Lessons from established breeding programs: terrestrial and aquatic animals

Some relevant components of selection program theory and implementation are reviewed. This includes pedigree recording, genetic evaluation, balancing genetic gains and genetic diversity and tactical integration of key issues. Lessons learned are briefly described – illustrating how existing method and tools can be useful when launching a program in a novel species, and yet highlighting the importance of proper understanding and custom application according to the biology and environments of that species

Lessons from established breeding programs: terrestrial and aquatic animals

Some relevant components of selection program theory and implementation are reviewed. This includes pedigree recording, genetic evaluation, balancing genetic gains and genetic diversity and tactical integration of key issues. Lessons learned are briefly described û illustrating how existing method and tools can be useful when launching a program in a novel species, and yet highlighting the importance of proper understanding and custom application according to the biology and environments of that species.Biotechnology, Genetics, Food fish, Genetic drift, Genetic diversity, Aquatic animals, Selective breeding, Cultured organisms

The use of non-additive components in selection policy

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An algorithm for efficient constrained mate selection

<p>Abstract</p> <p>Background</p> <p>Mate selection can be used as a framework to balance key technical, cost and logistical issues while implementing a breeding program at a tactical level. The resulting mating lists accommodate optimal contributions of parents to future generations, in conjunction with other factors such as progeny inbreeding, connection between herds, use of reproductive technologies, management of the genetic distribution of nominated traits, and management of allele/genotype frequencies for nominated QTL/markers.</p> <p>Methods</p> <p>This paper describes a mate selection algorithm that is widely used and presents an extension that makes it possible to apply constraints on certain matings, as dictated through a group mating permission matrix.</p> <p>Results</p> <p>This full algorithm leads to simpler applications, and to computing speed for the scenario tested, which is several hundred times faster than the previous strategy of penalising solutions that break constraints.</p> <p>Conclusions</p> <p>The much higher speed of the method presented here extends the use of mate selection and enables implementation in relatively large programs across breeding units.</p

A GENOTYPING STRATEGY TO MINIMISE THE COST OF DNA TESTING

SUMMARY This paper describes a method for reducing the cost of DNA typing by processing or &apos;genotyping&apos; only some of the individuals in the target population. The method is designed such that there is in fact good DNA information on the individuals that have not been genotyped. The method works in cycles, first genotyping the one individual that will contribute most information to the total population, through pedigree links. Following this, analysis is done to find which is the individual that can contribute most at this next stage, etc. After genotyping about 10 % of the population, about 50 % of the utility of genotyping all animals is reached, leading to potentially big savings in the cost of genotyping

Oligonucleotide Functionalised Microbeads: Indispensable Tools for High-Throughput Aptamer Selection

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Alanine scanning mutagenesis of a high-affinity nitrate transporter highlights the requirement for glycine and asparagine residues in the two nitrate signature motifs

Common to all of the nitrate nitrite porter family are two conserved motifs in transmembrane helices 5 and 11 termed NS (nitrate signature) 1 and NS2. Although perfectly conserved substrate-interacting arginine residues have been described in transmembrane helices 2 and 8, the role of NSs has not been investigated. In the present study, a combination of structural modelling of NrtA (nitrate transporter from Aspergillus nidulans) with alanine scanning mutagenesis of residues within and around the NSs has been used to shed light on the probable role of conserved residues in the NSs. Models show that Asn 168 in NS1 and Asn 459 in NS2 are positioned approximately midway within the protein at the central pivot point in close proximity to the substrate-binding residues Arg 368 and Arg 87 respectively, which lie offset from the pivot point towards the cytoplasmic face. The Asn 168 /Arg 368 and Asn 459 /Arg 87 residue pairs are relatively widely separated on opposite sides of the probable substrate translocation pore. The results of the present study demonstrate the critical structural contribution of several glycine residues in each NS at sites of close helix packing. Given the relative locations of Asn 168 /Arg 368 and Asn 459 /Arg 87 pairs, the validity of the models and possible role of the NSs together with the substrate-binding arginine residues are discusse

Periodicity of DNA in Exons

BACKGROUND: The periodic pattern of DNA in exons is a known phenomenon. It was suggested that one of the initial causes of periodicity could be the universal (RNY)npattern (R = A or G, Y= C or U, N = any base) of ancient RNA. Two major questions were addressed in this paper.Firstly, the cause of DNA periodicity, which was investigated by comparisons between real and simulated coding sequences. Secondly, quantification of DNA periodicity was made using anevolutionary algorithm, which was not previously used for such purposes.RESULTS: We have shown that simulated coding sequences, which were composed using codon usage frequencies only, demonstrate DNA periodicity very similar to the observed in real exons.It was also found that DNA periodicity disappears in the simulated sequences, when the frequencies of codons become equal.Frequencies of the nucleotides (and the dinucleotide AG) at each location along phase 0 exons were calculated for C. elegans, D. melanogaster and H. sapiens. Two models were used to fit thesedata, with the key objective of describing periodicity. Both of the models showed that the best-fit curves closely matched the actual data points. The first dynamic period determination modelconsistently generated a value, which was very close to the period equal to 3 nucleotides. The second fixed period model, as expected, kept the period exactly equal to 3 and did not detract from its goodness of fit.CONCLUSIONS: Conclusion can be drawn that DNA periodicity in exons is determined by codon usage frequencies. It is essential to differentiate between DNA periodicity itself, and the length ofthe period equal to 3. Periodicity itself is a result of certain combinations of codons with different frequencies typical for a species. The length of period equal to 3, instead, is caused by the triplet nature of genetic code. The models and evolutionary algorithm used for characterising DNA periodicity are proven to be an effective tool for describing the periodicity pattern in a species, when a number of exons in the same phase are analysed