Sturgeons belong to an extraordinarily old and highly endangered group of fish. Although the sex determining region in this taxon was recently discovered, there is still a great need for the ...development of reliable gene expression markers for sturgeon sexing in their different life stages which could be easily applied in field conditions. In this study an extensive screening of the Atlantic sturgeon genome was performed using: AFLP (202 PC) and MS-AFLP (256 PC) markers likewise the Siberian sturgeon transcripts deriving from the Whole Transcriptome Sequencing (WTS) and cDNA-AFLP (128 PC). Genetic material extracted from female and male fins was used. AFLP reactions were minimized and automatized and a novel method for SCAR identification was proposed (SCAR-NGS). The 204 primary selected markers were subjected to gDNA or cDNA PCR amplifications, semi- and RT-qPCRs in order to confirm the presence of unique sex-marker sequences in the genomes or sex-linked expression differences. We identified eleven loci in the Atlantic sturgeon genome which exhibited sex-linked polymorphisms of the restriction sites (SNP based). In case of the Siberian sturgeon, 41 transcripts were confirmed to be expressed in a sex specific manner; three of which were also significantly differentially amplified in the female and male genomes. Six of those markers were highly overexpressed in males, which was quantified using RT-qPCRs. The approach enabled the discovery of DNA and RNA candidate sequences suitable for application in sturgeon sexing, being important both for commercial aquaculture optimization and genetic variability maintenance of sturgeons.
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•Atlantic and Siberian sturgeon genomes and transcriptomes were screened for sex markers discovering.•41 sex specific transcripts with three of them showing DNA differences were found.•Six RNA markers have potential for commercial application in sturgeon aquaculture.•AFLP reactions were minimized and automatized.•A novel method for SCAR identification was proposed (SCAR-NGS).
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Aims
Genetic diversity and antimicrobial resistance of Campylobacter coli and Campylobacter jejuni were investigated along the broiler chicken production chain in central Italy.
Methods and Results
...Campylobacter sp. isolated from cloacal swabs in farms (n = 116) and from the neck skin of chilled and eviscerated carcasses at slaughter (n = 24) were identified as C. coli (n = 99) and C. jejuni (n = 41) by multiplex PCR. Characterization by single amplified fragment length polymorphism (s‐AFLP) revealed a specific genotype of Campylobacter for each farm. Minimal inhibitory concentration showed high prevalence of fluoroquinolones (70%), tetracycline (70%) and erythromycin (30%) resistance among C. coli isolates. Campylobacter jejuni isolates showed lower prevalence of fluoroquinolone (39%) and tetracycline (10%) resistance, and all isolates were susceptible to erythromycin. The S‐AFLP types of the C. coli and C. jejuni isolates were associated with their antimicrobial resistance profiles (P < 0·001).
Conclusions
The genetic diversity detected in Campylobacter isolates suggested that a specific genotype was harboured in each farm. A considerable number of C. coli isolates were resistant to erythromycin.
Significance and Impact of the Study
Campylobacter coli was detected more frequently than C. jejuni in contrast to common findings for poultry. The high prevalence of 30% resistance to erythromycin in C. coli strains isolated from poultry is worrisome, as this is the first antibiotic of choice to treat human campylobacteriosis.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SBCE, SBMB, UL, UM, UPUK
•Piriformospora indica mediate host resistance against early blight by priming of a versatile host-signaling component.•P. indica modulate downstream defense related genes.•P. indica primed ...transcriptome reprogramming fine tunes jasmonate/ethylene mediated basal defense against pathogen infection.
Piriformospora indica is an adaptable mycorrhiza-like fungus belonging to the Sebacinales order that can colonize roots of a wide range of plant species. Studies have shown that P. indica improves growth and enhances systemic defense against pathogens in host plants. However, the mechanism(s) through which these effects occur remain unclear. Therefore to gain more insight into the molecular basis of P. indica induced resistance, cDNA-AFLP (Amplified fragment length polymorphism) based transcript profiling was done to identify differentially expressed genes in P. indica-colonized tomato plants infected with Alternaria solani. Our results demonstrated that pre-colonization of tomato roots with P. indica systemically induced resistance against early blight. Transcript profiling of P. indica pre-colonized tomato plants revealed systemic modulation of several key components of signaling network transcriptional regulators including CBL-interacting protein kinase (CIPK), Mitogen activated protein kinases (MPKs), Lipid transfer proteins (LTPs), WRKY1, ethylene responsive transcription factors (ERF), and Jasmonate Zim Domain 1 (JAZ1), a negative regulator of jasmonic acid (JA) signaling. Expression of downstream defense related genes like Thaumatin-like protein, β-1, 3-glucanase and chitinases was also affected in leaves upon challenge inoculation with pathogen. Interestingly, P. indica pre-colonization alone was unable to induce transcript levels for most of the genes studied. However, pathogen attack on P. indica pre-colonized plants induced strong defense responses. In conclusion, P. indica induces transcriptome reprogramming in a manner that allows rapid and efficient activation of JA/ET (jasmonic acid/ethylene)-mediated basal defenses against pathogen infection by altering the expression of JA/ET related genes. P. indica colonization appears to potentiate the complete signal transduction cascade leading to the systemic expression of defense genes against foliar pathogens. It thus presents itself as a potential and sustainable method of activating multiple components of defense signaling thereby conveying durable horizontal defense against a range of pathogens.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
انجیلی گونۀ بومی و مختص جنگلهای هیرکانی است که از غرب تا شرق جنگلهای شمال ایران پراکنش دارد. در این پژوهش، تنوع ژنتیکی انجیلی با استفاده از اطلاعات مولکولی جمعیتهای جمعآوریشده از استانهای گیلان ...(سه رویشگاه)، مازندران (چهار رویشگاه) و گلستان (سه رویشگاه) بررسی شد. با کمک نشانگر AFLP، 826 باند بهدست آمد که بیش از 90 درصد آنها چندشکل بودند و میانگین محتوای اطلاعات چندشکل (PIC) و شاخص نشانگر (MI) بهترتیب 24/0 و 4/22 محاسبه شد. تجزیهوتحلیل خوشهای برمبنای ضریب تشابه جاکارد و الگوریتم UPGMA نشان داد که تنوع گستردهای در نمونههای جمعآوریشده وجود دارد، بهطوریکه براساس ضریب تشابه جاکارد، دامنۀ تشابه ژنتیکی از 26/0 تا 44/0 متغیر بود. نتایج تجزیۀ واریانس مولکولی (AMOVA) نشان داد که 21 درصد از تنوع ژنتیکی کل در جمعیتهای انجیلی ناشی از تنوع ژنتیکی بین جمعیتهای سه استان گلستان، مازندران و گیلان است و تنوع ژنتیکی درون جمعیتهای رویشگاهها، 79 درصد بهدست آمد. میتوان نتیجهگیری کرد که براساس تنوع اطلاعات مولکولی تنوع بین جمعیتهای انجیلی بهمراتب از تنوع درونجمعیتی آن کمتر است. به نظر میرسد که تنوع موجود بین جمعیتهای انجیلی بیشتر متأثر از محیط باشد تا ژنتیک. البته برای نتیجهگیری دقیقتر پیشنهاد میشود که اکوتونهای مختلف جمعیت انجیلی نیز با نشانگرهای مولکولی بررسی شوند.
Protected areas buffer species from anthropogenic threats and provide places for the processes that generate and maintain biodiversity to continue. However, genetic variation, the raw material for ...evolution, is difficult to capture in conservation planning, not least because genetic data require considerable resources to obtain and analyze. Here we show that freely available environmental and geographic distance variables can be highly effective surrogates in conservation planning for representing adaptive and neutral intraspecific genetic variation. We obtained occurrence and genetic data from the IntraBioDiv project for 27 plant species collected over the European Alps using a gridded sampling scheme. For each species, we identified loci that were potentially under selection using outlier loci methods, and mapped their main gradients of adaptive and neutral genetic variation across the grid cells. We then used the cells as planning units to prioritize protected area acquisitions. First, we verified that the spatial patterns of environmental and geographic variation were correlated, respectively, with adaptive and neutral genetic variation. Second, we showed that these surrogates can predict the proportion of genetic variation secured in randomly generated solutions. Finally, we discovered that solutions based only on surrogate information secured substantial amounts of adaptive and neutral genetic variation. Our work paves the way for widespread integration of surrogates for genetic variation into conservation planning.
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BFBNIB, NMLJ, NUK, PNG, SAZU, UL, UM, UPUK
Epigenetic modifications, such as DNA methylation variation, can generate heritable phenotypic variation independent of the underlying genetic code. However, epigenetic variation in natural plant ...populations is poorly documented and little understood. Here, we test whether northward range expansion of obligate apomicts of the common dandelion (Taraxacum officinale) is associated with DNA methylation variation. We characterized and compared patterns of genetic and DNA methylation variation in greenhouse‐reared offspring of T. officinale that were collected along a latitudinal transect of northward range expansion in Europe. Genetic AFLP and epigenetic MS‐AFLP markers revealed high levels of local diversity and modest but significant heritable differentiation between sampling locations and between the southern, central and northern regions of the transect. Patterns of genetic and epigenetic variation were significantly correlated, reflecting the genetic control over epigenetic variation and/or the accumulation of lineage‐specific spontaneous epimutations, which may be selectively neutral. In addition, we identified a small component of DNA methylation differentiation along the transect that is independent of genetic variation. This epigenetic differentiation might reflect environment‐specific induction or, in case the DNA methylation variation affects relevant traits and fitness, selection of heritable DNA methylation variants. Such generated epigenetic variants might contribute to the adaptive capacity of individual asexual lineages under changing environments. Our results highlight the potential of heritable DNA methylation variation to contribute to population differentiation along ecological gradients. Further studies are needed using higher resolution methods to understand the functional significance of such natural occurring epigenetic differentiation.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SBCE, SBMB, UL, UM, UPUK
Se utilizaron tres coeficientes de similitud: Simple Matching (SM), Jaccard (J) y Dice (D) para analizar la variabilidad genética mediante el uso de marcadores moleculares AFLP en 48 accesiones de ...Lupinus Mutabilis Sweet, 26 provenientes del Departamento de Cusco y 22 de departamentos y países distintos (Ecuador y Bolivia). A partir de matrices de similitud, se generaron dendrogramas con cada coeficiente, mediante el método UPGMA a través del software NTSYSpc versión 2.01, analizándose y comparándose entre sí, obteniendo un Coeficiente de correlación cofenética (r): SM=0,68674, J=0,79116 y D=0,79332; un Índice de consenso (Clc): SM–J=0,52, SM–D=0,52 y J–D=0,93; y niveles de similitud: SM=0,68, J=0,39 y D=0,56. Determinándose el coeficiente de Simple Matching como el más idóneo para análisis de variabilidad genética con marcadores dominantes como AFLP en L. mutabilis Sweet.
The evolution of the improvement in the field of agronomy is fundamental for its adaptation to the new exigencies that the current world context raises. In addition, within these improvements, this ...article focuses on those related to the biotechnology sector. More specifically, the use of DNA markers that allow the researcher to know the set of genes associated with a particular quantitative trait or QTL. The use of molecular markers is widely extended, including: restriction fragment length polymorphism, random-amplified polymorphic DNA, amplified fragment length polymorphism, microsatellites, and single-nucleotide polymorphisms. In addition to classical methodology, new approaches based on the next generation sequencing are proving to be fundamental. In this article, a historical review of the molecular markers traditionally used in plants, since its birth and how the new molecular tools facilitate the work of plant breeders is carried out. The evolution of the most studied cultures from the point of view of molecular markers is also reviewed and other parameters whose prior knowledge can facilitate the approach of researchers to this field of research are analyzed. The bibliometric analysis of molecular markers in plants shows that top five countries in this research are: US, China, India, France, and Germany, and from 2013, this research is led by China. On the other hand, the basic research using Arabidopsis is deeper in France and Germany, while other countries focused its efforts in their main crops as the US for wheat or maize, while China and India for wheat and rice.
A new clonal strain of Candida auris is an emerging etiologic agent of fungemia in Delhi, India. In 12 patients in 2 hospitals, it was resistant to fluconazole and genotypically distinct from ...isolates from South Korea and Japan, as revealed by M13 and amplified fragment length polymorphism typing.
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DOBA, IZUM, KILJ, NUK, ODKLJ, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
•This research demonstrated that there is genetic variability for the selection of strawberry genotypes adapted to the tropical climate;.•The multivariate analysis allowed the selection of superior ...genotypes concerning from a set of characters of agronomic, morphological, and post-harvest traits interest, simultaneously;.•Clustering based on AFLP markers and molecular descriptors contributed to the identification of variability in the species fragaria × ananassa Duch.;.•Genotypes derived from 'Monterey' performed better regarding the traits in the set of characters of interest than cultivar 'Albion';.•The selected genotypes showed higher yields than commercial cultivars.•Genotypes derived from 'Monterey' performed better than those from 'Albion'.
Although strawberry can be cultivated in all types of climate, it grows best in temperate climates, limiting its cultivation in certain countries or regions with tropical or subtropical climates. The objective of this study was to verify the genetic diversity of 34 pre-selected day-neutral strawberry genotypes in humid tropical and subtropical conditions through characterization of morpho-agronomic characteristics and molecular markers. The selection was based on qualitative and quantitative morpho-agronomic traits, using the Gower algorithm. Molecular characterization was performed with AFLP markers, using four combinations of selective primers. Six representative variables were subjected to principal component analysis (PCA) and the Mulamba and Mock selection index. Soluble solids and luminosity of the outer part of the fruit did not differ among genotypes but presented values above those usually found. AFLP markers detected 80% polymorphism, confirming high genetic variability among genotypes. Clustering based on molecular and agronomic data separated the genotypes into three groups, and the Mulamba and Mock index did not select individuals derived from 'Albion' or RVFS06. PCA highlighted the genotypes RVCA16M-1, RVDA11M-3, RVDA11M-4, and RVDA11M-25 as superior for most of the evaluated traits compared with the commercial cultivars 'Albion' and 'Monterey'. The PCA and selection index results indicate the reliability of the multivariate analysis for selecting superior strawberry genotypes for cultivation in tropical regions. Of the 34 genotypes analyzed, four stood out with potential for immediate cultivation.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
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