Method and arrangement for matching mammals by comparing genotypes

Abstract

A method for determining a matchmaking quality for a first mammal in relation to a plurality of different second mammals by comparing genotypes thereof, comprises steps of providing a first database and second database. The first database comprises genotyping data of known traits and coefficients weighting severity of said traits, and the second comprises genotyping data for at least certain loci common to each of said mammals to be matchmade. In determination of value of the match first results of the coefficients weighting the severities of the traits are determined for each potential breeding pair of the first mammal with each of said plurality of the different second mammals, and second results relating to a diversity are determined for each potential breeding pair of the first mammal with each of said plurality of the different second mammals. A total result determining the matchmaking quality for each potential breeding pair is determined by combining said first and second results for each of said potential breeding pair.

Claims

1. A method for determining an advised breeding choice or a matchmaking quality for a first mammal in relation to a plurality of different second mammals by comparing genotypes thereof, wherein the method comprises steps of: providing a first database comprising genotyping data of known traits and coefficients weighting severity of said traits, such as mutation, disease risk, lethality and/or affected breeds of mammal species of said mammals to be matchmade, providing a second database comprising genotyping data for at least certain loci common to each of said mammals to be matchmade, providing a group of markers for said loci to be determined for matchmaking, where i) at least first portion of the markers relates to loci to be compared in said second databases and having the coefficients in various known gene based traits in said first databases for possible breeding combinations derived in said second database, and ii) at least second portion of said markers used in determining differs from said first portion of said markers, wherein in determination of value of the match for said first mammal with said plurality of the different second mammals: first results of said coefficients weighting the severities of the traits are determined for each potential breeding pair of the first mammal with each of said plurality of the different second mammals by using said first portion of the markers, and second results relating to a diversity are determined for each potential breeding pair of the first mammal with each of said plurality of the different second mammals by using said second portion of the markers, a total result determining the matchmaking quality for each potential breeding pair is determined by combining said first and second results for each of said potential breeding pair, and said total results for each of said potential breeding pairs are processed in order to determine values of matches for said first mammal.

2. A method of claim 1 for determining said matchmaking quality, wherein first results of said coefficients weighting the severities of the traits are determined for the potential breeding partners of the first mammal with each of said plurality of the different second mammals by using said first portion of the markers, where a sub-result of the first results relates to a certain genotype and has a certain sub-coefficient, whereupon the first results are determined by summing said sub-coefficients of said sub-results, and second results relating to the diversity are determined by using said second portion of the markers so that if genotype of a certain locus is different for said first mammal than for the potential partner of said different second mammals in the second database, said sub-coefficient for said locus is rewarded and if genotype of said locus is same for both mammals, said sub-coefficient for said locus is not awarded or is penalized, whereupon the second results are determined by summing said sub-coefficients, whereupon said total result is determined by summing said first and second results.

3. The method of claim 1 for determining matchmaking quality, wherein a group of virtual descendants is provided for different combinations of said first and at least one of said second different mammals to be matchmade, where i) genotyping data of the first mammal's genome is compared with corresponding genotyping data of second different mammal's genome in the second database, ii) possible combined genotypes is determined based on said compared genotyping data for each of virtual descendants to be provided, iii) an individual index is determined for health related traits and/or genetic diversity for each of said virtual descendants to determine the value of disease risks of said descendants and breeding value of said two mammals to be matchmade, comprising the steps of: a) comparing the genotyping data of each of said individual virtual descendants' genome corresponding to said first portion of said markers with corresponding genotyping data of said first database in order to determine coefficients of the first results between said determined regions and data of said first database and thereby determine said individual index for each of said individual virtual descendants of a probability or risk or severity of the traits, and b) combining said first results and second results, such as averages of said first results and second results to determine said individual index of said virtual descendants and breeding value of said two mammals to be matchmade as said total result.

4. The method of claim 3, wherein the matchmaking quality and the breeding value is determined as: i) if said individual index<a threshold, the partners matchmade is invalid for breeding, ii) if said individual index=a threshold, the partners matchmade is invalid for breeding, and iii) if said individual index>a threshold, the partners matchmade is valid for breeding.

5. The method of claim 1, wherein a third database is provided for comprising phenotyping data of known phenotyping traits and coefficients weighting severity of said phenotyping traits, such as morphology, behaviour, color, temperament, hunting skills of mammal species of said mammals to be matchmade, for at least certain loci common to each of said mammals to be matchmade, whereupon at least one phenotype is selected as a seed.

6. The method of claim 5, wherein said seed relates to at least one phenotype to be desired or avoided for the potential descendants, whereupon: said loci related to said phenotype is analysed for both first mammal and said at least one of the second mammal to be matchmade in said second database and the corresponding coefficients weighting severity of said phenotyping trait is selected in said third database, and, if said seed is the desired phenotype and said coefficients>a threshold, the couple matchmade is valid for breeding for said phenotyping traits, and if said seed is the undesired phenotype and said coefficients>a threshold, the couple matchmade is invalid for breeding for said phenotyping traits.

7. The method of claim 1, wherein said first database comprises also neutral genotyping data used only for diversity determination in addition to said second portion of said markers, and/or wherein the method uses also neutral phenotyping data such as pedigrees for diversity determination.

8. The method of claim 1, wherein at least one genotyping data of the marker relating to a certain trait is defined as overruling all other genotyping data to be determined and thereby producing invalid breeding value for said two mammals to be matchmade, such as a carrier genotype for a lethal disease in both of the breeding partners, therefore, potentially producing unviable offsprings.

9. The method of claim 1, wherein the method comprises reporting said probability or severity of the traits of said mammal as well as DNA profile via a graphical interface and/or via simplified numerical data.

10. The method of claim 1, wherein the first portion of said markers comprises over 50 markers, more advantageously over 100 markers and most advantageously over about 150 markers, the majority of which are advantageously disease markers or markers associated with morphological, such as conformation, colour, fur type, hair length, or behavioural traits of the animal.

11. The method of claim 1, wherein the second portion of said markers comprises advantageously over 200 markers, more advantageously over about 500 markers and most advantageously over about 1000 markers, relating to microsatellite- and/or SNP-markers used for the measurement of genetic ancestry and diversity.

12. The method of claim 1, wherein genomic data for a gene test is achieved to the second database by a blood or cheek swab samples.

13. An arrangement for determining an advised breeding choice or a matchmaking quality for a first mammal in relation to a plurality of different second mammals by comparing genotypes thereof, wherein the arrangement comprises: an access to a first database comprising genotyping data of known traits and coefficients weighting severity of said traits, such as mutation, disease risk, lethality and/or affected breeds of mammal species of said mammals to be matchmade, an access to a second database comprising genotyping data for at least certain loci common to each of said mammals to be matchmade, an access to a group of markers for said loci to be determined for matchmaking, where i) at least first portion of the markers relates to loci to be compared in said second databases and having the coefficients in various known gene based traits in said first databases for possible breeding combinations derived in said second database, and ii) at least second portion of said markers used in determining differs from said first portion of said markers, wherein in determination of value of the match for said first mammal with said plurality of the different second mammals the arrangement is configured to: determine first results of said coefficients weighting the severities of the traits for each potential breeding pair of the first mammal with each of said plurality of the different second mammals by using said first portion of the markers, and determine second results relating to a diversity for each potential breeding pair of the first mammal with each of said plurality of the different second mammals by using said second portion of the markers, determine a total result determining the matchmaking quality for each potential breeding pair by combining said first and second results for each of said potential breeding pair, and manipulate said total results for each of said potential breeding pairs in order to determine values of matches for said first mammal.

14. The arrangement of claim 13 for determining said matchmaking quality, wherein the arrangement is configured to: determine first results of said coefficients weighting the severities of the traits for the potential breeding partners of the first mammal with each of said plurality of the different second mammals by using said first portion of the markers, where a sub-result of the first results relates to a certain genotype and has a certain sub-coefficient, whereupon the first results are determined by summing said sub-coefficients of said sub-results, and determine second results relating to the diversity by using said second portion of the markers so that if genotype of a certain locus is different for said first mammal than for the potential partner of said different second mammals in the second database, said sub-coefficient for said locus is rewarded and if genotype of said locus is same for both mammals, said sub-coefficient for said locus is not awarded or is penalized, whereupon the second results are determined by summing said sub-coefficients, and determine said total result by summing said first and second results.

15. The arrangement of claim 13 for determining said matchmaking quality, wherein the arrangement is configured to: provide a group of virtual descendants for different combinations of said first and at least one of said second different mammals to be matchmade, where the arrangement is further configured to: i) compare genotyping data of the first mammal's genome with corresponding genotyping data of second different mammal's genome in the second database, ii) determine possible combined genotypes based on said compared genotyping data for each of virtual descendants to be provided, iii) determine an individual index for health related traits and/or genetic diversity for each of said virtual descendants to determine the value of disease risks of said descendants and breeding value of said two mammals to be matchmade, comprising: a) comparing the genotyping data of each of said individual virtual descendants' genome corresponding to said first portion of said markers with corresponding genotyping data of said first database in order to determine coefficients of the first results between said determined regions and data of said first database and thereby determine said individual index for each of said individual virtual descendants of a probability or risk or severity of the traits, and b) combining said first results and second results, such as averages of said first results and second results to determine said individual index of said virtual descendants and breeding value of said two mammals to be matchmade as said total result.

16. A computer program product for determining an advised breeding choice or a matchmaking quality for a first mammal in relation to a plurality of different second mammals by comparing genotypes thereof, characterized in that it comprises program code means stored on a computer-readable medium, which code means are arranged to perform all the steps of the method of claim 1, when the program is run on a computer.

Description

BRIEF DESCRIPTION OF THE DRAWINGS

[0029] Next the invention will be described in greater detail with reference to exemplary embodiments in accordance with the accompanying drawings, in which:

[0030] FIG. 1 illustrates a principle of an exemplary method for determining an advised breeding choice or a matchmaking quality according to an advantageous embodiment of the invention, and

[0031] FIGS. 2A-2B illustrate principles of two exemplary methods for determining an advised breeding choice or a matchmaking quality according to an advantageous embodiment of the invention.

DETAILED DESCRIPTION

[0032] FIG. 1 illustrates a principle of an exemplary method 100 for determining an advised breeding choice or a matchmaking quality for a first mammal in relation to a plurality of different second mammals by comparing genotypes thereof according to an advantageous embodiment of the invention. In step 101 a first database is provided. The first database comprises genotyping data of known traits and coefficients weighting severity of said traits, such as mutation, disease risk, lethality and/or affected breeds of mammal species of said mammals to be matchmade. In second step 102 a second database is provided. The second database comprises genotyping data for at least certain loci common to each of said mammals to be matchmade, where said genotyping data is advantageously gathered via testing from the mammals to be matchmade.

[0033] In addition in step 103 a group of markers is provided for the loci to be determined for matchmaking. At least first portion used for determining health related traits of the markers relates to loci to be compared in the second databases and having the coefficients in various known gene based traits in said first databases for possible breeding combinations derived in said second database. At least second portion of said markers used in determining differs from said first portion of said markers.

[0034] Next value of the match for said first mammal with said plurality of the different second mammals is determined. In step 104 first results of said coefficients weighting the severities of the traits are determined for each potential breeding pair of the first mammal with each of said plurality of the different second mammals by using said first portion of the markers. In step 105 second results relating to a diversity are determined for each potential breeding pair of the first mammal with each of said plurality of the different second mammals by using said second portion of the markers.

[0035] Finally in step 106 a total result determining the matchmaking quality for each potential breeding pair is determined by combining said first and second results for each of said potential breeding pair. In addition in step 107 said total results for each of said potential breeding pairs are manipulated in order to determine values of matches for said first mammal. The manipulation may be for example sorting or ranking the total result into a certain order and thereby determining values of matches, such as the best match.

[0036] It is to be noted that the method 100 may comprise also additional step 108 for taking into account also phenotyping data. The step 108 comprises providing 108a a third database, where the third database comprises phenotyping data of known phenotyping traits and coefficients weighting severity of said phenotyping traits, such as morphology, behaviour, colour, temperament, hunting skills of mammal species of said mammals to be matchmade, for at least certain loci common to each of said mammals to be matchmade. The step 108 advantageously comprises selecting 108b at least one phenotype as a seed. The seed relates to at least one phenotype to be desired or avoided for the potential descendants. The seed may be one number, weighted by the desired severity, or averaged from the number of desired or undesired phenotyping traits, for example.

[0037] The step 108 additionally and advantageously comprises also analysing 108c the loci related to said phenotype for both first mammal and said at least one of the second mammal to be matchmade in said second database. In addition it comprises selecting 108d of the corresponding coefficients weighting severity of said phenotyping trait in said third database. Furthermore the step 108 comprises determination 108e of validity of the breeding pair. This may include e.g. following comparison: [0038] if the seed is the desired phenotype and said coefficients>a threshold, the breeding pair matchmade is valid for breeding for said phenotyping traits, and [0039] if said seed is the undesired phenotype and said coefficients>a threshold, the breeding pair matchmade is invalid for breeding for said phenotyping traits.

[0040] It is to be noted that step 108 is optional and can be performed in any step. Especially it is to be noted that it can be performed before, during or after the step 104-107.

[0041] FIGS. 2A-2B illustrate principles of two exemplary methods 200, 250 for determining an advised breeding choice or a matchmaking quality according to an advantageous embodiment of the invention, where both examples are based on 103 of providing first and second databases as well as group of markers are also comprised by the methods 200, 250. In addition also step 108 with its sub-steps 108a-108e can be included to the methods 200, 250.

[0042] In the first exemplary method 200 first results of said coefficients weighting the severities of the traits are determined in step 201 for the potential breeding partners of the first mammal with each of said plurality of the different second mammals by using said first portion of the markers. In the method a sub-result of the first results relates to a certain genotype, in particularly a genotype of a locus, pointed by one of the first marker and has a certain sub-coefficient, whereupon the first results are advantageously determined in step 201 by summing said sub-coefficients of said sub-results.

[0043] In addition second results relating to the diversity are determined in step 202 by using said second portion of the markers (e.g. similarly than in step 106 in FIG. 1). If genotype of a certain locus is different for said first mammal than for the potential partner of said different second mammals in the second database, said sub-coefficient for said locus is rewarded. Rewarding may be done e.g. by giving e.g. 1, as an example. If the genotype of said locus is same for both mammals, said sub-coefficient for said locus is not awarded or is penalized, for example by giving 0, for example. The second results are determined advantageously by summing said sub-coefficients.

[0044] The total result is determined in step 203 by summing said first and second results.

[0045] In the second exemplary method 250 a group of virtual descendants is provided, such as created, in step 251 for different combinations of said first and at least one of said second different mammals to be matchmade. According to an example e.g. 512 descendants is provided. In step 252 genotyping data relating advantageously to at least the first portion of the markers of the first mammal's genome is compared with corresponding genotyping data of second different mammal's genome in the second database.

[0046] Next possible combined genotypes are determined in step 253 based on said compared genotyping data for each of virtual descendants to be provided. In step 254 an individual index is determined for health related traits and/or genetic diversity for each of said virtual descendants to determine the value of disease risks of said descendants and breeding value of said two mammals to be matchmade. Determination includes comparing the genotyping data of each of said individual virtual descendants' genome corresponding to said first portion of said markers with corresponding genotyping data of said first database in order to determine coefficients of the first results between said determined regions and data of said first database and thereby determine said individual index for each of said individual virtual descendants of a probability or risk or severity of the traits. The first and second results are combined (as in step 106 in FIG. 1) to determine said individual index of said virtual descendants and breeding value of said two mammals to be matchmade as said total result (step 255). The combination of said first and second results may be e.g. combination of averages of said first results and second results, as an example.

[0047] The methods may also advantageously comprise additional step (not shown) for determining matchmaking quality and the breeding value. The step of determining matchmaking quality and the breeding value may comprise steps of comparison, where: [0048] if said individual index<a threshold, the partners matchmade is invalid for breeding, [0049] if said individual index=a threshold, the partners matchmade is invalid for breeding, and [0050] if said individual index>a threshold, the partners matchmade is valid for breeding.

[0051] The invention has been explained above with reference to the aforementioned embodiments, and several advantages of the invention have been demonstrated. It is clear that the invention is not only restricted to these embodiments, but comprises all possible embodiments within the spirit and scope of the inventive thought and the following patent claims. It is to be noticed that even though different databases are discussed above, they can also be implemented by a same physical database arrangement for example by allocating separated data structures for different types of data. In addition even if only few mammals are discussed as an example, the invention is not limited only to those but can be used in connection with different kinds of breeds and mammals.