Starch phosphorylation associated SNPs found by genome-wide association studies in the potato (Solanum tuberosum L.)

Abstract Background The natural variation of starch phosphate content in potatoes has been previously reported. It is known that, in contrast to raw starch, commercially phosphorylated starch is more stable at high temperatures and shear rates and has higher water capacity. The genetic improvement of phosphate content in potato starch by selection or engineering would allow the production of phosphorylated starch in a natural, environmentally friendly way without chemicals. The aim of the current research is to identify genomic SNPs associated with starch phosphorylation by carrying out a genome-wide association study in potatoes. Results A total of 90 S. tuberosum L. varieties were used for phenotyping and genotyping. The phosphorus content of starch in 90 potato cultivars was measured and then statistically analysed. Principal component analysis (PCA) revealed that the third and eighth principal components appeared to be sensitive to variation in phosphorus content (p = 0.0005 and p = 0.002, respectively). PC3 showed the correlation of starch phosphorus content with allelic variations responsible for higher phosphorylation levels, found in four varieties. Similarly, PC8 indicated that hybrid 785/8–5 carried an allele associated with high phosphorus content, while the Impala and Red Scarlet varieties carried alleles for low phosphorus content. Genotyping was carried out using an Illumina 22 K SNP potato array. A total of 15,214 scorable SNPs (71.7% success rate) was revealed. GWAS mapping plots were obtained using TASSEL based on several statistical models, including general linear models (GLMs), with and without accounting for population structure, as well as MLM. A total of 17 significant SNPs was identified for phosphorus content in potato starch, 14 of which are assigned to 8 genomic regions on chromosomes 1, 4, 5, 7, 8, 10, and 11. Most of the SNPs identified belong to protein coding regions; however, their allelic variation was not associated with changes in protein structure or function. Conclusions A total of 8 novel genomic regions possibly associated with starch phosphorylation on potato chromosomes 1, 4, 5, 7, 8, 10, and 11 was revealed. Further validation of the SNPs identified and the analysis of the surrounding genomic regions for candidate genes will allow better understanding of starch phosphorylation biochemistry. The most indicative SNPs may be useful for developing diagnostic markers to accelerate the breeding of potatoes with predetermined levels of starch phosphorylation

The In-Silico Development of DNA Markers for Breeding of Spring Barley Varieties That Are Resistant to Spot Blotch in Russia

The fungal pathogen Cochliobolus sativus Drechs. Ex Dastur, anamorph Bipolaris sorokiniana (Sacc.) Shoemaker is one of the most common barley pathogens worldwide and causes spot blotch and root rot in barley. Spot blotch is considered to be the major biotic stress hampering the commercial production of barley. During high disease severity, which occurs in the northwestern region of Russia once every three to four years, yield losses for barley may reach 40%. An increase in common root rot severity results in yield losses that can reach 80%. The goal of the current study was to identify significant markers that can be employed as diagnostic DNA markers to breed C. sativus pathogen-resistant varieties of barley. In 94 spring barley cultivars and lines, the resistance of seedlings and adult plants to the impact of C. sativus on their leaves and roots was investigated. Five genomic regions associated with resistance to Spot blotch were identified (on chromosome 1H (50–61.2 cM), 2H (68.7–69.68 cM), 3H (18.72–26.18 cM), 7H (7.52–15.44 cM)). No significant loci were determined to be associated with root rot. According to obtained data, 11 significant SNPs were converted into KASP markers and 6 markers located on chromosome 3H were determined to possess good accuracy and the potential to be employed in marker-assisted selection

The Initial Response to COVID-19 Disruptions for Older People with HIV in Ukraine

Ukraine imposed a COVID-19 lockdown in March 2020. From April to June 2020, we surveyed 123 older people with HIV (OPWH) by phone to assess their mental health, engagement in HIV and other healthcare, and substance use using standardised scales. Variables of key interest were symptoms of depression and symptoms of anxiety. Univariate and multivariable Firth logistic regression models were built to assess factors associated with: (1) symptoms of depression, and (2) symptoms of anxiety. Findings indicated high suicidal ideation (10.6%); 45.5% met the screening criteria for moderate to severe depression; and 35.0% met the criteria for generalised anxiety disorder (GAD). Independent correlates of having moderate to severe depression included being female (AOR: 2.83, 95%CI = 1.19–7.05), having concerns about potential barriers to HIV treatment (AOR: 8.90, 95%CI = 1.31–104.94), and active drug use (AOR: 34.53, 95%CI = 3.02–4885.85). Being female (AOR: 5.30, 95%CI = 2.16–14.30) and having concerns about potential barriers to HIV treatment (AOR: 5.33, 95%CI = 1.22–28.45) were independently correlated with GAD, and over half (58.5%) were willing to provide peer support to other OPWH. These results highlight the impact of the COVID-19 restrictions in Ukraine on mental health for OPWH and support the need to screen for psychiatric and substance use disorders, potentially using telehealth strategies

Influence of Structure of Detrital Food Webs on Fusarium Head Blight of Winter Wheat

Conventional methods for Fusarium head blight (FHB) control are ineffective. A better understanding of the mechanisms linking the abundance of Fusarium species in soil before winter wheat flowering and mycotoxin content in mature grain may help to improve the effectiveness of methods for FHB control. In this study, we established a field experiment aimed to trace the impact of three types of organic mulch with different C:N ratios on the structure of detrital food webs and the manifestation of winter wheat FHB. T2-toxin content in grain was significantly higher in N-poor treatment (52.1 ± 0.2 µg g−1) compared to N-rich treatment (40.4 ± 1.6 µg g−1). The structure of detrital food webs in the studied treatments changed significantly after mulch addition; the abundance of soil saprophages and mycophages increased up to 50%. Based on the results of mixed-effects modeling, the abundance of herpetobionts and soil mesofauna were positively associated with an increase in Fusarium biomass in grain. The increase in the content of T2-toxin in the grain was associated with an increase in the abundance of earthworms and phytophagous macrofauna in the soil. Results suggest the existence of a previously undescribed mechanism for FHB infection by transfer of pathogenic spores by soil invertebrates, while the content of mycotoxins in grain can be triggered by the grazing activity of soil phytophagous invertebrates