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Critical Reviews in Plant Sciences 27 (6), 377 (2008)
Plant Breeding 128 (1), 1-26 (2009)
TAG Theoretical and Applied Genetics 118 (4), 683-94 (26 Nov 2008)
Nature Biotechnology 27 (6), 487 (2009)
In contrast to the slow translation of human genome information into medicine, animal genomics is likely to have a rapid and tangible impact on agriculture.
Introduction
The immediate impact of the human genome sequence on human health and wellness has been rather underwhelming. Yes, sequence information from human and/or microbial genomes is immensely useful for understanding biology. But translating that into novel medicines and diagnostics is both complex and time consuming. Meanwhile, less anthropocentric genomic studies are forging ahead, with very little hype or fanfare. These livestock genomes are providing not only hugely valuable biological information but also immediate benefits to the way livestock breeders go about their business.
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Dwarf Hamster Breeding - Playing the Matchmaker
BMC Bioinformatics 10 (1), 176 (2009)
Background
Analysis of allelic variation for relevant genes and monitoring chromosome segment transmission during selection are important approaches in plant breeding and ecology. To minimize the number of required molecular markers for this purpose is crucial due to cost and time constraints. To date, software for identification of the minimum number of required markers has been optimized for human genetics and is only partly matching the needs of plant scientists and breeders. In addition, different software packages with insufficient interoperability need to be combined to extract this information from available allele sequence data, resulting in an error-prone multi-step process of data handling.
Results
PolyMin, a computer program combining the detection of a minimum set of single nucleotide polymorphisms (SNPs) and / or insertions/deletions (INDELs) necessary for allele differentiation with the subsequent genotype differentiation in plant populations has been developed. Its efficiency in finding minimum sets of polymorphisms is comparable to other available program packages.
Conclusions
A computer program detecting the minimum number of SNPs for haplotype discrimination and subsequent genotype differentiation has been developed, and its performance compared to other relevant software. The main advantages of PolyMin, especially for plant scientists, is the integration of procedures from sequence analysis to polymorphism selection within a single program, including both haplotype and genotype differentiation.
Current Opinion in Plant Biology 12 (2), 103 (2009)
During the past two decades, new technologies and enabling platforms have revolutionised our ability to dissect genomes and decipher gene function. This amazing journey has progressed in a ‘leaps and bounds’ fashion along with the adoption of the relevant platforms that have improved the resolution and throughput level in profiling the genome, transcriptome, proteome and metabolome. An equally important role has been played by the introduction of suitable statistical packages and bioinformatics tools that are required for handling the deluge of molecular data and sequence information. In this fast-evolving scenario, the 18 reviews of this special issue provide a timely update on the structure, evolution and functions of plant genomes and illustrate how this information can be harnessed to more effectively improve crops and trees. Notwithstanding the diversity of this collection of articles and the kaleidoscope of expertise and species that they represent, we have identified some common themes.
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