An integrated genetic linkage map with 1,137 markers constructed from five F2 crosses of autoimmune disease-prone and -resistant inbred rat strains

The rat (Rattus norvegicus) is an important experimental model for many human diseases including arthritis, diabetes, and other autoimmune and chronic inflammatory diseases. The rat genetic linkage map, however, is less well developed than those of mouse and human. Integrated rat genetic linkage maps have been previously reported by Pravenec et al. (1996, Mamm. Genome 7: 117-127) (500 markers mapped in one cross), Bihoreau et al. (1997, Genome Res. 7: 434-440) (767 markers mapped in three crosses), Wei et al. (1998, Mamm. Genome 9: 1002-1007) (562 markers mapped in two crosses), Brown et al. (1998, Mamm. Genome 9: 521-530) (678 markers mapped in four crosses), and Nordquist et al. (1999, Rat Genome 5: 15-20) (330 markers mapped in two crosses). The densest linkage map combined with a radiation hybrid map, reported by Steen et al. (1999, Genome Res. 9: AP1-AP8), includes 4736 markers mapped in two crosses. Here, we present an integrated linkage map with 1137 markers. We have constructed this map by genotyping F2 progeny of five crosses: F344/NHsd x LEW/NHsd (673 markers), DA/Bkl x F344/NHsd (531 markers), BN/SsN x LEW/N (714 markers), DA/Bkl x BN/SsNHsd (194 markers), and DA/Bkl x ACI/SegHsd (245 markers). These inbred rat strains vary in susceptibility/resistance to multiple autoimmune diseases and are used extensively for many types of investigation. The integrated map includes 360 loci mapped in three or more crosses. The map contains 196 new SSLP markers developed by our group, as well as many SSLP markers developed by other groups. Two hundred forty genes are incorporated in the map. This integrated map should allow comparison of rat genetic maps from different groups and thereby facilitate genetic studies of rat autoimmune and related disease models.     

Integration of the PiGMaP and USD A maps for porcine chromosome 14

In order to align two previously published genetic linkage maps, a set of four of the United States Department of Agriculture (USDA) microsatellite linkage markers was mapped in the International Pig Gene Mapping Project (PiGMaP) reference families. Two-point linkage analysis was used between these USDA markers and the set of genes and markers previously mapped on the PiGMaP chromosome 14 map-Markers with threshold lod scores of three or greater were used for multipoint map construction. The USDA and PigGMaP linkage maps of chromosome 14 were aligned using the four USDA microsatellite markers along with three markers that are common to both maps. The PiGMaP genetic linkage map order for chromosome 14 was confirmed and the map was expanded to 193 cM with addition of the new markers.     

Conservation and synteny of SSR loci and QTLs for vegetative propagation in four Eucalyptus species

Conservation of microsatellite loci, heterozygous in Eucalyptus grandis, Eucalyptus urophylla, Eucalyptus tereticornis and Eucalyptus globulus, allowed us to propose homeologies among genetic linkage groups in these species, supported by at least three SSR loci in two different linkage groups. Marker-trait associations for sprouting and adventitious rooting ability were also compared in the four species. Putative quantitative trait loci (QTLs) influencing vegetative propagation traits were located on homeologous linkage groups. Our findings indicate high transferability of microsatellite markers between Eucalyptus species of the Symphyomyrtus subgenus and establish foundations for the use of synteny in the genetic analysis of this genus. Microsatellite markers should help integrate eucalypt genetic linkage maps from various sources. The availability of comparative linkage maps provides a basis of more-efficient use of genetic information for molecular breeding and evolutionary studies in Eucalyptus.     

Inheritance and Organization of Glycinin Genes in Soybean

Five genes (Gy1, through Gy5) encode most of the subunits that are assembled into glycinin, a predominant seed storage protein found in soybeans. Restriction fragment length polymorphisms are described that identify four of these five genes (Gy1/Gy2, Gy3, and Gy5). The fifth gene (Gy4) is characterized by two alleles, one of which (gy4) causes absence of the subunit. Genetic segregation studies indicate that the five genes are located at four genetic loci within the genome. Gy1 and Gy2 are in a direct tandem repeat at one locus, whereas there is a single glycinin gene at each of the other three loci. All four loci segregate independently from one another, and they also segregate independently from the genetic markers for tawny/grey pubescence (T/t), purple/white flower color (W1/w1), light/dark hilum pigmentation (l/ll), black/brown seed coat (R/r), and brown/tan pod color (I1I1L2L2/I1I1I2I2). The latter genetic markers are located on linkage groups 1 (t), 8 (w1), 7 (i), and 2 (r) in the soybean genome, respectively.     

Genetics of adaptive radiation in Hawaiian and Cook Islands species of Tetramolopium (Asteraceae). II. Genetic linkage map and its implications for interspecific breeding barriers.

In a study of the genetic mechanisms associated with adaptive radiation in Hawaiian Tetramolopium, a genetic linkage map was constructed in an interspecific cross. A total of 125 RFLP and RAPD markers were mapped into 117 different loci on nine linkage groups for a map length of 665.7 cM. Segregation distortion occurred in 49% of the mapped probes, located primarily in four linkage groups. High percentages of one parental species genotype (Tetramolopium rockii) were recovered in three of these blocks and the second parental species (T. humile) in the remaining block. The high degree of distorted segregation suggests the buildup of internal crossing barriers, even though island plant species are typically characterized as highly cross compatible with few to no internal crossing barriers. This work and a review of previous crossing studies in island plants show that internal (postmating) crossing barriers do exist. The weak crossing barriers have likely been overlooked because the main focus has been on diversification and speciation through adaptation to extremely diverse environments.     

Molecular Tagging and Mapping of Quantitative Trait Loci for Lint Percentage and Morphological Marker Genes in Upland Cotton

Using 219 F2 Individuals developed by crossing the genetic standard line TM-1 and the multiple dominant marker line T586 In Gossyplum hirsutum L., a genetic linkage map with 19 linkage groups was constructed based on simple sequence repeat （SSR） markers. Compared with our tetraploid backboned molecular genetic map from a （TM-1xHal 7124）xTM-1 BC1 population, 17 of the 19 I｜nkage groups were combined and anchored to 12 chromosomes （sub-genomes）. Of these groups, four morphological marker genes In T586 had been mapped Into the molecular linkage map. Meanwhile, three quantitative trait loci for lint percentage were tagged and mapped separately on the A03 linkage group and chromosome 6.     

A Genetic Linkage Map for Cattle

We report the most extensive physically anchored linkage map for cattle produced to date. Three-hundred thirteen genetic markers ordered in 30 linkage groups, anchored to 24 autosomal chromosomes (n = 29), the X and Y chromosomes, four unanchored syntenic groups and two unassigned linkage groups spanning 2464 cM of the bovine genome are summarized. The map also assigns 19 type I loci to specific chromosomes and/or syntenic groups and four cosmid clones containing informative microsatellites to chromosomes 13, 25 and 29 anchoring syntenic groups U11, U7 and U8, respectively. This map provides the skeletal framework prerequisite to development of a comprehensive genetic map for cattle and analysis of economic trait loci (ETL).     

Identification of quantitative trait loci for wood quality and growth across eight full-sib coastal Douglas-fir families

Typical linkage and quantitative trait locus (QTL) analyses in forest trees have been conducted in single pedigrees with sex-averaged linkage maps. The results of a QTL analysis for wood quality and growth traits of coastal Douglas-fir using eight full-sib families, each consisting of 40 progeny, replicated on four sites are presented. The resulting map of segregating genetic markers consisted of 120 amplified fragment length polymorphism (AFLP) loci distributed across 19 linkage groups. The wood quality traits represent the widest suite of traits yet examined for QTL analysis in a tree species in a single study. Wood fiber traits showed the lowest number of QTLs (3) with relatively small effect (ca. 4%); wood density traits also showed just three QTLs but with slightly larger effect; wood chemistry traits showed more QTLs (7), while ring density traits showed many QTLs with large numbers of QTLs (78) and interesting patterns of temporal variation. Growth traits gave just five QTLs but of major effect (10–16%). Trees, with their long generation times, provide a rich resource for studies of temporal variation of QTL expression.     

A Genetic Map of Lettuce (Lactuca sativa L.) with Restriction Fragment Length Polymorphism, Isozyme, Disease Resistance and Morphological Markers

A detailed linkage map of lettuce was constructed using 53 genetic markers including 41 restriction fragment length polymorphism (RFLP) loci, five downy mildew resistance genes, four isozyme loci and three morphological markers. The genetic markers were distributed into nine linkage groups and cover 404 cM which may be 25-30% of the lettuce genome. The majority (31 of 34) of the RFLP probes detected single segregating loci, although seven of these may have been homologous to further monomorphic loci. When several loci were detected by a single probe, the loci were generally linked, suggesting tandem duplications. One probe, however, detected loci in three linkage groups suggesting translocations. The five downy mildew resistance genes (Dm1, Dm3, Dm4, Dm5/8 and Dm13), segregating in the Calmar x Kordaat cross, represented each of the four resistance gene linkage groups. Dm5/8 is flanked by two cDNA loci, each located 10 cM away. These flanking markers will be used to study the source of variation in downy mildew genes and are also part our strategy to clone resistance genes.     

Genetic linkage map in sour cherry using RFLP markers

 Restriction fragment length polymorphism (RFLP) linkage maps of two tetraploid sour cherry (Prunus cerasus L., 2n=4x=32) cultivars, Rheinische Schattenmorelle (RS) and Erdi Botermo (EB), were constructed from 86 progeny from the cross RS×EB. The RS linkage map consists of 126 single-dose restriction fragment (SDRF, Wu et al. 1992) markers assigned to 19 linkage groups covering 461.6 cM. The EB linkage map has 95 SDRF markers assigned to 16 linkage groups covering 279.2 cM. Fifty three markers mapped in both parents were used as bridges between both maps and 13 sets of homologous linkage groups were identified. Homoeologous relationships among the sour cherry linkage groups could not be determined because only 15 probes identified duplicate loci. Fifty nine of the markers on the linkage maps were detected with probes used in other Prunus genetic linkage maps. Four of the sour cherry linkage groups may be homologous with four of the eight genetic linkage groups identified in peach and almond. Twenty one fragments expected to segregate in a 1 : 1 ratio segregated in a 2 : 1 ratio. Three of these fragments were used in the final map construction because they all mapped to the same linkage group. Six fragments exhibited segregation consistent with the expectations of intergenomic pairing and/or recombination. Received: 1 April 1998 / Accepted: 9 June 1998     

Evaluation of inter-simple sequence repeat analysis for mapping in Citrus and extension of the genetic linkage map

Inter-simple sequence repeat (ISSR) analysis was evaluated for its usefulness in generating markers to extend the genetic linkage map of Citrus using a backcross population previously mapped with restriction fragment length polymorphism (RFLP), random amplified polymorphic DNA (RAPD) and isozyme markers. ISSR markers were obtained through the simple technique of PCR followed by analysis on agarose gels, using simple sequence repeat (SSR) primers. Optimization of reaction conditions was achieved for 50% of the SSR primers screened, and the primers amplified reproducible polymorphic bands in the parents and progeny of the backcross population. Mendelian segregation of the polymorphic bands was demonstrated, with an insignificant number of skewed loci. Most of the SSR primers produced dominant loci; however co-dominance was observed with loci derived from three primers. A new genetic map was produced by combining the segregation data for the ISSR markers and data for the RFLP, RAPD and isozyme markers from the previous map and creating genetic linkages among all the markers using JoinMap 2.0 mapping software. The new map has an improved distribution of markers along the linkage groups with fewer gaps, and marker order showed partial or complete conservation in the linkage groups. The incorporation of ISSR markers into the genetic linkage map demonstrates that ISSR markers are suitable for genetic mapping in Citrus. Received: 3 February 2000 / Accepted: 12 May 2000     

Centromere-linked microsatellite markers for linkage groups 3, 4, 6, 7, 13, and 20 of zebrafish (Danio rerio)

A large number of interesting mutations affecting development and organogenesis have been identified through genetic screens in zebrafish. Mapping of these mutations to a chromosomal region can be rapidly accomplished using half-tetrad analysis. However, knowledge of centromere-linked markers on every chromosome is essential to this mapping method. Centromeres on all 25 linkage groups have been mapped on the RAPD zebrafish genetic map. However, species specificity and the lack of codominance make RAPD markers less practical for mapping than microsatellite-based markers. On the microsatellite-based genetic map, centromere-linked markers have been identified for 19 linkage groups. No direct evidence has been published linking microsatellite markers to the centromeres of linkage groups 3, 4, 6, 7, 13, and 20. Therefore, we compared the microsatellite-based genetic map with the RAPD map to identify markers most likely linked to the centromeres of these 6 linkage groups. These candidate markers were tested for potential centromere linkage using four panels of half-tetrad embryos derived by early-pressure treatment of eggs from four different female zebrafish. We have identified microsatellite markers for linkage groups 3, 4, 6, 7, 13, and 20 to within 1.7 cM of their centromeres. These markers will greatly facilitate the rapid mapping of mutations in zebrafish by half-tetrad analysis.     

Microsatellite marker based genetic linkage maps of Oreochromis aureus and O. niloticus (Cichlidae): extensive linkage group segment homologies revealed

Partial genetic linkage maps, based on microsatellite markers, were constructed for two tilapia species, Oreochromis aureus and Oreochromis niloticus using an interspecific backcross population. The linkage map for O. aureus comprised 28 markers on 10 linkage groups and covered 212.8 CM. Nine markers were mapped to four linkage groups on an O. niloticus female linkage map covering 40.6 CM. Results revealed a high degree of conservation of synteny between the linkage groups defined in O. aureus and the previously published genetic linkage map of O. niloticus.     

Molecular-mapping analysis in Brassica napus using isozyme, RAPD and RFLP markers on a doubled-haploid progeny

We have undertaken the construction of a Brassica napus genetic map with isozyme (4%), RFLP (26.5%) and RAPD (68%) markers on a 152 lines of a doubled-haploid population. The map covers 1765 cM and comprises 254 markers including three PCR-specific markers and a morphological marker. They are assembled into 19 linkage groups, covering approximatively 71% of the rapeseed genome. Thirty five percent of the studied markers did not segregate according to the expected Mendelian ratio and tended to cluster in eight specific linkage groups. In this paper, the structure of the genetic map is described and the existence of non-Mendelian segregations in linkage analysis as well as the origins of the observed distortions, are discussed. The mapped RFLP loci corresponded to the cDNAs already used to construct B. napus maps. The first results of intraspecific comparative mapping are presented.     

An integrated and comparative genetic map of the turkey genome

An integrated genetic linkage map was developed for the turkey (Meleagris gallopavo) that combines the genetic markers from the three previous mapping efforts. The UMN integrated map includes 613 loci arranged into 41 linkage groups. An additional 105 markers are tentatively placed within linkage groups based on two-point LOD scores and 19 markers remain unlinked. A total of 210 previously unmapped markers has been added to the UMN turkey genetic map. Markers from each of the 20 linkage groups identified in the Roslin map and the 22 linkage groups of the Nte map are incorporated into the new integrated map. Overall map distance contained within the 41 linkage groups is 3,365 cM (sex-averaged) with the largest linkage group (94 loci) measuring 533.1 cM. Average marker interval for the map was 7.86 cM. Sequences of markers included in the new map were compared to the chicken genome sequence by 'BLASTN'. Significant similarity scores were obtained for 95.6% of the turkey sequences encompassing an estimated 91% of the chicken genome. A physical map of the chicken genome based on positions of the turkey sequences was built and 36 of the 41 turkey linkage groups were aligned with the physical map, five linkage groups remain unassigned. Given the close similarities between the turkey and chicken genomes, the chicken genome sequence could serve as a scaffold for a genome sequencing effort in the turkey.     

A SNP and SSR based genetic map of asparagus bean (Vigna. unguiculata ssp. sesquipedialis) and comparison with the broader species

Asparagus bean (Vigna. unguiculata ssp. sesquipedialis) is a distinctive subspecies of cowpea [Vigna. unguiculata (L.) Walp.] that apparently originated in East Asia and is characterized by extremely long and thin pods and an aggressive climbing growth habit. The crop is widely cultivated throughout Asia for the production of immature pods known as 'long beans' or 'asparagus beans'. While the genome of cowpea ssp. unguiculata has been characterized recently by high-density genetic mapping and partial sequencing, little is known about the genome of asparagus bean. We report here the first genetic map of asparagus bean based on SNP and SSR markers. The current map consists of 375 loci mapped onto 11 linkage groups (LGs), with 191 loci detected by SNP markers and 184 loci by SSR markers. The overall map length is 745 cM, with an average marker distance of 1.98 cM. There are four high marker-density blocks distributed on three LGs and three regions of segregation distortion (SDRs) identified on two other LGs, two of which co-locate in chromosomal regions syntenic to SDRs in soybean. Synteny between asparagus bean and the model legume Lotus. japonica was also established. This work provides the basis for mapping and functional analysis of genes/QTLs of particular interest in asparagus bean, as well as for comparative genomics study of cowpea at the subspecies level.     

An intersubspecific genetic map of<Emphasis Type="Italic"> Lens</Emphasis>

A Lens map was developed based on the segregational analysis of five kinds of molecular and morphological genetic markers in 113 F₂ plants obtained from a single hybrid of Lens culinaris ssp. culinaris × L. c. ssp. orientalis. A total of 200 markers were used on the F₂ population, including 71 RAPDs, 39 ISSRs, 83 AFLPs, two SSRs and five morphological loci. The AFLP technique generated more polymorphic markers than any of the others, although AFLP markers also showed the highest proportion (29.1%) of distorted segregation. At a LOD score of 3.0, 161 markers were grouped into ten linkage groups covering 2,172.4 cM, with an average distance between markers of 15.87 cM. There were six large groups with 12 or more markers each, and four small groups with two or three markers each. Thirty-nine markers were unlinked. A tendency for markers to cluster in the central regions of large linkage groups was observed. Likewise, clusters of AFLP, ISSR or RAPD markers were also observed in some linkage groups, although RAPD markers were more evenly spaced along the linkage groups. In addition, two SSR, three RAPD and one ISSR markers segregated as codominant. ISSR markers are valuable tools for Lens genetic mapping and they have a high potential in the generation of saturated Lens maps.Communicated by H.C. Becker     

The locus for the medium-chain acyl-CoA dehydrogenase gene on chromosome 1 is highly polymorphic

The gene for medium-chain acyl-CoA dehydrogenase (gene symbol ACADM; enzyme symbol MCAD) has been characterized for restriction fragment length polymorphisms (RFLPs) and mapped by linkage analysis to 4.2 cM from D1S2 and 11.7 cM from PGM1. The three RFLP systems described in detail show significant linkage disequilibrium but define four haplotypes with a PIC of 0.58. This makes ACADM informative for linkage mapping and for clinical genetic studies. By linkage studies, the orientation of these three loci relative to the centromere places ACADM most proximal. This is in direct conflict with the regional assignments of ACADM to 1p31 by in situ hybridization and of PGM1 to 1p22.1 by somatic cell studies. We suggest that this somatic cell localization of PGM1 may be incorrect.     

Characterization of a minimal screening set of 172 microsatellite markers for genome-wide screens of the canine genome

We have characterized a subset of 172 microsatellite markers from the canine map, termed 'Minimal Screening Set 1' (Canine MSS-1), which we propose be used for initial genome-wide genetic linkage studies. Three hierarchical criteria were used to select markers from the current meiotic linkage and radiation hybrid maps for MSS-1. Markers were selected that (1) provided as complete coverage as possible of the canine genome, (2) were highly informative, and (3) have been ordered in linkage groups with a high degree of statistical support. This resulting screening set spans all reported meiotic linkage and RH groups, leaving only 10 known gaps > or = 20 cM. The average polymorphic information content (PIC) value of markers tested is 0.74. Coverage estimates suggest 42% of the genome is within 5 cM of at least one marker in the minimal screening set, 77% of the genome is within 10 cM. This minimal mapping set therefore provides an efficient and cost effective way to begin screening pedigrees of interest for genetic linkage.     

A preliminary microsatellite genetic map of the ostrich (Struthio camelus)

Molecular genetic maps can provide information for the identification and localization of major genes associated with quantitative traits. However, there are currently no published genetic linkage maps for any ratites. Herein, a preliminary genetic map of ostrich was developed using a two-generation ostrich reference family by linkage analysis of 104 polymorphic microsatellite markers, including 40 novel markers reported in this study. A total of 35 microsatellite markers were placed into 13 linkage groups. Five linkage groups are composed of three or more loci, whereas the remaining eight groups each contained two markers. The sex-averaged map spans 365.4 cM. The marker interval of each linkage group ranges from 5.3 to 25.4 cM, and the average interval distance is 16.61 cM. The male map covers 342.7 cM, with an average intermarker distance of 15.58 cM, whereas the female map is 456.7 cM, with the average intermarker spacing of 20.76 cM. In order to screen the orthologous loci between ostrich and chicken, all of the flanking sequences of the 104 polymorphic loci, nine monomorphic loci and a further 12 reported microsatellite loci for ostrich were screened against the chicken genomic sequence using the BLAST algorithm (Altschul et al., 1990), and corresponding orthologs were found for 13 sequences. The microsatellite loci and genetic map developed in this study will be useful for QTL mapping, population genetics and phylogenetic studies in the ratite. In addition, the 13 orthologous loci identified in this study will be advantageous to the construction of a comparative genetic map between chicken and ostrich.