Detection of quantitative trait loci for wood strength in Cryptomeria japonica

2000 ◽  
Vol 30 (10) ◽  
pp. 1525-1533 ◽  
Author(s):  
Noritsugu Kuramoto ◽  
Teiji Kondo ◽  
Yoshitake Fujisawa ◽  
Ryogo Nakata ◽  
Eiji Hayashi ◽  
...  
Keyword(s):  
Cryptomeria Japonica ◽  
Rapd Markers ◽  
Forest Tree ◽  
Phenotypic Traits ◽  
Phenotypic Variance ◽  
Linkage Maps ◽  
Linkage Groups ◽  
Important Indicator ◽  
Wood Strength ◽  
Map Distance

Cryptomeria japonica D. Don (sugi) is one of the most important forest tree species in Japan. The progeny of a cross between the cultivars Iwao-sugi and Boka-sugi were analyzed using RAPD markers, with the pseudo-test-cross strategy, to construct linkage maps of the parental cultivars. A total of 355 segregating loci were detected among 72 offspring: 200 and 155 markers being distributed in Iwao-sugi and Boka-sugi, respectively. In Iwao-sugi, 119 markers with confirmed map positions were assigned to 21 linkage groups covering 1756.4 cM. In Boka-sugi, 84 markers with confirmed map positions were assigned to 14 linkage groups covering 1111.9 cM. The framework map distance in Iwao-sugi and Boka-sugi provides about 62 and 40% coverage, respectively, of the total genome, estimated to be approximately 2800 cM in length. Using genetic linkage maps constructed in this study, 15 QTLs were detected that are associated with the modulus of elasticity (MOE), an important indicator of wood strength. The QTLs for MOE explained about 45% of its total phenotypic variance. Some QTLs associated with different phenotypic traits were located on the same linkage groups. Some of the QTLs for MOE measured by two different methods (the hanging method and the tapping method) were located independently on the different linkage groups.

Two genetic linkage maps of mungbean using RFLP and RAPD markers

2000 ◽  
Vol 51 (4) ◽  
pp. 415 ◽  
Author(s):  
C. J. Lambrides ◽  
R. J. Lawn ◽  
I. D. Godwin ◽  
J. Manners ◽  
B. C. Imrie
Keyword(s):  
Linkage Map ◽  
Segregation Distortion ◽  
Recombinant Inbred ◽  
Genetic Linkage ◽  
Rapd Markers ◽  
Rflp Markers ◽  
Linkage Maps ◽  
Linkage Groups ◽  
Genetic Linkage Maps ◽  
Map Distance

Two genetic linkage maps of mungbean derived from the cross Berken ACC 41 are reported. The F2 map constructed from 67 individuals consisted of 110 markers (52 RFLP and 56 RAPD) that grouped into 12 linkage groups. The linked markers spanned a total map distance of 758.3 cM. A recombinant inbred (RI) population derived from the 67 F2 individuals was used for the generation of an additional linkage map. The RI map, composed entirely of RAPD markers, consisted of 115 markers in 12 linkage groups. The linked markers spanned a total map distance of 691.7 cM. Using a framework set of RFLP markers, the F2 map was compared with another F2 mungbean map constructed in Minnesota. In general, the order of these markers was consistent between maps. Segregation distortion was observed for some markers. 14.5% (16/110) of mapped F2 markers and 24% (28/115) of mapped RI markers segregated with distorted ratios. Segregation distortion occurred in each successive generation after the F2 . The regions of distortion identified in the Australian maps did not coincide with regions of the Minnesota map.

Genetic Linkage Maps of the Guppy ( Poecilia reticulata ): Assignment of RAPD Markers to Multipoint Linkage Groups

2003 ◽  
Vol 5 (3) ◽  
pp. 279-293 ◽  
Author(s):  
Gideon Khoo ◽  
Meng Huat Lim ◽  
Haridas Suresh ◽  
Damien K. Y. Gan ◽  
Kok Fang Lim ◽  
...  
Keyword(s):  
Genetic Linkage ◽  
Rapd Markers ◽  
Poecilia Reticulata ◽  
Linkage Maps ◽  
Linkage Groups ◽  
Multipoint Linkage ◽  
Genetic Linkage Maps

A genetic linkage map for Stevia rebaudiana

Genome ◽  
1999 ◽  
Vol 42 (4) ◽  
pp. 657-661 ◽  
Author(s):  
Y Yao ◽  
M Ban ◽  
J Brandle
Keyword(s):  
Linkage Map ◽  
Genetic Linkage ◽  
Rapd Markers ◽  
Genetic Linkage Map ◽  
Average Distance ◽  
Stevia Rebaudiana ◽  
Linkage Groups ◽  
Genome Map ◽  
High Level ◽  
Map Distance

To lay a foundation for molecular breeding efforts, the first genetic linkage map for Stevia rebaudiana has been constructed using segregation data from a pseudo test-cross F1 population. A total of 183 randomly amplified polymorphic DNA (RAPD) markers were analysed and assembled into 21 linkage groups covering a total distance of 1389 cM, with an average distance between markers of of 7.6 cM. The 11 largest linkage groups consisted of 4-19 loci, ranged in length from 56 to 174 cM, and accounted for 75% of the total map distance. Fifteen RAPD loci were found to be unlinked. From the 521 primers showing amplification products, 185 (35.5%) produced a total of 293 polymorphic fragments, indicating a high level of genetic diversity in stevia. Most of the RAPD markers in stevia segregated in normal Mendelian fashion.Key words: stevia, open-pollinated, genome map, RAPD.

scholarly journals Autopolyploidy versus Allopolyploidy and Low-density Randomly Amplified Polymorphic DNA Linkage Maps of Sweetpotato

1997 ◽  
Vol 122 (6) ◽  
pp. 822-828 ◽  
Author(s):  
Kittipat Ukoskit ◽  
Paul G. Thompson
Keyword(s):  
Genetic Analysis ◽  
Genome Size ◽  
Rapd Markers ◽  
Rapd Marker ◽  
Chromosome Length ◽  
Low Density ◽  
Linkage Maps ◽  
Randomly Amplified Polymorphic Dna ◽  
Linkage Groups ◽  
Genome Coverage

Low-density randomly amplified polymorphic DNA (RAPD) markers of sweetpotato [Ipomoea batatus (L.) Lam.; 2n = 6x = 90] were constructed from 76 pseudotestcross progenies obtained from `Vardaman' × `Regal'. Of 460 primers, 84 generating 196 well-resolved repeatable markers were selected for genetic analysis. `Vardaman' and `Regal' testcross progenies were analyzed for segregation and linkages of RAPD markers. Type of polyploidy, autopolyploidy, or allopolyploidy is uncertain in sweetpotato and was examined in this study using the ratio of nonsimplex to simplex RAPD markers and the ratio of simplex RAPD marker pairs linked in repulsion to coupling. Both measures indicated autopolyploidy. Low-density RAPD linkage maps of `Vardaman' and `Regal' were constructed from simplex RAPD marker linkage analysis. Duplex and triplex markers were then mapped manually into the simplex marker map. Homologous linkage groups were identified using nonsimplex RAPD markers and three homologous groups were found in each of the parent maps. Use of nonsimplex markers increased mapping efficiency. The `Vardaman' map had a predicted coverage of 10.5% at a 25-cM interval of the genome size of 5024 cM. In `Regal', genome coverage was estimated to be 5.6% at a 25-cM interval of the genome size of 6560 cM. Therefore, average chromosome length was ≈56 to 73 cM.

scholarly journals Genetic linkage maps of Eucalyptus grandis and Eucalyptus urophylla using a pseudo-testcross: mapping strategy and RAPD markers.

Genetics ◽  
1994 ◽  
Vol 137 (4) ◽  
pp. 1121-1137 ◽  
Author(s):  
D Grattapaglia ◽  
R Sederoff
Keyword(s):  
Genetic Linkage ◽  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Eucalyptus Grandis ◽  
Single Individual ◽  
Linkage Maps ◽  
Eucalyptus Urophylla ◽  
Linkage Groups ◽  
Mapping Strategy ◽  
Genetic Linkage Maps

Abstract We have used a "two-way pseudo-testcross" mapping strategy in combination with the random amplified polymorphic 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 F1 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, theta = 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 > or = 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 organisms. 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 genetic linkage map of crested wheatgrass based on AFLP and RAPD markers

Genome ◽  
2012 ◽  
Vol 55 (4) ◽  
pp. 327-335 ◽  
Author(s):  
Xiaoxia Yu ◽  
Xiaolei Li ◽  
Yanhong Ma ◽  
Zhuo Yu ◽  
Zaozhe Li
Keyword(s):  
Molecular Markers ◽  
Linkage Map ◽  
Genetic Linkage ◽  
Rapd Markers ◽  
Genetic Linkage Map ◽  
Mapping Population ◽  
Gene Localization ◽  
Linkage Groups ◽  
Crested Wheatgrass ◽  
Map Distance

Using a population of 105 interspecific F2 hybrids derived from a cross between Agropyron mongolicum Keng and Agropyron cristatum (L.) Gaertn. ‘Fairway’ as a mapping population, a genetic linkage map of crested wheatgrass was constructed based on AFLP and RAPD molecular markers. A total of 175 markers, including 152 AFLP and 23 RAPD markers, were ordered in seven linkage groups. The map distance was 416 cM, with a mean distance of 2.47 cM between markers. The number of markers ranged from 13 to 46 in each linkage group and the length of groups ranged from 18 to 104 cM. The research found that 30 out of 175 molecular markers showed segregation distortion, accounting for 17% of all markers. This is the first genetic linkage map of crested wheatgrass. This map will facilitate gene localization, cloning, and molecular marker-assisted selection in the future.

scholarly journals Genetic linkage maps of 'Pêra' sweet orange and 'Cravo' mandarin with RAPD markers

2004 ◽  
Vol 39 (2) ◽  
pp. 159-165 ◽  
Author(s):  
Roberto Pedroso de Oliveira ◽  
Mariângela Cristofani ◽  
Marcos Antônio Machado
Keyword(s):  
Linkage Map ◽  
Segregation Distortion ◽  
Rapd Markers ◽  
Sweet Orange ◽  
Citrus Canker ◽  
F1 Hybrids ◽  
Citrus Reticulata ◽  
Linkage Maps ◽  
Linkage Groups ◽  
Genetic Linkage Maps

The objective of this work was to construct linkage maps of 'Pêra' sweet orange [Citrus sinensis (L.) Osbeck] and 'Cravo' mandarin (Citrus reticulata Blanco) using RAPD markers and the pseudo-testcross strategy. The parents were chosen according to the resistance/susceptibility to citrus variegate chlorosis (CVC). The segregation of 176 markers was analyzed in 94 progeny of F1 hybrids, which were obtained from controlled crossings. The linkage map of 'Pêra' sweet orange had 117 markers defined by 12 linkage groups, which spanned 612.1 cM. Only six markers could not be linked to the linkage group and 48.7% of the markers showed segregation distortion. The linkage map of 'Cravo' mandarin had 51 markers defined by 12 linkage groups, which spanned 353.3 cM. Only two markers did not link to the groups and 15.7% showed segregation distortion. The construction of linkage maps is relevant to future mapping studies of the inheritance of CVC, citrus canker and leprosis.

Genetic mapping of hop (Humulus lupulus L.) applied to the detection of QTLs for alpha-acid content

Genome ◽  
2006 ◽  
Vol 49 (5) ◽  
pp. 485-494 ◽  
Author(s):  
Andreja Cerenak ◽  
Zlatko Satovic ◽  
Branka Javornik
Keyword(s):  
Acid Content ◽  
Acid Synthesis ◽  
Humulus Lupulus ◽  
Genetic Maps ◽  
Phenotypic Variance ◽  
Linkage Groups ◽  
Humulus Lupulus L ◽  
Bitter Acid ◽  
The Stability ◽  
Map Distance

The map locations and effects of quantitative trait loci (QTLs) were estimated for alpha-acid content in hop (Humulus lupulus L.) using amplified fragment length polymorphism (AFLP) and microsatellite marker (simple sequence repeat (SSR)) genetic linkage maps constructed from a double pseudotestcross. The mapping population consisted of 111 progeny from a cross between the German hop cultivar 'Magnum', which exhibits high levels of alpha-acids, and a wild Slovene male hop, 2/1. The progeny segregated quantitatively for alpha-acid content determined in 2002, 2003, and 2004. The maternal map consisted of 96 markers mapped on 14 linkage groups defining 661.90 cM of total map distance. The paternal map included 70 markers assigned to 12 linkage groups covering 445.90 cM of hop genome. QTL analysis indicated 4 putative QTLs (alpha1, alpha2, alpha3, and alpha4) on linkage groups (LGs) 03, 01, 09, and 03 of the female map, respectively. QTLs explained 11.9%–24.8% of the phenotypic variance. The most promising QTL to be used in marker-assisted selection is alpha2, the peak of which colocated exactly with the AFLP marker. Three chalcone synthase-like genes (chs2, chs3, and chs4) involved in hop bitter acid synthesis mapped together on LG04 of the female map. Saturation of the maps, particularly the putative QTL regions, will be carried out using SSR markers, and the stability of the QTLs will be tested in the coming years.Key words: Humulus lupulus L., genetic maps, alpha-acid content, QTLs.

scholarly journals Genome-Wide Variation in DNA Methylation Predicts Variation in Leaf Traits in an Ecosystem-Foundational Oak Species

Forests ◽  
2021 ◽  
Vol 12 (5) ◽  
pp. 569
Author(s):  
Luke Browne ◽  
Brandon MacDonald ◽  
Sorel Fitz-Gibbon ◽  
Jessica W. Wright ◽  
Victoria L. Sork
Keyword(s):  
Dna Methylation ◽  
Phenotypic Variation ◽  
Leaf Traits ◽  
Forest Tree ◽  
Genomic Variation ◽  
Causal Mechanism ◽  
Phenotypic Traits ◽  
Phenotypic Variance ◽  
Reduced Representation ◽  
Valley Oak

Epigenetic modifications such as DNA methylation are a potential mechanism for trees to respond to changing environments. However, it remains controversial the extent to which DNA methylation impacts ecologically important traits that influence fitness. In this study, we used reduced-representation bisulfite sequencing to associate genomic and epigenomic variation with seven phenotypic traits related to growth, leaf function, and disease susceptibility in 160 valley oak (Quercus lobata) saplings planted across two common gardens in California. We found that DNA methylation was associated with a significant fraction of phenotypic variance in plant height, leaf lobedness, powdery mildew infection, and trichome density. Two of the seven traits were significantly associated with DNA methylation in the CG context, three traits were significantly associated with CHG methylation, and two traits were significantly associated with CHH methylation. Notably, controlling for genomic variation in SNPs generally reduced the amount of trait variation explained by DNA methylation. Our results suggest that DNA methylation may serve as a useful biomarker to predict phenotypic variation in trees, though it remains unclear the degree to which DNA methylation is a causal mechanism driving phenotypic variation in forest tree species.

scholarly journals A Composite Genetic Map of the Parasitoid Wasp Trichogramma brassicae Based on RAPD Markers

Genetics ◽  
1998 ◽  
Vol 150 (1) ◽  
pp. 275-282 ◽  
Author(s):  
Valérie Laurent ◽  
Eric Wajnberg ◽  
Brigitte Mangin ◽  
Thomas Schiex ◽  
Christine Gaspin ◽  
...  
Keyword(s):  
Dna Markers ◽  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Parasitoid Wasp ◽  
Linkage Maps ◽  
Linkage Groups ◽  
Trichogramma Brassicae ◽  
Haploid Male ◽  
The Mean ◽  
Mapping Populations

Abstract Three linkage maps of the genome of the microhymenopteran Trichogramma brassicae were constructed from the analysis of segregation of random amplified polymorphic DNA markers in three F2 populations. These populations were composed of the haploid male progeny of several virgin F1 females, which resulted from the breeding of four parental lines that were nearly fixed for different random amplified polymorphic DNA markers and that were polymorphic for longevity and fecundity characters. As the order of markers common to the three mapping populations was found to be well conserved, a composite linkage map was constructed. Eighty-four markers were organized into five linkage groups and two pairs. The mean interval between two markers was 17.7 cM, and the map spanned 1330 cM.

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