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Design and Characterization of a 52K SNP Chip for Goats 总被引:3,自引:0,他引:3
Gwenola Tosser-Klopp Philippe Bardou Olivier Bouchez Cédric Cabau Richard Crooijmans Yang Dong Cécile Donnadieu-Tonon André Eggen Henri C. M. Heuven Saadiah Jamli Abdullah Johari Jiken Christophe Klopp Cynthia T. Lawley John McEwan Patrice Martin Carole R. Moreno Philippe Mulsant Ibouniyamine Nabihoudine Eric Pailhoux Isabelle Palhière Rachel Rupp Julien Sarry Brian L. Sayre Aurélie Tircazes Jun Wang Wen Wang Wenguang Zhang and the International Goat Genome Consortium 《PloS one》2014,9(1)
The success of Genome Wide Association Studies in the discovery of sequence variation linked to complex traits in humans has increased interest in high throughput SNP genotyping assays in livestock species. Primary goals are QTL detection and genomic selection. The purpose here was design of a 50–60,000 SNP chip for goats. The success of a moderate density SNP assay depends on reliable bioinformatic SNP detection procedures, the technological success rate of the SNP design, even spacing of SNPs on the genome and selection of Minor Allele Frequencies (MAF) suitable to use in diverse breeds. Through the federation of three SNP discovery projects consolidated as the International Goat Genome Consortium, we have identified approximately twelve million high quality SNP variants in the goat genome stored in a database together with their biological and technical characteristics. These SNPs were identified within and between six breeds (meat, milk and mixed): Alpine, Boer, Creole, Katjang, Saanen and Savanna, comprising a total of 97 animals. Whole genome and Reduced Representation Library sequences were aligned on >10 kb scaffolds of the de novo goat genome assembly. The 60,000 selected SNPs, evenly spaced on the goat genome, were submitted for oligo manufacturing (Illumina, Inc) and published in dbSNP along with flanking sequences and map position on goat assemblies (i.e. scaffolds and pseudo-chromosomes), sheep genome V2 and cattle UMD3.1 assembly. Ten breeds were then used to validate the SNP content and 52,295 loci could be successfully genotyped and used to generate a final cluster file. The combined strategy of using mainly whole genome Next Generation Sequencing and mapping on a contig genome assembly, complemented with Illumina design tools proved to be efficient in producing this GoatSNP50 chip. Advances in use of molecular markers are expected to accelerate goat genomic studies in coming years. 相似文献
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Gwenola Tosser-Klopp Philippe Bardou Olivier Bouchez Cédric Cabau Richard Crooijmans Yang Dong Cécile Donnadieu-Tonon André Eggen Henri C. M. Heuven Saadiah Jamli Abdullah Johari Jiken Christophe Klopp Cynthia T. Lawley John McEwan Patrice Martin Carole R. Moreno Philippe Mulsant Ibouniyamine Nabihoudine Eric Pailhoux Isabelle Palhière Rachel Rupp Julien Sarry Brian L. Sayre Aurélie Tircazes Jun Wang Wen Wang Wenguang Zhang International Goat Genome Consortium 《PloS one》2016,11(3)
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Syed Muhammad Usman Shah Che Che Radziah Saadiah Ibrahim Faazaz Latiff Mohd Fariduddin Othman Mohd Azmuddin Abdullah 《Annals of microbiology》2014,64(1):157-164
The aim of the present work was to study the effects of photoperiod, salinity and pH on growth and lipid content of Pavlova lutheri microalgae for biodiesel production in small-scale and large-scale open-pond tanks. In a 250-mL flask, the cultures grew well under 24 h illumination with maximum specific growth rate, μ max , of 0.12 day?1 and lipid content of 35 % as compared to 0.1 day?1 and 15 % lipid content in the dark. The salinity was optimum for the cell growth at 30–35 ppt, but the lipid content of 34–36 % was higher at 35–40 ppt. Algal growth and lipid accumulation was optimum at pH 8–9. Large-scale cultivation in 5-L and 30-L tanks achieved μ max of 0.13–0.14 day?1 as compared to 0.12 day?1 in small-scale and 300L cultures. 相似文献
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Lauren M. Hemara Jay Jayaraman Paul W. Sutherland Mirco Montefiori Saadiah Arshed Abhishek Chatterjee Ronan Chen Mark T. Andersen Carl H. Mesarich Otto van der Linden Minsoo Yoon Magan M. Schipper Joel L. Vanneste Cyril Brendolise Matthew D. Templeton 《PLoS pathogens》2022,18(5)
A pandemic isolate of Pseudomonas syringae pv. actinidiae biovar 3 (Psa3) has devastated kiwifruit orchards growing cultivars of Actinidia chinensis. In contrast, A. arguta (kiwiberry) is not a host of Psa3. Resistance is mediated via effector-triggered immunity, as demonstrated by induction of the hypersensitive response in infected A. arguta leaves, observed by microscopy and quantified by ion-leakage assays. Isolates of Psa3 that cause disease in A. arguta have been isolated and analyzed, revealing a 51 kb deletion in the exchangeable effector locus (EEL). This natural EEL-mutant isolate and strains with synthetic knockouts of the EEL were more virulent in A. arguta plantlets than wild-type Psa3. Screening of a complete library of Psa3 effector knockout strains identified increased growth in planta for knockouts of four effectors–AvrRpm1a, HopF1c, HopZ5a, and the EEL effector HopAW1a –suggesting a resistance response in A. arguta. Hypersensitive response (HR) assays indicate that three of these effectors trigger a host species-specific HR. A Psa3 strain with all four effectors knocked out escaped host recognition, but a cumulative increase in bacterial pathogenicity and virulence was not observed. These avirulence effectors can be used in turn to identify the first cognate resistance genes in Actinidia for breeding durable resistance into future kiwifruit cultivars. 相似文献
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