Triticale is making its way on dairy farms as an alternative forage crop. This requires the availability of high-yielding triticale varieties with good digestibility. Triticale forage breeding mainly ...focussed on biomass yield, but efforts to improve digestibility are increasing. We previously investigated the interrelationships among different quality traits in soft dough triticale: starch, acid detergent fibre and in vitro digestibility of organic matter (IVOMD) and of neutral detergent fibre (IVNDFD) of the total plant, IVNDFD and Klason lignin of the stems, and ear proportion and stem length. Here we determine the genetic control of these traits, using a genome-wide association (GWAS) approach. A total of 33,231 DArTseq SNP markers assessed in a collection of 118 winter triticale genotypes, including 101 varieties and 17 breeding lines, were used.
The GWAS identified a total of 53 significant marker-trait associations (MTAs). The highest number of significantly associated SNP markers (n = 10) was identified for total plant IVNDFD. A SNP marker on chromosome 1A (4211801_19_C/T; 474,437,796 bp) was found to be significantly associated with ear proportion, and plant and stem IVNDFD, with the largest phenotypic variation for ear proportion (R²
= 0.23). Based on MTAs, candidate genes were identified which were of particular relevance for variation in in vitro digestibility (IVD) because they are putatively involved in plasma membrane transport, cytoskeleton organisation, carbohydrate metabolic processes, protein phosphorylation, and sterol and cell wall biogenesis. Interestingly, a xyloglucan-related candidate gene on chromosome 2R, SECCE2Rv1G0126340, was located in close proximity of a SNP significantly associated with stem IVNDFD. Furthermore, quantitative trait loci previously reported in wheat co-localized with significantly associated SNP markers in triticale.
A collection of 118 winter triticale genotypes combined with DArTseq SNP markers served as a source for identifying 53 MTAs and several candidate genes for forage IVD and related traits through a GWAS approach. Taken together, the results of this study demonstrate that the genetic diversity available in this collection can be further exploited for research and breeding purposes to improve the IVD of triticale forage.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Knowledge of the diversity of microbial communities and their relationship with biogeochemical cycles is a key factor in understanding and improving the performance of constructed wetland (CW) ...systems, allowing improvements in design and operation methods to reach the desired effluent quality. Assemblies of microbial groups in CWs are driven by several factors, including the environmental conditions of the mesocosm and substrate availability. This study combined physicochemical analyses, high-throughput DNA sequencing, and statistical methods to gain an insight into the influence of operational conditions on the bacteria and archaea communities in a modified constructed wetland system treating raw-light greywater. The EvaTAC system is composed of an upflow evapotranspiration and treatment tank (CEvaT) which has an inbuilt anaerobic chamber (AnC), followed by a horizontal subsurface flow constructed wetland (HSSF-CW). Samples were collected after five years of system operation in both units: sludge from the AnC, coarse gravel from the CEvaT, and fine gravel from the CW. The results showed that the system operated predominantly in anaerobic conditions, with redox potential (Eh) increasing from the inlet (−364.1 mV) to the outlet (−240.4 mV) zone. The Eh was the environmental condition that most influenced the microbial community diversity and richness, and, as well as Eh, increased along the light greywater (LGW) flow. Conversely, the chemical oxygen demand (COD) decreased, thus suggesting a negative correlation among these factors. The clustering analyses of microbial community showed that, besides environmental conditions, the media filter and related depth could also be drivers of microbial community composition. The bottom layer of CEvaT was assigned to the Proteobacteria and Synergistetes phyla indicating the accomplishment of the first steps of anaerobic digestion. The next layer was characterised by the presence of Desulfovibrio, Syntrophobacter, and Methanobacterium, microorganisms responsible for the sulfidogenesis and methanogenesis processes. Finally, in the CW zone, the community composition was dominated by microorganisms involved in the methane oxidation, such as Methylosinus, Bradyrhizobium, and Candidatus Koribacter. This study explored the universe of bacteria and archaea communities, and is an initial step in elucidating microbial diversity conversions in CW systems treating greywater, which is important knowledge to steer the conversion pathway and establish the ideal environmental conditions for the development of desired microbial communities in these systems.
SUMMARY
Genetic analysis of type material of various Ulva species has shown that many names have been misapplied. DNA sequences of two of the specimens on the lectotype sheet of U. australis from ...South Australia showed that U. australis is conspecific with specimens called U. pertusa from Japan. However, type material of U. pertusa has not been sequenced, nor have other type specimens with type localities in Japan and Australia, including U. conglobata f. conglobata and U. conglobata f. densa from the former, and U. laetevirens and U. spathulata from the latter. To determine if these names have been correctly applied, targeted DNA sequencing of the rbcL gene was performed on (i) the lectotype specimen of U. laetevirens, (ii) the lectotype and two syntype specimens of U. pertusa, (iii) the lectotype and two syntype specimens of U. congoblata f. conglobata and (iv) two specimens on the holotype sheet of U. conglobata f. densa. In addition, high‐throughput sequencing (HTS) analysis was carried out on an isotype specimen of U. spathulata. Phylogenetic analysis of the resulting rbcL gene sequences supports the taxonomic conclusions that U. laetevirens, U. pertusa and U. spathulata are synonyms of U. australis, and U. conglobata f. conglobata and U. conglobata f. densa represent a single separate and distinct species, U. conglobata. These genetic data contribute to the taxonomy of Ulva and further demonstrate that analyzing DNA from type material is the only currently known reliable method to correctly apply names in this genus.
Telomeres are regions of repetitive DNA at the end of eukaryotic chromosomes, which prevent chromosomal instability. Telomere shortening is linked to age-related disease including Alzheimer's disease ...(AD) and has been reported to be reduced in leukocytes of AD patients. The aim of the present study was to measure telomere length in monocytes of patients with AD or mild cognitive impairment (MCI) compared to healthy subjects. Our data show significant shorter telomere length in AD patients (6.6±0.2kb; p=0.05) compared to controls (7.3±0.2kb). Telomere length of MCI patients did not differ compared to healthy subjects (7.0±0.2kb). We observe a strong correlation between telomere length and age (p=0.01, r=−0.38), but no association between telomere length and Mini-Mental State Examination score. In conclusion, the telomere length is age-dependent in monocytes and decreased in AD patients, which could mean that the AD pathology may contribute to telomere length shortening. The high variability of telomere lengths in individuals suggests that it will not be useful as a general biomarker for AD. However, it could become a biomarker in personalized long-term monitoring of an individuals’ health.
► Alzheimer‘s disease is a severe neurodegenerative disorder of the brain. ► Laboratory diagnosis of AD is difficult and not well established. ► Monocytes play a role in inflammation and may reflect AD pathology. ► Telomer length is reduced in monocytes of AD patients. ► Telomer length could be a putative (personalized) biomarker for diagnosis.
Negative population feedbacks mediated by natural enemies can promote species coexistence at the community scale through disproportionate mortality of numerically dominant (common) tree species. ...Simultaneously, associations with arbuscular mycorrhizal fungi (AMF) can result in positive effects on tree populations. Coupling data on seedling foliar damage from herbivores and pathogens and DNA sequencing of soil AMF diversity, we assessed the effects of these factors on tree seedling mortality at local (1 m2) and community (16 ha plot) scales in a tropical rainforest in Puerto Rico. At the local scale, AMF diversity in soil counteracted negative effects from foliar damage on seedling mortality. At the community scale, mortality of seedlings of common tree species increased with foliar damage while rare tree species benefited from soil AMF diversity. Together, the effects of foliar damage and soil AMF diversity on seedling mortality might foster tree species coexistence in this forest.
Display omitted
•We test whether parasite gene sequences accumulate as expected based on species richness.•Data from the London Natural History Museum and GenBank are integrated.•The number of gene ...sequences per country or family increases with their species richness.•We provide a list of the 20 countries with the greatest deficit in genetic research.•We also identify the 20 helminth families with the greatest deficit in genetic research.
The use of genetic information is now fundamental in parasite taxonomy and systematics, for resolving parasite phylogenies, discovering cryptic species, and elucidating patterns of gene flow among parasite populations. The accumulation of available gene sequences per geographical area or per parasite taxonomic group is likely proportional to species richness, but not without some biases. Certain areas and certain taxonomic groups receive more research effort than others, possibly causing a deficit in the relative number of parasite species being characterized genetically in some areas or taxonomic groups. Here, we use data on the number of parasite records per country or helminth family from the London Natural History Museum host-parasite database, and matching data on the number of gene sequences available from the National Center for Biotechnology Information (NCBI) GenBank database, to determine how available gene sequences scale with species richness across countries or parasitic helminth families. Our quantitative analysis identified countries/regions of the world and helminth families that have received the most effort in genetic research. More importantly, it allowed us to generate lists (based on residuals from the statistical model) of the 20 countries/regions and the 20 helminth families with the largest deficit in available gene sequences relative to their helminth species richness. We propose these lists as useful guides toward future allocation of effort to maximise advances in parasite biodiscovery, systematics and population structure.
The increase in detections of Plasmodium vivax infection in Duffy-negative individuals in Africa has challenged the dogma establishing the unique P. vivax Duffy Binding Protein-Duffy antigen receptor ...for chemokines (PvDBP-DARC) pathway used by P. vivax merozoites to invade reticulocytes. Information on the impact of Duffy antigen polymorphisms on the epidemiology of P. vivax malaria remains elusive. The objective of this study was to determine the distribution of asexual parasitaemia of P. vivax according to the Duffy antigen polymorphisms in Ethiopia.
DNA was extracted from dried blood spots (DBS) collected from prospectively recruited 138 P. vivax-infected patients from health centres. The identification and estimation of P. vivax asexual parasitaemia were performed by microscopic examination and quantitative real-time polymerase chain reaction (PCR). Duffy genotyping was conducted by DNA sequencing in a total of 138 P.vivax infected samples.
The proportion of Duffy-negatives (FY*B
/FY*B
) in P. vivax infected patients was 2.9% (4/138). Duffy genotype FY*B/FY*B
(48.6%) was the most common, followed by FY*A/FY*B
genotype (25.4%). In one patient, the FY*02 W.01/FY*02 N.01 genotype conferring a weak expression of the Fy
antigen was observed. All P.vivax infected Duffy-negative patients showed low asexual parasitaemia (≤ 110 parasites/µL). The median P. vivax parasitaemia in Duffy-negative patients (53 parasites/µL) was significantly lower than those found in homozygous and heterozygous individuals (P < 0.0001).
Plasmodium vivax in Duffy-negative patients shows invariably low asexual parasitaemia. This finding suggests that the pathway used by P. vivax to invade Duffy-negative reticulocytes is much less efficient than that used in Duffy-positives. Moreover, the low asexual parasitaemia observed in Duffy-negative individuals could constitute an 'undetected silent reservoir', thus likely delaying the elimination of vivax malaria in Ethiopia.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Aquaculture is an important sector for ensuring global food security. Due to the scarcity of freshwater available for expanding aquaculture, the development of omnivorous fish species and varieties ...that can tolerate high salinity will enhance fish production. Some tilapia species are good candidates for aquaculture in brackish and seawater because they can grow in high salinity. Among tilapia species, Oreochromis mossambicus, Oreochromis aureus, Oreochromis spilurus, Oreochromis urolepis hornorum, Sarotherodon galilaeus and Coptodon zillii are the most salinity‐tolerant. Hybrids derived from salinity‐tolerant tilapia species are tolerant to a certain level of salinity. They have been used in aquaculture production in brackish water and full seawater. Conventional selective breeding has been applied to increase the growth rate of salinity‐tolerant tilapias. However, their growth rate is lower than that of the freshwater Oreochromis niloticus. Recently, many genomic resources and tools have been developed for salinity‐tolerant tilapia. Quantitative trait locus (QTL) mapping and genome‐wide association studies (GWAS) for important economic traits, including salinity tolerance and other desired traits, have been carried out and applied in molecular breeding for superior salinity‐tolerant tilapia lines. In this review, we systematically analysed tilapia species that can be cultured in brackish and saltwater. We summarized previous works in conventional breeding and molecular breeding for salinity‐tolerant tilapia. We pointed out a few known and potential challenges in the selective breeding and culture of salinity‐tolerant tilapia. Due to the rapid advances in molecular and other disruptive technologies, we are optimistic that novel breeding approaches will significantly increase the production salinity‐tolerant tilapia.
PDF
