Recent advances in molecular marker techniques: Insight into QTL mapping,GWAS and genomic selection in plants

Recent advances in sequencing technology have brought several novel platforms for marker development and subsequent genotyping. The high-throughput and cost effective marker techniques have changed the entire scenario of marker applications. The huge genotypic data obtained with next generation sequencing (NGS) also demands analytical tools, statistical advances, and comprehensive understanding to cope with breeding applications. In the present review, we discussed different available marker techniques, their strengths, and limitations. Emphasis was given on software tools, analytical pipelines, workbenches, and online resources available for marker development. Comparison of SNP genotyping involving complexity reduction techniques like GBS, RRL, RAD, and array-based platforms were presented in a view to describe suitability for specific purposes. We found that genotyping by whole genome re-sequencing has great potential, and could be a routine application in the near future with continuously decreasing cost of sequencing. Microsatellites, still a valuable option for breeders, have also advanced with NGS. Here a catalogue of tools for microsatellite evaluation in short sequence reads was provided. The most common applications of molecular marker like QTL mapping, genome-wide association mapping (GWAS), and genomic selection were highlighted. The present review will be helpful for the effective utilization of available resources and for the planning of crop improvement programs employing molecular marker techniques.     

Species spectrum, diversity profile and infection indices of helminth parasite fauna of Chirruh snowtrout, Schizothorax esocinus (Heckel) in lake ecosystems of Kashmir Himalayas-Do similarity and host-parasite associations arise?

In order to assess the species richness and diversity profile of helminth parasite fauna in an endemic fish, an investigation was carried out in two urban and two rural lakes of Kashmir. Overall nine species of helminth parasites were observed in four lakes. Of these three were autogenic and six were allogenic. Heteroxenous parasite species were more in number than monoxenous species. Results showed significant differences in heteroxenous / monoxenous ratio between different lakes. Core species (Prevalence?>?20) were only found in hypertrophic lake (Anchar Lake). Overall, majority of helminth species were either secondary or satellite species. Prevalence of some helminth parasites showed significant differences in different lakes. In addition mean intensity showed significant differences between autogenic and allogenic parasites (P?<?0.05). Principle Component Analysis based on prevalence showed that Anchar Lake was strongly associated with most of helminth parasites. Diversity indices showed significant variation between different lakes. Maximum helminth species per host was in Anchar Lake. Finally we concluded that helminth parasite fauna showed significant differences in species richness and infection indices between different lakes. Diversity profile was higher in Anchar Lake in comparison to other three lakes. The results clearly show that environmental features of lake ecosystems have got an impact on distribution pattern of helminth parasites in S. esocinus. We suggest comparative parasitological study should be taken between different species of fish in order to have a clear picture regarding the species composition of helminth species in this region. Also we need to characterize the species spectrum of parasitic worms in fish of freshwater bodies of this region as well as other similar type of climatic zones because parasite fauna is an integral part of the inventory of biodiversity and as possible regulators of host populations in aquatic ecosystems.     

Dietary ginger administration attenuates oxidative stress and immunosuppression caused by oxytetracycline in rainbow trout (Oncorhynchus mykiss)

In the present study, potential ameliorative effects of dietary ginger (GN) were investigated on antioxidant and immune responses of rainbow trout (Oncorhynchus mykiss) during oxytetracycline (OX) administration. As a 2 × 3 factorial design, the fish were orally treated with OX (a daily dose of 100 mg/kg) and GN (either 10 or 20 g/kg diet) for 10 days. Then, blood samples were taken from each treatment to monitor plasma lysozyme, complement (ACH50), superoxide dismutase (SOD), catalase (CAT), glutathione peroxidase (GPx), glutathione‐S‐transferase (GST) activities, and reduced glutathione (GSH), malondialdehyde (MDA), total immunoglobulin (Ig) and globulin levels. OX treatment significantly decreased SOD (30%), GPx, (10%) and lysozyme (23%) activities, and GSH (19%) levels; however, it increased GST (16%) activity and MDA (28%) levels. Ten grams GN per kg levels significantly decreased SOD (35%), CAT (13%), GST (20%) and MDA (30%), but increased GSH (30%), lysozyme (48%) and globulin (16%). Twenty grams GN per kg diet significantly decreased SOD (26%) and MDA (17%), but increased lysozyme (31%) levels. Interaction effects of dietary GN and OX were observed on plasma MDA and GPx levels, as 10 g GN per kg diet prevented the OTC‐induced changes in these parameters. Moreover, 20 g GN per kg diet prevented the OX‐induced change in GPx activity and mitigated the MDA elevation by 20%. It is concluded that GN administration at 10 g/kg diet is beneficial in mitigating oxidative stress and immunosuppression of rainbow trout during OX administration.     

Comparison of symbiotic effectiveness of Rhizobium sp. with positive hydrogen-uptake activity compared with negative mutants in relation to nitrogen fixation in mungbean (Vigna radiata L.)

H₂ uptake activity was well distributed in Rhizobium sp. strains isolated from nodules of mung-bean (Vigna radiata L.). Two effective strains, RMP1 und RMP2, exhibiting significantly higher H₂ uptake activity were subjected to mutagenesis with nitrosoguanidine. The respective mutation frequencies were 0.18 and 0.19%. Three Hup^- mutants each of RMP1 und RMP2 were compared with the wild-type parent strains under pot culture experiments to evaluate the significance of the H₂ uptake system in biological N₂ fixation. Nodulation capabilities, plant growth characteristics, and the chlorophyll content of the leaves were significantly reduced in the plants treated with Hup^- mutants. Nitrogenase activity in Hup^- nodules was reduced by 8–41%. Similarly, N accumulation was also reduced singificantly.     

The Effect of Sodium Caseinate Coating Incorporated with Zataria moltiflora Essential Oil on the Quality and Shelf Life of Rainbow Trout During Refrigerated Storage

ABSTRACT

In the present study, aqueous solutions of sodium caseinate (SC) 8% (w/w) were provided in the form of four treatments—including SC without any essential oil (EO) as well as SC with 0.25, 0.5, and 1% (v/w) concentrations of Zataria moltiflora EO. Fish samples were treated with aqueous solutions and stored at 4 ± 1°C for 20 days. The control and treated fish samples were analyzed for chemical (total volatile basic nitrogen, pH, thiobarbituric acid, peroxide value), microbiological (total viable count and psychrotrophic count), and sensory analyses every 4 days. Based on results, SC edible coating had no antimicrobial effect but acted like a barrier against the fish flesh contamination. Moreover, incorporating Zataria moltiflora EO with SC edible coating reduces peroxide value and thiobarbituric acid-reactive substances values as well as the chemical and microbiological spoilage of refrigerated ?sh samples. Furthermore, sensory evaluation results showed that the presence of thyme oil improved the sensory quality of the rainbow trout.     

Growth performance,immune response and disease resistance of rainbow trout (Oncorhynchus mykiss) fed Thymus vulgaris essential oils

Efficacy of Thymus vulgaris essential oils was assessed on growth, immune response and disease resistance of rainbow trout (Oncorhynchus mykiss). Fish weighing 10 g were fed with dietary supplemented of the oils at 0.5, 1.0 and 2.0 ml/kg feed for 2 months. Fish fed with the oils at 0.5 ml/kg feed demonstrated a better weight gain and specific growth rate, compared to other treatments (p < .05). Fish fed with 1.0 ml the oils showed the highest up‐regulation of complement component 3 (C3) and (cluster of differentiation 4) (CD4) genes expression (p < .05), while lysozyme gene expression level significantly increased in fish fed with 2.0 ml of the oils. In addition, at the end of the experiment, the expression of C3 and CD4 genes were significantly up‐regulated in fish fed with 1.0 and 2.0 ml of the oils, while IL‐1ß and lysozyme genes expression levels were significantly decreased in fish fed 2.0 ml oils, towards the end of the trial (p < .05). There was a fluctuation in the levels of Alanine aminotransferase, Aspartate aminotransferase and Alkaline phosphatase in all treatments during the experiment. When treated fish were challenged with Aeromonas hydrophila, the highest survival rate was observed in 0.5 ml/kg treatment, followed by 2 and 1 mg/kg treatments. Overall, these findings demonstrated that dietary administration of T. vulgaris oils especially at 0.5 mg/kg feed can be considered as a potential component for enhancing of the growth, immune responses and disease resistance of trout against motile Aeromonas septicemia caused by A. hydrophila.     

Genetic diversity,population structure and genetic relationships in apricot (Prunus armeniaca L.) germplasm of Jammu and Kashmir,India using ISSR markers

Genetic Resources and Crop Evolution - The collection and characterization of apricot germplasm is an important step for its utilization, conservation, and breeding programs. In the present study,...     

First detection of koi herpesvirus from koi,Cyprinus carpio L. experiencing mass mortalities in Iran: clinical,histopathological and molecular study

Koi herpesvirus (KHV) is the aetiological agent of an emerging disease (KHVD) associated with mass mortalities in koi and common carp and reported from at least 30 countries. We report the first detection of KHV from koi in Iran using clinical, histopathological and molecular studies. KHV‐infected fish showed reduced swimming activity, sunken eyes and increased mucus production on skin and fins. On post‐mortem examination, gill necrosis was observed in the majority of fish. Histopathologically, the gill showed diffuse necrosis of the branchial epithelial cells. Margination of chromatin was detected in gills, kidney, heart, spleen, intestine and brain. In addition, sequence analyses of the TK gene, ORF 136 and marker I and II, demonstrates that Iranian KHV isolates were identical and classified as variant A1 of TUSMT1 (J strain) and displayed the I⁺⁺II⁺ allele of this Asian genotype.     

Field Bindweed (Convolvulus arvensis) Control and Winter Wheat Response to Post Herbicides Application

Journal of Crop Science and Biotechnology - Field bindweed is a deep-rooted and drought-tolerant perennial weed that can hardly be controlled once it has become established in wheat. Field...     

Evaluation of PRE and POST Herbicides on Growth Features,Nodulation, and Nitrogen Fixation of Three Cultivars of Chickpea (Cicer aritinium L.)

Journal of Crop Science and Biotechnology - It is exceptionally difficult to have productive farming without the use of herbicides. It has been found that they create difficulties in the growth and...