An algorithm for analyzing linkages affected by heterozygous translocations: QuadMap

Heterozygous chromosome rearrangements such as reciprocal translocations are most accurately displayed as two-dimensional linkage maps. Standard linkage mapping software packages, such as MapMaker, generate only one-dimensional maps and so reciprocal translocations appear as clusters of markers, even though they originate from two nonhomologous chromosomes. To more accurately map these regions, researchers have developed statistical methods that use the variance in map distance to distinguish among the four segments (two translocation, two interstitial) of the translocation. In this study, we describe modifications to one of these protocols, that proposed by Livingstone et al. (2000). We also introduce QuadMap, a new software application for dissecting heterozygous translocation-affected linkage maps.     

An SSR genetic map of Sorghum bicolor (L.) Moench and its comparison to a published genetic map.

Sorghum bicolor (L.) Moench is an important grain and forage crop grown worldwide. We developed a simple sequence repeat (SSR) linkage map for sorghum using 352 publicly available SSR primer pairs and a population of 277 F2 individuals derived from a cross between the Westland A line and PI 550610. A total of 132 SSR loci appeared polymorphic in the mapping population, and 118 SSRs were mapped to 16 linkage groups. These mapped SSR loci were distributed throughout 10 chromosomes of sorghum, and spanned a distance of 997.5 cM. More important, 38 new SSR loci were added to the sorghum genetic map in this study. The mapping result also showed that chromosomes SBI-01, SBI-02, SBI-05, and SBI-06 each had 1 linkage group; the other 6 chromosomes were composed of 2 linkage groups each. Except for 5 closely linked marker flips and 1 locus (Sb6_34), the marker order of this map was collinear to a published sorghum map, and the genetic distances of common marker intervals were similar, with a difference ratio 相似文献   

A genetic map of chromosome 1: comparison of different data sets and linkage programs

We have used 22 chromosome 1 loci to construct a genetic linkage map of this autosome using the Venezuelan Reference Pedigree. These markers formed two linkage groups separated by an interval of more than 30 cM. Linkage maps were constructed separately using the computer programs LINKAGE and MAPMAKER to determine their relative speed, efficiency, and accuracy. We found that both programs generated maps with the same order and distances, although the LINKAGE program derived more information from the data, allowing placement of one additional marker. Many of the probes have previously been mapped using the CEPH pedigrees. However, the current map is generated from a different data set and so can be used to increase the certainty of locus order and map position. Ultimately, the generation and confirmation of a 1-cM map of this chromosome will require such multiple data sets.     

Influence of epistatic segregation distortion loci on genetic marker linkages in Japanese flounder

For genetic linkage analysis of Japanese flounder, 160 doubled haploids (DH) were artificially produced using mitotic gynogenesis and were genotyped for 458 simple sequence repeat (SSR) markers, 101 of which show distortional segregation. The genetic linkage map was constructed by modifying recombination fractions between the distorted markers. Between the corrected and uncorrected genetic maps, there were considerable differences in genetic distance, but not in relative locations among markers. Using a liability model, a segregation distortion locus (SDL), with an additive genetic effect of 1.772, was mapped between markers BDHYP387 and Poli56TUF of chromosome 24 in the corrected genetic map. Additionally, six pairs of epistatic SDLs were identified on chromosomes 1, 5, 8, 9, 23, and 24. Changes in genetic distances between markers did not occur on chromosome regions with main effect SDLs. However, most chromosome regions where genetic distances changed covered the detected epistatic SDLs. This study concluded that epistatic SDLs decrease linkages between markers and lengthen genetic distances in Japanese flounder. This finding has been partially validated in other DH populations derived from three female Japanese flounders.     

Simple sequence repeat map of the sunflower genome

Several independent molecular genetic linkage maps of varying density and completeness have been constructed for cultivated sunflower ( Helianthus annuus L.). Because of the dearth of sequence and probe-specific DNA markers in the public domain, the various genetic maps of sunflower have not been integrated and a single reference map has not emerged. Moreover, comparisons between maps have been confounded by multiple linkage group nomenclatures and the lack of common DNA markers. The goal of the present research was to construct a dense molecular genetic linkage map for sunflower using simple sequence repeat (SSR) markers. First, 879 SSR markers were developed by identifying 1,093 unique SSR sequences in the DNA sequences of 2,033 clones isolated from genomic DNA libraries enriched for (AC)(n) or (AG)(n) and screening 1,000 SSR primer pairs; 579 of the newly developed SSR markers (65.9% of the total) were polymorphic among four elite inbred lines (RHA280, RHA801, PHA and PHB). The genetic map was constructed using 94 RHA280 x RHA801 F(7) recombinant inbred lines (RILs) and 408 polymorphic SSR markers (462 SSR marker loci segregated in the mapping population). Of the latter, 459 coalesced into 17 linkage groups presumably corresponding to the 17 chromosomes in the haploid sunflower genome ( x = 17). The map was 1,368.3-cM long and had a mean density of 3.1 cM per locus. The SSR markers described herein supply a critical mass of DNA markers for constructing genetic maps of sunflower and create the basis for unifying and cross-referencing the multitude of genetic maps developed for wild and cultivated sunflowers.     

Twelve loci form a continuous linkage map for human chromosome 18

We have constructed a primary genetic map of human chromosome 18 consisting of 11 DNA markers and one serological marker (JK). Two of these loci define highly polymorphic VNTR systems. The markers define a continuous genetic linkage map of 97 cM in males and 205 cM in females; female genetic distances in a panel of 59 three-generation families were consistently about twice those observed in males. The high odds in support of the linear order of the markers on this recombination map, and the extent of coverage of chromosome 18, indicate that this map will permit efficient linkage studies of human genetic diseases that may be segregating on chromosome 18 and will provide anchor points for development of high-resolution maps for this chromosome.     

Reciprocal Translocations and Translocation Disomics of Aspergillus and Their Use for Genetic Mapping

Two new techniques are described for genetic mapping of reciprocal translocations in A. nidulans, which can be used to locate centromeres and meiotically unlinked markers. They both make use of unbalanced disomics from heterozygous translocation crosses. These are mainly hyperhaploids of two classes: either typical-looking n + 1 with a normal chromosome in addition to a haploid set containing the translocation, or translocation disomics. When large chromosome segments are involved, such disomics, as well as stable aneuploids and duplication types, show characteristic phenotypes and can be classified visually. The first method maps translocation breaks qualitatively, since translocated markers can be identified when translocation disomics are analyzed for heterozygous markers. The second method measures meiotic linkage of any marker to the translocation breaks when allele ratios in the balanced haploid sectors of either or both classes of disomics are determined: linked markers show reciprocal deviations from 1:1—In addition, it can be shown that frequencies of nondisjunction and recovery of specific translocation disomics both depend on the relative position of the break within a chromosome arm. Such information can provide a rough estimate of the positions of breaks for a new translocation.—Using these techniques, as well as mitotic mapping in homo- and heterozygous translocation diploids, four reciprocal translocations were mapped. From these results, information on the sequence and orientation of most of the "meiotic fragments" of the current maps (groups III, VI, VII and VIII) was obtained, and the position of the centromeres of groups VI and VII were identified. Translocation disomics are also used to map meiotically unlinked single genes, e.g. oliA of group VII, to specify chromosome segments.     

Construction of an AFLP genetic map with nearly complete genome coverage in Pinus taeda

  De novo construction of complete genetic linkage maps requires large mapping populations, large numbers of genetic markers, and efficient algorithms for ordering markers and evaluating order confidence. We constructed a complete genetic map of an individual loblolly pine (Pinus taeda L.) using amplified fragment length polymorphism (AFLP) markers segregating in haploid megagametophytes and PGRI mapping software. We generated 521 polymorphic fragments from 21 AFLP primer pairs. A total of 508 fragments mapped to 12 linkage groups, which is equal to the Pinus haploid chromosome number. Bootstrap locus order matrices and recombination matrices generated by PGRI were used to select 184 framework markers that could be ordered confidently. Order support was also evaluated using log likelihood criteria in MAPMAKER. Optimal marker orders from PGRI and MAPMAKER were identical, but the implied reliability of orders differed greatly. The framework map provides nearly complete coverage of the genome, estimated at approximately 1700 cM in length using a modified estimator. This map should provide a useful framework for merging existing loblolly pine maps and adding multiallelic markers as they become available. Map coverage with dominant markers in both linkage phases will make the map useful for subsequent quantitative trait locus mapping in families derived by self-pollination. Received: 7 August 1998 / Accepted: 27 October 1998     

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.     

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.     

Genetic Map of Diploid Wheat, Triticum Monococcum L., and Its Comparison with Maps of Hordeum Vulgare L

A genetic map of diploid wheat, Triticum monococcum L., involving 335 markers, including RFLP DNA markers, isozymes, seed storage proteins, rRNA, and morphological loci, is reported. T. monococcum and barley linkage groups are remarkably conserved. They differ by a reciprocal translocation involving the long arms of chromosomes 4 and 5, and paracentric inversions in the long arm of chromosomes 1 and 4; the latter is in a segment of chromosome arm 4L translocated to 5L in T. monococcum. The order of the markers in the inverted segments in the T. monococcum genome is the same as in the B and D genomes of T. aestivum L. The T. monococcum map differs from the barley maps in the distribution of recombination within chromosomes. The major 5S rRNA loci were mapped on the short arms of T. monococcum chromosomes 1 and 5 and the long arms of barley chromosomes 2 and 3. Since these chromosome arms are colinear, the major 5S rRNA loci must be subjected to positional changes in the evolving Triticeae genome that do not perturb chromosome colinearity. The positional changes of the major 5S rRNA loci in Triticeae genomes are analogous to those of the 18S-5.8S-26S rRNA loci.     

Comparison off genetic distance and order off DNA markers in five populations of rice.

A group of about 300 evenly distributed DNA markers from a high density RFLP linkage map of rice constructed using an F2 population derived from a japonica variety, Nipponbare, and an indica variety, Kasalath, were used to evaluate gene order and genetic distance in four other rice mapping populations. The purpose of this study was to determine the degree to which information gained from the high density linkage map could be applied to other mapping populations, particularly with regard to its utility in bridging quantitative traits and molecular and physical mapping information. The mapping populations consisted of two F2 populations derived from Dao Ren Qiao/Fl-1084 and Kinandangputi/Fl-1007, recombinant inbred lines from Asominori/IR24, and a backcross population from Sasanishiki/Habataki//Sasanishiki. All DNA markers commonly mapped in the four populations showed the same linkage groups as in the Nipponbare/Kasalath linkage map with conserved linkage order. The genetic distance between markers among the different populations did not vary to a significant level in any of the 12 chromosomes. The differences in some markers could be attributed to the size of the population used in the construction of the linkage maps. Furthermore, the conservation of linkage order found in the distal region of chromosomes 11 and 12 was also confirmed in the RFLP maps based on the four populations of rice. These suggest that any major genetic information from the Nipponbare/Kasalath map can be expected to be approximately the same in other crosses or populations. This high density RFLP linkage map, which is being utilized in constructing a physical map of rice, can be very useful in interpreting genome structure with great accuracy in other populations. Key words : linkage map, japonica, indica, gene order, genetic distance.     

Physical location of homoeologous groups 5 and 6 molecular markers mapped in Triticum aestivum L

In situ hybridization was used to map 21 restriction fragment length polymorphism (RFLP) probes to linkage groups 5 and 6 of hexaploid wheat (Triticum aestivum L. em Thell.) in order to compare physical distances and genetic distances between adjacent markers. All 21 probes hybridized to the corresponding homoeologous chromosome arms. The linear order and linkage relationships among the DNA probes on the in situ-based physical maps were generally the same as those on the RFLP-based genetic maps. However, significant differences were observed between the centiMorgan distances on a linkage map and the physical distances of the probes using in situ-based techniques. The results indicated a clustering of polymorphic RFLP markers in the middle of all of the homoeologous group 5 and 6 chromosome arms. This suggests that the available linkage maps do not completely cover the physical length of the chromosomes. As with the genetic maps, the physical map clearly showed the presence of nonhomoeologous rearrangements in the terminal regions of chromosome arms 5AL and 6BS. However, the physical mapping gave an indication of the physical size of the rearrangements as well as their arm location.     

A reciprocal translocation between ’Garfi’ almond and ’Nemared’ peach

A map with 51 markers (46 RFLPs and five isozymes) was constructed using an interspecific F₂ population between ’Garfi’ almond (Prunus amygdalus Batsch.) and ’Nemared’ peach [Prunus persica (L.) Batsch.]. This map was developed by selecting markers covering most of the distance of the eight linkage groups from previously constructed Prunus maps. The markers studied in this population mapped to seven linkage groups instead of the eight expected in Prunus. Markers belonging to groups 6 and 8 in previous maps formed a single group in the ’Garfi’×’Nemared’ F₂ and several marker pairs placed in different groups in other maps exhibited tight linkages. The study of pollen fertility and chromosome behavior during meiosis in the F₁ generation allowed us to confirm the hypothesis that a reciprocal translocation exists between ’Garfi’ and ’Nemared’. Based on independent evidence of linkage between markers and pollen fertility data in the F₂ population, we concluded that the breakpoint of the reciprocal translocation was placed between markers AC50 and AG26A in group 6 and between markers AG112A and FG230A in group 8. Received: 28 June 2000 / Accepted: 17 October 2000     

High-density genetic linkage maps of Phytophthora infestans reveal trisomic progeny and chromosomal rearrangements

Detailed analysis of the inheritance of molecular markers was performed in the oomycete plant pathogen Phytophthora infestans. Linkage analysis in the sexual progeny of two Dutch field isolates (cross 71) resulted in a high-density map containing 508 markers on 13 major and 10 minor linkage groups. The map showed strong clustering of markers, particularly of markers originating from one parent, and dissimilarity between the parental isolates on linkage group III in the vicinity of the mating-type locus, indicating a chromosomal translocation. A second genetic map, constructed by linkage analysis in sexual progeny of two Mexican isolates (cross 68), contained 363 markers and is thus less dense than the cross 71 map. For some linkage groups the two independent linkage maps could be aligned, but sometimes markers appeared to be in a different order, or not linked at all, indicating chromosomal rearrangements between genotypes. Graphical genotyping showed that some progeny contained three copies of a homologous linkage group. This trisomy was found for several linkage groups in both crosses. Together, these analyses suggest a genome with a high degree of flexibility, which may have implications for evolution of new races and resistance development to crop protection agents.     

CONSTRUCTION OF A GENETIC LINKAGE MAP FOR PORPHYRA HAITANENSIS (BANGIALES,RHODOPHYTA) BASED ON SEQUENCE‐RELATED AMPLIFIED POLYMORPHISM AND SIMPLE SEQUENCE REPEAT MARKERS1

Molecular markers and molecular genetic maps are prerequisites for molecular breeding in any plant species. A comprehensive genetic linkage map for cultivated Porphyra haitanensis T. J. Chang et B. F. Zheng has not yet been developed. In this study, 157 double haploid (DH) lines [derived from a YSIII (wildtype) × RTPM (red‐type artificial pigmentation mutant) cross] were used as a mapping population in P. haitanensis. A total of 60 pairs of sequence‐related amplified polymorphism (SRAP) primers and 39 pairs of simple sequence repeat (SSR) primers were used to detect polymorphisms between the two parents. Fifteen SRAP and 16 SSR polymorphic primer pairs were selected to analyze the DH population. A linkage genetic map comprising 67 SRAP markers and 20 SSR markers in five linkage groups, with a total length of 830.6 cM and an average of 10.13 cM between markers, was constructed. The markers were distributed evenly in all linkage groups without clustering. The linkage groups comprised 12–23 markers ranging in length from 134.2 to 197.3 cM. The estimated genome length of P. haitanensis was 942.4 cM, with 88.1% coverage. This is the first report of a comprehensive genetic map in P. haitanensis. The map presented here will provide a basis for the development of high‐density genetic linkage maps and lay the foundation for molecular breeding work in P. haitanensis.     

Linkage map construction involving a reciprocal translocation

This paper is concerned with a novel statistical–genetic approach for the construction of linkage maps in populations obtained from reciprocal translocation heterozygotes of barley (Hordeum vulgare L.). Using standard linkage analysis, translocations usually lead to ‘pseudo-linkage’: the mixing up of markers from the chromosomes involved in the translocation into a single linkage group. Close to the translocation breakpoints recombination is severely suppressed and, as a consequence, ordering markers in those regions is not feasible. The novel strategy presented in this paper is based on (1) disentangling the “pseudo-linkage” using principal coordinate analysis, (2) separating individuals into translocated types and normal types and (3) separating markers into those close to and those more distant from the translocation breakpoints. The methods make use of a consensus map of the species involved. The final product consists of integrated linkage maps of the distal parts of the chromosomes involved in the translocation.     

A COSII genetic map of the pepper genome provides a detailed picture of synteny with tomato and new insights into recent chromosome evolution in the genus Capsicum

We report herein the development of a pepper genetic linkage map which comprises 299 orthologous markers between the pepper and tomato genomes (including 263 conserved ortholog set II or COSII markers). The expected position of additional 288 COSII markers was inferred in the pepper map via pepper–tomato synteny, bringing the total orthologous markers in the pepper genome to 587. While pepper maps have been previously reported, this is the first complete map in the sense that all markers could be placed in 12 linkage groups corresponding to the 12 chromosomes. The map presented herein is relevant to the genomes of cultivated C. annuum and wild C. annuum (as well as related Capsicum species) which differ by a reciprocal chromosome translocation. This map is also unique in that it is largely based on COSII markers, which permits the inference of a detailed syntenic relationship between the pepper and tomato genomes—shedding new light on chromosome evolution in the Solanaceae. Since divergence from their last common ancestor is approximately 20 million years ago, the two genomes have become differentiated by a minimum number of 19 inversions and 6 chromosome translocations, as well as numerous putative single gene transpositions. Nevertheless, the two genomes share 35 conserved syntenic segments (CSSs) within which gene/marker order is well preserved. The high resolution COSII synteny map described herein provides a platform for cross-reference of genetic and genomic information (including the tomato genome sequence) between pepper and tomato and therefore will facilitate both applied and basic research in pepper. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Construction of a genetic linkage map of the model legume Lotus japonicus using an intraspecific F2 population.

Among leguminous plants, the model legume Lotus japonicus (Regel) Larsen has many biological and genetic advantages. We have developed a genetic linkage map of L. japonicus based on amplified fragment length polymorphism (AFLP), simple sequence repeat polymorphism (SSRP) and derived cleaved amplified polymorphic sequence (dCAPS). The F2 mapping population used was derived from a cross between two L. japonicus accessions Gifu B-129 and Miyakojima MG-20. These parental accessions showed remarkable cytological differences, particularly with respect to size and morphology of chromosomes 1 and 2. Using fluorescence in situ hybridization (FISH) with BAC clones from Gifu B-129 and TAC (Transformation-competent Artificial Chromosome) clones from Miyakojima MG-20, a reciprocal translocation was found to be responsible for the cytological differences between chromosomes 1 and 2. The borders of the translocations were identified by FISH and by alignment toward the L. filicaulis x L. japonicus Gifu B-129 linkage map. The markers from the main translocated region were located on linkage groups 1 and 2 of the two accessions, Gifu B-129 and Miyakojima MG-20, respectively. The framework of the linkage map was constructed based on codominant markers, and then dominant markers were integrated separately in each linkage group of the parents. The resulting linkage groups correspond to the six pairs of chromosomes of L. japonicus and consist of 287 markers with 487.3 cM length in Gifu B-129 and 277 markers with 481.6 cM length in Miyakojima MG-20. The map and marker information is available through the World Wide Web at http://www.kazusa.or.jp/lotus/.