Mule Duck “Foie Gras” Shows Different Metabolic States According to Its Quality Phenotype by Using a Proteomic Approach

This study aimed at identifying the mechanisms implicated in “foie gras” quality variability through the study of the relationships between liver protein compositions and four liver quality phenotypes: liver weight, melting rate, and protein contents on crude or dry matter. Spots of soluble proteins were separated by bidimensional electrophoresis, and the relative abundance of proteins according to quality traits values was investigated. Twenty-three protein spots (19 unique identified proteins) showed different levels of abundance according to one or more of the traits’ values. These abundance differences highlighted two groups of livers with opposite trends of abundance levels. Proteins of the first group, associated with low liver weight and melting rate, are involved in synthesis and anabolism processes, whereas proteins of the second group, associated with high liver weight and melting rate, are proteins involved in stress response. Altogether, these results highlight the variations in metabolic states underlying foie gras quality traits

SNP dataset retrieved from 176 whole-genome sequences (117 A. m. iberiensis, 28 A. m. carnica and 31 A. m. ligustica)

The dataset contains a total of 2,366,382 SNPs detected between 117 A. m. iberiensis, 28 A. m. carnica and 31 A. m. ligustica. SNP calling was performed using three different variant calling tools: GATK's, SAMtools’ mpileup 1.1 and PLATYPUS 0.8.1 Details for SNP processing and quality control is provided in the paper and its supplementary information

El Progreso : semanario independiente: Ano VIII Número 1470 - 1914 novembro 1

Additional file 1: Table S1. List of identified protein spots for which QTL were detected. List of 104 protein spots with gene/protein symbol, protein name, spot number, accession number, Mascot score, number of amino acids, molecular weight and calculated isolectric point

Addition of the microchromosome GGA25 to the chicken genome sequence assembly through radiation hybrid and genetic mapping-2

Ochromosomes of similar size as the one hybridised by the BAC clone from E26C13 are shown: (a): BAC clones for GGA19, GGA21, GGA22, GGA23 (red) and BAC clone bw90F5 for E26C13 (green). (b): BAC clones for GGA24, GGA26, GGA27, GGA28 (red) and BAC clone bw90F5 for E26C13 (green).<p><b>Copyright information:</b></p><p>Taken from "Addition of the microchromosome GGA25 to the chicken genome sequence assembly through radiation hybrid and genetic mapping"</p><p>http://www.biomedcentral.com/1471-2164/9/129</p><p>BMC Genomics 2008;9():129-129.</p><p>Published online 17 Mar 2008</p><p>PMCID:PMC2275740.</p><p></p

Addition of the microchromosome GGA25 to the chicken genome sequence assembly through radiation hybrid and genetic mapping-1

Ome assembly. In green: RH linkage group assignment of the supercontigs; LG: linkage group, ND: not done, NLG: new linkage group. A: position of all chicken supercontigs larger than 10 kb on HSA1 in the May 2004 Hg17 assembly. Supercontigs with a low % (G+C) were not selected for genotyping. B: position of the supercontigs genotyped in the RH panel on HSA1 in the March 2006 Hg18 assembly.<p><b>Copyright information:</b></p><p>Taken from "Addition of the microchromosome GGA25 to the chicken genome sequence assembly through radiation hybrid and genetic mapping"</p><p>http://www.biomedcentral.com/1471-2164/9/129</p><p>BMC Genomics 2008;9():129-129.</p><p>Published online 17 Mar 2008</p><p>PMCID:PMC2275740.</p><p></p

Addition of the microchromosome GGA25 to the chicken genome sequence assembly through radiation hybrid and genetic mapping-3

Gion 144.1–159.5 Mb [37]. For each marker on the framework map, a line joins both positions (cR and Mb) together. Framework markers are in red. Left: conservation of synteny between HSA1 and chicken chromosomes. Pink: GGA25, blue: GGA08, orange: GGA01.<p><b>Copyright information:</b></p><p>Taken from "Addition of the microchromosome GGA25 to the chicken genome sequence assembly through radiation hybrid and genetic mapping"</p><p>http://www.biomedcentral.com/1471-2164/9/129</p><p>BMC Genomics 2008;9():129-129.</p><p>Published online 17 Mar 2008</p><p>PMCID:PMC2275740.</p><p></p

Addition of the microchromosome GGA25 to the chicken genome sequence assembly through radiation hybrid and genetic mapping-6

Ome assembly. In green: RH linkage group assignment of the supercontigs; LG: linkage group, ND: not done, NLG: new linkage group. A: position of all chicken supercontigs larger than 10 kb on HSA1 in the May 2004 Hg17 assembly. Supercontigs with a low % (G+C) were not selected for genotyping. B: position of the supercontigs genotyped in the RH panel on HSA1 in the March 2006 Hg18 assembly.<p><b>Copyright information:</b></p><p>Taken from "Addition of the microchromosome GGA25 to the chicken genome sequence assembly through radiation hybrid and genetic mapping"</p><p>http://www.biomedcentral.com/1471-2164/9/129</p><p>BMC Genomics 2008;9():129-129.</p><p>Published online 17 Mar 2008</p><p>PMCID:PMC2275740.</p><p></p

Addition of the microchromosome GGA25 to the chicken genome sequence assembly through radiation hybrid and genetic mapping-0

Ck of 20% and a maximum overlap with the chicken self-alignment table of 20%. A: schematic representation of the filtering and intersection queries in the UCSC table browser. B: screenshot of the UCSC browser, representing a supercontig selected with the above criteria. The overlap with the human alignment net track is about 75% and there is no overlap with another chicken region. The quality scores and repeat element tracks are displayed to guide the choice of PCR primers.<p><b>Copyright information:</b></p><p>Taken from "Addition of the microchromosome GGA25 to the chicken genome sequence assembly through radiation hybrid and genetic mapping"</p><p>http://www.biomedcentral.com/1471-2164/9/129</p><p>BMC Genomics 2008;9():129-129.</p><p>Published online 17 Mar 2008</p><p>PMCID:PMC2275740.</p><p></p

Addition of the microchromosome GGA25 to the chicken genome sequence assembly through radiation hybrid and genetic mapping-5

Ck of 20% and a maximum overlap with the chicken self-alignment table of 20%. A: schematic representation of the filtering and intersection queries in the UCSC table browser. B: screenshot of the UCSC browser, representing a supercontig selected with the above criteria. The overlap with the human alignment net track is about 75% and there is no overlap with another chicken region. The quality scores and repeat element tracks are displayed to guide the choice of PCR primers.<p><b>Copyright information:</b></p><p>Taken from "Addition of the microchromosome GGA25 to the chicken genome sequence assembly through radiation hybrid and genetic mapping"</p><p>http://www.biomedcentral.com/1471-2164/9/129</p><p>BMC Genomics 2008;9():129-129.</p><p>Published online 17 Mar 2008</p><p>PMCID:PMC2275740.</p><p></p

Whole genome comparative studies between chicken and turkey and their implications for avian genome evolution-0

Turkey metaphase (chromosome numbers are labeled with arrows and chicken (GGA) orthologues are indicated in brackets).<p><b>Copyright information:</b></p><p>Taken from "Whole genome comparative studies between chicken and turkey and their implications for avian genome evolution"</p><p>http://www.biomedcentral.com/1471-2164/9/168</p><p>BMC Genomics 2008;9():168-168.</p><p>Published online 14 Apr 2008</p><p>PMCID:PMC2375447.</p><p></p