Agricultural and Food Sience, Vol. 16 (2007): 177-187 A G R I C U L T U R A L A N D F O O D S C I E N C E Vol. 16 (2007): 177-187 177 © Agricultural and Food Science Manuscript received February 2007 Chromosome regions affecting body weight in egg layers Mervi Honkatukia, Maria Tuiskula-Haavisto and Johanna Vilkki MTT Agrifood Research Finland, Biotechnology and Food Research, Animal Genomics, FI-31600 Jokioinen, Finland, e-mail: mervi.honkatukia@mtt.fi We have previously mapped quantitative trait loci (QTL) affecting egg production and quality traits using a reciprocal cross of two divergent egg-layer lines. The lines differ also in body weight, and we initially identified genome-wide significant Mendelian QTL for adult body weight at 40 weeks of age and feed intake at 32–36 weeks of age. In addition, QTL with parent-of-origin effects were detected for feed intake and body weight. In the present study, a total of five body weight traits (weight at 16, 20, 24, 40 and 60 weeks of age) have been analysed in the same mapping population. New QTL affecting body weight at different ages were found on chromosomes 1, 4, 5, 6, and 13. Both Mendelian QTL and loci with parent-of-origin expression were found. Our findings are in good agreement with the results of previous studies on different mapping populations. The results elucidate the most important chromosome regions affecting weight in poultry in general and may add to the understanding of such loci among domestic animals. Key-words: Egg laying chickens, QTL mapping, body weight Introduction A large number of studies have reported quantita- tive trait loci (QTL) for economically important traits in poultry. The majority of the studies (21 of 50 published ones) have dealt with growth-relat- ed traits (Abasht et al. 2006). This may reflect the straightforward accessibility of the phenotypes for several growth traits. The recently updated chick- en QTL database contains a total of 657 QTL from poultry, 345 of which are growth related (http:// www.animalgenome.org/QTLdb/chicken.html). The mapping population structures and results are thoroughly summarized in recent reviews by Abasht et al. (2006) and Hocking (2005). The general out- line of the results regarding growth-related QTL is that there are numerous loci with moderate ef- fects rather than a few QTL with a major effect. A G R I C U L T U R A L A N D F O O D S C I E N C E Honkatukia, M. et al. Chromosome regions affecting body weight in egg layers 178 A G R I C U L T U R A L A N D F O O D S C I E N C E Vol. 16 (2007): 177-187 179 The studies have mainly concentrated on the first weeks of growth (in broilers) and very few have included measurements of the whole growth peri- od or adult weight. Growth can be measured relative to body weight, feed efficiency or body composition. Suc- cessive measurements are forming a growth curve. At least three different stages can be distinguished from the growth curve. Early growth is due to rap- id development of internal organs, such as the gastrointestinal tract, heart and liver (Lilja 1983). Most of the deposition of body mass takes place during the intermediate growth phase (between the age of 6–16 weeks). During the later period growth is more or less associated with deposition of fat (Jennen 2004). Individuals with high early growth rates have rapid development of the ‘sup- ply’ organs, which are necessary to fulfil the nutri- tional demands of the growing animal (Blom and Lilja 2005). This process in turn promotes over- all growth of the ‘demand’ organs (brain, muscles, skeleton and feathers) giving greater potential for growth. Weight gain is associated either with the above-mentioned developmental pattern or accu- mulation of abdominal fat. In broilers, long-term selection for fast growth and high yield has led to increased abdominal fat and feed intake (Wright et al. 2006). In our previous analyses we have identified QTL mainly for egg production and egg quali- ty traits (Tuiskula-Haavisto et al. 2002, Tuiskula- Haavisto et al. 2004). Some of the QTL, especial- ly those affecting adult body weight (at 40 weeks of age), feed intake, egg weight and sexual matu- rity were found to show parent-of origin effects, i.e. a specific QTL allele was expressed only when inherited through either parental germ line. In the present study, we investigated the role of Mendeli- an and parent-of-origin QTL affecting body weight throughout the life span (excluding early growth) in the same experimental population (Tuiskula- Haavisto et al. 2002). Material and methods The mapping population is an F2 cross between two extreme egg layer lines: Rhode Island Red (RIR) and White Leghorn (WL). The RIR line is a typi- cal brown egg layer with high feed intake and body weight. The WL line has been selected for several generations for high egg production and good feed efficiency. From each line two hens and two roost- ers were reciprocally crossed. From the F1, 32 hens and 8 roosters were crossed to produce a total of 305 F2 hens in three different hatches. All individu- als of the F0, F1 and F2 generations were genotyped and phenotypes were recorded on the F2 hens (Tu- iskula-Haavisto et al. 2002). Compared to the pre- vious study, new microsatellite markers were add- ed to chromosomes 2, 4, 7, 8 and 10. The Haldane map length was 2344 cM. The full cross design and the linkage maps used for mapping are available at http://www.mtt.fi/julkaisut/chickenqtl/. Body weight (g) Abbreviation Minimum Maximum Mean SD1 n2 Age 16 weeks BW16 800 1910 1402 181 303 20 weeks BW20 1226 2266 1635 198 303 24 weeks BW24 1240 2339 1690 209 299 40 weeks* BW40 1233 2782 1853 252 289 60 weeks* BW60 1202 2882 1922 273 282 *Included in Tuiskula-Haavisto et al. 2002 1 Standard deviation. 2 Number of individuals. Table 1. Description of the traits analysed in the F2 generation from the reciprocal cross between Rhode Island Red and White Leghorn lines. A G R I C U L T U R A L A N D F O O D S C I E N C E Honkatukia, M. et al. Chromosome regions affecting body weight in egg layers 178 A G R I C U L T U R A L A N D F O O D S C I E N C E Vol. 16 (2007): 177-187 179 Phenotypic measurements Body weight was measured at 16, 20, 24, 40, and at 60 weeks of age (BW16, BW20, BW24, BW40, BW60). The recorded traits are summarized in Ta- ble 1, including information on the variation in the F2 generation. BW40 and BW60 were included in the previous analyses (Tuiskula-Haavisto et al. 2002 and 2004), with slightly different marker maps. Systematic effects For part of the analyses, F2 records were pre-cor- rected for any significant effect of hatch number using least squares analysis (SAS proc GLM). The effect of hatch was significant for all the traits ana- lysed in the present study. Genetic Models The F2 data were analysed following a line cross model (Haley et al. 1994) where for every F2 indi- vidual the probabilities that it inherited two RIR al- leles (p11), two WL alleles (p22), or one allele from each line (p12 or p21; the first subscript indicating the paternally inherited, the second the maternal- ly inherited allele) were inferred at 1 cM intervals across the genome. At every position, the follow- ing Mendelian model was fitted: yj=m+apaj+dpdj+ej [1] where yj is the trait score of animal j, m is the population mean, a and d are the estimated additive and dominance effects of a putative QTL at the giv- en location, paj is the probability of animal j to car- ry two RIR alleles, pdj the conditional probability of animal j to be heterozygous, and ej is the resid- ual error. An outbred line cross design provides the possibility to trace the parental origin of alleles in F2 individuals back to F1 parents. This enables anal- ysis of potential parent-of-origin effects. Knott et al. (1998) introduced the contrast between hetero- zygous individuals with alternative parental origin as a test for parent-of-origin effects (pi = p12-p21): yj=m+apa j+dpd j+ipi j+ej [2] Variables are as in [1]; with the extension that i is the estimated imprinting effect. The model for parent-of-origin effects by Knott et al. (1998) was re-parameterised to enable a direct test for the con- tribution of the paternally and maternally inherit- ed effect (De Koning et al. 2000). Model [2] can be re-written with a specific maternal and paternal QTL component: yj=m+apat ppat j+amat pmat j+ dpd j +e j [3] where apat is the paternally inherited QTL ef- fect, amat is the maternally inherited QTL effect, ppat = [p11+p12]-[p22+p21] and pmat = [p11+p21]-[p22+p12]. Models [2] and [3] are identical in terms of total variance explained by the model. This re-parame- terisation allows additional models to be fitted with exclusive paternal or maternal expression: Yj=m+apat ppat j+ej Yj=m+amat pmat j+ej [4] QTL Mapping We analysed thirteen autosomes and the sex chro- mosome Z, genotyped for a total of 114 microsat- ellite markers, for Mendelian and parent-of-origin specific QTL. Details on genotyping and linkage map construction were given by Tuiskula-Haavis- to et al. (2002). Significance of the parent-of-ori- gin effect was assessed using an F test of whether a full model explains significantly more variation than a Mendelian model. Subsequently, all auto- somes were re-analysed using models with exclu- sive paternal or maternal expression. After deriva- tion of the genetic model, the significance level, the QTL effects, and the confidence intervals were es- timated using the inferred genetic model. A G R I C U L T U R A L A N D F O O D S C I E N C E Honkatukia, M. et al. Chromosome regions affecting body weight in egg layers 180 A G R I C U L T U R A L A N D F O O D S C I E N C E Vol. 16 (2007): 177-187 181 Significance thresholds Significance thresholds for the presence of QTL against the H0 of no QTL were determined em- pirically for individual chromosomes by permu- tation (Churchill and Doerge 1994). The first lev- el of significance was suggestive linkage where one false positive is expected in a genome scan (Lander and Kruglyak 1995). In order to claim significant linkage, we applied a 5% genome- wide significance level (Lander and Kruglyak 1995). To derive genome-wide significance levels from the chromosome-wide significance levels, we applied the following Bonferroni correction: P genome-wide = 1 - (1 – P chromosome-wise) 1/r, where r is the relative contribution of the studied chromosome to the total genome length (r = chromosome length/ genome length). The empirical genome-wide significance thresh- old for the presence of a QTL against the H0 of no QTL effect varied between 7.8 and 13.2 for the Men- delian QTL and 12.3 and 13.2 for analyses fitting only a single parental QTL effect. To facilitate graph- ical comparisons of different models, the negative logarithm of the comparison-wise P values [-log10 (P)] of the F statistics is presented in the graphs (de Koning et al. 2002). The thresholds are averaged over all models that are represented in the graph. Confidence intervals for QTL positions were ob- tained by bootstrapping. The sorted F ratios from the bootstrap replicates were used to determine the test statistic value corresponding to a desired (90%) con- fidence interval (de Koning et al. 2000). The meth- od used here allows for non-continuous confidence intervals and is close to the traditional LOD drop- off methods. Results Analysing 13 autosomes and the sex chromosome Z with a Mendelian model revealed a highly sig- Trait1 GGA2 cM3 CI904 F-ratio Genome- wide P Chromosome- wise P Additive5 effect ± SE Dominance6 effect ± SE R2 BW20 1 291 279–304 7.72 0.057 0.015 –45.2±20.9 129.2±41.0 4.8 BW60 1 297 291–303 7.75 0.053 0.014 –44.9±28.4 180.0±51.0 5.2 BW16 4 195 189-204 58.72 <0.0009 <0.0001 +127.5±11.8 –7.4±18.0 28.0 BW20 4 196 189–204 68.10 <0.0009 <0.0001 +163.6±14.1 –20.2±21.7 31.2 BW24 4 196 187–206 48.49 <0.0009 <0.0001 +154.1±15.7 –8.5±23.9 24.7 BW40 4 195 179–231 51.10 <0.0009 <0.0001 +190.2±18.9 –19.6±28.5 26.3 BW60 4 198 189–209 33.60 <0.0009 <0.0001 +189.2±23.3 –34.0±35.7 19.4 BW16 6 37 15–56 5.81 0.39 0.015 +33.4±14.1 –48.2±19.2 3.7 BW20 6 39 3–53 7.14 0.16 0.0054 +52.9±17.5 –57.2±24.7 4.5 BW24 6 36 13–49 5.97 0.34 0.013 +30.8±17.5 –70.8±23.1 3.8 Table 2. Quantitative trait loci (QTL) affecting body weight detected by Mendelian inheritance model in the reciprocal F2 cross between Rhode Island Red and White Leghorn. Significant results are shown in bold. 1 Trait definitions are given in Table 1. 2 Chicken chromosome (Gallus gallus). 3The most likely position of the QTL, at centiMorgan (cM). 4 90% confidence interval for the QTL position. 5 Additive QTL effect reported for the Rhode Island Red QTL allele is half of the average phenotypic difference between animals carrying two Rhode Island Red alleles and those carrying two White Leghorn alleles; estimates are given with standard errors (SE). 6The dominance effect is the deviation of the phenotypes of the heterozygous birds from the mean of the groups of ho- mozygous birds; estimates are given with standard errors. R2 refers to the proportion (%) of phenotypic variance ex- plained by the QTL. A G R I C U L T U R A L A N D F O O D S C I E N C E Honkatukia, M. et al. Chromosome regions affecting body weight in egg layers 180 A G R I C U L T U R A L A N D F O O D S C I E N C E Vol. 16 (2007): 177-187 181 nificant QTL region (Pgenome-wide < 0.0009) affect- ing all body weight measurements (BW16, BW20, BW24, BW40, BW60) on GGA4 (Gallus gallus chromosome 4) (Fig. 1), two suggestive QTL (Pg- enome-wide = 0.053 and 0.057) for BW20 and BW60 on GGA1 and three suggestive QTL (at 1% chro- mosome-wise significance level) for BW16, BW20 and BW24 on GGA6 (Table 2). At the chromosome region with genome-wide significant Mendelian QTL effected on all body weight measurements on chromosome 4, a sin- gle individual QTL explained 19.4–31.2% of the total phenotypic variance with the additive effect ranging from 0.7 to 1.05 standard deviation of the F2 (Table 2). The RIR allele effect for all these QTL was positive. The confidence intervals for all QTL were within the marker bracket ADL0331– LEI0073 (179–231 cM) and the highest F-ratio for all body weight measurements occurred of po- sitions between 195 and 200 cM close to mark- er MCW0180 (Fig. 1). This area was already de- tected in our previous study to affect BW40, egg weight and feed intake. Other research groups have also detected growth related QTL at this particu- lar region on GGA4. Jacobsson et al. (2005) and Sewalem et al. (2002) have observed body weight QTL at 187–217 cM, and 138–243 cM, respec- tively. Park et al. (2006) detected breast muscle QTL at 187–217 cM and McElroy et al. (2006) a QTL affecting abdominal fat (153–201 cM). Car- cass weight QTL of Ikeobi et al. (2002) located at a wider area (138–243 cM). The suggestive Mendelian QTL region on GGA1 affecting both BW20 and BW60 lay be- tween 279 and 304 cM. The F-ratio curves for BW20 and BW60 had almost overlapping confi- dence intervals (Fig. 2, Table 2). The dominance effects were remarkably high for both the traits. BW20 was not detected in the previous scan, where body weight was analysed only at 40 and 60 weeks of age. Moreover, a maternally expressed QTL for feed intake was identified in our previous study in this region. Hansen et al. (2005) have detect- ed a Mendelian QTL for feed intake in the same region. In addition, a suggestive Mendelian QTL re- gion was found on GGA6 affecting body weight Fig. 1 Test statistic profiles for Mendelian quantitative trait loci on chicken chromosome 4 affecting body weight at: 16 weeks , 20 weeks , 24 weeks , 40 weeks , and 60 weeks of age. The black solid horizontal line denotes the 5% genome- wise significance threshold for the Mendelian model. The marker names and locations are indicated on the X-axis. 30 25 20 15 10 5 0 30 25 20 15 10 5 0 22 7 17 4 17 6 18 8 19 4 20 8 23 3 -log (P) 1 48 82 95 14 0 M C W 00 47 A D L0 14 5 M C W 00 05 A D L0 26 6 M C W 02 76 A D L0 33 1 M C W 01 70 M C W 01 80 M C W 01 29 M C W 00 99 LE I0 07 3 10 1 M C W 00 23 M C W 01 02 M C W 01 45 A D L0 15 0 M C W 00 07 A D L0 16 0 H U J0 00 1 M C W 00 10 A D L0 01 9 M C W 00 43 M C W 00 18 M C W 00 58 M C W 00 68 M C W 00 46 M C W 00 36 M C W 00 49 M C W 01 15 A D L0 18 8 A D L0 25 2 A D L0 02 0 A D L0 03 7 50 31 22 39 99 13 5 20 2 21 6 25 9 31 8 36 6 43 5 47 6 50 7 10 7 21 1 25 0 31 0 37 5 51 2 60 3 -log 4 3.5 3 2.5 2 1.5 1 0.5 0 log10(P) 3.5 Fig. 2. Test statistic profiles for quantitative trait loci (QTL) on chicken chromosome 1. Mendelian QTL were found for body weight at 20 weeks of age and at 60 weeks of age. Maternally expressed QTL were found for body weight at 16 weeks of age , 20 weeks of age , 24 weeks of age , and 40 weeks of age , and paternally expressed QTL for body weight at 20 weeks of age . The black solid horizontal line denotes the 5% chromosome-wise significance threshold for the Mendelian model and the red solid horizontal line denotes the 5% genome-wise significance threshold for the model including uniparental effects. The marker names and locations are indicated on the X-axis. A G R I C U L T U R A L A N D F O O D S C I E N C E Honkatukia, M. et al. Chromosome regions affecting body weight in egg layers 182 A G R I C U L T U R A L A N D F O O D S C I E N C E Vol. 16 (2007): 177-187 183 at 16, 20 and 24 weeks of age. The highest test statistic for each QTL effect lay within three cen- timorgans (36–39 cM), at or close to the marker ADL0040 (at 64 cM in the 2005 consensus map). The RIR allele effects were dominant and nega- tive. Results of three other research groups (Se- walem et al. 2002, Siwek et al. 2004, Zhou et al. 2006a) are supporting the presence of QTL affect- ing juvenile body weight or weight gain at this par- ticular position. Searching the 13 autosomes using models with uniparental expression revealed three new genome- wide significant QTL (Pgenome-wide = 0.046 to 0.014) and one suggestive QTL (Pchromosome-wise = 0.026) on chromosome 1 (GGA1) and one suggestive QTL (Pchromosome-wise = 0.044) on chromosome 5 as well as three suggestive QTL on GGA13 (Table 3). The locations of body weight QTL with mater- nal expression on GGA1 for BW16, BW20, BW24 co-located with the QTL for BW40 observed pre- viously (Tuiskula-Haavisto et al. 2004). The con- fidence intervals for BW16, BW20, BW24, and BW40 were overlapping and the highest test sta- tistics lay between 239 and 267 cM in each case. These individual QTL explain from 3.4 to 4.6% of the phenotypic variance and the RIR allele effect was negative at all loci varying from –40.12 g to –66.5g. A suggestive QTL with paternal expression for BW20 was located on GGA1 at 107 cM (Fig. 2). The effect of the RIR allele at this QTL was also negative (-37.55g) (Table 3). The suggestive QTL on chromosome 5 (GGA5) showed maternal expression for BW16. The RIR al- lele effect was negative (–26 g). The highest F-ratio was located at the marker ADL0233. The suggestive QTL with paternal expression for BW24, BW40 and F-ratio Imprint vs Mendelian Maternal Paternal Dominance Genome- wide 4 P Chromo- some wide5 P QTL effect6 R² Trait1 GGA cM2 CI903 BW20 1 107 84–126 8.04** 0.54 10.72 0.89 0.089 0.026 –37.55±11.5 3.4 BW16 1 239 218–296 7.74** 12.26 0.07 0.09 0.046 0.013 –40.12±11.2 3.9 BW20 1 267 279-304 4.68* 14.55 0.67 0.96 0.014 0.004 –56.74±14.8 4.6 BW24 1 259 203–216 3.85* 12.94 1.19 0.004 0.014 0.004 –50.36±14.0 4.1 BW40 1 239 212–285 6.3* 13.87 2.33 0.02 0.018 0.005 –66.54±17.8 4.6 BW16 5 117 107–122 5.67* 7.64 0.48 1.4 0.55 0.044 –26.04±9.4 2.4 BW24 13 32 5–32 5.17* 0.32 6.47 0.11 0.78 0.022 –35.18±13.8 2.1 BW40 13 32 5–32 4.47* 0.92 7.18 0.11 0.64 0.015 –45.76±17.1 2.4 BW60 13 32 12–32 6.77* 0.03 5.96 0.54 0.85 0.028 –47.11±19.2 2.0 Table 3. Quantitative trait loci (QTL) affecting body weight showing significant parent-of-origin specific effects in the reciprocal F2 cross between Rhode Island Red and White Leghorn. Uniparentally expressed QTL that are significant- ly supported by comparison of the full model against a Mendelian model are shown. F ratios for the individual compo- nents of the model (maternal effect, paternal effect, dominance) at the most likely position of the QTL are shown. The F ratio for the inferred genetic model is shown in bold. 1 Trait definitions are given in Table 1. 2 The most likely position of the QTL. 3 90% confidence interval for the QTL position. 4 Genome-wide significance for the QTL under the inferred genetic model. 5 Chromosome-wise significance for the QTL under the inferred genetic model. 6 The deviation of the Rhode Island Red (RIR) allele from the White Leghorn (WL) allele under the inferred genetic model (maternal or paternal expression). * P ≤ 0.05, ** P ≤ 0.01. A G R I C U L T U R A L A N D F O O D S C I E N C E Honkatukia, M. et al. Chromosome regions affecting body weight in egg layers 182 A G R I C U L T U R A L A N D F O O D S C I E N C E Vol. 16 (2007): 177-187 183 BW60 found on chromosome 13 all have the high- est test statistics at the same point at 32 cM, at the marker MCW0104 (Table 3), and at all loci the RIR allele effect was negative. The suggestive paternal- ly expressed BW60 QTL was already detected in the earlier scan (Tuiskula-Haavisto et al. 2004), but it was not reported as only genome-wide significant results were then included. Discussion Our results give support to earlier findings on both Mendelian and parent-of-origin expressed QTL. The Mendelian QTL were found within areas, where many previous studies have shown QTL for growth related traits. At present it is impossible to estimate if similar results from different studies reflect the effects of same loci or regions with many QTL af- fecting these traits. Likewise, it is not possible to es- timate even for our own experiment how many dif- ferent genes may be involved in the effects at each region or, in other words, how many of the QTL ef- fects are due to pleiotropic effects of one gene or due to linked genes. Some tentative conclusions might be made based on the observed effects. For exam- ple, in the present study the QTL region on GGA4 has effects on body weight at all measured ages. In all cases the RIR allele effect is positive and of ap- proximately the same size. It could be concluded that these are all effects of the same locus, which is active throughout the life span. One of the po- tential candidate genes to permanently affect body weight in the region between markers MCW0276 and MCW0129 is PPARGC1A (NP_001006457.1) (also known as PGC-1α), a key regulator of energy metabolism (Liang and Ward 2006). It is involved in regulating energy homeostasis, thermal regula- tion, and glucose metabolism in the liver, fat and muscle tissues (Wu et al. 2006). In fact, Wu et al. (2006) have detected association between an ami- no acid substitution (Asp216Asn) of PPARGC1A and BW at 4 weeks and abdominal fat weight in different chicken populations like White Plymouth Rock and White Leghorn. On the other hand, at the QTL region on chro- mosome 6 the RIR allele effect on growth is similar for all three QTL found to affect the early measur- ing periods (16, 20 and 24 weeks of age). No QTL for later weight measurements, the other produc- tion traits or feed intake have been detected on this chromosome in any earlier studies (e.g. Tuiskula- Haavisto et al. 2002 and 2004). This might sug- gest the action of a single locus that is active only during the early or intermediate stages of growth (a possible maturity QTL), and is not involved in the later growth related to energy balance (fat dep- osition). The recent findings of QTL with parent-of-ori- gin specific effects in the chicken may provide one more explanation for the well-known reciprocal ef- fects in poultry, hypothesized to originate from sex- linked genes or maternal effects. Our initial find- ings of QTL with parent-of-origin effects (Tuisku- la-Haavisto et al. 2004) suggested that the phenom- enon deserves closer scrutiny. Parent-of-origin ef- fects have thereafter been reported for growth and carcass traits in chicken (McElroy et al. 2006) and for QTL for body weight and feed intake in Japa- nese quail (Minvielle et al. 2005). The best-known epigenetic phenomenon lead- ing to parent-of-origin-specific expression in mam- mals is genomic imprinting. Recent comparative mapping has provided evidence for the conser- vation of orthologous imprinted gene clusters on chicken chromosomes (Dunzinger et al. 2005). Fur- thermore, some of these genes exhibit asynchro- nous DNA replication, an epigenetic mark specific for all imprinted regions. Many of the mapped par- ent-of-origin specific QTL effects in poultry locate in or close to these conserved regions that show some of the basic features involved in monoallel- ic expression and thus raise a need to review the possible involvement of imprinting in parent-of- origin / reciprocal effects in poultry. A majority of the imprinted genes in mammals regulate embry- onic growth in all vertebrates. Although the pos- sible imprinting-like effects in birds may involve different mechanisms or genes than in mammals, the growth-related QTL with parent-of-origin ef- fects are prime candidates to study the phenome- non in chicken. A G R I C U L T U R A L A N D F O O D S C I E N C E Honkatukia, M. et al. Chromosome regions affecting body weight in egg layers 184 A G R I C U L T U R A L A N D F O O D S C I E N C E Vol. 16 (2007): 177-187 185 In the following we discuss our new results on body weight QTL with parent-of-origin ef- fects, with special emphasis on the co-location of the observed parent-of-origin effects, clustering of chicken orthologues of mammalian imprinted genes and asynchronously replicating regions in chicken. The QTL database (http://www.animalg- enome.org/QTLdb/chicken.html) indicates several discrete QTL areas affecting weight related traits across the chicken chromosome 1. In the present study we found evidence for the existence of two independent growth related QTL regions. The first QTL region is found within the marker bracket MCW0007–MCW0068 (202–310 cM on our link- age map and 215 cM–283 cM on the 2005 consen- sus map (http://www.thearkdb.org). This area in- cludes QTL with both Mendelian and parent-of-or- igin effects. The QTL with maternal expression for body weight at 16, 20, and 24 weeks of age are lo- cated within the same chromosome area as the ma- ternally expressed QTL affecting body weight at 40 weeks of age in our earlier scan (Tuiskula-Haavis- to et al. 2004). Studies by McElroy et al. (2006), van Kaam et al. (1999) and Sewalem et al. (2002) also support existence of Mendelian QTL affec- ting body weight at this location. Mendelian QTL have also been found in this area (between mark- ers LEI0174 and LEI0171) for body weight at 13 and 16 weeks of age in a F2 cross between two ge- netically different lines (slow growing native breed and heavy weight broiler) (Tatsuda and Fujinaka 2001). Jennen et al. (2004) found Mendelian QTL on the same chromosome area (between markers MCW0058 and MCW0101) affecting percentage of abdominal fat at 10 weeks of age in a cross be- tween two broiler dam lines. In a further study on the generation 9 of the same population, QTL were found for body weight at 5 and 7 weeks of age (Jen- nen et al. 2005) between markers MCW0018 and MCW0058. The other region in this study affecting growth traits on chromosome 1 is flanked by markers MCW0010 and MCW0043 (at 39 cM and 135 cM on our linkage map and 71 cM and 156 cM on the consensus linkage map). The suggestive paternally expressed QTL found in this region has an effect on body weight at the age of 20 weeks. Five other re- search groups have found Mendelian QTL affect- ing body weight in the same area around 80–160 cM (Tatsuda and Fujinaka 2001, Ikeobi et al. 2002, Sewalem et al. 2002, Kerje et al. 2003, Zhou et al. 2006b). Of these studies, Sewalem et al. (2002) and Ikeobi et al. (2002) analysed possibile parent-of-or- igin effects without finding any support for them. In the rest of the studies possible parent-of-origin effects were not considered, and therefore the ex- act nature of these QTL remains to be analysed. In addition, QTL affecting the weight of heart and leg muscle (drumstick) have been found at positions of 72–109 cM and 122–125 cM (Navarro et al. 2005, Zhou et al. 2006b). The human Prader-Willi/Angelman syndrome imprinted gene cluster (Nicholls and Knepper 2001) is to some extent conserved on chicken chro- mosome 1 in two different areas; the MKRN3 gene at 58.8 Mb corresponding to a linkage map loca- tion between markers ADL0188 and MCW0007 and gene cluster Gabrg3, Gabra5, Gabrb3, At- p10a and Ube3a at 135.0–136.0 Mb, correspond- ing to position around 400 cM in our linkage map. The MKRN3 region locates between the two QTL regions with parent-of-origin effects found in this study. On chromosome 5 we detected a suggestive QTL with maternal expression affecting BW16 at marker position ADL0233 (155 cM on the consen- sus 2005 map). This corresponds to the genomic region around 51.4 Mb (http://www.ensembl.org/ Gallus_gallus/index.html, assembly WASHUC2) harbouring the asynchronously replicating mam- malian imprinted gene orthologues DLK1 (delta- like homolog 1, cell surface transmembrane glyc- oprotein) and DIO3 (type 3 deiodinase, thyroid hormone inactivating enzyme) (Dunzinger et al. 2005). These genes could be studied for mono-al- lelic expression as candidates for the parent-of-or- igin effect. Zhou et al. (2006a) found a Mendelian QTL for body weight partly overlapping with our result. They have also detected leg muscle (drum- stick) and liver weight QTL at the same location. Jacobsson et al. (2005), Sewalem et al. (2002) and Jennen et al. (2004) have found QTL affect- ing early body weight in the same area on GGA13 that was identified in this study to harbour paternal- A G R I C U L T U R A L A N D F O O D S C I E N C E Honkatukia, M. et al. Chromosome regions affecting body weight in egg layers 184 A G R I C U L T U R A L A N D F O O D S C I E N C E Vol. 16 (2007): 177-187 185 ly expressed QTL for body weight. QTL affecting muscle growth (drumstick, heart, thigh) have been found within the same area (Ikeobi et al. 2002, Na- varro et al. 2005). No imprinted gene orthologues or asynchronously replicating genes have been found on this chromosome. In conclusion, our QTL findings are in good agreement with the results of previous studies from different mapping populations, confirming espe- cially the important and common QTL regions on chromosomes 1 and 4. These findings suggest that these regions include very important growth genes that may show pure Mendelian inheritance (chromosome 4) or both Mendelian inheritance and parent-of-origin expression. The fact that these re- gions are repeatedly detected as major QTL in var- ious types of populations/crosses indicates that pol- ymorphism is retained at these loci for some rea- son across poultry species and breeds. The results elucidate the most important chro- mosome regions affecting growth and fat deposi- tion in poultry in general and may add to the under- standing of such loci among domestic animals. Our results underline the possible involvement of par- ent-of-origin effects in the reciprocal differences in hybrid performance and give ground for further studies on imprinting-like mechanisms in poultry in specific QTL regions. References Abasht, B., Dekkers, J.C. & Lamont, S.J. 2006. Review of quantitative trait loci identified in the chicken. Poultry Science 85: 2079–2096. Blom, J. & Lilja, C. 2005. A comparative study of embry- onic development of some bird species with different patterns of postnatal growth. Zoology (Jena, Germa- ny) 108: 81–95. Churchill, G.A. & Doerge, R.W. 1994. Empirical thresh- old values for quantitative trait mapping. Genetics 138: 963–971. de Koning, D.J., Bovenhuis, H. & van Arendonk, J.A. 2002. On the detection of imprinted quantitative trait loci in ex- perimental crosses of outbred species. Genetics 161: 931–938. de Koning, D.J., Rattink, A.P., Harlizius, B., van Aren- donk, J.A., Brascamp, E.W. & Groenen, M.A. 2000. Ge- nome-wide scan for body composition in pigs reveals important role of imprinting. Proceedings of the Nation- al Academy of Sciences of the United States of Ameri- ca 97: 7947–7950. Dunzinger, U., Nanda, I., Schmid, M., Haaf, T. & Zech- ner, U. 2005. Chicken orthologues of mammalian im- printed genes are clustered on macrochromosomes and replicate asynchronously. Trends in Genetics : TIG 21: 488–492. Haley, C.S., Knott, S.A. & Elsen, J.M. 1994. Mapping quan- titative trait loci in crosses between outbred lines using least squares. Genetics 136: 1195–1207. Hansen, C., Yi, N., Zhang, Y.M., Xu, S., Gavora, J. & Cheng, H.H. 2005. Identification of QTL for production traits in chickens. Animal Biotechnology 16: 67–79. Hocking, P.M. 2005. Review on QTL mapping results in chickens. World’s Poultry Science Journal 61: 215– 226. Ikeobi, C.O., Woolliams, J.A., Morrice, D.R., Law, A., Wind- sor, D., Burt, D.W. & Hocking, P.M. 2002. Quantitative trait loci affecting fatness in the chicken. Animal Genet- ics 33: 428–435. Jacobsson, L., Park, H.B., Wahlberg, P., Fredriksson, R., Perez-Enciso, M., Siegel, P.B. & Andersson, L. 2005. Many QTLs with minor additive effects are associated with a large difference in growth between two selection lines in chickens. Genetical Research 86: 115–125. Jennen, D.G., Vereijken, A.L., Bovenhuis, H., Crooij- mans, R.M., van der Poel, J.J. & Groenen, M.A. 2005. Confirmation of quantitative trait loci affecting fatness in chickens. Genetics, Selection, Evolution.: GSE 37: 215–228. Jennen, D.G., Vereijken, A.L., Bovenhuis, H., Crooijmans, R.P., Veenendaal, A., van der Poel, J.J. & Groenen, M.A. 2004. Detection and localization of quantitative trait loci affecting fatness in broilers. Poultry Science 83: 295–301. Jennen, D.G.J. 2004. Chicken fatness: From QTL to can- didate gene. Thesis Wageningen University, The Neth- erlands. 176 p. Kerje, S., Carlborg, O., Jacobsson, L., Schutz, K., Hart- mann, C., Jensen, P. & Andersson, L. 2003. The twofold difference in adult size between the red junglefowl and White Leghorn chickens is largely explained by a limited number of QTLs. Animal Genetics 34: 264–274. Knott, S.A., Marklund, L., Haley, C.S., Andersson, K., Wil- liam, D., Ellegren, H., Fredholm, M., Hansson, I., Hoy- heim, B., Lundström, K., Moller, M., & Andersson, L. 1998. Multiple marker mapping of quantitative trait loci in a cross between outbred Wild Boar and Large White pigs. Genetics 149: 1069–1080. Lander, E. & Kruglyak, L. 1995. Genetic dissection of com- plex traits: guidelines for interpreting and reporting link- age results. Nature Genetics 11: 241–247. Liang, H. & Ward, W.F. 2006. PGC-1alpha: a key regula- tor of energy metabolism. Advances in Physiology Ed- ucation 30: 145–151. Lilja, C. 1983. A comparative study of postnatal growth and organ development in some species of birds. Growth 47: 317–339. McElroy, J.P., Kim, J.J., Harry, D.E., Brown, S.R., Dekkers, J.C. & Lamont, S.J. 2006. Identification of trait loci af- fecting white meat percentage and other growth and carcass traits in commercial broiler chickens. Poultry A G R I C U L T U R A L A N D F O O D S C I E N C E Honkatukia, M. et al. Chromosome regions affecting body weight in egg layers 186 A G R I C U L T U R A L A N D F O O D S C I E N C E Vol. 16 (2007): 177-187 187 Science 85: 593–605. Minvielle, F., Kayang, B.B., Inoue-Murayama, M., Miwa, M., Vignal, A., Gourichon, D., Neau, A., Monvoisin, J.L. & Ito, S. 2005. Microsatellite mapping of QTL affect- ing growth, feed consumption, egg production, tonic immobility and body temperature of Japanese quail. BMC Genomics 6: 87. Navarro, P., Visscher, P.M., Knott, S.A., Burt, D.W., Hock- ing, P.M. & Haley, C.S. 2005. Mapping of quantita- tive trait loci affecting organ weights and blood vari- ables in a broiler layer cross. British Poultry Science 46: 430–442. Nicholls, R.D. & Knepper, J.L. 2001. Genome organiza- tion, function, and imprinting in Prader-Willi and Angel- man syndromes. Annual Review of Genomics and Hu- man Genetics 2: 153–175. Park, H.B., Jacobsson, L., Wahlberg, P., Siegel, P.B. & Andersson, L. 2006. QTL analysis of body composition and metabolic traits in an intercross between chicken lines divergently selected for growth. Physiological Ge- nomics 25: 216–223. Sewalem, A., Morrice, D.M., Law, A., Windsor, D., Ha- ley, C.S., Ikeobi, C.O., Burt, D.W. & Hocking, P.M. 2002. Mapping of quantitative trait loci for body weight at three, six, and nine weeks of age in a broiler layer cross. Poultry Science 81: 1775–1781. Siwek, M., Cornelissen, S.J., Buitenhuis, A.J., Nieuwland, M.G., Bovenhuis, H., Crooijmans, R.P., Groenen, M.A., Parmentier, H.K. & van der Poel, J.J. 2004. Quantitative trait loci for body weight in layers differ from quantita- tive trait loci specific for antibody responses to sheep red blood cells. Poultry Science 83: 853–859. Tatsuda, K. & Fujinaka, K. 2001. Genetic mapping of the QTL affecting body weight in chickens using a F2 fam- ily. British Poultry Science 42: 333–337. Tuiskula-Haavisto, M., de Koning, D.J., Honkatukia, M., Schulman, N.F., Mäki-Tanila, A. & Vilkki, J. 2004. Quan- titative trait loci with parent-of-origin effects in chicken. Genetical Research 84: 57–66. Tuiskula-Haavisto, M., Honkatukia, M., Vilkki, J., de Ko- ning, D.J., Schulman, N.F. & Maki-Tanila, A. 2002. Mapping of quantitative trait loci affecting quality and production traits in egg layers. Poultry Science 81: 919–927. va n K a a m , J . B ., G r o e n e n , M . A ., B ove n h u i s , H ., Veenendaal, A., Vereijken, A.L. & van Arendonk, J.A. 1999. Whole genome scan in chickens for quantitative trait loci affecting growth and feed efficiency. Poultry Science 78: 15–23. Wright, D., Kerje, S., Lundstrom, K., Babol, J., Schutz, K., Jensen, P. & Andersson, L. 2006. Quantitative trait loci analysis of egg and meat production traits in a red junglefowl x White Leghorn cross. Animal Genetics 37: 529–534. Wu, G.Q., Deng, X.M., Li, J.Y., Li, N. & Yang, N. 2006. A po- tential molecular marker for selection against abdominal fatness in chickens. Poultry Science 85: 1896–1899. Zhou, H., Deeb, N., Evock-Clover, C.M., Ashwell, C.M. & Lamont, S.J. 2006a. Genome-wide linkage analysis to identify chromosomal regions affecting phenotypic traits in the chicken. I. Growth and average daily gain. Poultry Science 85: 1700–1711. Zhou, H., Deeb, N., Evock-Clover, C.M., Ashwell, C.M. & Lamont, S.J. 2006b. Genome-wide linkage analy- sis to identify chromosomal regions affecting pheno- typic traits in the chicken. II. Body composition. Poult- ry Science 85: 1712–1721. A G R I C U L T U R A L A N D F O O D S C I E N C E Honkatukia, M. et al. Chromosome regions affecting body weight in egg layers 186 A G R I C U L T U R A L A N D F O O D S C I E N C E Vol. 16 (2007): 177-187 187 SELOSTUS Munijakanojen painoon vaikuttavat kromosomialueet Mervi Honkatukia, Maria Tuiskula-Haavisto ja Johanna Vilkki MTT Biotekniikka- ja elintarviketutkimus Aiemmassa koko genomin kattavassa tuotantogeenien kartoituksessa on paikannettu kanan perimästä alueita, jotka vaikuttavat kananmunan laatuun ja munantuotan- non määrään. Tätä tutkimusta varten risteytettiin resip- rookkisesti eli vastavuoroisesti kaksi erilaista munija- kanalinjaa. Koska alkuperäiset kanalinjat poikkesivat toisistaan muun muassa kokonsa puolesta, pystyttiin näin paikantamaan kanan aikuispainoon ja syöntiin vaikuttavia tilastollisesti merkitseviä kromosomialueita. Seuraavassa vaiheessa tutkimusaineistoon sovellettiin tilastollisia menetelmiä, joiden avulla oli mahdollista havaita niin sanottu parent-of-origin-vaikutus. Parent- of-origin-vaikutuksella tarkoitetaan sitä, että geenin alleelilla on erilainen vaikutus sen mukaan, kummalta vanhemmalta se on peritty. Nämä vaikutukset huomioi- malla löydettiin uusia syöntikykyyn ja painoon vaikut- tavia kromosomialueita. Aineistoa analysoitiin myös kolmen uuden ominaisuuden kannalta, huomioimalla kanan paino 16:n, 20:n ja 24 viikon iässä. Analyysin tuloksena löytyi uusia, eri ikäkausina painoon vaikut- tavia alueita kromosomeista 1, 4, 5, 6 ja 13. Tulokset tukevat aiempia tutkimuksia ja korostavat tiettyjen kromosomialueiden merkitystä siipikarjan kasvulle ja painon kehitykselle. Chromosome regions affecting body weight in egg layers Introduction Material and methods Results Discussion References SELOSTUS