. The results revealed a new variant of the RS3 allele (rs3 snp5, rs3 snp6) contributed to the UL RFO phenotype when mutant alleles of RS2 were present. The variant RS3 allele identified was present in about 15% of a small set of soybean cultivars released in North America. A missense allele of the RS3 gene (rs3 G75E) also produced the UL RFO phenotype when combined with mutant alleles of RS2. The discoveries reported here enable direct marker-assisted selection for an improved soybean meal trait that has the potential to add value to soybean by improving the metabolizable energy of the meal.

Contextual risk among adolescents receiving opioid prescriptions for acute pain in pediatric ambulatory care settings.

Many adults with opioid use disorder (OUD) report that their first exposure to opioids was in the course of routine pain treatment in medical care settings. Adolescents receive opioid prescriptions with frequency, but are susceptible to a constellation of unique risks in the context of pain management. This empirical study presents the first cohort of adolescents recruited from ambulatory medical care within 72 h of their receipt of opioids to treat acute pain. The primary aim was to capture a time-sensitive report of the intersection of prescription opioid receipt and contextual risks for opioid misuse related to pain experience, mental health symptoms, and substance use at the adolescent and parental levels. Data were collected from 70 14-19-year-old adolescents and their accompanying parent. Results reflected that 90% of this sample of adolescents reported 2 or more risks and 35% reported 5 or more risks for future opioid misuse. Pain catastrophizing (46%) and alcohol use (40%) and were the most common adolescent-level risk factors; mother history of chronic pain (32%) and parent anxiety (21%) were the most common parent-level risk factors. Past-week parent pain intensity showed the strongest association with adolescent past-week pain intensity; neither was associated with adolescent OUD symptoms. Adolescent pain catastrophizing most reliably predicted OUD symptoms; parent pain interference was also associated. Seventy-one percent of parents reported keeping opioids at home, a relevant risk factor for future misuse. These findings illuminate the intersection between adolescent and parental risks in the context of pediatric opioid prescribing for acute pain management, and provide initial insight into potential points of prevention early in adolescent pain treatment, including avenues by which to inform and enhance prescriber decision-making regarding factors to be weighed in adolescent candidacy for opioid therapy.

Hunting for What Works: Adolescents in Addiction Treatment.

Although adolescents are developmentally distinct from adults, they often receive addiction treatment based on adult models. This is problematic because adolescents face significantly different conditions in addiction treatment, including distinct basic biological and neurodevelopmental stages, unique sociodevelopmental concerns, distinctive addiction trajectories, and, in turn, disparate treatment goals and outcomes. In sum, it can be difficult for even savvy clinicians to know how to approach addiction treatment with this important age group. In an effort to help clinicians and researchers consider substance use via a neurodevelopmental lens, we approached this review with 4 goals: (i) characterize the prevalence, and related health and safety implications of substance use within this age group; (ii) identify the nature of the adolescent brain, including characteristic features of this phase of neurodevelopment relevant to adolescent substance use treatment; (iii) provide an overview of current adolescent addiction interventions and avenues to improve clinical treatment and clinical research efforts for adolescents; and (iv) examine the intersection between the nature of the developing brain and adolescent substance use, and utilize that information to inform alternative routes and directions for substance use treatment in this critical age group. This review concludes by offering a novel neurodevelopmental model and framework to examine substance use interventions, along with a series of recommendations to optimize adolescent substance use treatment and clinical research.

Featured Article: Adolescent Condom Use and Connectivity in the Social-Planful Brain.

Objective: To reduce rates of sexually transmitted infections (STIs) and unwanted pregnancy among adolescents, it is critical to investigate brain connectivity that may underlie adolescents' sexual health decision-making in the context of intercourse. This study explored relationships between adolescent condom use frequency and the brain's resting-state functional connectivity, to identify differential patterns of social-affective processing among sexually active youth. Methods: In this study, N = 143 sexually active adolescents (68.5% male, Mage = 16.2 years, SD = 1.06) completed magnetic resonance imaging and reported past 3-month frequency of condom use. Resting-state connectivity, seeded on a social region of the brain, the temporoparietal junction (TPJ), was assessed to determine its correspondence with protected sex (condom use). Results: Condom use was associated with positive connectivity between the left TPJ and bilateral inferior frontal gyrus (IFG). This relationship was observed in adolescent males only; no connectivity differences were observed with adolescent females. Conclusions: This study reflects functional synchrony between nodes of the "social brain," including the TPJ, and a region of planfulness and control, the IFG. The relationship between these regions suggests that adolescents who have more coordinated systems of communication between these critical components of the brain are more likely to be successful in planning and engaging in safer sexual decision-making; for young males, this differentiated more frequent from less frequent condom use. In turn, interventions designed to reduce STIs/human immunodeficiency virus may benefit from targeting social-planfulness dimensions to help youth implement safer sex behaviors.

Sexual risk-taking and subcortical brain volume in adolescence.

Background: The developmental period of adolescence marks the initiation of new socioemotional and physical behaviors, including sexual intercourse. However, little is known about neurodevelopmental influences on adolescent sexual decision-making. Purpose: We sought to determine how subcortical brain volume correlated with condom use, and whether those associations differed by gender and pubertal development. Methods: We used FreeSurfer to extract subcortical volume among N = 169 sexually experienced youth (mean age 16.07 years; 31.95% female). We conducted multiple linear regressions to examine the relationship between frequency of condom use and subcortical volume, and whether these associations would be moderated by gender and pubertal development. Results: We found that the relationship between brain volume and condom use was better accounted for by pubertal development than by gender, and moderated the association between limbic brain volume and condom use. No significant relationships were observed in reward areas (e.g., nucleus accumbens) or prefrontal cortical control areas. Conclusions: These data highlight the potential relevance of subcortical socioemotional processing structures in adolescents' sexual decision-making.

A comparison of genotyping-by-sequencing analysis methods on low-coverage crop datasets shows advantages of a new workflow, GB-eaSy.

BACKGROUND: Genotyping-by-sequencing (GBS), a method to identify genetic variants and quickly genotype samples, reduces genome complexity by using restriction enzymes to divide the genome into fragments whose ends are sequenced on short-read sequencing platforms. While cost-effective, this method produces extensive missing data and requires complex bioinformatics analysis. GBS is most commonly used on crop plant genomes, and because crop plants have highly variable ploidy and repeat content, the performance of GBS analysis software can vary by target organism. Here we focus our analysis on soybean, a polyploid crop with a highly duplicated genome, relatively little public GBS data and few dedicated tools. RESULTS: We compared the performance of five GBS pipelines using low-coverage Illumina sequence data from three soybean populations. To address issues identified with existing methods, we developed GB-eaSy, a GBS bioinformatics workflow that incorporates widely used genomics tools, parallelization and automation to increase the accuracy and accessibility of GBS data analysis. Compared to other GBS pipelines, GB-eaSy rapidly and accurately identified the greatest number of SNPs, with SNP calls closely concordant with whole-genome sequencing of selected lines. Across all five GBS analysis platforms, SNP calls showed unexpectedly low convergence but generally high accuracy, indicating that the workflows arrived at largely complementary sets of valid SNP calls on the low-coverage data analyzed. CONCLUSIONS: We show that GB-eaSy is approximately as good as, or better than, other leading software solutions in the accuracy, yield and missing data fraction of variant calling, as tested on low-coverage genomic data from soybean. It also performs well relative to other solutions in terms of the run time and disk space required. In addition, GB-eaSy is built from existing open-source, modular software packages that are regularly updated and commonly used, making it straightforward to install and maintain. While GB-eaSy outperformed other individual methods on the datasets analyzed, our findings suggest that a comprehensive approach integrating the results from multiple GBS bioinformatics pipelines may be the optimal strategy to obtain the largest, most highly accurate SNP yield possible from low-coverage polyploid sequence data.

Transcriptional profiling of mechanically and genetically sink-limited soybeans.

The absence of a reproductive sink causes physiological and morphological changes in soybean plants. These include increased accumulation of nitrogen and starch in the leaves and delayed leaf senescence. To identify transcriptional changes that occur in leaves of these sink-limited plants, we used RNAseq to compare gene expression levels in trifoliate leaves from depodded and ms6 male-sterile soybean plants and control plants. In both sink-limited tissues, we observed a deferral of the expression of senescence-associated genes and a continued expression of genes associated with leaf maturity. Gene Ontology-terms (GO-terms) associated with growth and development and storage proteins were over-represented in genes that were differentially expressed in sink-limited tissues. We also identified basic helix-loop-helix, auxin response factor, and squamosa binding protein transcription factors expressed in sink-limited tissues, and the senescing control leaves expressed WRKY and NAC transcription factors. We identified genes that were not expressed during normal leaf development but that were highly expressed in sink-limited plants, including the SGR3b "non-yellowing" gene. These differences highlighted several metabolic pathways that were involved in distinct modes of resource partitioning of leaves with the "stay green" phenotype.

Orbitofrontal cortex connectivity as a mechanism of adolescent behavior change.

An increasing number of studies have implicated the role of network functional connectivity in addiction. Yet, none have examined functional connectivity as a potential mechanism of adolescent behavior change. We examined the underlying neural mechanism of a promising treatment for adolescents, motivational interviewing (MI). We began by employing psychophysiological interaction (PPI) to evaluate network response in a sample of adolescent cannabis users (N=30). Next, we examined correlations between network connectivity and clinical metrics of treatment outcome. PPI analyses seeded on the orbitofrontal cortex (OFC) showed significant increases in functional connectivity across the inferior frontal gyrus (IFG), precentral gyrus, anterior and posterior cingulate gyrus, supplementary motor area (SMA), superior frontal gyrus, pallidus, caudate, and parahippocampal gyrus. Further, greater functional connectivity between the OFC and anterior cingulate/medial frontal gyrus was associated with less behavior change (e.g., greater post-treatment cannabis problems). These data support the role of the OFC network as a mechanism of adolescent treatment response.

Overweight adolescents' brain response to sweetened beverages mirrors addiction pathways.

Many adolescents struggle with overweight/obesity, which exponentially increases in the transition to adulthood. Overweight/obesity places youth at risk for serious health conditions, including type 2 diabetes. In adults, neural substrates implicated in addiction (e.g., orbitofrontal cortex (OFC), striatum, amygdala, and ventral tegmental area) have been found to be relevant to risk for overweight/obesity. In this study, we examined three hypotheses to disentangle the potential overlap between addiction and overweight/obesity processing by examining (1) brain response to high vs. low calorie beverages, (2) the strength of correspondence between biometrics, including body mass index (BMI) and insulin resistance, and brain response and (3) the relationship between a measure of food addiction and brain response using an established fMRI gustatory cue exposure task with a sample of overweight/obese youth (M age = 16.46; M BMI = 33.1). Greater BOLD response was observed across the OFC, inferior frontal gyrus (IFG), nucleus accumbens, right amygdala, and additional frontoparietal and temporal regions in neural processing of high vs. low calorie beverages. Further, BMI scores positively correlated with BOLD activation in the high calorie > low calorie contrast in the right postcentral gyrus and central operculum. Insulin resistance positively correlated with BOLD activation across the bilateral middle/superior temporal gyrus, left OFC, and superior parietal lobe. No relationships were observed between measures of food addiction and brain response. These findings support the activation of parallel addiction-related neural pathways in adolescents' high calorie processing, while also suggesting the importance of refining conceptual and neurocognitive models to fit this developmental period.

Developmental profiling of gene expression in soybean trifoliate leaves and cotyledons.

BACKGROUND: Immediately following germination, the developing soybean seedling relies on the nutrient reserves stored in the cotyledons to sustain heterotrophic growth. During the seed filling period, developing seeds rely on the transport of nutrients from the trifoliate leaves. In soybean, both cotyledons and leaves develop the capacity for photosynthesis, and subsequently senesce and abscise once their function has ended. Before this occurs, the nutrients they contain are mobilized and transported to other parts of the plant. These processes are carefully orchestrated by genetic regulation throughout the development of the leaf or cotyledon. RESULTS: To identify genes involved in the processes of leaf or cotyledon development and senescence in soybean, we used RNA-seq to profile multiple stages of cotyledon and leaf tissues. Differentially expressed genes between stages of leaf or cotyledon development were determined, major patterns of gene expression were defined, and shared genes were identified. Over 38,000 transcripts were expressed during the course of leaf and cotyledon development. Of those transcripts, 5,000 were expressed in a tissue specific pattern. Of the genes that were differentially expressed between both later stage tissues, 90 % had the same direction of change, suggesting that the mechanisms of senescence are conserved between tissues. Analysis of the enrichment of biological functions within genes sharing common expression profiles highlights the main processes occurring within these defined temporal windows of leaf and cotyledon development. Over 1,000 genes were identified with predicted regulatory functions that may have a role in control of leaf or cotyledon senescence. CONCLUSIONS: The process of leaf and cotyledon development can be divided into distinct stages characterized by the expression of specific gene sets. The importance of the WRKY, NAC, and GRAS family transcription factors as major regulators of plant senescence is confirmed for both soybean leaf and cotyledon tissues. These results help validate functional annotation for soybean genes and promoters.

A classification of basic helix-loop-helix transcription factors of soybean.

The complete genome sequence of soybean allows an unprecedented opportunity for the discovery of the genes controlling important traits. In particular, the potential functions of regulatory genes are a priority for analysis. The basic helix-loop-helix (bHLH) family of transcription factors is known to be involved in controlling a wide range of systems critical for crop adaptation and quality, including photosynthesis, light signalling, pigment biosynthesis, and seed pod development. Using a hidden Markov model search algorithm, 319 genes with basic helix-loop-helix transcription factor domains were identified within the soybean genome sequence. These were classified with respect to their predicted DNA binding potential, intron/exon structure, and the phylogeny of the bHLH domain. Evidence is presented that the vast majority (281) of these 319 soybean bHLH genes are expressed at the mRNA level. Of these soybean bHLH genes, 67% were found to exist in two or more homeologous copies. This dataset provides a framework for future studies on bHLH gene function in soybean. The challenge for future research remains to define functions for the bHLH factors encoded in the soybean genome, which may allow greater flexibility for genetic selection of growth and environmental adaptation in this widely grown crop.