Construction of a linkage map of the Rennell Island Tall coconut type (Cocos nucifera L.) and QTL analysis for yield characters.

AFLP and SSR DNA markers were used to construct a linkage map in the coconut (Cocos nucifera L.; 2n = 32) type Rennell Island Tall (RIT). A total of 227 markers were arranged into 16 linkage groups. The total genome length corresponded to 1971 cM for the RIT map, with 5-23 markers per linkage group. QTL analysis for yield characters in two consecutive sampling periods identified nine loci. Three and two QTLs were detected for number of bunches and one and three QTLs for number of nuts. The correlation of trait values between characters and evaluation periods is partially reflected in identical QTLs. The QTLs represent characters that are important in coconut breeding. The cosegregation of markers with these QTLs provides an opportunity for marker-assisted selection in coconut breeding programmes.     

QTL analysis of flower and fruit traits in sour cherry

The map locations and effects of quantitative trait loci (QTLs) were estimated for eight flower and fruit traits in sour cherry (Prunus cerasus L.) using a restriction fragment length polymorphism (RFLP) genetic linkage map constructed from a double pseudo-testcross. The mapping population consisted of 86 progeny from the cross between two sour cherry cultivars, Rheinische Schattenmorelle (RS)×Erdi Botermo (EB). The genetic linkage maps for RS and EB were 398.2 cM and 222.2 cM, respectively, with an average interval length of 9.8 cM. The RS/EB linkage map that was generated with shared segregating markers consisted of 17 linkage groups covering 272.9 cM with an average interval length of 4.8 cM. Eleven putatively significant QTLs (LOD >2.4) were detected for six characters (bloom time, ripening time, % pistil death, % pollen germination, fruit weight, and soluble solids concentration). The percentage of phenotypic variation explained by a single QTL ranged from 12.9% to 25.9%. Of the QTLs identified for the traits in which the two parents differed significantly, 50% had allelic effects opposite to those predicted from the parental phenotype. Three QTLs affecting flower traits (bloom time, % pistil death, and % pollen germination) mapped to a single linkage group, EB 1. The RFLP closest to the bloom time QTL on EB 1 was detected by a sweet cherry cDNA clone pS141 whose partial amino acid sequence was 81% identical to that of a Japanese pear stylar RNase. Received: 4 March 1999 / Accepted: 27 August 1999     

Moderate-density molecular maps of Eucalyptus urophylla S. T. Blake and E. tereticornis Smith genomes based on RAPD markers

Moderate-density molecular maps were constructed for the genomes of Eucalyptus urophylla S. T. Blake and E. tereticornis Smith using RAPD markers and an interspecific cross between the two species. One hundred and eighty-three primers were employed to generate 245 and 264 parent-specific markers in E. urophylla and E. tereticornis, respectively, as well as 49 parent-shared markers. The normally segregating markers, including 208 (84.9%) specific to maternal E. urophylla, 175 (66.3%) to paternal E. tereticornis, and 48 shared by both parents, were used for framework map construction for each parental species. For maternal E. urophylla, the linkage map consisted of 23 linkage groups, 160 framework markers, and 60 accessory markers, defining a total map distance of 1504.6 cM and an average interval of 11.0 ± 8.07 cM. For paternal E. tereticornis, the linkage map contained 23 linkage groups, 126 framework markers, and 92 accessory markers, defining a total map distance of 1035.7 cM and an average interval of 10.1 ± 7.23 cM. Genome length was estimated at 1585.7 and 1507.5 cM for E. urophylla and E. tereticornis, respectively, indicating map coverage of 94.9 and 68.7% of the corresponding genomes. Construction of such maps will be valuable for quantitative trait loci (QTLs) detection, marker-assisted selection (MAS), comparative mapping, and whole genome based fingerprint characterization in Eucalyptus breeding programs.     

A high-density molecular map for ryegrass (Lolium perenne) using AFLP markers

AFLP markers have been successfully employed for the development of a high-density linkage map of ryegrass (Lolium perenne L.) using a progeny set of 95 plants from a testcross involving a doubled-haploid tester. This genetic map covered 930 cM in seven linkage groups and was based on 463 amplified fragment length polymorphism (AFLP) markers using 17 primer pairs, three isozymes and five EST markers. The average density of markers was approximately 1 per 2.0 cM. However, strong clustering of AFLP markers was observed at putative centromeric regions. Around these regions, 272 markers covered about 137 cM whereas the remaining 199 markers covered approximately 793 cM. Most genetic distances between consecutive pairs of markers were smaller than 20 cM except for five gaps on groups A, C, D, F and G. A skeletal map with a uniform distribution of markers can be extracted from this high-density map, and can be applied to detect and map QTLs. We report here the application of AFLP markers to genome mapping, in Lolium as a prelude to quantitative trait locus (QTL) identification for diverse agronomic traits in ryegrass and for marker-assisted plant breeding. Received: 4 November 1998 / Accepted:15 March 1999     

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.     

A genetic linkage map of Guinea yam ( Dioscorea rotundata Poir.) based on AFLP markers

A genetic linkage map of the tetraploid white yam (Dioscorea rotundata Poir.) was constructed based on 341 co-dominantly scored amplified fragment length polymorphism (AFLP) markers segregating in an intraspecific F₁ cross. The F₁ mapping population was produced by crossing a landrace cultivar TDr 93-1 as female parent to a breeding line TDr 87/00211 as the male parent. The marker segregation data were split into maternal and paternal data sets, and separate genetic linkage maps were constructed since the mapping population was an F₁ cross between two presumed heterozygous parents. The markers segregated like a diploid cross-pollinator population suggesting that the D. rotundata genome is an allo-tetraploid (2n = 4x = 40). The maternal map comprised 155 markers mapped on 12 linkage groups with a total map length of 891 cM. Three linkage groups consisted of maternal parent markers only. The paternal map consisted of 157 markers mapped on 13 linkage groups with a total map length of 852 cM. Three and one quantitative trait loci (QTLs) with effects on resistance to Yam Mosaic Virus (YMV) were identified on the maternal and paternal linkage maps, respectively. Prospects for detecting more QTLs and using marker-assisted selection in white yam breeding appear good, but this is subject to the identification of additional molecular markers to cover more of the genome.     

基于SRAP分子标记的冰草遗传连锁图谱构建

构建高密度遗传连锁图谱是冰草抗性、品质、产量等重要性状QTL精细定位及标记辅助育种研究的基础。该试验以四倍体杂交冰草F2群体的202个分离单株及其亲本为材料,利用SRAP分子标记技术和Join Map 4.0作图软件对冰草的遗传连锁图谱进行了构建。结果表明:(1)共筛选出22对多态性好、标记位点清晰稳定的SRAP适宜引物,对冰草杂种F2分离单株的基因组DNA进行PCR扩增,共获得510个SRAP多态性标记位点,其比率占88.2%。(2)偏分离分析表明,偏分离标记比率仅为14.12%,符合遗传作图的要求。(3)成功构建了冰草的SRAP分子标记遗传连锁图谱,该图谱有14个连锁群、510个标记,连锁群间长度范围86.4～179.0cM,覆盖基因组总长度1 912.9cM,标记间平均间距3.75cM,为高密度遗传图谱。     

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.     

An integrated genetic map of Populus deltoides based on amplified fragment length polymorphisms

Amplified fragment length polymorphism (AFLP) is an efficient molecular technique for generating a large number of DNA-based genetic markers in Populus. We have constructed an integrated genetic map for a Populus backcross population derived from two selected P. deltoides clones using AFLP markers. A traditional strategy for genetic mapping in outcrossing species, such as forest trees, is based on two-way pseudo-testcross configurations of the markers (testcross markers) heterozygous in one parent and null in the other. By using the markers segregating in both parents (intercross markers) as bridges, the two parent-specific genetic maps can be aligned. In this study, we detected a number of non-parental heteroduplex markers resulting from the PCR amplification of two DNA segments that have a high degree of homology to one another but differ in their nucleotide sequences. These heteroduplex markers detected have served as bridges to generate an integrated map which includes 19 major linkage groups equal to the Populus haploid chromosome number and 24 minor groups. The 19 major linkage groups cover a total of 2,927 cM, with an average spacing between two markers of 23. 3 cM. The map developed in this study provides a first step in producing a highly saturated linkage map of the Populus deltoides genome. Received: 10 September 1999 / Accepted: 3 November 1999     

Genetic Mapping and QTL Analysis of Growth-Related Traits in the Pacific Oyster

The Pacific oyster (Crassostrea gigas) is one of the most important oysters cultured worldwide. To analyze the oyster genome and dissect growth-related traits, we constructed a sex-averaged linkage map by combining 64 genomic simple sequence repeats, 42 expressed sequence tag-derived SSRs, and 320 amplified fragment length polymorphism markers in an F₁ full-sib family. A total of 426 markers were assigned to 11 linkage groups, spanning 558.2 cM with an average interval of 1.3 cM and 94.7% of genome coverage. Segregation distortion was significant for 18.8% of the markers (P < 0.05), and distorted markers tended to occur on some genetic regions or linkage groups. Most growth-related quantitative traits were highly significantly (P < 0.01) correlated, and principal component analysis obtained four principal components. Quantitative trait locus (QTL) analysis identified three significant QTLs for two principal components, which explained 0.6–13.9% of the phenotypic variation. One QTL for sex was detected on linkage group 6, and the inheritabilities of sex for parental alleles and maternal alleles on that locus C15 are 39.8% and 0.01%, respectively. The constructed linkage map and determined QTLs can provide a tool for further genetic analysis of the traits and be potential for marker-assisted selection in C. gigas breeding.     

An integrated AFLP and RFLP Brassica oleracea linkage map from two morphologically distinct doubled-haploid mapping populations

Genetical maps of molecular markers in two very different F₁-derived doubled-haploid populations of Brassica oleracea are compared and the first integrated map described. The F₁ crosses were: Chinese kale×calabrese (var. alboglabra×var. italica) and cauliflower×Brussels sprout (var. botrytis×var. gemmifera). Integration of the two component maps using Joinmap v.2.0 was based on 105 common loci including RFLPs, AFLPs and microsatellites. This provided an effective method of producing a high-density consensus linkage map of the B. oleracea genome. Based on 547 markers mapping to nine linkage groups, the integrated map covers a total map length of 893 cM, with an average locus interval of 2.6 cM. Comparisons back to the component linkage maps revealed similar sequences of common markers, although significant differences in recombination frequency were observed between some pairs of homologous markers. Map integration resulted in an increased locus density and effective population size, providing a stronger framework for subsequent physical mapping and for precision mapping of QTLs using substitution lines. Received: 5 February 1999 / Accepted: 16 June 1999     

Comparative molecular mapping in Ceratotropis species using an interspecific cross between azuki bean (Vigna angularis) and rice bean (V. umbellata)

A genetic linkage map was developed with 86 F₂ plants derived from an interspecific cross between azuki bean (Vigna angularis, 2n=2x=22) and rice bean (V. umbellata, 2n=2x=22). In total, 14 linkage groups, each containing more than 4 markers, were constructed with one phenotypic, 114 RFLP and 74 RAPD markers. The total map size was 1702 cM, and the average distance between markers was 9.7 cM. The loci showing significant deviation from the expected ratio clustered in several linkage groups. Most of the skewed loci were due to the predominance of rice bean alleles. The azuki-rice bean linkage map was compared with other available maps of Vigna species in subgenus Ceratotropis. Based on the lineage of the common mapped markers, 7 and 16 conserved linkage blocks were found in the interspecific map of azuki bean ×V. nakashimae and mungbean map, respectively. Although the present map is not fully saturated, it may facilitate gene tagging, QTL mapping and further useful gene transfer for azuki bean breeding. Received: 20 March 1999 / Accepted: 29 April 1999     

SSR-based genetic linkage map construction in pistachio using an interspecific F<Subscript>1</Subscript> population and QTL analysis for leaf and shoot traits

Pistachio is one of the most commercially important nut trees in the world. To characterize the genetic controls of horticultural traits and facilitate marker-assisted breeding in pistachio, we constructed an SSR-based linkage map using an interspecific F₁ population derived from a cross between the cultivar “Siirt” (Pistacia vera L.) and the monoecious Pa-18 genotype of Pistacia atlantica Desf. This population was also used for the first QTL analysis in pistachio on leaf and shoot characters. In total, 1312 SSR primers were screened, and 388 loci were successfully integrated into parental linkage maps. The Siirt maternal map contained 306 markers, while the “Pa-18” paternal map included 285 markers along the 15 linkage groups. The Siirt map spanned 1410.4 cM, with an average marker distance of 4.6 cM; the Pa-18 map covered 1362.5 cM with an average marker distance of 4.8 cM. Phenotypic data were collected during the growing seasons of 2015 and 2016 for four traits: leaf length (LL), leaf width (LW), leaf length/leaf width ratio (LWR), number of leaflet pairs (NLL), and young shoot color (YSC). A total of 17 QTLs were identified in the parental maps. Four QTLs for LL and LW were located on LG2 and LG4, while four QTLs for LWR ratio on LG13 and LG14, two QTLs for NLL and two QTLs for YSC were on LG7 and LG9, respectively, with similar positions in both parental maps. The SSR markers, linkage maps, and QTLs reported here will provide a valuable resource for future molecular and genetic studies in pistachio.     

Theobroma cacao L.: a genetic linkage map and quantitative trait loci analysis

A genetic linkage map of Theobroma cacao (cocoa) has been constructed from 131 backcross trees derived from a cross between a single tree of the variety Catongo and an F1 tree from the cross of Catongo by Pound 12. The map comprises 138 markers: 104 RAPD loci, 32 RFLP loci and two morphologic loci. Ten linkage groups were found which cover 1068 centimorgans (cM). Only six (4%) molecular-marker loci show a significant deviation from the expected 11 segregation ratio.The average distance between two adjacent markers is 8.3 cM. The final genome-size estimates based on two-point linkage data ranged from 1078 to 1112 cM for the cocoa genome. This backcross progeny segregates for two apparently single gene loci controlling (1) anthocyanidin synthesis (Anth) in seeds, leaves and flowers and (2) self-compatibility (Autoc). The Anth locus was found to be 25 cM from Autoc and two molecular markers co-segregate with Anth. The genetic linkage map was used to localize QTLs for early flowering, trunk diameter, jorquette height and ovule number in the BC₁ generation using both single-point ANOVA and interval mapping. A minimum number of 2–4 QTLs (P<0.01) involved in the genetic expression of the traits studied was detected. Coincident map locations of a QTL for jorquette height and trunk diameter suggests the possibility of pleiotropic effects in cocoa for these traits. The combined estimated effects of the different mapped QTLs explained between 11.2% and 25.8% of the phenotypic variance observed in the BC₁ population.     

Construction of the First High-Density Genetic Linkage Map and Analysis of Quantitative Trait Loci for Growth-Related Traits in <Emphasis Type="Italic">Sinonovacula constricta</Emphasis>

The razor clam (Sinonovacula constricta) is an important aquaculture species, for which a high-density genetic linkage map would play an important role in marker-assisted selection (MAS). In this study, we constructed a high-density genetic map and detected quantitative trait loci (QTLs) for Sinonovacula constricta with an F₁ cross population by using the specific locus amplified fragment sequencing (SLAF-seq) method. A total of 315,553 SLAF markers out of 467.71 Mreads were developed. The final linkage map was composed of 7516 SLAFs (156.60-fold in the parents and 20.80-fold in each F₁ population on average). The total distance of the linkage map was 2383.85 cM, covering 19 linkage groups with an average inter-marker distance of 0.32 cM. The proportion of gaps less than 5.0 cM was on average 96.90%. A total of 16 suggestive QTLs for five growth-related traits (five QTLs for shell height, six QTLs for shell length, three QTLs for shell width, one QTL for total body weight, and one QTL for soft body weight) were identified. These QTLs were distributed on five linkage groups, and the regions showed overlapping on LG9 and LG13. In conclusion, the high-density genetic map and QTLs for S. constricta provide a valuable genetic resource and a basis for MAS.     

Development of an integrated genetic map of a sugarcane (Saccharum spp.) commercial cross, based on a maximum-likelihood approach for estimation of linkage and linkage phases

Sugarcane (Saccharum spp.) is a clonally propagated outcrossing polyploid crop of great importance in tropical agriculture. Up to now, all sugarcane genetic maps had been developed using either full-sib progenies derived from interspecific crosses or from selfing, both approaches not directly adopted in conventional breeding. We have developed a single integrated genetic map using a population derived from a cross between two pre-commercial cultivars (‘SP80-180’ × ‘SP80-4966’) using a novel approach based on the simultaneous maximum-likelihood estimation of linkage and linkage phases method specially designed for outcrossing species. From a total of 1,118 single-dose markers (RFLP, SSR and AFLP) identified, 39% derived from a testcross configuration between the parents segregating in a 1:1 fashion, while 61% segregated 3:1, representing heterozygous markers in both parents with the same genotypes. The markers segregating 3:1 were used to establish linkage between the testcross markers. The final map comprised of 357 linked markers, including 57 RFLPs, 64 SSRs and 236 AFLPs that were assigned to 131 co-segregation groups, considering a LOD score of 5, and a recombination fraction of 37.5 cM with map distances estimated by Kosambi function. The co-segregation groups represented a total map length of 2,602.4 cM, with a marker density of 7.3 cM. When the same data were analyzed using JoinMap software, only 217 linked markers were assigned to 98 co-segregation groups, spanning 1,340 cM, with a marker density of 6.2 cM. The maximum-likelihood approach reduced the number of unlinked markers to 761 (68.0%), compared to 901 (80.5%) using JoinMap. All the co-segregation groups obtained using JoinMap were present in the map constructed based on the maximum-likelihood method. Differences on the marker order within the co-segregation groups were observed between the two maps. Based on RFLP and SSR markers, 42 of the 131 co-segregation groups were assembled into 12 putative homology groups. Overall, the simultaneous maximum-likelihood estimation of linkage and linkage phases was more efficient than the method used by JoinMap to generate an integrated genetic map of sugarcane. E.A. Kido, A.N. Meza and H.M.B. Souza contributed equally to this work.     

Construction of genetic linkage maps and QTL mapping for X-disease resistance in tetraploid chokecherry (Prunus virginiana L.) using SSR and AFLP markers

Chokecherry (Prunus virginiana L.) (2n = 4x = 32) is a unique Prunus species for both genetics and disease resistance research due to its tetraploid nature and known variations in X-disease resistance. X-disease is a destructive disease of stone fruit trees, causing yield loss and poor fruit quality. However, genetic and genomic information on chokecherry is limited. In this study, simple sequence repeat (SSR) and amplified fragment length polymorphism (AFLP) markers were used to construct genetic linkage maps and to identify quantitative trait loci (QTLs) associated with X-disease resistance in chokecherry. A segregating population (101 progenies) was developed by crossing an X-disease-resistant chokecherry line (RC) with a susceptible chokecherry line (SC). A total of 498 DNA markers (257 SSR and 241 AFLP markers) were mapped on the two genetic maps of the two parental lines (RC and SC). The map of RC contains 302 markers assigned to 14 linkage groups covering 2,089 cM of the genome. The map of SC has 259 markers assigned to 16 linkage groups covering 1,562.4 cM of the genome. The average distance between two markers was 6.9 cM for the RC map and 6.0 cM for the SC map. One QTL located on linkage group 15 on the map of SC was found to be associated with X-disease resistance. Genetic linkage maps and the identified QTL linked to X-disease resistance will further facilitate genetic research and breeding of X-disease resistance in chokecherry and other Prunus species.     

Identifying QTLs for fire-blight resistance via a European pear (<Emphasis Type="Italic">Pyrus communis</Emphasis> L.) genetic linkage map

The existence of different levels of susceptibility to fire blight (Erwinia amylovora) in European pear (Pyrus communis L.) cultivars suggests that it is possible to identify QTLs related to resistance in pear germplasm. Given the polygenic nature of this trait, we designed two genetic maps of the parental lines 'Passe Crassane' (susceptible) and 'Harrow Sweet' (resistant) using SSRs, MFLPs, AFLPs, RGAs and AFLP-RGAs markers. RGA-related markers should theoretically map in chromosome regions coding for resistance genes. The 'Passe Crassane' map includes 155 loci, for a total length of 912 cM organised in 18 linkage groups, and the 'Harrow Sweet' map 156 loci, for a total length of 930 cM divided in 19 linkage groups; both maps have a good genome coverage when compared to the more detailed apple maps. Four putative QTLs related to fire blight resistance were identified in the map. A suite of molecular markers, including two AFLP-RGAs, capable of defining resistant and susceptible haplotypes in the analysed population was developed.     

Construction of a genetic linkage map using MFLP and identification of molecular markers linked to domestication genes in narrow-leafed lupin (Lupinus angustifolius L.)

A mapping population of F(8)derived recombinant inbred lines (RILs) was established from a cross between a domesticated breeding line 83A:476 and a wild type P27255 in narrow-leaf lupin (Lupinus angustifolius L.). The parents together with the 89 RILs were subjected to DNA fingerprinting using microsatellite-anchored fragment length polymorphism (MFLP) to rapidly generate DNA markers to construct a linkage map. Five hundred and twenty two unique markers of which 21% were co-dominant, were generated and mapped. Phenotypic data for the domestication traits: mollis (soft seeds), leucospermus (white flower and seed colour); Lentus (reduced pod-shattering), iucundis (low alkaloid), Ku (early flowering) and moustache pattern on seed coats; were included. Three to 7 molecular markers were identified within 5 cM of each of these domestication genes. The anthracnose resistance gene Lanr1 was also mapped. Linkage groups were constructed using MapManager version QTXb20, resulting in 21 linkage groups consisting of 7 or more markers. The total map length was 1543 cM, with an average distance of 3.4 cM between adjacent markers. This is the first published map for a lupin species. The map can be exploited for marker assisted selection for genetic improvement in lupin breeding programs.     

Nearly complete genetic maps of <Emphasis Type="Italic">Pinus sylvestris</Emphasis> L. (Scots pine) constructed by AFLP marker analysis in a full-sib family

We have constructed nearly complete linkage maps of Pinus sylvestris (L.) using AFLP markers based on a two-way pseudo-testcross strategy in a full-sib family founded in an advanced breeding program. With 39 primer combinations, a total of 737 markers (320 from the mother and 417 from the father) segregated in a 1:1 ratio, corresponding to DNA polymorphism: heterozygous in one parent and null in the other. In the maternal parent, 188 framework markers were mapped in 12 linkage groups, equivalent to the Pinus haploid chromosome number, with a total coverage of 1,695.5 cM. In the paternal parent, 245 framework markers established a map with 15 linkage groups, spanning a genome length of 1,718.5 cM. The estimated total map length was L(F) = 1,681 cM for the female and L(M) = 1,645 cM for the male using a modified method-of-moment estimator. Combining these values with those estimated from the observed map lengths in both parents, we estimated the genome length in Scots pine to be between 1,600 and 2,100 cM. Our genome coverage was estimated to be more than 98% with a framework marker interval of 20 cM for both parents. Most of the female and male linkage groups were associated through the analysis of the intercross markers.