Summary Three informative pig F2 families based on European Wild Boar (W), Meishan (M) and Pietrain (P) crosses have been used for genome‐wide linkage and quantitative trait loci (QTL) analysis. Altogether 129 microsatellites, 56 type I loci and 46 trait definitions (specific to growth, fattening, fat deposition, muscling, meat quality, stress resistance and body conformation) were included in the study. In the linkage maps of M × P, W × P and W × M families, average spacing of markers were 18.4, 19.7 and 18.8 cM, the numbers of informative meioses were 582, 534 and 625, and the total lengths of autosomes measured were 27.3, 26.0 and 26.2 Morgan units, respectively. Maternal maps were on average 1.3 times longer than paternal maps. QTLs contributing more than 3% of F2 phenotypic variance could be identified at p < 0.05 chromosome‐wide level. Differences in the numbers and positions of QTLs were observed between families. Genome‐wide significant QTL effects were mapped for growth and fattening traits on eight chromosomes (1, 2, 4, 13, 14, 17, 18 and X), for fat deposition traits on seven chromosomes (1, 2, 3, 4, 6, 7 and X), for muscling traits on 11 chromosomes (1, 2, 3, 4, 6, 7, 8, 12, 14, 15 and X), for meat quality and stress resistance traits on seven chromosomes (2, 3, 6, 13, 16, 18 and X), and QTLs for body‐conformation traits were detected on 14 chromosomes. Closely correlated traits showed similar QTL profiles within families. Major QTL effects for meat quality and stress resistance traits were found on SSC6 in the interval RYR1‐A1BG in the W × P and M × P families, and could be attributed to segregation of the RYR1 allele T derived from Pietrain, whereas no effect in the corresponding SSC6 interval was found in family W × M, where Wild Boar and Meishan both contributed the RYR1 allele C. QTL positions were mostly similar in two of the three families for body conformation traits and for growth, fattening, fat deposition and muscling traits, especially on SSC4 (interval SW1073‐NGFB). QTLs with large effects were also mapped on SSC7 in the major histocompatibility complex (MHC) (interval CYP21A2‐S0102) and affected body length, weight of head and many other traits. The identification of DNA variants in genes causative for the QTLs requires further fine mapping of QTL intervals and a positional cloning. However, for these subsequent steps, the genome‐wide QTL mapping in F2 families represents an essential starting point and is therefore significant for animal breeding.

Summary Linkage maps have been constructed for Sus scrofa chromosome 6 (SSC6) based on 17 markers, of which 10 were used in all three F2 families of Wild Boar (W), Meishan (M) and Pietrain (P) crosses. The coverage of the linkage maps of SSC6 was almost complete. All loci were ordered identically in the families, but two intervals (RYR1‐A1BG‐EAH, S0146‐S0003‐SW824) differed from published maps. Major quantitative trait loci (QTLs) for meat quality, stress resistance and carcass composition explaining up to 59% of F2 phenotypic variance have been mapped in the M × P and W × P families centred on the segregating RYR1 T and C alleles. In the W × M family, which was homozygous for the RYR1 C allele, no QTL effects for meat quality and stress‐resistance, but moderate effects for carcass composition have been observed in this region. These findings indicate further loci closely linked with the RYR1 or/and further alleles at the RYR1 locus, involved in the variation of carcass and growth traits.

Properdin (BF) was investigated as a candidate gene influencing litter size in a commercial pig cross population. The BF gene was chosen because of its integral role in influencing uterine epithelium growth and because several quantitative trait loci (QTL) with impact on reproductive traits have been detected near the centromere of porcine chromosome 7. A total of 123 F2 (Large White x Landrace) x Leicoma sows were genotyped using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. The sows were divided into two extreme performance groups, one with a high litter size (n = 61, > or = 14.3 piglets per litter) and the other with a low litter size (n = 62, < or = 11.3 piglets per litter). Although genotype and allele frequencies were uneven with 2.4% (AA), 16.3% (AB), 81.3% (BB) and 0.11 (A): 0.89 (B), the allele A was the unfavourable one, leading to less offspring. With regard to the level of significance at p < 0.05, the total number of born (TNB) and number of born alive (NBA) piglets were associated with BF genotypes. The genotype AA led to 10.55 TNB and 10.00 NBA, whereas the genotype BB led to 13.19 TNB and 12.11 NBA. The genotype AB was intermediate. In future, a systematic mating test is necessary in order to obtain more balanced genotype frequencies. Furthermore, it should be taken into consideration that the investigated polymorphism is located in an intronic region and the causative mutation is not clear yet.

Summary For Sus scrofa chromosome 13 (SSC13) eleven markers were genotyped to generate linkage and QTL maps in three F2 families based on Wild Boar (W), Meishan (M) and Pietrain (P) crosses. Results of linkage maps were similar and agreed with published maps. Quantitative trait loci (QTLs) for body weights, meat conductivity and fat deposition were mapped in the M × P family to the interval S0076–S0068 (40–80 cM) and near the locus SW38 (120–150 cM). QTLs for the same traits were observed in the W × M family in different intervals explaining up to 5.3% of the F2 phenotypic variance. No significant QTLs for the traits under investigation were found in the W × P family. The effects of QTL alleles were mostly dominant. In the M × P and W × M families alleles inherited from Meishan were generally associated with high values of live weights, food consumption and fat deposition and low values of meat conductivity.

Summary Linkage and QTL maps of Sus scrofa chromosome 9 (SSC9) were constructed using 16 markers, with 13 to 15 used in three F2 families based on Wild Boar (W), Meishan (M) and Pietrain (P) crosses. The LPR and SLN loci were integrated into the linkage map of SSC9 for the first time. Only a few quantitative trait loci (QTLs), explaining up to 5.1% of the F2 phenotypic variance, were identified on SSC9 with chromosome‐wide significant effects on growth and fattening in the W × P family and on weight of liver, growth and fat‐to‐meat ratio in the W × M family. No QTLs were found in the M × P family. Gene effects were mainly dominant in the W × P family. In the W × M family, Wild Boar QTL alleles for weight of liver were superior over Meishan alleles.