A high-density genetic linkage map of a black spruce (Picea mariana) × red spruce (Picea rubens) interspecific hybrid

Genetic maps provide an important genomic resource of basic and applied significance. Spruce (Picea) has a very large genome size (between 0.85 × 1010 and 2.4 × 1010 bp; 8.5-24.0 pg/1C, a mean of 17.7 pg/1C ). We have constructed a near-saturated genetic linkage map for an interspecific backcross (BC1) hybrid of black spruce (BS; Picea mariana (Mill.) B.S.P.) and red spruce (RS; Picea rubens Sarg.), using selectively amplified microsatellite polymorphic loci (SAMPL) markers. A total of 2284 SAMPL markers were resolved using 31 SAMPL-MseI selective nucleotide primer combinations. Of these, 1216 SAMPL markers showing Mendelian segregation were mapped, whereas 1068 (46.8%) SAMPL fragments showed segregation distortion at α = 0.05. Maternal, paternal, and consensus maps consistently coalesced into 12 linkage groups, corresponding to the haploid chromosome number (1n = 1x = 12) of 12 in the genus Picea. The maternal BS map consisted of 814 markers distributed over 12 linkage groups, covering 1670 cM, with a mean map distance of 2.1 cM between adjacent markers. The paternal BS × RS map consisted of 773 markers distributed over 12 linkage groups, covering 1563 cM, with a mean map distance of 2.0 cM between adjacent markers. The consensus interspecific hybrid BC1 map consisted of 1216 markers distributed over 12 linkage groups, covering 1865 cM (98% genome coverage), with a mean map distance of 1.5 cM between adjacent markers. The genetic map reported here provides an important genomic resource in Picea, Pinaceae, and conifers.     

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 combined AFLP and microsatellite linkage map and pilot comparative genomic analysis of European sea bass Dicentrarchus labrax L

European sea bass (Dicentrarchus labrax L., Moronidae, Teleostei) sustains a regional fishery and is commonly farmed in the Mediterranean basin, but has not undergone much long-term genetic improvement. An updated genetic linkage map of the European sea bass was constructed using 190 microsatellites, 176 amplified fragment length polymorphisms and two single nucleotide polymorphisms. From the 45 new microsatellite markers (including 31 type I markers) reported in this study, 28 were mapped. A total of 368 markers were assembled into 35 linkage groups. Among these markers, 28 represented type I (coding) markers, including those located within the peptide Y, SOX10, PXN1, ERA and TCRB genes (linkage groups 1, 7, 16, 17 and 27 respectively). The sex-averaged map spanned 1373.1 centimorgans (cM) of the genome. The female map measured 1380.0 cM, whereas the male map measured 1046.9 cM, leading to a female-to-male (F:M) recombination rate ratio of 1.32:1. The intermarker spacing of the second-generation linkage map of the European sea bass was 3.67 cM, which is smaller than that of the first-generation linkage map (5.03 cM). Comparative mapping of microsatellite flanking regions was performed with five model teleosts and this revealed a high percentage (33.6%) of evolutionarily conserved regions with the three-spined stickleback.     

Construction of a genetic linkage map of black gram, Vigna mungo (L.) Hepper, based on molecular markers and comparative studies

A genetic linkage map of black gram, Vigna mungo (L.) Hepper, was constructed with 428 molecular markers using an F9 recombinant inbred population of 104 individuals. The population was derived from an inter-subspecific cross between a black gram cultivar, TU94-2, and a wild genotype, V. mungo var. silvestris. The linkage analysis at a LOD score of 5.0 distributed all 428 markers (254 AFLP, 47 SSR, 86 RAPD, and 41 ISSR) into 11 linkage groups. The map spanned a total distance of 865.1 cM with an average marker density of 2 cM. The largest linkage group spanned 115 cM and the smallest linkage group was of 44.9 cM. The number of markers per linkage group ranged from 11 to 86 and the average distance between markers varied from 1.1 to 5.6 cM. Comparison of the map with other published azuki bean and black gram maps showed high colinearity of markers, with some inversions. The current map is the most saturated map for black gram to date and will provide a useful tool for identification of QTLs and for marker-assisted selection of agronomically important characters in black gram.     

Linkage mapping of AFLP markers in a wild population of great reed warblers: importance of heterozygosity and number of genotyped individuals

Amplified fragment length polymorphisms (AFLP) are dominant markers frequently used to build linkage maps where heterozygosity could be inferred by a backcross breeding strategy. In the present study, we describe the utilization of an unmanipulated great reed warbler, Acrocephalus arundinaceus pedigree to infer heterozygous genotypes of AFLP markers in order to map these markers to a partial linkage map previously based on microsatellites. In total, 50 of the 83 autosomal AFLPs (60%) and 4 of 5 Z-linked AFLPs (80%) were mapped. For each marker, on average, 88% of the expected number of heterozygote parents was detected. The likelihood of map assignment was to a large extent due to the number and density of microsatellite markers already in the map. The 'parsimonious linkage map', that is the map based on the most parsimonious location of all significantly linked markers, consisted of 21 autosomal linkage groups with 2 to 15 markers and had a total map size of 552 cM in males and 858 cM in females. The Z-chromosome linkage group with 12 markers had a size of 155 cM. The autosomal 'framework linkage map', that is the map based only on markers with an unambiguous position, had a total size of 237 cM in males and 440 cM in females, respectively. The inclusion of AFLPs enlarged the previous map substantially (e.g. the autosomal parsimonious linkage map became 441 cM and 621 cM larger for male and female recombination, respectively). The probability that an AFLP became mapped increased with increasing level of heterozygosity, whereas the probability of mapping into a framework position increased with both heterozygosity and number of genotyped individuals. Our results suggest that AFLP provides a fast and inexpensive means of enlarging genetic maps already composed of markers with high polymorphism, also in wild populations with unmanipulated pedigrees.     

Genetic linkage map of the house musk shrew, Suncus murinus, constructed with PCR-based and RFLP markers.

A genetic linkage map for Suncus murinus was previously constructed with 11 marker loci. In this study, we developed 172 new microsatellite and three RFLP markers, and re-constructed a new framework map by combining all markers. The new map comprises 42 markers that are distributed into 12 linkage groups, two of which are assigned to chromosomes, and spans 403.5 cM with an average inter-marker distance of 13.5 cM.     

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.     

A first genetic linkage map of mulberry (Morus spp.) using RAPD, ISSR, and SSR markers and pseudotestcross mapping strategy

To lay the foundation for molecular breeding efforts, the first genetic linkage map of mulberry (2n=2x=28) was constructed with 50 F1 full-sib progeny using randomly amplified polymorphic DNA (RAPD), inter-simple sequence repeat (ISSR), and simple sequence repeat (SSR) markers and two-way pseudotestcross mapping strategy. We selected 100 RAPD, 42 ISSR, and 9 SSR primers that amplified 517 markers, of which 188 (36.36%) showed a test-cross configuration, corresponding to the heterozygous condition in one parent and null in the other. Two separate female and male maps were constructed using 94 each of female- and male-specific testcross markers, containing 12 female linkage groups and 14 male linkage groups. At a minimum logarithm of the odds (LOD) score threshold of 6.0 and at a maximum map distance of 20 cM, the female map covered a 1,196.6-cM distance, with an average distance of 15.75 cM and maximum map distance of 37.9 cM between two loci; the male-specific map covered a 1,351.7-cM distance, with an average distance of 18.78 cM and a maximum map distance between two loci is of 34.7 cM. The markers distributed randomly in all linkage groups without any clustering. All 12 linkage groups in the female-specific map consisted of 4–10 loci ranging in length from 0 to 140.4 cM, and in the male-specific map, the 13 largest linkage groups (except linkage group 12, which contained three loci) consisted of 4–12 loci, ranging in length from 53.9 to 145.9 cM and accounting for 97.22% of the total map distance. When mapping, progeny pass through their juvenile phase and assume their adult characters, mapping morphological markers and identification of quantitative trait loci for adaptive traits will be the primary target. In that sense, our map provides reference information for future molecular breeding work on Morus and its relatives.     

Genetic linkage map of a high yielding FELDA deli×yangambi oil palm cross

Enroute to mapping QTLs for yield components in oil palm, we constructed the linkage map of a FELDA high yielding oil palm (Elaeis guineensis), hybrid cross. The parents of the mapping population are a Deli dura and a pisifera of Yangambi origin. The cross out-yielded the average by 8-21% in four trials all of which yielded comparably to the best current commercial planting materials. The higher yield derived from a higher fruit oil content. SSR markers in the public domain - from CIRAD and MPOB, as well as some developed in FELDA - were used for the mapping, augmented by locally-designed AFLP markers. The female parent linkage map comprised 317 marker loci and the male parent map 331 loci, both in 16 linkage groups each. The number of markers per group ranged from 8-47 in the former and 12-40 in the latter. The integrated map was 2,247.5 cM long and included 479 markers and 168 anchor points. The number of markers per linkage group was 15-57, the average being 29, and the average map density 4.7 cM. The linkage groups ranged in length from 77.5 cM to 223.7 cM, with an average of 137 cM. The map is currently being validated against a closely related population and also being expanded to include yield related QTLs.     

A comparative genetic map of the turkey genome

Genetic markers (microsatellites and SNPs) were used to create and compare maps of the turkey and chicken genomes. A physical map of the chicken genome was built by comparing sequences of turkey markers with the chicken whole-genome sequence by BLAST analysis. A genetic linkage map of the turkey genome (Meleagris gallopavo) was developed by segregation analysis of genetic markers within the University of Minnesota/Nicholas Turkey Breeding Farms (UMN/NTBF) resource population. This linkage map of the turkey genome includes 314 loci arranged into 29 linkage groups. An additional 40 markers are tentatively placed within linkage groups based on two-point LOD scores and 16 markers remain unlinked. Total map distance contained within linkage groups is 2,011 cM with the longest linkage group (47 loci) measuring 413.3 cM. Average marker interval over the 29 linkage groups was 6.4 cM. All but one turkey linkage group could be aligned with the physical map of the chicken genome. The present genetic map of the turkey provides a comparative framework for future genomic studies.     

Genetic linkage map of the eastern oyster Crassostrea virginica Gmelin

Amplified fragment length polymorphisms (AFLPs), along with some microsatellite and Type I markers, were used for linkage analysis in Crassostrea virginica Gmelin, the eastern oyster. Seventeen AFLP primer combinations were selected for linkage analysis with two parents and their 81 progeny. The 17 primer combinations produced 396 polymorphic markers, and 282 of them were segregating in the two parents. Chi-square analysis indicated that 259 (91.8%) markers segregated in Mendelian ratio, while the other 23 (8.2%) showed significant (P < 0.05) segregation distortion, primarily for homozygote deficiency and probably due to deleterious recessive genes. Moderately dense linkage maps were constructed using 158 and 133 segregating markers (including a few microsatellite and Type I markers) from male and female parents, respectively. The male framework map consisted of 114 markers in 12 linkage groups, covering 647 cM. The female map had 84 markers in 12 linkage groups with a length of 904 cM. The estimated genome length was 858 cM for the male map and 1296 cM for the female map. The observed genome coverage was 84% for the male and female map when all linked markers were considered. Genetic maps observed in this study are longer than the cytogenetic map, possibly because of low marker density.     

The first genetic linkage map of Luohanguo (Siraitia grosvenorii ) based on ISSR and SRAP markers

In this study, the first genetic map of Luohanguo (Siraitia grosvenorii (Swingle) C. Jeffrey) was constructed with 150 F? population individuals using inter-simple sequence repeat (ISSR) and sequence-related amplified polymorphism (SRAP) markers. A total of 100 ISSRs and 196 SRAP primer combinations generated 51 and 222 polymorphic markers, respectively. Among the 273 markers obtained, 199 markers (29 ISSRs and 170 SRAPs) were mapped to 25 linkage groups. The map covered 1463.3 cM with a mean map distance of 7.35 cM between adjacent markers and a maximum map distance of 52.6 cM between two markers. The markers were distributed randomly in 25 groups except for minor clusters in the distal region of linkage groups. All 25 linkage groups consisted of 2-36 loci ranging in length from 19.5 to 152.6 cM and accounted for 59.8% of the total map distance. This map provides reference information for future molecular breeding work on Luohanguo.     

A molecular genetic map and electrophoretic karyotype of the plant pathogenic fungus Cochliobolus sativus

A molecular genetic map was constructed and an electrophoretic karyotype was resolved for Cochliobolus sativus, the causal agent of spot blotch of barley and wheat. The genetic map consists of 27 linkage groups with 97 amplified fragment length polymorphism (AFLP) markers, 31 restriction fragment length polymorphism (RFLP) markers, two polymerase chain reaction amplified markers, the mating type locus (CsMAT), and a gene (VHv1) conditioning high virulence on barley cv. Bowman. These linkage groups covered a map distance of 849 cM. The virulence gene VHv1 cosegregated with six AFLP markers and was mapped on one of the major linkage groups. Fifteen chromosome-sized DNAs were resolved in C. sativus isolates ND93-1 and ND9OPr with contour-clamped homogeneous electric field (CHEF) electrophoresis combined with telomere probe analysis of comigrating chromosome-sized DNAs. The chromosome sizes ranged from 1.25 to 3.80 Mbp, and the genome size of the fungus was estimated to be approximately 33 Mbp. By hybridizing genetically mapped RFLP and AFLP markers to CHEF blots, 25 of the 27 linkage groups were assigned to specific chromosomes. The barley-specific virulence locus VHv1 was localized on a chromosome of 2.80 Mbp from isolate ND9OPr in the CHEF gel. The total map length of the fungus was estimated to be at least 1,329 cM based on the map distance covered by the linked markers and the estimated gaps. Therefore, the physical to genetic distance ratio is approximately 25 kb/cM. Construction of a high-resolution map around target loci will facilitate the cloning of the genes conferring virulence and other characters in C. sativus by a map-based cloning strategy.     

A genetic map of the lettuce downy mildew pathogen,Bremia lactucae,constructed from molecular markers and avirulence genes

The genetic map of Bremia lactucae was expanded utilizing 97 F(1) progeny derived from a cross between Finnish and Californian isolates (SF5xC82P24). Genetic maps were constructed for each parent utilizing 7 avirulence genes, 83 RFLP markers, and 347 AFLP markers, and a consensus map was constructed from the complete data set. The framework map for SF5 contained 24 linkage groups distributed over 835cM; the map for C82P24 contained 21 linkage groups distributed over 606cM. The consensus map contained 12 linkage groups with markers from both parents and 24 parent-specific groups. Six avirulence genes mapped to different linkage groups; four were located at the ends of linkage groups. The closest linkages between molecular markers and avirulence genes were 3cM to Avr4 and 1cM to Avr7. Mating type seemed to be determined by a single locus, where the heterozygote determined the B(2) type and the homozygous recessive genotype determined the B(1) type.     

First comprehensive low-density horse linkage map based on two 3-generation, full-sibling, cross-bred horse reference families

Two 3-generation full-sibling reference families have been produced and form a unique resource for genetic linkage mapping studies in the horse. The F(2) generations, now comprising 61 individuals, consist of 28- to 32-day-old embryos removed nonsurgically from two pairs of identical twin mares. The same stallion sired all F(2)s such that the two full-sibling families are half-sibling with respect to each other. The families are crossbred to maximize levels of heterozygosity and include Arabian, Thoroughbred, Welsh Cob, and Icelandic Horse breeds. Milligram quantities of DNA have been isolated from each embryo and from blood samples of the parents and grandparents. The families have been genotyped with 353 equine microsatellites and 6 biallelic markers, and 42 linkage groups were formed. In addition, the physical location of 85 of the markers is known, and this has allowed 37 linkage groups to be anchored to the physical map. The inclusion of dams in the genotyping analysis has allowed the generation of a genetic map of the X chromosome. Markers have been assigned to all 31 autosomes and the X chromosome. The average interval between markers on the map is 10.5 cM, and the linkage groups collectively span 1780 cM. The results demonstrate the benefits for horse linkage mapping studies of genotyping on these unique full-sibling families, which comprise relatively few individuals, by the generation of a comprehensive low-density map of the horse genome.     

A microsatellite linkage map of the blacklip abalone, Haliotis rubra

There is considerable scope for genetic improvement of cultured blacklip abalone Haliotis rubra in Australia using molecular marker-assisted, selective-breeding practices. Such improvement is dependent on the availability of primary genetic resources, such as a genetic linkage map. This study presents a first-generation linkage map of H. rubra, containing 122 microsatellite markers typed in a single full-sib family. These loci mapped to 17 and 20 linkage groups for the male and female respectively, and when aligned, the consensus map represented 18 linkage groups. The male linkage map contained 102 markers (one unlinked) covering 621 cM with an average intermarker spacing of 7.3 cM, and the female map contained 98 markers (eight unlinked) covering 766 cM with an average intermarker spacing of 9.8 cM. Analysis of markers informative in both parents showed a significantly higher recombination rate in the female parent, with an average male-to-female recombination ratio of 1:1.45 between linked pairs of markers. This linkage map represents a significant advancement in the genetic resource available for H. rubra and provides a framework for future quantitative trait loci mapping and eventual implementation of marker-assisted selection.     

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.     

The first genetic linkage map of Eucommia ulmoides

In accordance with pseudo-testcross strategy, the first genetic linkage map of Eucommia ulmoides Oliv. was constructed by an F₁ population of 122 plants using amplified fragment length polymorphism (AFLP) markers. A total of 22 AFLP primer combinations generated 363 polymorphic markers. We selected 289 markers segregating as 1:1 and used them for constructing the parent-specific linkage maps. Among the candidate markers, 127 markers were placed on the maternal map LF and 108 markers on the paternal map Q1. The maternal map LF spanned 1116.1 cM in 14 linkage groups with a mean map distance of 8.78 cM; the paternal map Q1 spanned 929.6 cM in 12 linkage groups with an average spacing of 8.61 cM. The estimated coverage of the genome through two methods was 78.5 and 73.9% for LF, and 76.8 and 71.2% for Q1, respectively. This map is the first linkage map of E. ulmoides and provides a basis for mapping quantitative-trait loci and breeding applications.     

An amplified fragment length polymorphism map of the silkworm

The silkworm (Bombyx mori L.) is a lepidopteran insect with a long history of significant agricultural value. We have constructed the first amplified fragment length polymorphism (AFLP) genetic linkage map of the silkworm B. mori at a LOD score of 2.5. The mapping AFLP markers were genotyped in 47 progeny from a backcross population of the cross no. 782 x od100. A total of 1248 (60.7%) polymorphic AFLP markers were detected with 35 PstI/TaqI primer combinations. Each of the primer combinations generated an average of 35.7 polymorphic AFLP markers. A total of 545 (44%) polymorphic markers are consistent with the expected segregation ratio of 1:1 at the significance level of P = 0.05. Of the 545 polymorphic markers, 356 were assigned to 30 linkage groups. The number of markers on linkage groups ranged from 4 to 36. There were 21 major linkage groups with 7-36 markers and 9 relatively small linkage groups with 4-6 markers. The 30 linkage groups varied in length from 37.4 to 691.0 cM. The total length of this AFLP linkage map was 6512 cM. Genetic distances between two neighboring markers on the same linkage group ranged from 0.2 to 47 cM with an average of 18.2 cM. The sex-linked gene od was located between the markers P1T3B40 and P3T3B27 at the end of group 3, indicating that AFLP linkage group 3 was the Z (sex) chromosome. This work provides an essential basic map for constructing a denser linkage map and for mapping genes underlying agronomically important traits in the silkworm B. mori L.     

Construction of an integrated map of rose with AFLP, SSR, PK, RGA, RFLP, SCAR and morphological markers

A high-density genetic map with a number of anchor markers has been created to be used as a tool to dissect genetic variation in rose. Linkage maps for the diploid 94/1 population consisting of 88 individuals were constructed using a total of 520 molecular markers including AFLP, SSR, PK, RGA, RFLP, SCAR and morphological markers. Seven linkage groups, putatively corresponding to the seven haploid rose chromosomes, were identified for each parent, spanning 487 cM and 490 cM, respectively. The average length of 70 cM may cover more than 90% of the rose genome. An integrated map was constructed by incorporating the homologous parental linkage groups, resulting in seven linkage groups with a total length of 545 cM. The present linkage map is currently the most advanced map in rose with regard to marker density, genome coverage and with robust markers, giving good perspectives for QTL mapping and marker-assisted breeding in rose. The SSR markers, together with RFLP markers, provide good anchor points for future map alignment studies in rose and related species. Codominantly scored AFLP markers were helpful in the integration of the parental maps.