A comprehensive radiation hybrid map of bovine Chromosome 26 (BTA26): comparative chromosomal organization between HSA10q and BTA26 and BTA28

In this study, we present a comprehensive 3000-rad radiation hybrid (RH) map of bovine Chromosome (Chr) 26 (BTA26) with 80 markers including 50 genes or ESTs: 44 have an ortholog mapping to human Chr 10 (HSA10) and 29 to mouse Chr (MMU) 7, 10, and 19. Moreover, 12 other HSA10 genes were integrated in a newly developed RH map of BTA28 (seven represent new assignments). The available draft of the mouse genome allowed us to present a detailed picture of the distribution of conserved synteny segments among the three species (human, cattle, and mouse) and to propose a simple model of the comparative chromosomal organization between the long arm of HSA10 and BTA26 and 28. Finally, the INRA bovine BAC library was screened for most of the BTA26 markers considered in this study to provide anchors for the bovine physical map.     

Linkage of bilateral convergent strabismus with exophthalmus (BCSE) to BTA5 and BTA18 in German Brown cattle

Bilateral convergent strabismus with exophthalmus (BCSE) is a widespread inherited eye defect in several cattle populations. Its progressive condition often leads to blindness in affected cattle and decreases their usability. Furthermore, the German animal welfare laws prevent breeding with animals whose progeny are expected to be affected by genetic defects. Identifying genes involved in the heredity of BCSE should lead to insights into the molecular pathogenesis of this eye disease and permit the establishment of a genetic test for this disease. A whole-genome scan for 10 families containing a total of 159 genotyped individuals identified two BCSE loci. One BCSE locus mapped to the centromeric region on bovine chromosome (BTA) 5 and the other BCSE locus mapped to the telomeric region of BTA18. Thus, it is possible that two genes are involved in the development of BCSE. Alternatively, one of these loci could be the cause for the development of BCSE and the other locus could affect the progression and severity of the defect.     

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.     

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.     

Bovine UCP2 and UCP3 map to BTA15

Two recently described uncoupling proteins, UCP2 and UCP3, may have important roles in determining feed conversion and/or maintenance energy requirements in livestock. Sequence was determined for the entire coding region and four of the six introns for bovine UCP3. A partial cDNA sequence was obtained for bovine UCP2. Radiation hybrid mapping was used to place UCP3 on BTA15, a chromosome previously shown to harbor a locus influencing meat tenderness. In order to place UCP3 in the existing linkage map, five single nucleotide polymorphisms (SNPs) were developed. Linkage analysis using one of five SNPs was used to place UCP3 between 53.1 and 53.5 CM. No recombination was detected between UCP3 and IDVGA10, IDVGA32, and INRA145. The sequence of PCR products from a single BAC amplified with primers specific for either UCP2 or UCP3 indicate that UCP2 and UCP3 are separated by < 200 kb.     

Development of 47 new microsatellite markers from a BTA6 library

Chromosome-specific libraries provide a means to isolate genetic markers from specific chromosomal regions. A small-insert BTA6 library, constructed by microdissection, was screened for dinucleotide repeats (CA)15 and (GA)15. A total of 47 new microsatellite loci were developed and tested for polymorphism and informativeness using the MARC bovine mapping family.     

Characterization of a novel microdeletion polymorphism on BTA5 in cattle

We present a detailed breakpoint mapping and population frequency analysis of a 214-kb microdeletion that removes multiple olfactory receptor genes. Using progressive rounds of PCR assays, we mapped the upstream and downstream breakpoints of this microdeletion event to approximately 1 and 12 kb genomic regions, respectively. We developed PCR-based genotyping assays, characterized a dairy cattle panel of 96 samples and found that the frequency of the deletion allele was over 51%. Our results indicated that this microdeletion is an ancient event occurring in one of the earlier founders, and that it has been stably inherited across generations in the North American dairy cattle population.     

Modelling QTL effect on BTA06 using random regression test day models

In statistical models, a quantitative trait locus (QTL) effect has been incorporated either as a fixed or as a random term, but, up to now, it has been mainly considered as a time-independent variable. However, for traits recorded repeatedly, it is very interesting to investigate the variation of QTL over time. The major goal of this study was to estimate the position and effect of QTL for milk, fat, protein yields and for somatic cell score based on test day records, while testing whether the effects are constant or variable throughout lactation. The analysed data consisted of 23 paternal half-sib families (716 daughters of 23 sires) of Chinese Holstein-Friesian cattle genotyped at 14 microsatellites located in the area of the casein loci on BTA6. A sequence of three models was used: (i) a lactation model, (ii) a random regression model with a QTL constant in time and (iii) a random regression model with a QTL variable in time. The results showed that, for each production trait, at least one significant QTL exists. For milk and protein yields, the QTL effect was variable in time, while for fat yield, each of the three models resulted in a significant QTL effect. When a QTL is incorporated into a model as a constant over time, its effect is averaged over lactation stages and may, thereby, be difficult or even impossible to be detected. Our results showed that, in such a situation, only a longitudinal model is able to identify loci significantly influencing trait variation.     

Parallel RH mapping of BTA1 with HSA3 and HSA21

The development of radiation hybrid (RH) panels has elevated comparative gene mapping to a new level of resolution. In this study, we have constructed parallel RH maps defining rearrangements of gene order within conserved segments of bovine Chromosome (Chr) 1 (BTA1) and human Chrs 3 and 21 (HSA3, HSA21). Six new markers, including one gene, have been added to the bovine map, and 11 human genes were ordered with the human G3 panel. BTA1 is clearly a composite of genetic material conserved on these two human chromosomes with HSA21 homologs at each end of BTA1 flanking a large segment homologous to HSA3. Each of the three conserved segments of BTA1 contains rearrangements of gene order relative to their human counterparts. Received: 31 March 1999 / Accepted: 12 July 1999     

Revisiting the quantitative trait loci for milk production traits on BTA6

A parallel association study was performed in two independent cattle populations based on 41 validated, targeted single nucleotide polymorphisms (SNPs) and four microsatellite markers to re-evaluate the multiple quantitative trait loci (QTL) architecture for milk performance on bovine chromosome 6 (BTA6). Two distinct QTL located in the vicinity of the middle region of BTA6, but differing unambiguously regarding their effects on milk composition and yield traits were validated in the German Holstein population. A highly significant association of the protein variant ABCG2 p.Tyr581Ser with milk composition traits reconfirmed the causative molecular relevance of the ABCG2 gene in QTL region 1, whereas in QTL region 2, significant and tentative associations between gene variants RW070 and RW023 (located in the promoter region and exon 9 of the PPARGC1A gene for milk yield traits) were detected. For the German Fleckvieh population, only RW023 showed a tentative association with milk yield traits, whereas those loci with significant effects in German Holsteins (ABCG2 p.Tyr581Ser, RW070) showed fixed alleles. Even though our new data highlight two variants in the PPARGC1A gene (RW023, RW070) in QTL region 2, based on the results of our study, currently no unequivocal conclusion about the causal background of this QTL affecting milk yield traits can be drawn. Notably, the German Holstein and Fleckvieh populations, known for their divergent degree of dairy type, differ substantially in their allele frequencies for the growth-associated NCAPG p.Ile442Met locus.     

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.     

The variant red coat colour phenotype of Holstein cattle maps to BTA27

The variant red phenotype in Holstein cattle is indistinguishable from the traditional e/e recessive red phenotype caused by a mutation in melanocortin 1 receptor, but is inherited as a dominant trait in relation to black. Co-segregation analysis in four half-sib families segregating for variant red was conducted, excluding melanocortin 1 receptor , agouti signalling protein , attractin and melatonin receptor 1A as causative genes. However, variant red co-segregated with markers in a region of BTA27 that includes beta-defensin 103 ( DEFB103 ). Two newly identified microsatellites and 5 SNPs 5' of DEFB103 were used for linkage mapping in four segregating families (LOD = 3.26). One haplotype was inherited in VR cattle in a 6-generation pedigree.     

Genetic mapping of the belt pattern in Brown Swiss cattle to BTA3

The white belt pattern of Brown Swiss cattle is characterized by a lack of melanocytes in a stretch of skin around the midsection. This pattern is of variable width and sometimes the belt does not fully circle the body. To identify the gene responsible for this colour variation, we performed linkage mapping of the belted locus using six segregating half-sib families including 104 informative meioses for the belted character. The pedigree confirmed a monogenic autosomal dominant inheritance of the belted phenotype in Brown Swiss cattle. We performed a genome scan using 186 microsatellite markers in a subset of 88 animals of the six families. Linkage with the belt phenotype was detected at the telomeric region of BTA3. Fine-mapping and haplotype analysis using 19 additional markers in this region refined the critical region of the belted locus to a 922-kb interval on BTA3. As the corresponding human and mouse chromosome segments contain no obvious candidate gene for this coat colour trait, the mutation causing the belt pattern in the Brown Swiss cattle might help to identify an unknown gene influencing skin pigmentation.     

Development and mapping of microsatellites from a microdissected BTA 11-specific DNA library

A chromosome-specific library was developed for Bos taurus autosome 11 by chromosome microdissection and microcloning using a bovine primary fibroblast culture, obtained from a t(X;23) heifer, that spontaneously developed a translocation chromosome involving bovine chromosome 11. The library was screened using (AC)12 oligos, positive clones selected, sequenced and primers developed to generate bovine chromosome 11-specific microsatellite markers. This study suggests that chromosome-specific libraries have great potential for development of microsatellite markers for the construction of marker-saturated linkage maps for each chromosome.     

Characterization of a QTL region affecting clinical mastitis and protein yield on BTA6

Quantitative trait loci affecting clinical mastitis were detected and fine mapped to a narrow region on bovine chromosome 6 in the Norwegian Red cattle population. The region includes the casein gene cluster and several candidate genes thought to influence clinical mastitis. The most significant results were found for SNPs within the Mucin 7 gene. This gene encodes an antimicrobial peptide and constitutes part of the first line of defence for the mucosal immune system. Detection of long haplotypes extending several Mb may indicate that artificial selection has influenced the haplotype structures in the region. A search for selection sweeps supports this observation and coincides with association results found both by single SNP and haplotype analyses. Our analyses identified haplotypes carrying quantitative trait loci alleles associated with high protein yield and simultaneously fewer incidences of clinical mastitis. The fact that such haplotypes are found in relative high frequencies in Norwegian Red may reflect the combined breeding goal that is characterized by selection for both milk production and disease resistance. The identification of these haplotypes raises the possibility of overcoming the unfavourable genetic correlation between these traits through haplotype-assisted selection.     

Investigation of the genetic architecture of a bone carcass weight QTL on BTA6

A previous analysis of an F₂/Backcross Charolais × Holstein cross population identified the presence of a highly significant QTL on chromosome 6 (BTA6) affecting the proportion of bone in the carcass. Two closely linked QTL affected birth weight (BW) and body length at birth (BBL). In this report, the marker density around the QTL on BTA6 was increased, adding four additional microsatellite markers across the chromosome and 46 SNPs within the target QTL confidence interval. Of the SNPs, 26 were in positional candidate genes and the remaining 20 provided an even distribution of markers in the target QTL region. As a bone‐related trait, the sum of the bone weight for all the left fore‐ and hindquarter joints of the carcass was analysed. We also studied the BW and BBL. Analyses of the data substantially reduced the QTL confidence interval. No strong evidence was found that the QTL for the three traits studied are different, and we conclude that the results are consistent with a single pleiotropic QTL influencing the three traits, with the largest effects on the proportion of bone in the carcass. The analyses also suggest that none of the SNPs tested is the sole causative variant of the QTL effects. Specifically, the SNP in the NCAPG gene previously reported as a causal mutation for foetal growth and carcass traits in other cattle populations was excluded as the causal mutation for the QTL reported here. Polymorphisms located in other previously identified candidate genes including SPP1, ABCG2, IBSP, MEPE and PPARGC1A were also excluded. The results suggest that SNP51_BTA‐119876 is the polymorphism in strongest linkage disequilibrium with the causal mutation(s). Further research is required to identify the causal variant(s) associated with this bone‐related QTL.     

Homogeneity of recombination rate within a conserved region on BTA3 that contains QTL

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 (theta) among bulls in order to assess the suitability of population-based estimates of theta for marker assisted selection and to explore the relationship between variation in theta and chromosome breakpoints associated with mammalian evolution. Using sperm typing, thetaD3S20-D3S34 and theta D3S34-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 theta was not detected between bulls for either interval (D3S20-D3S34 chi(2)5 d.f.=2.59, P < 0.90; D3S34-D3S3 chi(2)5 d.f.=3.72, P < 0.75). The observed differences in theta 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 theta. 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 theta.     

Polymorphism at the bovine tumor necrosis factor alpha locus and assignment to BTA 23

We have identified four single-strand conformation variants of the bovine tumor necrosis factor alpha gene by analysis of PCR-amplified fragments. The variants are inherited in Mendelian fashion and are informative for linkage mapping. We have mapped the bovine gene to Chromosome (Chr) 23 in a panel of somatic cell hybrids and observed genetic linkage to the major histocompatibility complex (BoLA) genes and microsatellite markers on bovine Chr 23 in an international bovine reference family panel. The distribution of the alleles was determined in cattle of different breeds and of different geographical origins, which included trypano-susceptible and trypano-tolerant cattle. Received: 3 July 1995 / Accepted: 16 October 1995