WO2000029615A2 - A whole-genome radiation hybrid map of the dog genome and use thereof for identifying genes of interest - Google Patents
A whole-genome radiation hybrid map of the dog genome and use thereof for identifying genes of interest Download PDFInfo
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- WO2000029615A2 WO2000029615A2 PCT/IB1999/001907 IB9901907W WO0029615A2 WO 2000029615 A2 WO2000029615 A2 WO 2000029615A2 IB 9901907 W IB9901907 W IB 9901907W WO 0029615 A2 WO0029615 A2 WO 0029615A2
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- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
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- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12Q2600/00—Oligonucleotides characterized by their use
- C12Q2600/142—Toxicological screening, e.g. expression profiles which identify toxicity
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- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12Q2600/00—Oligonucleotides characterized by their use
- C12Q2600/156—Polymorphic or mutational markers
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- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12Q2600/00—Oligonucleotides characterized by their use
- C12Q2600/172—Haplotypes
Definitions
- the present invention concerns a map of the dog genome comprising the chromosome location of purified or isolated gene markers, TOASTs, and polymorphic microsatellite markers of said genome. Another aspect is the use of said map for identifying genes responsible for a phenotypic and behavioral trait of interest, for the identification of morbid genes, for analyzing diseases, for identifying the implicated genes of said diseases and their alleles, and for studying dog pedigrees.
- Canis familiaris the only domesticated species of the Canidae family, is composed of more than 350 breeds offering a very large spectrum of polymorphic traits, behaviours and capabilities.
- various breeds are plagued by numerous genetic disorders, many being similar to human diseases (Ettinger and Feldman, 1995).
- Most breeds have been generated over the past 250 years, a rather short period of time. This suggests that only a small number of key loci are likely to be responsible for the peculiar traits that define a breed (Serpell, 1995; Denis, 1997). It can be postulated that intrabreed uniformity is due to the high degree of genetic homogeneity, at least in the region of the genome submitted to selective pressure.
- dog appears as a particularly attractive and powerful model to study the nature and involvement of the genes responsible for such phenotypic and behavioural diversity (Ostrander and Giniger, 1997).
- the canine model should also prove very useful in human genetics when the identification of a morbid gene faces two major problems.
- the first problem is the difficulty to diagnose, down to the molecular level two diseases caused by two different mutated genes while displaying a unique symptomatology.
- the second comes from the scarcity of large and informative pedigrees. Whenever possible, these two problems are overcome by studying pedigrees from isolated populations in which a single founder effect can be postulated. Resorting to dog should be a promising alternative strategy (Galibert et al, 1998).
- dog pedigrees can be secured rather easily while the unique combination of interbreed diversity with intrabreed uniformity makes dog a model of choice to analyse diseases or other complex mammalian traits and to identify the implicated genes and their alleles.
- the key resource for tracking down genes responsible for various polymorphic traits or genetic diseases is a genome map including polymorphic icrosatellites (Type II markers) and functional genes (Type I markers) regularly spaced along the genome.
- Type II markers polymorphic icrosatellites
- Type I markers functional genes
- Second, detecting regions where synteny is conserved between different species will favor the identification of many more genes, which in turn will enrich the dog map and facilitate the identification of responsible genes through the candidate gene approach.
- Integrated maps, comprising Type I and Type II markers have been proven feasible through the use of Radiation Hybrid panels (Cox et al, 1990; Raeymaekers et al.,1995; McPherson et al., 1997).
- the present invention concerns an integrated RH map of the canine genome where 400 markers, consisting of gene markers, TOATS and microsatellites -some of which already integrated in meiotic maps-, have been mapped through the WGRH strategy, on a dog/hamster RH5 000 panel. Positioning these Type I and Type II markers led to a RH map covering approximately 80% of the dog genome. Moreover, gene order comparison in this RH map with that in human, mouse and pig maps allowed to characterize chromosomal segments where synteny has been conserved or, conversely, disrupted.
- the present invention is aimed at a map of the dog genome comprising the genome location of a marker selected from the group consisting of the markers of sequence SEQ ID N° 1-804, as depicted in table 2 below.
- the map can comprises the genome location of at least 50, 100, 200, 300 or preferably 400 markers selected from the group consisting of the markers of sequence SEQ ID N° 1-804, as depicted in table 2. This map can have any combination of markers depicted in table 2.
- location means any relative or absolute measure between two or more markers, any data showing that a given marker is unlinked to another marker, any positioning by membership to a given radiation group or any data showing that a given marker belongs to a radiation group that comprises no other markers.
- Another aspect of the invention relates to the use of a map as described above for identifying genes responsible for a phenotypic and behavioral trait of interest, for the identification of morbid genes, for analyzing diseases and for identifying the implicated genes of said diseases and their alleles, or for studying dog pedigrees.
- a third aspect concerns the use of a dog genome marker selected from the group consisting of the markers as depicted in table 2 of sequence SEQ ID N° 1-804, or sequence complementary thereto, for identifying genes responsible for a phenotypic and behavioral trait of interest, for the identification of morbid genes, for analyzing diseases and for identifying the implicated genes of said diseases and their alleles, or for studying dog pedigrees.
- Another object of the invention is a sequence selected from the group of sequences SEQ ID N° 1-804, which can be used for example as a primer for isolating corresponding human gene sequence, especially gene involved in genetic diseases.
- these sequences are the sequences in bold in table 2 below.
- RH mapping is a powerful method in view of its potential for integrating genetic and physical maps (Hudson et al., 1995; Gyapay et al., 1996; Schuler et al, 1996; McCarthy et al, 1996; Schlapfer et al, 1997; Yang et al, 1998).
- the major advantages of this strategy include (i) mapping polymorphic and non-polymorphic markers, (ii) unlimited DNA supply and (iii) higher resolution level of a panel of 100 to 200 hybrids compared to an equivalent number of meiosis in genetic linkage mapping. For example, from theoretical considerations (Stewart et al, 1997) the upper resolution limit expected from the RH panel used in the present invention can be estimated as follows.
- the coverage of the map has been estimated from the chances that any new marker will integrate into one of the linkage group. From the 180 marker on, we observe that any new marker had a 80% chance to be linked to another marker with a lod score 6 or greater. Assuming those markers are most probably randomly distributed within the genome, coverage can be estimated to ⁇ 80%.
- the total size of all 57 RH groups amounts 7995 cR.
- the data obtained from the RH2PT analysis computed at lod 6 allow detection of linkage between markers located 50 cR apart. This value can be added to each side of the RH groups, which extends the RH group coverage to 13,695 cR. This may be an overestimate due to the fact that some markers can be located close to telomeres. On the other hand, it does not take into consideration the estimated coverage corresponding to the 53 unlinked markers.
- RH mapping has been shown to constitute a particularly powerful tool in comparative gene mapping, since chromosomal order can be established for expressed genes that are usually conserved between species (O'Brien et al, 1993; Johansson et al, 1995; Chowdhary et al, 1996), but often do not led themselves to a genetic linkage mapping approach for lack of readily detectable allelic variation. In such a challenge, it is of paramount importance to anchor a maximum number of common markers, which could be facilitated by the use of reagents such as TOASTs (Jiang et al.
- RH groups containing at least three markers have been ordered and the distances calculated using the RHMAXLIK program of RHMAP 3.0 (Table 2). Distances between markers are expressed in centiRays (cR), 1 cRsooo being defined as 1% frequency of breakage between two markers after exposure to 5000 rads of gamma-rays (Cox et al, 1990). RH groups range in size from 9 cR (RH06 with two markers) to 588 cR (RH14 with 18 markers). The average distance observed between two adjacent markers is 23 cR. Table 1 : Type, number and reference of markers typed on the dog/hamster RH panel
- Type I markers coding sequences 218 Present
- Type II markers repeated sequences 182
- Tri- or di-nucleotides selected 35 Present in the lab invention markers selected from dog tetranucleotide repeats 72 4 dinucleotide repeats 49 5 previously published microsatellites 26 6
- Tsble 2 legend Groups of markers are termed sRHa (containing several RHa groups) or RHa (containing one RH group)
- the suffix a is added to date the RH map When the chromosome assignment is known, it is indicated as CFA (Canis Familiaris)
- Primer sequences characterized in the laboratory are indicated in bold For PCR conditions "Ta” is the annealing temperature
- the suffix L indicates an annealing step of 45 sec Sizes of the PCR products are indicated in bp, "int” indicates the presence of intron(s) and subsequently the size of the product is unknown
- Lod scores and distances values between two markers (locus 1 on the upper line and locus 2 on the lower) are indicated on the lower line Distances are shown in centiRays (cR) ND not determined PCR Programs:
- Marker retention The average retention frequency of the 400 markers on the RH panel is 21%, with 82% of the markers having a retention frequency between 10% and 40%. Four of the markers displaying extreme retention values were above 80%. This is not surprising for two genes (SRP68 and Galkl) known to be localized on canine chromosome 9 (Werner et al, 1997) in the vicinity of the TK gene used for the selection of the hybrid cell lines. Another marker, also presenting a high retention frequency and corresponding to the huEST L08069, has not yet been linked to any other. It encodes a member of the DNA J family of chaperone proteins and caution will be needed before incorporating this marker into a linkage group.
- the fourth marker corresponds to the anonymous microsatellite Ren01E15. It does not match any known dog repeated sequence and we have no explanation for its high retention value.
- the medium-high (40-80%) retention profile presented by 28 markers might be due to their specific chromosomal location. Indeed, as previously observed in the human genome, there is a general trend towards increased retention for landmarks located on smaller chromosomes (Gyapay et al, 1996). This may be related to the high retention frequencies of markers near the centromere. In the canine genome, this is illustrated by gene SR7, localized on the dog Y chromosome, that has a retention value of 40% on the RH panel.
- sRHOl 13 larger groups termed syntenic groups and designated as sRHOl to sRH13 in Table 2.
- sRHOl could be defined through the linkage of 3 RH groups (RH01, 02 and 03) using 7 markers belonging to a single meiotic group (Ll group described by Mellersh et al, 1997).
- the largest syntenic group, sRH06 contains 24 markers and reaches 674 cR in size. Alignment of RH and meiotic groups also permitted to join some previously published dog meiotic groups.
- mapping markers by two independent methods provided higher confidence in their order. Detailed comparisons of the most probable order of the 121 markers common to the RH and meiotic maps demonstrated both approaches to coincide, with only one discrepancy in the sRH06 group.
- Two microsatellite markers, Cxx246 and Cxx424, have permuted positions in radiation hybrid RH11 and meiotic Ll groups. However, as Cxx246 is a non-framework marker in the RH map, its position will be subjected to local optimization after integrating more markers. Correlation of RH map units with genetic and physical distances
- mapping Type I markers allows to exploit data gathered by cytogenetic studies and/or physical mapping in different mammalian species.
- HSA human
- MMU 93 on mouse
- SSC pig chromosomes
- HSA4 corresponds to CFA3 (sRHOl) and CFA 13 (RH29) and, conversely, CFA3 shares homologies with HSA4p, 5q and 15q (Table 2).
- CFA3 shares homologies with HSA4p, 5q and 15q (Table 2).
- the dog X chromosome (part of it being represented by the sRH05 group) displayed homology with its human and murine counterparts (O'Brien et al, 1993). Seven of the other RH groups were conserved en bloc between the dog, human and mouse species. The largest block is a part of the sRH03 group (CFA9), homologous to HSA17q and MMUl l, and reaches 300cR (slightly less than 50 Mb). A case of conservation of synteny between the four species is demonstrated in the sRH06 group over a distance of lOOcR (16.6Mb). The RH28 group, corresponding to CFA12, contains 14 markers ordered over 195 cR.
- MHC genes are genes commonly associated to the MHC locus, namely tumor necrosis factor (TNF) and colipase (CLPS).
- TNF tumor necrosis factor
- CLPS colipase
- EXAMPLE 1 GENERATION OF RADIATION HYBRID CELL LINES
- a panel of radiation hybrid cell lines was constructed as described by Vignaux et al, (in press). Mongrel dog fibroblasts were irradiated by a 5000-rad gamma ray exposure. Cells were then fused with thymidine-kinase deficient hamster cells (HTK3-1) in the presence of polyethylene-glycol according to Benham et al, 1989. Following selection in HAT medium and cell culture in roller bottles, DNA was extracted from individual clones (H ⁇ glund et al, 1995). After verification of the presence of dog DNA and analysis of the retention profiles, a total of 126 radiation hybrid cells were expanded to prepare a minimum of 2.5 mg genomic DNA. This WGRH panel, named RHDF5000, was used to map the canine genome.
- TOAST Raced Orthologous Amplified Sequence Tags
- Microsatellites A set of tri- and dinucleotide microsatellites characterized from a small insert canine genomic library as well as additional dog microsatellites from the literature were typed (Table 1).
- EXAMPLE 3 GENERATION OF A RADIATION HYBRID MAP Screening dog versus hamster specific markers - Each marker was tested on dog, hamster and a mix of dog/hamster (1:2) DNA in order to mimic RH DNA content. PCR were optimized to obtain a dog specific PCR product.
- PCR analysis on the radiation hybrid cell lines - PCR was performed on 50 ng RH DNA in a final volume of 10 ⁇ l containing 15 ng of each primer, 200 ⁇ M dNTPs, 1.5 to 3 mM MgCl 2 , 50 mM KC1, 10 mM Tris-HCl and 0.5 U of Taq Gold polymerase (Perkin Elmer). Amplification was carried out with Techne (Techne, Cambridge, MA) or MJ (MJ Research, Cambridge, MA) thermocyclers. PCR products were analyzed by migration in 1.8% agarose gels for 30 min at 120 V in 0.5X TBE buffer (Hybaid electrophoresis system) and were visualized under UN light after ethidium bromide staining.
- RHMAP 3.0 consists of three programs : RH2PT, RHMINBRK and RHMAXLIK.
- the two-point analysis program (RH2PT) was used to identify pairs of loci with lod scores greater than 6 and to derive RH groups from these data.
- RHMINBRK performs multilocus ordering by minimization of obligate breaks required to explain the data.
- the RHMINBRK order was used as candidate for RHMAXLIK analysis, which performs multilocus ordering by maximization of the likelihood of the hybrid data.
- Equal retention model was used for all marker analysis. Multipoint analysis was carried out by positioning markers as framework at 1000: 1 and 100: 1. Non- framework markers were then positioned with most favorable order. Stepwise locus ordering was used to reduce computing time. Finally, selected locus model 1, allowing one retention probability for a fragment containing the selectable locus, was used to verify locus order of the linkage group containing the TK locus.
- Cytogenetic data for human, mouse and pig genes were extracted from the Genome Databases: http://bisance.citi2.fr/GENATLAS : http://www.ncbi.nlm.nih. gov/Uni Gene/index, html.
- Radiation hybrid mapping a somatic cell genetic method for constructing high-resolution maps of mammalian chromosomes. Science 250: 245-250.
- Gyapay G., Schmitt, K., Fizames, C, Jones, H, Nega-Czarny, ⁇ ., Spillett, D., Muselet, D., Prud'Homme, J.-F., Dib, C, Auffray, C. et al. (1996).
- McPherson, J.D., may be a radiation hybrid map of human chromosome 5 with integration of cytogenetic, genetic, and transcript maps. Genome Res. 7: 897-909.
- Vignaux, F Priat, C , Jouquand, S , Hitte, C , Jiang, Z , Cheron, A , Renier, C , Andre, C and Galibert F Toward a dog radiation hybrid map J.Hered. in press
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EP99956263A EP1129218A2 (en) | 1998-11-13 | 1999-11-15 | A whole-genome radiation hybrid map of the dog genome and use thereof for identifying genes of interest |
CA002351881A CA2351881A1 (en) | 1998-11-13 | 1999-11-15 | A whole-genome radiation hybrid map of the dog genome and use thereof for identifying genes of interest |
JP2000582596A JP2002530091A (en) | 1998-11-13 | 1999-11-15 | Whole-genome radiohybrid map of the canine genome and its use for identification of genes of interest |
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US10819398P | 1998-11-13 | 1998-11-13 | |
US60/108,193 | 1998-11-13 |
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WO2000029615A3 WO2000029615A3 (en) | 2000-10-26 |
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Cited By (6)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
WO2002027014A2 (en) * | 2000-09-29 | 2002-04-04 | The State Of Oregon Acting By And Through The State Board Of Higher Education On Behalf Of Oregon State University | Detection of fecal contamination |
EP1609876A1 (en) * | 2004-06-21 | 2005-12-28 | Cornell Research Foundation, Inc. | Identification of the gene and mutation for progressive rod-cone degeneration in dog and method for testing same |
US7118870B2 (en) | 2001-09-28 | 2006-10-10 | The State Of Oregon Acting By And Through The State Board Of Higher Education On Behalf Of Oregon State University | Detection of fecal contamination using nucleic acid molecules that recognize bacterial 16S rDNA sequences |
WO2008031846A1 (en) * | 2006-09-12 | 2008-03-20 | Institut National De La Recherche Agronomique | Genomic marker for meat tenderness |
KR101156047B1 (en) * | 2009-09-18 | 2012-06-27 | 대한민국 | Microsatellite marker and methods for identification of dogs |
FR3012470A1 (en) * | 2013-10-31 | 2015-05-01 | Christian Doutremepuich | METHOD AND KIT FOR IDENTIFYING A DOG BY ANALYZING A BIOLOGICAL SAMPLE |
Citations (1)
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WO1997013876A1 (en) * | 1995-09-28 | 1997-04-17 | Pe Zoogen | Microsatellite sequences for canine genotyping |
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- 1999-11-15 CA CA002351881A patent/CA2351881A1/en not_active Abandoned
- 1999-11-15 JP JP2000582596A patent/JP2002530091A/en not_active Withdrawn
- 1999-11-15 EP EP99956263A patent/EP1129218A2/en not_active Withdrawn
- 1999-11-15 WO PCT/IB1999/001907 patent/WO2000029615A2/en not_active Application Discontinuation
Patent Citations (1)
Publication number | Priority date | Publication date | Assignee | Title |
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WO1997013876A1 (en) * | 1995-09-28 | 1997-04-17 | Pe Zoogen | Microsatellite sequences for canine genotyping |
Non-Patent Citations (7)
Title |
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ACLAND G M ET AL: "Linkage analysis and comparative mapping of canine progressive rod-cone degeneration (prcd) establishes potential locus homology with retinitis pigmentosa (RP17) in humans." PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, (1998 MAR 17) 95 (6) 3048-53., XP002136285 * |
GALIBERT F ET AL: "ÄThe importance of the canine model in medical geneticsÜ. Interet du mod ele canin pour la genetique medicale." BULLETIN DE L ACADEMIE NATIONALE DE MEDECINE, (1998) 182 (4) 811-21;DISCUSSION 822., XP000904980 cited in the application * |
LANGSTON A A ET AL: "Construction of a panel of canine-rodent hybrid cell lines for use in partitioning of the canine genome." GENOMICS, (1997 DEC 15) 46 (3) 317-25., XP000905060 cited in the application * |
LINGAAS F ET AL: "Towards construction of a canine linkage map: establishment of 16 linkage groups." MAMMALIAN GENOME, (1997 MAR) 8 (3) 218-21., XP000891974 cited in the application * |
MELLERSH C S ET AL: "A linkage map of the canine genome." GENOMICS, (1997 DEC 15) 46 (3) 326-36., XP000905058 cited in the application * |
PRIAT C ET AL: "A whole-genome radiation hybrid map of the dog genome" GENOMICS, (1998 DEC 15) 54 (3) 361-78., XP000905171 * |
PRIAT, C. ET AL: "A whole-genome radiation hybrid map of the dog genome" ANIMAL GENETICS, (DEC., 1998) VOL. 29, NO. SUPPL. 1, PP. 44. MEETING INFO.: 26TH INTERNATIONAL CONFERENCE ON ANIMAL GENETICS AUCKLAND, NEW ZEALAND AUGUST 9-14, 1998, XP000905057 * |
Cited By (12)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
WO2002027014A2 (en) * | 2000-09-29 | 2002-04-04 | The State Of Oregon Acting By And Through The State Board Of Higher Education On Behalf Of Oregon State University | Detection of fecal contamination |
WO2002027014A3 (en) * | 2000-09-29 | 2002-07-18 | Oregon State | Detection of fecal contamination |
US7118870B2 (en) | 2001-09-28 | 2006-10-10 | The State Of Oregon Acting By And Through The State Board Of Higher Education On Behalf Of Oregon State University | Detection of fecal contamination using nucleic acid molecules that recognize bacterial 16S rDNA sequences |
EP1609876A1 (en) * | 2004-06-21 | 2005-12-28 | Cornell Research Foundation, Inc. | Identification of the gene and mutation for progressive rod-cone degeneration in dog and method for testing same |
US7312037B2 (en) | 2004-06-21 | 2007-12-25 | Cornell Research Foundation, Inc. | Identification of the gene and mutation responsible for progressive rod-cone degeneration in dog and a method for testing same |
US7671187B2 (en) | 2004-06-21 | 2010-03-02 | Cornell Research Foundation, Inc. | Identification of the gene and mutation responsible for progressive rod-cone degeneration in dog and a method for testing same |
WO2008031846A1 (en) * | 2006-09-12 | 2008-03-20 | Institut National De La Recherche Agronomique | Genomic marker for meat tenderness |
AU2007296198B2 (en) * | 2006-09-12 | 2011-12-15 | Apis Gene | Genomic marker for meat tenderness |
US8097411B2 (en) | 2006-09-12 | 2012-01-17 | Institut National De La Recherche Agronomique | Genomic marker for tenderness meat |
KR101156047B1 (en) * | 2009-09-18 | 2012-06-27 | 대한민국 | Microsatellite marker and methods for identification of dogs |
FR3012470A1 (en) * | 2013-10-31 | 2015-05-01 | Christian Doutremepuich | METHOD AND KIT FOR IDENTIFYING A DOG BY ANALYZING A BIOLOGICAL SAMPLE |
WO2015063429A1 (en) * | 2013-10-31 | 2015-05-07 | Christian Doutremepuich | Method and kit for identifying a dog by analysing a biological sample |
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EP1129218A2 (en) | 2001-09-05 |
WO2000029615A3 (en) | 2000-10-26 |
CA2351881A1 (en) | 2000-05-25 |
JP2002530091A (en) | 2002-09-17 |
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