Mutations in the bovine ABCG2 and the ovine MSTN gene added to the few quantitative trait nucleotides identified in farm animals: a mini-review.

The progress in molecular genetics in animal breeding is moderately effective as compared to traditional animal breeding using quantitative genetic approaches. There is an extensive disparity between the number of reported quantitative trait loci (QTLs) and their linked genetic variations in cattle, pig, and chicken. The identification of causative mutations affecting quantitative traits is still very challenging and hampered by the cloudy relationship between genotype and phenotype. There are relatively few reports in which a successful identification of a causative mutation for an animal production trait was demonstrated. The examples that have attracted considerable attention from the animal breeding community are briefly summarized and presented in a table. In this mini-review, the recent progress in mapping quantitative trait nucleotides (QTNs) are reviewed, including the ABCG2 gene mutation that underlies a QTL for fat and protein content and the ovine MSTN gene mutation that causes muscular hypertrophy in Texel sheep. It is concluded that the progress in molecular genetics might facilitate the elucidation of the genetic architecture of QTLs, so that also the high-hanging fruits can be harvested in order to contribute to efficient and sustainable animal production.

Short communication: duplication in the 5'-flanking region of the beta-lactoglobulin gene is linked to the BLG A allele.

beta-Lactoglobulin (beta-LG) is the major whey protein in the milk of cows and other ruminants. It is well established that the predominant genetic variants beta-LG A and B are differentially expressed. Extensive investigation of the genetic variation in the promoter region of the BLG gene revealed the existence of specific haplotypes associated with the A and B variants. However, the genetic basis for the differentially expressed BLG A and B alleles is still elusive. In this study additional genetic variation further upstream in the 5'-flanking region of the BLG gene was identified, including 6 single nucleotide substitutions, a single nucleotide deletion, and a 7-bp duplication. Comparison of DNA sequences showed that the investigated 5'-flanking region is highly conserved between ruminants, and the duplication g.-1885_-1879dupCTCTCGC and the substitution g.-1888A>G are only found in the BLG A and D alleles in cattle. The cytosine at position g.-1957 and the thymines at positions g.-2008 and g.-2049 are only found in BLG B alleles of cattle. It is suggested that the described genetic variability contributes to the differential allelic expression of the BLG gene.

The locus for bovine dilated cardiomyopathy maps to chromosome 18.

Bovine dilated cardiomyopathy (BDCMP) is a severe and terminal disease of the heart muscle observed in Holstein-Friesian cattle over the last 30 years. There is strong evidence for an autosomal recessive mode of inheritance for BDCMP. The objective of this study was to genetically map BDCMP, with the ultimate goal of identifying the causative mutation. A whole-genome scan using 199 microsatellite markers and one SNP revealed an assignment of BDCMP to BTA18. Fine-mapping on BTA18 refined the candidate region to the MSBDCMP06-BMS2785 interval. The interval containing the BDCMP locus was confirmed by multipoint linkage analysis using the software loki. The interval is about 6.7 Mb on the bovine genome sequence (Btau 3.1). The corresponding region of HSA19 is very gene-rich and contains roughly 200 genes. Although telomeric of the marker interval, TNNI3 is a possible positional and a functional candidate for BDCMP given its involvement in a human form of dilated cardiomyopathy. Sequence analysis of TNNI3 in cattle revealed no mutation in the coding sequence, but there was a G-to-A transition in intron 6 (AJ842179:c.378+315G>A). The analysis of this SNP using the study's BDCMP pedigree did not conclusively exclude TNNI3 as a candidate gene for BDCMP. Considering the high density of genes on the homologous region of HSA19, further refinement of the interval on BTA18 containing the BDCMP locus is needed.

Aberrant low expression level of bovine beta-lactoglobulin is associated with a C to A transversion in the BLG promoter region.

Beta-lactoglobulin (beta-LG) is the major whey protein in cow's milk. It is well established that the predominant 2 genetic variants, beta-LG A and B, are differentially expressed. Extensive investigation of the genetic variation in the promoter region of the BLG gene revealed the existence of specific haplotypes associated with the A and B variants, respectively. However, the genetic basis for the differential expression of BLG A and B alleles is still elusive. We have previously reported a quantitative beta-LG B variant, characterized by a very low beta-LG protein expression level. Here, we report that the corresponding BLG allele (BLG B*) shows a correspondingly low mRNA expression level. Comparative DNA sequencing of 7,670 bp of the BLG B* allele and the established BLG B allele revealed a unique difference of a C to A transversion at position 215 bp upstream of the translation initiation site (g.-215C>A). This mutation segregated perfectly with the differential phenotypic expression in a paternal half-sib family and could be confirmed in 2 independent cases. The sequence of the BLG B allele in the region of the mutation is highly conserved among 4 related ruminant species. The site of the mutation corresponds to a putative consensus-binding sequence for the transcription factors c-Rel and Elk-1 as predicted by searching the TRANSFAC database. The beta-LG B* site might be relevant in the natural production of milk of low beta-LG content.

Genome-wide identification of quantitative trait loci in a cross between Hampshire and Landrace I: carcass traits.

We report the identification of quantitative trait loci (QTL) affecting carcass composition, carcass length, fat deposition and lean meat content using a genome scan across 462 animals from a combined intercross and backcross between Hampshire and Landrace pigs. Data were analysed using multiple linear regression fitting additive and dominance effects. This model was compared with a model including a parent-of-origin effect to spot evidence of imprinting. Several precisely defined muscle phenotypes were measured in order to dissect body composition in more detail. Three significant QTL were detected in the study at the 1% genome-wide level, and twelve significant QTL were detected at the 5% genome-wide level. These QTL comprise loci affecting fat deposition and lean meat content on SSC1, 4, 9, 10, 13 and 16, a locus on SSC2 affecting the ratio between weight of meat and bone in back and weight of meat and bone in ham and two loci affecting carcass length on SSC12 and 17. The well-defined phenotypes in this study enabled us to detect QTL for sizes of individual muscles and to obtain information of relevance for the description of the complexity underlying other carcass traits.

The phylogeny of Chinese indigenous pig breeds inferred from microsatellite markers.

A genetic study of 32 local Chinese, three foreign pig breeds [Duroc (DU), Landrace and Yorkshire], and two types of wild boar (Hainan and Dongbei wild boar) based on 34 microsatellite loci was carried out to clarify the phylogeny of Chinese indigenous pig breeds. The allele frequencies, effective numbers of alleles, and the average heterozygosity within populations were calculated. The results showed that the genetic variability of the Lingao pig was the largest, while the Jiaxing pig was the lowest. The greatest distance between domestic pigs was found between Shanggao and DU pig and the shortest was found between Wuzhishan and Lingao pig, respectively. A neighbour-joining tree constructed from Modified Cavalli-Sforza genetic distances divided Chinese pigs into two clusters; four subclusters were also identified. Our results only partly agree with the traditional types of classification and also provide a new relationship among Chinese local pig breeds. Our data also confirmed that Chinese pig breeds have a different origin from European/American breeds and can be utilized in programmes that aim to maintain Chinese indigenous pig breeds.

Generation and exploration of a dense genetic map in a region of a QTL affecting corpora lutea in a Meishan x Yorkshire cross.

Previously genomic scans revealed quantitative trait loci (QTL) on porcine Chromosome 8 (SSC8) as significantly affecting the number of corpora lutea (CL) in swine. In one study, statistical evidence for the putative QTL was found in the chromosomal region defined by the microsatellites (MS) SW205, SW444, SW206, and SW29. A Yeast Artificial Chromosome library was screened by using the corresponding primers for clones containing these MS by PCR. From five positive YAC clones, 10 additional MS were isolated and mapped to SSC8 with the INRA-University of Minnesota porcine Radiation Hybrid (IMpRH) panel. The genetic map position of the QTL has been refined by addition of these 10 markers. The QTL evaluation included pedigrees of F2-intercross Meishan x Yorkshire design, with phenotypic data of 108 F2 female offspring and genotypic data for 29 MS markers on SSC8. The analysis was performed by using the least squares regression method. The calculated QTL effect for CL obtained by the multilocus least squares method showed a maximum test statistic (F value = 13.98) at position 99 cM between three MS derived from YACs containing SW205 and SW1843 spanning an interval of 7.1 cM. The point-wise (nominal) P-value was 5.21 x 10-6 corresponding to a genome-wide P-value of 0.009. The additive QTL effect explained 17.4% of the phenotypic variance.

Porcine factor V: cDNA cloning, gene mapping, three-dimensional protein modeling of membrane binding sites and comparative anatomy of domains.

Factor V is a plasma protein essential for blood coagulation. This protein is involved in activated protein C resistance, the most common inherited thrombotic disorder known. We utilized the polymerase chain reaction to clone the porcine factor V gene by generating overlapping clones amplified with primers chosen by comparison with known nucleotide sequences. The porcine factor V cDNA contig encodes a predicted 2258-amino acid protein, making it the largest in comparison to the bovine, human, and murine proteins. Porcine factor V has the highest level of homology with bovine factor V, but also has high levels of conservation of important residues with all the species. Radiation hybrid mapping assigned the porcine factor V gene to chromosome 4. Three-dimensional models of factor V were generated and used to analyze membrane-binding sites in terms of conserved, and therefore likely important residues.

Associations between casein haplotypes and milk production traits of Swiss Brown cattle.

Effects of casein haplotypes and beta-lactoglobulin (LG) genotypes on milk protein fractions and on daughter yield deviations for milk performance traits were estimated from a daughter design. Offspring of seven Swiss Brown sires with the haplotypes B-A-B-A and B-A-B-B for alpha s1-, alpha s2-, beta-, and kappa-caseins were selected. The milk of daughter groups with paternal haplotype B-A-B-A was associated with lower casein content and higher whey protein content compared with B-A-B-B. Because of these contrary effects, the true protein content was not affected by the paternal haplotypes. The effects of maternal haplotypes were significant on true protein and casein content but not on whey protein content. The beta-LG genotypes had highly significant effects on casein and whey protein content. The effect of beta-LG BB was positive on casein and negative on whey protein content compared with beta-LG AA; the effect of beta-LG AB was intermediate. No significant effects of paternal haplotypes were found for daughter yield deviation on kilograms of milk, fat, and protein or percentages of fat and protein. The effects of the beta-LG genotypes were, independent of the parental haplotypes, close to significant on daughter yield deviation for percentage of protein. The beta-LG BB tended to be associated with a higher protein content compared with beta-LG AA. The effects for beta-LG genotypes showed additive gene effects. The analysis of paternal haplotypes within sires revealed a contrary effect of haplotypes for two of the seven sires for casein content. The paternal haplotypes within sire showed, although not significant, that haplotypes of the two sires had a contrary effect on daughter yield deviation for percentage of protein as well.

Power-based colour coded duplex sonography for evaluation of calf veins.

BACKGROUND: Power-based colour coded duplex sonography (PD) has been described to display lower flow velocities compared to frequency-based colour coded duplex sonography (CD). This study was undertaken to study the clinical usefulness of PD in the evaluation of calf veins in suspected deep vein thrombosis. EXPERIMENTAL DESIGN: A prospective, comparative study. SETTING: University hospital, Switzerland. PATIENTS AND MEASURES: CD of the complete deep venous system and complementary PD of paired calf veins were performed in 50 consecutive patients with clinically suspected DVT. All except three patients, with failed vein puncture at the dorsum of the foot, had a venography used as reference test for confirmatory diagnosis of DVT. RESULTS: Complete identification of calf veins increased from 80.5% using CD to 97.9% using complementary PD (p=0.007). Overall accuracy to detect an acute calf DVT was 96% (95% Ci, 85-99%) and 95% (95% CI, 83-99%), respectively. Accuracy was 95% (95% CI, 83-99%) using CD vs 94% (95% CI, 82-98%) using PD in posterior tibial, 87% (95% CI, 74-95%) vs 85% (95% CI, 71-94%) in anterior tibial, and 95% (95% CI, 83-99%) vs 96% (95% CI, 85-99%) in peroneal veins. Chronic post-thrombotic changes (10.6%) were more reliably recognized using CD (accuracy 83% [95% CI, 72-94%]) compared to PD (accuracy 66% [95% CI, 59-85%]) due to tissue motion artifacts and inability to discriminate the direction of blood flow. CONCLUSIONS: PD used complementary with CD is capable of significantly improving identification of paired calf veins without loss of diagnostic accuracy in the diagnosis of acute DVT.

Adventitial cystic disease of the popliteal artery: percutaneous US-guided aspiration.

PURPOSE: To evaluate percutaneous ultrasound (US)-guided aspiration as an alternative therapy for adventitial cystic disease. MATERIALS AND METHODS: Between September 1993 and June 1996, seven patients (six men, one woman; age range, 42-62 years; mean age, 48 years) presented with symptomatic adventitial cystic disease of the popliteal artery (one patient with subacute foot paresthesia, six patients with chronic calf claudication). Color Doppler sonography showed stenosis due to eccentric cysts. Five of the patients also underwent digital subtraction angiography, and four patients underwent magnetic resonance imaging. With real-time sonographic guidance, a 14-gauge needle was forwarded percutaneously into the cysts for aspiration. The aspiration procedure was performed on an outpatient basis with local anesthetics. RESULTS: The procedure was technically and clinically successful in all cases. No complications were noted. Follow-up color duplex sonography performed between 1 and 32 months (mean, 14.8 months) after the procedure showed no relevant recurrent stenosis. CONCLUSION: Percutaneous US-guided aspiration is an easy, safe, efficacious method for treating adventitial cystic disease. In symptomatic patients who do not have thrombotic occlusion, it may be considered the treatment of choice.