APPROACHES AND CHALLENGES IN MEASURING GENETIC DIVERSITY IN PIGS (AVANCES Y RETOS EN LA MEDICIÓN DE LA DIVERSIDAD GENÉTICA EN LOS CERDOS)
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APPROACHES AND CHALLENGES IN MEASURING GENETIC DIVERSITY IN PIGS (AVANCES Y RETOS EN LA MEDICIÓN DE LA DIVERSIDAD GENÉTICA EN LOS CERDOS)

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Abstract
While the number of diverse genetic breeds of pigs may exceed 600 worldwide, there is a limited amount of information to assess their genetic and functional diversity. Efforts have primarily been conducted to examine genetic diversity using anonymous markers and to a more limited extent individual gene markers and mtDNA. This paper discusses the methods used to date and the need to examine other methods to more fully understand not only the genetic diversity but the functional diversity of different pig breeds.
Resumen
Aunque el número de razas genéticas de cerdos distintas excede de las 600 en todo el mundo, hay una disposición limitada de información para acceder al conocimiento de su diversidad genética y funcional. Los esfuerzos deben ir preliminarmente conducidos a examinar la diversidad genética utilizando marcadores anónimos y con una extensión más limitada a marcadores génicos individuales y ADNmt. Este trabajo discute los métodos utilizados hasta la fecha y la necesidad de examinar otros métodos para un conocimiento más profundo no sólo la de la diversidad genética, sino la diversidad funcional de las distintas razas porcinas.

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Publié le 01 janvier 2003
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APPROACHES AND CHALLENGES IN MEASURING GENETIC
1DIVERSITY IN PIGS
AVANCES Y RETOS EN LA MEDICIÓN DE LA DIVERSIDAD GENÉTICA EN LOS CERDOS
Rothschild, M.F.
Department of Animal Science. 2255 Kildee Hall. Iowa State University. Ames, Iowa 50011. USA.
ADDITIONAL KEYWORDS PALABRAS CLAVE ADICIONALES
Pig. Breeds. Genetic diversity. Functional diver Cerdo. Razas. Diversidad genética. Diversidad
sity. Genes. funcional. Genes.
SUMMARY RESUMEN
While the number of diverse genetic breeds Aunque el número de razas genéticas de
of pigs may exceed 600 worldwide, there is a cerdos distintas excede de las 600 en todo el
limited amount of information to assess their mundo, hay una disposición limitada de informa
genetic and functional diversity. Efforts have ción para acceder al conocimiento de su diver
primarily been conducted to examine genetic sidad genética y funcional. Los esfuerzos deben
diversity using anonymous markers and to a ir preliminarmente conducidos a examinar la di
more limited extent individual gene markers and versidad genética utilizando marcadores anóni
mtDNA. This paper discusses the methods used mos y con una extensión más limitada a marca
to date and the need to examine other methods dores génicos individuales y ADNmt. Este trabajo
to more fully understand not only the genetic discute los métodos utilizados hasta la fecha y la
diversity but the functional diversity of different necesidad de examinar otros métodos para un
pig breeds. conocimiento más profundo no sólo la de la
diversidad genética, sino la diversidad funcional
de las distintas razas porcinas.
1Presented at Symposium on Pig Biodiversity,
Córdoba, Spain November 7 10, 2002. This is a
INTRODUCTIONjournal paper of the Iowa Agriculture and Home
Economics Experiment Station, Ames, Iowa,
Project No. 3609, and was supported in part by The pig was one of the first animals
Hatch Act and State of Iowa funds and funding
likely to have been domesticated over
from NRSP 8 and the USDA/CSREES Pig Genome
5,000 years ago (Rothschild andCoordination program. The author gratefully
acknowledges input received from Graham Ruvinsky, 1998). To date there are
Plastow, Louis Ollivier and Juan Vicente Delga likely over 600 breeds or lines
do. By no means will this be an exhaustive review
worldwide of which the most reside in
of the literature but it will touch on issues central
China and Europe and over 200 areto livestock. The author apologizes for references
of work that he has failed to cite. considered endangered (Ollivier et al .,
Arch. Zootec. 52: 129 135. 2003.ROTHSCHILD
2001). Considerable differences appear diversity should be used to help in the
to exist both morphologically and determination of breed differences and
physiologically between the various in determining those which must be
domestic breeds and their wild boar preserved.
ancestors from Europe and Asia The objectives of this paper are to
(Giuffra et al., 2000). These changes review in general terms ways to
in the domestic pig have reflected the measure genetic diversity among and
rather plastic nature of the pig and within pig breeds and to discuss
humankind's ability to genetically methods to quantify diversity and rela
manipulate it to fit certain needs and te it to functional importance.
markets.
A large percentage of pig breeds
METHODS TO DETERMINE GENETICare now in danger of extinction and
DIVERSITYothers are threatened by inefficient
use and loss due to crossbreeding.
Over the past ten years considera Efforts to determine the level of such
ble improvements in molecular geneticsrisk are underway, especially in Europe
have led to the development of geneticbut also in other parts of the world. In
maps of many organisms. TheseEurope, at the European Association
advances in molecular biology havefor Animal Production, an Animal
made it possible to develop compre Genetic Data Bank has been establis
hensive genetic linkage maps in the pighed as a repository to record such
(e.g. Archibald et al., 1995; Rohrer etbreeds and to assess risk (see Simianer
al., 1994; 1996). To date, over 6,000and Meyer, 2003, in this Proceedings).
genes and anonymous markers haveAlong with assessment of risk is the
been added to the gene map of the pigconsideration of which breeds should
(see www.thearkdb.org or http://be preserved. Certainly there is the
iowa.thearkdb.org)increased interest in this approach and
In addition to identifying andthere is some support by private
mapping genes and markers, animalorganizations and governmental
geneticists have begun to search forprograms. Ruane (1999) has provided
the individual genes that affect traits ofa set of criteria to be considered when
interest in the pig. Since the earliestchoosing a specific breed for a con
quantitative trait loci (QTL) scan inservation program. The degree of
pigs by Andersson et al. (1994) manyendangerment and genetic uniqueness
others have followed and a number ofof the breed are two of seven essential
criteria discussed. However, while regions are now identified (see review
breeds have cultural and historical by Bidanel and Rothschild, 2002). In
value, from an economic point of view,addition, the candidate gene approach
the functional diversity for a set of (Rothschild and Soller, 1997) has been
important economic traits should be employed and many candidate genes
considered the most important criterion. have been shown to be associated with
Efforts therefore to determine both traits of interest (Rothschild and
genetic diversity and functional Plastow, 1999). These QTL and
Archivos de zootecnia vol. 52, núm. 198, p. 130.MEASURING PIG GENETIC DIVERSITY
candidate genes form the basis of A number of genetic methods exist
comparison of genetics related to to measure genetic diversity. These
functional differences. include comparison of anonymous
Key issues to discuss include but markers such as microsatellites,
are not limited to 1) What is genetic minisatellites, and amplified fragment
homology/diversity? 2) How is it best length polymorphisms (AFLPs), gene
measured? 3) What is functional markers/SNPs (single nucleotide
diversity and how is it best assessed? polymorphisms), large scale or directed
Some examination of what has occurred sequencing, mitochondrial genotyping,
in other fields may be useful for and Y chromosome genotyping. Mini
discussion purposes. Evolutionists are satellites are the preferred method in
interested in knowing if two species human studies and allow for seeing
are related. Therefore, interest is in expansion and hence direction of
evolutionary changes and knowing that evolution. Mitochondrial (mtDNA)
the genes are the same is not enough. genotyping has also been used to look
Given two DNA sequences, a resear for different female lineages and Y
cher can ask the question: How much chromosome genotyping has also been
evolutionary change has occurred used for measuring ethnic differences.
between these two sequences? Dealing with only 2 narrow genomic
Seemingly this appears to be a simple regions, Y and mtDNA, give some
question but the answer may prove insight into possible phylogenetic
elusive. Researchers can use observed origins, among the many others that
differences and the simplest measure SNPs in autosomal regions might
of distance is to count the number of indicate.
nucleotides that differ between the In livestock early measures of
two sequences. This approach has been diversity were associated with protein
used in livestock (Giuffra et al ., 2000; polymorphisms measured on 2D gels.
Kijas and Andersson, 2001) to exami More recently, several recommen
ne evolutionary changes in the pig. dations have been made for genetic
However, there are potential problems diversity studies (Barker et al ., 1998).
with such an approach because if These recommendations include use
change has been common then the of 2 5 microsatellites per chromosome
same site may have undergone repeated and genotyping of 50 animals (25 of
substitution. So as more time passes, each sex) that are unrelated. Breeds
the number of differences between that differ in the frequency of alleles at
two sequences becomes a less accuratethese loci are declared different or
estimate of the actual number of diverse after determination of genetic
substitutions that truly occurred. As a relationships or genetic distances
general rule animal geneticists and between breeds (Barker et al., 1998).
breeders have a different problem in Examples of these approaches include
that they are not only interested in an European Community project that
homology but also genetic and functio was recently completed to evaluate
nal diversity, even so the same types of the genetic diversity of European pig
concern exist relative to comparisons. resources (considering more than 50
Archivos de zootecnia vol. 52, núm. 198, p. 131.ROTHSCHILD
breeds) using primarily microsatellites considered were disease resistance,
and AFLP markers (Laval et al ., 2000; growth, coat color, meat quality and
San Cristobal et al ., 2002). For details prolificacy. Ciobanu et al . (2001) found
see http://databases.roslin.ac.uk/ significant differences in five of the
pigbiodiv. However, just as with ten characterized polymorphisms and
evolutionary comparisons of gene they concluded the observed allele
sequence differences, the number of frequency differences were related to
differences between two microsatellite gene function and the phenotype of the
sequences, as time passes, becomes a breed. A limitation in such studies is
less accurate estimate of the actual that the number of animals in such
number of substitutions that truly populations is usually small
occurred. Certainly, given the accepted Candidate gene approaches can be
4rate of mutation in microsatellites (10 ) combined with QTL scans for traits
it is possible that mutations may changethat are economically important and
in one direction and then back again, could be a better approach to measure
confounding such comparisons further. of functional diversity [e.g. new
Another important question to ask mutations with PRKAG3 affecting
is do microsatellites measure functional meat quality (Ciobanu et al., 2001)].
diversity? For major genes like The use of exotic or local or country
Halothane (HAL), RN (PRKAG3) and breeds in scans is less likely due to cost
E.coli K88 resistance we have of the QTL scan and such scans
examples of genetic and functional represent more limited sampling of the
diversity. For other traits in which major breeds. When more is known about the
genes do not appear to exist would genes of interest then anonymous
sequence differences or polymorphisms markers will be irrelevant. The
within proteins or SNPs within genes challenge is to pick the right genes and
(introns or exons) be a better measurecompare breeds. The European
of genetic and functional diversity than Community Pig Biodiversity II project
microsatellites? Today use of SNPs PigBioDiv 2 (QLRT 2001 01059) has
within genes, especially those shown accepted the idea that real gene
to be associated with traits of interest,differences are important and has
may be a better measure of functional expanded to include SNPs (see Blott
differences. This approach has been et al., 2003, in the present procee
recommended and employed but on a ding).
limited basis for both genes and
mtDNA.
Ciobanu et al. (2001) examined NEW DIRECTIONS AND NEEDS FOR
animals from two local Romanian pig FUTURE STUDY
breeds, Mangalitsa and Bazna.
Polymorphism was assessed at nine Technical problems with use of
genes known to cause phenotypic many of these types of markers do
variation, were potentially involved in exist. These methods (PCR RFLP,
trait differences or were putative microsatellites, and AFLPs) are
candidate genes. The traits they constrained generally by gel electro
Archivos de zootecnia vol. 52, núm. 198, p. 132.MEASURING PIG GENETIC DIVERSITY
phoresis resulting in low throughput. lowering of genotyping costs a new
Use of microsatellites or SNPs requiresDNA genotyping chip may have
previous identification of a polymor possibilities for diversity studies. It is
phism. Recognition of the polymor likely that technology may advance
phisms is based on size separation andrapidly once sequencing is underway.
correlating bands among labs can be Some examination of the larger
difficult and differences could be picture is also required. First if breeds
misleading. This has certainly been the are found to be different which methods
situation for pig microsatellite genoty should be used to choose animals that
ping between labs where using control represent unrelated samples of a par
DNAs showed that the range of allele ticular breed. Clearly, selection of
size usually differed by less than one representative animals from a breed
bp between PigMaP and PigBioDiv depends on availability of animals both
labs, though for 2 microsatellites out ofwithin and across families. The use of
26 differences exceeded 2 bp (Ollivier,microsatellites to determine more
personal communication). accurately the relatedness with family
One approach designed to overcome and to make decisions on mating pairs
many of these limitations is the use offor breed preservation is quite
hybridization based methods using appropriate. Additionally, the use of
nucleic acids fixed to solid state specific SNPs to represent trait
surfaces. An example of such an diversity could be included as ways to
approach is the use of DNA chips for select diverse animals.
genotyping for SNPs. This technique Researchers should consider the
is again limited by first knowing the needs and solutions required for future
genes and SNPs and then also by cost.trait gene mapping and diversity
An alternative approach that uses partsstudies. These include, but are not
of genes but also the random nature of limited to:
variation is the use of so called Diversity 1) Available gene (allele) frequency
TMArray Technology (DArT ). This screens will tests work in all
approach uses methods similar to a populations?.
combination of RFLP analysis and 2) DNA from large phenotyped
array technology to measure gene populations of diverse breeds.
expression and has been used in 3) Ability to accomplish high density
examining differences in rice (Jaccoud (throughput) genotyping HDG.
et al ., 2001). This technology certainly 4) Inexpensive, high throughput
has promise because genes can later phenotyping.
be identified that are associated with 5) Development of advanced statis
differences and function inferred or tical analysis tools (bioinformatics).
later studied. 6) Large scale gene expression
Whole genome sequencing has yet screens chips and arrays.
to be undertaken for the pig but efforts 7) Real financial investment in
are underway to begin in the near diversity data.
future. Such results could lead to whole Point 4 requires more discussion.
genome SNP discovery and with The ability to measure functional
Archivos de zootecnia vol. 52, núm. 198, p. 133.ROTHSCHILD
diversity relies on phenotypic traits that CONCLUSIONS
are accurate and easily collected. Ani
mal scientists will need to assist in this Diversity studies have come along
process so that data are reliable and way in attempting to measure genetic
phenotyping costs can be reduced. differences in pigs from a variety of
Other issues also cloud the picture breeds and countries. The use of anony
of future research and the results that mous markers has limitations but has
are likely to come from it. Backgroundbeen useful to date and has value in
genetics (epistasis) makes single gene measuring relatedness within breeds.
comparison's difficult and limited on a Gene differences will be better than
per gene/breed basis. In the future, anonymous markers for determining
large scale studies involving hundreds both genetic and functional diversity.
or thousands of genes would provide Their use will require considerable new
the ability to look for functional diversityinformation about many more genes
among interacting genes and gene than those presently know to be
pathways. Since discovery of functional associated with traits of interest. New
gene differences are the preferred end technologies such as array methods or
point of diversity studies then protection those resulting from large scale
of intellectual property (IP) and exclusive sequencing may revolutionize approa
vs non exclusive use of IP from diversity ches for determining genetic and functi
studies may be an issue. Certainly main onal diversity. Researchers should
taining a real public and scientific interestconsider new technologies as they
in diversity issues will be challenging. approach the challenges ahead.
REFERENCES
Andersson, L., C.S. Haley, H. Ellegren, S.A. Andersson, H. Ellegren, M. Johansson, L.
Knott, M. Johansson, K. Andersson, L. Marklund, J.R. Miller, D.V. Anderson, Dear, E.
Andersson Eklund, I. Edfors Lilja, M. Signer, A.J. Jeffreys, C. Moran, P. Le Tissier,
Fredholm, I. Hansson, J. Hakansson and K. M.F. Rothschild, C.K. Tuggle, D. Vaske, J.
Lundström. 1994. Genetic mapping of Helm, H.C. Liu, A. Rahman, T.P. Yu, R.G.
quantitative trait loci for growth and fatness Larson and C.B. Schmitz. 1995. The PiGMaP
in pigs. Science, 263: 1771 1774. consortium linkage map of the pig ( Sus
Archibald, A.L., J.F. Brown, S. Couperwhite, scrofa). Mammalian Genome, 6: 157 175.
H.A. Mc Queen, D. Nicholson, C.S. Haley, W. Barker, J.S.F. 1999. Conservation of livestock
Coppieters, A. Van de Weghe, A. Stratil, A.K. breed diversity. Anim. Genet. Resource
Winterø, M. Fredholm, N.J. Larsen, V.H. Inform., 25: 33 43.
Nielsen, D. Milan, N. Woloszyn, A. Robic, M. Barker, J.S.F., W.G. Hill, D. Bradley, M. Nei, R.
Dalens, J. Riquet, J. Gellin, J.C. Caritez, D. Fries and R.K. Wayne. 1998. Measurement
Hue, G. Burgaud, L. Ollivier, J.P. Bidanel, M. of domestic animal diversity (MoDAD): Origi
Vaiman, C. Renard, H. Geldermann, R. Davoli, nal Working Group Report, FAO, Rome.
D. Ruyter, E.J.M. Versteger, M.A.M. Groenen, Bidanel, J.P. and M.F. Rothschild. 2002. Current
W. Davies, B. Høyheim, A. Keiserud, L. status of quantitative trait locus mapping in
Archivos de zootecnia vol. 52, núm. 198, p. 134.MEASURING PIG GENETIC DIVERSITY
pigs. Pig News and Inform., 23: 39N 53N. Genetic Resources in Europe ( Eds) Ollivier L.
Blott, S., L. Andersson, M. Groenen, M. F. Labroue, P. Glodek, G. Gandini and J.V.
Sancristobal, C. Chevalet, R. Cardellino, N. Li, Delgado Wageningen Pers.
L. Huang, K. Li, G. Plastow and C. Haley . Rohrer, G.A., L.J. Alexander, J.W. Keele, T.P.L.
2003. Characterisation of genetic variation in Smith and C.W. Beattie. 1994. A microsatellite
the pig breeds of China and Europe. The Pig linkage map of the porcine genome. Genetics,
BioDiv2 project. Arch. Zootec., 52: 207 217. 136: 231 245.
Ciobanu, D.C., J. Bastiaansen, M. Malek, J. Helm, Rohrer, G.A., L.J. Alexander, Z. Hu, T.P.L. Smith,
J. Woollard, G.S. Plastow and M.F. Rothschild. J.W. Keele and C.W. Beattie. 1996. A
2001. Evidence for new alleles in the protein comprehensive map of the porcine genome.
kinase AMP activated, subunit gene Genome Research, 6: 371 391.
associated with low glycogen content in pig Rothschild, M.F. and G.S. Plastow. 1999.
skeletal muscle and improved meat quality. Advances in pig genomics and industry
Genetics, 159: 1151 1162. applications. Ag. Biotech. Net 1: February,
Ciobanu, D.C., A. Nagy, R. Wales, A.E. Day, M.F. ABN 007.
Rothschild and G.S. Plastow. 2001. Genetic Rothschild, M.F. and A. Ruvinsky. 1998. The
variation in two conserved local Romanian Genetics of the Pig. CABI Press. Pgs. 622.
pig breeds using type 1 DNA markers. Genet. Rothschild, M.F. and M. Soller.1997. Candidate
Sel. Evol., 33: 417 432. gene analysis to detect traits of economic
Giuffra, E., J.M.H. Kijas, V. Amarger, O. Carlborg, importance in domestic livestock. Probe, 8:
J. T. Jeon and L. Andersson. 2000. The origin 13 18.
of the domestic pig: independent domestica Ruane, J. 1999. A critical review of the value of
tion and subsequent introgression, Genetics, genetic distance studies in conservation of
154: 1785 1791. animal genetics resources. J. Anim. Breed.
Jaccoud, D., K. Peng, D. Feinstein and A. Kilian. Genet., 116: 317 323.
2001. Diversity arrays: a solid state techno San Cristobal, M., C. Chevalet, C.S. Haley, G.
logy for sequence information independent Russell, G. Plastow, K. Siggens, M. Bagga,
genotyping. Nucleic Acids Res., 29, e 25. M.A.M. Groenen, Y. Amigues, K. Hammond,
Kijas, J.M.H. and L. Andersson. 2001. A G. Laval, M Y. Boscher, D. Milan, A. Law, E.
phylogenetic study of the origin of the Fimland, R. Davoli, V. Russo, G. Gandini, A.
domestic pig estimated from near complete Archibald, J.V. Delgado, M. Ramos, C.
mtDNA genome. J. Mol. Evol., 52: 302 308. Désautés, L. Alderson, P. Glodek, J. N. Meyer,
Laval, G., N. Iannuccelli, C. Legault, D. Milan, M. J.L. Foulley and L. Ollivier. 2002. Genetic
Groenen, E. Giuffra, L. Andersson, P. Nissen, diversity in pigs. Preliminary results on 58
thC. Jorgensen, P. Beeckmann, H. Geldermann, European breeds and lines. Proceedings 7
J.L. Foulley, C. Chevalet and L. Ollivier. 2000. World Congress on Genetics Applied to
Genetic diversity of eleven European pig Livestock Production, August 19 23, 2002,
breeds. Genet. Sel. Evol., 32: 187 203. Montpellier, France. Prod., 33: 523 528.
Ollivier, L., J. Wrede and O. Distl. 2001. An Simianer, H. and J. N. Meyer. 2003. Past and
overview of the genetic resources of pigs future activities to harmonize farm animal
and their management and conservation. In: biodiversity studies on a global scale. Arch.
Characterisation and Conservation of Pig Zootec., 52: 193 199.
Archivos de zootecnia vol. 52, núm. 198, p. 135.

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