Fine mapping QTL for female fertility on BTA04 and BTA13 in dairy cattle using HD SNP and sequence data

Background

Female fertility is important for the maintenance of the production in a dairy cattle herd. Two QTL regions on BTA04 and on BTA13 previously detected in Nordic Holstein (NH) and validated in the Danish Jersey (DJ) and Nordic Red (NR) were investigated further in the present study to further refine the QTL locations. Refined QTL regions were imputed to the full sequence data. The genes in the regions were then studied to ascertain their possible effect on fertility traits.

Results

BTA04 was screened for number of inseminations (AIS), 56-day non-return rate (NRR), days from first to last insemination (IFL), and the interval from calving to first insemination (ICF) in the range of 38,257,758 to 40,890,784 bp, whereas BTA13 was screened for ICF only in the range from 21,236,959 to 46,150,079 with the HD bovine SNP array for NH, DJ and NR. No markers in the DJ and NR breeds reached significance. By analyzing imputed sequence data the QTL position on BTA04 was narrowed down to two regions in the NH. In these two regions a total of 9 genes were identified. BTA13 was analyzed using sequence data for the NH breed. The highest –log₁₀(P-value) was 19.41 at 33,903,159 bp. Two regions were identified: Region 1: 33,900,143-33,908,994 bp and Region 2: 34,051,815-34,056,728 bp. SNPs within and between these two regions were annotated as intergenic.

Conclusion

Screening BTA04 and BTA13 for female fertility traits in NH, NR and DJ suggested that the QTL for female fertility were specific for NH. A missense mutation in CD36 showed the strongest association with fertility traits on BTA04. The annotated SNPs on BTA13 were all intergenic variants. It is possible that BTA13 at this stage is poorly annotated such that the associated polymorphisms are located in as-yet undiscovered genes. Fertility traits are complex traits as many different biological and physiological factors determine whether a cow is fertile. Therefore it is not expected that there is a simple explanation with an obvious candidate gene but it is more likely a network of genes and intragenic variants that explain the variation of these traits.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-790) contains supplementary material, which is available to authorized users.     

Mapping of quantitative trait loci for carcass traits in a Japanese Black (Wagyu) cattle population

To detect quantitative trait loci (QTL) that influence economically important traits in a purebred Japanese Black cattle population, we performed a preliminary genome-wide scan using 187 microsatellite markers across a paternal half-sib family composed of 258 offspring. We located six QTL at the 1% chromosome-wise level on bovine chromosomes (BTA) 4, 6, 13, 14 and 21. A second screen of these six QTL regions using 138 additional paternal offspring half-sib from the same sire, provided further support for five QTL: carcass weight on BTA14 (22-39 cM), one for rib thickness on BTA6 (27-58 cM) and three for beef marbling score (BMS) on BTA4 (59-67 cM), BTA6 (68-89 cM) and BTA21 (75-84 cM). The location of QTL for subcutaneous fat thickness on BTA13 was not supported by the second screen (P > 0.05). We determined that the combined contribution of the three QTLs for BMS was 10.1% of the total variance. The combined phenotypic average of these three Q was significantly different (P < 0.001) from those of other allele combinations. Analysis of additional half-sib families will be necessary to confirm these QTL.     

Oligogenic transmission of abnormal teat patterning phenotype (ATPP) in cattle

Abnormal teat patterning phenotype (ATPP) is characterized by one (moderate form) or two (severe form) absent teats in cattle. Using an allele-sharing non-parametric linkage strategy, significant associations with severe ATPP animals were detected on BTA17 (Z(max) = 7.3 at 21 cM), centromeric BTA1 (Z(max) = 3.7 at 8 cM) and telomeric BTA1 (Z(max) = 4.8 at 142 cM). The BTA17 region was also significantly associated in the analysis of the moderate ATPP animals (Z(max) = 5.3 at 0 cM). The transmission disequilibrium test in severe ATPP animals demonstrated significant over-transmission of paternal alleles in the BTA17 region (P = 2.2 x 10(-9)), the centromeric BTA1 region (P = 0.035) and the telomeric BTA1 region (P = 0.005). Significant over-transmission of the BTA17 region was also observed among the moderate ATPP animals (P = 2.3 x 10(-4)). These findings indicate that the BTA17 locus plays a key role in risk of the disease, and that the BTA17 locus contributes temporally in combination with the two other loci on BTA1 and/or possibly unknown modifier(s) in a probabilistic oligo- or polygenic manner of transmission. Haplotypes of these three loci can be used for marker-assisted animal breeding to control the recurrence of affected progeny with ATPP.     

Genome-wide association and biological pathway analysis for milk-fat composition in Danish Holstein and Danish Jersey cattle

Background

The milk fat profile of the Danish Holstein (DH) and Danish Jersey (DJ) show clear differences. Identification of the genomic regions, genes and biological pathways underlying the milk fat biosynthesis will improve the understanding of the biology underlying bovine milk fat production and may provide new possibilities to change the milk fat composition by selective breeding. In this study a genome wide association scan (GWAS) in the DH and DJ was performed for a detailed milk fatty acid (FA) profile using the HD bovine SNP array and subsequently a biological pathway analysis based on the SNP data was performed.

Results

The GWAS identified in total 1,233 SNPs (FDR < 0.10) spread over 18 chromosomes for nine different FA traits for the DH breed and 1,122 SNPs (FDR < 0.10) spread over 26 chromosomes for 13 different FA traits were detected for the DJ breed. Of these significant SNPs, 108 SNP markers were significant in both DH and DJ (C14-index, BTA26; C16, BTA14; fat percentage (FP), BTA14). This was supported by an enrichment test. The QTL on BTA14 and BTA26 represented the known candidate genes DGAT and SCD. In addition we suggest ACSS3 to be a good candidate gene for the QTL on BTA5 for C10:0 and C15:0. In addition, genetic correlations between the FA traits within breed showed large similarity across breeds. Furthermore, the biological pathway analysis revealed that fat digestion and absorption (KEGG04975) plays a role for the traits FP, C14:1, C16 index and C16:1.

Conclusion

There was a clear similarity between the underlying genetics of FA in the milk between DH and DJ. This was supported by the fact that there was substantial overlap between SNPs for FP, C14 index, C14:1, C16 index and C16:1. In addition genetic correlations between FA showed a similar pattern across DH and DJ. Furthermore the biological pathway analysis suggested that fat digestion and absorption KEGG04975 is important for the traits FP, C14:1, C16 index and C16:1.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-1112) contains supplementary material, which is available to authorized users.     

Changes in gut microbiota in children with atopic dermatitis administered the bacteria Lactobacillus casei DN--114001

Gut microbiota was analyzed in children, aged 6-18 months and suffering from atopic dermatitis before and after 3 month supplementation of their diet with Lactobacillus casei DN--114001 in a dose of 109 cells daily. On completion of this period the total number of fecal Lactobacillus sp. cells decreased from 7.86 Log10 CFU/g to 6.40 Log10 CFU/g. After the next 5 months (without dietary supplementation with the probiotic bacteria) the level of Lactobacillus sp. cells was maintained at the latter value. During the dietary supplementation with the probiotic strain, the level of Bifidobacterium cells was maintained at 6.15-6.89 Log10 CFU/g while after 5 months it decreased to 5.57 Log10 CFU/g. The population of Clostridium sp. was reduced after 3 months of dietary supplementation from 6.49 to 5.83 Log10 CFU/g and was maintained at the latter level during the next 5 months. The dietary supplementation had no effect on populations of Bacteroides sp., Enterococcus sp. and Enterobacteriaceae. Supplementation of children who developed atopic dermatitis with the preparation of Lactobacillus casei DN - 114001 positively affected their gut microbiota in terms of bifidobacteria and clostridia populations.     

A microsatellite-based analysis for the detection of selection on BTA1 and BTA20 in northern Eurasian cattle (Bos taurus) populations

Background

Microsatellites surrounding functionally important candidate genes or quantitative trait loci have received attention as proxy measures of polymorphism level at the candidate loci themselves. In cattle, selection for economically important traits is a long-term strategy and it has been reported that microsatellites are linked to these important loci.

Methods

We have investigated the variation of seven microsatellites on BTA1 (Bos taurus autosome 1) and 16 on BTA20, using bovine populations of typical production types and horn status in northern Eurasia. Genetic variability of these loci and linkage disequilibrium among these loci were compared with those of 28 microsatellites on other bovine chromosomes. Four different tests were applied to detect molecular signatures of selection.

Results

No marked difference in locus variability was found between microsatellites on BTA1, BTA20 and the other chromosomes in terms of different diversity indices. Average D'' values of pairwise syntenic markers (0.32 and 0.28 across BTA 1 and BTA20 respectively) were significantly (P < 0.05) higher than for non-syntenic markers (0.15). The Ewens-Watterson test, the Beaumont and Nichol''s modified frequentist test and the Bayesian F_ST-test indicated elevated or decreased genetic differentiation, at SOD1 and AGLA17 markers respectively, deviating significantly (P < 0.05) from neutral expectations. Furthermore, lnRV, lnRH and lnRθ'' statistics were used for the pairwise population comparison tests and were significantly less variable in one population relative to the other, providing additional evidence of selection signatures for two of the 51 loci. Moreover, the three Finnish native populations showed evidence of subpopulation divergence at SOD1 and AGLA17. Our data also indicate significant intergenic linkage disequilibrium around the candidate loci and suggest that hitchhiking selection has played a role in shaping the pattern of observed linkage disequilibrium.

Conclusion

Hitchhiking due to tight linkage with alleles at candidate genes, e.g. the POLL gene, is a possible explanation for this pattern. The potential impact of selective breeding by man on cattle populations is discussed in the context of selection effects. Our results also suggest that a practical approach to detect loci under selection is to simultaneously apply multiple neutrality tests based on different assumptions and estimations.     

Whole genome scan to detect quantitative trait loci for bovine milk protein composition

The objective of this study was to perform a whole genome scan to detect quantitative trait loci (QTL) for milk protein composition in 849 Holstein–Friesian cows originating from seven sires. One morning milk sample was analysed for the major milk proteins using capillary zone electrophoresis. A genetic map was constructed with 1341 single nucleotide polymorphisms, covering 2829 centimorgans (cM) and 95% of the cattle genome. The chromosomal regions most significantly related to milk protein composition ( P _genome < 0.05) were found on Bos taurus autosomes (BTA) 6, 11 and 14. The QTL on BTA6 was found at about 80 cM, and affected α_S1-casein, α_S2-casein, β-casein and κ-casein. The QTL on BTA11 was found at 124 cM, and affected β-lactoglobulin, and the QTL on BTA14 was found at 0 cM, and affected protein percentage. The proportion of phenotypic variance explained by the QTL was 3.6% for β-casein and 7.9% for κ-casein on BTA6, 28.3% for β-lactoglobulin on BTA11, and 8.6% for protein percentage on BTA14. The QTL affecting α_S2-casein on BTA6 and 17 showed a significant interaction. We investigated the extent to which the detected QTL affecting milk protein composition could be explained by known polymorphisms in β-casein , κ -casein , β-lactoglobulin and DGAT1 genes. Correction for these polymorphisms decreased the proportion of phenotypic variance explained by the QTL previously found on BTA6, 11 and 14. Thus, several significant QTL affecting milk protein composition were found, of which some QTL could partially be explained by polymorphisms in milk protein genes.     

A 型肉毒毒素治疗半侧面肌痉挛的临床疗效评价

目的：观察A型肉毒毒素对面肌痉挛患者的痉挛程度、抑郁症状和焦虑症状的改善。方法：对58例面肌痉挛患者进行局部注射A型肉毒毒素。在治疗前后对痉挛程度改善情况进行评定以及用汉密顿焦虑量表（HAMA）、汉密顿抑郁量表（HAMD）对焦虑状态、抑郁状态进行评分,并对药物的副作用进行观察。结果：A型肉毒毒素明显改善面肌痉挛患者的痉挛程度,治疗后2周的HAMA、HA肋评分较治疗前明显下降,且差异具有统计学意义（P〈0．01）。结论：局部注射A型肉毒毒素可迅速缓解或消除面肌痉挛患者肌肉痉挛及相关的抑郁和焦虑状态,提高患者的生活质量。     

Administration of different Lactobacillus strains in fermented oatmeal soup: in vivo colonization of human intestinal mucosa and effect on the indigenous flora.

In vivo colonization by different Lactobacillus strains on human intestinal mucosa of healthy volunteers was studied together with the effect of Lactobacillus administration on different groups of indigenous bacteria. A total of 19 test strains were administered in fermented oatmeal soup containing 5 x 10(6) CFU of each strain per ml by using a dose of 100 ml of soup per day for 10 days. Biopsies were taken from both the upper jejunum and the rectum 1 day before administration was started and 1 and 11 days after administration was terminated. The administration significantly increased the Lactobacillus counts on the jejunum mucosa, and high levels remained 11 days after administration was terminated. The levels of streptococci increased by 10- to 100-fold in two persons, and the levels of sulfite-reducing clostridia in the jejunum decreased by 10- to 100-fold in three of the volunteers 1 day after administration was terminated. In recta, the anaerobic bacterium counts and the gram-negative anaerobic bacterium counts decreased significantly by the end of administration. Furthermore, a decrease in the number of members of the Enterobacteriaceae by 1,000-fold was observed on the rectal mucosa of two persons. Randomly picked Lactobacillus isolates were identified phenotypically by API 50CH tests and genotypically by the plasmid profiles of strains and by restriction endonuclease analysis of chromosomal DNAs.(ABSTRACT TRUNCATED AT 250 WORDS)     

Comparative mapping of bovine chromosome 13 by fluorescence in situ hybridization

We present chromosomal fluorescence in situ hybridization (FISH) results that both extend the HSA20/BTA13 comparative map as well as cytogenetically anchor two microsatellite markers. A bovine bacterial artificial chromosome (BAC) library was screened for conserved genes (type I loci) previously assigned to HSA10 or HSA20 and BTA13, and for microsatellites selected from two published BTA13 linkage maps. Clones from six out of nine comparative loci and both microsatellites were found represented in the BAC library. These BAC clones were used as probes in single colour FISH to determine the chromosome band position of each locus. As predicted by the human/bovine comparative map, all type I loci mapped to BTA13. Because single colour FISH analysis revealed that the loci were clustered within the distal half of BTA13, dual colour FISH was used to confirm the locus order. Established order was centromere- PRNP-(SODIL/AVP/OXT)-(BL42/GNAS1)-HCK-CSSM30 . The findings confirm the presence of a conserved HSA20 homologous synteny group on BTA13 distal of a HSA10 homologous segment.     

Targeted development of microsatellite markers from the defined region of bovine Chromosome 6q21-31

A methodical strategy for the isolation of microsatellite markers specific for targeted regions of bovine chromosomes is presented. The procedure involves directed microdissection of one defined subchromosomal area, its DOP-PCR-amplification and cloning. With this approach, a library specific to the BTA 6q21-31 chromosomal region was constructed. Eleven unique microsatellite-containing sequences were isolated, converted into sequence-tagged microsatellite sites, and characterized concerning their species-specific origin. Seven primer pairs generated bovine-specific PCR products and provided a set of microsatellite markers that generally revealed high informativity in the HF breed. Linkage analysis assigned six of them to their predefined subchromosomal origin on BTA 6 corresponding to the specific rehybridization signal of the DOP-PCR product generated from the microdissected chromosome area 6q21-31. The results underline the usefulness of the BTA 6q21-31 library for targeted isolation of unique sequences that are specific for the dissected chromosomal region as demonstrated here by the isolation of microsatellite markers. Received: 27 March 1997 / Accepted: 14 July 1997     

Bovine umbilical hernia maps to the centromeric end of Bos taurus autosome 8

Twelve bull calves were produced by mating elite Israeli cows to "Glenhapton Enhancer", a Canadian Holstein bull. The frequency of umbilical hernia (UH) in the progeny of the sons ranged from 1 to 21%, consistent with the hypothesis that Enhancer is the carrier of major dominant or codominant gene with partial penetrance for UH. Five sons of Enhancer produced progeny with >10% frequency of UH including sire 3259, whereas progeny of three sons had <3% UH. A total of 116 grand-progeny of Enhancer, all progeny of 3259, were genotyped for 59 microsatellites spanning the 29 bovine autosomes. Of these offspring, 41 were affected. Significant differences in paternal allele frequencies between the affected and unaffected progeny groups were found for marker BMS1591 on bovine chromosome 8 (BTA8). The UH-associated paternal allele originated from Enhancer. The chromosomal segment associated with UH was more precisely mapped between UWCA47, on the centromeric end of BTA8 and RM321, 12 cM from the centromere. A maximum LOD score of 3.84 was obtained 2.5 cM from the centromere with a support interval of 8 cM. Haplotype analysis of eight sons of Enhancer suggested that the UH gene is located in the centromeric end of BTA8 beyond ARO71/ARO72. Thus, by integrating the results from progeny of sire 3259 and sons of Enhancer the location of the UH gene was further refined to the BTA8 segment between ARO71/ARO72 and UWCA47.     

Microbiological and biochemical changes during the fermentation of maize (Zea mays) grains formasa production

Microorganisms associated with fermentation ofmasa wereLactobacillus plantarum, Pediococcus acidilactici, Lactobacillus fermentum andSaccharomyces cerevisiae. During the fermentation of maize grains, the temperature and moisture increased and the pH decreased. Most amino acids decreased in concentration during fermentation, with glutamic acid being the most abundant amino acid, but he protein content of the masa increased during fermentation. The bacteria played the major role in the fermentation.

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Résumé Les microorganismes associés avec la fermentation demasa sontLactobacillus plantarum, pediococcus acidilactici, Lactobacillus fermentum etSaccharomyces cerevisiae. Durant la fermentation de grains de mais, la température et l'humidité augmentent, et le pH diminue. La concentration de la plupart des acides aminés diminue durant la fermentation. L'acide aminé le plus abondant est l'acide glutamique. Toutefois, le contenu en protéines dumasa augmente au cours de la fermentation. Les bactéries jouent le rôle majeur dans la fermentation.

     

Changes in the diversity of pig ileal lactobacilli around weaning determined by means of 16S rRNA gene amplification and denaturing gradient gel electrophoresis

Our study aimed to provide a comprehensive characterization of changes in porcine intestinal Lactobacillus populations around the time of weaning based on 16S rRNA gene amplification and denaturing gradient gel electrophoresis (DGGE). DNA was extracted from the ileal contents of piglets at weaning (28 days of age) and after 1, 2, 5 and 11 days. PCR amplicons (V2-V3 fragments of 16S rRNA genes) were separated using DGGE. Predominant bands were excised and sequenced after reamplification. A band corresponding to Lactobacillus salivarius was present 1 and 2 days post-weaning (pw), while Lactobacillus crispatus was detected only 1 and 11 days pw. Lactobacillus sobrius gave the most dominant band in all animals. The number of bands decreased from 13+/-3 at weaning to 9+/-1 at 5 days pw, but the species richness had recovered by 11 days pw. The similarity of profiles between sampling days was high for 1 and 2 days pw (>91%), but was low for 5 and 11 days pw (<59%). The diversity of the profiles was lower 5 days pw, based on the Shannon diversity index (0.83+/-0.076 vs. 1.02+/-0.127 at weaning, P=0.042), but had recovered to preweaning values by 11 days pw. The application of group-specific DGGE showed that the Lactobacillus community within the porcine ileum undergoes dramatic, partly reversible changes as a consequence of weaning.     

The bovine 5′ AMPK gene family: mapping and single nucleotide polymorphism detection

The 5-AMP-activated protein kinase (AMPK) family is an ancient stress response system whose primary function is regulation of cellular ATP. Activation of AMPK, which is instigated by environmental and nutritional stresses, initiates energy-conserving measures that protect the cell by inhibition and phosphorylation of key enzymes in energy-consuming biochemical pathways. The seven genes that comprise the bovine AMPK family were mapped in cattle by using a radiation hybrid panel. The seven genes mapped to six different cattle chromosomes, each with a LOD score greater than 10.0. PRKAA1 mapped to BTA 20, PRKAA2 and PRKAB2 to BTA 3, PRKAB1 to BTA 17, PRKAG1 to BTA 5, PRKAG2 to BTA 4, and PRKAG3 to BTA 2. Five of the seven genes mapped to regions expected from human/cattle comparative maps. PRKAB2 and PRKAG3, however, have not been mapped in humans. We predict these genes to be located on HSA 1 and 2, respectively. Additionally, one synonymous and one non-synonymous single nucleotide polymorphism (SNP) were detected in PRKAG3 in Bos taurus cattle. In an effort to determine ancestral origins, various herds of mixed breed cattle as well as other ruminant species were characterized for sequence variation in this region of PRKAG3. Owing to the physiological importance of this gene family, we believe that its individual genes are candidate genes for conferring resistance to diseases in cattle.     

A medium density microsatellite map of BTA10: reassignment of INRA69

We have developed a genetic map of BTA10 based on 8952 informative meioses for 13 microsatellite markers and the erythrocyte antigen Z. With the exception of OarAE64 , the support for the order of all loci in the map exceeded a LOD > 3·0. The length of the BTA10 genetic map was 87·0 centimorgans (cM). The 14-marker, sex-average map in Kosambi cM was: CSSM38 –8·9- BM1237 –5·2- HH8A –2·6- INRA69 –10·6- TGLA378 –0·8- BM6305 –17·2- TGLA102 –17·9- INRA96 –0·3- CSRM60 –9·2- DIK20 –3·0- EAZ –6·7- CSSM46 –3·7- SRCRSP3 –1·0- OarAE64 with an average interval of 6·70 cM. The microsatellite INRA69 was recently assigned to the pseudoautosomal region of the bovine X chromosome by linkage analysis. However, we found that twopoint support for linkage between INRA69 and 15 X-linked bovine microsatellites was LOD < 0·50 in 529 reciprocal backcross and F₂ fullsib progeny. We performed twopoint analyses of INRA69 against 275 markers distributed throughout the bovine genome and found significant associations with a LOD > 3·0 only between INRA69 and eight BTA10 microsatellite loci. Consequently, we excluded INRA69 from the genetic map of the X chromosome and reassign this microsatellite to BTA10.     

Comparison of automated culture systems with a CFR/USP-compliant method for sterility testing of cell-therapy products

BACKGROUND: Although widely used, commercially available automated culture methods are not US Food and Drug Administration-approved for sterility testing of cell-therapy products. For cell-therapy products regulated under Section 351 of the Public Health Service Act, sterility testing must be performed by the methods described in 21 CFR 610.12 and USP <71> (CFR/USP method), or by methods demonstrated to be equivalent. METHODS: Two automated methods, BacT/Alert (BTA; bioMerieux) and Bactec (Becton Dickinson), were compared with the CFR/USP method. Representative mononuclear cell (MNC) products were formulated using six different product media. MNC product aliquots containing 10-50 x 10(6) cells in a 0.5 mL volume were seeded with organisms, and cultured for 14 days in aerobic and anaerobic bottles of each system. Ten different organisms at target concentrations of 10 and 50 colony-forming units (CFU) per bottle were tested. RESULTS: Positives were detected in a mean (range) of 72% (7-100%) of cultures for CFR/USP, 82% (0-100%) for BTA, and 93% (57-100%) for Bactec. For nine of the 10 organisms tested, overall detection rates for BTA and Bactec were equivalent to or higher than CFR/USP. Of the six product media tested, detection of organisms was impaired only by the medium containing multiple antibiotics: this occurred in all three systems. Both BTA and Bactec had shorter times to detection than the CFR/USP method, with overall means (ranges) of 87 (24-264) h for CFR/USP, 24 (12-54) h for BTA, and 33 (12-80) h for Bactec. Detection occurred consistently within 7 days for both BTA and Bactec, but not for CFR/USP. DISCUSSION: Both BTA and Bactec are superior to the CFR/USP method for overall detection and time to detection of organisms in MNC products suspended in commonly used media. These data support general use of either BTA or Bactec for sterility testing of a variety of cell-therapy products, and suggest that a 7-day culture period is sufficient to detect clinically relevant organisms. These results confirm the need for bacteriostasis and fungistasis testing of antibiotic-containing products, even when antibiotic-binding substances are used.     

Mapping of the bovine genes of the de novo AMP synthesis pathway

Summary The purine nucleotides adenosine monophosphate (AMP) and guanosine monophosphate (GMP) are critical for energy metabolism, cell signalling and cell reproduction. Despite their essential function, little is known about the regulation and in vivo expression pattern of the genes involved in the de novo purine synthesis pathway. The complete coding region of the bovine phosphoribosylaminoimidazole carboxylase gene (PAICS), which catalyses steps 6 and 7 of the de novo purine biosynthesis pathway, as well as bovine genomic sequences of the six other genes in the pathway producing inosine monophosphate (IMP) and AMP [phosphoribosyl pyrophosphate amidotransferase (PPAT), phosphoribosylglycinamide formyltransferase (GART), phosphoribosylformylglycinamidine synthase (PFAS), adenylosuccinate lyase (ADSL), 5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase (ATIC) and adenylosuccinate synthase (ADSS)], were identified. The genes were mapped to segments of six different bovine chromosomes using a radiation hybrid (RH) cell panel. The gene PPAT, coding for the presumed rate-limiting enzyme of the purine de novo pathway was closely linked to PAICS on BTA6. These, and the other bovine locations i.e. GART at BTA1, PFAS at BTA19, ADSL at BTA5, ATIC at BTA2 and ADSS at BTA16, are in agreement with published comparative maps of cattle and man. PAICS and PPAT genes are known to be closely linked in human, rat and chicken. Previously, an expressed sequence fragment of PAICS (Bos taurus corpus luteum, BTCL9) was mapped to BTA13. By isolation and characterization of a BAC clone, we have now identified a PAICS processed pseudogene sequence (psiPAICS) on BTA13. Processed pseudogene sequences of PAICS and other genes of the purine biosynthesis pathway were identified in several mammalian species, indicating that the genes of this pathway have been susceptible to retrotransposition. The seven bovine genes are expressed at a higher level in testicular and ovary tissues compared with skeletal muscle.     

Resolution of conflicting assignments for the bovine casein kinase II alpha (CSNK2A2) gene

The casein kinase II alpha' gene (CSNK2A2), which physically maps to human chromosome 16 (HSA16), has previously been mapped to bovine chromosome 5 (BTA5). Based on these results, a new segment of homology between the human and bovine genomes was suggested. In this paper we demonstrate linkage between CSNK2A2 and several markers on BTA18. Our result is supported by the extensive conservation of synteny between HSA16q and BTA18. Bovine chromosome 18 markers used in this study included several microsatellites, as well as the MC1R gene previously mapped to HSA16q24.3. Sequencing of the PCR-fragment mapped to BTA5 reveals that a CSNK-like retroposon was responsible for the conflicting assignments. The present results further extend the observed conservation of synteny between HSA16q and BTA18.