Genetic Variability and Correlation of Biochemical and Sensory Characteristics of Coffee

Organoleptic and biochemical attributes in the coffee bean determine the final cup quality of coffee which is a critical factor in the price determination of coffee in the market. The study aimed at determining the genetic variability of the green coffee bean. The trial sites were located at Siaya and Busia counties in Kenya. Nineteen different genotypes were established and included Arabusta coffee hybrids, backcrosses of Arabica to tetraploid Robusta, Arabica coffee, Robusta coffee, and Arabusta coffee. Randomized Complete Block Design with three replications in each site was used in conducting the experiment. The coffee beans were harvested in the year 2018 and extraction and calculation of sucrose, trigonelline, caffeine, and chlorogenic acids was carried using the recommended methods. The cupping procedure involved the use of five judges in assessing the flavor, aroma, balance, overall standard, acidity, body, and aftertaste of the roasted coffee beans. The sensory evaluation used the Specialty Coffee Association (SCA) method. There were significant variations recorded for the traits that were measured. All the traits were highly heritable registering values of > 50% for heritability whereby, caffeine and oil were highly heritable traits with 90.8% and 88.9% respectively. Oil had a high phenotypic coefficient of variation, genotypic variation, and response values when compared to the other traits. All the organoleptic traits were positively correlated with sucrose, trigonelline, and oil but the correlation with caffeine and chlorogenic acids was negative. The genotypic effects contributed largely to the high heritability recorded with a low influence from the environmental factors.

Selection and Characterization of Burkholderia spp. for Their Plant-Growth Promoting Effects and Influence on Maize Seed Germination

Burkholderia sp. is a bacterial genus extremely versatile in the environment and has been reported for a great potential to promote plant growth via different mechanisms. Here we evaluate the plant growth-promoting mechanisms in twenty-six Burkholderia strains. Strains were evaluated for their ability to promote plant growth by means of: indole-3-acetic acid (IAA) production under different conditions of pH, salt stress and the presence or absence of L-tryptophan; exopolysaccharides (EPS) production and quorum sensing (ALH). The strains were also characterized in terms of their genetic variability and species identification through Sanger sequencing. Then, the bacteria most responsive in the greatest number of plant-growth promotion mechanisms were selected for a corn seed germination test. All bacteria synthesized IAA in medium with 0.0 or 5.0 mM of L-tryptophan in combination with either 1 or 5% of NaCl, and pH values of either 4.5 or 7.2. The EPS production was confirmed for 61.54% of the bacterial strains. Quorum sensing also occurred in 92.3% of the selected bacteria. The Jaccard similarity coefficient revealed 16 clusters with high genetic variability between bacterial strains. Bacterial strains were assigned to seven species: B. anthina, B. cepacia, B. gladioli, B. ambifaria, B. graminis, B. heleia, and Burkholderia spp. The corn seed bacterization did not affect the germination velocity index (GSI), as well as the first count of germinated seeds (FC). However, inoculations formulated with B. heleia strain G28, B. gladioli strain UAGC723, and B. graminis strain UAGC348 promoted significant increases in root length, seedling height and fresh and dry seedling phytomass, respectively. These results indicate the high biotechnological potential of several strains in the genus Burkholderia sp. as seed inoculants, favoring germination and seedling initial development.

Elucidating Hexanucleotide Repeat Number and Methylation within the X-Linked Dystonia-Parkinsonism (XDP)-Related SVA Retrotransposon in TAF1 with Nanopore Sequencing

Background: X-linked dystonia-parkinsonism (XDP) is an adult-onset neurodegenerative disorder characterized by progressive dystonia and parkinsonism. It is caused by a SINE-VNTR-Alu (SVA) retrotransposon insertion in the TAF1 gene with a polymorphic (CCCTCT)n domain that acts as a genetic modifier of disease onset and expressivity. Methods: Herein, we used Nanopore sequencing to investigate SVA genetic variability and methylation. We used blood-derived DNA from 96 XDP patients for amplicon-based deep Nanopore sequencing and validated it with fragment analysis which was performed using fluorescence-based PCR. To detect methylation from blood- and brain-derived DNA, we used a Cas9-targeted approach. Results: High concordance was observed for hexanucleotide repeat numbers detected with Nanopore sequencing and fragment analysis. Within the SVA locus, there was no difference in genetic variability other than variations of the repeat motif between patients. We detected high CpG methylation frequency (MF) of the SVA and flanking regions (mean MF = 0.94, SD = ±0.12). Our preliminary results suggest only subtle differences between the XDP patient and the control in predicted enhancer sites directly flanking the SVA locus. Conclusions: Nanopore sequencing can reliably detect SVA hexanucleotide repeat numbers, methylation and, lastly, variation in the repeat motif.

Identification of Hotspot Mutations in the N Gene of SARS-CoV-2 in Russian Clinical Samples That May Affect the Detection by Reverse Transcription-PCR

Sensitive and reliable diagnostic test systems based on real-time PCR are of great importance in the fight against the ongoing SARS-CoV-2 pandemic. The genetic variability of the SARS-CoV-2 virus leads to the accumulation of mutations, some of which may affect the sensitivity of modern PCR assays. The aim of this study was to search in Russian clinical samples for new mutations in SARS-CoV-2 gene N that can affect the detection by RT-PCR. In this study, the polymorphisms in the regions of the target gene N causing failed or poor detection of the target N in the RT-PCR assay on 12 selected samples were detected. Sequencing the entire N and E genes in these samples along with other 195 samples that were positive for both target regions was performed. Here, we identified a number of nonsynonymous mutations and one novel deletion in the N gene that affected the ability to detect a target in the N gene as well a few mutations in the E gene of SARS-CoV-2 that did not affect detection. Sequencing revealed that majority of the mutations in the N gene were located in the variable region between positions 193 and 235 aa, inside and nearby the phosphorylated serine-rich region of the protein N. This study highlights the importance of the further characterization of the genetic variability and evolution of gene N, the most common target for detecting SARS-CoV-2. The use of at least two targets for detecting SARS-CoV-2, including one for the E gene, will be necessary for reliable diagnostics.