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Background: We sought research experiences of caregivers and their children were enrolled in the Environmental Determinants of Islet Autoimmunity (ENDIA) study. Methods: ENDIA is a pregnancy–birth cohort investigating early-life causes of type 1 diabetes (T1D). Surveys were sent to 1090 families between June 2021 and March 2022 with a median participation of >5 years. Caregivers completed a 12-item survey. Children ≥ 3 years completed a four-item survey. Results: The surveys were completed by 550/1090 families (50.5%) and 324/847 children (38.3%). The research experience was rated as either “excellent” or “good” by 95% of caregivers, and 81% of children were either “ok”, “happy” or “very happy”. The caregivers were motivated by contributing to research and monitoring their children for T1D. Relationships with the research staff influenced the experience. The children most liked virtual reality headsets, toys, and “helping”. Blood tests were least liked by the children and were the foremost reason that 23.4% of the caregivers considered withdrawing. The children valued gifts more than their caregivers. Only 5.9% of responses indicated dissatisfaction with some aspects of the protocol. The self-collection of samples in regional areas, or during the COVID-19 pandemic restrictions, were accepted. Conclusions: This evaluation identified modifiable protocol elements and was conducted to further improve satisfaction. What was important to the children was distinct from their caregivers.

Reciprocal recurrent selection is the selection of purebreds for crossbred performance and takes advantage of additive and non-additive variance by using pedigreed progeny performance records. Developed in maize, the adoption of this approach in livestock breeding has been limited to the pork and poultry industries; genomic selection may facilitate its extension into the beef industry by replacing pedigree. The literature regarding the relative importance of additive versus non-additive variance and reciprocal recurrent genomic selection models was reviewed. The potential for using reciprocal recurrent genomic selection in a terminal Wagyu × Angus cross scenario was examined. Non-additive variance is more important for fitness traits and accounts for a small proportion of variance related to production traits such as marbling. In general, reciprocal recurrent selection was not significantly better at improving performance of crossbreds than was traditional selection within parental breeds using only additive variance in the studies examined. Simulation studies showed benefits of including dominance or breed-specific allele effects in prediction models but advantages were small as more realistic simulations were examined. On the basis of the evidence, it is likely that in a terminal two-way cross-beef scenario utilising Wagyu sires and Angus dams, where selection emphasis is on marbling, selection of purebreds on the basis of additive variance will allow substantial progress to be realised.

Context Significant opportunities have been identified in the northern Australian beef industry that can improve efficiency and profitability by using composite or crossbred cattle and genomic selection. The improved performance of composite cattle is partly due to heterosis. One of the major genetic bases of heterosis is dominance. Traditionally, dominance is ignored in genetic evaluation but could improve the accuracy of breeding values and help maintain genetic diversity. Aims The aim of this study is to describe the impact of including a dominance relationship matrix with different parameterisation methods and including heterozygosity fraction on estimated breeding values for 400-day weight in a composite population. Methods Genotype and phenotype data were obtained from 2364 tropical composite animals and were imputed to 27 648 single nucleotide polymorphisms. Genetic parameters and breeding values were estimated for 400-day weight from a linear mixed model using a genomic relationship matrix, heterozygosity fraction and three different parameterisation methods for the dominance relationship matrix, including genotypic, classical and the natural and orthogonal interaction approach. Genetic parameters and breeding values where compared over the three different parameterisation methods. Key results The heritability for all models when heterozygosity was not fitted ranged from 0.25 to 0.35, with the genotypic dominance model having the lowest additive heritability. Including heterozygosity fraction in the model as a fixed covariate resulted in substantial (39–49%) reductions in dominance variance across all models but a minimal change in the additive variance and, therefore, heritability (0.29–0.35). Conclusions and Implications In a composite population, including heterozygosity fraction in the model was important due to directional dominance. When heterozygosity fraction was not included, the genetic variance was incorrectly partitioned, and the dominance estimates were biased. Including the dominance relationship matrix improved the accuracy of breeding values. Parameterisation methods for forming the dominance relationship matrix are largely a matter of what estimates are required from the models and convenience. The additive values were largely independent of dominance parameterisation when heterozygosity was in the model.

Islet autoantibody screening of infants and young children in the Northern Hemisphere, together with semi-annual metabolic monitoring, is associated with a lower risk of ketoacidosis (DKA) and improved glucose control after diagnosis of clinical (stage 3) type 1 diabetes (T1D). We aimed to determine if similar benefits applied to older Australians and New Zealanders monitored less rigorously.DKA occurrence and metabolic control were compared between T1D relatives screened and monitored for T1D and unscreened individuals diagnosed in the general population, ascertained from the Australasian Diabetes Data Network.Between 2005 and 2019, 17,105 relatives (mean (SD) age 15.7 (10.8) years; 52% female) were screened for autoantibodies against insulin, glutamic acid decarboxylase, and insulinoma-associated protein 2. Of these, 652 screened positive to a single and 306 to multiple autoantibody specificities, of whom 201 and 215, respectively, underwent metabolic monitoring. Of 178 relatives diagnosed with stage 3 T1D, 9 (5%) had DKA, 7 of whom had not undertaken metabolic monitoring. The frequency of DKA in the general population was 31%. After correction for age, sex and T1D family history, the frequency of DKA in screened relatives was80% lower than in the general population. HbA1c and insulin requirements following diagnosis were also lower in screened relatives, consistent with greater beta cell reserve.T1D autoantibody screening and metabolic monitoring of older children and young adults in Australia and New Zealand, by enabling pre-clinical diagnosis when beta cell reserve is greater, confers protection from DKA. These clinical benefits support ongoing efforts to increase screening activity in the region and should facilitate the application of emerging immunotherapies.

We thank King Abdullah University of Science and Technology (KAUST) for funding this work, and Photon Systems Instruments (PSI) for their scientific and technical support. Special thanks to Dr. Xavier Sirault (CSIRO, Australia) for suggesting the use of the saturation method for salt imposition, Radka Mezulanikova and Jaromir Pytela (PSI, Czech Republic) for assisting with the phenotyping and Prof. Christa Testerink (UVA, Netherlands) for providing the HapMap seeds. We also thank the KAUST Greenhouse Core-lab personnel: Dr. Richard Soppe, Mr. Mupalla Reddy, Mr. Gomerito Sagun, Mr. John Rahmer, Mr. Thomas Hoover and Mr. Johnard Balangue for their help in propagating the plant material that was used in this study and for running the highthroughput phenotyping facility at KAUST.

OBJECTIVE Pregnancy and type 1 diabetes are each associated with increased anxiety and depression, but the combined impact on wellbeing is unresolved. We compared the mental health of women with and without type 1 diabetes during pregnancy and postpartum, and examined the relationship between mental health and glycaemic control. RESEARCH DESIGN AND METHODS Participants were women enrolled from 2016 to 2020 in the Environmental Determinants of Islet Autoimmunity (ENDIA) study, a pregnancy-birth prospective cohort following children with a first-degree relative with type 1 diabetes. Edinburgh Postnatal Depression Scale (EPDS) and Perceived Stress Scale (PSS) were completed during the third trimester (T3) (median [IQR] 34 [32, 36] weeks) and postpartum (14 [13, 16] weeks) by 737 women (800 pregnancies) with (n=518) and without (n=282) type 1 diabetes. RESULTS EPDS and PSS scores did not differ between women with and without type 1 diabetes during T3 and postpartum. EPDS scores were marginally higher in T3: predicted mean (95% CI) 5.7 (5.4, 6.1) than postpartum: 5.3 (5.0, 5.6), independent of type 1 diabetes status (p=0.01). HbA1c levels in type 1 diabetes were 6.3 [5.8, 6.9] % in T3 and did not correlate with EPDS or PSS scores. Reported use of psychotropic medications was similar in women with (n=44/518 [8%]) and without type 1 diabetes (n=17/282 [6%]), as was their amount of physical activity. CONCLUSIONS Overall, mental health in late pregnancy and postpartum did not differ between women with and without type 1 diabetes and mental health scores were not correlated with glycaemic control.

OBJECTIVE Pregnancy and type 1 diabetes are each associated with increased anxiety and depression, but the combined impact on well-being is unresolved. We compared the mental health of women with and without type 1 diabetes during pregnancy and postpartum and examined the relationship between mental health and glycemic control. RESEARCH DESIGN AND METHODS Participants were women enrolled from 2016 to 2020 in the Environmental Determinants of Islet Autoimmunity (ENDIA) study, a pregnancy to birth prospective cohort following children with a first-degree relative with type 1 diabetes. Edinburgh Postnatal Depression Scale (EPDS) and Perceived Stress Scale (PSS) were completed during the third trimester (T3) (median [interquartile range] 34 [32, 36] weeks) and postpartum (14 [13, 16] weeks) by 737 women (800 pregnancies) with (n = 518) and without (n = 282) type 1 diabetes. RESULTS EPDS and PSS scores did not differ between women with and without type 1 diabetes during T3 and postpartum. EPDS scores were marginally higher in T3: predicted mean (95% CI) 5.7 (5.4, 6.1) than postpartum: 5.3 (5.0, 5.6), independent of type 1 diabetes status (P = 0.01). HbA1c levels in type 1 diabetes were 6.3% [5.8, 6.9%] in T3 and did not correlate with EPDS or PSS scores. Reported use of psychotropic medications was similar in women with (n = 44 of 518 [8%]) and without type 1 diabetes (n = 17 of 282 [6%]), as was their amount of physical activity. CONCLUSIONS Overall, mental health in late pregnancy and postpartum did not differ between women with and without type 1 diabetes, and mental health scores were not correlated with glycemic control.

BACKGROUND Recruitment and retention of research participants is challenging. Social media, particularly Facebook, has emerged as a tool for connecting with participants due to its high uptake in the community. The Environmental Determinants of Islet Autoimmunity (ENDIA) study is an Australia-wide prospective pregnancy-birth cohort following children who have a first-degree relative with type 1 diabetes (ACTRN1261300794707). A dedicated Facebook page was established for the ENDIA study in 2013 with the aim to enhance recruitment and support participant retention. OBJECTIVE The purpose of this investigation was to evaluate the long-term impact of Facebook as a recruitment and retention tool. The hypotheses were that (1) Facebook was an important source of referral to the ENDIA study, (2) the sociodemographic characteristics of participants recruited by Facebook would be different from those of participants recruited by other means (i.e., ‘conventional recruits’), and (3) recruitment by Facebook would be associated with long-term retention. We also evaluated the most effective types of Facebook content based on post engagement. METHODS Recruitment of 1511 ENDIA participants was completed in December 2019. Characteristics of participants recruited through Facebook were compared to conventional recruits using linear, logistic, and multinomial logistic regression models. A logistic regression model was used to determine the risk of study withdrawal. Data pertaining to 794 Facebook posts over 7.5 years from June 2013 until December 2020 were extracted using the Facebook ‘Insights’ function for thematic analysis. RESULTS Facebook was the third largest source of referral to the ENDIA study (300/1511; 19.9%) behind in-person clinics (500/1511, 33.1%) and healthcare professional referrals (347/1511, 23.0%). The ENDIA Facebook page had 2337 followers at the close of recruitment. Approximately 20% of these could be identified as participating parents. Facebook recruits were more frequently Australian-born (P CONCLUSIONS Facebook was a valuable recruitment tool for the ENDIA study and participants recruited through Facebook were three times less likely to withdraw during long-term follow-up. The sociodemographic characteristics of Facebook recruits were different to conventional recruits, but perhaps in unintended ways. Facebook content featuring stories and images of participants received the highest engagement despite the fact that most Facebook followers were not enrolled in the study. These findings should inform social media strategies for future cohort studies involving pregnant women and young families, and for type 1 diabetes risk studies. CLINICALTRIAL Australia New Zealand Clinical Trials Registry: ACTRN1261300794707 INTERNATIONAL REGISTERED REPORT RR2-https://doi.org/10.1186/1471-2431-13-124

Studies of the gut microbiome have focused on its bacterial composition. We aimed to characterize the gut fungal microbiome (mycobiome) across pregnancy in women with and without type 1 diabetes.Faecal samples (n = 162) were collected from 70 pregnant women (45 with and 25 without type 1 diabetes) across all trimesters. Fungi were analysed by internal transcribed spacer 1 amplicon sequencing. Markers of intestinal inflammation (faecal calprotectin) and intestinal epithelial integrity (serum intestinal fatty acid binding protein; I-FABP), and serum antibodies to Saccharomyces cerevisiae (ASCA) were measured.Women with type 1 diabetes had decreased fungal alpha diversity by the third trimester, associated with an increased abundance of Saccharomyces cerevisiae that was inversely related to the abundance of the anti-inflammatory butyrate-producing bacterium Faecalibacterium prausnitzii. Women with type 1 diabetes had higher concentrations of calprotectin, I-FABP and ASCA.Women with type 1 diabetes exhibit a shift in the gut mycobiome across pregnancy associated with evidence of gut inflammation and impaired intestinal barrier function. The relevance of these findings to the higher rate of pregnancy complications in type 1 diabetes warrants further study.

Background: Rural/remote blood collection can cause delays in processing, reducing PBMC number, viability, cell composition and function. To mitigate these impacts, blood was stored at 4 °C prior to processing. Viable cell number, viability, immune phenotype, and Interferon-γ (IFN-γ) release were measured. Furthermore, the lowest protective volume of cryopreservation media and cell concentration was investigated. Methods: Blood from 10 individuals was stored for up to 10 days. Flow cytometry and IFN-γ ELISPOT were used to measure immune phenotype and function on thawed PBMC. Additionally, PBMC were cryopreserved in volumes ranging from 500 µL to 25 µL and concentration from 10 × 106 cells/mL to 1.67 × 106 cells/mL. Results: PBMC viability and viable cell number significantly reduced over time compared with samples processed immediately, except when stored for 24 h at RT. Monocytes and NK cells significantly reduced over time regardless of storage temperature. Samples with &gt, 24 h of RT storage had an increased proportion in Low-Density Neutrophils and T cells compared with samples stored at 4 °C. IFN-γ release was reduced after 24 h of storage, however not in samples stored at 4 °C for &gt, 24 h. The lowest protective volume identified was 150 µL with the lowest density of 6.67 × 106 cells/mL. Conclusion: A sample delay of 24 h at RT does not impact the viability and total viable cell numbers. When long-term delays exist (&gt, 4 d) total viable cell number and cell viability losses are reduced in samples stored at 4 °C. Immune phenotype and function are slightly altered after 24 h of storage, further impacts of storage are reduced in samples stored at 4 °C.

The Environmental Determinants of Islet Autoimmunity (ENDIA) Study is an Australia-wide observational pregnancy-birth cohort of children at genetic risk on account of a first-degree relative with type 1 diabetes (1). 1511 participants were recruited from all Australian States and Territories from 2013-2019 with 1473 live-born infants in follow-up. The standard protocol involves 3-monthly face-to-face visits from pregnancy until the child is 2 years of age, then 6-monthly visits. Study staff across nine centres in five States collect biospecimens (blood, urine, stool, swabs) and administer lifestyle and dietary questionnaires. Approximately 10% of the cohort are engaged in a Regional Participant Program (2) that requires self-collection of sample types except for venepuncture performed at local pathology services.

Rice is the most salt-sensitive cereal, suffering yield losses above 50% with soil salinity of 6 dS/m. Thus, understanding the mechanisms of rice salinity tolerance is key to address food security. In this chapter, we provide guidelines to assess rice salinity tolerance using a high-throughput phenotyping platform (HTP) with digital imaging at seedling/early tillering stage and suggest improved analysis methods using stress indices. The protocols described here also include computer scripts for users to improve their experimental design, run genome-wide association studies (GWAS), perform multi-testing corrections, and obtain the Manhattan plots, enabling the identification of loci associated with salinity tolerance. Notably, the computer scripts provided here can be used for any stress or GWAS experiment and independently of HTP.

Rice is the most salt-sensitive cereal, suffering yield losses above 50% with soil salinity of 6 dS/m. Thus, understanding the mechanisms of rice salinity tolerance is key to address food security. In this chapter, we provide guidelines to assess rice salinity tolerance using a high-throughput phenotyping platform (HTP) with digital imaging at seedling/early tillering stage and suggest improved analysis methods using stress indices. The protocols described here also include computer scripts for users to improve their experimental design, run genome-wide association studies (GWAS), perform multi-testing corrections, and obtain the Manhattan plots, enabling the identification of loci associated with salinity tolerance. Notably, the computer scripts provided here can be used for any stress or GWAS experiment and independently of HTP.

Background The conversion of lignocellulosic biomass from agricultural waste into biofuels and chemicals is considered a promising way to provide sustainable low carbon products without compromising food security. However, the use of lignocellulosic biomass for biofuel and chemical production is limited by the cost-effectiveness of the production process due to its recalcitrance to enzymatic hydrolysis and fermentable sugar release (i.e., saccharification). Rice straw is a particularly attractive feedstock because millions of tons are currently burned in the field each year for disposal. The aim of this study was to explore the underlying natural genetic variation that impacts the recalcitrance of rice (Oryza sativa) straw to enzymatic saccharification. Ultimately, we wanted to investigate whether we could identify genetic markers that could be used in rice breeding to improve commercial cultivars for this trait. Here, we describe the development and characterization of a Vietnamese rice genome-wide association panel, high-throughput analysis of rice straw saccharification and lignin content, and the results from preliminary genome-wide association studies (GWAS) of the combined data sets. We identify both QTL and plausible candidate genes that may have an impact on the saccharification of rice straw. Results We assembled a diversity panel comprising 151 rice genotypes (Indica and Japonica types) from commercial, historical elite cultivars, and traditional landraces grown in Vietnam. The diversity panel was genotyped using genotype by sequencing (GBS) methods yielding a total of 328,915 single nucleotide polymorphisms (SNPs). We collected phenotypic data from stems of these 151 genotypes for biomass saccharification and lignin content. Using GWAS on the indica genotypes over 2 years we identified ten significant QTL for saccharification (digestibility) and seven significant QTL for lignin. One QTL on chromosome 11 occurred in both GWAS for digestibility and for lignin. Seven QTL for digestibility, on CH2, CH6, CH7, CH8, and CH11, were observed in both years of the study. The QTL regions for saccharification include three potential candidate genes that have been previously reported to influence digestibility: OsAT10; OsIRX9; and OsMYB58/63-L. Conclusions Despite the difficulties associated with multi-phasic analysis of complex traits in novel germplasm, a moderate resolution GWAS successfully identified genetic associations encompassing both known and/or novel genes involved in determining the saccharification potential and lignin content of rice straw. Plausible candidates within QTL regions, in particular those with roles in cell wall biosynthesis, were identified but will require validation to confirm their value for application in rice breeding.

Background Current excitement about the opportunities for gene editing in plants have been prompted by advances in CRISPR/Cas and TALEN technologies. CRISPR/Cas is widely used to knock-out or modify genes by inducing targeted double-strand breaks (DSBs) which are repaired predominantly by error-prone non-homologous end-joining or microhomology-mediated end joining resulting in mutations that may alter or abolish gene function. Although such mutations are random, they occur at sufficient frequency to allow useful mutations to be routinely identified by screening. By contrast, gene knock-ins to replace entire genes with alternative alleles or copies with specific characterised modifications, is not yet routinely possible. Gene replacement (or gene targeting) by homology directed repair occurs at extremely low frequency in higher plants making screening for useful events unfeasible. Homology directed repair might be increased by inhibiting non-homologous end-joining and/or stimulating homologous recombination (HR). Here we pave the way to increasing gene replacement efficiency by evaluating the effect of expression of multiple heterologous recombinases on intrachromosomal homologous recombination (ICR) in Nicotiana tabacum plants. Results We expressed several bacterial and human recombinases in different combinations in a tobacco transgenic line containing a highly sensitive β-glucuronidase (GUS)-based ICR substrate. Coordinated simultaneous expression of multiple recombinases was achieved using the viral 2A translational recoding system. We found that most recombinases increased ICR dramatically in pollen, where HR will be facilitated by the programmed DSBs that occur during meiosis. DMC1 expression produced the greatest stimulation of ICR in primary transformants, with one plant showing a 1000-fold increase in ICR frequency. Evaluation of ICR in homozygous T2 plant lines revealed increases in ICR of between 2-fold and 380-fold depending on recombinase(s) expressed. By comparison, ICR was only moderately increased in vegetative tissues and constitutive expression of heterologous recombinases also reduced plant fertility. Conclusion Expression of heterologous recombinases can greatly increase the frequency of HR in plant reproductive tissues. Combining such recombinase expression with the use of CRISPR/Cas9 to induce DSBs could be a route to radically improving gene replacement efficiency in plants.

During plant growth, sodium (Na+) in the soil is transported via the xylem from the root to the shoot. While excess Na+ is toxic to most plants, non-toxic concentrations have been shown to improve crop yields under certain conditions, such as when soil K+ is low. We quantified grain Na+ across a barley genome-wide association study panel grown under non-saline conditions and identified variants of a Class 1 HIGH-AFFINITY-POTASSIUM-TRANSPORTER (HvHKT1;5)-encoding gene responsible for Na+ content variation under these conditions. A leucine to proline substitution at position 189 (L189P) in HvHKT1;5 disturbs its characteristic plasma membrane localisation and disrupts Na+ transport. Under low and moderate soil Na+, genotypes containing HvHKT1:5P189 accumulate high concentrations of Na+ but exhibit no evidence of toxicity. As the frequency of HvHKT1:5P189 increases significantly in cultivated European germplasm, we cautiously speculate that this non-functional variant may enhance yield potential in non-saline environments, possibly by offsetting limitations of low available K+.

Backgrounds: We aimed to monitor pancreatic exocrine function longitudinally in relation to the development of islet autoimmunity (IA) and type 1 diabetes (T1D) in at-risk children with a first-degree relative with T1D, who were followed prospectively in the Environmental Determinants of Islet Autoimmunity (ENDIA) study. Methods: Fecal elastase-1 (FE-1) concentration was measured longitudinally in 85 ENDIA children from median age 1.0 (IQR 0.7,1.3) year. Twenty-eight of 85 children (progressors) developed persistent islet autoantibodies at median age of 1.5 (IQR 1.1,2.5) years, of whom 11 went on to develop clinical diabetes. The other 57 islet autoantibody-negative children (non-progressors) followed similarly were age and gender-matched with the progressors. An adjusted linear mixed model compared FE-1 concentrations in progressors and non-progressors. Results: Baseline FE-1 did not differ between progressors and non-progressors, or by HLA DR type or proband status. FE-1 decreased over time in progressors in comparison to non-progressors (Wald statistic 5.46, P =.02); in some progressors the fall in FE-1 preceded the onset of IA. Conclusions: Pancreatic exocrine function decreases in the majority of young at-risk children who progress to IA and T1D.

We quantified grain sodium (Na+) content across a barley GWAS panel grown under optimal conditions. We identified a strong association with a region containing two low and one high Na+ accumulating haplotypes of a Class 1 HIGH-AFFINITY POTASSIUM TRANSPORTER (HKT1;5) known to be involved in regulating plant Na+ homeostasis. The haplotypes exhibited an average 1.8-fold difference in grain Na+ content. We show that an L189P substitution disrupts Na+ transport in the high Na+ lines, disturbs the plasma membrane localisation typical of HKT1;5 and induces a conformational change in the protein predicted to compromise function. Under NaCl stress, lines containing P189 accumulate high levels of Na+, but show no significant difference in biomass. P189 increases in frequency from wild-species to elite cultivars leading us to speculate that the compromised haplotype is undergoing directional selection possibly due to the value of Na+ as a functional nutrient in non-saline environments.

During plant growth, sodium (Na+) in the soil is transported via the xylem from the root to the shoot. While excess Na+ is toxic to most plants, non-toxic concentrations have been shown to improve crop yields under certain conditions, such as when soil K+ is low. We quantified grain Na+ across a barley genome-wide association study panel grown under non-saline conditions and identified variants of a Class 1 HIGH-AFFINITY-POTASSIUM-TRANSPORTER (HvHKT1;5)-encoding gene responsible for Na+ content variation under these conditions. A leucine to proline substitution at position 189 (L189P) in HvHKT1;5 disturbs its characteristic plasma membrane localisation and disrupts Na+ transport. Under low and moderate soil Na+, genotypes containing HvHKT1:5P189 accumulate high concentrations of Na+ but exhibit no evidence of toxicity. As the frequency of HvHKT1:5P189 increases significantly in cultivated European germplasm, we cautiously speculate that this non-functional variant may enhance yield potential in non-saline environments, possibly by offsetting limitations of low available K+., Kelly Houston et al. report a genome-wide association study for sodium content in barley to find genetic variants that may improve yield under low soil K + levels. They identify variants of the Na+ transporter-encoding gene HvHKT1;5 as important for sodium content variation in non-saline conditions.

Summary To optimize shoot growth and structure of cereals, we need to understand the genetic components controlling initiation and elongation. While measuring total shoot growth at high throughput using 2D imaging has progressed, recovering the 3D shoot structure of small grain cereals at a large scale is still challenging. Here, we present a method for measuring defined individual leaves of cereals, such as wheat and barley, using few images. Plant shoot modelling over time was used to measure the initiation and elongation of leaves in a bi‐parental barley mapping population under low and high soil salinity. We detected quantitative trait loci (QTL) related to shoot growth per se, using both simple 2D total shoot measurements and our approach of measuring individual leaves. In addition, we detected QTL specific to leaf elongation and not to total shoot size. Of particular importance was the detection of a QTL on chromosome 3H specific to the early responses of leaf elongation to salt stress, a locus that could not be detected without the computer vision tools developed in this study., Significance Statement To dissect overall shoot growth in small grain cereals, a computer vision‐based approach was developed for the measurement of individual leaves, which requires only few input images, making image acquisition fast and high throughput. The applicability of this approach is shown by mapping QTL for leaf elongation in a barley mapping population in response to salinity.

International audience; Caffeic acid O-methyltransferase (COMT), the lignin biosynthesis gene modified in many brown-midrib high-digestibility mutants of maize and sorghum, was targeted for downregulation in the small grain temperate cereal, barley (Hordeum vulgare), to improve straw properties. Phylogenetic and expression analyses identified the barley COMT orthologue(s) expressed in stems, defining a larger gene family than in brachypodium or rice with three COMT genes expressed in lignifying tissues. RNAi significantly reduced stem COMT protein and enzyme activity, and modestly reduced stem lignin content while dramatically changing lignin structure. Lignin syringyl-to-guaiacyl ratio was reduced by similar to 50%, the 5-hydroxyguaiacyl (5-OH-G) unit incorporated into lignin at 10--15-fold higher levels than normal, and the amount of p-coumaric acid ester-linked to cell walls was reduced by similar to 50%. No brown-midrib phenotype was observed in any RNAi line despite significant COMT suppression and altered lignin. The novel COMT gene family structure in barley highlights the dynamic nature of grass genomes. Redundancy in barley COMTs may explain the absence of brown-midrib mutants in barley and wheat. The barley COMT RNAi lines nevertheless have the potential to be exploited for bioenergy applications and as animal feed.

Genomic selection in crop breeding introduces modeling challenges not found in animal studies. These include the need to accommodate replicate plants for each line, consider spatial variation in field trials, address line by environment interactions, and capture nonadditive effects. Here, we propose a flexible single-stage genomic selection approach that resolves these issues. Our linear mixed model incorporates spatial variation through environment-specific terms, and also randomization-based design terms. It considers marker, and marker by environment interactions using ridge regression best linear unbiased prediction to extend genomic selection to multiple environments. Since the approach uses the raw data from line replicates, the line genetic variation is partitioned into marker and nonmarker residual genetic variation (i.e., additive and nonadditive effects). This results in a more precise estimate of marker genetic effects. Using barley height data from trials, in 2 different years, of up to 477 cultivars, we demonstrate that our new genomic selection model improves predictions compared to current models. Analyzing single trials revealed improvements in predictive ability of up to 5.7%. For the multiple environment trial (MET) model, combining both year trials improved predictive ability up to 11.4% compared to a single environment analysis. Benefits were significant even when fewer markers were used. Compared to a single-year standard model run with 3490 markers, our partitioned MET model achieved the same predictive ability using between 500 and 1000 markers depending on the trial. Our approach can be used to increase accuracy and confidence in the selection of the best lines for breeding and/or, to reduce costs by using fewer markers.

In many cereal crops, meiotic crossovers predominantly occur toward the ends of chromosomes and 30 to 50% of genes rarely recombine. This limits the exploitation of genetic variation by plant breeding. Previous reports demonstrate that chiasma frequency can be manipulated in plants by depletion of the synaptonemal complex protein ZIPPER1 (ZYP1) but conflict as to the direction of change, with fewer chiasmata reported in Arabidopsis thaliana and more crossovers reported for rice (Oryza sativa). Here, we use RNA interference (RNAi) to reduce the amount of ZYP1 in barley (Hordeum vulgare) to only 2 to 17% of normal zygotene levels. In the ZYP1(RNAi) lines, fewer than half of the chromosome pairs formed bivalents at metaphase and many univalents were observed, leading to chromosome nondisjunction and semisterility. The number of chiasmata per cell was reduced from 14 in control plants to three to four in the ZYP1-depleted lines, although the localization of residual chiasmata was not affected. DNA double-strand break formation appeared normal, but the recombination pathway was defective at later stages. A meiotic time course revealed a 12-h delay in prophase I progression to the first labeled tetrads. Barley ZYP1 appears to function similarly to ZIP1/ZYP1 in yeast and Arabidopsis, with an opposite effect on crossover number to ZEP1 in rice, another member of the Poaceae.

High-throughput phenotyping produces multiple measurements over time, which require new methods of analyses that are flexible in their quantification of plant growth and transpiration, yet are computationally economic. Here we develop such analyses and apply this to a rice population genotyped with a 700k SNP high-density array. Two rice diversity panels, indica and aus, containing a total of 553 genotypes, are phenotyped in waterlogged conditions. Using cubic smoothing splines to estimate plant growth and transpiration, we identify four time intervals that characterize the early responses of rice to salinity. Relative growth rate, transpiration rate and transpiration use efficiency (TUE) are analysed using a new association model that takes into account the interaction between treatment (control and salt) and genetic marker. This model allows the identification of previously undetected loci affecting TUE on chromosome 11, providing insights into the early responses of rice to salinity, in particular into the effects of salinity on plant growth and transpiration., Image-based plant phenotyping can be used to collect data with high temporal and spatial resolution. Here, the authors develop a computationally efficient method using smoothing splines and a new marker-by-trait association model to identify loci in a diverse rice population associated with early response to salinity.

Producing sufficient food for nine billion people by 2050 will be constrained by soil salinity, especially in irrigated systems. To improve crop yield, greater understanding of the genetic control of traits contributing to salinity tolerance in the field is needed. Here, we exploit natural variation in exotic germplasm by taking a genome-wide association approach to a new nested association mapping population of barley called HEB-25. The large population (1,336 genotypes) allowed cross-validation of loci, which, along with two years of phenotypic data collected from plants irrigated with fresh and saline water, improved statistical power. We dissect the genetic architecture of flowering time under high salinity and we present genes putatively affecting this trait and salinity tolerance. In addition, we identify a locus on chromosome 2H where, under saline conditions, lines homozygous for the wild allele yielded 30% more than did lines homozygous for the Barke allele. Introgressing this wild allele into elite cultivars could markedly improve yield under saline conditions.

Objective To evaluate maternal and neonatal outcomes associated with birth at term by week of gestational age and also by onset of labor. Design Cohort study. Setting A state-wide perinatal outcome database. Population 28,626 women with spontaneous onset of labor, induction of labor for recognized indications and induction of labor for non-recognized indications. Methods Cohort study utilizing a validated dataset comparing outcomes with type of onset of labor using a log binomial model. Main outcome measures Cesarean section, assisted vaginal birth, important measures of maternal and neonatal morbidity. Results Induction of labor for non-recognized indications was associated with a significantly increased risk of a range of outcomes, including cesarean section (RR 1.67, 95% CI 1.55-1.80). The lowest risk of adverse maternal and infant outcome occurred with birth between 38 and 39 weeks and with the spontaneous onset of labor. Conclusions Induction of labor for non-recognized indications at term is associated with an increased risk of adverse outcomes. Caution is warranted with a liberal policy of induction of labor at term in an otherwise uncomplicated pregnancy.

Phragmidium violaceum (Pv) isolate F15 was released for biological control of invasive European blackberry in Australia in 1991–1992. This study reports variation in the pathogenicity of isolate F15 and Pv isolates SA1, V1 and V2, collected in southeastern Australia in 1997 or 1998, on a broad sample of genetically variable European blackberry clones collected in 1996–2000. The use of whole shoots or detached leaflet discs led to the same conclusions about the relative susceptibility of a blackberry clone to a particular Pv isolate. Moderate to relatively high numbers of uredinia developed on all 25 blackberry clones inoculated with isolate V1, whereas no or few uredinia of isolates V2 and SA1 developed on Rubus erythrops clone EB20, three clones of Rubus leucostachys (EB9, EB19 and 960804) or Rubus sp. clone SR43. Pv isolate F15 differed from the three isolates collected in Australia in that no or few uredinia of F15 developed on Rubus polyanthemus clone 961107 or three clones of Rubus laciniatus (EB22, KE1, SR14). Isolate F15 also differed from isolates V1 and V2 for the density of uredinia as a function of leaf age in a clone of Rubus anglocandicans found widely in Australia. Isolates V1 and V2 ceased production of uredinia on leaves older than 16 days, whereas Pv isolate F15 continued production of uredinia beyond this leaf age. This study informed selection of additional Pv isolates from Europe for release in Australia in 2004.

OBJECTIVE Gestational diabetes mellitus (GDM) may cause obesity in the offspring. The objective was to assess the effect of treatment for mild GDM on the BMI of 4- to 5-year-old children. RESEARCH DESIGN AND METHODS Participants were 199 mothers who participated in a randomized controlled trial of the treatment of mild GDM during pregnancy and their children. Trained nurses measured the height and weight of the children at preschool visits in a state-wide surveillance program in the state of South Australia. The main outcome measure was age- and sex-specific BMI Z score based on standards of the International Obesity Task Force. RESULTS At birth, prevalence of macrosomia (birth weight ≥4,000 g) was 5.3% among the 94 children whose mothers were in the intervention group, and 21.9% among the 105 children in the routine care control group. At 4- to 5-years-old, mean (SD) BMI Z score was 0.49 (1.20) in intervention children and 0.41 (1.40) among controls. The difference between treatment groups was 0.08 (95% CI −0.29 to 0.44), an estimate minimally changed by adjustment for maternal race, parity, age, and socio-economic index (0.08 [−0.29 to 0.45]). Evaluating BMI ≥85th percentile rather than continuous BMI Z score gave similarly null results. CONCLUSIONS Although treatment of GDM substantially reduced macrosomia at birth, it did not result in a change in BMI at age 4- to 5-years-old.

Barley (Hordeum vulgare) is a crop of global significance. However, a third of the genes of barley are largely inaccessible to conventional breeding programmes as crossovers are localised to the ends of the chromosomes. This work examines whether crossovers can be shifted to more proximal regions simply by elevating growth temperature. We utilised a genome-wide marker set for linkage analysis combined with cytological mapping of crossover events to examine the recombination landscape of plants grown at different temperatures. We found that barley shows heterochiasmy, that is, differences between female and male recombination frequencies. In addition, we found that elevated temperature significantly changes patterns of recombination in male meiosis only, with a repositioning of Class I crossovers determined by cytological mapping of HvMLH3 foci. We show that the length of synaptonemal complexes in male meiocytes increases in response to temperature. The results demonstrate that the distribution of crossover events are malleable and can be shifted to proximal regions by altering the growth temperature. The shift in recombination is the result of altering the distribution of Class I crossovers, but the higher recombination at elevated temperatures is potentially not the result of an increase in Class I events.

A statistical approach is presented for selection of best performing lines for commercial release and best parents for future breeding programs from standard agronomic trials. The method involves the partitioning of the genetic effect of a line into additive and non-additive effects using pedigree based inter-line relationships, in a similar manner to that used in animal breeding. A difference is the ability to estimate non-additive effects. Line performance can be assessed by an overall genetic line effect with greater accuracy than when ignoring pedigree information and the additive effects are predicted breeding values. A generalized definition of heritability is developed to account for the complex models presented.

This paper presents the results from an investigation to assess the development of a Riesling and a wooded Chardonnay wine over five years. The wines were bottled either with or without added ascorbic acid and stored under controlled temperature and humidity conditions. Ascorbic acid addition to wine at bottling had little effect on wine aroma and flavour when the wines in this study had been in bottle for 6 months or less. For both wines, at bottle storage times of 3 years or more, addition of ascorbic acid at bottling resulted in wines with no difference in aroma or less oxidised and/or more fresh fruity aromas, even if all the ascorbic acid had been depleted at the time of assessment, compared to wines without addition of ascorbic acid at bottling. In terms of colour, for the Chardonnay wines, the effect of ascorbic acid addition at bottling assessed between two weeks and two years after bottling suggested that wines without addition were browner and had more overall colour intensity. For the Riesling wines, ascorbic acid addition had no significant effect on brownness and overall colour intensity although the Riesling wines with ascorbic acid were generally higher in yellow colour. The A420 measurements, which are widely used to estimate the brown colour of wines, did not always appear to correlate with the brown scores obtained by visual assessment or colour measures by CIELAB when wines with and without ascorbic acid addition were compared together. For both wines, after three and five years storage, the concentration of the antioxidant sulfur dioxide was either little different or else slightly(statistically significantly) higher in wines to which ascorbic acid was added at bottling than those without addition.

This paper presents the results from an investigation to assess the development of a Riesling and a wooded Chardonnay wine over five years following the imposition of several treatments at bottling. The wines were bottled under a screw cap closure, two different natural corks, a synthetic closure and in a glass ampoule. In addition, the effect of storage orientation was investigated. The bottled wines were stored under controlled temperature and humidity conditions. Various analyses were carried out on replicate bottles from each treatment, including sulfur dioxide and ascorbic acid concentration, sensory analysis of appearance and aroma attributes, and spectral measures. The largest treatment effect resided with the nature of the closure. Wines sealed with the synthetic closure were relatively oxidised in aroma, brown in colour, and low in sulfur dioxide compared to wines held under the other closures. A struck flint/rubber (reduced) aroma was discernible in the wines sealed under the screw caps or in glass ampoules. Wines sealed under natural bark corks in this study showed negligible reduced characters. The bottle orientation during storage under the conditions of this study had little effect on the composition and sensory properties of the wines examined.

Background (1,3;1,4)-β-Glucan is an important component of the cell walls of barley grain as it affects processability during the production of alcoholic beverages and has significant human health benefits when consumed above recommended threshold levels. This leads to diametrically opposed quality requirements for different applications as low levels of (1,3;1,4)-β-glucan are required for brewing and distilling and high levels for positive impacts on human health. Results We quantified grain (1,3;1,4)-β-glucan content in a collection of 399 2-row Spring-type, and 204 2-row Winter-type elite barley cultivars originating mainly from north western Europe. We combined these data with genotypic information derived using a 9 K Illumina iSelect SNP platform and subsequently carried out a Genome Wide Association Scan (GWAS). Statistical analysis accounting for residual genetic structure within the germplasm collection allowed us to identify significant associations between molecular markers and the phenotypic data. By anchoring the regions that contain these associations to the barley genome assembly we catalogued genes underlying the associations. Based on gene annotations and transcript abundance data we identified candidate genes. Conclusions We show that a region of the genome on chromosome 2 containing a cluster of CELLULOSE SYNTHASE-LIKE (Csl) genes, including CslF3, CslF4, CslF8, CslF10, CslF12 and CslH, as well as a region on chromosome 1H containing CslF9, are associated with the phenotype in this germplasm. We also observed that several regions identified by GWAS contain glycoside hydrolases that are possibly involved in (1,3;1,4)-β-glucan breakdown, together with other genes that might participate in (1,3;1,4)-β-glucan synthesis, re-modelling or regulation. This analysis provides new opportunities for understanding the genes related to the regulation of (1,3;1,4)-β-glucan content in cereal grains. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-907) contains supplementary material, which is available to authorized users.

Natural bark corks which were exposed to an atmosphere saturated with deuterium-labelled 2,4,6-trichloroanisole (d5-TCA) absorbed the d5-TCA rapidly. A commercially applied surface treatment did not prevent the ingress of the d5-TCA into the corks. d5-TCA was lost from contaminated corks by aeration relatively slowly. Nevertheless, the observation that TCA can be desorbed in this manner suggests that aeration, albeit under modified conditions, may yet prove useful in improving the quality of wine corks. Most of the absorbed d5-TCA was localised in the outer 2 mm of the cork cylinder, but a significant amount migrated to the interior of the cork cylinder after as little as twenty-four hours of exposure. Significantly more d5-TCA was found in the older growth compared to the younger growth bark after this time.

Effects of several inoculation protocols using Saccharomyces cerevisiae strain AWRI 838 (an isolate of Lalvin EC1118) and Candida stellata strain AWRI 1159 (CBS 2649) upon the aroma properties and chemical composition of Chardonnay wine were determined. An increase in the concentration of glycerol and acetic acid was observed when fermentation was performed with C. stellata AWRI 1159, which did not progress to dryness. Sensory descriptive analysis showed a substantial difference in aroma between the wines produced by monocultures of the two yeast species. The Candida stellata AWRI 1159 produced significantly more intense 'honey', 'apricot', and 'sauerkraut' aromas, and diminished the 'lime', 'banana' 'tropical fruit' and 'floral' aromas ascribed to S. cerevisiae AWRI 838. When C. stellata AWRI 1159 was co-inoculated at ten times the initial concentration of strain S. cerevisiae AWRI 838, the non-Saccharomyces yeast had only a minor impact upon wine aroma and composition despite maintaining a significant viable population of 5-10 X 106 colony forming units per mL throughout fermentation. Wine of a different aroma profile to either of the reference monoculture wines was produced by sequential fermentation, whereby C. stellata AWRI 1159 conducted the first half of fermentation, before inoculation with S. cerevisiae AWRI 838, and the subsequent completion of fermentation. This wine had 'floral', 'banana', 'lime', 'tropical fruit' and 'sauerkraut' aroma scores intermediate to the two reference monoculture wines, 'apricot' and 'honey' aroma ratings similar to the S. cerevisiae AWRI 838 wine, and 'ethyl acetate' aroma that exceeded that of both reference wines. These results suggest the potential of a reliable mixed culture fermentation strategy for exploiting unconventional, fermentation-impaired yeasts for producing greater flavour diversity in wine.