Microsatellite diversity of the Nordic type of goats in relation to breed conservation: how relevant is pure ancestry?

In the last decades, several endangered breeds of livestock species have been re-established effectively. However, the successful revival of the Dutch and Danish Landrace goats involved crossing with exotic breeds and the ancestry of the current populations is therefore not clear. We have generated genotypes for 27 FAO-recommended microsatellites of these landraces and three phenotypically similar Nordic-type landraces and compared these breeds with central European, Mediterranean and south-west Asian goats. We found decreasing levels of genetic diversity with increasing distance from the south-west Asian domestication site with a south-east-to-north-west cline that is clearly steeper than the Mediterranean east-to-west cline. In terms of genetic diversity, the Dutch Landrace comes next to the isolated Icelandic breed, which has an extremely low diversity. The Norwegian coastal goat and the Finnish and Icelandic landraces are clearly related. It appears that by a combination of mixed origin and a population bottleneck, the Dutch and Danish Land-races are separated from the other breeds. However, the current Dutch and Danish populations with the multicoloured and long-horned appearance effectively substitute for the original breed, illustrating that for conservation of cultural heritage, the phenotype of a breed is more relevant than pure ancestry and the genetic diversity of the original breed. More in general, we propose that for conservation, the retention of genetic diversity of an original breed and of the visual phenotype by which the breed is recognized and defined needs to be considered separately.

Longitudinal analysis of residual feed intake and BW in mink using random regression with heterogeneous residual variance.

The aim of this study was to determine the genetic background of longitudinal residual feed intake (RFI) and BW gain in farmed mink using random regression methods considering heterogeneous residual variances. The individual BW was measured every 3 weeks from 63 to 210 days of age for 2139 male+female pairs of juvenile mink during the growing-furring period. Cumulative feed intake was calculated six times with 3-week intervals based on daily feed consumption between weighing's from 105 to 210 days of age. Genetic parameters for RFI and BW gain in males and females were obtained using univariate random regression with Legendre polynomials containing an animal genetic effect and permanent environmental effect of litter along with heterogeneous residual variances. Heritability estimates for RFI increased with age from 0.18 (0.03, posterior standard deviation (PSD)) at 105 days of age to 0.49 (0.03, PSD) and 0.46 (0.03, PSD) at 210 days of age in male and female mink, respectively. The heritability estimates for BW gain increased with age and had moderate to high range for males (0.33 (0.02, PSD) to 0.84 (0.02, PSD)) and females (0.35 (0.03, PSD) to 0.85 (0.02, PSD)). RFI estimates during the growing period (105 to 126 days of age) showed high positive genetic correlations with the pelting RFI (210 days of age) in male (0.86 to 0.97) and female (0.92 to 0.98). However, phenotypic correlations were lower from 0.47 to 0.76 in males and 0.61 to 0.75 in females. Furthermore, BW records in the growing period (63 to 126 days of age) had moderate (male: 0.39, female: 0.53) to high (male: 0.87, female: 0.94) genetic correlations with pelting BW (210 days of age). The result of current study showed that RFI and BW in mink are highly heritable, especially at the late furring period, suggesting potential for large genetic gains for these traits. The genetic correlations suggested that substantial genetic gain can be obtained by only considering the RFI estimate and BW at pelting, however, lower genetic correlations than unity indicate that extra genetic gain can be obtained by including estimates of these traits during the growing period. This study suggests random regression methods are suitable for analysing feed efficiency and BW gain; and genetic selection for RFI in mink is promising.

Identifying QTL and genetic correlations between fur quality traits in mink (Neovison vison).

Mapping of QTL affecting fur quality traits (guard hair length, guard hair thickness, density of wool, surface of the fur and quality) and skin length was performed in a three-generation mink population (F2 design). In the parental generation, Nordic Brown mink were crossed reciprocally with American Black short nap mink. In all, 1082 mink encompassing three generations were used for the analyses. The mink were genotyped for 104 microsatellites covering all 14 autosomes. The QTL analyses were performed by least-square regression implemented in gridqtl software. Genetic and phenotypic correlations and heritabilities were estimated using the average information-restricted maximum-likelihood method. Evidence was found for QTL affecting fur quality traits on nine autosomes. QTL were detected for guard hair thickness on chromosomes 1, 2, 3, 6 and 13; for guard hair length on chromosomes 2, 3 and 6; for wool density on chromosomes 6 and 13; for surface on chromosomes 7, 12 and 13; for quality on chromosomes 6, 7, 11 and 13; and for skin length on chromosomes 7 and 9. Proximity of locations of QTL for guard hair length, guard hair thickness and for wool density and quality suggests that some of the traits are in part under the influence of the same genes. Traits under the influence of QTL at close or identical positions also were traits that were strongly genotypically correlated. Based on the results of correlation analyses, the most important single traits influencing the quality were found to be density of wool, guard hair thickness and appearance of the surface.

Inbreeding affects fecundity of American mink (Neovison vison) in Danish farm mink.

Inbreeding is an increasing problem in farmed mink, because of limited exchange of individuals between farms. In this study, genetic relatedness within seven American mink (Neovison vison) colour strains originating from 13 different mink farms in Denmark was analysed using 21 polymorphic microsatellite loci. We detected large differences in the level of relatedness (range 0.017-0.520) within colour strains. Moreover, a very strong and highly significant negative correlation between the level of relatedness and fecundity was observed (r = 0.536, P < 0.001) [Correction added after online publication on 9 March 2011: r(2) has been changed to r]. To our knowledge, this is the first time that such a correlation has been demonstrated for commercially farmed mink.

Effect of selection for growth on normal and reduced protein diets on weight gain, feed intake, feed efficiency and body composition in mice.

Mice selected for weight gain from 3 to 9 weeks of age on a normal (N) protein diet containing 19.3% protein and a reduced (R) protein diet with 5.1% protein were reared on both diets in generations 7 and 9. The lines NH, NC, NL, RH, RC and RL (H, high; C, control; L, low) were tested for weight gain on diet N and R and for feed intake and feed efficiency on diet N in generation 7. In generation 9, the lines were tested for body composition traits (fat, protein and water percentage) at 3, 6, 9 and 12 weeks of age on both diets. A significant (p < 0.0001) genotype x environment interaction for growth rate was observed in generation 7. Weight gain at both the protein levels was best improved by selection at the protein level itself. Furthermore, the ranking of the lines on diet N was similar for weight gain, feed intake and feed efficiency. In generation 9 at 9 weeks of age, the ranking of the lines for fat percentage was equal to the ranking for weight gain in generation 7 on both test-diets. The association between weight gain and protein or water percentage was less pronounced, particularly on diet R. These results suggest that the largest genetic improvement in growth rate is obtained when the protein content of the feed is the same in selection and production. However, when selection is carried out in one environment while the animals have to perform under conditions with varying nutrient protein contents, selection in an inferior environment may be advantageous.

Evaluation of the porcine melanocortin 4 receptor (MC4R) gene as a positional candidate for a fatness QTL in a cross between Landrace and Hampshire.

Melanocortin 4 receptor (MC4R) is expressed in the appetite-regulating areas of the brain where it is central in the regulation of feed intake and energy balance. A mutation in MC4R causing an Asp298Asn substitution has been associated with fatness, high daily gain and feed intake in the pig. In a previously performed genome scan based on a Hampshire x Landrace cross, we detected one quantitative trait loci (QTL) affecting carcass fat/meat ratio and one QTL affecting the biceps femoris muscle, both close to the position of MC4R on porcine chromosome 1. In this study, the two lines were found to be close to fixation for alternative alleles of the Asp298Asn polymorphism. Additional QTL analyses supported our hypothesis of MC4R as a positional candidate gene but only for the fat/meat QTL. The Asp298Asn polymorphism was also evaluated as a selection target for daily gain in a Danish pig breeding population that included four breeds (Hampshire, Duroc, Landrace and Yorkshire). Over a 12-year period (1990-2002), a significant increase in the allele frequency of 298Asn was found in Landrace and Duroc, whereas a non-significant decrease in the 298Asn allele frequency was observed in Yorkshire. The Hampshire breed was fixed for the 298Asn allele in 1990. The high 298Asn allele frequencies in Hampshire, Landrace and Duroc are most likely due to selection for daily gain, whereas selection for daily gain in the Yorkshire breed apparently focuses on other loci.

Multitrait quantitative trait Loci mapping for milk production traits in danish Holstein cattle.

The aims of this study were (1) to confirm previously identified quantitative trait loci (QTL) on bovine chromosomes 6, 11, 14, and 23 in the Danish Holstein cattle population, (2) to assess the pleiotropic nature of each QTL on milk production traits by building multitrait and multi-QTL models, and (3) to include pedigree information on nongenotyped individuals to improve the estimation of genetic parameters underlying the random QTL model. Nineteen grandsire families were analyzed by single-trait (ST) and multitrait (MT) QTL mapping methods. The variance component-based QTL mapping model was implemented via restricted maximum likelihood (REML) to estimate QTL position and parameters. Segregation of the previously identified QTL was confirmed on bovine chromosomes 6, 11, and 14, but not on 23. A highly significant (1% chromosome-wise level) QTL was found on chromosome 6, between 37 and 73 cM. This QTL had a strong effect on protein percentage (PP) and fat percentage (FP) according to ST analyses, and effects on PP, FP, milk yield (MY), fat yield (FY), and protein yield (PY) in MT analyses. A QTL affecting PP was detected on chromosome 11 (at 70 cM) using ST analysis. The MT analysis revealed a second QTL (at 67 cM) approaching significance with an effect on MY. The ST analysis identified a QTL for MY and FP on chromosome 14, between 10 and 24 cM. The extended pedigree (nongenotyped animals) was included to estimate genetic parameters underlying the random QTL model; that is, additive polygenic and QTL variances. In general, the estimates of the QTL variance components were smaller but more precise when the extended pedigree was considered in the analysis.

Chromosome location, genomic organization of the porcine COL10A1 gene and model structure of the NC1 domain.

The porcine COL10A1 gene, encoding the alpha1(X) chain of type X collagen, has been sequenced. The gene structure is evolutionarily conserved, consisting of three exons and two introns spanning 7100 bp. Linkage mapping localized the gene to chromosome 1, which is in agreement with human-pig homology maps. Furthermore, protein structure comparison of the functionally important carboxyl domain between species revealed that amino acid changes were few and mainly situated in loop regions.

Abnormal growth plate function in pigs carrying a dominant mutation in type X collagen.

We have identified a naturally occurring, dominant mutation that causes dwarfism in domestic pigs (Sus scrofa). With a positional candidate gene approach, the dwarf phenotype was shown to be a result of a single amino acid change, G590R, in the alpha1 (X) chain of type X collagen. Type X collagen is a homotrimer of alpha1(X) chains encoded by the COL10A1 gene, which is expressed in hypertrophic chondrocytes during the process of endochondral ossification. An amino acid substitution at the equivalent position in human type X collagen, G595E, has previously been shown to cause Schmid metaphyseal chondrodysplasia (SMCD), which is a relatively mild skeletal disorder associated with dwarfism and growth plate abnormality. Consistent with the clinical phenotype of SMCD patients, radiological and histological examination of the dwarf pigs revealed metaphyseal chondrodysplasia in the long bones. Yeast-based, two-hybrid protein interaction studies and in vitro assembly experiments demonstrated that the amino acid substitution interfered with the ability of the mutated collagen molecules to engage in trimerization. This work establishes that the chondrodysplastic dwarf pigs by genetic, biochemical, radiological and histological criteria provide a valid animal model of SMCD.

Growth hormone gene polymorphism associated with selection for milk fat production in lines of cattle.

Fifty-eight calves of both sexes from lines of Red Danish dairy breed selected for high (n = 36) and low (n = 22) milk fat production, and 32 heifers from lines of Norwegian Red dairy breed selected for high (n = 16) and low (n = 16) milk fat yield were typed for two previously reported restriction fragment length polymorphisms (RFLPs) in the growth hormone gene. The RFLPs are consistent with: (1) an insertion(I)/deletion(D) of approximately 0.9 kb in the 3'-region of the growth hormone gene and (2) a polymorphic MspI(+/-) site in the third intron. A traditional RFLP procedure was used for typing the I/D polymorphism and a polymerase chain reaction (PCR) procedure was developed for typing the MspI polymorphism. Only the I-MspI(+) and D-MspI(-) haplotypes were found. In the Red Danish lines the frequency of D-MspI(-) haplotype was 0.28 in high line and 0.05 in low line calves, this difference was significant (P < 0.01). The corresponding frequencies in the Norwegian Red lines were 0.09 in the high line and 0.0 in the low line. Attempts to screen for RFLPs in the growth hormone receptor gene and in the insulin-like growth factor-I gene were unsuccessful.