Genetic Linkage Maps of Eucalyptus Grandis and Eucalyptus Urophylla Using a Pseudo-Testcross: Mapping Strategy and Rapd Markers

We have used a ``two-way pseudo-testcross' mapping strategy in combination with the random amplified polymorhic DNA (RAPD) assay to construct two moderate density genetic linkage maps for species of Eucalyptus. In the cross between two heterozygous individuals many single-dose RAPD markers will be heterozygous in one parent, null in the other and therefore segregate 1:1 in their F(1) progeny following a testcross configuration. Meiosis and gametic segregation in each individual can be directly and efficiently analyzed using RAPD markers. We screened 305 primers of arbitrary sequence, and selected 151 to amplify a total of 558 markers. These markers were grouped at LOD 5.0, θ = 0.25, resulting in the maternal Eucalyptus grandis map having a total of 240 markers into 14 linkage groups (1552 cM) and the paternal Eucalyptus urophylla map with 251 markers in 11 linkage groups (1101 cM) (n = 11 in Eucalyptus). Framework maps ordered with a likelihood support >/=1000:1 were assembled covering 95% of the estimated genome size in both individuals. Characterization of genome complexity of a sample of 48 mapped random amplified polymorphic DNA (RAPD) markers indicate that 53% amplify from low copy regions. These are the first reported high coverage linkage maps for any species of Eucalyptus and among the first for any hardwood tree species. We propose the combined use of RAPD markers and the pseudo-testcross configuration as a general strategy for the construction of single individual genetic linkage maps in outbred forest trees as well as in any highly heterozygous sexually reproducing living organism. A survey of the occurrence of RAPD markers in different individuals suggests that the pseudo-testcross/RAPD mapping strategy should also be efficient at the intraspecific level and increasingly so with crosses of genetically divergent individuals. The ability to quickly construct single-tree genetic linkage maps in any forest species opens the way for a shift from the paradigm of a species index map to the heterodox proposal of constructing several maps for individual trees of a population, therefore mitigating the problem of linkage equilibrium between marker and trait loci for the application of marker assisted strategies in tree breeding.     

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.     

Towards a genus-wide reference linkage map for Eucalyptus based exclusively on highly informative microsatellite markers

A novel set of 50 highly polymorphic microsatellite markers were developed and mapped on existing RAPD framework maps of Eucalyptus grandis and E. urophylla. Together with the twenty previously developed microsatellite markers, these were used to align the existing maps for the two most commercially important Eucalyptus species in the tropics. Sixty-three microsatellite markers were placed on the E. grandis map in 11 linkage groups, and 53 on the E. urophylla map distributed in 10 linkage groups. Approximately 66% of the microsatellite markers segregated in a fully informative fashion, allowing the establishment of colinear syntenic linkage groups between the two maps. The 50 new microsatellite markers were highly informative, with an average of 14 alleles per locus, and average expected heterozygosity between 0.82 and 0.87. Furthermore, within the subgenus Symphyomyrtus, to which the vast majority of commercially important Eucalyptus species belong, these markers display on average 90% transportability. This set of 70 mapped microsatellite markers represents a significant step toward the development of a genus-wide reference linkage map for Eucalyptus. These highly multiallelic and transportable markers constitute a powerful tool for QTL discovery and validation, and can be used in directed searches for QTL allele variation across Eucalyptus pedigrees.     

A gene controlling sex in grapevines placed on a molecular marker-based genetic map.

Genetic maps of Vitis (2n = 38) have been constructed from an interspecific hybrid population of 58 seedlings of the cross 'Horizon' ('Seyval' x 'Schuyler') x Illinois 547-1 (V. cinerea B9 x V. rupestris B38). The maps were initially constructed based on 277 RAPD (random amplified polymorphic DNA) markers using a double-pseudotestcross strategy. Subsequently, 25 microsatellites, 4 CAPS (cleaved amplified polymorphic sequence), and 12 AFLP (amplified fragment length polymorphism) markers were added to the maps. Another 120 markers, mostly those segregating 3:1, were also assigned but not positioned on the linkage groups in the two maps. The 'Horizon' map consisted of 153 markers covering 1199 cM, with an average map distance of 7.6 cM between markers. The Illinois 547-1 map had 179 markers covering 1470 cM, with an average map distance of 8.1 cM. There were 20 linkage groups in each map, one more than the basic number of chromosomes in grapes. Ten linkage groups in each map were identified as homologous using 16 microsatellite and 2 CAPS markers polymorphic in both parents. A single locus controlling sex in grapes mapped close to a microsatellite marker. These maps provide enough coverage of the genome for QTL (quantitative trait loci) analysis and as a starting point for positional gene cloning in grapes.     

Genetic linkage maps of two apricot cultivars ( Prunus armeniaca L.), and mapping of PPV (sharka) resistance

Genetic linkage maps for two apricot cultivars have been constructed using AFLP, RAPD, RFLP and SSR markers in 81 F1 individuals from the cross 'Goldrich' x 'Valenciano'. This family segregated for resistance to 'plum pox virus' (PPV), the most-important virus affecting Prunus species. Of the 160 RAPD arbitrary primers screened a total of 44 were selected. Sixty one polymorphic RAPD markers were scored on the mapping population: 30 heterozygous in 'Goldrich', 19 heterozygous in 'Valenciano', segregating 1:1, and 12 markers heterozygous in both parents, segregating 3:1. A total of 33 and 19 RAPD markers were mapped on the 'Goldrich' and 'Valenciano' maps respectively. Forteen primer combinations were used for AFLPs and all of them detected polymorphism. Ninety five markers segregating 1:1 were identified, of which 62 were heterozygous in the female parent 'Goldrich' and 33 in the male parent 'Valenciano'. Forty five markers were present in both parents and segregated 3:1. A total of 82 and 48 AFLP markers were mapped on the 'Goldrich' and 'Valenciano' maps. Twelve RFLPs probes were screened in the population, resulting in five loci segregating in the family, one locus heterozygous for 'Valenciano' and four heterozygous for both, segregating 1:2:1. Of the 45 SSRs screened 17 segregated in the mapping family, resulting in seven loci heterozygous for the maternal parent and ten heterozygous for both, segregating 1:2:1 or 1:1:1:1. A total of 16 and 13 co-dominant markers were mapped in the female and male parent maps respectively. A total of 132 markers were placed into eight linkage groups on the 'Goldrich' map, defining 511 cM of the total map-length. The average distance between adjacent markers was 3.9 cM. A total of 80 markers were placed into seven linkage groups on the 'Valenciano' map, defining 467.2 cM of the total map-distance, with an average interval of 5.8 cM between adjacent markers. Thirty six marker loci heterozygous in both parents revealed straightforward homologies between five linkage groups in both maps. The sharka resistance trait mapped on linkage group 2. The region containing sharka resistance is flanked by two co-dominant markers that will be used for targeted SSR development employing a recently constructed complete apricot BAC library. SSRs tightly linked to sharka resistance will facilitate MAS in breeding for resistance in apricot.     

A genetic linkage map for hazelnut (Corylus avellana L.) based on RAPD and SSR markers.

A linkage map for European hazelnut (Corylus avellana L.) was constructed using random amplified polymorphic DNA (RAPD) and simple sequence repeat (SSR) markers and the 2-way pseudotestcross approach. A full-sib population of 144 seedlings from the cross OSU 252.146 x OSU 414.062 was used. RAPD markers in testcross configuration, segregating 1:1, were used to construct separate maps for each parent. Fifty additional RAPD loci were assigned to linkage groups as accessory markers whose exact location could not be determined. Markers in intercross configuration, segregating 3:1, were used to pair groups in one parent with their homologues in the other. Eleven groups were identified for each parent, corresponding to the haploid chromosome number of hazelnut (n = x = 11). Thirty of the 31 SSR loci were able to be assigned to a linkage group. The maternal map included 249 RAPD and 20 SSR markers and spanned a distance of 661 cM. The paternal map included 271 RAPD and 28 SSR markers and spanned a distance of 812 cM. The maps are quite dense, with an average of 2.6 cM between adjacent markers. The S-locus, which controls pollen-stigma incompatibility, was placed on chromosome 5S where 6 markers linked within a distance of 10 cM were identified. A locus for resistance to eastern filbert blight, caused by Anisogramma anomala, was placed on chromosome 6R for which two additional markers tightly linked to the dominant allele were identified and sequenced. These maps will serve as a starting point for future studies of the hazelnut genome, including map-based cloning of important genes. The inclusion of SSR loci on the map will make it useful in other populations.     

A molecular linkage map of olive (Olea europaea L) based on RAPD, microsatellite, and SCAR markers.

An integrated molecular linkage map of olive (Olea europaea L.) was constructed based on randomly amplified polymorphic DNA (RAPD), sequence characterized amplified region (SCAR), and microsatellite markers using the pseudo-testcross strategy. A mapping population of 104 individuals was generated from an F1 full-sib family of a cross between 'Frantoio' and 'Kalamata'. The hybridity of the mapping population was confirmed by genetic similarity and nonmetric multidimensional scaling. Twenty-three linkage groups were mapped for 'Kalamata', covering 759 cM of the genome with 89 loci and an average distance between loci of 11.5 cM. Twenty-seven linkage groups were mapped for 'Frantoio', covering 798 cM of the genome with 92 loci and an average distance between loci of 12.3 cM. For the integrated map, 15 linkage groups covered 879 cM of the genome with 101 loci and an average distance between loci of 10.2 cM. The size of the genomic DNA was estimated to be around 3000 cM. A sequence characterized amplified region marker linked to olive peacock disease resistance was mapped to linkage group 2 of the integrated map. These maps will be the starting point for studies on the structure, evolution, and function of the olive genome. When the 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 targets.     

Integration genetic linkage map construction and several potential QTLs mapping of Chinese shrimp (Fenneropenaeus chinensis) based on three types of molecular markers

In this study, totally 54 selected polymorphic SSR loci of Chinese shrimp (Fenneropenaeus chinensis), in addition with the previous linkage map of AFLP and RAPD markers, were used in consolidated linkage maps that composed of SSR, AFLP and RAPD markers of female and male construction, respectively. The female linkage map contained 236 segregating markers, which were linked in 44 linkage groups, and the genome coverage was 63.98%. The male linkage map contained 255 segregating markers, which were linked in 50 linkage groups, covering 63.40% of F. chinensis genome. There were nine economically important traits and phenotype characters of F. chinensis were involved in QTL mapping using multiple-QTL mapping strategy. Five potential QTLs associated with standard length (q-standardl-01), with cephalothorax length (q-cephal-01), with cephaloghorax width (q-cephaw-01), with the first segment length (q-firsel-01) and with anti-WSSV (q-antiWSSV-01) were detected on female LG1 and male LG44 respectively with LOD> 2.5. The QTL q-firsel-01 was at 73.603 cM of female LG1. Q-antiWSSV-01 was at 0 cM of male LG44. The variance explained of these five QTLs was from 19.7-33.5% and additive value was from -15.9175 to 7.3675. The closest markers to these QTL were all SSR, which suggested SSR marker was superior to AFLP and RAPD in the QTL mapping.     

RAPD Linkage Mapping in a Populus adenopoda×P. alba F1 Family

Random amplified polymorphic DNAs(RAPDs) were used to construct linkage maps of the parents of a Populus adenopoda Maxim. x P. alba L. Fl family. A set of 620 random oligonucleotide primers were screened and 128 primers were selected to generate RAPD markers within a sample of 80 Fl progenies. A total of 333 segregating loci [ (326( 1:1 ) ,7(3:1 ) ] were identified. Among the 326 1:1 segregating loci (238 loci from P. adenopoda and 88 loci from P. dba),36 loci (26 loci in P. adenopoda and 10 loci in P. dba) were found distorted from the normal 1:1 ratio. Altogether 290 loci segregating 1:1 (testcross configuration) were used to construct parent-specific linkage maps,212 for P. alba and 78 for P. adenopoda. The resulting linkage maps consisted of 189 marker loci in 20 groups (four or more loci per group), 6 triples and 16 pairs for P. dba, which cover the map distance about 2 402.4 cM, and 41 linked marker loci for P. adenopoda which cover map distance about 479.4 cM. Further study is warranted to locate some important quantitative trait loci (QTLs) based on the maps.     

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 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.     

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.     

Linkage map of Japanese black pine based on AFLP and RAPD markers including markers linked to resistance against the pine needle gall midge

Macrogametophytes derived from the seeds of a tree resistant to pine needle gall midge (PGM) were analyzed using amplified fragment length polymorphism (AFLP). A total of 244 segregating loci were detected among 71 macrogametophytes. Combining the AFLP results with previously reported segregation data for 127 random amplified polymorphic DNA (RAPD) markers, 157 AFLP and 50 RAPD markers with confirmed map positions were assigned to 20 linkage groups and three pairs covering 2085.5 cM with an average distance of 10.1 cM. The total map distance covers about 77.1–78.4% of the total genome, estimated to be approximately 2665–2719 cM in length. Thus, using AFLP markers, the previous RAPD map of this tree was improved in terms of the average distance between markers, the total map distance, and coverage of the genome. Three RAPD markers linked to a gene associated with resistance to PGM were also located on this map. Rceived: 14 April 2000 / Accepted: 21 August 2000     

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.     

AFLP genetic maps of Eucalyptus globulus and E. tereticornis

 Amplified fragment length polymorphism (AFLP) analysis is a rapid and efficient technique for detecting large numbers of DNA markers in eucalypts. We have used AFLP markers in a two-way pseudo-testcross strategy to generate genetic maps of two clones of different Eucalyptus species (E. tereticornis and E. globulus). Of 606 polymorphic fragments scored, 487 segregated in a 1 : 1 ratio, corresponding to DNA polymorphisms heterozygous in one parent and null in the other. In the maternal E. tereticornis map, 268 markers were ordered in 14 linkage groups (919 cM); the paternal E. globulus map had 200 markers in 16 linkage groups (967 cM). Results from PGRI software were compared with MAPMAKER. The average density of markers was approximately 1 per 3.9 cM. Framework markers were ordered with an average confidence level of 90%, covering 80–100% of the estimated Eucalyptus genome size. In order to investigate the homologies between the E. tereticornis and the E. globulus genetic linkage maps, we included 19 markers segregating 3 : 1 in the analysis. Some homeologous linkage groups were recognized. The linkage data developed in these maps will be used to detect loci controlling commercially important traits. Received: 17 July 1997 / Accepted: 13 October 1997     

Combined RAPD and RFLP molecular linkage map of asparagus.

Two linkage maps of asparagus (Asparagus officinalis L.) were constructed using a double pseudotestcross mapping strategy with restriction fragment length polymorphisms (RFLPs), random amplified polymorphic DNAs (RAPDs), and allozymes as markers in a population generated from crossing MW25 x A19, two heterozygous parents. All data were inverted and combined with the natural data to detect linkages in repulsion phase. Two sets of data, one for each parent, were formed according to the inheritance patterns of the markers. The maternal MW25 map has a total of 163 marker loci placed in 13 linkage groups covering 1281 cM, with an average and a maximum distance between adjacent loci of 7.9 and 29 cM, respectively. The paternal A19 map has 183 marker loci covering 1324 cM in 9 linkage groups, with an average and a maximum distance between two adjacent loci of 7.7 and 29 cM, respectively. Six multiallelic RFLPs segregating in the pattern a/c x b/c and eight heterozygous loci (four RAPDs, and four RFLPs segregating in the pattern a/b x a/b (HZ loci)) were common to both maps. These 14 loci were used as bridges to align homologous groups between the two maps. In this case, RFLPs were more frequent and informative than RAPDs. Nine linkage groups in the MW25 map were homologous to six groups in the A19 map. In two cases, two or more bridge loci were common to a group; thus, the orientation of homologous linkage groups was also determined. In four other cases, only one locus was common to the two homologous groups and the orientation was unknown. Mdh, four RFLPs, and 14 RAPDs were assigned to chromosome L5, which also has the sex locus M.     

Megagametophyte-derived linkage maps of white spruce ( Picea glauca) based on RAPD,SCAR and ESTP markers

We have constructed linkage maps for two parents of white spruce [ Picea glauca (Moench) Voss]. Haploid megagametophytes from 92 and 96 seeds of parents M2 and 80132, respectively, were analysed with RAPD, SCAR and ESTP markers. Fragments segregating in a 1:1 Mendelian ratio were classified and mapped using MAPMAKER, GMENDEL and JOINMAP. For M2, the analysis with JOINMAP resulted in 165 loci (152 RAPDs, 3 SCARs and 10 ESTPs) mapping to 23 linkage groups and covering 2,059.4 cM(Kosambi function, K). For 80132, the analysis resulted in 144 loci (137 RAPDs, 1 SCAR and 7 ESTPs) mapping to 19 linkage groups and covering 2,007.7 cM(K). The maps covered 87 and 73% of the entire genome of parents M2 and 80132, respectively. Similar results were obtained with MAPMAKER and GMENDEL. A comparison was made between the two individual maps and 16 loci were shared between the two maps.     

AFLP-based genetic linkage map for the red flour beetle (Tribolium castaneum)

The red flour beetle (Tribolium castaneum) is a major pest of stored grain and grain products and a popular model species for a variety of ecological, evolutionary, and developmental biology studies. Development of a linkage map based on reproducible and highly polymorphic molecular markers would greatly facilitate research in these disciplines. We have developed a genetic linkage map using 269 amplified fragment length polymorphism (AFLP) markers. Ten previously known random amplified polymorphic DNA (RAPD) markers were used as anchor markers for linkage group assignment. The linkage map was constructed through genotyping two independent F(2) segregating populations with 48 AFLP primer combinations. Each primer combination generated an average of 4.6 AFLP markers eligible for linkage mapping. The length of the integrated map is 573 cM, giving an average marker resolution of 2.0 cM and an average physical distance per genetic distance of 350 kb/cM. A cluster of loci on linkage group 3 exhibited significant segregation distortion. We have also identified six X-linked and two Y-linked markers. Five mapped AFLP fragments were sequenced and converted to sequence-tagged site (STS) markers.     

RAPD-based genetic linkage maps of yellow passion fruit (Passiflora edulis Sims. f. flavicarpa Deg.).

A single cross between two clones of passion fruit (Passiflora edulis Sims. f. flavicarpa Deg., 2n = 18) was selected for genetic mapping. The mapping population was composed of 90 F1 plants derived from a cross between 'IAPAR 123' (female parent) and 'IAPAR 06' (male parent). A total of 380 RAPD primers were analyzed according to two-way pseudo-testcross mapping design. The linkage analysis was performed using Mapmaker version 3.0 with LOD 4.0 and a maximum recombination fraction (theta) of 0.30. Map distances were estimated using the Kosambi mapping function. Linkage maps were constructed with 269 loci (2.38 markers/primer), of which 255 segregated 1:1, corresponding to a heterozygous state in one parent and null in the other. The linkage map for 'IAPAR123' consisted of 135 markers. A total of nine linkage groups were assembled covering 727.7 cM, with an average distance of 11.20 cM between framework loci. The sizes of the linkage groups ranged from 56 to 144.6 cM. The linkage map for 'IAPAR 06' consisted of 96 markers, covering 783.5 cM. The average distance between framework loci was 12.2 cM. The length of the nine linkage groups ranged from 20.6 to 144.2 cM. On average, both maps provided 61% genome coverage. Twenty-four loci (8.9%) remained unlinked. Among their many applications, these maps are a starting point for the identification of quantitative trait loci for resistance to the main bacterial disease affecting passion fruit orchards in Brazil, caused by Xanthomonas campestris pv. passiflorae, because parental genotypes exhibit diverse responses to bacterial inoculation.     

Integration genetic linkage map construction and several potential QTLs mapping of Chinese shrimp (<Emphasis Type="Italic">Fenneropenaeus chinensis</Emphasis>) based on three types of molecular markers

In this study, totally 54 selected polymorphic SSR loci of Chinese shrimp (Fenneropenaeus chinensis), in addition with the previous linkage map of AFLP and RAPD markers, were used in consolidated linkage maps that composed of SSR, AFLP and RAPD markers of female and male construction, respectively. The female linkage map contained 236 segregating markers, which were linked in 44 linkage groups, and the genome coverage was 63.98%. The male linkage map contained 255 segregating markers, which were linked in 50 linkage groups, covering 63.40% of F. chinensis genome. There were nine economically important traits and phenotype characters of F. chinensis were involved in QTL mapping using multiple-QTL mapping strategy. Five potential QTLs associated with standard length (q-standardl-01), with cephalothorax length (q-cephal-01), with cephaloghorax width (q-cephaw-01), with the first segment length (q-firsel-01) and with anti-WSSV (q-antiWSSV-01) were detected on female LG1 and male LG44 respectively with LOD > 2.5. The QTL q-firsel-01 was at 73.603 cM of female LG1. Q-antiWSSV-01 was at 0 cM of male LG44. The variance explained of these five QTLs was from 19.7–33.5% and additive value was from −15.9175 to 7.3675. The closest markers to these QTL were all SSR, which suggested SSR marker was superior to AFLP and RAPD in the QTL mapping.