Quantitative trait loci segregating in crosses between New Hampshire and White Leghorn chicken lines: I. egg production traits

Transcription

1 doi: /j x Quantitative trait loci segregating in crosses between New Hampshire and White Leghorn chicken lines: I. egg production traits Z. S. Goraga, M. K. Nassar and G. A. Brockmann Department for Crop and Animal Sciences, Humboldt Universität zu Berlin, Invalidenstraße 42, D Berlin, Germany Summary A genome scan was performed to detect chromosomal regions that affect egg production traits in reciprocal crosses between two genetically and phenotypically extreme chicken lines: the partially inbred line New Hampshire (NHI) and the inbred line White Leghorn (WL77). The NHI line had been selected for high growth and WL77 for low egg weight before inbreeding. The result showed a highly significant region on chromosome 4 with multiple QTL for egg production traits between 19.2 and 82.1 Mb. This QTL region explained 4.3 and 16.1% of the phenotypic variance for number of eggs and egg weight in the F 2 population, respectively. The egg weight QTL effects are dependent on the direction of the cross. In addition, genome-wide suggestive QTL for egg weight were found on chromosomes 1, 5, and 9, and for number of eggs on chromosomes 5 and 7. A genome-wide significant QTL affecting age at first egg was mapped on chromosome 1. The difference between the parental lines and the highly significant QTL effects on chromosome 4 will further support fine mapping and candidate gene identification for egg production traits in chicken. Keywords egg production trait, inbred chicken line, quantitative trait loci. Introduction Quantitative traits such as age at first egg, number of eggs and egg weight determine the economic gain in egg production. Background knowledge of genes contributing to egg production can be used to identify variability in these genes in chicken production lines to improve breeding efficiency. QTL detection is an important step in identifying genes that contribute to genetic variability. QTL for egg production traits were detected on chromosomes 1, 2, 3, 4, 5, 7, 8, 9, 11, 13, 17, 27 and Z in experimental chicken populations derived from crosses between layers and broilers, in particular between White Leghorn and either Rhode Island Red (Tuiskula-Haavisto et al. 2002, 2004; Honkatukia et al. 2005; Sasaki et al. 2004), Broiler (Schreiweis et al. 2005), Red Junglefowl (Kerje et al. 2003) Address for correspondence G. A. Brockmann, Breeding Biology and Molecular Genetics, Department for Crop and Animal Sciences, Faculty of Agriculture and Horticulture, Humboldt Universität zu Berlin, Invalidenstraße 42, D Berlin, Germany. gudrun.brockmann@agrar.hu-berlin.de Accepted for publication 14 March 2011 or Cornish breeds (Hansen et al. 2005). Phenotypic variances explained by QTL range from 3 to 17%. In each cross, a different set of QTL was detected, which demonstrates the complex and polygenetic nature of the genetic determination of laying performance. To further improve our understanding of genetic determinants of egg production, it is desirable to map additional loci that could contribute to the phenotypic variation between and within breeds. Crosses between extreme lines for egg-laying performance could contribute to the pinpointing of the location of genes with major effects, which can in turn facilitate the fine mapping and identification of the causative gene or mutations. Here, we report results of a reciprocal cross-breed experiment between two genetically extreme chicken lines: the partially inbred line New Hampshire (NHI) of dual purpose type and the inbred line White Leghorn (WL77), which had been selected for low egg weight before inbreeding (Goraga et al. 2010). NHI hens reached sexual maturity 9 days earlier and had 35% increase in egg production rate over WL77 hens. Eggs laid by NHI hens were on average 6 g heavier than those of WL77. The aim of the study was to map genomic regions influencing age at first egg, number of eggs, egg weight and egg production rate, as a first step for the identification of causative genes. 183

2 184 Goraga et al. Materials and methods Chicken lines The study was performed with two parental lines, New Hampshire (NHI) and White Leghorn (WL77). Previously, the history of the two lines as well as husbandry and feeding conditions were described in detail (Goraga et al. 2010). In brief, the NHI line was selected for high growth rate until 20 weeks, and WL77 was selected for low egg weight. Afterwards, the lines were inbred. The inbreeding levels in NHI and WL77 lines were 86% and close to 100% after brother sister mating for six and more than 40 generations, respectively. Pedigree structure Reciprocal crosses between the lines NHI and WL77 were generated. In the cross (NHI WL77), one male of the strain NHI was initially mated with two WL77 females. Subsequently, 24 F 1 chickens (two males and 22 females) were intercrossed to generate 276 F 2 chickens (127 males and 149 females). In the reciprocal cross (WL77 NHI), one WL77 male was mated with three NHI females, and 28 F 1 chickens (three males and 25 females) were intercrossed to generate 303 F 2 chickens (151 males and 152 females). Of 301 F 2 hens, 295 had full phenotypic records and were used for this QTL study (Fig. S1). Phenotypes Individual data on age at first egg (AFE), number of eggs (EN), egg weight (EW) and body weights (BW) were recorded. Eggs were collected every day from the beginning of egg-laying to 60 weeks of age. For the determination of egg weights, two eggs of every hen were weighed every 4 weeks until the end of the experimental period. Egg weights and number of eggs were analysed separately for the early (EW18 40, EN18 40), late (EW41 60, EN41 60) and whole production period (EW18 60, EN18 60). Egg production rate between days 169 and 280 was calculated as the number of eggs divided by the number of days (Sasaki et al. 2004). Body weights of hens were measured at hatch, 5, 10, 15, 20, 24, 32 and 56 weeks of age. Statistical analyses PearsonÕs correlation coefficients between traits were estimated using the PROC CORR procedure of SAS, Version 9. 2 (SAS Institute 2008). The phenotypic data were checked for normal distribution using the PROC UNIVARIATE procedure. Number of eggs and egg production rate were transformed by squaring to obtain normal distribution. Age at first egg was transformed into inverse square root. Family, hatch and cross effects on phenotypes were detected using the GLM procedure and thus used as a fixed effect in the model for linkage analysis. A Tukey Kramer test was used to test significant differences between genotype classes at marker positions that are located next to QTL peaks. Heritabilities of traits were estimated between F 1 and F 2 hens based on both sire and dam variance components (Falconer & Mackay 1996). The variance components were estimated using the restricted maximum-likelihood method PROC VARCOMP in SAS. Genotypes Genotype information was generated for all parents, F 1 and F 2 chickens. Two hundred and sixteen microsatellite markers were selected from the chicken genetic consensus map ( based on their chromosomal location and polymorphic information content to cover the entire genome with linkage groups (Fig. S2). To fill gaps on chromosome 4, two SNPs (rs and rs ) were genotyped. In one cross (NHI WL77), 109 markers were fully informative and had alternative alleles between NHI and WL77 parents; 13 markers were partially informative, sharing one common allele between parental lines. In another cross (WL77 NHI), 103 markers were fully and 19 partially informative. Marker MCW0249 was partially informative in one cross (NHI WL77) and was not informative in another cross (WL77 NHI). Marker MCW0230 was not informative in one cross (NHI WL77). Among the 122 markers which were informative between the parental lines, 93 markers had two alleles, 28 had three alleles and one marker (ROS0018) had four alleles. Construction of linkage map The program CRIMAP (Green et al. 1990) was used to build a pedigree-specific genetic map. All informative markers were assigned to 25 linkage groups. The first marker on every chromosome was placed on 0 cm. The total map length in our chicken population was 2335 cm (Kosambi). The average marker distance was 26.8 cm. The markers had on average a polymorphism information content of The pedigree-specific marker map (Fig. S2) was consistent with the marker order and distances in the consensus linkage map (Groenen et al. 2000), except for the positions of markers LEI0138 and ADL0199. In our population, marker LEI0138 was mapped to chromosome 1 between markers MCW0058 and LEI0101, which is in agreement with the marker position in the East Lansing Population (Levin et al. 1994). The marker order we obtained for microsatellites MCW0330, ADL0202 and ADL0199 on chromosome 17 was not in agreement with the consensus linkage map, where it is MCW0330, ADL0199 and ADL0202.

3 Quantitative trait loci for egg traits 185 QTL analysis The program QTL express ( Seaton et al. 2002) was used for QTL mapping. Sex-averaged genetic maps (Kosambi) were used for the QTL scan. F- statistic thresholds were obtained using chromosome- and genome-wide permutation tests (n = 1000) (Lander & Kruglyak 1995). We used the genome-wide 5% (F = 8.52) and 1% (F = 10.43) thresholds for reporting significant and highly significant QTLs, respectively. The 5% chromosomewise thresholds were taken as suggestive level of significance, defined as one expected false positive result per trait in a whole genome scan. Using bootstrap analysis, 95% confidence intervals of the QTL positions were determined (n = 1000) (Visscher et al. 1996). Family and hatch were included in all models as fixed factors. In the analysis of both crosses together, cross was included as an additional fixed effect in the model. QTL by cross-interaction was tested using a second model including direction of cross as interactive covariate. In a similar manner, we tested the effect of family within a cross. QTL by cross- or family interaction were considered significant if the F-value difference at the QTL peak position between the model with and without cross or family as covariate was >4.6; an F-value of 4.6 corresponds to a LOD value of 2.0 in our F 2 chicken population, as determined by the formula described previously (Neuschl 2009), and corresponds to significant interaction at P < 0.05 (Li et al. 2006). A test for two QTL in a linkage group was performed if the QTL effects covered a large chromosomal region. The two QTL models were considered significantly better than the one QTL model if F > 9.2. The QTL positions are given as cm distance of the highest F-value from the first marker on the chromosome at 0 cm. The positions of the closest markers are used to translate genetic positions into physical positions according to the sequence information of the ENSEMBL53 WASHUC2 Chicken Assembly. Body weight at 32 weeks of age was highly correlated (0.28 r 0.55) (P < 0.001) with most egg production traits. Therefore, it was included as a covariate in additional analyses to test the relationship between egg production traits and body weight at different QTL positions. The phenotypic variance explained by a QTL was calculated as reduction of residual sum of squares in the full model, with QTL compared with the reduced model without QTL. Results Phenotypic characteristics of reciprocal crosses The performance of the NHI line for egg production rate, number of eggs (EN18 40, EN41 60, EN18 60) and egg weight (EW41 60, EW18 60) was significantly (P < 0.05) higher than of the WL77 line (Table 1). Means of egg number and weights in both F 1 and F 2 chickens shifted towards the respective values of the NHI parental line, which had the higher laying performance (Table 1, Fig. S3). The number of eggs in F 1 hens was particularly high and dominant over the parental phenotypes during the early production period (EN18 40), in both crosses. The mean egg weight of F 1 and F 2 hens also exceeded the average performances of their parents. F 1 hens Table 1 Means and standard errors of egg production traits in the parent, F 1 and F 2 hens. Parents F 1 F 2 Trait NHI n =26 WL77 n =15 NHI WL77 n =22 WL77 NHI n =25 NHI WL77 n = 149 WL77 NHI n = 146 AFE (days) 146 ± ± ± ± ± ± 1 EPR (%) 88 ± 2 65 ± 4* 93 ± 2 97 ± 1 76 ± 2 79 ± 1 EN18 60 (n) 204 ± ± 10* 214 ± ± 2* 177 ± ± 3* EN41 60 (n) 94 ± 3 64 ± 6* 93 ± 2 97 ± 1* 92 ± 2 95 ± 2 EN18 40 (n) 110 ± 3 77 ± 6* 121 ± ± 2 91 ± 2 94 ± 2 EW18 60 (g) 52 ± 1 46 ± 2* 56 ± ± 0.4* 54 ± ± 0.3* EW41 60 (g) 60 ± 1 50 ± 2* 61 ± ± 0.4* 58 ± ± 0.4* EW18 40 (g) 45 ± 1 42 ± 1 52 ± 1 50 ± 1* 50 ± ± 0.3 BW20 (g) 2123 ± ± 44* 1848 ± ± 23* 1760 ± ± 15* BW24 (g) 2342 ± ± 49* 1911 ± ± 25* 1980 ± ± 16* BW32 (g) 2567 ± ± 73* 2052 ± ± 29* 2128 ± ± 18* BW56 (g) 2827 ± ± 92* 2360 ± ± 38* 2338 ± ± 21* AFE, age at first egg; EPR, egg production rate; EN18 40, number of eggs from 18 to 40 weeks; EN41 60, number of eggs from 41 to 60 weeks; EN18 60, number of eggs from 18 to 60 weeks; EW18 40, egg weight from 18 to 40 weeks; EW41 60, egg weight from 41 to 60 weeks; EW18 60, egg weight from 18 to 60 weeks; BW20, body weight of hens at 20 weeks of age; BW24, body weight of hens at 24 weeks of age; BW32, body weight of hens at 32 weeks of age, BW56, body weight of hens at 56 weeks of age. * refers to significance at P < 0.05 either between the parental lines, the two F 1 crosses, or between the two F 2 crosses.

4 186 Goraga et al. had the first egg at a similar age (146 ± 2) to NHI hens (146 ± 2). In contrast, F 2 hens reached sexual maturity (164 ± 2) on average later in life than their parents (NHI: 146 ± 2), and even later than WL77 hens (155 ± 4). Comparing the reciprocal crosses, F 2 hens of the cross (WL77 NHI) with the parental female of the NHI line performed better than those of the cross (NHI WL77) for all traits, except for egg weights and body weights of hens (Table 1). F 1 and F 2 hens of the cross (NHI WL77) were heavier than their counterparts of the reciprocal cross. Their eggs were 1 3 g heavier, but they had less eggs during the 60 weeks of production. The heritability of egg production traits ranged from 0.02 to 0.42 in cross (NHI WL77) and in the reciprocal cross (WL77 NHI) (Table S1). In both crosses, egg weight had the highest heritability, ranging from 0.18 to Heritability estimates for egg number were higher in the cross (WL77 NHI). Correlation between traits in the F 2 population Age of first egg and egg number including egg production rate as well as egg number and egg weight were highly negatively correlated (Table S1). The body weight of hens was always positively correlated with egg weights (0.32 r 0.55). The highest correlation was found for body weight at 32 weeks with most traits. Therefore, body weight at 32 weeks was included as a covariate in the QTL analysis. The correlation between body weight of hens and either age at first egg or number of eggs differed between reciprocal crosses. The correlation between body weight of hens and age at first egg was positive (0.19 r 0.28) in the cross (NHI WL77) and negative (r = )0.38) in the reciprocal cross, while the relationship with number of eggs was in the opposite direction. QTL effects In the joint analysis of both crosses, a genome-wide highly significant QTL for egg weight (P < 0.01) was identified on chromosome 4 at 154 cm (76.4 Mb) (Table 2). The flanking markers of the QTL region are MCW0251 (19.2 Mb) and rs (82.1 Mb), covering a length of 62.9 Mb. A search for multiple QTL in the chromosome 4 region provided evidence for two QTL affecting egg weight, one QTL at 154 cm (76.4 Mb) (F = 24.04) and a second QTL at 93 cm (37.6 Mb) (F = 9.57). The two QTL model improved the one QTL model by an F-value difference of Body Table 2 QTL positions, significance levels and effects. Trait Chr. Position cm (Mb) 1 95% CI (cm) 2 Marker 3 F 4 DF 5 Additive (SE) 6 Dominance (SE) 6 % Var 7 AFE (103.9) LEI ** 4.55 )5.5 (1.92) 3.20 (2.71) 6.5 EW (51.9) LEI * (0.36) )0.47 (0.52) 5.9 EW (51.6) LEI * (0.35) )0.17 (0.52) 5.1 EW (50.6) LEI * (0.33) )1.10 (0.51) 5.6 EN (58) MCW * 0.37 )0.27 (4.2) (5.51) 4.3 EW (37.6) LEI ** (0.35) 1.99 (0.57) 7.1 EW (37.6) LEI * (0.36) 1.91 (0.59) 5.5 EW (37.6) LEI * (0.32) 1.51 (0.53) 4.9 EW (76.4) UMA *** (0.34) )0.46 (0.50) 16.1 EW (76.4) UMA *** (0.35) )0.68 (0.50) 12.3 EW (75.8) UMA *** (0.31) 0.36 (0.44) 12.3 BW (78.9) UMA *** (19.4) )13.4 (29.3) 15.9 EN (11.1) 1 94 ADL * (1.94) 7.28 (2.69) 4.2 EW (19.8) LEI * (0.43) )2.10 (0.6) 5.0 EW (17.4) MCW * (0.41) )1.8 (0.57) 4.3 EN (24.0) 2 27 MCW * 2.76 )6.7 (1.94) )3.5 (2.67) 4.6 EW (11.5) MCW * 3.74 )1.3 (0.48) 2.78 (0.89) 5.6 EW (11.1) MCW * 3.66 )1.4 (0.51) 2.94 (1.0) 5.3 Abbreviations are as for Table 1. NHI, New Hampshire. 1 most likely chromosomal location of QTL in cm (Mb). 2 The 95% confidence interval (CI) of QTL determined by bootstrap analysis. 3 Marker closest to the chromosomal position with the highest F-value. 4 Peak of the F-value curve. 5 Difference between the F-values of the standard model (model including fixed effects of hatch, family, cross) and cross-interaction model. DF-values 4.6 provide evidence for significant QTL by cross-interaction. 6 Additive and dominance effects and their standard errors (using untransformed data) are given for the NHI allele. 7 Phenotypic F 2 variance explained by the QTLs. Mb positions are according to the ENSEMBL53 WASHUC2 Chicken Assembly. *, ** and *** refer to genome-wide suggestive, significant, and highly significant QTLs, respectively.

5 Quantitative trait loci for egg traits 187 (a) (b) (c) (d) in the one QTL model for egg weight, the position of the highest peak of the egg weight QTL shifted from 154 cm (76.4 Mb) to 93 cm (37.6 Mb) (Fig. 1). The QTL at 93 cm (37.6 Mb) was genome-wide significant (P < 0.05) for the average egg weight during the laying period between 18 and 60 weeks. The directions and magnitudes of the two QTL effects were consistent in the reciprocal crosses (Fig. S4). The QTL at 93 cm (37.6 Mb) had dominance effects (1.51 d 1.99) on egg weights, while the genetic effect of the QTL at 154 cm (76.4 Mb) was additive (1.93 a 2.40) (Table 2). The effects were evident over the whole egg-laying period (Fig. S5). The phenotypic F 2 variance for egg weights in the early and late production periods explained by the QTL at 93 (37.6 Mb) and 154 cm (76.4 Mb) ranged from 4.9 to 7.1% and 12.3 to 16.1%, respectively. As expected, the favourable allele for higher egg weight at the two QTL positions was inherited from the superior line NHI (Fig. S4). In addition to the chromosome 4 effects, genome-wide suggestive QTL for egg weight were mapped on chromosomes 1 (66 70 cm), 5 (22 27 cm) and 9 (58 61 cm). These QTL explained % of the phenotypic F 2 variance of egg weight. A QTL for number of eggs (EN18 60) was identified on chromosome 4 at 125 cm (58 Mb). The confidence interval overlapped with the QTL regions for egg weight. The egg number QTL was highly significant in the cross (WL77 NHI), but could not be detected in the reciprocal cross. Additional genome-wide suggestive QTL affecting number of eggs were mapped to chromosome 5 at 3 cm (11.1 Mb) and 7 at 20 cm (24 Mb). The QTL affecting number of eggs on chromosome 7 had additive effect, while the QTL on chromosomes 4 and 5 had dominance effects (Table 2). A genome-wide significant QTL for age at first egg was mapped on chromosome 1 at 207 cm (103.9 Mb). The NHI QTL allele contributed to early age at first egg (a = )5.52) and explained 6.5% of the phenotypic F 2 variance (Table 2). Discussion Figure 1 F-value curves belonging to linkage analysis on chromosome 4. (a) One QTL model for EW18 60, (b) One QTL model for EW18 60 with body weight at 32 weeks as a covariate, (c) Absolute difference of F-values in the model with and without body weight as a covariate and (d) One QTL model for body weight at 32 weeks. The horizontal lines represent F-value thresholds at the genome-wide highly significant (dashed lines separated by dots), significant (dashed lines) and suggestive levels (dotted lines), respectively. weight at 32 weeks was also influenced by the chromosome 4 region. A highly significant QTL for body weight of hens (F = 26.7) was detected at 158 cm (78.9 Mb) (Fig. 1). When body weight at 32 weeks was included as a covariate The most interesting result of this study is the multiple QTL region on chromosome 4 between 19.2 and 82.1 Mb. At least two QTLs in this region at 37.6 and 76.4 Mb affected egg weight. The distal QTL at 76.4 Mb had pleiotropic effects on egg weight and body weight of the hens, suggesting that one gene or two closely linked genes affected both correlating traits. In addition, a QTL at 58 Mb affected the number of eggs. In our study, the WL77 allele was the low allele for egg weight, which was consistent with the selection for low egg weight in this line (Goraga et al. 2010). The identified chromosome 4 QTL position and direction of effects confirmed QTL that have been reported previously in crosses between layers and broilers. In crosses of White Leghorn and Rhode Island Red, QTLs for egg weight were

6 188 Goraga et al. repeatedly discovered in a region between 59.9 and 82.8 Mb, with alleles from the Rhode Island Red increasing egg weight (Tuiskula-Haavisto et al. 2002; Sasaki et al. 2004). Schreiweis et al. (2005) also reported a QTL for egg weight between 62.1 and 75.8 Mb in a cross between Broiler and White Leghorn; the favourable allele for egg weight came from the broiler strain. In a cross between Red Junglefowl and White Leghorn, a QTL for egg weight was identified on the same chromosome between 51.6 and 67.1 Mb (Kerje et al. 2003), with the increased weight allele inherited from the White Leghorn. Our study is the first to provide evidence for two QTL on chromosome 4 in a region of 39 Mb affecting egg weight. The central QTL at 37.6 Mb has not been reported in other crosses. While the distal QTL for egg weight is highly dependent on the body weight of the hens, the central QTL at 37.6 Mb is not significantly affected by body weight in our cross. However, in other crosses, QTL for body weight were also found in the central region around 37.6 Mb (Jacobsson et al. 2005; Zhou et al. 2006; Atzmon et al. 2008). The support interval of the identified QTL region on chromosome 4 between 19.2 and 82.1 Mb harbours over 668 genes (Ensembl genome browser: org/index.html). Among the many genes, there are several candidates that could contribute to reproduction traits and egg-laying performances. For example, the chicken CLOCK gene might affect egg-laying by regulating the circadian rhythm (Tuiskula-Haavisto et al. 2002). The gene hematopoietic prostaglandin-d synthase (HPGDS) has shown different expression levels between layers and broilers (Shiue et al. 2006). For a targeted selection of positional candidate genes, fine mapping of the chromosome 4 region is required. In addition to the QTL on chromosome 4, genome-wide suggestive QTL for egg weight were mapped in our study on chromosomes 1, 5 and 9. QTL on the same chromosomes have been reported in other crosses between layers and broilers (Tuiskula-Haavisto et al. 2002; Kerje et al. 2003; Sasaki et al. 2004), but the QTL positions on the chromosomes were different from those identified in our study. We found transgressive QTL alleles where the superior allele for number of eggs on chromosomes 4 (at 125 cm) and 7 (at 20 cm) and for egg weight on chromosome 9 (at cm) was inherited from the inferior line WL77. Such alleles are not uncommon. For example, Tuiskula-Haavisto et al. (2002) reported a low egg weight allele from a high egg weight line. Transgressive alleles may segregate in a population because of no or limited selection for the trait, drift, pleiotropic effects of the QTL allele, linkage to other traits that are under selection, as result of interaction between genes, or as modifier alleles (Abasht et al. 2006). Our study confirmed that chromosome 4 carries an interesting genomic region for egg production traits in diverse chicken populations. Moreover, our data provide evidence for several loci affecting the laying performance in a 62.9 Mb region on chromosome 4. A new QTL for egg weight was detected at 37.6 Mb. Because the effects of the chromosome 4 QTL are large, this region can be targeted for candidate gene identification and future searches for gene variations in production lines. The additional QTL effects on chromosomes other than chromosome 4 are in part novel findings, which contribute to our understanding of the complex inheritance pattern of the traits underlying egglaying performance. Acknowledgements This work was supported by grants from the DAAD (Z.S.G.) and Yousef Jameel Foundation (M.K.N.). References Abasht B., Dekkers J.C.M. & Lamont S.J. (2006) Review of quantitative trait loci identified in the chicken. Poultry Science 85, Atzmon G., Blum S., Feldman M., Cahaner A., Lavi U. & Hillel J. (2008) QTL detected in a multigenerational resource chicken population. Journal of Heredity 99, Falconer D.S. & Mackay T.F.C. (1996) Introduction to Quantitative Genetics, edn 4. Longmans Group, Essex, UK. 463 pp Goraga Z., Nassar M., Schramm G.-P. & Brockmann G.A. (2010) Phenotypic characterization of chicken inbred lines that differ extremely in growth, body composition and egg production traits. Archiv Tierzucht 53, Green P., Falls K. & Crook S. (1990) Documentation of CRIMAP, Version 2.4. Washington University School of Medicine, St. Louis. Groenen M.A.M., Cheng H.H., Bumstead N. et al. (2000) A consensus linkage map of the chicken genome. Genome Research 10, 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, Honkatukia M., Tuiskula-Haavisto M., Koning D.-J.D., Virta A., Mäki-Tanila A. & Vilkki J. (2005) A region on chicken chromosome 2 affects both egg white thinning and egg weight. Genetics, Selection, Evolution 37, Jacobsson L., Park H., Wahlberg P., Fredriksson R., Perez-Enciso M., Siegel P. & Andersson L. (2005) Many QTL with minor additive effects are associated with a large difference ingrowth between two selection lines in chickens. Genetical Research 86, Kerje S., Carlborg O., Jacobsson L., tz K.S., Hartmann 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, Lander E. & Kruglyak L. (1995) Genetic dissection of complex traits: guidelines for interpreting and reporting linkage results. Nature Genetics 11, Levin I., Santangelo L., Cheng H., Crittenden L.B. & Dodgson J.B. (1994) An autosomal genetic linkage map of the chicken. Journal of Heredity 85, Li R., Tsaih S.W., Shockley K., Stylianou I.M., Wergedal J., Paigen B. & Churchill G.A. (2006) Structural model analysis of multiple quantitative traits. PLoS Genetics 2, e114.

7 Quantitative trait loci for egg traits 189 Neuschl C. (2009) Analyses of body weight, body composition, and the fat distribution pattern in a reciprocal cross of Berlin Fat Mouse Inbred line 860 and C57BL/6NCrl. Ph.D. Dissertation. Humboldt University of Berlin, Germany, Sasaki O., Odawara S., Takahashi H. et al. (2004) Genetic mapping of quantitative trait loci affecting body weight, egg character and egg production in F 2 intercross chickens. International Society for Animal Genetics, Animal Genetics 35, Schreiweis M.A., Hester P.Y., Settar P. & Moody D.E. (2005) Identification of quantitative trait loci associated with egg quality, egg production, and body weight in an F 2 resource population of chickens. International Society for Animal Genetics, Animal Genetics 37, Seaton G., Haley C.S., Knott S.A., Kearsey M. & Visscher P.M. (2002) QTL Express: mapping quantitative trait loci in simple and complex pedigrees. Bioinformatics 18, Shiue Y.-L., Chen L.-R., Chen C.-F., Chen Y.-L., Ju J.-P., Chao C.-H., Lin Y.-P., Kuo Y.-M., Tang P.-C. & Lee Y.-P. (2006) Identification of transcripts related to high egg production in the chicken hypothalamus and pituitary gland. Theriogenology 66, Tuiskula-Haavisto M., Honkatukia M., Vilkki J., Koning D.-Jd., Schulman N.F. & Mäki- Tanila A. (2002) Mapping of quantitative trait loci affecting quality and production traits in egg layers. Poultry Science 81, Tuiskula-Haavisto M., Koning D.-J.D., Honkatukia M., Schulman N.F., Mäki-Tanila A. & Vilkki J. (2004) Quantitative trait loci with parent-of-origin effects in chicken. Genetics Research 84, Visscher P.M., Thompson R. & Haley C.S. (1996) Confidence intervals in QTL mapping by bootstrapping. Genetics 143, Zhou H., Deeb N., Evock-Clover C.M., Ashwell C.M. & Lamont S.J. (2006) Genome-wide linkage analysis to identify chromosomal regions affecting phenotypic traits in the chicken. I. growth and average daily gain. Poultry Science 85, Supporting Information Additional supporting information may be found in the online version of this article. Figure S1 Population structure describing the origin of F 1, and F 2 chickens in both crosses. Figure S2 Map of 121 microsatellite markers and two SNPs genotyped in the chicken population used for QTL mapping. Figure S3 Plots showing means and standard errors for parental lines (NHI, WL77), F 1, and F 2 hens. Figure S4 Effect plot (means and standard error) for egg weights between 18 and 60 weeks (EW18 60) at the two QTL positions on chromosome 4. Figure S5 Mean egg weights of the three genotype classes NHI/NHI (h symbol), WL77/WL77 (D symbol), and NHI/ WL77 (solid line) of markers ADL0246 (a) and UMA4.034 (b) at 37.6 and 76.4 Mb on chromosome 4, respectively, during the laying period (20 60 weeks). Table S1 PearsonÕs correlation coefficients among egg production traits and body weights and heritability estimates (diagonal) for egg production traits in the reciprocal F 2 populations. As a service to our authors and readers, this journal provides supporting information supplied by the authors. Such materials are peer-reviewed and may be re-organized for online delivery, but are not copy-edited or typeset. Technical support issues arising from supporting information (other than missing files) should be addressed to the authors.