A putative resistant DNA marker for wool yellowing susceptibility in sheep

An Australian Merino flock was screened for low (resistant) and high (susceptible) yellow predictive colour (YPC) breeding values in order to compare extreme individuals using the differential display of mRNA technique. One differentially expressed cDNA band was visualised only in the resistant group. This band showed no identity with the DNA sequences of public databases; however, they showed short homologies with three database sequences related to transmembrane signalling functions. The use of these candidate genes as DNA markers needs to be confirmed against sheep with a wide range of susceptibility to wool yellowing to verify the results.

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Marker assisted selection in BMQ related breeding programs

Genetika ◽

10.2298/gensr0801039o ◽

2008 ◽

Vol 40 (1) ◽

pp. 39-49 ◽

Cited By ~ 1

Author(s):

Dragana Obreht ◽

Borislav Kobiljski ◽

Mihajla Djan ◽

Ljiljana Vapa

Keyword(s):

Dna Sequences ◽

Dna Markers ◽

Marker Assisted Selection ◽

Wheat Breeding ◽

Quality Traits ◽

Vegetable Crops ◽

Bread Making ◽

Technological Parameters ◽

Breeding Programs ◽

Wide Range

Implementation of marker assisted selection (MAS) in bread making quality (BMQ) oriented breeding programs could allow genetic potential assessment of genotypes prior to their phenotypic evaluation. The mechanisms underlying some quality traits in wheat are now understood. This knowledge, coupled with the availability of the DNA sequences of the genes encoding gluten proteins and the wide application of the PCR, has enabled the design of diagnostic DNA markers for these quality traits. Bread wheat breeding programs developed in Institute of Field and Vegetable Crops, Novi Sad have originated a wide range of quality cultivars with strong flours and hard grain texture. During twenty years, in the process of bread-making quality prediction, composition of HMW glutenin subunits were analyzed beside standard technological parameters. However, in order to improve our breeding strategies new generations of PCR-based BMQ related markers were included in selection programs. This paper provides an overview of diagnostic DNA markers that are currently in use in foreign and domestic wheat selection programs. .

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Genome-wide association study and gene network analyses reveal potential candidate genes for high night temperature tolerance in rice

Scientific Reports ◽

10.1038/s41598-021-85921-z ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Raju Bheemanahalli ◽

Montana Knight ◽

Cherryl Quinones ◽

Colleen J. Doherty ◽

S. V. Krishna Jagadish

Keyword(s):

Grain Size ◽

Candidate Genes ◽

Gene Network ◽

Genome Wide Association ◽

Potential Candidate ◽

Genetic Loci ◽

Stay Green ◽

Yield And Quality ◽

Genome Wide ◽

Wide Range

AbstractHigh night temperatures (HNT) are shown to significantly reduce rice (Oryza sativa L.) yield and quality. A better understanding of the genetic architecture of HNT tolerance will help rice breeders to develop varieties adapted to future warmer climates. In this study, a diverse indica rice panel displayed a wide range of phenotypic variability in yield and quality traits under control night (24 °C) and higher night (29 °C) temperatures. Genome-wide association analysis revealed 38 genetic loci associated across treatments (18 for control and 20 for HNT). Nineteen loci were detected with the relative changes in the traits between control and HNT. Positive phenotypic correlations and co-located genetic loci with previously cloned grain size genes revealed common genetic regulation between control and HNT, particularly grain size. Network-based predictive models prioritized 20 causal genes at the genetic loci based on known gene/s expression under HNT in rice. Our study provides important insights for future candidate gene validation and molecular marker development to enhance HNT tolerance in rice. Integrated physiological, genomic, and gene network-informed approaches indicate that the candidate genes for stay-green trait may be relevant to minimizing HNT-induced yield and quality losses during grain filling in rice by optimizing source-sink relationships.

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A New Statistic for Detecting Genetic Differentiation

Genetics ◽

10.1093/genetics/155.4.2011 ◽

2000 ◽

Vol 155 (4) ◽

pp. 2011-2014 ◽

Cited By ~ 10

Author(s):

Richard R Hudson

Keyword(s):

Genetic Differentiation ◽

Dna Sequences ◽

Genetic Data ◽

Island Model ◽

Wide Range ◽

Infinite Sites Model ◽

Parameter Values

Abstract A new statistic for detecting genetic differentiation of subpopulations is described. The statistic can be calculated when genetic data are collected on individuals sampled from two or more localities. It is assumed that haplotypic data are obtained, either in the form of DNA sequences or data on many tightly linked markers. Using a symmetric island model, and assuming an infinite-sites model of mutation, it is found that the new statistic is as powerful or more powerful than previously proposed statistics for a wide range of parameter values.

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Parasites in Antarctic krill guts inferred from DNA sequences

Antarctic Science ◽

10.1017/s0954102018000469 ◽

2019 ◽

Vol 31 (1) ◽

pp. 16-22 ◽

Cited By ~ 2

Author(s):

Alison C. Cleary ◽

Maria C. Casas ◽

Edward G. Durbin ◽

Jaime Gómez-Gutiérrez

Keyword(s):

Dna Sequences ◽

High Frequency ◽

Dna Analysis ◽

Antarctic Krill ◽

Euphausia Superba ◽

Gut Contents ◽

The West ◽

West Antarctic ◽

Wide Range

AbstractThe keystone role of Antarctic krill,Euphausia superbaDana, in Southern Ocean ecosystems, means it is essential to understand the factors controlling their abundance and secondary production. One such factor that remains poorly known is the role of parasites. A recent study of krill diet using DNA analysis of gut contents provided a snapshot of the parasites present within 170E. superbaguts in a small area along the West Antarctic Peninsula. These parasites includedMetschnikowiaspp. fungi,Haptoglossasp. peronosporomycetes,LankesteriaandParalecudinaspp. apicomplexa,Stegophorussp. nematodes, andPseudocolliniaspp. ciliates. Of these parasites,Metschnikowiaspp. fungi andPseudocolliniaspp. ciliates had previously been observed inE. superba, as had other genera of apicomplexans, though notLankesteriaandParalecudina.In contrast, nematodes had previously only been observed in eggs ofE. superba, and there are no literature reports of peronosporomycetes in euphausiids.Pseudocolliniaspp., parasitoids which obligately kill their host, were the most frequently observed infection, with a prevalence of 12%. The wide range of observed parasites and the relatively high frequency of infections suggest parasites may play a more important role than previously acknowledged inE. superbaecology and population dynamics.

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Species-specific duplex PCR for the detection of Pratylenchus penetrans

Nematology ◽

10.1163/156854109x428016 ◽

2009 ◽

Vol 11 (6) ◽

pp. 847-857 ◽

Cited By ~ 21

Author(s):

Lieven Waeyenberge ◽

Nicole Viaene ◽

Maurice Moens

Keyword(s):

Internal Control ◽

Dna Sequences ◽

Rrna Gene ◽

Duplex Pcr ◽

Specific Primers ◽

5.8S Rrna Gene ◽

5.8S Rrna ◽

Wide Range ◽

Pcr Products ◽

Species Specific

Abstract ITS1, the 5.8S rRNA gene and ITS2 of the rDNA region were sequenced from 20 different Pratylenchus species. Additionally, the same region was sequenced from seven populations of P. penetrans. After purifying, cloning and sequencing the PCR products, all sequences were aligned in order to find unique sites suitable for the design of species-specific primers for P. penetrans. Since ITS regions showed variability between and even within populations of P. penetrans, only three small DNA sequences were suitable for the construction of three potentially useful species-specific primers. New species-specific primers were paired with existing universal ITS primers and tested in all possible primer combinations. The best performing primer set, supplemented with a universal 28S rDNA primer set that served as an internal control, was tested in duplex PCR. The ideal annealing temperature, Mg2+ concentration and primer ratios were then determined for the most promising primer set. The optimised duplex PCR was subsequently tested on a wide range of different Pratylenchus spp. and 25 P. penetrans populations originating from all over the world. To test the sensitivity, the duplex PCR was conducted on DNA extracted from a single P. penetrans nematode mixed with varying amounts of nematodes belonging to another Pratylenchus species. Results showed that a reliable and sensitive P. penetrans species-specific duplex PCR was constructed.

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Progression of the transformed phenotype in clonal lines of Abelson virus-infected lymphocytes

Molecular and Cellular Biology ◽

10.1128/mcb.3.4.596-604.1983 ◽

1983 ◽

Vol 3 (4) ◽

pp. 596-604

Author(s):

C A Whitlock ◽

S F Ziegler ◽

O N Witte

Keyword(s):

Cell Lines ◽

Dna Sequences ◽

Lymphoid Cells ◽

Growth Potential ◽

Malignant Growth ◽

Wide Range ◽

Feeder Layers ◽

Growth Phenotype ◽

Abelson Virus

Some molecular changes which correlate with the tumorigenic progression of neoplastic cells can best be studied with in vitro cell lines that represent each stage in the progression. Lymphoid cells infected by Abelson murine leukemia virus exhibit a wide range of growth potential in vitro and in vivo. Uncloned populations that are poorly oncogenic early after infection become progressively more oncogenic with successive passages of the cells in culture. In such mass cultures, it is difficult to evaluate whether a rare subpopulation of highly oncogenic cells becomes dominant in the culture or whether the individual cells progress in oncogenic phenotype. To examine this latter possibility, Abelson virus-infected lymphoid cells were cloned by limiting-dilution culture 10 days postinfection. We isolated two clones that grew poorly in agar, required feeder layers of adherent bone marrow cells for growth in liquid culture, and were extremely slow to form tumors in syngeneic animals. Both clones, after passage in the presence of adherent feeder layers for 3 months, grew well in liquid and agar-containing cultures in the absence of feeder layers and formed tumors in animals at a rapid rate. The progression of these clonal cell lines to a more malignant growth phenotype occurred in the absence of detectable changes in the concentration, half-life, phosphorylation, in vitro kinase activity, or cell localization of the Abelson virus-encoded transforming protein. No change in the concentration or arrangement of integrated Abelson viral DNA sequences was detected in either clone. Thus, perhaps changes in the expression of cellular genes would appear to alter the growth properties of lymphoid cells after their initial transformation by Abelson virus. Such cellular changes could complement the activity of the Abelson virus transforming protein in producing the fully malignant growth phenotype.

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In vitro analysis of a transcription termination site for RNA polymerase II.

Molecular and Cellular Biology ◽

10.1128/mcb.10.11.5782 ◽

1990 ◽

Vol 10 (11) ◽

pp. 5782-5795 ◽

Cited By ~ 19

Author(s):

D K Wiest ◽

D K Hawley

Keyword(s):

Rna Polymerase ◽

Rna Polymerase Ii ◽

Dna Sequences ◽

Nuclear Extract ◽

Transcription Unit ◽

Dependent Manner ◽

Wide Range ◽

Vitro Analysis

Transcription from the adenovirus major late (ML) promoter has previously been shown to pause or terminate prematurely in vivo and in vitro at a site within the first intron of the major late transcription unit. We are studying the mechanism of elongation arrest at this site in vitro to define the DNA sequences and proteins that determine the elongation behavior of RNA polymerase II. Our assay system consists of a nuclear extract prepared from cultured human cells. With standard reaction conditions, termination is not observed downstream of the ML promoter. However, in the presence of Sarkosyl, up to 80% of the transcripts terminate 186 nucleotides downstream of the start site. Using this assay, we showed that the DNA sequences required to promote maximal levels of termination downstream of the ML promoter reside within a 65-base-pair region and function in an orientation-dependent manner. To test whether elongation complexes from the ML promoter were functionally homogeneous, we determined the termination efficiency at each of two termination sites placed in tandem. We found that the behavior of the elongation complexes was different at these sites, with termination being greater at the downstream site over a wide range of Sarkosyl concentrations. This result ruled out a model in which the polymerases that read through the first site were stably modified to antiterminate. We also demonstrated that the ability of the elongation complexes to respond to the ML termination site was promoter specific, as the site did not function efficiently downstream of a heterologous promoter. Taken together, the results presented here are not consistent with the simplest class of models that have been proposed previously for the mechanism of Sarkosyl-induced termination.

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Tissue-specific cis-regulatory divergence implicates a fatty acid elongase necessary for inhibiting interspecies mating in Drosophila

10.1101/344754 ◽

2018 ◽

Author(s):

Peter A. Combs ◽

Joshua J. Krupp ◽

Neil M. Khosla ◽

Dennis Bua ◽

Dmitri A. Petrov ◽

...

Keyword(s):

Fatty Acid ◽

Candidate Genes ◽

Molecular Mechanisms ◽

Sister Species ◽

F1 Hybrids ◽

Rna Seq ◽

Fatty Acid Elongase ◽

Tissue Specific ◽

Regulatory Changes ◽

Wide Range

AbstractPheromones known as cuticular hydrocarbons are a major component of reproductive isolation in Drosophila. Individuals from morphologically similar sister species produce different sets of hydrocarbons that allow potential mates to identify them as a suitable partner. In order to explore the molecular mechanisms underlying speciation, we performed RNA-seq in F1 hybrids to measure tissue-specific cis-regulatory divergence between the sister species D. simulans and D. sechellia. By focusing on cis-regulatory changes specific to female oenocytes, we rapidly identified a small number of candidate genes. We found that one of these, the fatty acid elongase eloF, broadly affects both the complement of hydrocarbons present on D. sechellia females and the propensity of D. simulans males to mate with those females. In addition, knockdown of eloF in the more distantly related D. melanogaster led to a similar shift in hydrocarbons as well as lower interspecific mate discrimination by D. simulans males. Thus, cis-regulatory changes in eloF appear to be a major driver in the sexual isolation of D. simulans from multiple other species. More generally, our RNA-seq approach proved to be far more efficient than QTL mapping in identifying candidate genes; the same framework can be used to pinpoint cis-regulatory drivers of divergence in a wide range of traits differing between any interfertile species.

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Cross-border Investigations on the Prevalence and Transmission Dynamics of Cryptosporidium Species in Dairy Cattle Farms in Western Mainland Europe

10.20944/preprints202110.0273.v1 ◽

2021 ◽

Author(s):

Pedro Pinto ◽

Claudia A Ribeiro ◽

Sumaiya Hoque ◽

Ourida Hammouma ◽

Hélène Leruste ◽

...

Keyword(s):

The Netherlands ◽

Human Health ◽

Dna Sequences ◽

Significant Risk ◽

Dairy Farms ◽

Economic Loss ◽

Cryptosporidium Spp ◽

Wide Range ◽

Parasitic Protist ◽

Cattle Farms

Cryptosporidium is comprised an apicomplexan parasitic protist, which infects a wide range of hosts, causing cryptosporidiosis. In cattle farms, the incidence of cryptosporidiosis results in high mortality in calves leading to considerable economic loss in the livestock industry. Infected animals may also act as a major reservoir of Cryptosporidium spp., in particular C. parvum, the most common cause of cryptosporidiosis in calves. This poses a significant risk to other farms via breeding centres, to trading of livestock and to human health. This study, funded by the Interreg-2-seas programme, is a part of a global project aimed at strategies to tackle cryptosporidiosis. To reach this target, it was essential to determine whether prevalence was dependent on the studied countries or if the issue was borderless. Indeed, C. parvum occurrence was assessed across dairy farms in certain regions of Belgium, France and the Netherlands. At the same time, the animal-to-animal transmission of the circulating C. parvum subtypes was studied. To accomplish this, 1084 faecal samples, corresponding to 57 dairy-farms from all three countries, were analysed. Well-established protocols amplifying the 18S rDNA and gp60 genes fragments, followed by DNA sequencing, were used for the detection and subtyping C. parvum; the DNA sequences obtained were further characterised using a combination of bioinformatics and phylogenetics methods. Our results show 25.7%, 24.9% and 20.8% prevalence of Cryptosporidium spp. in Belgium, France and the Netherlands respectively. Overall, 93% of the farms were Cryptosporidium positive. The gp60 subtyping demonstrated a significant number of the C. parvum positives belonged to the IIa allelic family, which has been also detected in humans. Consequently, this study highlights how widespread is C. parvum in dairy farms and endorses cattle as a major carrier of zoonotic C. parvum subtypes, which subsequently pose a significant threat to human health.

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The Genetic Variability of Sicilian Lemon Germplasm Revealed by Molecular Marker Fingerprints

Journal of the American Society for Horticultural Science ◽

10.21273/jashs.133.2.242 ◽

2008 ◽

Vol 133 (2) ◽

pp. 242-248 ◽

Cited By ~ 3

Author(s):

Mirko Siragusa ◽

Fabio De Pasquale ◽

Loredana Abbate ◽

Letizia Martorana ◽

Nicasio Tusa

Keyword(s):

Dna Markers ◽

Random Amplified Polymorphic Dna ◽

Citrus Limon ◽

Genetic Isolation ◽

Breeding Programs ◽

Bud Mutation ◽

Italian Regions ◽

Wide Range ◽

High Level ◽

Polymorphic Nature

There is a high level of diversity among lemons [Citrus limon (L.) Burm. f. (2n = 2x = 18)] in Sicily, where each growing area has a wide range of landraces mostly derived from bud mutation. Because this variability represents an important resource for future breeding programs and genetic improvement, the relationships among the principal 36 accessions of Sicilian lemon, belonging to three different cultivars (Femminello, Monachello, and Lunario), were examined by intersimple sequence repeat and random amplified polymorphic DNA markers. Three ‘Femminello’ accessions from nearby Italian regions were also examined to study the genetic flow from the continent. The disputed case of the accession ‘Eureka Messina lemon’ was also examined, using ‘Frost Eureka’ as a control. Our results confirmed the extreme polymorphic nature of the three principal Sicilian cultivars and the presence of a wide range of different genotypes. Twenty-two Sicilian genotypes were recognized as unique accessions, reflecting the richness of the lemon germplasm present in Sicily. Each growing area showed the presence of several genetically different landraces, probably preserved by genetic isolation, whereas the continental accessions appeared extremely similar to the island genotypes, showing an exchange of germplasm from the island to the continent.

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