Toward developing a genome-wide microsatellite marker set for linkage analysis in the rhesus macaque (Macaca mulatta): identification of 76 polymorphic markers

Linkage analysis can be problematic in humans because of the lack of large, multigenerational pedigrees and the difficulties in obtaining phenotypic data on all family members. In contrast, large, captive colonies of rhesus macaque are a potentially valuable resource for linkage studies because detailed phenotypic and genealogical data are kept, inbreeding is avoided, and DNA samples can usually be obtained. Microsatellite marker sets for genome-wide screening are available in a number of species, but not for the rhesus macaque. We tested primers to 400 human microsatellite markers from a genome-wide mapping set using DNA from nine unrelated female rhesus macaques. We found that 76 (19%) of the primers amplified a polymorphic product using the standard protocols for human DNA. The average heterozygosity of the markers in humans was 0.80, compared to 0.65 in the rhesus macaques. This study provides preliminary data, which could be used toward the development of a linkage mapping set in this species. There would be a need, however, to confirm the Mendelian inheritance of the markers.     

Genetic variation and biochemical properties of esterase-18 (ES-18) in the laboratory rat (Rattus norvegicus): A new locus of esterase cluster 2 in linkage group V

A new liver-specific rat carboxylesterase isozyme (EC 3.1.1.1) designated esterase-18 (ES-18) is described. Genetic variation of ES-18 was examined in 93 inbred strains and substrains and a structural locusEs-18 was suggested, coding for either the presence (Es-18 ^a) or the absence (Es-18 ^b) of the isozyme. Linkage studies involving two backcross series revealed thatEs-18 resides in cluster 2 of LGV. No recombination betweenEs-18 and other cluster 2 loci was found in 19 lines of two RI strain sets or in the backcross series.R. K. was supported by the Sonderforschungsbereich 146 (Versuchstierforschung). O.D. was supported by the Deutsche Forschungsgemeinschaft (De 315/2). This is communication No. 65 of a research program devoted to the cellular distribution, regulation, and genetics of nonspecific esterases.     

Immunohistochemistry of Grandry corpuscles in the oral mucosa of the duck bill: a light- and electron-microscopic study

Grandry corpuscles in the oral mucosa of the upper bill of the duck were immunohistochemically studied using antisera against calcitonin gene-related peptide (CGRP), galanin, methionine-enkephalin, neuropeptide Y (NPY), somatostatin, substance P (SP) and vasoactive intestinal peptide (VIP). Grandry corpuscles in the lamina propria selectively showed only SP-like immunoreactivity. Herbst corpuscles distributed near Grandry corpuscles were negative to all antisera applied. Although immunoreactive products in the Grandry corpuscles were found as granules in the peripheral cytoplasm of the Grandry cell, the axon terminals and satellite cells exhibited no reactivity. In pre-embedding electron-microscopic sections, SP-like immunoreactive products visualized with 3,3-diaminobezidine were localized in the granules of Grandry cells, but no labeling was observed in the cytoplasmic matrix or cell organelles. Electron-immunocytochemical labeling with colloidal gold by the post-embedding method clearly demonstrated that the SP antigen was localized only in the granules. It is presumed that Grandry cells have a secretory function. However, the function and the method of release of the SP contained in the observed granules remains obscure. Some CGRP-, NPY-, SP- and VIP-like-immunoreactive nerve fibers with varicosities associated with blood vessels and nerve fiber bundles of various sizes were observed in the lamina propria, but no such fibers penetrated into the intraepitherial layer. Nerve fibers positive for SP and VIP were also found in the interlobular connective tissue of the palatine glands. Some SP-positive neurons were detected in the vicinity of the palatine glands.     

Genetic linkage between the loci for phosphohexose isomerase (PHI) and a serum protein (Xk) in horses

Genetic linkage between the equine loci for phosphohexose isomerase (PHI) and serum Xk protein was demonstrated by means of segregation data from three sire families. The recombination frequency was estimated from pooled data to be 0.23 ± 0.02; a significant heterogeneity between sires for estimates of the recombination frequency was observed. No indication of linkage was detected between Xk and 14 other blood marker loci. Linkage between the Xk locus and the locus for soluble malic enzyme ( ME1 ) has recently been reported in horses. An equine linkage group designated LG IV comprising the three loci ME1, PH1 , and Xk has thus been established. The possibility that the linkage between PH1 and Xk is homologous to the linkage between the loci for PHI and a serum postalbumin (PO-2) in pigs was discussed.     

Biochemical genetics of Es-14 (formerly Es-Si) and a new esterase variation,Es-15, of the laboratory rat (Rattus norvegicus): Biochemistry,tissue expression,and linkage to Es-1 in linkage group V

The segregation of rat esterases controlled by loci residing in linkage group V (LGV) has been studied in two backcross series, (LEW/Han × BN/Han)F₁ × LEW/Han and (LEW/Han × LE/Han)F₁ × LEW/Han. Es-14 (formerly Es-Si) was shown to be closely linked to Es-1. A new esterase locus, Es-15, was described which codes for a liver isozyme. The distribution pattern of three alleles at the Es-15 locus is presented for 52 independent inbred strains. Close linkage of Es-15 to Es-14 and to Es-1 was established, proposing the following gene order: [Es-2, Es-10]—[ES-1, ES-14, ES-15]. The esterase loci on LGV are thus separated into two gene clusters, cluster 1 and cluster 2. These conclusions are supported by the strain distribution patterns of the two RI strain series, LXB and DXE.Otto von Deimling was supported by the Deutsche Forschungsgemeinschaft (De 315/2-1, communication No. 56).     

Preliminary linkage map of the turkey (Meleagris gallopavo) based on microsatellite markers

The turkey is an agriculturally important species for which, until now, there is no published genetic linkage map based on microsatellite markers--still the markers most used in the chicken and other farm animals. In order to increase the number of markers on a turkey genetic linkage map we decided to map new microsatellite sequences obtained from a GT-enriched turkey genomic library. In different chicken populations more than 35-55% of microsatellites are polymorphic. In the turkey populations tested here, 43% of all turkey primers tested were found to be polymorphic, in both commercial and wild type turkeys. Twenty linkage groups (including the Z chromosome) containing 74 markers have been established, along with 37 other unassigned markers. This map will lay the foundations for further genetic mapping and the identification of genes and quantitative trait loci in this economically important species. Genome comparisons, based on genetic maps, with related species such as the chicken would then also be possible. All primer information, polymerase chain reaction (PCR) conditions, allele sizes and genetic linkage maps can be viewed at http://roslin.thearkdb.org/. The DNA is also available on request through the Roslin Institute.     

家蚕AFLP连锁框架图谱的构建

利用改进的AFLP分子标记方法,对家蚕Bombyx mori回交一代BC1群体进行连锁图谱的构建。经17组AFLP引物的选择性扩增,共得到430个多态位点,卡方检验后有253个为有效位点。利用Mapmaker/Exp (Version 3.0b)软件作连锁分析,其中163个标记分属28个连锁群,连锁群标记数变化范围是2～28个,平均每个连锁群标记数为5.8个,该图覆盖的基因组长度为2.998.9cM(图距单位),连锁群长度变化范围为4.5～652.8 cM,连锁群的平均长度为107.1 cM,平均图距为4.5～36.7 cM。     

Dissecting linkage disequilibrium in African-American genomes: roles of markers and individuals

Substantial increases of linkage disequilibrium (LD) both in magnitude and in range have been observed in recently admixed populations such as African-American (AfA). On the other hand, it has also been shown that LD in AfAs was very similar to that of African. In this study, we attempted to resolve these contradicting observations by conducting a systematic examination of the LD structure in AfAs by genotyping a sample of AfA individuals at 24,341 single nucleotide polymorphisms (SNPs) spanning almost the entire chromosome 21, with an average density of 1.5 kb/SNP. The overall LD in AfAs is similar to that in African populations and much less than that in European populations. Even when the ancestry-informative markers (AIMs) were used, extended LD in AfA was found to be limited to certain magnitude range (0.2 < or = r(2) < or = 0.8) and certain distance range, that is, between-marker distance more than 200 kb. Furthermore, the inclusion of AfA individuals with predominant African ancestry was found to reduce the overall magnitude of LD. Elevation of LD in the AfA population, compared with its parental populations, can only be observed at the markers with large allele frequency differences between 2 parental populations at limited scenario. AfA individuals of wholly African ancestry contribute little to the extended LD in the AfA population, and further genotyping or association analysis conducted using only admixed individuals may lead to higher statistical power and possibly reduced cost.     

Vibrotactile thresholds of the Non-Pacinian I channel: II. Predicting the effects of contactor location on the phalanx

The firing-rate-based population model for rapidly-adapting (RA) mechanoreceptive fibers by Güçlü and Bolanowski (Güçlü B, Bolanowski SJ. 2002. Modeling population responses of rapidly-adapting mechanoreceptive fibers. Journal of Computational Neuroscience 12:201–218.) is extended by including temporal-response properties of RA fibers. This representation allows for the generation of action-potential (spike) times for each fiber when a sinusoidal, steady-state stimulus is applied onto the skin. Signal detection theory was used to predict human psychophysical thresholds. Specifically, the effects of sensorineural innervation pattern, stimulus-contactor location and selected decision rules on the model predictions were studied. The predicted thresholds were lowest when the decision rule was one spike and highest when many active fibers were required for detection. These predictions were empirically tested by measuring vibrotactile thresholds of the Non-Pacinian I (NP I) channel, which required the special techniques discussed in the preceding article. Although the model predicted thresholds to decrease distally due to the known innervation density which is higher distally, the thresholds of the NP I psychophysical channel were found to be approximately constant (20–25?dB re 1?µm peak amplitude) from the proximal site on the terminal phalanx to the most distal portion. Interestingly, the mechanical impedance of the skin was found not to be constant along the proximo-distal axis. This latter result implies that the space-invariant mechanical attenuation function used in the model may not be valid at every location on the fingertip. Because of this, the discrepancy between the model's predictions and the psychophysical results may be reconciled.     

Repurposing population genetics data to discern genomic architecture: A case study of linkage cohort detection in mountain pine beetle (Dendroctonus ponderosae)

Genetic surveys of the population structure of species can be used as resources for exploring their genomic architecture. By adjusting filtering assumptions, genome‐wide single‐nucleotide polymorphism (SNP) datasets can be reused to give new insights into the genetic basis of divergence and speciation without targeted resampling of specimens. Filtering only for missing data and minor allele frequency, we used a combination of principal components analysis and linkage disequilibrium network analysis to distinguish three cohorts of variable SNPs in the mountain pine beetle in western Canada, including one that was sex‐linked and one that was geographically associated. These marker cohorts indicate genomically localized differentiation, and their detection demonstrates an accessible and intuitive method for discovering potential islands of genomic divergence without a priori knowledge of a species’ genomic architecture. Thus, this method has utility for directly addressing the genomic architecture of species and generating new hypotheses for functional research.     

Assignment of Lap-1 to linkage group I of the rat (Rattus norvegicus)

Genetic analysis of backcross progeny from previously characterized rat inbred strains revealed that the biochemical marker Lap-1 is localized in linkage group I (LG I). Lap-1 codes for leucine arylaminopeptidase (EC 3.4.11). The distances of Lap-1 to c, RT6, and Hbb, based on recombination frequencies, are 3.1±1.5, 8.3±4.0, and 11.4±2.8 cM, respectively. Acon-1 codes for aconitase (EC 4.2.1.3). The calculated distances of Acon-1 to c and Hbb are 30.1±5.0 and 36.1±5.3 cM, respectively. This suggests that Acon-1 is also in LG I, but the observed high frequency of double crossovers requires further confirmation of this linkage. Ahd-2, Es-6, and Gdc-1 are linked neither to markers of LG I nor to one another.     

家蚕高密度AFLP连锁图谱的构建

为了进行家蚕Bombyx mori数量性状的QTL定位研究,以白色茧系品种C₁₀₀ (♀)和近交系大造(P50)(♂)杂交得到F₁,用F₁(♂)与双隐性标记的C₁₀₀ (♀)回交,得到回交一代(BC₁),用改进的AFLP分子标记方法,经96组选择性扩增引物扩增,获得分离比为1∶1(P≤0.05)的1 744个AFLP位点。用Map Manager QTXb19（Version 0.29）连锁图谱构建软件,构建了具有814个标记,36个连锁群的家蚕高密度AFLP分子标记连锁图谱。该连锁图谱覆盖的家蚕基因组长度为13 005 cM,连锁群长度变化范围为109.0～1 573.7 cM,连锁群的平均长度为361.25 cM,其标记间平均图距15.98 cM,最小图距2.3 cM,最大图距47.7 cM,标记间大于30 cM的gap共有39个。该连锁图平均每个连锁群23个标记,最多一个连锁群有92个标记,最少8个标记。该连锁图谱确定了与经典实验遗传图谱第15连锁群和W染色体连锁群相对应的两个连锁群。     

Genetic linkage between loci for a red cell alloantigen (U) and serum protease inhibitor (Pi) in the horse

Preliminary evidence for the fifth autosomal linkage group in the horse, comprised of the loci for a red cell alloantigen (U) and serum protease inhibitor (Pi), was demonstrated by means of paternal half-sib groups in thoroughbred, standardbred and Arabian breeds. Recombination frequency in males was estimated to be 0.125 +/- 0.019.     

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

A comprehensive linkage map, including 236 linked markers with a total sex-average map length of about 2300 cM, covering nearly all parts of the pig genome has been established. Linkage groups were assigned to all 18 autosomes, the X chromosome and the X/Y pseudoautosomal region. Several new gene assignments were made including the assignment of linkage group U1 (EAK-HPX) to chromosome 9. The linkage map includes 77 type I loci informative for comparative mapping and 72 in situ mapped markers physically anchoring the linkage groups on chromosomes. A highly significant heterogeneity in recombination rates between sexes was observed with a general tendency towards an excess of female recombination. The average ratio of female to male recombination was estimated at 1–4:1 but this parameter varied between chromosomes as well as between regions within chromosomes. An intriguing finding was that blood group loci were overrepresented at the distal ends of linkage groups.     

AFLP-based genetic linkage maps of the blue mussel (Mytilus edulis)

We report the construction of the first genetic linkage map in the blue mussel, Mytilus edulis. AFLP markers were used in 86 full-sib progeny from a controlled pair mating, applying a double pseudo-test cross strategy. Thirty-six primer pairs generated 2354 peaks, of which 791 (33.6%) were polymorphic in the mapping family. Among those, 341 segregated through the female parent, 296 through the male parent (type 1:1) and 154 through both parents (type 3:1). Chi-square goodness-of-fit tests revealed that 71% and 73% of type 1:1 and 3:1 markers respectively segregated according to Mendelian inheritance. Sex-specific linkage maps were built with mapmaker 3.0 software. The female framework map consisted of 121 markers ordered into 14 linkage groups, spanning 862.8 cM, with an average marker spacing of 8.0 cM. The male framework map consisted of 116 markers ordered into 14 linkage groups, spanning 825.2 cM, with an average marker spacing of 8.09 cM. Genome coverage was estimated to be 76.7% and 75.9% for the female and male framework maps respectively, rising to 85.8% (female) and 86.2% (male) when associated markers were included. Twelve probable homologous linkage group pairs were identified and a consensus map was built for nine of these homologous pairs based on multiple and parallel linkages of 3:1 markers, spanning 816 cM, with joinmap 4.0 software.     

Assignment of the gene for porcine insulin-like growth factor 1 (IGF1) to chromosome 5 by linkage mapping

Investigation of published sequence data from the porcine insulin-like growth factor 1 (IGF1) gene, resulted in the detection of a microsatellite in the first intron of the gene. Polymerase chain reaction (PCR) primers flanking the (CA)₁₉ repeat were constructed. Polymorphism and Mendelian segregation were documented in a three-generation pedigree and allele frequencies were determined in 74 unrelated animals from four different breeds. Seven alleles were encountered. Linkage analysis was performed in a large pedigree established for gene mapping. Linkage between the IGF1 microsatellite and an anonymous microsatellite marker, S0005, was detected. Furthermore, IGF1 and S0005 was found to be linked to the porcine submaxillary gland mucin (MUC) gene, previously assigned to chromosome 5. The results presented here extend the linkage group on pig chromosome 5 and are in accordance with conserved synteny between human chromosome 12, cattle chromosome 5, mouse chromosome 10 and pig chromosome 5.     

Absence of detectable linkage between the G and H blood group loci in the pig

Morton's lod score method used for the analysis of data from 168 backcross matings (1094 offspring) did not indicate linkage between the G and H blood group loci of the pig. Linkage closer than 0.413 could be excluded at the 1% significance level.     

The first linkage map of the American mink (Mustela vison)

Described herein, the first microsatellite linkage map for the American mink consists of 85 microsatellite markers resolved into 17 linkage groups. The map was constructed using 92 F(1) progeny from five sire families created by crossing mink with different colour types. The linkage groups ranged from 0 to 137 cM. These linkage groups were assigned to 12 of the 14 mink autosomes using a somatic cell hybrid panel. The total map covered 690 sex-averaged Kosambi units with an average marker spacing of 8 cM. This map will facilitate further genetic mapping of monogenic characters and QTL.     

Construction of a genetic linkage map for silver carp (Hypophthalmichthys molitrix)

For silver carp (Hypophthalmichthys molitrix), a combined microsatellite (or simple sequence repeat) and amplified fragment length polymorphism (AFLP) sex average linkage map was constructed. A total of 483 markers (245 microsatellites and 238 AFLPs) were assigned to 33 linkage groups. The map spanned 1352.2 cM, covering 86.4% of the estimated genome size of silver carp. The maximum and average spaces between 420 loci were 21.5 cM and 3.2 cM, respectively. The length of linkage groups ranged from 3.6 cM to 98.5 cM with an average of 41.0 cM. The number of markers per group varied from 2 to 44 with an average of 14.6. The AFLP markers significantly improved the integrity of microsatellite-based linkage groups and increased the genome coverage and marker evenness. A genome-wide recombination suppression was observed in male. In an extreme case, six microsatellites co-segregated in male, but spanned a 45.1 cM region in female.