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A porcine genome linkage map composed of 194 microsatellite markers was constructed with a large-scale White Duroc x Erhualian resource population. The marker order on this linkage map was consistent with the USDA-MARC reference map except for two markers on SSC3, two markers on SSC13 and two markers on SSCX. The length of the sex-averaged map (2344.9 cM) was nearly the same as that of the USDA-MARC and NIAI map. Highly significant heterogeneity in recombination rates between sexes was observed. Except for SSC1 and SSC13, the female autosomes had higher average recombination rates than the male autosomes. Moreover, recombination rates in the pseudoautosomal region were greater in males than in females. These observations are consistent with those of previous reports. The recombination rates on each paternal and maternal chromosome of F(2) animals were calculated. Recombination rates were not significantly affected by the age (in days) or parity of the F(1) animals. However, recombination rates on paternal chromosomes were affected by the mating season of the F(1) animals. This could represent an effect of environmental temperature on spermatogenesis.

There is evidence that NR6A1 is a strong candidate for being a causal gene underlying vertebral number in pigs. The Licha Black is one of the leanest Chinese indigenous pig breeds, having an average vertebral number of 21.5. The introgression of Western germplasm into Licha Black, resulting in increased vertebral number, has been assumed but is not confirmed. This study detected allele frequencies of the NR6A1 causative mutation (c.575T>C) in 519 pigs from three Western and seven Chinese breeds including Licha Black, and evaluated the genetic variation in a 650-kb region containing NR6A1 in the 10 breeds. Allele T for increased vertebral number was fixed in Western breeds. In contrast, this allele was very rare in most of the Chinese native breeds. Notably, the T allele was present in the Licha Black at a rather higher frequency (0.585) and in the Laiwu at lower frequency (0.250). As expected, selection pressure has wiped out the genetic variability in the 650 kb region in Western breeds. Conversely, Chinese indigenous breeds showed a high degree of genetic variability in this region. However, the Licha Black displayed dramatically reduced heterozygosity at the loci proximal to the causative mutation. Moreover, a high proportion (45.9%) of Licha Black pigs and a small number (21%) of Laiwu pigs had the Western NR6A1 haplotype, and the two breeds showed closer relationships with Western commercial breeds than other Chinese breeds in the phylogenic tree. When the results are taken together, this study supports the assumption that the Western NR6A1 haplotypes were introduced into Licha Black and possibly Laiwu and are associated with increased vertebral number.