Closure of a genetic linkage map of human chromosome 7q with centromere and telomere polymorphisms.

We have constructed a 2.4-cM resolution genetic linkage map for chromosome 7q that is bounded by centromere and telomere polymorphisms and contains 66 loci (88 polymorphic systems), 38 of which are uniquely placed with odds for order of at least 1000:1. Ten genes are included in the map and 11 markers have heterozygosities of at least 70%. This map is the first to incorporate several highly informative markers derived from a telomere YAC clone HTY146 (locus D7S427), including HTY146c3 (HET 92%). The telomere locus markers span at least 200 kb of the 7q terminus and no crossovers within the physical confines of the locus were observed in approximately 240 jointly informative meioses. The sex-equal map length is 158 cM and the largest genetic interval between uniquely localized markers in this map is 11 cM. The female and male map lengths are 181 and 133 cM, respectively. The map is based on the CEPH reference pedigrees and includes over 4000 new genotypes, our previously reported data plus 29 allele systems from the published CEPH version 5 database, and was constructed using the program package CRI-MAP. This genetic linkage map can be considered a baseline map for 7q, and will be useful for defining the extent of chromosome deletions previously reported for breast and prostate cancers, for developing additional genetic maps such as index marker and 1-cM maps, and ultimately for developing a fully integrated genetic and physical map for this chromosome.     

A detailed multipoint map of human chromosome 4 provides evidence for linkage heterogeneity and position-specific recombination rates

Utilizing the CEPH reference panel and genotypic data for 53 markers, we have constructed a 20-locus multipoint genetic map of human chromosome 4. New RFLPs are reported for four loci. The map integrates a high-resolution genetic map of 4p16 into a continuous map extending to 4q31 and an unlinked cluster of three loci at 4q35. The 20 linked markers form a continuous linkage group of 152 cM in males and 202 cM in females. Likely genetic locations are provided for 25 polymorphic anonymous sequences and 28 gene-specific RFLPs. The map was constructed employing the LINKAGE and CRIMAP computational methodologies to build the multipoint map via a stepwise algorithm. A detailed 10-point map of the 4p16 region constructed from the CEPH panel provides evidence for heterogeneity in the linkage maps constructed from families segregating for Huntington disease (HD). It additionally provides evidence for position-specific recombination frequencies in the telomeric region of 4p.     

Long homozygous chromosomal segments in reference families from the centre d'Etude du polymorphisme humain

Using genotypes from nearly 8,000 short tandem-repeat polymorphisms typed in eight of the reference families from the Centre d'Etude du Polymorphisme Humain (CEPH), we identified numerous long chromosomal segments of marker homozygosity in many CEPH individuals. These segments are likely to represent autozygosity, the result of the mating of related individuals. Confidence that the complete segment is homozygous is gained only with markers of high density. The longest segment in the eight families spanned 77 cM and included 118 homozygous markers. All individuals in family 884 showed at least one segment of homozygosity: the father and mother were homozygous in 8 and 10 segments with an average length of 13 and 16 cM, respectively, and covering a total of 105 and 160 cM, respectively. The progeny in family 884 were homozygous over 5-16 segments with average length 11 cM. The progeny in family 102 were homozygous over 4-12 segments with average length 19 cM. Of the 100 individuals in the other six families, 1 had especially long homozygous segments, and 19 had short but significant homozygous segments. Our results indicate that long homozygous segments are common in humans and that these segments could have a substantial impact on gene mapping and health.     

The CEPH consortium primary linkage map of human chromosome 10

The first CEPH consortium map, that of chromosome 10, is presented. This primary linkage map contains 28 continuously linked loci defined by genotypes generated from CEPH family DNAs with 37 probe and enzyme combinations. Cytogenetic localization of some of the genetic markers indicates that the consortium map extends, at least, from 10p13 to 10q26. The order of loci on the consortium map agrees with the physical localization data. The female map spans 309 cM (206 cM if an approximation of interference is included in the mapping function used to construct the map), and the mean genetic distance of intervals is 11 cM (7 cM). Also presented are maps of chromosome 10 from each of five CEPH collaborating laboratories, based on genotypes for all relevant markers in the CEPH database. The CEPH consortium map of chromosome 10 should be useful for localization of any gene of interest falling within the span covered. The genotypes in the chromosome 10 consortium map database are now available to the scientific community.     

A Primary Genetic Linkage Map of 14 Polymorphic Loci for the Short Arm of Human Chromosome 8

A genetic linkage map of markers for the short arm of human chromosome 8 has been constructed with 14 polymorphic DNA markers on the basis of genotypes obtained in 40 CEPH reference families. This unbroken map spans 45 cM in males and 79 cM in females. The 14 markers include three genes, MSR, LPL, and NEFL, and one anonymous DNA segment that were previously assigned to chromosome 8. The other 10 marker had been isolated from a chromosome 8-specific cosmid library and physically localized to chromosomal bands by fluorescence in situ hybridization. The order of loci determined by genetic linkage was consistent with their physical locations. This map will facilitate efficient linkage studies of human genetic diseases that may be segregating on chromosome 8p and will provide anchor points for development of high-resolution maps for this chromosomal region.     

A genetic map of human chromosome 17p

A genetic linkage map was constructed with 18 loci from the short arm and pericentric region of chromosome 17 typed on the CEPH reference families. The genetic map includes three markers extracted from the CEPH public database. Nine loci could be ordered using a threshold of odds of at least 1000:1 against alternative orders during the map construction process. With a reduced tolerance of 100:1, a total of 13 loci could be placed on the map spanning a distance of approximately 60 cM in females and 46 cM in males. There were statistically significant differences between the male and the female genetic maps. The order inferred from the genetic data was consistent with the physical localizations of these probes obtained from somatic cell hybrids and tumor deletion studies. This map should be useful for genetic fine mapping of 17p loci.     

Constructing genetic linkage maps for Pinus elliottii var. elliottii and Pinus caribaea var. hondurensis using SRAP, SSR, EST and ISSR markers

A total of 122 F₁ individuals from a single full-sib interspecific hybrid family crossed between Pinus elliottii var. elliottii (PEE) and P. caribaea var. hondurensis (PCH) were used to construct a detailed genetic linkage maps using four types of molecular markers: sequence-related amplified polymorphism (SRAP), microsatellite (SSR), expressed sequence tag polymorphism (ESTP) and inter-simple sequence repeat (ISSR). There were 381 SRAP, 108 SSR, 25 ESTP and 32 ISSR loci, segregating in the interspecific F₁ hybrid individuals. Framework maps were constructed at a LOD score threshold of 4.0 using the JoinMap^® 3.0. The map for the male parent (PCH) had 108 markers in 16 linkage groups (LGs), with a total length of 1,065.9 cM (Kosambi) and an average marker interval of 9.87 cM. The map for the female parent (PEE) contained 93 markers in 19 LGs, with a total length of 1,006.7 cM (Kosambi) and an average marker interval of 10.82 cM. The maps for PCH and PEE covered 56.5 and 70.3 % of their respective genomes. Based on the position of 36 loci segregating in both parents, 8 homologous LGs between PEE and PCH were identified.     

A collection of ordered tetranucleotide-repeat markers from the human genome. The Utah Marker Development Group.

A collection of 1,069 human PCR-based genetic markers has been developed, and their distribution over the 22 autosomes and the X chromosome has been determined. Each marker was developed around a short-tandem-repeat DNA sequence. The majority (85%) of the markers described here were selected to contain tetranucleotide repeats, because these repeats show better stability during PCR than do dinucleotide repeats. Linkage maps constructed from genotypes collected with these markers in four CEPH pedigrees (1331, 1332, 1362, and 884) covered 3,417 cM of the human genome. More than 600 of the loci revealed heterozygosities > .70. Overall, 444 loci were ordered, with odds > 100:1 against inversion of adjacent loci. The average distance between markers was 7.4 cM on the autosomes and 24.8 cM on the X chromosome. Likely locations (100:1 odds intervals) were assigned for the remaining 621 short-tandem-repeat polymorphisms, as well as for 160 other markers that are present on the framework maps published by the Cooperative Human Linkage Center. Four markers specific to the Y chromosome are also reported here. From our maps, 347 markers were chosen to define "index" maps for each of the 22 autosomes. The index markers detect loci with an average heterozygosity of .85 and cover 3,169 cM of the autosomes, with an average distance between markers of 9.2 cM. These polymorphic short tandem repeats will be highly useful as reagents for the ongoing genetic and physical mapping of the human genome and for characterization of genetic changes in cancer.     

Construction of a High-Density Microsatellite Genetic Linkage Map and Mapping of Sexual and Growth-Related Traits in Half-Smooth Tongue Sole (Cynoglossus semilaevis)

High-density genetic linkage maps of half-smooth tongue sole were developed with 1007 microsatellite markers, two SCAR markers and an F1 family containing 94. The female map was composed of 828 markers in 21 linkage groups, covering a total of 1447.3 cM, with an average interval 1.83 cM between markers. The male map consisted of 794 markers in 21 linkage groups, spanning 1497.5 cM, with an average interval of 1.96 cM. The female and male maps had 812 and 785 unique positions, respectively. The genome length of half-smooth tongue sole was estimated to be 1527.7 cM for the females and 1582.1 cM for the males. Based on estimations of the map lengths, the female and male maps covered 94.74 and 94.65% of the genome, respectively. The consensus map was composed of 1007 microsatellite markers and two SCAR markers in 21 linkage groups, covering a total of 1624 cM with an average interval of 1.67 cM. Furthermore, 159 sex-linked SSR markers were identified. Five sex-linked microsatellite markers were confirmed in their association with sex in a large number of individuals selected from different families. These sex-linked markers were mapped on the female map LG1f with zero recombination. Two QTLs that were identified for body weight, designated as We-1 and We-2, accounted for 26.39% and 10.60% of the phenotypic variation. Two QTLs for body width, designated Wi-1 and Wi-2, were mapped in LG4f and accounted for 14.33% and 12.83% of the phenotypic variation, respectively. Seven sex-related loci were mapped in LG1f, LG14f and LG1m by CIM, accounting for 12.5–25.2% of the trait variation. The results should prove to be very useful for improving growth traits using molecular MAS.     

Alignment of the PiGMaP and USDA linkage maps of porcine chromosomes 2 and 5

The PiGMaP and USDA porcine linkage maps for chromosomes 2 and 5 have been aligned by typing five USDA microsatellite markers from chromosomes 2 and 4 from chromosome 5 on the PiGMaP reference families. The markers in the two maps can be successfully aligned except for Sw395 on chromosome 2, which is the end-most marker in the USDA map 22 cM remote from the next marker, but which maps to a more central location and in the same position as Sw776 in the PiGMaP families. The mapping of four additional chromosome 5 markers has enabled amalgamation of the two previously separate PiGMaP linkage groups assigned to chromosome 5 and has more than doubled the length of its map. The USDA map of chromosome 5 is considerably shorter than the revised PiGMaP version, particularly between DAGK and Sw1071 , where the corresponding lengths are 9 cM versus 33 cM.     

Linkage maps of microsatellite DNA markers for the Pacific oyster Crassostrea gigas

We constructed male and female consensus linkage maps for the Pacific oyster Crassostrea gigas, using a total of 102 microsatellite DNA markers typed in 11-day-old larvae from three families. We identified 11 and 12 linkage groups in the male and female consensus maps, respectively. Alignment of these separate maps, however, suggests 10 linkage groups, which agrees with the haploid chromosome number. The male linkage map comprises 88 loci and spans 616.1 cM, while the female map comprises 86 loci and spans 770.5 cM. The male and the female maps share 74 loci; 2 markers remain unlinked. The estimated coverages for the consensus linkage maps are 79% for the male and 70-75% for the female, on the basis of two estimates of genome length. Ninety-five percent of the genome is expected to lie within 16 and 21 cM of markers on the male and female maps, respectively, while 95% of simulated minimum distances to the male and female maps are within 10.1 and 13.6 cM, respectively. Females have significantly more recombination than males, across 118 pairs of linked markers in common to the parents of the three families. Significant differences in recombination and orders of markers are also evident among same-sex parents of different families as well as sibling parents of opposite sex. These observations suggest that polymorphism for chromosomal rearrangements may exist in natural populations, which could have profound implications for interpreting the evolutionary genetics of the oyster. These are the first linkage maps for a bivalve mollusc that use microsatellite DNA markers, which should enable them to be transferred to other families and to be useful for further genetic analyses such as QTL mapping.     

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.     

Index, Comprehensive Microsatellite, and Unified Linkage Maps of Human Chromosome 14 with Cytogenetic Tie Points and a Telomere Microsatellite Marker

Three sets of linkage maps (index, comprehensive microsatellite, and unified) have been constructed for human chromosome 14 based on genotypes from the CEPH reference pedigrees. The index maps consist of 18 microsatellite markers, with heterozygosities of at least 68% and intermarker spacing no greater than 11 cM. The sex-average comprehensive microsatellite map is 125 cM in length and includes 115 markers with 54 loci uniquely placed with odds for marker order of at least 1000:1. The sex-average index map length is 121 cM, and the female- and male-specific maps are 143 and 101 cM, respectively. A unified map was also constructed from 147 loci (162 marker systems), which includes 32 RFLP markers in addition to the 115 microsatellites. The sex-average length of the unified map is 128 cM with 69 loci uniquely placed. Our maps are anchored by a microsatellite telomere marker sCAW1 (D14S826), developed from a telomere YAC clone TYAC196, which extends the linkage map to the physical terminus of the long arm of chromosome 14. Furthermore, we have also physically mapped seven of the loci by fluorescencein situhybridization of cosmid clones orAlu-PCR products amplified from YACs containing the marker sequences. Together with previously established cytogenetic map designations for other loci, our maps display links between genetic markers for 10 of 13 cytogenetic bands of chromosome 14 at the 550 genome band resolution.     

Heterozygous Mapping Strategy (HetMappS) for High Resolution Genotyping-By-Sequencing Markers: A Case Study in Grapevine

Genotyping by sequencing (GBS) provides opportunities to generate high-resolution genetic maps at a low genotyping cost, but for highly heterozygous species, missing data and heterozygote undercalling complicate the creation of GBS genetic maps. To overcome these issues, we developed a publicly available, modular approach called HetMappS, which functions independently of parental genotypes and corrects for genotyping errors associated with heterozygosity. For linkage group formation, HetMappS includes both a reference-guided synteny pipeline and a reference-independent de novo pipeline. The de novo pipeline can be utilized for under-characterized or high diversity families that lack an appropriate reference. We applied both HetMappS pipelines in five half-sib F₁ families involving genetically diverse Vitis spp. Starting with at least 116,466 putative SNPs per family, the HetMappS pipelines identified 10,440 to 17,267 phased pseudo-testcross (Pt) markers and generated high-confidence maps. Pt marker density exceeded crossover resolution in all cases; up to 5,560 non-redundant markers were used to generate parental maps ranging from 1,047 cM to 1,696 cM. The number of markers used was strongly correlated with family size in both de novo and synteny maps (r = 0.92 and 0.91, respectively). Comparisons between allele and tag frequencies suggested that many markers were in tandem repeats and mapped as single loci, while markers in regions of more than two repeats were removed during map curation. Both pipelines generated similar genetic maps, and genetic order was strongly correlated with the reference genome physical order in all cases. Independently created genetic maps from shared parents exhibited nearly identical results. Flower sex was mapped in three families and correctly localized to the known sex locus in all cases. The HetMappS pipeline could have wide application for genetic mapping in highly heterozygous species, and its modularity provides opportunities to adapt portions of the pipeline to other family types, genotyping technologies or applications.     

RAPD-based genetic linkage maps of yellow passion fruit (Passiflora edulis Sims. f. flavicarpa Deg.).

A single cross between two clones of passion fruit (Passiflora edulis Sims. f. flavicarpa Deg., 2n = 18) was selected for genetic mapping. The mapping population was composed of 90 F1 plants derived from a cross between 'IAPAR 123' (female parent) and 'IAPAR 06' (male parent). A total of 380 RAPD primers were analyzed according to two-way pseudo-testcross mapping design. The linkage analysis was performed using Mapmaker version 3.0 with LOD 4.0 and a maximum recombination fraction (theta) of 0.30. Map distances were estimated using the Kosambi mapping function. Linkage maps were constructed with 269 loci (2.38 markers/primer), of which 255 segregated 1:1, corresponding to a heterozygous state in one parent and null in the other. The linkage map for 'IAPAR123' consisted of 135 markers. A total of nine linkage groups were assembled covering 727.7 cM, with an average distance of 11.20 cM between framework loci. The sizes of the linkage groups ranged from 56 to 144.6 cM. The linkage map for 'IAPAR 06' consisted of 96 markers, covering 783.5 cM. The average distance between framework loci was 12.2 cM. The length of the nine linkage groups ranged from 20.6 to 144.2 cM. On average, both maps provided 61% genome coverage. Twenty-four loci (8.9%) remained unlinked. Among their many applications, these maps are a starting point for the identification of quantitative trait loci for resistance to the main bacterial disease affecting passion fruit orchards in Brazil, caused by Xanthomonas campestris pv. passiflorae, because parental genotypes exhibit diverse responses to bacterial inoculation.     

A genetic linkage map of 27 markers on human chromosome 21.

We have constructed a genetic linkage map of the long arm of human chromosome 21 comprising 27 DNA markers. This map is an updated version of that reported earlier by group (1989, Genomics 4: 579-591), which contained 17 DNA markers. The current markers consist of 10 genes and 17 anonymous sequences. Traditional methods (restriction fragment length polymorphisms) were used to map 25 of these markers, whereas 2 markers were studied by polymerase chain reaction amplification of (GT)n dinucleotide repeats. Linkage analysis was performed on 40 CEPH families using the computer program packages LINKAGE, CRI-MAP, and MAPMAKER. Recombination rates were significantly different between the sexes, with the male map being 132 cM and the female map being 161 cM, assuming Kosambi interference and a variable ratio of sex difference in recombination. Approximately one-half of the crossovers in either sex occur distally, in terminal band 21q22.3, which also contains 16 of the markers studied. The average distance between adjacent markers was 6 cM.     

A strategy for constructing high-resolution genetic maps of the human genome: a genetic map of chromosome 17p, ordered with meiotic breakpoint-mapping panels.

Genetic linkage analyses with genotypic data obtained from four CEPH reference families initially assigned 24 new PCR-based markers to chromosome 17 and located the markers at specific intervals of an existing genetic map of chromosome 17p. Each marker was additionally genotyped with an ordered set of obligate, phase-known recombinant chromosomes. The breakpoint-mapping panels for each family consisted of two parents, one sib with a nonrecombinant chromosome, and one or more sibs with obligate recombinant chromosomes. The relative order of markers was determined by sorting segregation patterns of new markers and ordered anchor markers and by minimizing double-recombination events. Consistency of segregation patterns with multiple flanking loci constituted support for order. A genetic map of chromosome 17p was completed with 39 markers in 23 clusters, with an average space of 3 cM between clusters. The collection of informative genotypes was highly efficient, requiring fivefold fewer genotypes than would be collected with all the CEPH families. Given the availability of large numbers of highly informative PCR-based markers, meiotic breakpoint mapping should facilitate construction of a human genomic map with 1-cM resolution.     

Molecular mapping in tropical maize (Zea mays L.) using microsatellite markers. 1. Map construction and localization of loci showing distorted segregation

Microsatellites have become the most important class of markers for mapping procedures. Primarily based on restriction fragment length polymorphism (RFLP) markers, several molecular genetic maps of maize have been developed, mainly using temperate inbred maize lines. To characterize the level of polymorphism of microsatellite loci and construct a genetic map in tropical maize, two elite inbred lines, L-08-05F and L-14-4B, were crossed to produce 400 F(2) individuals that were used as a mapping population. A survey of 859 primer pair sequences of microsatellites was used. The polymorphism screens of each microsatellite and genotype assignment were performed using high-resolution agarose gels. About 54 % of the primer sets gave clearly scorable amplification products, 13 % did not amplify and 33 % could not be scored on agarose gels. A total of 213 polymorphic markers were identified and used to genotype the mapping population. Among the polymorphic markers, 40 showed loci deviating from expected Mendelian ratios and clusters of deviating markers were located in three chromosome regions. Non-Mendelian scoring was present in 19 markers. The final genetic map with 117 markers spanned 1634 cM in length with an average interval of 14 cM between adjacent markers.     

A genetic linkage map of 96 loci on the short arm of human chromosome 3.

We constructed a genetic map of 96 loci on the short arm of human chromosome 3 (3p) in 59 families provided by the Centre d'Etude du Polymorphisme Humaine (CEPH). Twenty-nine continuously linked loci were placed on the map with likelihood support of at least 1000:1; one locus, D3S213, was placed on the map with likelihood support of 871:1; D3Z1, an alpha satellite centromeric repeat probe, was placed on the map with likelihood support of 159:1; 65 loci were assigned regional locations. The average heterozygosity of the uniquely ordered markers was 49%. The map extends from 3p26, the terminal band of 3p, to the centromere (from D3S211 to D3Z1). Multipoint linkage analysis indicated that the male, female, and sex-averaged maps extend for 102, 147, and 116 cM, respectively. The mean genetic distance between uniquely ordered loci on the sex-averaged map was 4.0 cM. Probe density was greatest for the region of 3p between D3F15S2e and the telomere. The sex-averaged map contained two intervals greater than 10 cM. Seventeen probes were localized by fluorescence in situ hybridization. The loci described in this report will be useful in building an integrated genetic and physical map of this chromosome.     

The CEPH consortium linkage map of human chromosome 2

This paper describes the Centre d'Etude du Polymorphisme Humain (CEPH) consortium linkage map of chromosome 2. The map contains 36 loci defined by genotyping generated from the CEPH family DNAs. A total of 73 different markers were typed by 14 contributing laboratories; of these, 36 loci are ordered on the map with likelihood support of at least 1000:1. Markers are placed along the length of the chromosome but no markers were available to anchor the map at either telomere or the centromere. Multilocus linkage analysis has produced male, female, and sex-averaged maps extending for 261, 430, and 328 cM, respectively. The sex-averaged map contains five intervals greater than 15 cM and the mean genetic distance between the 36 uniquely placed loci is 9.1 cM.