bluuebunny/crossref_metadata_2025 huggingface dataset:
Complete sequence of the Japanese quail (Coturnix japonica) mitochondrial genome and its genetic relationship with related species
Authors: Nishibori M. , Hayashi T. , Tsudzuki M. , Yamamoto Y. , Yasue H.
Published: March 2003

The Japanese quail (Coturnix japonica; JQ) is one of the domesticated fowl species of Japan. To provide DNA sequence information for examination of its phylogenetic position in the order Galliformes, the complete sequence of the JQ mitochondria was determined. Sequence analysis revealed that the JQ mitochondrial genome is a circular DNA of 16 697 basepairs (bp), which is smaller than the chicken mitochondrial DNA of 16 775 bp, but the genomic structure of JQ mitochondria was the same as that of the chicken. The sequence homologies of all mitochondrial genes including those for 12S and 16S ribosomal RNA (rRNA), between Japanese quail and chicken ranged from 78.0 to 89.9%. Because the sequences of NADH dehydrogenase subunit 2 and cytochrome b genes had been reported in five species [Phasianus colchicus (ring‐neck pheasant: RP), Gallus gallus domesticus (chicken: CH), Perdix perdix (grey partridge: GP), Bambusicola thoracia (Chinese bamboo partridge: CP), and Aythya americana (redhead: RH)], the concatenated nucleotide sequences (2184 bp) and amino acid sequences of these two genes were used in a phylogenetic analysis of JQ against these five species using a maximum likelihood (ML) method. Using the first and second bases of the codons, and the third base of the codons indicated a phylogenic tree of [RH, (RP, GP), (JQ, (CH, CP))]. A phylogenic tree of [RH, JQ, (RP, GP), (CH, CP)] was determined using amino acid sequences. Because the local bootstrap values for the JQ branch in these trees are not high, additional sequence is necessary for construction of a reliable tree.
Identification of porcine Lhx3 and SF1 as candidate genes for QTL affecting growth and reproduction traits in swine
Authors: Smith T. P. L. , Showalter A. D. , Sloop K. W. , Rohrer G. A. , Fahrenkrug S. C. , Meier B. C. , Rhodes S. J.
Published: March 2003

The distal portion of the long arm of porcine chromosome 1 has been shown to harbour several quantitative trait loci affecting growth and reproductive traits in swine. In order to identify potential candidate genes that might underlie these effects, a comparative mapping analysis was undertaken to define the extent of orthologous segments of human chromosome 9. A microsatellite associated with heat shock protein (HSP) A5 was used to define the proximal boundary of the quantitative trait loci (QTL) region, which suggests the human orthologue of the gene(s) responsible for the observed effects lies between HSPA5 and the q arm telomere of human chromosome 9. Examination of this region revealed two candidate genes with known roles in production of hormones essential to growth and reproductive function. The steroidogenic factor 1 and Lhx3 LIM homeodomain transcription factor genes were mapped to 123 and 155 cM, respectively, of the Sus scrofa chromosome 1 (SSC1) linkage group, placing both genes within the confidence interval for the observed QTL. To further evaluate Lhx3, we examined the expression profile during porcine embryonic development. Low levels were detected at early embryonic stages, when development of the nervous system is proceeding. A transient increase in expression level is observed during the time of pituitary organogenesis and again at the time of differentiation of anterior pituitary cells, with relatively high levels of expression persisting in the adult pituitary gland. This ontology is consistent with Lhx3 being a candidate gene for the QTL.
A strategy to identify positional candidate genes conferring Marek’s disease resistance by integrating DNA microarrays and genetic mapping
Authors: Liu H.‐C. , Cheng H. H. , Tirunagaru V. , Sofer L. , Burnside J.
Published: March 2003

Marker‐assisted selection (MAS) to enhance genetic resistance to Marek’s disease (MD), a herpesvirus‐induced T cell cancer in chicken, is an attractive alternative to augment control with vaccines. Our earlier studies indicate that there are many quantitative trait loci (QTL) containing one or more genes that confer genetic resistance to MD. Unfortunately, it is difficult to sufficiently resolve these QTL to identify the causative gene and generate tightly linked markers. One possible solution is to identify positional candidate genes by virtue of gene expression differences between MD resistant and susceptible chicken using deoxyribonucleic acid (DNA) microarrays followed by genetic mapping of the differentially‐expressed genes. In this preliminary study, we show that DNA microarrays containing ∼1200 genes or expressed sequence tags (ESTs) are able to reproducibly detect differences in gene expression between the inbred ADOL lines 63 (MD resistant) and 72 (MD susceptible) of uninfected and Marek’s disease virus (MDV)‐infected peripheral blood lymphocytes. Microarray data were validated by quantitative polymerase chain reaction (PCR) and found to be consistent with previous literature on gene induction or immune response. Integration of the microarrays with genetic mapping data was achieved with a sample of 15 genes. Twelve of these genes had mapped human orthologues. Seven genes were located on the chicken linkage map as predicted by the human–chicken comparative map, while two other genes defined a new conserved syntenic group. More importantly, one of the genes with differential expression is known to confer genetic resistance to MD while another gene is a prime positional candidate for a QTL.
Phylogenetic relationships of Asian and European pig breeds determined by mitochondrial DNA D‐loop sequence polymorphism
Authors: Kim K‐I. , Lee J‐H. , Li K. , Zhang Y‐P. , Lee S‐S. , Gongora J. , Moran C.
Published: March 2003

Phylogenetic relationships among Asian and European pig breeds were assessed using 1036 bp of mitochondrial DNA (mtDNA) D‐loop sequences. An unweighted pair‐group method with arithmetic mean (UPGMA) tree was constructed on the basis of maximum likelihood distances using sequences determined for three Cheju (Korea), 11 Chinese, one Westran (Australian feral origin) and two European pigs (Berkshire and Welsh), and also published sequences for four Japanese (including two Wild Boars), one Yucatan miniature, five European (including Large White, Landrace, Duroc, Swedish and Wild Boar) and two Meishan pigs. The Colombian collared peccary (Tayassu tajacu) sequence was also determined and used as an outgroup. The maximum parsimony with heuristic search method was used to determine bootstrap support values. Asian‐type pigs clustered together (bootstrap support 33%), but were separate from European‐type pigs that also clustered together (93%). The Westran pig, derived from the feral descendants of pigs inhabiting Kangaroo Island of South Australia, clustered with Asian pigs, demonstrating Asian origin of their mitochondria. Berkshire and Large White clustered with Asian pigs, indicating that Asian pigs were involved in the development of these breeds. Our findings clearly demonstrate that pigs indigenous to China, Korea and Japan are only recently diverged from each other and distinctly different from European‐type pigs. European pig breeds consist of pigs with mitochondria of Asian and non‐Asian type, some of which were formed from closely related maternal ancestors, if not from a single ancestor.
A case of intersexuality in pigs associated with a de novo paracentric inversion 9 (p1.2; p2.2)
Authors: Pinton A. , Pailhoux E. , Piumi F. , Rogel‐Gaillard C. , Darré R. , Yerle M. , Ducos A. , Cotinot C.
Published: March 2003

In several mammalian species, genetic defects can be responsible for the interruption of and/or the deviation from the sequential steps of normal gonadal differentiation, leading to a sex‐reversal syndrome. In pigs, female‐to‐male sex‐reversal conditions are particularly frequent, but their aetiologies remain unclear. Chromosomal abnormalities that co‐occur with sex‐reversal disorders can be useful in the identification of loci containing responsible or susceptibility genes. This report describes a female‐to‐male SRY‐negative intersex pig with a de novo paracentric inversion of the short arm of one chromosome 9 (p1.2; p2.2). We have fine mapped the proximal chromosomal breakpoint of this rearrangement because it corresponded to a region potentially involved in the pig intersexuality. Fluorescent in situ hybridization (FISH) experiments carried out with Bacterial Artificial Chromosome (BAC) clones located within the critical region defined by genetic linkage analysis and ordered on the porcine RH map allowed us to locate the proximal breakpoint between markers SW2571 and SW539. Further investigations are currently in progress to find new markers inside this interval, in order to determine the BAC in which the break occurred.
Homogeneity of recombination rate within a conserved region on BTA3 that contains QTL
Authors: Frank M. T. , Park C. , Rodriguez‐Zas S. , Lewin H. A.
Published: March 2003

The D3S20‐D3S34‐D3S3 region on BTA3 contains quantitative trait loci (QTL) controlling milk production traits. This region also displays extensive conservation of synteny among several species including cattle, humans, mice and sheep. In this study, we evaluated the adjacent intervals D3S20‐D3S34 and D3S34‐D3S3 for differences in recombination rate (θ) among bulls in order to assess the suitability of population‐based estimates of θ for marker assisted selection and to explore the relationship between variation in θ and chromosome breakpoints associated with mammalian evolution. Using sperm typing, θD3S20‐D3S34 and θD3S34‐D3S3 were estimated for six triply heterozygous bulls. Recombination frequency ranged from 6.2 to 12.5% and from 9.7 to 19.2% for the D3S20‐D3S34 and D3S34‐D3S3 intervals, respectively. However, significant variation in θ was not detected between bulls for either interval (D3S20‐D3S34χ25 d.f.=2.59, P < 0.90; D3S34‐D3S3χ25 d.f.=3.72, P < 0.75). The observed differences in θ were most readily attributed to differences in allele‐specific amplification efficiencies among bulls. Our results suggest that the positions of QTL in this region can be reliably determined from population data and therefore accurate marker‐assisted selection can be performed for desirable alleles without concern for variation in θ. Furthermore, when considered with results of earlier studies, these findings support a correlation between the existence of evolutionary breakpoints or chromosome rearrangements and variation in θ.
Precise mapping of breakpoints in conserved synteny between human chromosome 1 and pig chromosomes 4, 6 and 9
Authors: Sun H. S. , Tuggle C. K. , Goureau A. , Fitzsimmons C. J. , Pinton P. , Chardon P. , Yerle M.
Published: March 2003

Previous comparative mapping suggested that at least five pig chromosomes (Sscr4, 6, 9, 10 and 14) share homology with human chromosome 1 (Hsap1). A significant quantitative trait loci (QTL) for fat deposition has been identified on Sscr4 that appears to be near the junction region between Sscr4 and Sscr9 relative to Hsap1. It is of interest to define the boundaries of conserved synteny between pig chromosomes and Hsap1 to use human map information to identify putative comparative positional candidates for this QTL. Eleven genes, including Janus kinase 1 (JAK1), Prostaglandin E receptor3 (PTGER3), urate oxidase (UOX), coagulation factor 3 (F3), vascular cell adhesion molecule 1 (VCAM1), ribosomal protein L5 (RPL5), POU domain, class 2, transcription factor 1 (POU2F1), coagulation factor 5 (F5), Prostaglandin endoperoxide synthase‐2 (PTGS2), myosin binding protein H (MYBPH) and Antithrombin III (SERPINC1), were selected to refine the boundaries of the blocks of conserved synteny between Hsap1 and pig chromosomes. Pig sequence tagged sites (STSs) were developed and used to physically map these 11 genes using a somatic cell hybrid panel. Eight loci have been mapped by using fluorescent in situ hybridization (FISH) to improve map resolution. Heterologous FISH was used to refine the location of VCAM1 on human chromosomes. In addition, human yeast artificial chromosomes (YACs) were mapped by heterologous FISH on pig metaphases to refine the boundaries of the regions of homology between Sscr4 and Sscr9 on Hsap1. Results from this study suggest the precise break in conserved synteny on Hsap1 corresponding to the Sscr4/6 and Sscr4/9 transitions are most likely on the Hsap1p22 and Hsap1q24–25 regions, respectively. Further, our data predict that Hsap1q21–24 is a candidate region for the backfat QTL localized to Sscr4.
A genome scan for quantitative trait loci affecting resistance toTrichostrongylus colubriformisin sheep
Authors: Beh K. J. , Hulme D. J. , Callaghan M. J. , Leish Z. , Lenane I. , Windon R. G. , Maddox J. F.
Published: March 2003

A genome linkage scan was carried out using a resource flock of 1029 sheep in six half‐sib families. The families were offspring of sires derived by crossing divergent lines of sheep selected for response to challenge with the intestinal parasitic nematodeTrichostrongylus colubriformis. All animals in the resource flock were phenotypically assessed for worm resistance soon after weaning using a vaccination/challenge regime. After correcting for fixed effects using a least squares linear model the faecal egg count data obtained following the first challenge and the faecal egg count data obtained after the second challenge were designated Trait 1 and Trait 2, respectively. A total of 472 lambs drawn from the phenotypic extremes of the Trait 2 faecal egg count distribution were genotyped with a panel of 133 microsatellite markers covering all 26 sheep autosomes. Detection of quantitative trait loci (QTL) for each of the faecal egg count traits was determined using interval analysis with the Animap program with recombination rates between markers derived from an existing marker map. No chromosomal regions attained genome‐wide significance for QTL influencing either of the traits. However, one region attained chromosome‐wide significance and five other regions attained point‐wise significance for the presence of QTL affecting parasite resistance.
Single nucleotide polymorphism (SNP) discovery in porcine expressed genes
Authors: Fahrenkrug S. C. , Freking B. A. , Smith T. P. L. , Rohrer G. A. , Keele J. W.
Published: March 2003

High‐throughput genotyping of swine populations is a potentially efficient method for establishing animal lineage and identification of loci important to animal health and efficient pork production. Markers were developed based upon single nucleotide polymorphisms (SNPs), which are abundant and amenable to automated genotyping platforms. The focus of this research was SNP discovery in expressed porcine genes providing markers to develop the porcine/human comparative map. Locus specific amplification (LSA) and comparative sequencing were used to generate PCR products and allelic information from parents of a swine reference family. Discovery of 1650 SNPs in 403 amplicons and strategies for optimizing LSA‐based SNP discovery using alternative methods of PCR primer design, data analysis, and germplasm selection that are applicable to other populations and species are described. These data were the first large‐scale assessment of frequency and distribution of porcine SNPs.
DNA markers and crossbreeding scheme as means to select sires for heterosis in egg production of chickens
Authors: Atzmon G. , Cassuto D. , Lavi U. , Cahaner A. , Zeitlin G. , Hillel J.
Published: March 2003

Genotypes for 24 microsatellite markers, dispersed across the chicken genome, were used to predict progeny performance and heterosis for egg production (number and mass) in `layers' (egg‐type chickens). These markers were used to evaluate genetic distance between each of 39 sires sampled from two‐layer male‐lines; Rhode Island Red (RIR) and White egg Leghorn (Leghorn), and a DNA pool of 30 randomly sampled females from a Brown‐egg female line (Silver). Each sire was analysed for egg production across months in the laying period and cumulatively in each of three subperiods; onset (2 month), mid (9 month) and late (1 month). The average Reynolds' genetic distance between Leghorn sires and the Silver female line (θ=0.6) was significantly higher than that between RIR sires and the Silver female line (θ=0.5). Neither performance nor heterosis values in the RIR sire's daughters were associated with genetic distance values between sires and the Silver female line. On the other hand, performance as well as heterosis values of Leghorn's daughters were positively associated with genetic distance. This association was particularly evident in the mid‐subperiod. If 25% of the most genetically distant Leghorn sires from the Silver female line had been selected in a single generation on the basis of DNA markers information only, average egg production of the crossbred daughters would have been improved by about nine eggs (3%). In principle, further improvement is possible if selection to increase genetic distance between the parental lines is carried on.
Chromosomal assignments for porcine genes encoding enzymes in hepatic metabolic pathways
Authors: Wimmers K. , Ponsuksili S. , Bläser U. , Gellin J. , Schellander K.
Published: March 2003

Increasing the number of mapped genes will facilitate (1) the identification of potential candidate genes for a trait of interest within quantitative trait loci regions and (2) comparative mapping. The metabolic activities of the liver are essential for providing fuel to peripheral organs, for regulation of amino acid, carbohydrate and lipid metabolism and for homoeostasis of vitamins, minerals and electrolytes. We aimed to identify and map genes coding for enzymes active in the liver by somatic cell genetics in order to contribute to the improvement of the porcine gene map. We mapped 28 genes of hepatic metabolic pathways including six genes whose locations could be confirmed and 22 new assignments. Localization information in human was available for all but one gene. In total 24 genes were assigned to in the expected chromosomal regions on the basis of the currently available information on the comparative human and pig map while for four genes our results suggest a new correspondence or extended regions of conservation between porcine and human chromosomes.
Improvement of the comparative map of chicken chromosome 13
Authors: Buitenhuis A. J. , Crooijmans R. P. M. A. , Van Coppenraet E. S. Bruijnesteijn , Veenendaal A. , Groenen M. A. M. , Van Der Poel J. J.
Published: March 2003

A comparative map was made of chicken chromosome 13 (GGA13) with a part of human chromosome 5 (HSA5). Microsatellite markers specific for GGA13 were used to screen the Wageningen chicken bacterial artificial chromosome (BAC) library. Selected BAC clones were end sequenced and 57 sequence tag site (STS) markers were designed for contig building. In total, 204 BAC clones were identified which resulted in a coverage of about 20% of GGA13. Identification of genes was performed by a bi‐directional approach. The first approach starting with sequencing mapped chicken BAC subclones, where sequences were used to identify orthologous genes in human and mouse by a basic local alignment search tool (BLAST) database search. The second approach started with the identification of chicken orthologues of human genes in the HSA5q23‐35 region. The chicken orthologous genes were subsequently mapped by fluorescentin situhybridisation (FISH) and/or single neucleotide polymorphism typing. The total number of genes mapped on GGA13 is increased from 14 to a total of 20 genes. Genes mapped on GGA13 have their orthologues on HSA5q23‐5q35 in human and on Mmu11, Mmu13 and Mmu18 in mouse.
Genetic distances within and across cattle breeds as indicated by biallelic AFLP markers
Authors: Ajmone‐Marsan P. , Negrini R. , Milanesi E. , Bozzi R. , Nijman I. J. , Buntjer J. B. , Valentini A. , Lenstra J. A.
Published: March 2003

We tested the use of biallelic Amplified fragment length polymorphism (AFLP) polymorphisms for the estimation of relative genetic distances of cattle individuals within or across breeds. An allele permutation procedure was developed to estimate the stochastic variation of the genetic distance that is inherent to a given dataset. In a panel of 47 Holstein‐Friesian cattle analysed with 248 polymorphic markers, the average genetic distance of bulls selected for breeding was slightly lower than the distance of the cows. The observed standard deviation (SD) of the distance indicated genetic subdivision, which for the bulls was explained by variation in the additive relationship derived from herdbook data. Animals from three different breeds, the highly selected Holstein‐Friesian, the Italian Brown and the historic Maremmana, were compared on the basis of 106 polymorphic markers. No breed‐specific fragments were observed. The mean pair‐wise genetic distance within breeds was 85% of the value across breeds, but principal coordinates analysis clustered the animals according to their breed of origin. Calculation of distances between the breeds indicated a relatively divergent position of the Maremmana, relative to the two other breeds. However, biallelic markers indicate that the process of breed formation had only a limited effect on the diversity at marker loci.
A high‐resolution comparative RH map of the proximal part of bovine chromosome 1
Authors: Drögemüller C. , Bader A. , Wöhlke A. , Kuiper H. , Leeb T. , Distl O.
Published: March 2003

Current comparative maps between human chromosome 21 and the proximal part of cattle chromosome 1 are insufficient to define chromosomal rearrangements because of the low density of mapped genes in the bovine genome. The recently completed sequence of human chromosome 21 facilitates the detailed comparative analysis of corresponding segments on BTA1. In this study eight bovine bacterial artificial chromosome (BAC) clones containing bovine orthologues of human chromosome 21 genes, i.e. GRIK1, CLDN8, TIAM1, HUNK, SYNJ1, OLIG2, IL10RB, and KCNE2 were physically assigned by fluorescence in situ hybridization (FISH) to BTA1q12.1‐q12.2. Sequence tagged site (STS) markers derived from these clones were mapped on the 3000 rad Roslin/Cambridge bovine radiation hybrid (RH) panel. In addition to these eight novel markers, 17 known markers from previously published BTA1 linkage or RH maps were also mapped on the Roslin/Cambridge bovine RH panel resulting in an integrated map with 25 markers of 355.4 cR3000 length. The human–cattle genome comparison revealed the existence of three chromosomal breakpoints and two probable inversions in this region.
History and integrity of thoroughbred dam lines revealed in equine mtDNA variation
Authors: Hill E. W. , Bradley D. G. , Al‐Barody M. , Ertugrul O. , Splan R. K. , Zakharov I. , Cunningham E. P.
Published: March 2003

Mitochondrial DNA (mtDNA) D‐loop sequences (381 bp) from 100 thoroughbreds in 19 of the most common matrilineal female families were used to reconstruct a founder female population for the thoroughbred (∼1650–1750 AD). Seventeen haplotypes were found to have contributed to the 19 female lineages. In order to place the reconstructed founder population in wider historical context, we examined, using both single strand conformation polymorphism and direct sequence analysis, variation in a 343 bp mtDNA fragment in that population and 13 other horse populations of disparate provenance. Interpopulation diversity analyses revealed no significant difference in variation between the thoroughbred founder population and the 13 other diverse horse populations and suggested a non‐random partitioning of diversity among geographically diverse horse populations. Within thoroughbreds, almost half of the female families, which are each considered from pedigrees to have matrilines converging to one of >30 historically recognized female ancestors, contained sequences which were inconsistent with common descent. Examination of the anomalies in the context of pedigree records suggests the majority might be best explained as confusion of mares at the foundation stages, although some could have some bearing on more recent (19th century – 1980) lineages. We have used this combination of molecular and historical information to identify some of the founder dams and to make new interpretations about the early history of the thoroughbred.
Restriction fragment alleles of the rabbit IGHG genes with reference to the rabbit IGHGCH2 or e locus polymorphism
Authors: Esteves P. J. , Alves P. C. , Ferrand N. , Van Der Loo W.
Published: March 2003

Among domesticated mammals, rabbit (Oryctolagus cuniculus) is the only species possessing not more than one subclass of immunoglobulin (IgG) antibodies. The rabbit IGHGCH2 or e locus presents two serologically defined alleles, the e14 and e15 allotypes, which are correlated with amino acid variation at the IgG CH2–CH3 interface. Genetic studies, while revealing the adaptive value of this polymorphism, have relied so far entirely upon allo‐antisera. Here we show how these alleles can be distinguished by polymerase chain reaction–restriction fragment length polymorphism (PCR–RFLP) methods. The proposed PCR–RFLP approach allows the monitoring of IGHG locus diversity in rabbit.
An integrated comparative map of the porcine X chromosome
Authors: McCoard S. A. , Fahrenkrug S. C. , Alexander L. J. , Freking B. A. , Rohrer G. A. , Wise T. H. , Ford J. J.
Published: March 2003

The objectives of this study were to assign both microsatellite and gene‐based markers on porcine chromosome X to two radiation hybrid (RH) panels and to develop a more extensive integrated map of SSC‐X. Thirty‐five microsatellite and 20 gene‐based markers were assigned to T43RH, and 16 previously unreported microsatellite and 15 gene‐based markers were added to IMpRH map. Of these, 30 microsatellite and 12 gene‐based markers were common to both RH maps. Twenty‐two gene‐based markers were submitted to BLASTN analysis for identification of orthologues of genes on HSA‐X. Single nucleotide polymorphisms (SNPs) were detected for 12 gene‐based markers, and nine of these were placed on the genetic map. A total of 92 known loci are present on at least one porcine chromosome X map. Thirty‐seven loci are present on all three maps; 31 loci are found on only one map. Location of 33 gene‐based markers on the comprehensive map translates into an integrated comparative map that supports conservation of gene order between SSC‐X and HSA‐X. This integrated map will be valuable for selection of candidate genes for porcine quantitative trait loci (QTLs) that map to SSC‐X.
Genetic diversity of three donkey populations in the Croatian coastal region
Authors: Ivankovic A. , Kavar T. , Caput P. , Mioc B. , Pavic V. , Dovc P.
Published: March 2003

Genetic variation in three Croatian donkey populations, Istrian (IS), North Adriatic (NA) and Littoral‐Dinaric (LD), was analysed using eight microsatellite loci and by sequence and SSCP analysis of the proximal portion of the mtDNA D‐loop region. The analysis of microsatellite loci revealed observed heterozygosities in the range of 0.37 (MPZ002in LD) to 0.85 (AHT21in LD) and polymorphic information content values in the range of 0.36 (MPZ002in NA) to 0.78 (AHT21in LD). The overall probability of exclusion was 0.991. Two populations (IS and NA) were closely related (Fst=0.0034), whereas genetic distances between IS and LD (Fst=0.021) and NA and LD (Fst=0.027) were higher. UsingAMOVA, 97.6% of the total genetic variance was portioned within populations, while 2.7% was portioned between the Littoral‐Dinaric population and the Istrian/North Adriatic population group. Sequencing of the proximal part of the mtDNA D‐loop region revealed 36 polymorphic sites representing 19 haplotypes which clustered into three haplotype groups (Y, W, Ws). Only the Y haplotype was found in the IS population which is characterized by a large body size. Haplotypes W and Ws were found in the NA and LD populations which include smaller animals. All three haplotypes were found in the LD population, indicating sporadic migration events from the IS into LD donkey population.
Microsatellite markers associated with quantitative trait loci controlling antibody response to Escherichia coli and Salmonella enteritidis in young broilers
Authors: Yunis R. , Heller E. D. , Hillel J. , Cahaner A.
Published: March 2003

A unique resource population was produced to facilitate detection of microsatellite markers associated with quantitative trait loci controlling antibody (Ab) response in broiler chickens. Three F1 males were produced by mating two lines divergently selected on Ab response to Escherichia coli vaccination. Each F1 male was mated with females from four genetic backgrounds: F1, high‐Ab line (HH), low‐Ab line and commercial line, producing three resource families, each with four progeny types. About 1700 chicks were immunized with E. coli and Salmonella enteritidis vaccines. Selective genotyping was conducted on the individuals with highest or lowest average Ab to E. coli and S. enteritidis within each progeny type in each sire family. Twelve markers were significantly associated with Ab to E. coli and six of them were also associated with Ab to S. enteritidis, mostly exhibiting a similar low effect (∼ 0.35 phenotypic SD) in all progeny types. Four markers exhibited a highly significant and much larger effect (∼1.7 SD), but only in progeny of females from the HH, suggesting that a backcross to the high parental line should be preferred over the commonly used F2 population. Results from two markers suggested a quantitative trait locus on chromosome 2 around 400 cM. The marker MCW0083, significant in two sire families, is closely linked to the bone morphogenetic protein 2 (BMP2) gene, known to be associated with the control of T‐cell transformation in humans.
Characterization of the porcine melanocortin 2 receptor gene (MC2R )
Authors: Jacobs K. , Van Poucke M. , Mattheeuws M. , Chardon P. , Yerle M. , Rohrer G. , Van Zeveren A. , Peelman L. J.
Published: March 2003

A porcine bacterial artificial chromosome (BAC) clone, containing the melanocortin 2 receptor gene (MC2R) was isolated. The complete coding sequence of the MC2R gene, contained in 1 exon, was determined. Polymerase chain reaction‐single stranded conformational polymorphism (PCR‐SSCP) was performed on a 241‐bp coding fragment. An AluI polymorphism, detecting a silent mutation, was found and typed on unrelated animals of five different pig breeds. The Meishan, Piétrain and Large White breeds differ significantly in allele frequencies from the Landrace and Czech Meat Pig breeds. The melanocortin 5 receptor gene (MC5R) was detected by PCR in the same BAC clone, as could be expected from the human and porcine mapping data. PCR‐SSCP was performed on a 200‐bp coding of MC5R, but no polymorphisms were detected. The BAC clone was mapped to Sscr6q27 by fluorescent in situ hybridization (FISH). A (CA)n microsatellite (SGU0002), isolated from the BAC, was localized on chromosome 6 by RH mapping near marker SW1473 and by linkage mapping on the MARC reference family at the same position as the marker SW2173 (97 cM). Allele frequencies, heterozygosity and polymorphism information contents (PIC) values were calculated for the five different pig breeds examined.

The transcription of both genes in porcine liver, heart, kidney, fat, brain, pancreas, stomach, bladder, ovaries, lung, spleen, skin, adrenal gland and muscle tissues was examined by reverse transcriptase‐polymerase chain reaction. Transcription was detected in skin and adrenal gland tissues for MC2R, while a positive signal was detected for MC5R in kidney, fat, pancreas, skin, adrenal gland and spleen tissues.
Quantitative trait loci affecting fatness in the chicken
Authors: Ikeobi C. O. N. , Woolliams J. A. , Morrice D. R. , Law A. , Windsor D. , Burt D. W. , Hocking P. M.
Published: March 2003

An F2 chicken population of 442 individuals from 30 families, obtained by crossing a broiler line with a layer line, was used for detecting and mapping Quantitative Trait Loci (QTL) affecting abdominal fat weight, skin fat weight and fat distribution. Within‐family regression analyses using 102 microsatellite markers in 27 linkage groups were carried out with genome‐wide significance thresholds. The QTL for abdominal fat weight were found on chromosomes 3, 7, 15 and 28; abdominal fat weight adjusted for carcass weight on chromosomes 1, 5, 7 and 28; skin and subcutaneous fat on chromosomes 3, 7 and 13; skin fat weight adjusted for carcass weight on chromosomes 3 and 28; and skin fat weight adjusted for abdominal fat weight on chromosomes 5, 7 and 15. Interactions of the QTL with sex or family were unimportant and, for each trait, there was no evidence for imprinting or of multiple QTL on any chromosome. Significant dominance effects were obtained for all but one of the significant locations for QTL affecting the weight of abdominal fat, none for skin fat and one of the three QTL affecting fat distribution. The magnitude of each QTL ranged from 3.0 to 5.2% of the residual phenotypic variation or 0.2–0.8 phenotypic standard deviations. The largest additive QTL (on chromosome 7) accounted for more than 20% of the mean weight of abdominal fat. Significant positive and negative QTL were identified from both lines.
Fine‐mapping of the intestinal receptor locus for enterotoxigenic Escherichia coli F4ac on porcine chromosome 13
Authors: Python P. , Jörg H. , Neuenschwander S. , Hagger C. , Stricker C. , Bürgi E. , Bertschinger H. U. , Stranzinger G. , Vögeli P.
Published: March 2003

The aim of this study was to refine the localization of the receptor locus for fimbriae F4ac. Small intestinal enterocyte preparations from 187 pigs were phenotyped by an in vitro adhesion test using two strains of Escherichia coli representing the variants F4ab and F4ac. The three‐generation pedigree comprised eight founders, 18 F1 and 174 F2 animals, for a total of 200 pigs available for the linkage analysis. Results of the adhesion tests on 171 F2 pigs slaughtered at 8 weeks of age show that 23.5% of the pigs were adhesive for F4ab and non‐adhesive for F4ac (phenotype F4abR+/F4acR–; R means receptor). Pigs of this phenotype were characterized by a weak adhesion receptor for F4ab. No pigs were found expressing only F4acR and lacking F4abR. Receptors for F4ab and F4ac (F4abR+/F4acR+) were expressed by 54.5% of the pigs. Animals of this phenotype strongly bound both F4ab and F4ac E. coli. In the segregation study, the serum transferrin (TF) gene and 10 microsatellites on chromosome 13 were linked with F4acR (recombination fractions (θ) between 0.00 and 0.11 and lod score values (Z) between 11.4 and 40.4). The 11‐point analysis indicates the F4acR locus was located in the interval S0068‐Sw1030 close to S0075 and Sw225, with recombination fractions (θ) of 0.05 between F4acR and S0068, 0.04 with Sw1030, and 0.00 with S0075 and Sw225.

The lack of pigs displaying the F4abR–/F4acR+ phenotype and the presence of two phenotypes for F4abR (a strong receptor present in phenotype F4abR+/F4acR+ and a weak receptor in phenotype F4abR+/F4acR–) led us to conclude that the receptor for F4ac binds F4ab bacteria as well, and that it is controlled by one gene localized between S0068 and Sw1030 on chromosome 13.
Putative in silico mapping of DNA sequences to livestock genome maps using SSLP flanking sequences
Authors: Farber C. R. , Medrano J. F.
Published: March 2003

In this study, an in silico approach was developed to identify homologies existing between livestock microsatellite flanking sequences and GenBank nucleotide sequences. Initially, 1955 bovine, 1570 porcine and 1121 chicken microsatellites were downloaded and the flanking sequences were compared with the nr and dbEST databases of GenBank. A total of 74 bovine, 44 porcine and 37 chicken microsatellite flanking sequences passed our criteria and had at least one significant match to human genomic sequence, genes/expressed sequence tags (ESTs) or both. GenBank annotation and BLAT searches of the UCSC human genome assembly revealed that 38 bovine, 13 porcine and 17 chicken microsatellite flanking sequences were highly similar to known human genes. Map locations were available for 67 bovine, 44 porcine and 21 chicken microsatellite flanking sequences, providing useful links in the comparative maps of humans and livestock. In support of our approach, 112 alignments with both microsatellite and match mapping information were located in the expected chromosomal regions based on previously reported syntenic relationships. The development of this in silico mapping approach has significantly increased the number of genes and EST sequences anchored to the bovine, porcine and chicken genome maps and the number of links in various human–livestock comparative maps.
Comparative mapping of a region on chromosome 10 containing QTL for reproduction in swine1
Authors: Nonneman D. J. , Rohrer G. A.
Published: March 2003

Several quantitative trait loci (QTL) for important reproductive traits (age of puberty, ovulation rate, nipple number and plasma FSH) have been identified on the long arm of porcine chromosome 10. Bi‐directional chromosome painting has shown that this region is homologous to human chromosome 10p. Because few microsatellite or type I markers have been placed on SSC10, we wanted to increase the density of known ESTs mapped in this region of the porcine genome. Genes were chosen for their position on human chromosome 10, sequence availability from the TIGR pig gene indices, and their potential as a candidate gene. The PCR primers were designed to amplify across introns or 3′‐UTR to maximize single nucleotide polymorphism (SNP) discovery. Parents of the mapping population (one sire and seven dams) were amplified and sequenced to find informative markers. The SNPs were genotyped using primer extension and mass spectrometry. These amplification products were also used to probe a BAC library (RPCI‐44, Roswell Park Cancer Institute) for positive clones and screened for microsatellites. Six genes from human chromosome 10p (AKR1C2, PRKCQ, ITIH2, ATP5C1, PIP5K2A and GAD2) were mapped in the MARC swine mapping population. Gene order was conserved within these markers from centromere to telomere of porcine chromosome 10q, as compared with human chromosome 10p. Four of these genes (PIP5K2A, ITIH2, GAD2 and AKR1C2), which map under QTL, are potential candidate genes. Identification of porcine homologues near important QTL and development of a comparative map for this chromosome will allow further fine‐ mapping and positional cloning of candidate genes affecting reproductive traits.
Polymorphism at the ovine β3‐adrenergic receptor locus: associations with birth weight, growth rate, carcass composition and cold survival
Authors: Forrest R. H. , Hickford J. G. H. , Hogan A. , Frampton C.
Published: March 2003

The β3‐adrenergic receptors (ADRB3s) are predominantly found on the surface of adipocytes and are the major mediators of the lipolytic and thermogenic effects of high catecholamine concentrations. Polymerase chain reaction–single strand conformational polymorphism (PCR–SSCP) analysis of part of the ovine β3‐adrenergic receptor gene (ADRB3) intron was used to screen 12 large Merino half‐sib families for sequence variation. Six different alleles that segregated in a Mendelian fashion were observed. The genetic basis for the allelic differences were identified by sequencing the ADRB3 (coding and non‐coding regions) from animals that were homozygous for each of the alleles. Five sire lines (two Merino × Merino, two Merino × Coopworth, one Dorset Down × Coopworth) provided phenotypic and genotypic data used to ascertain the effects of allelic variation at the ADRB3 locus on birth weight, weaning weight, growth rate (up until weaning), carcass composition at 63 days post‐weaning and cold survival. Statistical analyses within each half‐sib family showed that in some sire lines (S13, S15, and S17) the inheritance of a particular allele was associated with increased birth weights and/or increased growth rates up until weaning. The inheritance of a particular sire allele was associated with fatter carcasses in sire line S16. Chi‐squared analysis revealed the association of the E allele with cold survival and the D allele with cold‐related mortality in sire line S14. Such associations support the hypothesis that ADRB3s are involved in energy homeostasis. With more research, the variation detected at the ADRB3 locus may assist in the genetic selection for desirable animal production traits.
Genetic diversity and relationships of indigenous Kenyan camel (Camelus dromedarius) populations: implications for their classification
Authors: Mburu D. N. , Ochieng J. W. , Kuria S. G. , Jianlin H. , Kaufmann B. , Rege J. E. O. , Hanotte O.
Published: March 2003

The genetic diversity and relationships amongst the dromedary (Camelus dromedarius) populations are poorly documented. Four recognized Kenyan dromedary breeds (Somali, Turkana, Rendille, Gabbra) and dromedary from Pakistan and the Arabian Peninsula (Saudi Arabia, United Arab Emirates) were studied using 14 microsatellite loci. Phylogenetic analysis showed that Kenyan dromedaries are distinct from Arabian and Pakistani populations. Expected heterozygosity and allelic diversity values indicate that Kenyan dromedaries are less diverse than non‐Kenyan populations. With the exception of the Somali population, the Kenyan dromedaries are poorly differentiated (average FST=0.009), with only one to two loci separating the Gabbra, Rendille and Turkana populations studied (P < 0.05). Individual assignments were performed using the maximum likelihood method. A correct breed assignment of only 39–48% was observed for the Kenyan dromedaries, using an allocation stringency of a log of the odds ratio >2. Our results do not support the present classification of the indigenous Kenyan dromedary into four distinct breeds based on socio‐geographical criteria. Instead, our results point to just two separate genetic entities, the Somali and a group including the Gabbra, Rendille and Turkana populations.
Physical mapping of the brain and ovarian aromatase genes in the Nile Tilapia, Oreochromis niloticus, by fluorescence in situ hybridization
Authors: Harvey S. C. , Kwon J. Y. , Penman D. J.
Published: March 2003

Cytochrome P450‐aromatase enzyme (CYP19), which catalyses the conversion of androgens to oestrogens, is critical in ovarian differentiation and hence in the sex differentiation pathways of non‐mammalian vertebrates. As in other fish species, distinct ovarian and brain aromatase genes have been identified in the Nile Tilapia, Oreochromis niloticus. Here we demonstrate by in situ hybridization that the two aromatase genes of this species are present on different chromosomes and that neither are located on the sex chromosomes. Hence, the aromatase genes are not the primary sex determination genes in O. niloticus.
Effect of altered gastric emptying and gastrointestinal motility on metformin absorption
Authors: Marathe, Punit H. , Wen Yandong , Norton Jean , Greene Douglas S. , Barbhaiya Rashmi H. , Wilding Ian R.
Published: March 2003

Aims
The purpose of this in vivo human study was to assess the effect of altered gastric emptying and gastrointestinal motility on the absorption of metformin in healthy subjects.

Methods
An open‐label, three treatment, three period crossover study was conducted in 11 healthy volunteers. Each subject received 550 mg metformin hydrochloride in solution alone; 5 min after a 10 mg i.v. dose of metoclopramide; and 30 min after a 30 mg oral dose of propantheline. Metformin solution was radiolabeled by the addition of 99mTc‐DTPA. The gastrointestinal transit of the solution was monitored by gamma scintigraphy and the pharmacokinetic data were correlated with the scintigraphic findings.

Results
Scintigraphic data indicated that pretreatment with metoclopramide decreased gastric emptying time and increased gastrointestinal motility while pretreatment with propantheline had the opposite effect. The systemic disposition of metformin was not altered by pretreatment with metoclopramide and propantheline, as judged by unchanged renal clearance and elimination half‐life of metformin. Extent of metformin absorption was essentially unchanged after pretreatment with metoclopramide. However, AUC(0,∞) and % UR (percent dose excreted unchanged in urine) generally increased with increase in gastric emptying time and small intestinal transit times. GI overlay plots showed that the absorption phase of metformin plasma profile always coincided with gastric emptying and the beginning of decline of metformin plasma concentrations was usually associated with the colon arrival. Only in cases where the intestinal transit was drastically prolonged by propantheline pretreatment, was a decline in plasma levels observed prior to colon arrival.

Conclusions
Metformin is primarily absorbed from the small intestine. The extent of metformin absorption is improved when the gastrointestinal motility is slowed. These findings have significant implications in the design of a metformin modified release dosage form.
Sudden unexpected death in infants under 3 months of age and vaccination status – a case‐control study
Authors: Jonville‐Béra Annie‐Pierre , Autret‐Leca Elisabeth , Barbeillon Florence , Paris‐Llado Josepha ,   the French Reference Centers for SIDS
Published: March 2003

Aims  To determine whether DTPP+Hib vaccination (diphtheria, tetanus, pertussis, poliomyelitis +/− haemophilus) increased the risk of sudden unexpected death (SUD) in children under 3 months of age.

Methods  We conducted a multicentre case‐control study in the 28 French ‘SIDS Centers’. Case selection was based on death labelled sudden infant death syndrome (SIDS) of an infant aged between 30 and 90 days. Three living controls were selected, matched for sex, gestational age and born immediately after the victim in the same maternity unit.

Results  We identified 114 cases of SUD aged between 30 and 90 days and 341 live controls matched for age and sex and born in the same maternity unit as the case. DTPP±Hib immunization did not increase the risk of SUD (OR 1.08) (95% CI 0.49, 2.36) in children under 3 months of age when adjusted for sleeping position, illness in the week before death, maternal tobacco consumption, birth weight, type of mattress, breastfeeding and sex. However, low birth‐weight (6.53 [2.29, 18.9]), multiple birth (5.1 [1.76, 15.13]), no breastfeeding (1.77 [1.1, 2.85]), prone sleeping position (9.8 [5, 8, 18, 9]), soft mattress (3.26 [1.69, 6.29]), recent illness (3.44 [1.84, 6.41]) and parental smoking (1.74 [1.2, 2.96]) were confirmed as risk factors in early SIDS.

Conclusions  DTPP±Hib immunization is not a risk factor for early SUD. In this population, we found the same risk factors as described for SIDS.
An Immunohistochemical Survey of Catecholamine‐synthesizing Enzyme‐immunoreactive Nerves and Endocrine Cells in the Bovine Pancreas
Authors: Kitamura N. , Mori Y. , Hondo E. , Baltazar E. T. , Yamada J.
Published: March 2003

The distribution of catecholamine‐synthesizing enzyme‐immunoreactive nerves and endocrine cells in the pancreas of the calf and cow was studied immunohistochemically using antisera against tyrosine hydroxylase (TH) and dopamine β‐hydroxylase (DBH). TH‐ and DBH‐immunoreactive nerve fibres were abundant both within and around the islet of Langerhans. A few TH‐ and DBH‐immunoreactive nerve fibres were seen around the large islets characteristic of calf pancreas, but the majority of cells in the large islets, and some in islets of Langerhans, showed TH immunoreactivity. In the exocrine pancreas, both TH‐ and DBH‐immunoreactive nerve fibres were distributed randomly among the acini, with the DBH‐immunoreactive fibres being more numerous. Abundant TH‐ and DBH‐immuno‐ reactive nerve fibres were seen in close association with blood vessels and in the connective tissue around the interlobular duct. Immunoreactivity for both enzymes was also observed in the nerve cell bodies and fibres of the intrapancreatic ganglia. The findings suggest an important role for catecholamines in the regulation of bovine pancreatic function.