Genetic linkage map of Coffea canephora: effect of segregation distortion and analysis of recombination rate in male and female meioses.

Two complementary segregating plant populations of Coffea canephora were produced from the same clone. One population (DH) comprised 92 doubled haploids derived from female gametes, while the other population (TC) was a test cross consisting of 44 individuals derived from male gametes. Based on the DH population, a genetic linkage map comprising 160 loci was constructed. Eleven linkage groups that putatively correspond to the 11 gametic chromosomes of C. canephora were identified. The mapped loci included more than 40 specific sequence-tagged site markers, either single-copy RFLP probes or microsatellites, that could serve as standard landmarks in coffee-genome analyses. Furthermore, comparisons for segregation distortion and recombination frequency between the two populations were performed. Although segregation distortions were observed in both populations, the frequency of loci exhibiting a very pronounced degree of distortion was especially high in the DH population. This observation is consistent with the hypothesis of strong zygotic selection among the DH population. The recombination frequencies in both populations were found to be almost indistinguishable. These results offer evidence in favour of the lack of significant sex differences in recombination in C. canephora.     

A comparison of RFLP maps based on anther culture derived, selfed, and hybrid progenies of Solanum chacoense.

Comparative RFLP linkage maps were constructed using five segregating populations derived from two self-incompatible lines (termed PI 230582 and PI 458314) of diploid tuber-bearing Solanum chacoense Bitt. The analysis was based on 84 RFLP loci identified by 73 different cDNA clones. Distortion of expected Mendelian segregation ratios was observed; less than 10% of the markers showed a skewed segregation in the gametes forming the F1, hybrid population compared with 30% in the selfed population and 46 and 70% in the two populations produced by anther culture. For the anther culture derived populations, most of the skewed loci were scattered throughout the genome, whereas in the populations derived from selfing, they were found primarily in linkage group 1, around the S locus. In this study, we also found that the rate of meiotic recombination could differ between the male and female gametes produced by our parental lines. Thus, male gametes of line PI 458314 showed significantly less recombination as assessed by the total length of the map (206 cM for male gametes vs. 375 cM for female gametes) and the phenomenon was genome-wide. In contrast, the maps from the gametes of PI 230582 had about the same length, but some linkage groups were longer in the female gametes, while others were longer in the male gametes. Key words : Solanum chacoense, RFLP, anther culture, skewed segregation, self-incompatibility, sex differences in recombination.     

Indistinguishable patterns of recombination resulting from male and female meioses in Brassica napus (oilseed rape).

An F1 individual derived from a cross between two distinct lines of spring oilseed rape (Brassica napus) was used to produce a pair of complementary backcross populations, each consisting of 90 individuals. The F1 donated male gametes to the Male population and female gametes to the Female population. Genetic maps were generated from both populations and aligned using 117 common loci to form an integrated genome map of B. napus with 243 RFLP-defined loci. A comparison of the frequency and distribution of crossovers in the two populations of F1 gametes (assayed in the Male and Female populations) detected no differences. The genetic maps derived from the Male and Female populations each consisted of 19 linkage groups spanning 1544 and 1577 cM, respectively. The maps were aligned with other B. napus maps, and all 19 equivalent linkage groups were unambiguously assigned. The genetic size and general organisation of the new maps were comparable with those of pre-existing B. napus maps in most respects, except that the levels of polymorphism in the constituent A and C genomes were unusually similar in the new cross.     

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 genetic linkage map of Pacific white shrimp (<Emphasis Type="Italic">Litopenaeus vannamei</Emphasis>): sex-linked microsatellite markers and high recombination rates

Pacific white shrimp (Litopenaeus vannamei) is the leading species farmed in the Western Hemisphere and an economically important aquaculture species in China. In this project, a genetic linkage map was constructed using amplified fragment length polymorphism (AFLP) and microsatellite markers. One hundred and eight select AFLP primer combinations and 30 polymorphic microsatellite markers produced 2071 markers that were polymorphic in either of the parents and segregated in the progeny. Of these segregating markers, 319 were mapped to 45 linkage groups of the female framework map, covering a total of 4134.4 cM; and 267 markers were assigned to 45 linkage groups of the male map, covering a total of 3220.9 cM. High recombination rates were found in both parental maps. A sex-linked microsatellite marker was mapped on the female map with 6.6 cM to sex and a LOD of 17.8, two other microsatellite markers were also linked with both 8.6 cM to sex and LOD score of 14.3 and 16.4. The genetic maps presented here will serve as a basis for the construction of a high-resolution genetic map, quantitative trait loci (QTLs) detection, marker-assisted selection (MAS) and comparative genome mapping.     

RFLP mapping in Brassica nigra indicates differing recombination rates in male and female meioses.

A genetic linkage map of Brassica nigra, comprised of 288 loci in eight linkage groups, was constructed. The linkage groups varied in size from 72 to 159 cM and the total map length was 855 cM. The recurrent parent used in the backcross was extremely heterozygous. This allowed recombination to be estimated separately for female (recurrent parent) meiosis and male (F1) meiosis over a large proportion of the genome. Significant differences between male and female recombination frequencies were observed on all six linkage groups where data was available for both sexes. Enhanced male recombination frequencies were observed that were associated with proterminal regions, while enhanced female recombination frequencies were adjacent to putative centromeres. It is possible that the distinct genotypes of the F1 (male) and recurrent (female) parents contributed to the observed differences in recombination. However, this study emphasizes the need to consider potential sex differences, in both the rate and the position of recombination, when planning genetic experiments and breeding programmes.     

Genetic linkage mapping in Acacia mangium. 2. Development of an integrated map from two outbred pedigrees using RFLP and microsatellite loci

An integrated genetic linkage map, comprised of 219 RFLP and 33 microsatellite loci in 13 linkage groups, was constructed using two outbred pedigrees of Acacia mangium Willd. The linkage groups ranged in size from 23 to 103 cM and the total map length was 966 cM. Individual maps were made for each pedigree and the ordering of loci was consistent with the integrated map. The use of two independent pedigrees allowed a comparison of recombination rates between linked loci in male and female meioses as well as between parents. Differences were confined to specific regions and were not uniform across the male and female genomes or between genotypes. The heterogeneity in recombination frequencies did not result in major differences in the ordering of loci between pedigrees; hence, the integrated map provides a sound basis for QTL detection, leading to marker-assisted selection in A. mangium. It also provides a reference map for comparative genome analysis in acacias. The co-dominant markers used for mapping provide a useful resource in population studies and for quality control in acacia breeding programs. Detection of a relatively high proportion of selfs in pods derived from flowers which were not emasculated (30%), compared with emasculated flowers (0.01%), indicates that emasculation is desirable for efficient delivery of control-crossed seed in acacia breeding programs. Received: 25 March 2000 / Accepted: 30 April 2000     

A microsatellite‐based linkage map for song sparrows (Melospiza melodia)

Although linkage maps are important tools in evolutionary biology, their availability for wild populations is limited. The population of song sparrows (Melospiza melodia) on Mandarte Island, Canada, is among the more intensively studied wild animal populations. Its long‐term pedigree data, together with extensive genetic sampling, have allowed the study of a range of questions in evolutionary biology and ecology. However, the availability of genetic markers has been limited. We here describe 191 new microsatellite loci, including 160 high‐quality polymorphic autosomal, 7 Z‐linked and 1 W‐linked markers. We used these markers to construct a linkage map for song sparrows with a total sex‐averaged map length of 1731 cM and covering 35 linkage groups, and hence, these markers cover most of the 38–40 chromosomes. Female and male map lengths did not differ significantly. We then bioinformatically mapped these loci to the zebra finch (Taeniopygia guttata) genome and found that linkage groups were conserved between song sparrows and zebra finches. Compared to the zebra finch, marker order within small linkage groups was well conserved, whereas the larger linkage groups showed some intrachromosomal rearrangements. Finally, we show that as expected, recombination frequency between linked loci explained the majority of variation in gametic phase disequilibrium. Yet, there was substantial overlap in gametic phase disequilibrium between pairs of linked and unlinked loci. Given that the microsatellites described here lie on 35 of the 38–40 chromosomes, these markers will be useful for studies in this species, as well as for comparative genomics studies with other species.     

A Preliminary Genetic Linkage Map of the Pacific Abalone Haliotis discus hannai Ino

Preliminary genetic linkage maps were constructed for the Pacific abalone (Haliotis discus hannai Ino) using amplified fragment length polymorphism (AFLP), randomly amplified polymorphic DNA (RAPD), and microsatellite markers segregating in a F₁ family. Nine microsatellite loci, 41 RAPD, and 2688 AFLP markers were genotyped in the parents and 86 progeny of the mapping family. Among the 2738 markers, 384 (including 365 AFLP markers, 10 RAPD markers, and 9 microsatellite loci) were polymorphic and segregated in one or both parents: 241 in the female and 146 in the male. The majority of these markers, 232 in the female and 134 in the male, segregated according to the expected 1:1 Mendelian ratio (α = 0.05). Two genetic linkage maps were constructed using markers segregating in the female or the male parent. The female framework map consisted of 119 markers in 22 linkage groups, covering 1773.6 cM with an average intermarker space of 18.3 cM. The male framework map contained 94 markers in 19 linkage groups, spanning 1365.9 cM with an average intermarker space of 18.2 cM. The sex determination locus was mapped to the male map but not to the female map, suggesting a XY-male determination mechanism. Distorted markers showing excess of homozygotes were mapped in clusters, probably because of their linkage to a gene that is incompatible between two parental populations.     

High-density linkage mapping revealed suppression of recombination at the sex determination locus in papaya

A high-density genetic map of papaya (Carica papaya L.) was constructed using 54 F(2) plants derived from cultivars Kapoho and SunUp with 1501 markers, including 1498 amplified fragment length polymorphism (AFLP) markers, the papaya ringspot virus coat protein marker, morphological sex type, and fruit flesh color. These markers were mapped into 12 linkage groups at a LOD score of 5.0 and recombination frequency of 0.25. The 12 major linkage groups covered a total length of 3294.2 cM, with an average distance of 2.2 cM between adjacent markers. This map revealed severe suppression of recombination around the sex determination locus with a total of 225 markers cosegregating with sex types. The cytosine bases were highly methylated in this region on the basis of the distribution of methylation-sensitive and -insensitive markers. This high-density genetic map is essential for cloning of specific genes of interest such as the sex determination gene and for the integration of genetic and physical maps of papaya.     

Linkage maps of porcine Chromosomes 3, 6, and 9 based on 31 polymorphic markers

Linkage maps of porcine Chromosomes (Chrs) 3, 6, and 9, based on 31 polymorphic markers, are reported. The markers include 14 microsatellites, 12 RFLPs, three protein polymorphisms, and two blood group loci. The genetic interpretations of 11 RFLPs are documented. The markers were scored in a three-generation Wild Boar/Large White pedigree, and genetic maps were constructed on the basis of two-point and multi-point linkage analysis. Altogether the maps span a genetic distance of 216 cM, and previous physical assignments indicate that the linkage groups cover major parts of the three chromosomes. Significant differences in recombination rates between the sexes were observed for all three chromosomes. The recombination rate on the q arm of Chr 6 was markedly low. Sixteen loci are informative with regard to comparative mapping, that is, they have previously been mapped in the human and/or mouse genomes.     

An integrated genetic linkage map for eucalypts using RFLP,RAPD and isozyme markers

An integrated genetic linkage map for E. nitens was constructed in an outbred three-generation pedigree. Analysis of 210 RFLP, 125 RAPD and 4 isozyme loci resulted in 330 markers linked in 12 linkage groups covering 1462 cM (n=11 in eucalypts). The 12th linkage group is comprised of only 5 markers and will probably coalesce with another linkage group when further linked loci are located. Co-dominant RFLP loci segregating in both parents were used to integrate linkages identified in the male and female parents. Differences in recombination frequencies in the two parents were observed for a number of pairs of loci, and duplication of sequences was identified both within and between linkage groups. The markers were distributed randomly across the genome except for the RFLPs in linkage group 10 and for some loci showing segregation distortion, which were clustered into three regions of the map. The use of a large number of co-dominant RFLP loci in this map enables it to be used in other pedigrees of E. nitens and forms a basis for the detection and location of QTL in E. nitens and other eucalypt species.     

AFLP mapping and detection of quantitative trait loci (QTLs) for economically important traits in Pinus sylvestris: a preliminary study

We have applied a two-way pseudo-testcross strategy in an analysis of Pinus sylvestris for genetic mapping and detection of quantitative trait loci (QTLs) associated with economically important traits targeted in the Swedish tree-breeding programme. Based on 94 full-sib progeny of a cross between two plus-trees from northern Sweden we generated two parental maps using AFLP markers. The female map was comprised of 94 markers assigned to 15 linkage groups giving a size of 796 cM. On the male map 155 markers were assigned to 15 linkage groups, giving a total size of 1335 cM. The recombination frequency was found to be sex-dependent, being 29.3% higher in male than in female gametes. On the female map, 12 QTLs were detected (but none for branch diameter or wood density). Three QTLs for tree height accounted for 25.8% of the total phenotypic variation of this trait. When the QTLs detected for all the traits were taken independently, the percentages of phenotypic variance ranged from 9.3% to 22.7%. The highest value was observed for frost hardiness, an important trait in northern Sweden for which a major gene seemed to be involved. A cluster of QTLs for tree height, trunk diameter and volume was located on one linkage group. On the male map, four QTLs for trunk diameter and volume were detected. Due to the reduced number of individuals under study, the results are preliminary and have to be validated on more trees.     

Generation of a Restriction Fragment Length Polymorphism Linkage Map for Toxoplasma Gondii

We have constructed a genetic linkage map for the parasitic protozoan, Toxoplasma gondii, using randomly selected low copy number DNA markers that define restriction fragment length polymorphisms (RFLPs). The inheritance patterns of 64 RFLP markers and two phenotypic markers were analyzed among 19 recombinant haploid progeny selected from two parallel genetic crosses between PLK and CEP strains. In these first successful interstrain crosses, these RFLP markers segregated into 11 distinct genetic linkage groups that showed close correlation with physical linkage groups previously defined by molecular karyotype. Separate linkage maps, constructed for each of the 11 chromosomes, indicated recombination frequencies range from approximately 100 to 300 kb per centimorgan. Preliminary linkage assignments were made for the loci regulating sinefungin resistance (snf-1) on chromosome IX and adenine arabinoside (ara-1) on chromosome V by linkage to RFLP markers. Despite random segregation of separate chromosomes, the majority of chromosomes failed to demonstrate internal recombination events and in 3/19 recombinant progeny no intramolecular recombination events were detected. The relatively low rate of intrachromosomal recombination predicts that tight linkage for unknown genes can be established with a relatively small set of markers. This genetic linkage map should prove useful in mapping genes that regulate drug resistance and other biological phenotypes in this important opportunistic pathogen.     

Within‐population polymorphism of sex‐determination systems in the common frog (Rana temporaria)

In sharp contrast with birds and mammals, the sex chromosomes of ectothermic vertebrates are often undifferentiated, for reasons that remain debated. A linkage map was recently published for Rana temporaria (Linnaeus, 1758) from Fennoscandia (Eastern European lineage), with a proposed sex‐determining role for linkage group 2 (LG2). We analysed linkage patterns in lowland and highland populations from Switzerland (Western European lineage), with special focus on LG2. Sibship analyses showed large differences from the Fennoscandian map in terms of recombination rates and loci order, pointing to large‐scale inversions or translocations. All linkage groups displayed extreme heterochiasmy (total map length was 12.2 cM in males, versus 869.8 cM in females). Sex determination was polymorphic within populations: a majority of families (with equal sex ratios) showed a strong correlation between offspring phenotypic sex and LG2 paternal haplotypes, whereas other families (some of which with female‐biased sex ratios) did not show any correlation. The factors determining sex in the latter could not be identified. This coexistence of several sex‐determination systems should induce frequent recombination of X and Y haplotypes, even in the absence of male recombination. Accordingly, we found no sex differences in allelic frequencies on LG2 markers among wild‐caught male and female adults, except in one high‐altitude population, where nonrecombinant Y haplotypes suggest sex to be entirely determined by LG2. Multifactorial sex determination certainly contributes to the lack of sex‐chromosome differentiation in amphibians.     

The Evolution of the Y Chromosome with X-Y Recombination

A theoretical population genetic model is developed to explore the consequences of X-Y recombination in the evolution of sex chromosome polymorphism. The model incorporates one sex-determining locus and one locus subject to natural selection. Both loci have two alleles, and the rate of classical meiotic recombination between the loci is r. The alleles at the sex-determining locus specify whether the chromosome is X or Y, and the alleles at the selected locus are arbitrarily labeled A and a. Natural selection is modeled as a process of differential viabilities. The system can be expressed in terms of three recurrence equations, one for the frequency of A on the X-bearing gametes produced by females, one for each of the frequency of A on the X- and Y-bearing gametes produced by males. Several special cases are examined, including X chromosome dominance and symmetric selection. Unusual equilibria are found with the two sexes having very different allele frequencies at the selected locus. A significant finding is that the allowance of recombination results in a much greater opportunity for polymorphism of the Y chromosome. Tighter linkage results in a greater likelihood for equilibria with a large difference between the sex chromosomes in allele frequency.     

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.     

A saturated genetic linkage map of rubber tree (Hevea spp.) based on RFLP, AFLP, microsatellite, and isozyme markers

The first genetic map for Hevea spp. (2n=36) is presented here. It is based on a F₁ progeny of 106 individuals allowing the construction of a female, a male, and a synthetic map according to the pseudo-testcross strategy. Progeny were derived from an interspecific cross between PB260, a H. brasiliensis cultivated clone, and RO38, a H. brasiliensis×H. benthamiana interspecific hybrid clone. The disomic inheritance observed for all the codominant markers scattered on the 2n=36 chromosomes revealed that Hevea behaves as diploids. Homologous linkage groups between the two parental maps were merged using bridge loci. A total of 717 loci constituted the synthetic map, including 301 RFLPs, 388 AFLPs, 18 microsatellites, and 10 isozymes. The markers were assembled into 18 linkage groups, thus reflecting the basic chromosome number, and covered a total distance of 2144 cM. Nine markers were found to be unlinked. Segregation distortion was rare (1.4%). Average marker density was 1 per 3 cM. Comparison of the distance between loci in the parental maps revealed significantly less meiotic recombination in the interspecific hybrid male parent than in the female parent. Hevea origin and genome organisation are discussed. Received: 2 February 1999 / Accepted: 11 March 1999     

A linkage map of Atlantic salmon (Salmo salar) reveals an uncommonly large difference in recombination rate between the sexes

A genetic linkage map of the Atlantic salmon (Salmo salar) was constructed, using 54 microsatellites and 473 amplified fragment length polymorphism (AFLP) markers. The mapping population consisted of two full-sib families within one paternal half-sib family from the Norwegian breeding population. A mapping strategy was developed that facilitated the construction of separate male and female maps, while retaining all the information contributed by the dominant AFLP markers. By using this strategy, we were able to map a significant number of the AFLP markers for which all informative offspring had two heterozygous parents; these markers then served as bridges between the male and female maps. The female map spanned 901 cM and had 33 linkage groups, while the male spanned 103 cM and had 31 linkage groups. Twenty-five linkage groups were common between the two maps. The construction of the genetic map revealed a large difference in recombination rate between females and males. The ratio of female recombination rate vs. male recombination rate was 8.26, the highest ratio reported for any vertebrate. This map constitutes the first linkage map of Atlantic salmon, one of the most important aquaculture species worldwide.     

A genetic linkage map of red drum,Sciaenops ocellatus

Second‐generation, sex‐specific genetic linkage maps were generated for the economically important estuarine‐dependent marine fish Sciaenops ocellatus (red drum). The maps were based on F₁ progeny from each of two single‐pair mating families. A total of 237 nuclear‐encoded microsatellite markers were mapped to 25 linkage groups. The female map contained 226 markers, with a total length of 1270.9 centiMorgans (cM) and an average inter‐marker interval of 6.53 cM; the male map contained 201 markers, with a total length of 1122.9 cM and an average inter‐marker interval of 6.03 cM. The overall recombination rate was approximately equal in the two sexes (♀:♂ = 1.03:1). Recombination rates in a number of linkage intervals, however, differed significantly between the same sex in both families and between sexes within families. The former occurred in 2.4% of mapped intervals, while the latter occurred in 51.2% of mapped intervals. Sex‐specific recombination rates varied within chromosomes, with regions of both female‐biased and male‐biased recombination. Original clones from which the microsatellite markers were generated were compared with genome sequence data for the spotted green puffer, Tetraodon nigroviridis; a total of 43 matches were located in 17 of 21 chromosomes of T. nigroviridis, while seven matches were in unknown portions of the T. nigroviridis genome. The map for red drum provides a new, useful tool for aquaculture, population genetics, and comparative genomics of this economically important marine species.