Genetic Control of Sweetness, Acidity, and Seediness in Blackberry

The global blackberry (Rubus L. subgenus Rubus Watson) industry has experienced rapid growth during the past 15 years. Even so, many industry stakeholders report complaints from consumers and grocers stating blackberries are often too tart, too seedy, or not sweet enough for their liking. The development of molecular markers for high sweetness, low acidity, and reduced seediness would allow breeding programs to expeditiously make selection and crossing decisions in the early stages of the breeding pipeline. The objective of this study was to use a Genome-Wide Association Study (GWAS) to identify marker-trait associations, locate quantitative trait loci (QTL), and find possible candidate genes related to sweetness, acidity, and seediness in autotetraploid blackberries. A panel of 307 commercially-available cultivars and University of Arkansas System Division of Agriculture (UA) breeding selections grown at the Fruit Research Station in Clarksville, Arkansas, was phenotyped for soluble solids content (SSC) and pH in 2019, 2020, and 2021. Samples from a subset of 277 cultivars and breeding selections harvested during the summers of 2019 and 2020 were also evaluated for titratable acidity (TA), 100-seed weight, seed width to length (WL) ratio, seed area, and seeds per berry. The Rubus argutus Link. reference genome was used to design 35,054 Capture-Seq probes distributed across the genome, which were used to genotype the GWAS panel. Heritability estimates for flavor attributes concluded SSC had the lowest broad sense entry mean heritability at 61%, while pH and TA had heritabilities of 67% and 69%, respectively. Seediness attribute heritability estimates were 91% for 100-seed weight and WL ratio, 89% for seed area, and 70% for seeds per berry. Association analysis was performed in GWASpoly with 124,564 single nucleotide polymorphisms (SNPs) generated by Capture-Seq genotyping and a total of six QTL were identified. Three of the six QTL were related to flavor attributes; one for TA on Ra01, one for SSC on Ra02, and a shared QTL for TA and pH on Ra05. The remaining three QTL were related to seediness; one for WL ratio on Ra01, one for 100-seed weight on Ra03, and one for seed area on Ra05. No significant markers or QTL were identified for seeds per berry. Ten possible candidate genes for blackberry flavor attributes were identified, including an H+-ATPase 8 and a vacuolar proton-translocating pyrophosphatase associated with the QTL for TA on Ra01, a sucrose binding protein for the SSC QTL on Ra02, and two ALMT9 proteins, a MYB1, a PEPC, and three malate synthase genes for the shared TA and pH QTL on Ra05. Six seediness candidates were identified consisting of genes annotated for BRI1, CKX2, and GG3 associated with the WL ratio QTL on Ra01, an RPT2A and an AP2C1 in the QTL for 100-seed weight on Ra03, and a DA1 protein in the seed area QTL on Ra05. These results will be used to develop diagnostic markers for attributes related to sweetness, acidity, and seediness and as a training population for genomic selection

Multiorgan MRI findings after hospitalisation with COVID-19 in the UK (C-MORE): a prospective, multicentre, observational cohort study

Introduction: The multiorgan impact of moderate to severe coronavirus infections in the post-acute phase is still poorly understood. We aimed to evaluate the excess burden of multiorgan abnormalities after hospitalisation with COVID-19, evaluate their determinants, and explore associations with patient-related outcome measures. Methods: In a prospective, UK-wide, multicentre MRI follow-up study (C-MORE), adults (aged ≥18 years) discharged from hospital following COVID-19 who were included in Tier 2 of the Post-hospitalisation COVID-19 study (PHOSP-COVID) and contemporary controls with no evidence of previous COVID-19 (SARS-CoV-2 nucleocapsid antibody negative) underwent multiorgan MRI (lungs, heart, brain, liver, and kidneys) with quantitative and qualitative assessment of images and clinical adjudication when relevant. Individuals with end-stage renal failure or contraindications to MRI were excluded. Participants also underwent detailed recording of symptoms, and physiological and biochemical tests. The primary outcome was the excess burden of multiorgan abnormalities (two or more organs) relative to controls, with further adjustments for potential confounders. The C-MORE study is ongoing and is registered with ClinicalTrials.gov, NCT04510025. Findings: Of 2710 participants in Tier 2 of PHOSP-COVID, 531 were recruited across 13 UK-wide C-MORE sites. After exclusions, 259 C-MORE patients (mean age 57 years [SD 12]; 158 [61%] male and 101 [39%] female) who were discharged from hospital with PCR-confirmed or clinically diagnosed COVID-19 between March 1, 2020, and Nov 1, 2021, and 52 non-COVID-19 controls from the community (mean age 49 years [SD 14]; 30 [58%] male and 22 [42%] female) were included in the analysis. Patients were assessed at a median of 5·0 months (IQR 4·2–6·3) after hospital discharge. Compared with non-COVID-19 controls, patients were older, living with more obesity, and had more comorbidities. Multiorgan abnormalities on MRI were more frequent in patients than in controls (157 [61%] of 259 vs 14 [27%] of 52; p<0·0001) and independently associated with COVID-19 status (odds ratio [OR] 2·9 [95% CI 1·5–5·8]; padjusted=0·0023) after adjusting for relevant confounders. Compared with controls, patients were more likely to have MRI evidence of lung abnormalities (p=0·0001; parenchymal abnormalities), brain abnormalities (p<0·0001; more white matter hyperintensities and regional brain volume reduction), and kidney abnormalities (p=0·014; lower medullary T1 and loss of corticomedullary differentiation), whereas cardiac and liver MRI abnormalities were similar between patients and controls. Patients with multiorgan abnormalities were older (difference in mean age 7 years [95% CI 4–10]; mean age of 59·8 years [SD 11·7] with multiorgan abnormalities vs mean age of 52·8 years [11·9] without multiorgan abnormalities; p<0·0001), more likely to have three or more comorbidities (OR 2·47 [1·32–4·82]; padjusted=0·0059), and more likely to have a more severe acute infection (acute CRP >5mg/L, OR 3·55 [1·23–11·88]; padjusted=0·025) than those without multiorgan abnormalities. Presence of lung MRI abnormalities was associated with a two-fold higher risk of chest tightness, and multiorgan MRI abnormalities were associated with severe and very severe persistent physical and mental health impairment (PHOSP-COVID symptom clusters) after hospitalisation. Interpretation: After hospitalisation for COVID-19, people are at risk of multiorgan abnormalities in the medium term. Our findings emphasise the need for proactive multidisciplinary care pathways, with the potential for imaging to guide surveillance frequency and therapeutic stratification