bluuebunny/crossref_metadata_2025 huggingface dataset:
Power of 22 microsatellite markers in fluorescent multiplexes for parentage testing in goats (Capra hircus)
Authors: Luikart G , Biju‐Duval M‐P , Ertugrul O , Zagdsuren Y , Maudet C , Taberlet P
Published: March 2003

Two multiplex systems, each containing 11 microsatellite loci, were developed for semi‐automated parentage testing in goats. Eight of the loci originate from goats, nine from cattle and five from sheep. Eighteen of the loci have been mapped to 16 different autosomes (in goats and cattle). Parentage exclusion probabilities were computed from allele frequencies in ∼30 unrelated individuals from each of four economically important breeds: Mongolian Native Cashmere, Turkish Angora, Swiss Saanen, and Spanish Murciana‐Grenadina. In cases where genotypes are known for one parent and an offspring, the 22 markers will exclude an (erroneously) alleged parent with a probability of > 0 ·999999 in the cashmere breed, > 0 ·99999 in Angora and Murciana‐Grenadina, and > 0 ·9999 in Saanen. The multiplexes provide very high power for individual identification as the probability of finding two identical genotypes for the 22 loci is < 1 in 1 ·1015 in each of the four breeds. The multiplexes will also be useful for studies of population structure, history, and diversity in goats and also in wild Capra species that represent important resources for genetic improvement of domestic breeds.
Determination of genetic relationships among five indigenous Chinese goat breeds with six microsatellite markers
Authors: Yang L , Zhao S H , Li K , Peng Z Z , Montgomery G W
Published: March 2003

Microsatellite variation was analyzed in five Chinese indigenous goat breeds, which include four Cashmere breeds (Tibetan, Neimonggol, Liaoning, Taihang) and one Hubei local breed (Matou) used for meat production. Five ovine and one bovine microsatellites, selected from eight ovine microsatellites and five bovine microsatellites were suitable for use in this study. With these six microsatellites, allele frequencies, heterozygosity, polymorphism in‐formation content (PIC) and effective allele number were calculated. A neighbor‐joining tree was constructed using Nei's standard genetic distance (1978). In the tree, Neimonggol and Liaoning were grouped together, then with Taihang; while Tibetan and Matou individually had their own branch. The genetic relationship of five breeds corresponds to their history and geographic origins.
Mitochondrial D‐loop sequence variation among the 16 maternal lines of the Lipizzan horse breed
Authors: Kavar T , Habe F , Brem G , Dovč P
Published: March 2003

Mitochondrial DNA from 49 Lipizzan horses representing 16 maternal lines from the original stud at Lipica was used for SSCP analysis and DNA sequencing. The SSCP analysis of the 444 bp long fragment of the d‐loop region extending from the tRNAPro gene to the central conserved sequence block revealed three distinct groups of SSCP patterns. Both ends of the
d‐loop region (378 bp and 310 bp), which are considered as the most variable regions within the mammalian mitochondrial DNA, were sequenced. According to 49 polymorphic sites identified within the both parts of the
d‐loop region, the 16 maternal lines were grouped into 13 distinct mitochondrial haplotypes. The minimal difference between two different haplotype DNA sequences was one nucleotide and the maximal 24 nucleotides. The inheritance of mitochondrial haplotypes was stable and no sequence variation potentially attributable to mutation within maternal line was observed. Considerable DNA sequence similarity of Lipizzan mitochondrial haplotypes with the haplotypes from other breeds was observed. Phylogenetic analysis of the sequence data revealed a dendrogram with three separated branches, supporting the historical data about the multiple origin of the Lipizzan breed.
Nomenclature for factors of the Dog Major Histocompatibility System (DLA), 1998: first report of the ISAG DLA Nomenclature Committee
Authors: Kennedy L J , Altet L , Angles J M , Barnes A , Carter S D , Francino O , Gerlach J A , Happ G M , Ollier W E R , Polvi A , Thomson W , Wagner J L
Published: March 2003

A Nomenclature committee for Factors of the Dog Major Histocompatibility System or Dog Leukocyte Antigen (DLA) has been convened under the auspices of the International Society for Animal Genetics (ISAG) to define a sequence based nomenclature for the genes of the DLA system. The remit of this committee includes:

assignment of gene names

rules for naming alleles

assignment of names to published alleles

assignment of names to new alleles

rules for acceptance of new alleles
Integration of the genetic and physical maps of the chicken macrochromosomes
Authors: Smith J , Paton I R , Bruley C K , Windsor D , Burt D W , Ponce de Leon F A , Burke D
Published: March 2003

A large amount of genetic mapping information has been obtained in the chicken from the East Lansing, Compton and Wageningen reference populations. Physical mapping information has however, been more limited. We have mapped 14 new clones, both genetically and physically, and all 14 have been assigned to macrochromosomes. The orientation of linkage groups E01C01C11W01 (Chr 1), E06C02W02 (Chr 2), E02C03W03 (Chr 3), E05C04W04 (Chr 4), E07E34C05W05 (Chr 5), E11C10W06 (Chr 6), E45C07W07 (Chr 7) and E43C12W11 (Chr 8) has been established. Here we present integrated maps of the eight macrochromosomes and the Z chromosome of the chicken and correlate genetic with physical distances for chromosomes 1–3 and the Z sex chromosome.
A pedigree‐based study of mitochondrial d‐loop DNA sequence variation among Arabian horses
Authors: Bowling A T , Del Valle A , Bowling M
Published: March 2003

Through DNA sequence comparisons of a mitochondrial d‐loop hypervariable region, we investigated matrilineal diversity for Arabian horses in the United States. Sixty‐two horses were tested. From published pedigrees they traced in the maternal line to 34 mares acquired primarily in the mid to late 19th century from nomadic Bedouin tribes. Compared with the reference sequence (GenBank X79547), these samples showed 27 haplotypes with altogether 31 base substitution sites within 397 bp of sequence. Based on examination of pedigrees from a random sampling of 200 horses in current studbooks of the Arabian Horse Registry of America, we estimated that this study defined the expected mtDNA haplotypes for at least 89% of Arabian horses registered in the US. The reliability of the studbook recorded maternal lineages of Arabian pedigrees was demonstrated by haplotype concordance among multiple samplings in 14 lines. Single base differences observed within two maternal lines were interpreted as representing alternative fixations of past heteroplasmy. The study also demonstrated the utility of mtDNA sequence studies to resolve historical maternity questions without access to biological material from the horses whose relationship was in question, provided that representatives of the relevant female lines were available for comparison. The data call into question the traditional assumption that Arabian horses of the same strain necessarily share a common maternal ancestry.
Microsatellite analysis reveals substantial genetic differentiation between contemporary New World and Old World Holstein Friesian populations
Authors: Hanslik S , Harr B , Brem G , Schlötterer C
Published: March 2003

Genotypic data from 39 microsatellite loci typed in 211 animals were used to assess the genetic differentiation between Old World and New World Holstein Friesian cattle populations. Gene diversities were similar in all five Holstein Friesian populations surveyed, ranging from 0.43 to 0.48. A tree of individuals based on the proportion of shared alleles indicated a clear distinction between Old World and New World Holstein Friesian populations. Similarly, genetic differentiation between populations, as measured byF⊂ST⊂, was highly significant. Using the split decomposition method, we were able to visualize the significant introgression of New World Holstein Friesian into European Holstein Friesian populations.
Identification and characterization of a new allele for the beta subunit of follicle‐stimulating hormone in Chinese pig breeds*
Authors: Li M D , Rohrer G A , Wise T H , Ford J J
Published: March 2003

During evaluation of follicle‐stimulating hormone‐beta (FSHB) expression in anterior pituitary glands by an RNase protection assay (RPA), the expected fragment of 205 nucleotides at positions 759–963 was not detected in one boar that had moderate plasma and pituitary FSH concentrations. After subcloning and sequencing, mRNA from this boar lacked an 11‐bp fragment (5′‐CATTTGGAAAC‐3′) at nucleotide positions 807–817 of the 3′‐untranslated region (3′‐UTR, D allele). Wild‐type FSHB (WT allele) was present in pituitary RNA and genomic DNA in both Meishan (MS) and White Composite (WC) pigs; whereas the D allele was present only in MS pigs (P< 0·01; 5/6 MS vs. 0/6 WC). Also, we found the D allele in five other Chinese breeds but absent in ten American Landrace, 11 Yorkshire and 17 Berkshire pigs. Additionally, the D allele had one silent nucleotide change in the coding region plus six, single nucleotide changes in the 3′‐UTR.
Biochemical, molecular and physiological characterization of a new β‐casein variant detected in Korean Cattle
Authors: Han S K , Shin Y C , Byun H D
Published: March 2003

There are seven known genetic variants of bovine β‐casein (β‐CN) ‐ A1, A2, A3, B, C, D and E. In this study, we identified a new genetic variant (named β‐CN H) which migrates slower than the other variants in acidic starch gel electrophoresis. We confirmed through protein and DNA sequence analyses that the H variant differs at five residues from the A2 sequence: Arg25/Cys, Leu88/Ile, Gln117/Glu, Glu175/Gln and Gln195/Glu. Of these substitutions the 25th residue was contained in the casein phosphopeptide (CPP) region. In rats, calcium solubilizing effect of the CPP of bovine variant H was increased by ≈ 23% compared with that of the CPP of non‐H. Using extensive Korean Bos taurus pedigrees, we confirmed that β‐CN H was controlled by a codominant allele.
The genetic structure of Spanish Celtic horse breeds inferred from microsatellite data
Authors: Cañon J , Checa M L , Carleos C , Vega‐Pla J L , Vallejo M , Dunner S
Published: March 2003

Partition of the genetic variability, genetic structure and relationships among seven Spanish Celtic horse breeds were studied using PCR amplification of 13 microsatellites on 481 random individuals. In addition, 60 thoroughbred horses were included. The average observed heterozygosity and the mean number of alleles were higher for the Atlantic horse breeds than for the Balearic Islands breeds. Only eight percentage of the total genetic variability could be attributed to differences among breeds (mean Fst ;≈ 0.08; P < 0.01). Atlantic breeds clearly form a separate cluster from the Balearic Islands breeds and among the former only two form a clear clustering, while the rest of Atlantic breeds (Jaca Navarra, Caballo Gallego and Pottoka) are not consistently differentiated. Multivariate analysis showed that Asturcon populations, Losina and Balearic Islands breeds are clearly separated from each other and from the rest of the breeds. In addition to this, the use of the microsatellites proved to be useful for breed assignment.
Patterns of ribosomal gene variation in elite commercial chicken pure line populations
Authors: Delany M E
Published: March 2003

The nucleolus organizer region (NOR) encodes the tandemly repeated 18S, 5 ·8S and 28S ribosomal (r) RNA genes. The NORs of broiler and layer commercial chicken pure lines were studied to establish the type and extent of genetic variation at this important locus. The parameters studied were gene copy number, repeat size, and diversity of NOR‐types. The populations were organized into three groups for analysis including brown‐egg broiler (13 lines), brown‐egg layer (six lines), and white‐egg layer (eight lines). The ribosomal gene copy number average of the white‐egg layer populations was significantly lower (329 genes) than that of the brown‐egg layers (372 genes); the brown‐egg broiler ribosomal gene average was intermediate (350 genes). The white‐egg layer populations exhibited a ribosomal repeat unit average size of 36 kb, significantly different from the brown‐egg layer and brown‐egg broiler average repeat unit size of 32 ·5 and 33 ·9 kb, respectively. NOR array size was similar among the three groups (6 mb). The brown‐egg broiler populations exhibited polymorphic NOR patterns, intra‐and interline, whereas the white‐egg layer populations were essentially monomorphic for NOR‐type; brown‐egg layers exhibited an intermediate level of NOR diversity. Some NOR array characteristics may be a function of breed origin as brown‐egg commercial populations, both broilers and layers, have similar breed origins and exhibited similarities for predominant repeat unit size as compared with white‐egg layer populations. However, the finding that brown‐egg broiler lines typically exhibit a greater number of segregating NOR‐types than brown‐egg layer lines suggests that the selection schemes of broiler vs. layer pure line populations may also have influenced the degree of variation at this gene complex.
Genetic distinctness of African, Asian and South American local chickens
Authors: Wimmers K , Ponsuksili S , Hardge T , Valle‐Zarate A , Mathur P K , Horst P
Published: March 2003

The genetic variability of various local chicken populations derived from Bolivia, India, Nigeria and Tanzania was evaluated with 22 microsatellites. Between two and 11 alleles per locus were detected. All populations showed high levels of heterozygosity with the lowest value of 45% for the population named Aseel from India and the highest value of 67% for Arusha from Tanzania. A dendrogram was constructed based on CHORD distance by upg ma analysis. Within this tree the populations were assorted according to their geographical origin. Bootstrapping values within the dendrogram were between 37 and 99%. The contribution of the determination of genetic variability with genetic markers to the decision on conservation and/or further use of the populations in crossbreeding programs designed to create genetic stocks with improved adaptability and productivity in tropical countries is discussed.
Localization of the locus responsible for Chediak–Higashi syndrome in cattle to bovine chromosome 28
Authors: Kunieda T , Ide H , Nakagiri M , Yoneda K , Konfortov B , Ogawa H
Published: March 2003

Chediak–Higashi syndrome in Japanese black cattle is a hereditary disease with prolonged bleeding time and partial albinism. In the present study, we mapped the locus responsible for the disease (CHS) by linkage analysis using microsatellite genotypes of paternal half‐sib pedigrees obtained from commercial herds. Analysis revealed significant linkage between theCHSlocus and marker loci on the proximal end of bovine chromosome 28. TheCHSlocus was mapped on the region incorporating the microsatellite markersBMC6020,BM2892, andRM016with recombination fraction 0 and lod score 4 ·9–11 ·2. We also assigned the bovine CHS1/LYST, the homologue of the gene responsible for human Chediak–Higashi syndrome, to bovine chromosome 28 using a bovine/murine somatic cell hybrid panel. These findings suggest that a mutation in the CHS1/LYST gene is likely to be responsible for Chediak–Higashi syndrome in Japanese black cattle.
Phylogenetic analysis of the tribe Bovini using microsatellites
Authors: Ritz L R , Glowatzki‐Mullis M‐L , MacHugh D E , Gaillard C
Published: March 2003

The objective of the present study was to determine if the generally accepted phylogenetic relationships in the tribe Bovini correspond to a phylogenetic scheme derived from polymorphisms at 20 bovine microsatellite loci. This study comprises 17 representative populations: eight Bos taurus, two Bos indicus, one Poëphagus, one Bibos, one Bison, three Bubalus and one Syncerus. Phylogenetic analyses using (δμ)2 and chord (DC) distances revealed substantial divergence among species. Neighbor‐joining trees with both distance measures showed only minor differences. Bos taurus and Bos indicus grouped first, followed by Bos frontalis (Mithan) and Bos grunniens (Yak), Bison bison branched off next and Bubalus bubalis and Syncerus caffer emerged as the two most divergent species from the Bos clade. These findings would suggest that Bos, Poëphagus, and Bibos should be integrated into the Bos genus with each group classified as a subgenus. On the other hand, Bison, Bubalus and Syncerus should each be considered a separate genus. Direct estimates of the divergence times were calculated using the (δμ)2 genetic distance. Bos taurus and Bos indicus were estimated to have diverged 0·31–0·82 MYA, Bos and Poëphagus: 0·57–1·53 MYA, Bos and Bibos: 0·57–1·52 MYA, Bos and Bison: 0·46–1·23 MYA, Bos and Bubalus: 1·85–4·93 MYA and Bos and Syncerus: 0·98–2·61 MYA.
Mapping quantitative trait loci for stress induced alterations in porcine leukocyte numbers and functions
Authors: Edfors‐Lilja I , Wattrang E , Andersson L , Fossum C
Published: March 2003

To identify quantitative trait loci (QTLs) with effects on ‘stress’ induced alterations of porcine immune functions, a number of immune capacity traits were analysed in the F2 generation of a Wild Boar ‐ Yorkshire intercross. All traits were measured prior, and one day after, exposure to experimental ‘stress’ (mixing and transport). The ‘stress’ protocol induced a decrease in numbers of circulating neutrophils and in spontaneous proliferation in vitro, whereas phagocytic capacity, mitogen induced proliferation and spontaneous IL‐2 activity increased. The IFN‐α production tended to decrease, although the individual variation was pronounced. More than 200 genetic markers have been scored in the entire pedigree and were used to trace the inheritance of individual chromosome segments. Wild Boar alleles were on average associated with higher mitogen induced IL‐2 activity and a slightly lower decrease in IFN‐α production after mixing and transport. Four QTLs with significant effects were identified; one influencing ‘stress’ induced alteration in numbers of neutrophils (chromosome 8), one influencing spontaneous proliferation after ‘stress’ (chromosome 2), one influencing mitogen induced IL‐2 activity after ‘stress’ (chromosome 6) and one influencing ‘stress’ induced alterations in mitogen induced IL‐2 activity (chromosome 12). In addition, several suggestive QTLs were indicated.
Sequence and transfection of BoLA‐DRB3 cDNAs
Authors: Russell G C , Fraser D C , Craigmile S , Oliver R A , Dutia B M , Glass E J
Published: March 2003

Bovine MHC (BoLA‐) DRB3 alleles encoded by the DH8A, DH22A and DH24A class II haplotypes were cloned from cDNA and characterized by sequence analysis. Comparison with other full‐length DRB3 sequences suggested that DRB3 alleles may have evolved through multiple lineages. All three BoLA‐DRB3 alleles were shown to express on the surface of transfected cells, and the transfectants were used to define or confirm the class II specificity of a panel of monoclonal antibodies.
Evolution of the ovine MHC DQA region
Authors: J G H Hickford , H J Ridgway , A P Escayg
Published: March 2003

Southern hybridisation was used to define an apparent gene duplication event at the ovine DQA2 locus. Approximately 500 sheep from five different breeds were genotyped at their DQA1 and DQA2 loci. A subset of these were selected for further characterisation. Southern hybridisation of TaqI digested DNA revealed no DQA1 region in some sheep. It was also noted in these DQA1 null animals the DQA2 specific probe hybridised to two bands. An EcoRV‐RFLP designed to distinguish copy number confirmed this duplication of the DQA2 region. The results showed that the duplication was exclusively associated with the DQA1 null haplotype and occured only in alleles DQA2‐F, ‐G, ‐I and ‐J. Comparison with bovine MHC genes revealed that they also contained a DQA1 null haplotype and that this haplotype was associated with a putative DQA3 gene. The potential for an ovine DQA3 locus is discussed.
Identification of a premature stop codon in the melanocyte‐stimulating hormone receptor gene (MC1R) in Labrador and Golden retrievers with yellow coat colour
Authors: Everts R E , Rothuizen J , van Oost B A
Published: March 2003

We have examined whether black/yellow coat colour in Labrador retrievers is controlled by allelic variants at the extension locus. As the gene encoding the melanocyte‐stimulating hormone receptor (MC1R) has been shown to correspond to the extension locus in several species, we have determined the genomic MC1R sequence in Labrador retrievers with black and with yellow coat colour. Using primers based on the fox (Vulpes vulpes) MC1R sequence we initially isolated and sequenced the innerpart of the canine MC1R. By means of inverse PCR we succeeded in the characterization of both flanking regions of the MC1R gene (Genbank: AF064455). Comparison of the complete MC1R sequences of a yellow and a black Labrador retriever revealed a single C→T mutation at nucleotide position 916 in the yellow dog. This transition changed the codon for arginine at position 305 into a stop codon, resulting in the elimination of the evolutionary strongly conserved 10 carboxyterminal amino acid residues. With an allele‐specific‐oligonucleotide (ASO) test it was shown that the mutation cosegregated with the recessively inherited yellow coat colour in the Labrador retriever. Golden retrievers also appeared to be homozygous for the mutation. Seventeen other breeds were all negative for the mutation. Since the Labrador and Golden retriever are closely related, we suggest a common founder for the yellow coat colour in Labrador and Golden retrievers.
Identification and characterization of a set of 100 tri‐ and dinucleotide microsatellites in the canine genome
Authors: Jouquand S , Priat C , Hitte C , Lachaume P , André C , Galibert F
Published: March 2003

A set of 100 canine microsatellite markers – 83 dinucleotides and 17 trinucleotides – is reported. A study of their frequency in the dog genome showed that, while the frequency of the CA repeats is one (CA)n every 47 kb, the 10 trinucleotidic frequencies vary from one every 117 kb (AGG)n to one every 875 kb (AGT)n. Polymorphism analysis performed on 16 unrelated mongrel dogs showed that 80% of dinucleotides are polymorphic, while only 30% of the trinucleotides are so. Of this set of 100 markers, 56 have been mapped on the RHDF5000 dog/hamster whole genome radiation hybrid panel. Moreover, through systematic BLAST analogy searches of the microsatellite‐containing clone sequence, three new dog genes could be identified, based on their human ortholog. All of the markers presented may prove useful in physical mapping methods, and polymorphic microsatellites in genetic linkage studies or parentage controls in dog.
Molecular characterization of major and minor MHC class I and II genes in B21‐like haplotypes in chickens
Authors: Juul‐Madsen H R , Dalgaard T S , Afanassieff M
Published: March 2003

The major histocompatibility complex (MHC) sequences of three B21‐like haplotypes deriving from very different origins including the Red Jungle Fowl Gallus Gallus gallus were compared with the MHC sequences of the standard B21 haplotype from Scandinavian White Leghorn Gallus domesticus. The present analysis reveals two cDNA sequences for B‐F and two cDNA sequences for B‐LB for every B21‐like haplotype, including B21 itself. Contrary to expectation, no sequence polymorphism in the antigen‐binding domains of the MHC genes, between the investigated haplotypes, was found. The relative level of MHC class I molecules on the surface of leukocytes measured by flow cytometry was also analysed and found to be low in Marek's Disease (MD)‐resistant B haplotypes (B21 and B21‐like) and high in MD‐susceptible B haplotypes (B15 and B19). However, in heterozygous (resistant/susceptible) animals, the relative level was almost as high as in susceptible haplotypes.
Detection of the causal mutation for canine leukocyte adhesion deficiency (CLAD) using pyrosequencing
Authors: Kijas J M H , Juneja R K , Gäfvert S , Andersson L
Published: March 2003

A missense mutation in the ITGB2 gene causes canine leukocyte adhesion deficiency (CLAD) in Irish setters. We constructed a diagnostic test to identify heterozygous CLAD carriers based on a newly developed technology termed pyrosequencing. Although primarily designed for high‐speed generation of DNA sequence in a gel‐free system, the technology can be applied to rapid single‐nucleotide polymorphism analysis in a clinical setting. The testing of 339 dogs originating from a total of 10 countries was conducted and CLAD carriers were identified within every country where more than one sample was analysed. This indicates that the CLAD mutation is widespread and that there is a strong need for a robust diagnostic test.
Male‐mediated introgression of Bos indicus genes into Argentine and Bolivian Creole cattle breeds
Authors: Giovambattista G , Ripoli M V , De Luca J C , Mirol P M , Lirón J P , Dulout F N
Published: March 2003

The geographic distribution and frequency of Bos taurus and Bos indicus Y chromosome haplotypes amongst Argentine and Bolivian Creole cattle breeds were studied, using cytogenetic and molecular genetic techniques. A complete correspondence between Y chromosome morphology and the haplotype of the Y‐linked microsatellite marker INRA 124 was found in all males examined. The taurine and indicine haplotypes were detected in 85·7 and 14·3% of the males studied, respectively, although these frequencies varied amongst the different breeds examined. The geographic distribution of this polymorphism suggests a pattern of zebu introgression in South America. The highest frequencies of the Zebu Y‐chromosome are found in Brazilian populations (43–90%), in the eastern part of the continent, while it is absent in the southermost breeds from Uruguay and Argentina. Bolivan breeds, at the centre of the continent, exhibit intermediate values (17–41%). This east/west and north/south gradient of male Zebu introgression could be explained by historical events and environmental factors.
Construction and characterization of an ovine BAC contig spanning the callipyge locus
Authors: Segers K , Berghmans S , Georges M , Charlier C , Vaiman D , Shay T , Cockett N , Meyers S , Beever J
Published: March 2003

We describe the construction of an ovine BAC contig spanning a 4·6 centimorgan (cM) chromosome segment known to contain the callipyge (CLPG) locus. The contig comprises 21 ovine BAC clones jointly covering approximately 900 kilobases (Kb). Two gaps in the BAC contig, spanning 10 and 7·5 Kb, respectively, were bridged by long range PCR. The corresponding chromosome region was shown to be characterized by an unusually low Kb to cM ratio (164 Kb/cM) and a high density of NotI sites (1:126 Kb) possibly reflecting a high gene density in the corresponding chromosome region. Equivalent amplification of 64 sequence tagged sites spanning the corresponding region from homozygous +/+ and CLPG/CLPG individuals disproves the hypothesis of a major deletion causing the CLPG mutation.
cDNA cloning and genetic polymorphism of the swine major histocompatibility complex (SLA) class II DMA gene
Authors: Ando A. , Kawata H. , Murakami T. , Shigenari A. , Shiina T. , Sada M. , Tsuji T. , Toriu A. , Nakanishi Y. , Mitsuhashi T. , Sekikawa K. , Inoko H.
Published: March 2003

cDNA clones corresponding to the swine histocompatibility complex (SLA: swine leucocyte antigen)‐DM α chain were isolated using the polymerase chain reaction (PCR) products from the third exon in the human HLA‐DMA gene as a probe. Amino acid comparative analysis revealed that these clones were more closely related to the bovine and human DMA genes than to the other swine class II genes α chain genes, DRA, DQA and DOA. These results suggest that the SLA‐DMA gene is expressed and may function, like HLA‐DM, as an important modulator in class II restricted antigen processing in swine. Furthermore, based on the sequences and PCR–restriction fragment length polymorphism (PCR–RFLP) patterns in the SLA‐DMA gene, no allelic variation was recognized in the second exon, but five allelic variations were recognized in the third exon in five different breeds of swine. These DMA alleles were defined by variation at four nucleotide positions. Two of these alleles resulted in an amino acid substitution. These results suggest that SLA‐DMA has little polymorphism as observed in HLA‐DMA and mouse H2‐Ma.
Differential introgression of uniparentally inherited markers in bison populations with hybrid ancestries
Authors: Ward T. J. , Skow L. C. , Gallagher D. S. , Schnabel R. D. , Nall C. A. , Kolenda C. E. , Davis S. K. , Taylor J. F. , Derr J. N.
Published: March 2003

Historical hybridization between Bison bison (bison) and Bos taurus (cattle) has been well documented and resulted in cattle mitochondrial DNA (mtDNA) introgression, previously identified in six different bison populations. In order to examine Y chromosome introgression, a microsatellite marker (BYM‐1) with non‐overlapping allele size distributions in bison and cattle was isolated from a bacterial artificial chromosome (BAC) clone, and was physically assigned to the Y chromosome by fluorescence in situ hybridization. BYM‐1 genotypes for a sample of 143 male bison from 10 populations, including all six populations where cattle mtDNA haplotypes were previously identified, indicated that cattle Y chromosome introgression had not occurred in these bison populations. The differential permeability of uniparentally inherited markers to introgression is consistent with observations of sterility among first generation hybrid males and a sexual asymmetry in the direction of hybridization favouring matings between male bison and female cattle.
Linked markers exclude KIT as the gene responsible for appaloosa coat colour spotting patterns in horses
Authors: Terry R. R. , Bailey E. , Bernoco D. , Cothran E. G.
Published: March 2003

The appaloosa coat colour pattern of the horse is similar to that caused by the rump‐white (Rw) gene in the mouse. In the mouse Rw colour pattern is the result of an inversion involving the proto‐oncogene c‐kit (KIT). Therefore, we investigated KIT as a candidate gene that encodes the appaloosa coat colour gene (Lp) in horses. KIT plays a critical role in haematopoiesis, gametogenesis, and melanogenesis and encodes a transmembrane tyrosine kinase receptor that belongs to the PDGF/CSF‐1/c‐KIT receptor subfamily. Half‐sib families segregating for Lp were uninformative for a reported polymorphism in KIT. However, KIT is located on horse chromosome 3 close to albumin (ALB), serum carboxylesterase (ES), vitaminD‐binding protein (GC) and microsatellite markers ASB23, LEX007, LEX57, and UCDEQ437. Indeed, KIT and ASB23 were localized to ECA3q21–22.1 and 3q22.1–22.3, respectively, by fluorescent in situ hybridization. Family studies were conducted to investigate linkage of Lp to these markers using eight half‐sib families in which Appaloosa stallions were mated to solid coloured mares. Linkage of Lp to the chromosome region containing ES, ALB, GC, ASB23, UCDEQ437, LEX57, and LEX007 was investigated by a multipoint linkage analysis using the computer program GENEHUNTER. LOD scores over the interval under investigation ranged from –4.28 to –12.48, with a score of –12.48 at the location for ASB23. Therefore, it was concluded that appaloosa (Lp) is not linked to any of the tested markers on ECA3, and thus Lp is unlikely to be the product of KIT.
Three new MHC haplotypes in broiler breeder chickens
Authors: Livant E. J. , Zheng D. , Johnson L. W. , Shi W. , Ewald S. J.
Published: March 2003

Six distinct serotypes of the chicken B blood group system (which encodes the major histocompatibility complex) were identified in a commercial broiler breeder line (Line C). The B serotypes were compared by B‐G restriction fragment length polymorphism (RFLP) analysis, allele‐specific PCR typing test for B‐LBII family genes and nucleotide sequence analysis of expressed B‐F and B‐LBII family genes. The results indicated the existence of seven distinct B haplotypes. Nucleotide sequence analysis demonstrated that three of the Line C haplotypes encode new B‐F and B‐LB alleles.
Radiation hybrid comparative mapping between human chromosome 17 and porcine chromosome 12 demonstrates conservation of gene order
Authors: Shi X.‐W. , Fitzsimmons C. J. , Genêt C. , Prather R. , Whitworth K. , Green J. A. , Tuggle C. K.
Published: March 2003

A comparative study of human chromosome 17 (HSA17) and pig chromosome 12 (SSC12) was conducted using both somatic cell hybrid panel (SCHP) and radiation hybrid (RH) panel analysis. Sequences from an expressed sequence tag (EST) project in pig reproduction were examined and six genes and ESTs originally believed to map to HSA17 were selected for this study. The genes/ESTs were TATA box binding protein‐associated factor (TAF2N/RBP56), α‐2‐plasmin inhibitor (SERPINF2/PLI), H3 histone family 3B (H3F3B), aminopeptidase puromycin sensitive (NPEPPS), an expressed sequence tag (ESTMI015) and P311 protein (P311). The SCHP analysis mapped five genes/ESTs (TAF2N, H3F3B, SERPINF2, NPEPPS and ESTMI015) to SSC12q11‐q15 and SSC12p11‐p15 with 100% concordance, and assigned P311 to SSC2 (1/2q24)‐q29 with 100% concordance. Radiation hybrid analysis of all six genes confirmed the SCHP mapping results, with average retention frequency of 25%. Recent human sequence data demonstrated that P311 is actually located on HSA5q. As HSA5q and SSC2q show conserved syntenic regions predicted from bi‐directional painting, our P311 mapping data is consistent with these results. An expanded comparative SSC12 RH map integrating the five new type I markers and 23 previously mapped loci was established using a LOD score threshold of 4.8. The gene order of the five genes/ESTs on the SSC12 framework RH map (H3F3B–ESTMI015–NPEPPS–TAF2N–SERPINF2) is identical to the HSA17 GB4 map but with inversion of the map as conventionally drawn.
Bovine melanocortin receptor 4: cDNA sequence, polymorphisms and mapping
Authors: Haegeman A. , Coopman F. , Jacobs K. , Mattheeuws M. , Van Zeveren A. , Peelman L.
Published: March 2003

A cDNA encoding the bovine melanocortin receptor 4 (MC4R) was cloned and sequenced. Comparing human, pig and rat homologues showed a 87, 85 and 89% identity on the DNA level, respectively, and over 90% on the protein level. The bovine MC4R gene was mapped to BTU 24 by radiation hybrid mapping. Two nucleotide changes were identified by single stranded conformation polymorphism (SSCP) and sequencing. The substitutions proved to be a T to C and G (allele B) to A (allele A) resulting, respectively, in a conservative valine to alanine substitution (Val 145 Ala) and an alanine to threonine (Ala 172 Thr). Using PCR‐RFLP, 13 different cattle breeds were screened for the presence of the Ala 172 Thr substitution. With the exception of one Red Pied animal, allele A could only be detected in Red Holstein animals.
Transcriptome of channel catfish (Ictalurus punctatus): initial analysis of genes and expression profiles of the head kidney
Authors: Cao D. , Kocabas A. , Ju Z. , Karsi A. , Li P. , Patterson A. , Liu Z.
Published: March 2003

Analysis of expressed sequence tags (ESTs) is an efficient approach for gene discovery, expression profiling, and development of resources useful for functional genomics studies. As part of the transcriptome analysis in channel catfish (Ictalurus punctatus), we have conducted EST analysis using a cDNA library made from the head kidney. We analysed 2228 EST clones. Orthologues were established for 1495 (67.1%) clones representing 748 genes, of which 545 (36.5%) clones were singletons. The remaining 733 (32.9%) clones represent unknown gene clones, for which the number of genes has not yet been determined.
Molecular cloning, expression analysis, promoter characterization, and chromosomal localization of the bovine PREF1 gene
Authors: Minoshima Y. , Taniguchi Y. , Tanaka K. , Yamada T. , Sasaki Y.
Published: March 2003

Pre‐adipocyte factor‐1 (pref‐1), originally identified in mouse 3T3‐L1 pre‐adipocytes, is known to play a key role in inhibiting the adipose conversion. As a first step to study the involvement of the PREF1 gene in intramuscular adipose tissue development in cattle, which has an economic importance for beef cattle, we have isolated the bovine PREF1 cDNA and genomic clones and characterized expression in abdominal adipose and promoter region of the bovine PREF1 gene. We have detected two bovine PREF1 splice‐isoforms, PREF1C2 and PREF1A, in abdominal fat tissue. The RT‐PCR experiment revealed that the two isoforms are identified in neonatal, but no in adult abdominal fat tissue, suggesting age‐dependent suppression of the bovine PREF1 gene expression in the form of PREF1C2 and PREF1A in abdominal fat tissue. By mapping the regulatory region of this gene, we have shown that at least two regions within 1121 bp upstream of putative transcription start site are sufficient to confer promoter activity, when accompanied by a short region including the transcription start site. The chromosomal location of the PREF1 gene was determined by fluorescence in situ hybridization (FISH). The PREF1 gene locates on bovine chromosome 21q24.
Physical localization and order of genes in the class I region of the bovine MHC
Authors: McShane R. D. , Gallagher D. S. , Newkirk H. , Taylor J. F. , Burzlaff J. D. , Davis S. K. , Skow L. C.
Published: March 2003

Fluorescence in situ hybridization (FISH) analyses were used to order 16 bacterial artificial chromosomes (BAC) clones containing loci from the bovine lymphocyte antigen (BoLA) class I and III regions of bovine chromosome 23 (BTA23). Fourteen of these BACs were assigned to chromosomal band locations of mitotic and pachytene chromosomes by single‐ and dual‐colour FISH. Dual‐colour FISH confirmed that class II DYA is proximal to and separated from BoLA class I genes by approximately three chromosome bands. The FISH results showed that tumour necrosis factor α (TNFA), heat shock protein 70 (HSP70.1) and 21 steroid dehydrogenase (CYP21) are closely linked in the region of BTA23 band 22 along with BoLA class I genes, and that male enhanced antigen (MEA) mapped between DYA and the CYP21/TNFA/HSP70·1 gene region. All BAC clones containing BoLA class I genes mapped distal to CYP21/TNFA/HSP70.1 and centromeric to prolactin (PRL). Myelin oligodendrocyte glycoprotein (MOG) was shown to be imbedded within the BoLA class I gene cluster. The cytogenetic data confirmed that the disrupted distribution of BoLA genes is most likely the result of a single large chromosomal inversion. Similar FISH results were obtained when BoLA DYA and class I BAC clones were mapped to discrete chromosomal locations on the BTA homologue in white‐tailed deer, suggesting that this chromosomal inversion predates divergence of the advanced ruminant families from a common ancestor.
Nomenclature for factors of the dog major histocompatibility system (DLA), 2000: second report of the ISAG DLA Nomenclature Committee
Authors: Kennedy L. J. , Angles J. M. , Barnes A. , Carter S. D. , Francino O. , Gerlach J. A. , Happ G. M. , Ollier W. E. R. , Thomson W. , Wagner J. L.
Published: March 2003

The International Society for Animal Genetics (ISAG) Dog Leukocyte Antigen (DLA) Nomenclature Committee met during the ‘Comparative Evolution of the Mammalian major Histocompatibility Complex (MHC)’ meeting in Manchester, UK on 10 September 2000. The main points discussed were the naming of class I genes and alleles, and the inclusion of alleles from other canidae.
Polymorphic microsatellites developed by cross‐species amplifications in common pheasant breeds
Authors: Baratti M. , Alberti A. , Groenen M. , Veenendaal T. , Fulgheri F. D.
Published: March 2003

Genetic variability was analysed in two common breeds of pheasant (Phasianus colchicus L. 1758) by means of cross‐species amplifications of microsatellite loci: 154 chicken, Gallus gallus and 32 turkey, Meleagris gallopavo, primers were tested for amplification of pheasant DNA. Thirty‐six primers (25 specific for chicken and 11 for turkey) amplified pheasant DNA. Fifteen markers yielded specific products and were tested for polymorphism. Eight of them (55%) were polymorphic, with an average polymorphism of two alleles per locus. Specific polymerase chain reaction (PCR) products were sequenced; repeats were found in 11 of the 15 markers, although only two loci showed the same repeat and could be homologous to chicken ones.
cDNA cloning and physical mapping of porcine 3β‐hydroxysteroid dehydrogenase/Δ5‐Δ4 isomerase
Authors: Von Teichman A. , Joerg H. , Werner P. , Brenig B. , Stranzinger G.
Published: March 2003

The 3β‐hydroxysteroid dehydrogenase/Δ5‐Δ4‐isomerase (3β‐HSD) enzymes are essential for the biosynthesis of steroid hormones. The 3β‐HSD gene family has been reported to encode for different isoenzymes which function either as dehydrogenase/isomerase or as reductase. The 3β‐HSD enzymes are involved in the formation of the pheromone androstenone (5α‐androst‐16‐ene‐3‐one) which contributes to the unpleasant odour present in the meat of uncastrated boars. An reverse‐transcription–polymerase chain reaction (RT–PCR) probe from porcine testicular tissue of a 3β‐HSD enzyme was used to screen a porcine adipose tissue cDNA library. Both strands of the positive clones were sequenced and the putative coding sequence of 1122 nucleotides encodes 374 amino acids. Comparison of the putative open reading frame with the bovine and the human type I homologues revealed 85.6 and 79.3% identity, respectively. Fluorescence in situ hybridization (FISH) was performed with a labelled PAC clone containing the gene of interest. The 3β‐HSD gene was mapped to the porcine chromosome 4q16‐4q21 which is in accordance with the comparative gene map.
Mapping of rabbit chromosome 1 markers generated from a microsatellite‐enriched chromosome‐specific library
Authors: Korstanje R. , Gillissen G. F. , Den Bieman M. G. , Versteeg S. A. , Van Oost B. , Fox R. R. , Van Lith H. A. , Van Zutphen L. F. M.
Published: March 2003

A genomic DNA library was produced from flow‐sorted rabbit chromosome 1 and enriched for fragments containing CA‐repeats. Clones containing CA‐repeats were identified and primers for amplification of the microsatellite were developed after sequencing the clone. The degree of polymorphism was tested in rabbits from different breeds. This approach identified 12 microsatellite markers which could be used for studying linkage relationships in the progeny of an F2‐intercross: (AX/JUxIIIVO/JU) F2, and two backcrosses: (OS/JxX/J)X/J and (WH/JxX/J)X/J. Seven of these markers were mapped on chromosome 1.
Microsatellite diversity, pedigree relatedness and the contributions of founder lineages to thoroughbred horses
Authors: Cunningham E. P. , Dooley J. J. , Splan R. K. , Bradley D. G.
Published: March 2003

The thoroughbred (TB) horse is one of the oldest breeds of domestic animals, with pedigree records spanning three centuries. Because the population is essentially closed, there is concern about loss of genetic variation. Here we report two parallel analyses. In the first, genetic variation in the current population is measured using data from 13 microsatellite loci in 211 horses with relationships calculated based on allele sharing. In the second analysis, pedigree information is used to calculate genetic relationships between animals based on shared ancestry. These two measures of relationship are compared and shown to be closely related. Together, they provide an estimate of the amount of genetic variation which existed in founder animals. This study confirms the narrow genetic base of the breed and provides comprehensive analysis of contributions of founder animals. Seventy‐eight percent of alleles in the current population are derived from 30 founders, 27 of these male. Ten founder females account for 72% of maternal lineages, while one founder stallion is responsible for 95% of paternal lineages.
Assessing genetic diversity in Italian goat populations using AFLP® markers
Authors: Ajmone‐Marsan P. , Negrini R. , Crepaldi P. , Milanesi E. , Gorni C. , Valentini A. , Cicogna M.
Published: March 2003

Amplified fragment length polymorphism (AFLP®) markers were used to investigate the genetic variation in a sample of seven goat (Capra hircus) populations. A total of 210 individuals (30 per population) were analysed using seven selected AFLP primer combinations that produced 219 clear polymorphisms. Four autochthonous goat breeds (Bionda dell’Adamello, Frisa, Orobica and Verzaschese), two primary populations, one from the Lombardy Alps (Val di Livo) and the other from Sardinia island (Sarda) and a reference cosmopolitan breed (Saanen) were included in the analysis. The expected heterozygosity (Het) did not differ significantly among breeds (range 0.21–0.24). No breed specific markers were identified. The variability at AFLP loci was largely maintained within breeds, as indicated by the coefficient of genetic differentiation (Gst) value (0.11). Dice similarities calculated between pairs of individuals belonging to the same or to different breeds largely overlapped. Bootstrapping on markers indicated that the coefficient of variation (CV) of the genetic indexes tested decreases only marginally by adding markers over 100 AFLPs. Cluster analysis based on standard genetic distance between breeds indicates that Sarda is the most distant population, while Bionda, Frisa, Verzaschese and Val di Livo seem to be highly related populations. Interestingly, Saanen is closer than Orobica to the other four goat populations of the Lombardy Alps. Principal co‐ordinates analysis based on Dice similarities confirms these observations. Genetic diversity of the goat populations investigated confirms what is expected on the basis of their geographical location. Results from Orobica are not correlated with geographical distances and may reflect undocumented migrations and gene flows and identify an original genetic resource.
Development of 112 unique expressed sequence tags from chicken liver using an arbitrarily primed reverse transcriptase–polymerase chain reaction and single strand conformation gel purification method
Authors: Carré W. , Diot C. , Fillon V. , Crooijmans R. P. M. A. , Lagarrigue S. , Morrisson M. , Vignal A. , Groenen M. A. M. , Douaire M.
Published: March 2003

In order to provide information on chicken genome expression, expressed sequence tags (ESTs) were developed from chicken liver RNAs using a method based on arbitrarily primed reverse transcription–polymerase chain reaction (RT–PCR) of total RNAs. The method is similar to differential display, using one base anchored oligo‐d(T) reverse‐primers and 20‐mer arbitrary forward‐primers. A purification step by single strand conformation gel electrophoresis was added before sequencing. With a ratio of 112 unique sequences out of 155, we found this method to be highly effective when compared with EST production with randomly selected clones from non‐subtracted, non‐normalized libraries. A large proportion of the ESTs sequenced correspond to genes involved in transcriptional and post‐transcriptional events. Cytogenetic mapping was performed for a subset of ESTs and four regions of conserved synteny between chicken and human were confirmed.
Cloning of porcine IGF1 receptor cDNA and detection of sequence polymorphisms using RT‐PCR
Authors: Harumi T. , Maruyama K. , Kagami H. , Sano A. , Matsubara Y. , Tagami T. , Naito M.
Published: March 2003

A cDNA encoding the porcine type 1 insulin‐like growth factor receptor (IGF1R) was amplified by reverse transcriptase‐polymerase chain reaction (RT‐PCR). The sequence of a 4.2‐kb product was determined and had an open reading frame, encoding 1367 amino acids with 98.1 and 95.2% sequence similarity to the human and rat IGF1R, respectively. In the comparison of RT‐PCR derived IGF1R sequences from 12 unrelated pigs, 12 silent sequence variants were found.