Positional identification of a regulatory mutation in the

porcine IGF2 gene having a major QTL effect on muscle

mass.

M. Georges et al. ; IWMGQSG

Acknowledgments

ULg:ULg: Minh NguyenMinh Nguyen Carine NezerCarine Nezer Catherine ColletteCatherine Collette Laurence MoreauLaurence Moreau Michel GeorgesMichel Georges

Gentec:Gentec: Nadine BuysNadine Buys

Uppsala:Uppsala: Anne-Sophie Van LaereAnne-Sophie Van Laere Martin BraunschweigMartin Braunschweig Michael TallyMichael Tally Valérie AmargerValérie Amarger Goran AnderssonGoran Andersson Leif AnderssonLeif Andersson

Roslin:Roslin: Chris HaleyChris Haley Alan ArchibaldAlan Archibald

M. Georges et al. ; IWMGQSG

Molecular dissection of complex traits The majority of medically and agronomically The majority of medically and agronomically

important phenotypes are continuously distributed important phenotypes are continuously distributed multifactorial traits.multifactorial traits.

““The nature of quantitative-trait variation is one of The nature of quantitative-trait variation is one of the last unexplored frontiers in genetics, awaiting the last unexplored frontiers in genetics, awaiting the future cloning and definitive identification of the future cloning and definitive identification of quantitative-trait determinants, whether they be quantitative-trait determinants, whether they be genetic or epigenetic.”genetic or epigenetic.” Rutherford and Henikoff Rutherford and Henikoff (2003) (2003)

M. Georges et al. ; IWMGQSG

Livestock populations offer unique advantages for complex trait analysis A growing list of phenotypes is being A growing list of phenotypes is being

systematically recorded on a substantial systematically recorded on a substantial proportion of the breeding population.proportion of the breeding population.

Individual phenotypes are being processed to Individual phenotypes are being processed to compute environmental and genetic variance compute environmental and genetic variance components, from which estimates of heritability components, from which estimates of heritability can be derived.can be derived.

Extant pedigrees with a suitable structure for the Extant pedigrees with a suitable structure for the mapping of QTL underlying the mapping of QTL underlying the within-populationwithin-population genetic variance can often be readily collected. genetic variance can often be readily collected.

M. Georges et al. ; IWMGQSG

Livestock populations offer unique advantages for complex trait analysis The effective population size is typically The effective population size is typically

restricted:restricted: The genetic complexity of the trait in terms of allelic and locus The genetic complexity of the trait in terms of allelic and locus

heterogeneity is bound to be reduced.heterogeneity is bound to be reduced. Linkage disequilibrium (LD) in livestock extends over tens of Linkage disequilibrium (LD) in livestock extends over tens of

centimorgans.centimorgans. Livestock populations now resemble advanced Livestock populations now resemble advanced

inter-cross lines between highly divergent inter-cross lines between highly divergent genomes exhibiting nucleotide diversities as high genomes exhibiting nucleotide diversities as high as 1/200.as 1/200.

Experimental livestock inter- and back-cross Experimental livestock inter- and back-cross pedigrees can be generated at will to map QTL pedigrees can be generated at will to map QTL that underlie the that underlie the between populationbetween population genetic genetic variance.variance.

I. An imprinted QTL with major effect on muscle mass maps to

the porcine IGF2 locus.

M. Georges et al. ; IWMGQSG

A QTL with major effect on muscle mass and fat deposition maps to distal SSC2p

Piétrain x Large White F2

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SSC2p is orthologous to HSA11pter-q13

Igf2MyoD1

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The QTL co-localizes with IGF2

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IGF2 is imprinted in the pig

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The QTL is imprinted and expressed exclusively from the paternal allele

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The Piétrain & Large White IGF2 coding sequences are identical

Large White x Large White x PiétrainPiétrain F2 (Nezer et al., 1999) F2 (Nezer et al., 1999) Large WhiteLarge White x Wild Boar F2 (Jeon et al., 1999) x Wild Boar F2 (Jeon et al., 1999) Large WhiteLarge White x Meishan F2 (De Koning et al., x Meishan F2 (De Koning et al.,

2000)2000) Large WhiteLarge White x Berkshire F2 (Thomsen et al., x Berkshire F2 (Thomsen et al.,

2002)2002)

Similar results were obtained by others …

II. Haplotype sharing refines the QTL location to a 250 Kb

segment containing the IGF2 gene

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Principle underlying proposed approach

QQ

qq

M. Georges et al. ; IWMGQSG

QTL genotyping by « MASA »

Identify large paternal half-sib pedigrees Identify large paternal half-sib pedigrees (Piétrain x Large White cross-bred boars)(Piétrain x Large White cross-bred boars)

Genotype for distal SSC2p microsatellitesGenotype for distal SSC2p microsatellites Compute z = log(H1/H0) assuming a = 2%Compute z = log(H1/H0) assuming a = 2% « MASA »:« MASA »:

If z > 2, sire = « Qq »If z > 2, sire = « Qq » If z < 2, sire = « QQ » or « qq »If z < 2, sire = « QQ » or « qq »

M. Georges et al. ; IWMGQSG

M. Georges et al. ; IWMGQSG

Generate a denser map spanning the HSA 11p imprinted domain

Develop CATSDevelop CATS Identify SNPs Identify SNPs Screen BAC libraryScreen BAC library BAC-end sequencesBAC-end sequences

51 SNPs (9 multisite haplotypes)51 SNPs (9 multisite haplotypes)11 micro’s11 micro’s

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Assemble pools of « Q » and « q » chromosomes

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All "All "QQ" chromosomes share a " chromosomes share a 250 Kb 250 Kb common haplotype encompassing the common haplotype encompassing the INSINS and and IGF2IGF2 genes not present in the "q" chromosomes genes not present in the "q" chromosomes

M. Georges et al. ; IWMGQSG

All "All "QQ" chromosomes share a " chromosomes share a 250 Kb 250 Kb common haplotype encompassing the common haplotype encompassing the INSINS and and IGF2IGF2 genes not present in the "q" chromosomes genes not present in the "q" chromosomes

III. Positional identification of a regulatory mutation in IGF2

causing a major QTL effect on muscle development in the pig.

A. « Genetic » analysis

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Comparative sequence analysis of the INS-IGF2-H19 gene

cluster identifies 97 evolutionary footprints (Amarger et al., 2002)

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Resequencing 3 Q and 8 q chromosomes for 28.5 Kb spanning INS-IGF2 identifies 33 putative QTN

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Resequencing 3 Q and 8 q chromosomes for 28.5 Kb spanning INS-IGF2 identifies 33 putative QTN

« Q »: 1 clade, « q »: 2 « Q »: 1 clade, « q »: 2 cladesclades

253 SNPs !! (1/186)253 SNPs !! (1/186)

33 candidate QTN (2 in 33 candidate QTN (2 in evolutionary footprint)evolutionary footprint)

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Resequencing a heterozygous, non-segregating Hampshire sire identifies a recombination excluding TH-IGF2(I1) (- 9 candidate QTN)

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Resequencing a heterozygous, non-segregating Large White x Meishan sire identifies the QTN

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Resequencing a heterozygous, non-segregating Large White x Meishan sire identifies the QTN

Meishan chromosome belongs to « Meishan chromosome belongs to « QQ » clade, from  » clade, from which it differs at one of the two candidate QTN in which it differs at one of the two candidate QTN in an evolutionary conserved footprint.an evolutionary conserved footprint.

Large White chromosome belongs to « Large White chromosome belongs to « qq » clade,  » clade, and is identical to all « and is identical to all « qq »’s at all 33 candidate  »’s at all 33 candidate QTN.QTN.

« MASA » in Edinburgh, confirms « « MASA » in Edinburgh, confirms « qq » status of  » status of Meishan chromosome.Meishan chromosome.

« Identifies the QTN !! »« Identifies the QTN !! »

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III. Positional identification of a regulatory mutation in IGF2

causing a major QTL effect on muscle development in the pig.

B. « Functional » analysis

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Background information

Expected effect of the QTN:Expected effect of the QTN:« « Increase IGF2 expression levels without altering the Increase IGF2 expression levels without altering the

imprinting status. »imprinting status. »

Information from the mouse:Information from the mouse: « QTN is part of a region that contains a mesodermal « QTN is part of a region that contains a mesodermal

silencer binding GCF2 when unmethylated (maternal silencer binding GCF2 when unmethylated (maternal allele) »allele) »

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In vivo analysis of the QTN effect

The QTN does not The QTN does not affect imprintingaffect imprinting

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In vivo analysis of the QTN effect

A 3-fold increase of postnatal A 3-fold increase of postnatal IGF2IGF2 mRNA mRNA expression is observed in skeletal muscle in (expression is observed in skeletal muscle in (Q/QQ/Q or or QQpatpat/q/qmatmat) versus () versus (qqpatpat/Q/Qmatmat or or q/qq/q).).

Northern blotNorthern blot RT-PCR RT-PCR

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In vivo analysis of the QTN effect

The QTN is located in a novel DMR.The QTN is located in a novel DMR.

Methytlation Methytlation is not is not affected by affected by genotypegenotype

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In vitro analysis of the QTN effect

« EMSA »:« EMSA »:

The QTN abrogates binding The QTN abrogates binding of a nuclear factor present of a nuclear factor present in C2C12 myoblasts.in C2C12 myoblasts.

M. Georges et al. ; IWMGQSG

In vitro analysis of the QTN effect

« Reporter assay »:« Reporter assay »:

In C2C12 cells,In C2C12 cells, the « Q » allele the « Q » allele increases P3-driven luciferase increases P3-driven luciferase expression by 3.5 when expression by 3.5 when compared to « q »compared to « q »

IV. Conclusions

M. Georges et al. ; IWMGQSG

Conclusions

We herein report the first identification of a We herein report the first identification of a regulatory point mutation underlying a regulatory point mutation underlying a QTL.QTL.

This work illustrates the extraordinary This work illustrates the extraordinary resolution that is achievable in the resolution that is achievable in the molecular dissection of complex traits when molecular dissection of complex traits when using domestic animal resources.using domestic animal resources.

M. Georges et al. ; IWMGQSG

Conclusions

This work demonstrates that This work demonstrates that IGF2IGF2 has an has an important role in regulating mostnatal important role in regulating mostnatal myogenesis,myogenesis,

… … and opens new avenues for modulating and opens new avenues for modulating muscle development by targetting the muscle development by targetting the identified sequence and the binding trans-identified sequence and the binding trans-acting factor.acting factor.

M. Georges et al. ; IWMGQSG Thank you for your attention