A population of wheat multiple synthetic derivatives: an effective platform to explore, harness and utilize genetic diversity of Aegilops tauschii for wheat improvement

Introducing genes from wild relatives is the best option to increase genetic diversity and discover new alleles necessary for wheat improvement. A population harboring genomic fragments from the diploid wheat progenitor Aegilops tauschii Coss. in the background of bread wheat (Triticum aestivum L.) was developed by crossing and backcrossing 43 synthetic wheat lines with the common wheat cultivar Norin 61. We named this population multiple synthetic derivatives (MSD). To validate the suitability of this population for wheat breeding and genetic studies, we randomly selected 400 MSD lines and genotyped them by using Diversity Array Technology sequencing markers. We scored black glume as a qualitative trait and heading time in two environments in Sudan as a quantitative trait. Our results showed high genetic diversity and less recombination which is expected from the nature of the population. Genome-wide association (GWA) analysis showed one QTL at the short arm of chromosome 1D different from those alleles reported previously indicating that black glume in the MSD population is controlled by new allele at the same locus. For heading time, from the two environments, GWA analysis revealed three QTLs on the short arms of chromosomes 2A, 2B and 2D and two on the long arms of chromosomes 5A and 5D. Using the MSD population, which represents the diversity of 43 Ae. tauschii accessions representing most of its natural habitat, QTLs or genes and desired phenotypes (such as drought, heat and salinity tolerance) could be identified and selected for utilization in wheat breeding

Antiretroviral Genotypic Resistance Mutations in HIV-1 Infected Korean Patients with Virologic Failure

Resistance assays are useful in guiding decisions for patients experiencing virologic failure (VF) during highly-active antiretroviral therapy (HAART). We investigated antiretroviral resistance mutations in 41 Korean human immunodeficiency virus type 1 (HIV-1) infected patients with VF and observed immunologic/virologic response 6 months after HAART regimen change. Mean HAART duration prior to resistance assay was 45.3±27.5 months and commonly prescribed HAART regimens were zidovudine/lamivudine/nelfinavir (22.0%) and zidovudine/lamivudine/efavirenz (19.5%). Forty patients (97.6%) revealed intermediate to high-level resistance to equal or more than 2 antiretroviral drugs among prescribed HAART regimen. M184V/I mutation was observed in 36 patients (87.7%) followed by T215Y/F (41.5%) and M46I/L (34%). Six months after resistance assay and HAART regimen change, median CD4+ T cell count increased from 168 cells/µL (interquartile range [IQR], 62-253) to 276 cells/µL (IQR, 153-381) and log viral load decreased from 4.65 copies/mL (IQR, 4.18-5.00) to 1.91 copies/mL (IQR, 1.10-3.60) (P<0.001 for both values). The number of patients who accomplished viral load <400 copies/mL was 26 (63.4%) at 6 months follow-up. In conclusion, many Korean HIV-1 infected patients with VF are harboring strains with multiple resistance mutations and immunologic/virologic parameters are improved significantly after genotypic resistance assay and HAART regimen change

Genomic traces of Japanese malting barley breeding in two modern high-quality cultivars, ‘Sukai Golden’ and ‘Sachiho Golden’

Two modern high-quality Japanese malting barley cultivars, ‘Sukai Golden’ and ‘Sachiho Golden’, were subjected to RNA-sequencing of transcripts extracted from 20-day-old immature seeds. Despite their close relation, 2,419 Sukai Golden-specific and 3,058 Sachiho Golden-specific SNPs were detected in comparison to the genome sequences of two reference cultivars: ‘Morex’ and ‘Haruna Nijo’. Two single nucleotide polymorphism (SNP) clusters respectively showing the incorporation of (1) the barley yellow mosaic virus (BaYMV) resistance gene rym5 from six-row non-malting Chinese landrace Mokusekko 3 on the long arm of 3H, and (2) the anthocyanin-less ant2 gene from a two-row Dutch cultivar on the long arm of 2H were detected specifically in ‘Sukai Golden’. Using 221 recombinant inbred lines of a cross between ‘Ishukushirazu’ and ‘Nishinochikara’, another BaYMV resistance rym3 gene derived from six-row non-malting Japanese cultivar ‘Haganemugi’ was mapped to a 0.4-cM interval on the proximal region of 5H. Haplotype analysis of progenitor accessions of the two modern malting cultivars revealed that rym3 of ‘Haganemugi’ was independently introduced into ‘Sukai Golden’ and ‘Sachiho Golden’. Residual chromosome 5H segments of ‘Haganemugi’ surrounding rym3 were larger in ‘Sukai Golden’. Available results suggest possibilities for malting quality improvement by minimizing residual segments surrounding rym3

A metabolome genome-wide association study implicates histidine N-pi-methyltransferase as a key enzyme in N-methylhistidine biosynthesis in Arabidopsis thaliana

A genome-wide association study (GWAS), which uses information on single nucleotide polymorphisms (SNPs) from many accessions, has become a powerful approach to gene identification. A metabolome GWAS (mGWAS), which relies on phenotypic information based on metabolite accumulation, can identify genes that contribute to primary and secondary metabolite contents. In this study, we carried out a mGWAS using seed metabolomic data from Arabidopsis thaliana accessions obtained by liquid chromatography–mass spectrometry to identify SNPs highly associated with the contents of metabolites such as glucosinolates. These SNPs were present in genes known to be involved in glucosinolate biosynthesis, thus confirming the effectiveness of our analysis. We subsequently focused on SNPs detected in an unknown methyltransferase gene associated with N-methylhistidine content. Knockout and overexpression of A. thaliana lines of this gene had significantly decreased and increased N-methylhistidine contents, respectively. We confirmed that the overexpressing line exclusively accumulated histidine methylated at the pi position, not at the tau position. Our findings suggest that the identified methyltransferase gene encodes a key enzyme for N-methylhistidine biosynthesis in A. thaliana

Clinical Review of Endogenous Endophthalmitis in Korea: A 14-Year Review of Culture Positive Cases of Two Large Hospitals

PURPOSE: To identify the clinical features and outcomes of endogenous endophthalmitis in Korea. MATERIALS AND METHODS: We reviewed 18 patients with endogenous endophthalmitis at 2 Korean hospitals, treated over a 14 year period between January 1993 and December 2006. RESULTS: The comorbidities observed in these cases were diabetes mellitus and liver cirrhosis. The most common pathogens, which were found in 7 patients each (38.9%), were Klebsiella pneumonia and Pseudomonas aeruginosa. All patients were treated with systemic antibiotics and fortified topical antibiotics. A surgical approach including vitrectomy was performed in 9 cases (50.0%). The prognosis was generally poor, and visual acuity improved slightly in 6 patients (33.3%). CONCLUSION: In this study, diabetes mellitus and Klebsiella pneumonia showed a close relationship with endogenous endophthalmitis, respectively. Endogenous endophthalmitis is a serious risk to sight and careful attention to establishing the diagnosis and management may decrease the ocular morbidity.ope

Efficient anchoring of alien chromosome segments introgressed into bread wheat by new Leymus racemosus genome-based markers

Background: The tertiary gene pool of bread wheat, to which Leymus racemosus belongs, has remained underutilized due to the current limited genomic resources of the species that constitute it. Continuous enrichment of public databases with useful information regarding these species is, therefore, needed to provide insights on their genome structures and aid successful utilization of their genes to develop improved wheat cultivars for effective management of environmental stresses. Results: We generated de novo DNA and mRNA sequence information of L. racemosus and developed 110 polymorphic PCR-based markers from the data, and to complement the PCR markers, DArT-seq genotyping was applied to develop additional 9990 SNP markers. Approximately 52% of all the markers enabled us to clearly genotype 22 wheat-L. racemosus chromosome introgression lines, and L. racemosus chromosome-specific markers were highly efficient in detailed characterization of the translocation and recombination lines analyzed. A further analysis revealed remarkable transferability of the PCR markers to three other important Triticeae perennial species: L. mollis, Psathyrostachys huashanica and Elymus ciliaris, indicating their suitability for characterizing wheat-alien chromosome introgressions carrying chromosomes of these genomes. Conclusion: The efficiency of the markers in characterizing wheat-L. racemosus chromosome introgression lines proves their reliability, and their high transferability further broadens their scope of application. This is the first report on sequencing and development of markers from L. racemosus genome and the application of DArT-seq to develop markers from a perennial wild relative of wheat, marking a paradigm shift from the seeming concentration of the technology on cultivated species. Integration of these markers with appropriate cytogenetic methods would accelerate development and characterization of wheat-alien chromosome introgression lines