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M A M Groenen

Publications and source records attributed to M A M Groenen.

At least 19 recordsLinked to original sources
PubMed2007

Variance component analysis of quantitative trait loci for pork carcass composition and meat quality on SSC4 and SSC11.

In a previous study, QTL for carcass composition and meat quality were identified in a commercial finisher cross. The main objective of the current study was to confirm and fine map the QTL on SSC4 and SSC11 by genotyping an increased number of individuals and markers and to analyze the data using a combined linkage and linkage disequilibrium analysis method. A modified version of the method excludes linkage disequilibrium information from the analysis, enabling the comparison of results based on linkage information only or results based on combined linkage and linkage disequilibrium information. Nine additional paternal half-sib families were genotyped for 18 markers, resulting in a total of 1,855 animals genotyped for 15 and 13 markers on SSC4 and SSC11, respectively. The QTL affecting meat color on SSC4 was confirmed, whereas the QTL affecting LM weight could not be confirmed. The combined linkage and linkage disequilibrium analysis resulted in the identification of new significant effects for 14 traits on the 2 chromosomes. Heritabilities of the QTL effects ranged from 1.8 to 13.2%. The analysis contributed to a more accurate positioning of QTL and further characterized their phenotypic effect. However, results showed that even greater marker densities are required to take full advantage of linkage disequilibrium information and to identify haplotypes associated with favorable QTL alleles.

Adipose Tissue↗
PubMed2006

Genetic diversity analysis using lowly polymorphic dominant markers: the example of AFLP in pigs.

DNA markers are commonly used for large-scale evaluation of genetic diversity in farm animals, as a component of the management of animal genetic resources. AFLP markers are useful for such studies as they can be generated relatively simply; however, challenges in analysis arise from their dominant scoring and the low level of polymorphism of some markers. This paper describes the results obtained with a set of AFLP markers in a study of 59 pig breeds. AFLP fingerprints were generated using four primer combinations (PC), yielding a total of 148 marker loci, and average harmonic mean of breed sample size was 37.3. The average proportion of monomorphic populations was 63% (range across loci: 3%-98%). The moment-based method of Hill and Weir (2004, Mol Ecol 13:895-908) was applied to estimate gene frequencies, gene diversity (F(ST)), and Reynolds genetic distances. A highly significant average F(ST) of 0.11 was estimated, together with highly significant PC effects on gene diversity. The variance of F(ST) across loci also significantly exceeded the variance expected under the hypothesis of AFLP neutrality, strongly suggesting the sensitivity of AFLP to selection or other forces. Moment estimates were compared to estimates derived from the square root estimation of gene frequency, as currently applied for dominant markers, and the biases incurred in the latter method were evaluated. The paper discusses the hypotheses underlying the moment estimations and various issues relating to the biallelic, dominant, and lowly polymorphic nature of this set of AFLP markers and to their use as compared to microsatellites for measuring genetic diversity.

Animals↗
PubMed2006

Genetic diversity within and between European pig breeds using microsatellite markers.

An important prerequisite for a conservation programme is a comprehensive description of genetic diversity. The aim of this study was to use anonymous genetic markers to assess the between- and the within-population components of genetic diversity for European pig breeds at the scale of the whole continent using microsatellites. Fifty-eight European pig breeds and lines were analysed including local breeds, national varieties of international breeds and commercial lines. A sample of the Chinese Meishan breed was also included. Eleven additional breeds from a previous project were added for some analyses. Approximately 50 individuals per breed were genotyped for a maximum of 50 microsatellite loci. Substantial within-breed variability was observed, with the average expected heterozygosity and observed number of alleles per locus being 0.56 [range 0.43-0.68] and 4.5 respectively. Genotypic frequencies departed from Hardy-Weinberg expectations (P < 0.01) in 15 European populations, with an excess of homozygotes in 12 of them. The European breeds were on average genetically very distinct, with a Wright F(ST) index value of 0.21. The Neighbour-Joining tree drawn from the Reynolds distances among the breeds showed that the national varieties of major breeds and the commercial lines were mostly clustered around their breeds of reference (Duroc, Hampshire, Landrace, Large White and Piétrain). In contrast, local breeds, with the exception of the Iberian breeds, exhibited a star-like topology. The results are discussed in the light of various forces, which may have driven the recent evolution of European pig breeds. This study has consequences for the interpretation of biodiversity results and will be of importance for future conservation programmes.

Alleles↗
PubMed2006

Genetic diversity in European pigs utilizing amplified fragment length polymorphism markers.

The use of DNA markers to evaluate genetic diversity is an important component of the management of animal genetic resources. The Food and Agriculture Organisation of the United Nations (FAO) has published a list of recommended microsatellite markers for such studies; however, other markers are potential alternatives. This paper describes results obtained with a set of amplified fragment length polymorphism (AFLP) markers as part of a genetic diversity study of European pig breeds that also utilized microsatellite markers. Data from 148 AFLP markers genotyped across samples from 58 European and one Chinese breed were analysed. The results were compared with previous analyses of data from 50 microsatellite markers genotyped on the same animals. The AFLP markers had an average within-breed heterozygosity of 0.124 but there was wide variation, with individual markers being monomorphic in 3-98% of the populations. The biallelic and dominant nature of AFLP markers creates a challenge for their use in genetic diversity studies as each individual marker contains limited information and AFLPs only provide indirect estimates of the allelic frequencies that are needed to estimate genetic distances. Nonetheless, AFLP marker-based characterization of genetic distances was consistent with expectations based on breed and regional distributions and produced a similar pattern to that obtained with microsatellites. Thus, data from AFLP markers can be combined with microsatellite data for measuring genetic diversity.

Alleles↗
PubMed2006

Identification of quantitative trait loci for carcass composition and pork quality traits in a commercial finishing cross.

A QTL study for carcass composition and meat quality traits was conducted on finisher pigs of a cross between a synthetic Piétrain/Large White boar line and a commercial sow cross. The mapping population comprised 715 individuals evaluated for a total of 30 traits related to growth and fatness (4 traits), carcass composition (11 traits), and meat quality (15 traits). Offspring of 8 sires (n = 715) were used for linkage analysis and genotyped for 73 microsatellite markers covering 14 chromosomal regions representing approximately 50% of the pig genome. The regions examined were selected based on previous studies suggesting the presence of QTL affecting carcass composition or meat quality traits. Thirty-two QTL exceeding the 5% chromosome-wise significance level were identified. Among these, 5 QTL affecting 5 different traits were significant at the 1% chromosome-wise level. The greatest significance levels were found for a QTL affecting loin weight on SSC11 and a QTL with an effect on the Japanese color scale score of the loin on SSC4. About one-third of the identified QTL were in agreement with QTL previously reported. Results showed that QTL affecting carcass composition and meat quality traits segregated within commercial lines. Use of these results for marker-assisted selection offers opportunities for improving pork quality by within-line selection.

Animals↗
PubMed2005

Chromosomal assignment of chicken clone contigs by extending the consensus linkage map.

The bacterial artificial clone-based physical map for chicken plays an important role in the integration of the consensus linkage map and the whole-genome shotgun sequence. It also provides a valuable resource for clone selection within applications such as fluorescent in situ hybridization and positional cloning. However, a substantial number of clone contigs have not yet been assigned to a chromosomal location or have an ambiguous chromosome assignment. In this study, 86 single nucleotide polymorphism markers derived from 86 clones were mapped on the genetic map. These markers added anchoring information for 56 clone contigs and 13 individual clones, covering a total of 57,145 clones.

Animals↗
PubMed2005

Genetic mapping of quantitative trait loci affecting susceptibility in chicken to develop pulmonary hypertension syndrome.

Pulmonary hypertension syndrome (PHS), also referred to as ascites syndrome, is a growth-related disorder of chickens frequently observed in fast-growing broilers with insufficient pulmonary vascular capacity at low temperature and/or at high altitude. A cross between two genetically different broiler dam lines that originated from the White Plymouth Rock breed was used to produce a three-generation population. This population was used for the detection and localization of quantitative trait loci (QTL) affecting PHS-related traits. Ten full-sib families consisting of 456 G2 birds were typed with 420 microsatellite markers covering 24 autosomal chromosomes. Phenotypic observations were collected on 4202 G3 birds and a full-sib across family regression interval mapping approach was used to identify QTL. There was statistical evidence for QTL on chicken chromosome 2 (GGA2), GGA4 and GGA6. Suggestive QTL were found on chromosomes 5, 8, 10, 27 and 28. The most significant QTL were located on GGA2 for right and total ventricular weight as percentage of body weight (%RV and %TV respectively). A related trait, the ratio of right ventricular weight as percentage to total ventricular weight (RATIO), reached the suggestive threshold on this chromosome. All three QTL effects identified on GGA2 had their maximum test statistic in the region flanked by markers MCW0185 and MCW0245 (335-421 cM).

Animals↗
PubMed2004

Identification of QTLs involved in open-field behavior in young and adult laying hens.

Line differences for open-field behavior in chickens have been observed, and it has been shown that this behavior has a genetic component. The aim of this study was to detect quantitative trait loci (QTL) involved in open-field behavior. For this purpose, open-field behavior was studied at 5 and 29 weeks of age in F(2) hens coming from an intercross between two commercial White Leghorn laying lines selected for egg production traits. Latencies, durations, and frequencies of general activity (sitting, standing, walking, and stepping), defecation, and vocalizations were recorded individually for each bird, and a factor score was calculated. All animals (F(0), F(1), and F(2)) were screened with 180 microsatellite markers. Regression interval mapping was applied using both a paternal half-sib analysis and a line-cross analysis method. For general activity at 5 weeks of age, a significant QTL was detected on GGA4 and a suggestive QTL on GGA2 under the line-cross model. For general activity at 29 weeks of age, a significant QTL was detected on GGA4 and two suggestive QTLs were detected on GGA1 and on GGA10, respectively, also using the line-cross analysis. The QTL on GGA4 at 5 weeks of age did not overlap with the QTL on GGA4 at 29 weeks of age. The current study indicated that open-field behavior in young chickens was regulated by QTL that differ from the QTL for open-field behavior in adult chickens.

Animals↗
PubMed2004

Detection and localization of quantitative trait loci affecting fatness in broilers.

A cross between 2 genetically different outcross broiler dam lines, originating from the White Plymouth Rock breed, was used to produce a large 3-generation broiler population. This population was used to detect and localize QTL affecting fatness in chicken. Twenty full-sib birds in generation 1 and 456 full-sib birds in generation 2 were typed for microsatellite markers, and phenotypic observations were collected for 3 groups of generation 3 birds (approximately 1,800 birds per group). Body weight, abdominal fat weight, and percentage abdominal fat was recorded at the age of 7, 9, and 10 wk. To study the presence of QTL, an across-family weighted regression interval mapping approach was used in a full-sib QTL analysis. Genotypes from 410 markers mapped on 25 chromosomes were available. For the 3 traits, 26 QTL were found for 18 regions on 12 chromosomes. Two genomewise significant QTL (P < 0.05) were detected, one for percentage abdominal fat at the age of 10 wk on chicken chromosome 1 at 241 cM (MCW0058 to MCW0101) with a test statistic of 2.75 and the other for BW at the age of 10 wk on chicken chromosome 13 at 9 cM (MCW0322 to MCW0110) with a test statistic of 2.77. Significance levels were obtained using the permutation test. Multiple suggestive QTL were found on chromosomes 1, 2, 4, 13, 15, and 18, whereas chromosomes 3, 7, 10, 11, 14, and 27 had a single suggestive QTL.

Abdomen↗
PubMed2004

Quantitative trait loci for body weight in layers differ from quantitative trait loci specific for antibody responses to sheep red blood cells.

Quantitative trait loci for BW at 4, 6, 8, 12, and 18 wk of age were detected in an experimental F2 cross of layers divergently selected for primary antibody response to SRBC. A negative phenotypic correlation between levels of antibody titers and BW, was reported earlier within founder lines. The entire experimental population was genotyped with 174 microsatellite markers equally distributed over the genome. Two genetic models were applied in the QTL analysis: a half-sib model and a line-cross model, both using the regression interval method. In the half-sib model, 3 QTL for BW at 4 wk of age on chromosomes GGA2, GGA3, and GGA9 were detected. For BW at 6 wk of age, 3 QTL were detected on GGA2, GGA3, and GGA6. For BW at 8 wk of age, a QTL was detected on GGA7, and for BW at 12 and 18 wk of age, a QTL was detected on GGAZ. With the line-cross analysis model, one QTL on GGA7 for BW at 4 wk of age was detected. Two QTL were detected on GGA3 and GGA7 for BW at 6 wk of age, and one on GGA3 was detected for BW for 8 and 12 wk of age. For BW at 18 wk of age, there were no QTL under the line-cross analysis model. The present data suggest that 1) a different set of genes affects the early and the late growth, and 2) genes selected to humoral immune responsiveness are different from genes underlying growth.

Aging↗
PubMed2004

A radiation hybrid map of chicken chromosome 15.

We have constructed a radiation hybrid (RH) map of chicken chromosome (GGA) 15. This map can be used as a resource to efficiently map genes to this chromosome. The map has been developed using a 6000 rad chicken-hamster whole-genome radiation hybrid panel (ChickRH6). In total, six microsatellite loci, 18 sequence tagged sites (STSs) from BAC end sequences and 11 genes were typed on the panel. The initial framework map comprised eight markers, and an additional 23 markers were then added to generate the final map. The total map length was 334 centiRay6000 (cR6000). The estimated retention frequency for the data set was 18%. Using an estimated physical length of 21 Mb, the ratio between cR6000 and physical distance over GGA15 was estimated to be 0.063 Mb/cR6000. The present map increases the marker density and the marker resolution on GGA15 and enables fast mapping of new chicken genes homologous to genes from human chromosomes 12 and 22.

Animals↗
PubMed2003

Detection of QTL for immune response to sheep red blood cells in laying hens.

The aim of this study is to detect quantitative trait loci (QTL) involved in the regulation of the primary and the secondary immune response to sheep red blood cells (SRBC) in a resource population using microsatellite DNA markers. The F2 resource population originates from a cross of two divergently selected lines for either high (H line) or low (L line) primary antibody response to SRBC. The F2 population consisted of six half-sib families, three families per each of reciprocal crosses. Total antibody titres to SRBC were determined by agglutination in serum from all birds. F2, F1 and F0 generations were genotyped for 170 microsatellite markers, using a whole-genome scan approach. The half-sib and the line-cross analyses were performed to determine QTL regions associated with regulation of the immune response. In the half-sib analysis, four QTL for SRBC primary response have been identified: on GGA3, GGA5, GGA16 and GGA23. No QTL was identified for SRBC secondary response under the half-sib model. In the line-cross analysis, three QTL were identified on GGA10, GGA16 and GGA27 for SRBC primary response and five QTL were identified on GGA6, GGA9, GGA15, GGA16 and GGA27 for SRBC secondary response. Subsequently, the family contribution of individual families to the QTL was analysed. The family with the largest contribution was genotyped with additional microsatellite markers in the QTL region on GGA5. The extended half-sib analysis with additional genotype information results in narrowing down the QTL region on GGA5.

Animals↗
PubMed2003

Development of a single nucleotide polymorphism map of porcine chromosome 2.

Single nucleotide polymorphism markers are developed on SSC2, predominantly on the p-arm. Several studies reported a quantitative trait loci (QTL) for backfat thickness in this region. Single nucleotide polymorphisms were identified by comparative re-sequencing of polymerase chain reaction (PCR) products from a panel of eight individuals. The panel consisted of five Large Whites (each from a different Dutch breeding company), a Meishan, a Pietrain and a Wild Boar. In total, 67 different PCR products were sequenced and 301 SNPs were identified in 32,429 bp of consensus sequence, an average of one SNP in every 108 bp. After correction for sample size, this polymorphism rate corresponds to a heterozygosity value of one SNP in every 357 bp. For 63% of the SNPs, there was variation among the five Large Whites, and these SNPs are relevant for linkage and association studies in commercial populations. Comparing the Whites with other breeds revealed higher variation rates with: (i) Meishan, 89%; (ii) Pietrain, 69%; (iii) Wild Boar, 70%. Because many of the experimental populations to identify QTL are based on crosses between these breeds, these SNPs are relevant for the fine mapping of the QTL identified within these crosses.

Animals↗
PubMed2003

Identification of quantitative trait loci for receiving pecks in young and adult laying hens.

Feather pecking (FP) is a major problem in cage and free-range housing systems. In free-range systems, FP is more difficult to control. It is not known why a victim is being pecked. It could be that a bird is genetically predisposed to be pecked. To study the genetics of FP behavior, a large F2 population of 630 hens was generated from a cross between two commercial laying lines differing in their propensity to feather peck. The traits measured at 6 and 30 wk of age were receiving gentle FP, receiving severe FP, and receiving aggressive pecking. In addition, receiving toe pecking (TP) was also measured at 30 wk of age. For receiving gentle FP at 6 wk of age, a significant QTL on GGA1 and three different suggestive QTL were identified on GGA2, GGA6, and GGA7, respectively. For receiving gentle FP at 30 wk of age, a suggestive QTL on GGA5 was detected. For receiving aggressive pecking, a suggestive QTL was detected on GGA3. For receiving TP, three suggestive QTL were detected on GGA1, GGA5, and GGA23, respectively. The different QTL detected for receiving gentle FP at different ages indicate that this trait is regulated by different genes in young and adult hens.

Aggression↗
PubMed2003

Detection of different quantitative trait loci for antibody responses to keyhole lympet hemocyanin and Mycobacterium butyricum in two unrelated populations of laying hens.

Quantitative trait loci involved in the primary antibody response to keyhole lympet hemocyanin (KLH) and Mycobacterium butyricum were detected in two independent populations of laying hens. The first population was an F2 cross (H/L) of lines divergently selected for either high or low primary antibody responses to SRBC, and the second population was an F2 cross between 2 commercial layer lines displaying differences in feather pecking behavior (FP). Both populations were typed with microsatellite markers widely distributed over the genome with similar intervals between markers. Titers of antibodies binding KLH and M. butyricum were measured for all individuals by ELISA. Two genetic models were applied to detect QTL involved in the humoral immune response: a half-sib model and a line-cross model, both using the regression interval method. In the half-sib analysis, 2 QTL (on GGA14 and GGA27) were detected for the antibody response to KLH for the H/L population, and 2 QTL (on GGA14 and GGA18) were detected for the FP population. Only 1 QTL was detected for M. butyricum on GGA14 in the FP population using the half-sib analysis model. Two QTL were detected for the FP population on GGA2 and GGA3 using the line-cross analysis model. A QTL for the primary antibody response to KLH detected on GGA14 was validated in both populations under the half-sib analysis model. The present data suggest differences in the genetic regulation of antibody responses to two different T-cell dependent antigens.

Aggression↗
PubMed2003

Mapping quantitative trait loci affecting feather pecking behavior and stress response in laying hens.

In the European Union, legislation concerning animal housing is becoming stricter because of animal welfare concerns. Feather pecking (FP) in large group housing systems is a major problem. It has been suggested that corticosterone (CORT) response to manual restraint as a measure for stress is associated with FP behavior. The aim of the current study was to identify QTL involved in FP behavior and stress response in laying hens. An F2 population of 630 hens was established from a cross between two commercial lines of laying hens differing in their propensity to feather peck. The behavioral traits, measured at 6 and 30 wk of age, were gentle FP, severe FP, and aggressive pecking. Toe pecking was measured at 30 wk of age and CORT response to manual restraint was measured at 32 wk. All animals were genotyped for 180 microsatellite markers. A QTL analysis was performed using a regression interval mapping method. At 6 wk of age, a suggestive QTL on GGA10 was detected for gentle FP. At 30 wk of age, suggestive QTL were detected on GGA1 and GGA2 for gentle FP. A significant QTL was detected on GGA2 for severe FP. At 32 wk of age, a suggestive QTL was detected on GGA18 for CORT response to manual restraint. In addition, a suggestive QTL was detected on GGA5 with possible maternal parent-of-origin effect for CORT response.

Aggression↗