# Epigenetics and phenotypic variability: some interesting insights from birds

Laure Frésard, Mireille Morisson, Jean-Michel Brun, Anne Collin, Bertrand

Pain, Francis Minvielle, Frederique Pitel

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Laure Frésard, Mireille Morisson, Jean-Michel Brun, Anne Collin, Bertrand Pain, et al.. Epigenetics and phenotypic variability: some interesting insights from birds. Genetics Selection Evolution, 2013, 45 (1), pp.16. 10.1186/1297-9686-45-16. inserm-00838907

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# Epigenetics and phenotypic variability: some interesting insights from birds

Laure Frésard<sup>1,2†</sup>, Mireille Morisson<sup>1,2†</sup>, Jean-Michel Brun<sup>3</sup>, Anne Collin<sup>4</sup>, Bertrand Pain<sup>5</sup>, Francis Minvielle<sup>6,7</sup>
and Frédérique Pitel<sup>1,2*</sup>

**Abstract**

Little is known about epigenetic mechanisms in birds with the exception of the phenomenon of dosage compensation of sex chromosomes, although such mechanisms could be involved in the phenotypic variability of birds, as in several livestock species. This paper reviews the literature on epigenetic mechanisms that could contribute significantly to trait variability in birds, and compares the results to the existing knowledge of epigenetic mechanisms in mammals. The main issues addressed in this paper are: (1) Does genomic imprinting exist in birds? (2) How does the embryonic environment influence the adult phenotype in avian species? (3) Does the embryonic environment have an impact on phenotypic variability across several successive generations? The potential for epigenetic studies to improve the performance of individual animals through the implementation of limited changes in breeding conditions or the addition of new parameters in selection models is still an open question.

**Review**

Most economically relevant traits in animal production exhibit continuous phenotypic variations due to polygenic and environmental factors. Whereas many quantitative trait loci (QTL) have been identified for agronomic traits, in most cases, the underlying genes remain largely unknown. Genome-wide association studies have shown that, except for rare monogenic traits, the variability of complex traits is only partially explained by genetic variation [1]. Possible explanations include epistatic effects, structural variations, and insufficient detection power due to lack of individuals or markers [1,2]. Both epidemiological studies in humans and genetic studies in animals have revealed that, in addition to the DNA sequence, epigenetic marks may be transmitted across generations and influence the phenotype of offspring [3]. There are many discussions in the literature on what the term “epigenetics” refers to and this leads to numerous definitions [3-11]. While some definitions restrict epigenetics to modifications of the phenotype

without changes of the DNA sequence that are transmitted to the next generations [4], other broader definitions include any form of information storage that maintains the DNA sequence intact, as described by Bird: "the structural adaptation of chromosomal regions so as to register, signal or perpetuate altered activity states" [7]. The former definitions link the term "epigenetic" to inheritance and the latter also refer to any phenomenon that leads to phenotypic plasticity. These two visions share a common feature i.e. the molecular mechanisms involved. The epigenetic machinery encompasses chromatin folding and its attachment to the nuclear matrix, packaging of DNA around nucleosomes, covalent modifications of histone tails, DNA methylation, and regulatory non coding RNA (such as miRNA, snoRNA, lncRNA). Epigenetic marks have been shown to actively contribute to the determination of patterns of gene silencing or active transcription, and to participate in the lineage and tissue-specific expression of genes [12-14]. Epigenetic marks are heritable from cell to cell through lineage development, and when acquired in early life, they can have an impact on the adult phenotype. They can also have an impact on the phenotypes of subsequent generations through multigenerational effects that occur either via epigenetic changes acquired during embryonic development, or through the inheritance of

<footnote>* Correspondence: frederique.pitel@toulouse.inra.fr</footnote>

<footnote>†Equal contributors</footnote>

<footnote n="1">¹INRA, UMR444, Laboratoire de Génétique Cellulaire, Castanet-Tolosan F-31326, France</footnote>

<footnote n="2">²ENVT, UMR444, Laboratoire de Génétique Cellulaire, Toulouse, F-31076, France</footnote>

<footnote>Full list of author information is available at the end of the article</footnote>
epigenetic marks via the gametes [3,15]. In this review, we retain the definition given by Feil and Fraga [14]: "Epigenetics is the study of mitotically and/or meiotically heritable changes in gene function that cannot be explained by changes in DNA sequence".

Understanding the epigenetic regulation of gene ex-
pression due to environmental factors should provide
important new insights into animal breeding, since the
same genetic information may be used differently by
individuals grown in different environments. However,
epigenetic regulation of gene expression is not always
environment-dependent as for parental imprinting in
which parent-of-origin-specific expression of a subset of
genes is regulated by epigenetic mechanisms. Examples
of such loci have been documented in livestock species
i.e. the locus responsible for the callipyge phenotype in
sheep [16] and the locus that controls IGF2 expression
in pigs [17].

The first agricultural species to be fully sequenced was
the chicken, however, to date, there are few studies on
the relation between epigenetic processes and economic-
ally important phenotypes in birds. This review focuses
on how epigenetic phenomena can have an impact on
the adult phenotype of farmed birds.

The importance of sex-linked genes that account for
some of the phenotypic variability has been shown in the
chicken [18] and X inactivation that involves epigenetic
mechanisms is well known in mammals [19,20]. In birds,
only partial dosage compensation between the hetero-
(ZW, female) and homogametic (ZZ, male) sexes has been
described [21,22] and this was previously known as "lack
of global dosage compensation" [23]. A region of hy-
permethylation (MHM for Male Hypermethylated Region,
[24]) is associated with dosage-compensation of several
genes in the male chicken [25-27], but not in zebra finch
[21]. Many questions about the mechanisms of regional
dosage-compensation still remain [26,28]. Since this topic
has already been extensively reviewed, we refer the reader
to the literature, including the references given above. By
contrast, little is known about the mechanisms of genomic
imprinting, if present, or developmental programming in
birds although they may play a role in phenotypic variabil-
ity as shown in mammalian farm animals. Similarly, epi-
genetic information that can be transmitted through
several generations could have a significant impact on ani-
mal selection.

This review addresses the following questions: (1) Are
there molecular mechanisms leading to genomic im-
printing in birds? (2) While the influence of fetal envir-
onment on adult phenotypes is largely documented in
mammals, what are the developmental and metabolic
phenotypes due to specific environmental cues in birds?
(3) Are there examples indicating that embryonic envir-
onment has multigenerational effects in birds?

Genomic imprinting

To discuss the state of knowledge regarding genomic im-
printing in birds, the mechanisms known in mammals will
be compared to the information available in avian species.
To date, among vertebrates, genomic imprinting has been
described only in eutherian mammals and marsupials.
Parental imprinting (Figure 1), a process that leads to the
differential expression of alleles depending on their pa-
rental origin (see [29] for a review), is stage- and tissue-
specific [30,31]. The major theory explaining genomic
imprinting is the parental conflict hypothesis [32,33],
which states that the genes responsible for controlling the
supply of maternal resources have a parentally biased ex-
pression, with the maternal genome tending to restrain re-
source allocations to preserve the mother and future
progeny, while the paternal genome tends to facilitate this
allocation to produce stronger offspring. Based on this
theory, it can be assumed that genomic imprinting is re-
stricted to organisms in which the maternal resources
affect directly the embryonic genes, and thus its existence
would be unlikely in oviparous animals [34].

In avian species, important reciprocal effects involving asymmetry in the contributions of the sire and dam to the offspring phenotype have been described for some traits. They explain 15 to 20% of the phenotypic variability in broiler body weight and egg viability in layers, and up to 47% in turkey egg production, and they have been extensively used to improve production in layers by

<figure><img src="image_2.png" /><figcaption>**Figure 1 Principles of genomic imprinting.** Each chromosome pair of an offspring consists of a maternal chromosome (in red) and a paternal chromosome (in blue). In this example, the offspring resulting from the cross expresses only its maternal allele (red), since the paternally inherited allele is inactive.</figcaption></figure>
designing optimized mating schemes [35]. These effects
are mainly due to sex-linked genes, underlying the im-
portance of chromosome Z in epigenetic effects, direct
maternal effects ("larger females produce larger eggs")
or mitochondrial DNA transmission [18]. However, this
does not exclude the hypothesis that some of these ef-
fects may originate from parent-of-origin preferential al-
lelic expression [36,37], and efforts to identify the genes
involved in quantitative traits are increasingly taking epi-
static and epigenetic effects into account. In the chicken
and quail, many parent-of-origin QTL have been
detected for traits linked with production [37-41], im-
mune responses [42] and behavior [43]. However, such
studies can detect spurious QTL due to linkage disequi-
librium or bias generated by the experimental design
[44,45]. A study reported by Rowe et al. [37] was specif-
ically designed to avoid these biases i.e. it included a suf-
ficient number of sires and dams to ensure segregation
and a sufficient number of offspring to detect QTL with
roughly equal allele frequencies in sires and dams for both
QTL and molecular markers, and it fitted the common
maternal environment in the linear model. Interestingly,
this work confirmed the presence of a parent-of-origin
QTL on chicken chromosome 1, in a region correspond-
ing to orthologous imprinted regions in the human and
mouse genomes. These results confirm the importance of
studying genomic imprinting in birds.

Several studies have clearly demonstrated that some
genes are paternally or maternally expressed during em-
bryonic development in mammals [46-48]. Until recently,
less than 200 imprinted genes were described (http://igc.
otago.ac.nz/home.html) but a transcriptome sequencing
approach reported in 2010 [49] uncovered parent-of-ori-
gin allelic effects for more than 1300 loci in the mouse.
However, this large number is the subject of much debate
[50,51], and to date, no consensus on the number of
imprinted genes in mammals has been reached.

Some genes, known to be imprinted in mammals, have
been examined in non eutherian vertebrates, in particular
oviparous species [52], including birds, viviparous marsu-
pials [53], and monotremes [54,55]. The *IGF2* gene, which
has long been known to be paternally expressed in the
mouse and man [56], has also been analyzed in the
chicken. A preliminary report suggested that its expres-
sion is probably monoallelic [57], but later studies agreed
that it is in fact biallelic [52,58-61]. In this case, analyses of
different chicken tissues and at different growth stages led
to divergent conclusions, emphasizing the importance of
tissue sampling and time scaling in imprinting studies.
The orthologs of other genes known to be imprinted in
mammals, such as *ASCL2/MASH2* (a fully imprinted re-
gion in mammals), *M6PR/IGF2R*, *DLK1* and *UBE3A* were
found to be biallelically expressed in the chicken [61-63].
Moreover, the *H19* imprinting center identified in

mammals and controlling an imprinted cluster that in-
cludes *IGF2*, appears to be absent in the chicken [61].

However, such studies are limited to few genes (less
than 5% of the genes known to be imprinted in the
mouse) in different chicken embryonic tissues at differ-
ent developmental stages. They are not sufficiently ex-
haustive to conclude that imprinting does not exist in
birds, especially since different sets of genes might be
imprinted in mammals versus birds.

Several studies have examined imprinted-related mole-
cules and phenomena to better understand genomic im-
printing in mammals. If applied to the chicken, this
approach may also help test for the existence of genomic
imprinting in birds.

One feature of imprinted regions in mammals is the
asynchronous replication of parental alleles [64]. Inter-
estingly, replication of the chicken orthologs of some
imprinted genes is asynchronous [65], even when they
are biallelically expressed. It is hypothesized that mam-
malian imprinted gene clusters originate from an ances-
tor common to all vertebrates and that they evolved
from preimprinted to imprinted regions [66]. Since the
orthologous mammalian imprinted genes are biallelically
expressed in the chicken, it is impossible to strictly link
the asynchronous replication to imprinting in birds.

Another feature of mammalian imprinting is its associ-
ation with several molecular signatures. As recently
reviewed, these signatures need to differentiate paternal
and maternal inherited chromosomes in order to in-
fluence transcription, and to be transmitted through
generations [67]. Changes in DNA methylation patterns
represent an ideal mechanism to generate such signatures
or epigenetic marks. DNA methylation is involved in the
regulation of gene expression, and specific methylation
patterns can be inherited across generations in mammals.
The enzymes that control DNA methylation, such as
DNA methyltransferases (DNMT), are crucial for embry-
onic survival in the mouse (recently reviewed in [68,69]).
DNMT include proteins that act in the maintenance of
DNA methylation, such as DNMT1, and proteins that are
involved in *de novo* DNA methylation, either by directly
interacting with DNA (DNMT3A and DNMT3B) or indir-
ectly as supporting factors (DNMT3L) [70-74]. The re-
spective roles of DNMT in genomic imprinting have been
brought to light mainly through loss-of-function (knock-
down or knockout) experiments [75,76]. Identification of
methylation-related DNMT in chickens would stimulate
the search for allele-specific expression in oviparous ani-
mals. *DNMT1*, *DNMT3A* and *DNMT3B* cDNA have been
cloned in the chicken, and their encoded proteins have
been shown to share 50-80% amino acid identities with
the corresponding mouse orthologs [77,78]. However,
*DNMT3L*, a gene that encodes a protein essential for the
establishment of imprinted marks in the mouse [79] has
not been detected in birds [77], which may explain why
some genes imprinted in mammals are not imprinted in
the chicken.

Another approach for investigating genomic imprinting is to explore the chicken genome for differentially methylated regions (DMR) that are involved in the differential methylation of maternal and paternal chromosomal DNA in mammalian imprinting. A genome-wide methylome map of chicken muscle and liver tissues was completed recently [80], and the authors did not identify any DMR associated with genes known to be imprinted in mammals. However, this search was performed for only a few genes in two tissues, and thus it is difficult to draw conclusions on the existence of imprinted genes across the chicken genome.

Although methylation patterns play a major role in the
process of allele silencing, other mechanisms (e.g., histone
modifications or non-coding RNA) are also known to be
involved at several stages [81-84]. Among the numerous
studies on this subject, two deserve particular attention.
First, a study on mouse placenta has shown that genetic
ablation of DNA methylation does not suppress imprint-
ing of paternally repressed genes located in the distal
region of mouse chromosome 7 [85] but that histone
methylation seems sufficient to confer a silenced status to
the paternal alleles of the relevant genes. The authors sug-
gest the existence of an older imprinting mechanism that
is limited to extra-embryonic tissues and that involves
histone modification. In the second study, the authors
examined the mouse *Gnas* cluster (located on mouse
chromosome 2, containing a gene coding for stimulatory
G-protein alpha subunit, giving rise to alternatively spliced
isoforms that show maternal-, paternal- and biallelic ex-
pression as well as a non-coding antisense transcript
[86]). They demonstrated that *Nespas*, a non-coding
RNA, could silence *Nesp* by a mechanism independent
of a DNA methylation mark [87]. Again, a DNA-
methylation-independent role of chromatin marks in
gene silencing was highlighted. These two studies show
that imprinting mechanisms other than DNA methyla-
tion exist, and it is interesting to note that such mecha-
nisms have not yet been investigated in birds.

Genome-wide approaches [49,88,89] and developments
such as next-generation sequencing have recently opened
up new perspectives for the investigation of imprinting
mechanisms, including the possibility of identifying un-
known mechanisms and gaining insight into new interac-
tions or alternative processes. As suggested in a recent
review [90], it is essential to explore other vertebrate line-
ages for epigenetic marks and allele-specific expression.

Environmental epigenomics

The environment can influence developmental plasticity
and thus phenotypes in a wide variety of animals, from

insects to man [14]. Environmental epigenomics refers
to the study of how environmental exposures (e.g.,
toxins, stress or maternal nutrition) during early devel-
opment influence gene regulation through epigenetic
mechanisms (e.g., DNA methylation or histone modifi-
cations) that, in turn, influence the adult phenotype
[14,91-93]. As described below, the environment may
have a much broader impact on the adult phenotype
when the marks occur early during development.

Post-hatch environmental influences

Several studies on DNA and histone methylation levels
in chicks subjected to heat stimulation demonstrated
that epigenetic marks vary with the environmental
conditions experienced during the post-hatch period
[94-97]. They showed that the expression of BDNF
(brain-derived neurotrophic factor), which is a key regu-
lator of thermotolerance acquisition in the chick hypo-
thalamus, differs between control birds and animals
acclimated to heat early in their post-hatch life. Further-
more, alterations were observed in the methylation level
of CpG sites in the promoter of the *BDNF* gene. It was
also shown that modifications of histone H3 lysine 9
(H3K9) and methylation of histone H3 lysine residue 27
(H3K27) in the promoter of *BDNF* occur in the hypo-
thalamus during thermotolerance acquisition on day 3
post-hatch.

Epigenetic modifications are involved in the immune
mechanisms underlying chicken susceptibility to *Sal-
monella enteritidis* [98] or Marek disease [99,100] and
include changes in the DNA methylation pattern of host
defense genes. Indeed, the Marek disease virus (MDV)
can induce changes in the expression levels of all three
*DNMT* genes (*DNMT1*, *DNMT3A*, and *DNMT3B*). Vari-
ous histone profiles and gene promoters were identified
as being differentially modified and methylated in MDV-
sensitive and -resistant chicken strains, indicating that
epigenetic mechanisms may participate in the modula-
tion of the resistance and/or susceptibility to specific
poultry diseases [99,100].

Other environmental changes are known to affect the
adult phenotype, but to date, no molecular evidence of
epigenetic phenomena is available. For instance, phos-
phorus- or calcium-restricted diets during the early grow-
ing period trigger a compensatory adaptation of the
chicken [101], possibly mediated by epigenetic mecha-
nisms [102]. Although little is known about the underlying
molecular mechanisms in birds, it seems that feed stress
may alter gene transcription at least partly via epigenetic
mechanisms. For example, Xu et al. [103] reported that 3-
day-old chicks subjected to a 24-hour fasting underwent
histone H3 methylation modifications in the preoptic
anterior hypothalamus, which is the center of body
temperature and food intake control.
Influence of the environment during development

In addition to post-hatch environmental factors, changes applied directly to the egg or the resources contained in the egg (e.g., nutrients, hormones, carotenoids, vitamins or RNA transcripts) can have an impact on newborn fitness and later on the adult phenotype [104,105]. Thus, these environmental effects on development are either directly applied to the embryo itself, or are transmitted by the mother.

In birds, direct abiotic environmental factors (e.g., temperature) can influence embryonic development and the adult phenotype (see [106]). It has been shown that exposure of embryos to different temperatures at the end of egg incubation, which is a critical developmental period, can be a way of adapting poultry embryos to later climatic conditions (see [106]). Epigenetic processes are good candidates for mediating these mechanisms [107-110]. Another example of abiotic stress influencing embryonic development is the exposure to green monochromatic LED light during embryogenesis that has a growth-promoting effect observed on adult turkeys and broiler chickens [111-114]. One explanation may be enhanced proliferation and differentiation of adult myoblasts and myofiber synchronization [113], but further work is needed to better characterize the underlying processes.

The impact of the mother's environment on the F1 generation phenotype has been well documented in mammals. For example, it has been reported in humans, that the gestational diet affects offspring phenotypes (part of the "nutritional programming") (see [115]). A well-documented example comes from studies after the Dutch famine during World War II, which revealed that prenatal under-nutrition had an effect on later health [116] and that epigenetic mechanisms were involved [117]. The resulting chronic degenerative diseases associated with this famine include cardiovascular diseases, metabolic diseases, breast cancer and obesity. Another famous example of an adult phenotype induced by maternal nutrition in mammals is the viable yellow agouti (A<sup>VY</sup>) mouse model, in which the *Agouti* gene is genetically and epigenetically dysregulated by an upstream retrotransposon insertion. In this model, the diet of the mother influences coat color and other pleiotropic outcomes, such as diabetes, obesity and tumorigenesis in the offspring. Both methylation patterns and histone modifications are involved in the epigenetic variations of this mutation [118,119].

Maternal under-nutrition can also affect the phenotype
of offspring in birds. For example, Rao et al. showed that
4-week-old chicks from mothers fed a low-protein diet
had significantly heavier body weight and *Pectoralis major* muscle weight [120]. Another approach consists
in experimentally increasing brood size, which induces

developmental deficits (including nutrient deficits) in the
early life of birds. For example, in zebra finches, Naguib
et al. [121,122] imposed different degrees of develop-
mental stress on nestlings by forming broods ranging in
size from two to six nestlings, and then examined the
offspring of the dams that had been differentially
stressed as nestlings. As the brood size experienced by
the dams increased, the weight of their offspring de-
creased. The effects on body mass and size were sex-
specific. Female offspring grew larger than male off-
spring when their dam was raised in a small brood, but
females from dams reared in large broods were smaller
than their brothers. Furthermore, the reproductive suc-
cess of the female progeny was negatively associated
with the brood size in which the dam was raised
[121,122]. These maternal effects could result from
modifications in egg content of the females that were
stressed during their early development, leading to sex-
dependent impacts on the phenotype of F1 individuals.
Epigenetic mechanisms might be involved in this
process, and deserve to be examined in this context.
Several studies have also proven the existence of a ma-
ternal influence on the immune system of F1 individuals
in birds (see [123] for a review).

From a genetic point of view, it is interesting that the
priming effect of these induced responses seems to de-
pend on the maternal genetic background [124].

The most in-depth research on epigenetic effects in
birds over a single generation focused on the effects of
environmental challenges on behavioral traits, gene ex-
pression and DNA methylation in offspring [125-128].
In one of these studies [128], spatial learning was af-
fected in individuals subjected to unpredictable light
rhythms compared to animals exposed to predictable
light rhythms. In the White Leghorn but not the Red
Jungle Fowl, these effects were transmitted to the F1
generation reared under normal conditions, indicating a
difference in the transmission of information to the next
generation between these two chicken breeds. Exposure
of commercial chicks to an unpredictable light schedule
also triggered transmission of adaptive behavior to the
next generation, with female offspring showing greater
effects than males [127]. Molecular analyses showed that
transcription differences acquired by the parents in re-
sponse to environmental challenges are partially passed
on to the F1 generation, and that the *BDNF* gene [128],
immune genes [127], and stress-related genes [125] seem
to be involved in these transmitted effects. This work
also provides new insight into the role of DNA methyla-
tion in multigenerational epigenetic effects, by showing
heritable differences of DNA methylation between differ-
ent chicken breeds [126]. The influence of the genetic
background is a particularly interesting feature and it
has been reported that the impact of the parental
environment on the offspring's phenotype depends on
the chicken line [128]. Observations in quail have also
demonstrated a genetic component of maternal influ-
ence. Cross-fostering of chicks by mothers from two
quail lines, divergently selected for tonic immobility (a
fear-related behavioral trait), showed that the level of
maternal influence on the offspring's behavioral develop-
ment depends on the chick's genetic origin [129]. This
maternal influence is at least partially carried by egg com-
position, as shown in a study of F1 quails from stressed fe-
males [130] and using an *ex-ovo* embryo transfer strategy
between chicken layers and broilers [104].

Collectively, the above-described examples yield two
noteworthy conclusions. First, some of the early envir-
onmental effects on the offspring's phenotype are
sex-specific in both birds and mammals. Second, the
environment experienced during early development
seems to have a greater impact on the adult phenotype
than that experienced later in life (Figure 2).

Taken together, these examples show that the environ-
ment influences gene expression in avian species, per-
haps via epigenetic mechanisms. An interesting feature
in the context of poultry production and selection is the
possibility that these influences may be retained across
several successive generations.

Transgenerational memory of the ancestors' environment

An example of transgenerational epigenetic transmission comes from the plant world. Johannes et al. showed that alterations in DNA methylation can be inherited for several generations in *Arabidopsis thaliana* [131]. Using epiRIL (epigenetic Recombinant Inbred Lines), these authors and others [132] examined the transmission of epigenetic marks for at least eight generations, and observed that some were conserved while others gradually returned to their original methylation state.

Similarly, interesting cases have been highlighted in
animals. Erasure of methylation patterns during meiosis
results in the establishment of new parent-specific
imprints in oocytes and spermatocytes ([15,133], see
Figure 2). However, some loci can escape DNA methyla-
tion reprogramming, as for example, repeated elements
such as retrotransposons [15,134]. Moreover, miRNA
were shown to be involved in the transmission of epi-
genetic information via the gametes [15,135]. Thus, epi-
genetic information can be transmitted and have an
impact on the next generations.

Parental environment has an effect on the F1 gene-
ration and this is particularly clear in mammals, since
the mother hosts the offspring's development from the
zygote stage to birth. Such effects will also occur in the

<figure><img src="image_3.png" /><figcaption>**Figure 2** The epigenetic genome-wide reprogramming cycle involves two phases of DNA erasure in the mouse (from [91,161,162]).</figcaption></figure>

(1) A first wave of DNA demethylation takes place in the male (blue curve) or female (red curve) primordial germ cells (PGC) of the F1 individuals; this occurs throughout the genome, including the imprinted genes (embryonic day (E10.5-13.5). (2) Then, the genome of the gametes undergoes *de novo* methylation, with maternal methylation marks established at a later stage (ovulation) than paternal marks (E14). (3) A second wave of DNA demethylation takes place after fertilization in the F2 zygote (E0.5), with a more rapid demethylation in the paternal than the maternal genome. However, the paternal and maternal imprinted genes maintain their methylation pattern throughout this preimplantation reprogramming (dotted curves), allowing the inheritance of parent-specific monoallelic expression in somatic tissues of the F2 individual.

(4) Finally, genome-wide remethylation occurs in both parental genomes at about the time of implantation (E3.5). Altogether the very early embryonic development corresponds to an epigenomic reprogramming step, during which the new epigenetic marks are more prone to being impacted by the environment. This explains why the environment experienced during early development has a greater impact on the adult phenotype than that experienced later in life [163]. Moreover, the timing of the two global DNA demethylation and remethylation waves differs between male and female genomes, possibly explaining why they may be differently impacted by a stress applied during these stages [91,164].
F2 generation, since the developing F1 generation bears the primordial germ cells that will differentiate into gamete precursor cells and eventually form an F2 animal. In this way, the maternal environment can affect the next two generations (Figure 3), which means that the first generation for which an individual's cells are not directly exposed to an environmental effect is the F3 generation if it was the female that was exposed and the F2 generation if it was the male. Thus, evidence for transgenerational epigenetic transmission, i.e. incomplete erasure of epigenetic marks between generations resulting in unusual patterns of inheritance from one generation to the next, is unquestionable only if the effect is detected in the F3 generation or beyond [136]. Investigating the male-path is an interesting approach to examine transgenerational epigenetic impacts.

Paternal environmental influences on the phenotype of the F1 generation (or even the F2 generation) have been shown in mammals (reviewed in [137]). For example, the female offspring of adult male rats fed a high-fat diet showed modified β-cell functions that were associated with an altered expression of more than 600 genes in the F1 generation, and hypomethylation of a cytosine proximal to the transcription start site of the *IL13RA2* gene [138]. Similarly, offspring from male rats fed a low-

protein diet showed impaired lipid metabolism, notably associated with increased methylation at a putative enhancer of the *PPARα* gene [139]. These results strongly suggest transmission of epigenetic information, but since the methylation patterns were not examined in the following generation, it is difficult to conclude to an unquestionable transgenerational epigenetic phenomenon, as defined above.

Transgenerational epigenetic transmission may be rare, but it has already been reported in different mammalian species. In man, Pembrey reported that the paternal grandfather's food supply affected the mortality rate of grandsons but not of granddaughters, whereas the paternal grandmother's food supply affected the mortality rate of granddaughters but not of grandsons [140,141]. Another study by Heijmans and collaborators showed that the risk of mortality in grandchildren, with respect to the grandparents' food supply, was associated with modifications of DNA methylation in the differentially methylated region of the *IGF2* gene [117].

Recently, Zeybel et al. [142] described an adaptive mechanism involving epigenetic mechanisms in rats. After inducing liver injury in F0 and/or F1 males, they showed a reduction of liver fibrogenesis in F2 male offspring, illustrating an unquestionable transgenerational inheritance. The authors observed epigenetic modifications in a number of genes, with alterations observed in CpG methylation (PPARγ, PPARα and TGF-β1), histone H3 acetylation (PPARγ and TGF-β1) and other chromatin modifications (PPARγ). However, the mechanisms that transmit epigenetic modifications from the environment to the sperm and from the sperm to the offspring's liver have not yet been deciphered [142]. In rats, an epigenetic inheritance induced by different environmental components was observed in the sperm of the F3 generation by detecting differentially methylated regions depending on the environmental exposure of the ancestors [143].

Some studies have even revealed transmission of epigenetic marks to at least the F4 generation. Recently, Wolstenholme et al. reported that exposure to bisphenol A during the gestation of female mice reduced the expression of the genes encoding two neuropeptides (oxytocin and vasopressin) in the brain of the F1 individuals. The expression of oxytocin was still reduced in the brain of the F4 males and females, whereas decreased vasopressin expression was maintained only in the F4 males. Moreover, impacts on social behavior were detected until the F4 generation [144]. Another report on the analysis of the phenotype and epigenetic marks of female rats subjected to a high-energy diet for four generations, demonstrated that transgenerational effects involving altered epigenetic marks at each generation were induced (at least partly) *de novo* [145]. Finally, the best-studied

<figure><img src="image_4.png" /></figure>
example of transgenerational epigenetic inheritance in vertebrates concerns the influence of vinclozolin on the health (fertility problems or organic diseases) of rat male offspring in the F1 to F4 generations. This occurs via DNA methylation and a putative induction of copy number variation to generate new imprinted-like sites that are transmitted to subsequent generations through the male germ line, thus creating transgenerational transmission of adult phenotypes [146-149]. Other studies have suggested putative intergenerational transmission of epigenetic marks through the gametes [15,135].

To our knowledge, no transgenerational transmission of epigenetic marks has been reported in birds, either prior to the exhaustive reviews by Jablonka and Raz [3] and Ho and Burggren [4], or since then.

## Conclusions

A phenotype results from the interplay between the genome and the epigenome, which itself depends on the environment the animal experiences during its development and adult life. Epigenetic variations during early life play a role in producing inter-individual differences in phenotypes. Consequently, analyses of inter-individual phenotypic diversity should consider both epigenetic and genetic variations [93]. In this review, we describe epigenetic phenomena in birds in comparison to the related studies in mammals. Much more work is needed to fully comprehend the importance of epigenetics in the phenotypic variability of birds, and hence to exploit it for genetic selection.

In the chicken, epigenetic modifications occur from the first egg stage, i.e. a stage at which the dam provides an environmental signature through the egg content [150]. These environmental influences may have agronomic value via their effect on the adult phenotype. Given the likelihood that climate will change in the more or less near future and demands for food supplies will increase, a better understanding of the epigenetic mechanisms governing the embryo's response to environmental changes could open new ways to improve efficiency, animal welfare and food quality. For example, one interesting issue is the nutrient profile and restriction level of the diet of breeders, which is tailored to produce the largest possible number of fertile eggs and may thus not fill the requirements for future adult broiler performance [151].

Transgenerational inheritance associated with mechanisms other than DNA sequence variation (i.e., epigenetics, parental effects or "cultural inheritance") is thought to affect evolutionary dynamics [152]. This "non-classical" inheritance is known to play a role in phenotypic variability, especially in the response to environmental changes [153]. An important question in animal selection is the extent to which this non-genetic inheritance also affects the efficiency of genetic selection. Indeed, epigenetics may help

to better explain environmental and non-Mendelian variability of complex traits [154]. Several authors have proposed quantitative models including epigenetic inheritance and environmental interactions [155-157], potentially paving the way for future inclusion of these mechanisms in genetic selection studies. The reversibility of epigenetic modifications (i.e., their potentially transient nature) could constitute a challenge in the modeling of inheritance [158]. Aside from putative epigenetic inheritance, Feinberg and coworkers proposed a model in which DNA mutations could, via epigenetic mechanisms, modify phenotypic variability without changing the mean phenotype [159]. This model should be considered by geneticists aiming at studying the adaptation of livestock to changing environments.

From a genetic point of view, the contribution of heritable epigenetic effects to important phenotypic variations is an exciting research area, not only for fundamental science, but also because of its possible breeding applications, as recently suggested by a primary poultry genetics organization [160].

## Competing interests

The authors declare that they have no competing interests.

## Author's contributions

LF, MM and FP drafted and finalized the manuscript. JMB, BP, AC and FM participated in bibliographic analyses and writing of the paper. All authors read and approved the final manuscript.

## Acknowledgements

The authors thank Hervé Acloque for critical reading of the manuscript and Hélène Hayes for helpful comments. LF is supported by the Région Midi-Pyrénées and Animal Genetics Division (INRA). This work is supported by the French ANR EpiBird grant (ANR-009-GENM-004).

## Author details

¹INRA, UMR444, Laboratoire de Génétique Cellulaire, Castanet-Tolosan F-31326, France. ²ENVT, UMR444, Laboratoire de Génétique Cellulaire, Toulouse, F-31076, France. ³INRA, UR631, Station d'Amélioration Génétique des Animaux, Castanet-Tolosan, F-31326, France. ⁴INRA, UR83, Recherche Avicoles, Nouzilly F-37380, France. ⁵INSERM, U846, INRA, USC1361, Institut Cellule Souche et Cerveau, Bron F-69500, France. ⁶INRA, UMR1313, Génétique animale et biologie intégrative, Jouy-en-Josas F-78350, France.

⁷AgroParisTech UMR1313, Génétique animale et biologie intégrative, Jouy-en-Josas F-78350, France.

Received: 13 November 2012 Accepted: 26 April 2013

Published: 11 June 2013

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doi:10.1186/1297-9686-45-16

**Cite this article as:** Frésard et al.: Epigenetics and phenotypic variability: some interesting insights from birds. *Genetics Selection Evolution* 2013 **45**:16.

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