Deciphering salt stress responses in Solanum pimpinellifolium through high-throughput phenotyping.

Soil salinity is a major environmental stressor affecting agricultural productivity worldwide. Understanding plant responses to salt stress is crucial for developing resilient crop varieties. Wild relatives of cultivated crops, such as wild tomato, Solanum pimpinellifolium, can serve as a useful resource to further expand the resilience potential of the cultivated germplasm, S. lycopersicum. In this study, we employed high-throughput phenotyping in the greenhouse and field conditions to explore salt stress responses of a S. pimpinellifolium diversity panel. Our study revealed extensive phenotypic variations in response to salt stress, with traits such as transpiration rate, shoot mass, and ion accumulation showing significant correlations with plant performance. We found that while transpiration was a key determinant of plant performance in the greenhouse, shoot mass strongly correlated with yield under field conditions. Conversely, ion accumulation was the least influential factor under greenhouse conditions. Through a Genome Wide Association Study, we identified candidate genes not previously associated with salt stress, highlighting the power of high-throughput phenotyping in uncovering novel aspects of plant stress responses. This study contributes to our understanding of salt stress tolerance in S. pimpinellifolium and lays the groundwork for further investigations into the genetic basis of these traits, ultimately informing breeding efforts for salinity tolerance in tomato and other crops.

Genetic mapping of the early responses to salt stress in Arabidopsis thaliana.

Salt stress decreases plant growth prior to significant ion accumulation in the shoot. However, the processes underlying this rapid reduction in growth are still unknown. To understand the changes in salt stress responses through time and at multiple physiological levels, examining different plant processes within a single set-up is required. Recent advances in phenotyping has allowed the image-based estimation of plant growth, morphology, colour and photosynthetic activity. In this study, we examined the salt stress-induced responses of 191 Arabidopsis accessions from 1 h to 7 days after treatment using high-throughput phenotyping. Multivariate analyses and machine learning algorithms identified that quantum yield measured in the light-adapted state (Fv' /Fm' ) greatly affected growth maintenance in the early phase of salt stress, whereas the maximum quantum yield (QYmax ) was crucial at a later stage. In addition, our genome-wide association study (GWAS) identified 770 loci that were specific to salt stress, in which two loci associated with QYmax and Fv' /Fm' were selected for validation using T-DNA insertion lines. We characterized an unknown protein kinase found in the QYmax locus that reduced photosynthetic efficiency and growth maintenance under salt stress. Understanding the molecular context of the candidate genes identified will provide valuable insights into the early plant responses to salt stress. Furthermore, our work incorporates high-throughput phenotyping, multivariate analyses and GWAS, uncovering details of temporal stress responses and identifying associations across different traits and time points, which are likely to constitute the genetic components of salinity tolerance.

Corrigendum: The genome of Chenopodium quinoa.

This corrects the article DOI: 10.1038/nature21370.

The genome of Chenopodium quinoa.

Chenopodium quinoa (quinoa) is a highly nutritious grain identified as an important crop to improve world food security. Unfortunately, few resources are available to facilitate its genetic improvement. Here we report the assembly of a high-quality, chromosome-scale reference genome sequence for quinoa, which was produced using single-molecule real-time sequencing in combination with optical, chromosome-contact and genetic maps. We also report the sequencing of two diploids from the ancestral gene pools of quinoa, which enables the identification of sub-genomes in quinoa, and reduced-coverage genome sequences for 22 other samples of the allotetraploid goosefoot complex. The genome sequence facilitated the identification of the transcription factor likely to control the production of anti-nutritional triterpenoid saponins found in quinoa seeds, including a mutation that appears to cause alternative splicing and a premature stop codon in sweet quinoa strains. These genomic resources are an important first step towards the genetic improvement of quinoa.

A pilot study using lactulose in management of minimal hepatic encephalopathy in children with extrahepatic portal vein obstruction.

BACKGROUND: Minimal hepatic encephalopathy (MHE) is not associated with overt neuropsychiatric symptoms but rather with subtle changes in psychometric and/or neurophysiologic tests. We aimed to diagnose MHE in children with extrahepatic portal vein obstruction (EHPVO) and to evaluate the effect of lactulose on MHE. METHODS: A prospective study was carried out on 30 patients with EHPVO (21 males; mean age 10±2.5 years). The study was carried out in the Pediatric Hepatology Unit, Cairo University Pediatric Hospital, Cairo, Egypt, between 2011 and 2013. All patients were subjected to clinical and laboratory assessment, neuropsychmetric testing using the arabic version of Wechsler intelligence tests, neurophysiological testing by visual electroencephalogram and P300 event related potentials (ERP). RESULTS: The prevalence of MHE among children with EHPVO was 20% (6/30). After randomization to treatment and no-treatment groups using lactulose, all tests were repeated after three months. Among four patients with MHE who received lactulose, three (75%) improved. On the other hand, one of the patients in the no-treatment group developed MHE. Only one patient in the treatment arm had to discontinue lactulose because of severe diarrhea. CONCLUSIONS: This pilot study revealed that the prevalence of MHE was 20%. Improvement on psychometic tests was seen in 75% of our patients (3/4) after treatment with lactulose. Lactulose treatment was well tolerated.

The prevalence of congenital heart defects in infants with cholestatic disorders of infancy: a single-centre study.

BACKGROUND: There is deficiency of data about congenital heart defects (CHDs) in cholestatic disorders of infancy other than Alagille syndrome (AGS). We aimed to define the prevalence and types of CHDs in infants with various causes of cholestatic disorders of infancy. METHODS: This cross-sectional study was conducted on 139 infants presenting with cholestasis whether surgical or non-surgical. The study was carried out at the Pediatric Hepatology Unit, Cairo University Children's Hospital, Egypt. Full examination and investigations were done in an attempt to reach an aetiologic diagnosis for cholestasis, in addition to a comprehensive echocardiographic study. RESULTS: The age at the onset of cholestasis ranged from 1 day to 7 months. Males constituted 61.2%. Biliary atresia (BA) was diagnosed in 39 patients (28%), AGS in 16 patients (11.5%), 27 patients had miscellaneous diagnoses and 57 cases had indeterminate aetiology. CHDs were detected in 55 patients (39.5%). Shunt lesions were detected in 24 patients (43.6%), pulmonary stenosis in 18 patients (32.7%) and combined lesions in 9 patients (16.4%). Three patients (5.5%) had abnormal cardiac situs. Only seven patients had clinical presentation suggestive of CHD. CHDs were detected in 14 patients with BA (35.9%), 15 patients with AGS (93.7%) and 26 patients in the remaining group (30.9%). CONCLUSION: CHDs are not uncommon among cholestatic infants and are mostly asymptomatic. Echocardiographic examination of cholestatic infants is recommended particularly for patients with BA before undergoing hepatic portoenterostomy as presence of CHD may impact the anaesthetic planning and affect the outcome of hepatobiliary surgery.