Characterization of Brassica napus (Canola) Germplasm Based on Microsatellite Markers

Brassica napus L. is a major oilseed crop all over the world. The aim of this study was to investigate the genetic diversity of B. napus germplasm by using simple sequence repeats (SSR) markers. In the current study, ten SSR markers were used for studying genetic diversity of ten Brassica cultivars. Out of 110 total bands, 68 bands were polymorphic with 52.11% average polymorphism. Mean value of Nei’s genetic diversity and Polymorphism Information Content was 1.7, and 0.2630, respectively. These mean values show that there are moderate allelic differences between Brassica cultivars. The Nei’s genetic distance among various cultivars was 0.3281 and 0.125 which showed that germplasm of Brassica cultivars are different from each other, which is probably due to anthropogenic interventions and environmental factors. Thus, genetically different lines identified in this study could be employed in breeding programmes to develop higher-quality canola inbred varieties in future.

Allelic variants of full-length VAR2CSA, the placental malaria vaccine candidate, differ in antigenicity and receptor binding affinity

Plasmodium falciparum-infected erythrocytes (IE) sequester in the placenta via surface protein VAR2CSA, which binds chondroitin sulfate A (CSA) expressed on the syncytiotrophoblast surface, causing placental malaria (PM) and severe adverse outcomes in mothers and their offspring. VAR2CSA belongs to the PfEMP1 variant surface antigen family; PfEMP1 proteins mediate IE adhesion and facilitate parasite immunoevasion through antigenic variation. Here we produced deglycosylated (native-like) and glycosylated versions of seven recombinant full-length VAR2CSA ectodomains and compared them for antigenicity and adhesiveness. All VAR2CSA recombinants bound CSA with nanomolar affinity, and plasma from Malian pregnant women demonstrated antigen-specific reactivity that increased with gravidity and trimester. However, allelic and glycosylation variants differed in their affinity to CSA and their serum reactivities. Deglycosylated proteins (native-like) showed higher CSA affinity than glycosylated proteins for all variants except NF54. Further, the gravidity-related increase in serum VAR2CSA reactivity (correlates with acquisition of protective immunity) was absent with the deglycosylated form of atypical M200101 VAR2CSA with an extended C-terminal region. Our findings indicate significant inter-allelic differences in adhesion and seroreactivity that may contribute to the heterogeneity of clinical presentations, which could have implications for vaccine design.

WGS analysis of Listeria monocytogenes from rural, urban, and farm environments in Norway: Genetic diversity, persistence, and relation to clinical and food isolates

Listeria monocytogenes is a ubiquitous environmental bacterium associated with a wide variety of natural and man-made environments, such as soil, vegetation, livestock, food processing environments, and urban areas. It is also among the deadliest foodborne pathogens, and knowledge about its presence and diversity in potential sources is crucial to effectively track and control it in the food chain. Isolation of L. monocytogenes from various rural and urban environments showed higher prevalence in agricultural and urban developments than in forest or mountain areas, and that detection was positively associated with rainfall. Whole genome sequencing (WGS) was performed for the collected isolates and for L. monocytogenes from Norwegian dairy farms and slugs, in total 218 isolates. The data was compared with available datasets from clinical and food associated sources in Norway collected within the last decade. Multiple examples of clusters of isolates with 0?8 wgMLST allelic differences were collected over time in the same location, demonstrating persistence of L. monocytogenes in natural, urban and farm environments. Furthermore, several clusters with 6?20 wgMLST allelic differences containing isolates collected across different locations, times and habitats were identified, including nine clusters harbouring clinical isolates. The most ubiquitous clones found in soil and other natural and animal ecosystems (CC91, CC11, and CC37) were distinct from clones predominating among both clinical (CC7, CC121, CC1) and food (CC9, CC121, CC7, CC8) isolates. The analyses indicated that ST91 was more prevalent in Norway than other countries and revealed a high proportion of the hypovirulent ST121 among Norwegian clinical cases.

Inheritance of some quantitative traits in the hybrid generations ‘Kuboyar × Gagat’

Rice is an important food for humans. In the world, for food purposes white-grain rice varieties are mainly used, but there are varieties in which kernel pericarp is of red, brown, purple or black color. Such rice is more beneficial for health promotion. The current paper has presented the results of genetic analysis of the inheritance of a number of variable quantitative traits in rice hybrid populations of the first and third generations obtained by the hybridization of the varieties ‘Kuboyar’ and ‘Gagat’. The variety ‘Kuboyar’ is medium-sized, with a compact erect panicle, an oval caryopsis and white pericarp. The variety ‘Gagat’ is tall, with a long drooping panicle, a long kernel and black pericarp. The work was carried out on the territory of the OP ‘Proletarskoe’ of the Rostov region in 2018–2020. The analysis of the inheritance of some quantitative traits that have a direct impact on the rice productivity made it possible to establish new inheritance regularities. According to the trait ‘plant height’ there has been identified partial dominance of the largest values of the trait in the hybrids F2 and F3. Allelic differences of 3 pairs of genes were identified in parental forms. The trait ‘panicle length’ showed overdominance of the trait in F2, it was absent in F3, and there were digenic differences in parental forms. The trait ‘number of spikelets per panicle’ demonstrated overdominance of large values and positive transgression. According to the trait ‘1000-grain weight’, the hybrids of both generations were split by the digenic scheme in a ratio of 1:4:6:4:1. There was no dominance in the trait ‘kernel length’; the initial varieties had differences in 2 pairs of genes. According to the trait ‘kernel width’, there was identified incomplete dominance of smaller values, and there was monohybrid split. There have been selected the best plants F3 with a black pericarp, average values of the traits ‘plant height’, ‘panicle length’, ‘1000-grain weight’ and an increased number of grains per panicle for the further breeding process.

Differentially accessible, single copy sequences form contiguous domains along metaphase chromosomes that are conserved among multiple tissues

Background During mitosis, chromatin engages in a dynamic cycle of condensation and decondensation. Condensation into distinct units to ensure high fidelity segregation is followed by rapid and reproducible decondensation to produce functional daughter cells. Factors contributing to the reproducibility of chromatin structure between cell generations are not well understood. We investigated local metaphase chromosome condensation along mitotic chromosomes within genomic intervals showing differential accessibility (DA) between homologs. DA was originally identified using short sequence-defined single copy (sc) DNA probes of < 5 kb in length by fluorescence in situ hybridization (scFISH) in peripheral lymphocytes. These structural differences between metaphase homologs are non-random, stable, and heritable epigenetic marks which have led to the proposed function of DA as a marker of chromatin memory. Here, we characterize the organization of DA intervals into chromosomal domains by identifying multiple DA loci in close proximity to each other and examine the conservation of DA between tissues. Results We evaluated multiple adjacent scFISH probes at 6 different DA loci from chromosomal regions 2p23, 3p24, 12p12, 15q22, 15q24 and 20q13 within peripheral blood T-lymphocytes. DA was organized within domains that extend beyond the defined boundaries of individual scFISH probes. Based on hybridizations of 2 to 4 scFISH probes per domain, domains ranged in length from 16.0 kb to 129.6 kb. Transcriptionally inert chromosomal DA regions in T-lymphocytes also demonstrated conservation of DA in bone marrow and fibroblast cells. Conclusions We identified novel chromosomal regions with allelic differences in metaphase chromosome accessibility and demonstrated that these accessibility differences appear to be aggregated into contiguous domains extending beyond individual scFISH probes. These domains are encompassed by previously established topologically associated domain (TAD) boundaries. DA appears to be a conserved feature of human metaphase chromosomes across different stages of lymphocyte differentiation and germ cell origin, consistent with its proposed role in maintenance of intergenerational cellular chromosome memory.

Whole-genome sequencing and ad hoc shared genome analysis of Staphylococcus aureus isolates from a New Zealand primary school

Epidemiological studies of communicable diseases increasingly use large whole-genome sequencing (WGS) datasets to explore the transmission of pathogens. It is important to obtain an initial overview of datasets and identify closely related isolates, but this can be challenging with large numbers of isolates and imperfect sequencing. We used an ad hoc whole-genome multi locus sequence typing method to summarise data from a longitudinal study of Staphylococcus aureus in a primary school in New Zealand. Each pair of isolates was compared and the number of genes where alleles differed between isolates was tallied to produce a matrix of “allelic differences”. We plotted histograms of the number of allelic differences between isolates for: all isolate pairs; pairs of isolates from different individuals; and pairs of isolates from the same individual. 340 sequenced isolates were included, and the ad hoc shared genome contained 445 genes. There were between 0 and 420 allelic differences between isolate pairs and the majority of pairs had more than 260 allelic differences. We found many genetically closely related S. aureus isolates from single individuals and a smaller number of closely-related isolates from separate individuals. Multiple S. aureus isolates from the same individual were usually very closely related or identical over the ad hoc shared genome. Siblings carried genetically similar, but not identical isolates. An ad hoc shared genome approach to WGS analysis can accommodate imperfect sequencing of the included isolates, and can provide insights into relationships between isolates in epidemiological studies with large WGS datasets containing diverse isolates.

Investigation of possible transmission of a susceptible microorganism through a contaminated duodenoscope; a case report

Background Despite compliance to extensive reprocessing protocols, duodenoscopes have been linked to outbreaks of susceptible and multi-drug resistant organisms (MDRO) due to persistent duodenoscope contamination. Duodenoscope-associated infections (DAIs) based on transmission of susceptible microorganisms are likely to be underreported due to detection bias. Case presentation We describe the retrospective detection of a DAI case caused by a susceptible microorganism which at the time of clinical infection was not recognized as such. During 2017 and 2018, duodenoscopes were cultured on a daily basis due to research activities. While analyzing this data, it was found that a duodenoscope had been contaminated with Enterobacter cloacae complex over a period of 3 months. We checked whether patients treated with this duodenoscope had developed infections and found one patient with an E. cloacae cholangitis 3 months after the ERCP (Endoscopic retrograde cholangiopancreaticography) procedure. The isolates on the duodenoscope and in the patients’ blood culture were indistinguishable by amplified fragment length polymorphism (AFLP). By classical multi-locus sequence typing (MLST), both strains were of the same (but novel) sequence type. Application of whole genome MLST showed 93 (out of 3757) allelic differences. Conclusion This case report describes a plausible link between a contaminated duodenoscope and a patient infection with E. cloacae. Transmission of susceptible E. cloacae was highly suspected from AFLP and MLST results; by WGS, 93 allelic differences were found which proves closely related strains. This report shows that DAIs by susceptible microorganisms can be easily missed and therefore its true prevalence remains underscored.

Listeria monocytogenes Contamination Characteristics in Two Ready-to-Eat Meat Plants From 2019 to 2020 in Shanghai

Listeria monocytogenes is a ubiquitous foodborne pathogen that causes listeriosis and is mostly linked to consumption of ready-to-eat (RTE) foods. Lack of hygiene in food processing environments may be a primary reason for contamination by L. monocytogenes isolates. In this study, L. monocytogenes strains isolated from two RTE meat processing plants in the Shanghai municipality, China, were characterized during 2019–2020 using pulsed-field gel electrophoresis and whole-genome sequencing. Results showed that 29 samples (12.2%) out of 239 were positive for L. monocytogenes, with 21 (18.9%) and 8 (6.25%) isolates from plants A and B, respectively. The packaging room at plant A had the most contamination (14, 48.3%; p &lt; 0.05), with a peak occurrence of 76.5% in processing environments. Nineteen L. monocytogenes isolates belonging to the pulsotype (PT) 7 group were indistinguishable (≥ 95.7%). Furthermore, core-genome multiple loci sequencing typing identified up to nine allelic differences, and the closet pairwise differences among these ST5 isolates included 0–16 small nucleotide polymorphisms. Therefore, L. monocytogenes likely persisted at plant A during 2019–2020 with ongoing clone transmission. In contrast, no L. monocytogenes isolates were identified from processing environments at plant B. Most L. monocytogenes isolates were sampled from raw materials (62.5%). Several isolates (ST378, ST8, and ST120) were detected only once in 2020 and were considered as transient isolates. However, three ST121 isolates with the same PT (PT2) were detected in 2020 and should be noted for their stronger survival ability in harsh environments. These results suggest that continuous monitoring, stringent surveillance, and source tracking are crucial to guaranteeing food safety in RTE food plants.

Emergence of Multidrug-Resistant Escherichia coli Producing CTX-M, MCR-1, and FosA in Retail Food From Egypt

In this study, multidrug-resistant (MDR) Escherichia coli isolates from retail food and humans assigned into similar Multilocus Sequence Types (MLST) were analyzed using whole genome sequencing (WGS). In silico analysis of assembled sequences revealed the existence of multiple resistance genes among the examined E. coli isolates. Of the six CTX-M-producing isolates from retail food, blaCTX-M-14 was the prevalent variant identified (83.3%, 5/6). Two plasmid-mediated fosfomycin resistance genes, fosA3, and fosA4, were detected from retail food isolates (one each from chicken and beef), where fosA4 was identified in the chicken isolate 82CH that also carried the colistin resistance gene mcr-1. The blaCTX-M-14 and fosA genes in retail food isolates were located adjacent to insertion sequences ISEcp1 and IS26, respectively. Sequence analysis of the reconstructed mcr-1 plasmid (p82CH) showed 96–97% identity to mcr-1-carrying IncI2 plasmids previously identified in human and food E. coli isolates from Egypt. Hierarchical clustering of core genome MLST (HierCC) revealed clustering of chicken isolate 82CH, co-harboring mcr-1 and fosA4 genes, with a chicken E. coli isolate from China at the HC200 level (≤200 core genome allelic differences). As E. coli co-harboring mcr-1 and fosA4 genes has only been recently reported, this study shows rapid spread of this genotype that shares similar genetic structures with regional and international E. coli lineages originating from both humans and food animals. Adopting WGS-based surveillance system is warranted to facilitate monitoring the international spread of MDR pathogens.

Agronomic, Physiological and Genetic Changes Associated With Evolution, Migration and Modern Breeding in Durum Wheat

A panel of 172 Mediterranean durum wheat landraces and 200 modern cultivars was phenotyped during three years for 21 agronomic and physiological traits and genotyped with 46,161 DArTseq markers. Modern cultivars showed greater yield, number of grains per spike (NGS) and harvest index (HI), but similar number of spikes per unit area (NS) and grain weight than the landraces. Modern cultivars had earlier heading but longer heading-anthesis and grain-filling periods than the landraces. They had greater RUE (Radiation Use Efficiency) up to anthesis and lower canopy temperature at anthesis than the landraces, but the opposite was true during the grain-filling period. Landraces produced more biomass at both anthesis and maturity. The 120 genotypes with a membership coefficient q &gt; 0.8 to the five genetic subpopulations (SP) that structured the panel were related with the geographic distribution and evolutionary history of durum wheat. SP1 included landraces from eastern countries, the domestication region of the “Fertile Crescent.” SP2 and SP3 consisted of landraces from the north and the south Mediterranean shores, where durum wheat spread during its migration westward. Decreases in NS, grain-filling duration and HI, but increases in early soil coverage, days to heading, biomass at anthesis, grain-filling rate, plant height and peduncle length occurred during this migration. SP4 grouped modern cultivars gathering the CIMMYT/ICARDA genetic background, and SP5 contained modern north-American cultivars. SP4 was agronomically distant from the landraces, but SP5 was genetically and agronomically close to SP1. GWAS identified 2,046 marker-trait associations (MTA) and 144 QTL hotspots integrating 1,927 MTAs. Thirty-nine haplotype blocks (HB) with allelic differences among SPs and associated with 16 agronomic traits were identified within 13 QTL hotspots. Alleles in chromosomes 5A and 7A detected in landraces were associated with decreased yield. The late heading and short grain-filling period of SP2 and SP3 were associated with a hotspot on chromosome 7B. The heavy grains of SP3 were associated with hotspots on chromosomes 2A and 7A. The greater NGS and HI of modern cultivars were associated with allelic variants on chromosome 7A. A hotspot on chromosome 3A was associated with the high NGS, earliness and short stature of SP4.