Genome-Wide Association Study of Acute Renal Graft Rejection

Acute renal rejection is a major risk factor for chronic allograft dysfunction and long-term graft loss. We performed a genome-wide association study to detect loci associated with biopsy-proven acute T cell-mediated rejection occurring in the first year after renal transplantation. In a discovery cohort of 4127 European renal allograft recipients transplanted in eight European centers, we used a DNA pooling approach to compare 275 cases and 503 controls. In an independent replication cohort of 2765 patients transplanted in two European countries, we identified 313 cases and 531 controls, in whom we genotyped individually the most significant single nucleotide polymorphisms (SNPs) from the discovery cohort. In the discovery cohort, we found five candidate loci tagged by a number of contiguous SNPs (more than five) that was never reached in iterative in silico permutations of our experimental data. In the replication cohort, two loci remained significantly associated with acute rejection in both univariate and multivariate analysis. One locus encompasses PTPRO, coding for a receptor-type tyrosine kinase essential for B cell receptor signaling. The other locus involves ciliary gene CCDC67, in line with the emerging concept of a shared building design between the immune synapse and the primary cilium.

Identifying cows with subclinical mastitis by bulk single nucleotide polymorphism genotyping of tank milk

Mastitis remains the most important health issue in dairy cattle. Improved methods to identify cows developing subclinical mastitis would benefit farmers. We herein describe a novel method to determine the somatic cell counts (SCC) of individual cows by bulk genotyping a sample of milk from the milk tank with panels of genome-wide single nucleotide polymorphisms (SNP). We developed a simple linear model to estimate the contribution of individual cows to the genomic DNA present in the tank milk from 1) the known genotypes of individual cows for the interrogated SNP and 2) the ratio of SNP alleles in the tank milk. Using simulations, we estimate that 3,000, 50,000, and 700,000 SNP are sufficient to accurately (R(2)>0.98) estimate individual SCC in tanks containing milk from 25, 100, and 500 cows, respectively. Using actual data, we demonstrate that the SCC of 21 cows can be estimated with a coefficient of determination of 0.60 using approximately 9,000 SNP. The proposed method increases the value of the proposition of SNP genotyping individual cows for genomic selection purposes.

135 BREEDING VALUES CONCORDANCE BETWEEN EMBRYOS AND CORRESPONDING CALVES

Genomic tools are now available for most livestock species and are used routinely for genomic selection in cattle. Recently, biopsies of pre-implantation-stage embryos were genotyped for multiple markers. This strategy provides the opportunity to estimate breeding values for traits of particular interest and the presence of genetic abnormalities, thus allowing selection of embryos before transfer (Le Bourhis et al. 2011 Reprod. Fertil. Dev. 23, 197 abst). The present work aimed to compare the genotype and the breeding values from biopsied bovine embryos with the corresponding calves. Bovine embryos were obtained after superovulation (8 cows) and flushing at Day 6 or 7. A total of 11 embryos (1 or 2 Grade 1 embryos per flush per cow) were washed and biopsied using a microblade. Biopsies of 5 to 10 cells were transferred individually as dry samples in tubes and frozen before whole genome amplification (WGA). The genomic DNA of each biopsy was amplified using a WGA kit according to the manufacturer's instructions (WGA; QIAGEN REPLI-g® Mini Kit, Qiagen, Valencia, CA, USA). Biopsied embryos were transferred either frozen or fresh to synchronized recipients. At birth a blood sample was taken from the calf for subsequent genotyping. Genotyping was done using the Illumina BovineSNP50TM beadchip. Only embryos with call rate (CR) higher than 80% were selected for breeding values comparisons. Because of allele dropout, heterozygous markers are turned into homozygous makers artificially. Only markers that were still heterozygous in genotypes of an embryo were selected and error rates were calculated with the same markers from the corresponding calf. Imputation was done using Beagle and taking into account the 50 k genotyping results of the parents. Breeding values (milk production and morphological traits) were calculated and compared with those of the 7 corresponding calves. From 11 embryos analysed, only 1 (9%) gave a CR lower than 80% and a higher percentage error with calf genotype (Table 1). These results indicate that, using embryonic DNA after WGA, genotyping errors between embryo and calf are low and correlated with the CR of embryos. For embryos with CR higher than 84, the concordance of genomic values between embryo and calf is very high. More embryo–calf pairs are needed to assess the reliability of this method and to validate the breeding value at the embryo stage. This new technique offers new possibilities in managing breeding schemes by selecting the embryos before transfer. Table 1.Embryo call rate (CR) and genotyping and breeding value concordances between embryos and calves

Genetic variation in PLAG1 associates with early life body weight and peripubertal weight and growth in Bos taurus

Variation at the pleiomorphic adenoma gene 1 (PLAG1) locus has recently been implicated in the regulation of stature and weight in Bos taurus. Using a population of 942 outbred Holstein-Friesian dairy calves, we report confirmation of this effect, demonstrating strong association of early life body weight with PLAG1 genotype. Peripubertal body weight and growth rate were also significantly associated with PLAG1 genotype. Growth rate per kilogram of body weight, daily feed intake, gross feed efficiency and residual feed intake were not significantly associated with PLAG1 genotype. This study supports the status of PLAG1 as a key regulator of mammalian growth. Further, the data indicate the utility of PLAG1 polymorphisms for the selection of animals to achieve enhanced weight gain or conversely to aid the selection of animals with lower mature body weight and thus lower maintenance energy requirements.

193 BOVINE EMBRYO GENOTYPING USING A 50K SINGLE NUCLEOTIDE POLYMORPHISM CHIP

Genomic tools are now available for most livestock species and are used routinely for marker-assisted selection (MAS) and genomic selection (GS) in cattle. Recently, multiple-marker detection has been achieved from biopsies of preimplantation stage embryos, thus allowing embryos to be selected before transfer (Le Bourhis et al. 2009 Reprod. Fertil. Dev. 21, 192 abst). This strategy provides the opportunity to estimate some traits of particular interest, the presence of genetic abnormalities, or both. The present work aimed to assess the efficiency of MAS/GS evaluation from biopsied bovine embryos by using the bovine 50K single nucleotide polymorphism (SNP) Illumina chip. A biopsy of 5 to 10 cells was obtained under laboratory conditions, using a microblade under a stereomicroscope, from 29 in vitro-cultured morulae and blastocysts. Biopsies were transferred individually as dry samples in tubes and sent frozen (n = 13) or at room temperature (n = 16) to the genotyping laboratory. The genomic DNA of each biopsy was amplified using a whole-genome amplification (WGA) kit according to the manufacturer’s instructions (Qiagen REPLI-g® Mini Kit, Qiagen, Valencia, CA). Following WGA, DNA concentration was determined by using PicoGreen. For subsequent genotyping, a custom CRV 50K Illumina chip was used. Call rates were calculated from 50 905 SNP. Percentage of allele drop-out (%ADO), which was estimated from the number of heterozygous markers [%ADO = (calculated hetero – observed hetero)/calculated hetero]. Parentage error was estimated from 12 embryos by using the genotypes of the parents of the embryos. Both groups of transport conditions were compared using Student’s t-test. Results are presented as mean ± SEM. A greater quantity of DNA was obtained after amplification of biopsies that were sent frozen to the laboratory when compared with those at room temperature (P < 0.05). However, the SNP call rate, %ADO, and parentage error did not differ between groups. These results indicate that genotyping from embryo biopsies following WGA can be achieved with good efficiency when using high-density marker chips. To validate the use of MAS/GS from early embryos in breeding schemes, a larger number of in vivo embryos are currently genotyped under field conditions. This will allow the reliability of this method to be assessed and the correlation between embryo and calf genetic evaluation to be quantified with the current WGA efficiency. Table 1.Amount of DNA after WGA and genotyping results

A 2.5-Mb contig constructed from Angus, Longhorn and horned Hereford DNA spanning the polled interval on bovine chromosome 1

The polled locus has been mapped by genetic linkage analysis to the proximal region of bovine chromosome 1. As an intermediate step in our efforts to identify the polled locus and the underlying causative mutation for the polled phenotype, we have constructed a BAC-based physical map of the interval containing the polled locus. Clones containing genes and markers in the critical interval were isolated from the TAMBT (constructed from Angus and Longhorn genomic DNA) and CHORI-240 (constructed from horned Hereford genomic DNA) BAC libraries and ordered based on fingerprinting and the presence or absence of 80 STS markers. A single contig spanning 2.5 Mb was assembled. Comparison of the physical order of STSs to the corresponding region of human chromosome 21 revealed the same order of genes within the polled critical interval. This contig of overlapping BAC clones from horned and polled breeds is a useful resource for SNP discovery and characterization of positional candidate genes.

Results of a whole-genome quantitative trait locus scan for growth, carcass composition and meat quality in a porcine four-way cross

A whole-genome quantitative trait locus (QTL) scan for 31 phenotypes related to growth, carcass composition and meat quality was conducted using 1187 progeny of a commercial four-way cross. Animals were genotyped for 198 microsatellite markers that spanned the entire porcine genome. QTL analysis was conducted to extract information from paternal and maternal meioses separately using a rank-based nonparametric approach for half-sib designs. Nine QTL exceeded genome-wide significance: one QTL affecting growth (average daily gain on SSC1), two QTL influencing carcass composition (fatness on SSC3 and muscle mass on SSC15) and six QTL influencing meat quality (tenderness on SSC4 and SSC14; colour on SSC5, SSC6 and SSCX; and conductivity on SSC16). All but one of these coincided with previously reported QTL. In addition, we present evidence for 78 suggestive QTL with a combined false discovery rate of 40%.

Measuring the extent of linkage disequilibrium in commercial pig populations

To evaluate the extent of linkage disequilibrium in domestic pigs, we genotyped 33 and 44 unrelated individuals from two commercial populations for 29 and five microsatellite markers located on chromosomes 15 and 2 respectively. A high proportion of marker pairs up to 40 cM apart exhibited significant linkage disequilibrium in both populations. Pair-wise r(2) values averaged between 0.15 and 0.50 (depending on chromosome and population) for markers <1 cM apart and declined to values of 0.05 for more distant syntenic markers. Our results suggest that both populations underwent a bottleneck approximately 20 generations ago, which reduced the effective population size from thousands to <200 animals.

Non-parametric interval mapping in half-sib designs: use of midranks to account for ties

In QTL analysis of non-normally distributed phenotypes, non-parametric approaches have been proposed as an alternative to the use of parametric tests on mathematically transformed data. The non-parametric interval mapping test uses random ranking to deal with ties. Another approach is to assign to each tied individual the average of the tied ranks (midranks). This approach is implemented and compared to the random ranking approach in terms of statistical power and accuracy of the QTL position. Non-normal phenotypes such as bacteria counts showing high numbers of zeros are simulated (0-80% zeros). We show that, for low proportions of zeros, the power estimates are similar but, for high proportions of zeros, the midrank approach is superior to the random ranking approach. For example, with a QTL accounting for 8% of the total phenotypic variance, a gain from 8% to 11% of power can be obtained. Furthermore, the accuracy of the estimated QTL location is increased when using midranks. Therefore, if non-parametric interval mapping is chosen, the midrank approach should be preferred. This test might be especially relevant for the analysis of disease resistance phenotypes such as those observed when mapping QTLs for resistance to infectious diseases.

Statistical power of QTL mapping methods applied to bacteria counts

Most QTL mapping methods assume that phenotypes follow a normal distribution, but many phenotypes of interest are not normally distributed, e.g. bacteria counts (or colony-forming units, CFU). Such data are extremely skewed to the right and can present a high amount of zero values, which are ties from a statistical point of view. Our objective is therefore to assess the efficiency of four QTL mapping methods applied to bacteria counts: (1) least-squares (LS) analysis, (2) maximum-likelihood (ML) analysis, (3) non-parametric (NP) mapping and (4) nested ANOVA (AN). A transformation based on quantiles is used to mimic observed distributions of bacteria counts. Single positions (1 marker, 1 QTL) as well as chromosome scans (11 markers, 1 QTL) are simulated. When compared with the analysis of a normally distributed phenotype, the analysis of raw bacteria counts leads to a strong decrease in power for parametric methods, but no decrease is observed for NP. However, when a mathematical transformation (MT) is applied to bacteria counts prior to analysis, parametric methods have the same power as NP. Furthermore, parametric methods, when coupled with MT, outperform NP when bacteria counts have a very high proportion of zeros (70.8%). Our results show that the loss of power is mainly explained by the asymmetry of the phenotypic distribution, for parametric methods, and by the existence of ties, for the non-parametric method. Therefore, mapping of QTL for bacterial diseases, as well as for other diseases assessed by a counting process, should focus on the occurrence of ties in phenotypes before choosing the appropriate QTL mapping method.

Convenient genotyping of six myostatin mutations causing double-muscling in cattle using a multiplex oligonucleotide ligation assay

We herein describe a procedure that allows for simultaneous genotyping of six loss-of-function mutations in the bovine myostatin gene associated with the double-muscling phenotype. The proposed method relies on a multiplex oligonucleotide ligation assay and detection of the fluorescently labelled products using automatic sequencers.

Whole genome scan to detect quantitative trait loci for conformation and functional traits in dairy cattle

A granddaughter design was used to locate quantitative trait loci determining conformation and functional traits in dairy cattle. In this granddaughter design, consisting of 20 Holstein Friesian grandsires and 833 sons, genotypes were determined for 277 microsatellite markers covering the whole genome. Breeding values for 27 traits, regarding conformation (18), fertility (2), birth (4), workability (2), and udder health (1), were evaluated in an across-family analysis using multimarker regression. Significance thresholds were determined using a permutation test. The across-family analysis suggested the presence of 61 quantitative trait loci when 27 (i.e., one for each trait) were expected by chance. The test statistic exceeded the genomewise significance threshold for the following traits and chromosomes: chest width on chromosome 2; gestation length on chromosome 4; stature, body capacity, and size on chromosome 5; dairy character on chromosome 6; angularity on chromosome 12; fore udder attachment on chromosome 13; and fore udder attachment and front teat placement on chromosome 19. The quantitative trait loci for size traits on chromosomes 2, 5, and 6 may also have an effect on calving ease. The quantitative trait loci for udder traits on chromosomes 13 and 19 may also affect somatic cell score and mastitis resistance. If there are no negative effects on other economically important traits, marker assisted selection using markers associated with these quantitative trait loci can be applied.

Extensive genome-wide linkage disequilibrium in cattle

A genome-wide linkage disequilibrium (LD) map was generated using microsatellite genotypes (284 autosomal microsatellite loci) of 581 gametes sampled from the dutch black-and-white dairy cattle population. LD was measured between all marker pairs, both syntenic and nonsyntenic. Analysis of syntenic pairs revealed surprisingly high levels of LD that, although more pronounced for closely linked marker pairs, extended over several tens of centimorgan. In addition, significant gametic associations were also shown to be very common between nonsyntenic loci. Simulations using the known genealogies of the studied sample indicate that random drift alone is likely to account for most of the observed disequilibrium. No clear evidence was obtained for a direct effect of selection ("Bulmer effect"). The observation of long range disequilibrium between syntenic loci using low-density marker maps indicates that LD mapping has the potential to be very effective in livestock populations. The frequent occurrence of gametic associations between nonsyntenic loci, however, encourages the combined use of linkage and linkage disequilibrium methods to avoid false positive results when mapping genes in livestock.

Short communication: quantitative trait loci analysis on 17 nonproduction traits in the New Zealand dairy population

Seven New Zealand Holstein-Friesian families and two Jersey families, a total of 274 sires, were analyzed in a granddaughter design for marker-quantitative trait loci associations. For 17 nonproduction traits (management, size, and conformation traits), an across-family analysis was undertaken using multimarker regression procedures. Threshold levels were set empirically by permuting the data. A quantitative trait locus for stature was identified on chromosome 14, which was significant at the 15% experimentwise level (suggestive linkage). The quantitative trait locus was identified to be segregating in three of the nine families.

Fine-mapping of quantitative trait loci by identity by descent in outbred populations: application to milk production in dairy cattle

We previously mapped a quantitative trait locus (QTL) affecting milk production to bovine chromosome 14. To refine the map position of this QTL, we have increased the density of the genetic map of BTA14q11-16 by addition of nine microsatellites and three single nucleotide polymorphisms. Fine-mapping of the QTL was accomplished by a two-tiered approach. In the first phase, we identified seven sires heterozygous "Qq" for the QTL by marker-assisted segregation analysis in a Holstein-Friesian pedigree comprising 1,158 individuals. In a second phase, we genotyped the seven selected sires for the newly developed high-density marker map and searched for a shared haplotype flanking an hypothetical, identical-by-descent QTL allele with large substitution effect. The seven chromosomes increasing milk fat percentage were indeed shown to carry a common chromosome segment with an estimated size of 5 cM predicted to contain the studied QTL. The same haplotype was shown to be associated with increased fat percentage in the general population as well, providing additional support in favor of the location of the QTL within the corresponding interval.

A rank-based nonparametric method for mapping quantitative trait loci in outbred half-sib pedigrees: application to milk production in a granddaughter design

We describe the development of a multipoint nonparametric quantitative trait loci mapping method based on the Wilcoxon rank-sum test applicable to outbred half-sib pedigrees. The method has been evaluated on a simulated dataset and its efficiency compared with interval mapping by using regression. It was shown that the rank-based approach is slightly inferior to regression when the residual variance is homoscedastic normal; however, in three out of four other scenarios envisaged, i.e., residual variance heteroscedastic normal, homoscedastic skewed, and homoscedastic positively kurtosed, the latter outperforms the former one. Both methods were applied to a real data set analyzing the effect of bovine chromosome 6 on milk yield and composition by using a 125-cM map comprising 15 microsatellites and a granddaughter design counting 1158 Holstein-Friesian sires.

A QTL with major effect on milk yield and composition maps to bovine chromosome 14

A whole genome scan was undertaken in a granddaughter design comprising 1158 progeny-tested bulls in order to map QTL influencing milk yield and composition. In this paper we report the identification of a locus on the centromeric end of bovine Chromosome (Chr) 14, with major effect on fat and protein percentage as well as milk yield. The genuine nature of this QTL was verified using the grand2-daughter design, that is, by tracing the segregating QTL alleles from heterozygous grandsires to their maternal grandsons and confirming the predicted QTL allele substitution effect.

A QTL affecting milk yield and composition maps to bovine chromosome 20: a confirmation

As part of a whole genome scan undertaken to detect quantitative trait loci (QTL) affecting milk yield and composition, we have genotyped a granddaughter design comprising 1152 sons for six microsatellite markers spanning bovine chromosome 20. An analysis performed across families provided strong evidence (experiment-wise P-values < 0.01) for the presence of a QTL affecting primarily protein percentage towards the telomeric end of the chromosome. A founder sire, shown in a previous study to segregate for a similar QTL in the corresponding chromosome region, was characterized by 29 and 57 sons and maternal grandsons, respectively, in the present design. Sorting corresponding sons and grandsons by paternal or grandpaternal allele provided significant evidence for the segregation of a QTL on chromosome 20. Altogether these results confirm the location of a QTL affecting milk production on bovine chromosome 20.

The effect of mixed selected and unselected samples on the power of QTL mapping

It is known from previous work that selection by truncation can lead to substantial loss of power to detect linkage with a QTL We examine the effect of mixed selected and unselected samples. We show that even if a modest proportion of the sample originates from an unselected population, this loss of power is quite effectively neutralized. Moreover, we reach the unexpected conclusion that if the selection intensity in the selected subpopulation is high, the power to detect QTL may actually increase.

Quantitative trait loci analysis for five milk production traits on chromosome six in the Dutch Holstein-Friesian population

Twenty Dutch Holstein-Friesian families, with a total of 715 sires, were evaluated in a granddaughter experiment design for marker-QTL associations. Five traits-milk, fat and protein yield and fat and protein percent-were analyzed. Across-family analysis was undertaken using multimarker regression principles. One and two QTL models were fitted. Critical values for the test statistic were calculated empirically by permuting the data. Individual trait distributions of permuted test statistics differed and, thus distributions, had to be calculated for each trait. Experimentwise critical values, which account for evaluating marker-QTL associations on all 29 autosomal-bovine chromosomes and for five traits, were calculated. A QTL for protein percent was identified in one, and two QTL models and was significant at the 1 and 2% level, respectively. Extending the multimarker regression approach to an analysis including two QTL was limited by families not being informative at all markers, which resulted in singularity. Below average heterozygosity for the first and last marker lowered information content for the first and last marker bracket. Highly informative markers at the ends of the mapped chromosome would overcome the decrease in information content in the first and last marker bracket and singularity for the two QTL model.

A comprehensive linkage map of the pig based on a wild pig-Large White intercross

A comprehensive linkage map, including 236 linked markers with a total sex-average map length of about 2300 cM, covering nearly all parts of the pig genome has been established. Linkage groups were assigned to approximately all 18 autosomes, the X chromosome and the X/Y pseudoautosomal region. Several new gene assignments were made including the assignment of linkage group U1 (EAK-HPX) to chromosome 9. The linkage map includes 77 types I loci informative for comparative mapping and 72 in situ mapped markers physically anchoring the linkage groups on chromosomes. A highly significant heterogeneity in recombination rates between sexes was observed with a general tendency towards an excess of female recombination. The average ratio of female to male recombination was estimated at 1.4:1 but this parameter varied between chromosomes as well as between regions within chromosomes. An intriguing finding was that blood group loci were overrepresented at the distal ends of linkage groups.

Microsatellite mapping of the bovine roan locus: a major determinant of White Heifer disease

In the Belgian Blue Cattle breed, coat color variation is mainly under the influence of a single autosomal locus, the roan locus, characterized by a pair of codominant alleles: r+ (black) and R (white). Heterozygous r+R animals have intermingled black and white hairs, yielding the "blue" phenotype typical of the breed. Major interest for the roan locus stems from its pleiotropic effect on fertility, owing to the critical role of the R allele in the determinism of White Heifer Disease. We describe the linkage mapping of the roan locus to bovine Chromosome (Chr) 5, in the interval between microsatellite markers BPI and AGLA293, with an associated lodscore of 11.2. Moreover, we map a candidate gene, the Steel locus coding for the mast cell growth factor, to bovine Chr 5.

The mh gene causing double-muscling in cattle maps to bovine Chromosome 2

While the hereditary nature of the "double-muscling" phenotype (a generalized muscular hypertrophy documented in several cattle breeds) is well established, its precise segregation mode has remained controversial. Both monogenic models (autosomal dominant or recessive) and oligogenic models have been proposed. Using a panel of 213 bovine microsatellite markers, and an experimental pedigree obtained by backing "double-muscled (Belgian Blue) x conventional (Friesian)"1 dams to double-muscle sire, we have mapped a locus on bovine Chromosome (CHr) 2 that accounts for all the phenotypic variance in the backcross generation. This locus, referred to as mh (muscular hypertrophy), has been positioned with respects to a map composed of seven Chr 2-specific microsatellites, at 2 cM from the closet marker. This result confirms the validity in the Belgian Blue population of the monogenic model involving an autosomal mh locus, characterized by a wild-type "+" and a recessive "mh" allele, causing the double-muscling phenotype in the homozygous condition. The linkage relationship between the mh locus and the Chr 2 markers was confirmed in three informative pedigrees collected from the general Belgian Blue Cattle population, reinforcing the notice of genetic homogeneity of the double-muscling trait in this breed. This work paves the way towards marker-assisted selection for or against the double muscling trait, and towards positional cloning of the corresponding gene.

Polymorphic CAC/T repetitive sequences in the pig genome 1

Three genomic clones were isolated from a size-selected pig DNA library by hybridization with a DNA-fingerprint probe. Analysis at the sequence level revealed that all three clones contain interrupted stretches of triplet repeats mainly composed of CAC and CAT triplets. Evaluation of the corresponding loci for polymorphism by Southern blot hybridization showed considerable length variation. For two loci the polymorphism was also demonstrated by polymerase chain reaction (PCR) amplification. The PiGMaP reference pedigree was typed for all three loci.

Pig plasma alpha-protease inhibitors PI2, PI3 and PI4 are members of the antichymotrypsin family

Three related alpha-protease inhibitors, PI2 I, PI3 C and PI4 C2, of blood serum of the pig (Sus scrofa) were isolated. PI2 I inhibited both trypsin and chymotrypsin; PI3 C and PI4 C2 strongly inhibited chymotrypsin, but did not significantly inhibit trypsin. By using SDS-PAGE, the three proteins were found to be composed of single polypeptide chains, and molecular weights were 63,000 for PI2 I, 58,000 for PI3 C and 64,000 for PI4 C2. All three proteins were shown to be glycoproteins. In PI3 C, eight sialic acid residues were found, and in PI4 C2 (similarly as in PI2 F) 10-11 residues were found. Amino acid composition as well as N-terminal sequences of the three proteins were very similar, indicating close homology. Comparison of these partial amino acid sequences with the cDNA-deduced amino acid sequence of pig alpha-antichymotrypsin (AACT; Buchman, 1989, GenBank, Accession No. M29508) revealed great similarities, the sequence of PI2 I being virtually identical with the pig AACT. On the basis of all available results, PI2 is proposed to be pig AACT, an orthologue of human AACT.

The BAT1 gene in the MHC encodes an evolutionarily conserved putative nuclear RNA helicase of the DEAD family

The BAT1 gene has previously been identified about 30 kb upstream from the tumor necrosis factor (TNF) locus and close to a NF kappa b-related gene of the nuclear factor family in the major histocompatibility complex (MHC) of human, mouse, and pig. We now show that the BAT1 translation product is the homolog of the rat p47 nuclear protein, the WM6 Drosophila gene product, and probably also Ce08102 of Caenorhabditis elegans, all members of the DEAD protein family of ATP-dependent RNA helicases. This family has more than 40 members, including the eukaryotic translation initiation factor-4A (eIF-4A), the human nuclear protein p68, and the Drosophila oocyte polar granule component vasa. BAT1 spans about 10 kb, is split into 10 exons of varying length, and encodes a protein of 428 amino acids (approximately 48 kDa). Human and pig BAT1 cDNAs display 95.6% identity in the coding region and 80% identity in the 5' and 3' noncoding regions. Several repeat sequences of different types were identified in introns of the porcine BAT1 gene. Three different mRNAs, 4.1, 1.7, and 0.9 kb, respectively, were detected in all tissues analyzed upon hybridization with porcine BAT1 cDNA. Transfection and expression of human BAT1 cDNA after tagging with a heterologous antibody recognition epitope revealed a nuclear localization of the hybrid protein. An MspI RFLP was detected in an SLA class I typed family, confirming the localization of the BAT1 gene in the porcine MHC. BAT1 thus encodes a putative nuclear ATP-dependent RNA helicase and is likely to have an indispensable function.

The PiGMaP consortium linkage map of the pig (Sus scrofa)

A linkage map of the porcine genome has been developed by segregation analysis of 239 genetic markers. Eighty-one of these markers correspond to known genes. Linkage groups have been assigned to all 18 autosomes plus the X Chromosome (Chr). As 69 of the markers on the linkage map have also been mapped physically (by others), there is significant integration of linkage and physical map data. Six informative markers failed to show linkage to these maps. As in other species, the genetic map of the heterogametic sex (male) was significantly shorter (approximately 16.5 Morgans) than the genetic map of the homogametic sex (female) (approximately 21.5 Morgans). The sex-averaged genetic map of the pig was estimated to be approximately 18 Morgans in length. Mapping information for 61 Type I loci (genes) enhances the contribution of the pig gene map to comparative gene mapping. Because the linkage map incorporates both highly polymorphic Type II loci, predominantly microsatellites, and Type I loci, it will be useful both for large experiments to map quantitative trait loci and for the subsequent isolation of trait genes following a comparative and candidate gene approach.

Linkage maps of porcine chromosomes 3, 6, and 9 based on 31 polymorphic markers

Linkage maps of porcine Chromosomes (Chrs) 3, 6, and 9, based on 31 polymorphic markers, are reported. The markers include 14 microsatellites, 12 RFLPs, three protein polymorphisms, and two blood group loci. The genetic interpretations of 11 RFLPs are documented. The markers were scored in a three-generation Wild Boar/Large White pedigree, and genetic maps were constructed on the basis of two-point and multi-point linkage analysis. Altogether the maps span a genetic distance of 216 cM, and previous physical assignments indicate that the linkage groups cover major parts of the three chromosomes. Significant differences in recombination rates between the sexes were observed for all three chromosomes. The recombination rate on the q arm of Chr 6 was markedly low. Sixteen loci are informative with regard to comparative mapping, that is, they have previously been mapped in the human and/or mouse genomes.

Characterization of porcine polymorphic microsatellite loci

Twenty-seven (CA)n and two (GA)n microsatellite clones were isolated out of a size-selected genomic pig library. These were sequenced and the number of uninterrupted dinucleotides was found to range from 12 to 26. Flanking primers were chosen for 11 dinucleotide repeats and optimal conditions for polymerase chain reaction (PCR) amplifications were established. Different microsatellite loci were amplified simultaneously by combining primer sets. Related and unrelated pigs were screened for length polymorphisms of the different microsatellite loci. The polymorphic information content (PIC) of these loci ranged between 0.62 and 0.83. Segregation studies in pig reference families established Mendelian inheritance. Locus S0022 was found to be X-linked.

A hypervariable pig DNA fragment

A new hypervariable tandem repeat was isolated from the pig genome and characterized by DNA sequence. The use of this DNA fragment as a probe in order to follow allelic segregation and DNA fingerprinting in pigs, horses and rabbits is documented.

The homology between the serum proteins PO2 in pig, Xk in horse and alpha 1B-glycoprotein in human

1. Pig serum Po2 protein and horse Xk protein were purified by FPLC, non-denaturing 2D agarose-PAGE and 2D IPG-PAGE. 2. The separated fractions were electroblotted to poly(4-vinyl-N-methylpyridinium iodide) coated GF/C glass fiber sheets. 3. The partial amino acid sequences and amino acid compositions of different genetic variants of the proteins were determined. 4. The results proved that previously reported polymorphic serum post-albumins in each of these species were homologous to human plasma alpha 1B-glycoprotein.