Figure 3

Detailed haplotype analysis in AY population and parent pigs of F ₂ families. Nine novel microsatellite markers (underlined) were developed from the sequences of BAC clones, CH242-92H3 and CH242-154M12. These markers were added to the haplotype analysis of the AY population. In this population, some of the genetic intervals between SJ7059 and SJ7001 had identical haplotypes, and two individuals are shown for each haplotype: 5901/L and 8502/L for allele types no. 1 to no. 6; 5910/L and 2904/L for allele types no. 8 to no. 11; 1606/L and 9404/R for allele types no. 15 to no. 17; and 2206/L and 5901/R for allele types no. 22 to no. 29. Numbering is the same as in Figure 3. Haplotype analysis was also performed in the parent pigs of the F₂ families of our previous study, in which the QTL types of the parent pigs had been determined (Lower part). Numbers in each marker column are the sizes of alleles as amplified DNA fragments (in bp). Red boxes indicate conserved regions detected in the 95% confidence interval for the number-increase (Q) allele in the AY population and in the parent pigs of the F₂ families. Markers common to the two conserved regions are indicated in red letters (i.e. SJ7121 and SJ7114). The QTL was likely to be located between the flanking markers (SJ7126 and SJ7099). Breeds are: W, Large White; L, Landrace; B, Berkshire; D, Duroc. Family AY is the Awa-York population and the others are F₂ families constructed with a Japanese wild boar and two Landrace females (LWb), a Landrace male and two Meishan females (ML), a Meishan male and a Landrace female (LM), a Large White male and a Meishan female (MW), a Large White male and a Jinhua female (JW), a Clawn miniature male and a Berkshire female (BC), a Duroc male and five Jinhua females (JD), and a Japanese wild boar and three Large White females (WWb).