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In the livestock industry, meat color has become important because consumer acceptance is subject to the appearance of the product in the market-place. Our previous analyses of a whole genome QTL scan for various meat qualities using 2 F2 families from Japanese wild bar (known as a red meat) x Large White and from Duroc x Chinese Jinhua suggested that a meat color (heme content) QTL is located on SSC6. The objective, of this study was to fine-map this SSC6 meat color QTL and subsequently investigate positional candidate genes for polymorphisms that may cause changes in meat color. Therefore, we conducted interval mapping on SSC6 using an additional 9 gene markers through combined analyses of the 2 F2 families of Japanese wild boar x Large White (353 progeny) and Duroc x Chinese Jinhua (204 progeny). Comparative analysis with humans, mice, and cattle suggested that there were 10 functional genes in the region. Among these genes, we suggested that a novel pig gene encoding a nudix (nucleoside diphosphate linked moiety X)-type motif 7 (NUDT7, a member of the nudix hydrolases) is a strong candidate for the QTL because the mouse Nudt7 is reported to hydrolyze succinyl- CoA, a substrate of the reaction limiting the rate of heme biosynthesis. We therefore determined the pig NUDT7 gene sequence including the 5' promoter region and explored genetic polymorphisms between Japanese wild boar and Large White. We identified 116 polymorphisms within the NUDT7 CDS or in the 5' region. None of the AA substitutions were associated with the meat color QTL; however, 3 polymorphisms were found in putative transcription factor recognition sites. We then investigated the differential expression of NUDT7 in Japanese wild boar and Large White by'allele-specific quantitative real-time PCR. The expression level of the Large White type allele was greater than that of the Japanese wild-boar-type allele. Consequently, we speculated that the difference in meat color between Japanese wild boar and Large White is caused partly by differential expression of this candidate gene. Up- regulation of NUDT7 expression in muscle may reduce succinyl-CoA content and thus reduce the level of herne biosynthesis. [ABSTRACT FROM AUTHOR]

The objective of the research was to identify QTL affecting the number of vertebrae in swine, one of the major determining factors of growth and body composition. Previously, we reported a QTL for the number of vertebrae located on SSC 1qter (terminal band of the q arm of SSC 1) in an F2 family produced by crossing a Göttingen miniature male with two Meishan females. Eight other swine families were subsequently produced by crosses between different breeds of European, Asian, and miniature pigs. In these families, the QTL on SSC 1qter for the number of vertebrae was detected. Unlike the Asian alleles, all European alleles in this study had the effect of increasing the number of vertebrae by 0.44 to 0.69 and acted additively without dominance. The Göttingen miniature sire, for which we previously reported a smaller additive effect, seemed to be heterozygous at the QTL. In the present study, another QTL was found for the number of vertebrae on SSC7. This QTL was not fixed in the European pigs used as parents in our experimental families, and some of the European alleles increased the number of vertebrae. A half-sib analysis confirmed that this QTL was segregating in a commercial Large White population. Analysis in an F2 family in which the parental pigs were fixed for alternative alleles revealed that the effects of the QTL on SSC1 and on SSC7 were additive and similar in size. The two QTL acted independently without epistatic effects and explained an increase of more than two vertebrae. [ABSTRACT FROM AUTHOR]

Three generations of a swine family produced by crossing a Japanese wild boar and three Large White female pigs were used to map QTL for various production traits. Here we report the results of QTL analyses for skeletal muscle fiber composition and meat quality traits based on phenotypic data of 353 F2 animals and genotypic data of 225 markers covering almost the entire pig genome for all of the F2 animals as well as their F1 parents and F0 grandparents. The results of a genome scan using least squares regression interval mapping provided evidence that QTL (<1% genome-wise error rate) affected the proportion of the number of type IIA muscle fibers on SSC2, the number of type IIB on SSC14, the relative area (RA) of type I on SSCX, the BA of type IIA on SSC6, the RA of type IIB on SSC6 and SSC 14, the Minolta a* values of loin On SSC4 and SSC6, the Minolta b* value of loin on SSC15, and the hematin content of the LM on SSC6. Quantitative trait loci (<5% genome-wise error rate) were found for the number of type I on SSC1, SSCI4, and SSCX, for the number of type IIA on SSCI4, for the number of type JIB on SSC2, for the RA of type hA on SSC2, for the Minolta b* value of loin on SSC3, for the pH of loin on SSC15, and for the i.m. fat content on SSC15. Twenty-four QTL were detected for 11 traits at the 5% genome-wise level. Some traits were associated with each other, so the 24 QTL were located on 11 genomic regions. In five QTL located on SSC2, SSCG, and SSC14, each wild boar allele had the effect of increasing types I and IJA muscle fibers and decreasing type IIB muscle fibers. These effects are expected to improve meat quality. [ABSTRACT FROM AUTHOR]

A genome-wide scan for QTL affecting economically important traits in beef production was performed using an F2 resource family from a Japanese Black × Limousin cross, where 186 F2 animals were measured for growth, carcass, and meat-quality traits. All family members were genotyped for 313 informative microsatellite markers that spanned 2,382 cM of bovine autosomes. The centromeric region of BTA2 contained significant QTL (i.e., exceeding the genomewide 5% threshold) for 5 carcass grading traits [LM area, beef marbling standards (BMS) number, luster, quality grade, and firmness), 8 computer image analysis (CIA) traits [LM lean area, ratio of fat area (RFA) to LM area, LM area, RFA to musculus (M.) trapezius area, M. trapezius lean area, M. semispinalis lean area, RFA to M. semispinalis area, and RFA to M. semispinalis capitis area], and 5 meat quality traits (contents of CP, crude fat, moisture, C16:1, and C18:2 of LM). A significant QTL for withers height was detected at 80.3 cM on BTA5. We detected significant QTL for the C 14:0 content in backfat and C14:0 and C 14:1 content in intermuscular fat around the 62.3 to 71.0 cM region on BTA19 and for C14:0, C14:1, C18:1, and C16:0 content and ratio of total unsaturated fatty acid content to total SFA content in intramuscular fat at 2 different regions on BTA19 (41.1 cM for C14:1 and 62.3 cM for the other 4 traits). Overall, we identified 9 significant QTL regions controlling 27 traits with genomewide significance of 5%; of these, 22 traits exceeded the 1% genome-wide threshold. Some of the QTL affecting meat quality traits detected in this study might be the same QTL as previously reported. The QTL we identified need to be validated in commercial Japanese Black cattle populations. [ABSTRACT FROM AUTHOR]

Understanding of the genetic control of female reproductive performance in pigs would offer the opportunity to utilize natural variation and improve selective breeding programs through marker-assisted selection. The Chinese Meishan is one of the most prolific pig breeds known, farrowing 3 to 5 more viable piglets per litter than Western breeds. This difference in prolificacy is attributed to the Meishan's superior prenatal survival. Our study utilized a 3-generation resource population, in which the founder grandparental animals were purebred Meishan and Duroc pigs, in a genome scan for QTL. Grandparent, F1, and F2 animals were genotyped for 180 microsatellite markers. Reproductive traits, including number of corpora lutea (number of animals = 234), number of fetuses per animal (n = 226), number of teats (n = 801), and total number born (n = 288), were recorded for F2 females. Genome- wide significance level thresholds of 1, 5, and 10% were calculated using a permutation approach. We identified 9 QTL for 3 traits at a 10% genome-wise significance level. Parametric interval mapping analysis indicated evidence of a 1% genome-wise significant QTL for corpora lutea on SSC 3. Nonparametric interval mapping for number of teats found 4 significant QTL on chromosomes SSC3 (P < 0.01), SSC7 (P < 0.01), SSC8 (P < 0.01), and SSC12 (P < 0.05). Partial imprinting of a QTL affecting teat number (P < 0.10) was detected on SSC8. Using the likelihood-ratio test for a categorical trait, 2 QTL for pin nipples were detected on SSC2 and SSC16 (P < 0.01). Fine mapping of the QTL regions will be required for their application to introgression programs and gene cloning. [ABSTRACT FROM AUTHOR]