501
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502
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LOD significance thresholds for QTL analysis in experimental populations of diploid species. Heredity (Edinb) 1999; 83 (Pt 5):613-24. [PMID: 10620035 DOI: 10.1038/sj.hdy.6886230] [Citation(s) in RCA: 126] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Linkage analysis with molecular genetic markers is a very powerful tool in the biological research of quantitative traits. The lack of an easy way to know what areas of the genome can be designated as statistically significant for containing a gene affecting the quantitative trait of interest hampers the important prediction of the rate of false positives. In this paper four tables, obtained by large-scale simulations, are presented that can be used with a simple formula to get the false-positives rate for analyses of the standard types of experimental populations with diploid species with any size of genome. A new definition of the term 'suggestive linkage' is proposed that allows a more objective comparison of results across species.
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503
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Abstract
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 F1population. 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.
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504
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Abstract
Two framework linkage maps were constructed for the genome of the dioecious wild yam species Dioscorea tokoro. The pseudo-testcross strategy was employed, using 271 amplified fragment length polymorphisms (AFLPs), five sequence-tagged microsatellite sites, one isozyme, and one morphological marker. For the two parents DT7 and DT5 used in the cross, 13 and 12 linkage groups, respectively, were identified. The total map lengths were 669 and 613 cM, respectively, for DT7 and DT5, which cover more than 75% of the D. tokoro genome. Ten AFLP markers heterozygous only in the male parent showed tight linkages with the sex of its progeny, which suggests that male is the heterogametic sex (XY) and the female is the homogametic sex (XX).Key words: Dioscorea tokoro, yam, linkage map, AFLP, sex determination.
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505
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Abstract
Mapping strategies based on a half- or full-sib family design have been developed to map quantitative trait loci (QTL) for outcrossing species. However, these strategies are dependent on controlled crosses where marker-allelic frequency and linkage disequilibrium between the marker and QTL may limit their application. In this article, a maximum-likelihood method is developed to map QTL segregating in an open-pollinated progeny population using dominant markers derived from haploid tissues from single meiotic events. Results from the haploid-based mapping strategy are not influenced by the allelic frequencies of markers and their linkage disequilibria with QTL, because the probabilities of QTL genotypes conditional on marker genotypes of haploid tissues are independent of these population parameters. Parameter estimation and hypothesis testing are implemented via expectation/conditional maximization algorithm. Parameters estimated include the additive effect, the dominant effect, the population mean, the chromosomal location of the QTL in the interval, and the residual variance within the QTL genotypes, plus two population parameters, outcrossing rate and QTL-allelic frequency. Simulation experiments show that the accuracy and power of parameter estimates are affected by the magnitude of QTL effects, heritability levels of a trait, and sample sizes used. The application and limitation of the method are discussed.
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Affiliation(s)
- R L Wu
- Forest Biotechnology Group, Department of Forestry, North Carolina State University, Raleigh, North Carolina 27695-8008, USA.
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506
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Abstract
A new statistical method for mapping quantitative trait loci (QTL), called multiple interval mapping (MIM), is presented. It uses multiple marker intervals simultaneously to fit multiple putative QTL directly in the model for mapping QTL. The MIM model is based on Cockerham's model for interpreting genetic parameters and the method of maximum likelihood for estimating genetic parameters. With the MIM approach, the precision and power of QTL mapping could be improved. Also, epistasis between QTL, genotypic values of individuals, and heritabilities of quantitative traits can be readily estimated and analyzed. Using the MIM model, a stepwise selection procedure with likelihood ratio test statistic as a criterion is proposed to identify QTL. This MIM method was applied to a mapping data set of radiata pine on three traits: brown cone number, tree diameter, and branch quality scores. Based on the MIM result, seven, six, and five QTL were detected for the three traits, respectively. The detected QTL individually contributed from approximately 1 to 27% of the total genetic variation. Significant epistasis between four pairs of QTL in two traits was detected, and the four pairs of QTL contributed approximately 10.38 and 14.14% of the total genetic variation. The asymptotic variances of QTL positions and effects were also provided to construct the confidence intervals. The estimated heritabilities were 0.5606, 0.5226, and 0. 3630 for the three traits, respectively. With the estimated QTL effects and positions, the best strategy of marker-assisted selection for trait improvement for a specific purpose and requirement can be explored. The MIM FORTRAN program is available on the worldwide web (http://www.stat.sinica.edu.tw/chkao/).
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Affiliation(s)
- C H Kao
- Institute of Statistical Science, Academia Sinica, Taipei 11529, Taiwan, Republic of China.
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507
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Properties of AFLP markers in inheritance and genetic diversity studies of pinus sylvestris L. Heredity (Edinb) 1999; 82 (Pt 3):252-60. [PMID: 10336699 DOI: 10.1038/sj.hdy.6884720] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
We analysed the properties of AFLP markers in Pinus sylvestris. Using primers with three selective nucleotides, the AFLP protocol produced large numbers of amplified bands and could only be used with a restricted number of primer combinations. Replacement of the EcoRI +3 primer by an EcoRI +4 primer halved the number of bands, facilitating analysis. The inheritance of all but about 8.4% of the amplified bands has been confirmed to be Mendelian. We compared band patterns among selected P. sylvestris trees from northern Sweden, two Asian species of Pinus and one species from the genus Picea. The dendrogram obtained was generally concordant with the taxonomic data, although the genetic similarity values between trees from different genera did not entirely follow accepted inter- and intraspecific relationships. This deviation was less pronounced using primer combinations that generated fewer bands. More than 69.1% of the bands that were polymorphic in two P. sylvestris trees or 29 of their F1 progeny were in a pseudo-testcross configuration and thus were useful for the development of a linkage map for each parent. These markers have been analysed in four other crosses, and 83% of the bands could be mapped in at least one cross. Depending on the level of heterozygosity of the parents, the efficiency of such mapping will vary, but the AFLP technique appears to be a powerful way to generate, very quickly, large numbers of markers that are useful for constructing and comparing linkage maps.
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508
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Nikaido A, Yoshimaru H, Tsumura Y, Suyama Y, Murai M, Nagasaka K. Segregation distortion for AFLP markers in Cryptomeria japonica. Genes Genet Syst 1999. [DOI: 10.1266/ggs.74.55] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Affiliation(s)
- Asako Nikaido
- Bio-resources Technology Division, Forestry and Forest Products Research Institute
- Bio-oriented Technology Research Advancement Institution
| | - Hiroshi Yoshimaru
- Bio-resources Technology Division, Forestry and Forest Products Research Institute
| | - Yoshihiko Tsumura
- Bio-resources Technology Division, Forestry and Forest Products Research Institute
| | | | - Masahumi Murai
- Bio-resources Technology Division, Forestry and Forest Products Research Institute
| | - Kazutoshi Nagasaka
- Bio-resources Technology Division, Forestry and Forest Products Research Institute
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509
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Yi HY, Rufty RC, Wernsman EA, Conkling MC. Mapping the Root-Knot Nematode Resistance Gene (Rk) in Tobacco with RAPD Markers. PLANT DISEASE 1998; 82:1319-1322. [PMID: 30845463 DOI: 10.1094/pdis.1998.82.12.1319] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Random amplified polymorphic DNA (RAPD) analysis was conducted to map the Rk gene in tobacco which conditions resistance to races 1 and 3 of the root-knot nematode, Meloidogyne incognita. Resistant burley tobacco genotype NC 528, containing the Rk gene, and the susceptible cultivar Ky 14 were screened with 1,500 random decamers. A low rate of genetic polymor-phism (<10%) was detected among these lines. Two populations (F1 and F3) of maternally de-rived doubled haploid (MDH) lines of burley tobacco, developed from the cross NC 528 × Ky 14, were used to map the Rk gene. NC 528, Ky 14, three Rk-resistant (Rk-R) DNA bulks, andthree Rk-susceptible (Rk-S) bulks generated from F1-derived MDH individuals were screenedwith the primers that amplified bands polymorphic between Rk-R and Rk-S lines. A total of 67 F1MDH lines and 59 F3MDH lines were screened with the primers that amplified bands polymorphic between Rk-R bulks and Rk-S bulks to confirm linkage between candidate markers and the Rk gene. Sixteen RAPD markers were positioned at six loci in a map 24.1 centimorgans long. Six RAPD markers, including one identified in the F3MDH population, were mapped at the Rk locus.
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Affiliation(s)
- H-Y Yi
- Department of Crop Science
| | | | | | - M C Conkling
- Department of Genetics, North Carolina State University, Raleigh 27695-7620
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510
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Laurent V, Wajnberg E, Mangin B, Schiex T, Gaspin C, Vanlerberghe-Masutti F. A composite genetic map of the parasitoid wasp Trichogramma brassicae based on RAPD markers. Genetics 1998; 150:275-82. [PMID: 9725846 PMCID: PMC1460326 DOI: 10.1093/genetics/150.1.275] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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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Affiliation(s)
- V Laurent
- Laboratoire de Biologie des Invertébrés, Biologie des Populations, INRA, 06606 Antibes, France
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511
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Lefèvre F, Goué-Mourier MC, Faivre-Rampant P, Villar M. A Single Gene Cluster Controls Incompatibility and Partial Resistance to Various Melampsora larici-populina Races in Hybrid Poplars. PHYTOPATHOLOGY 1998; 88:156-163. [PMID: 18944985 DOI: 10.1094/phyto.1998.88.2.156] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
ABSTRACT Complete cosegregation for race-specific incompatibility with three Melampsora larici-populina rust races was observed in five F(1) hybrid progenies of Populus, with different patterns among the various progenies. A single gene cluster could explain these segregations: one locus with multiple alleles or two tightly linked loci controlling complete resistance to E1 and E3, and two tightly linked loci for E2. The random amplified polymorphic DNA marker OPM03/04_480 was linked to that cluster in all families (<1 cM). This marker accounted for more than 70% of the genetic variation for field resistance in each family (heritability approximately 0.40). The same marker accounted for up to 64% of the clonal variation for growth in the nursery under natural inoculum pressure; the weak tolerance to rust of F(1) interspecific hybrids was attributed to a genetic background effect. Partial resistance was split into epidemiological components (heritability ranged from 0.35 to 0.87). Genotypic correlations among resistance traits for the different races were high (0.73 to 0.90). However, correlations among different resistance components for a single race were not all significant. A major quantitative trait locus for all components of partial resistance to E2 was associated to the cluster controlling incompatibility to E1 and E3 and marked by OPM03/04_480 (R(2)from 48 to 68%).
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512
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Nilsson NO, Halldén C, Hansen M, Hjerdin A, Säll T. Comparing the distribution of RAPD and RFLP markers in a high density linkage map of sugar beet. Genome 1997; 40:644-51. [DOI: 10.1139/g97-085] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The distribution of RAPD markers was compared with that of RFLP markers in a high density linkage map of sugar beet. The same mapping population of 161 F2individuals was used to generate all the marker data. The total map comprises 160 RAPD and 248 RFLP markers covering 508 cM. Both the RAPD and the RFLP markers show a high degree of clustering over the nine linkage groups. The pattern is compatible with a strong distal localization of recombination in the sugar beet. It leads generally to one major cluster of markers in the centre of each linkage group. In regions of high marker density, dominant RAPD markers present in either linkage phase and codominant RFLP markers are subclustered relative to each other. This phenomenon is shown to be attributable to: (i) effects of the mapping procedure when dominant and codominant data are combined, (ii) effects of the mapping procedure when dominant data in both linkage phases are combined, and (iii) genuine differences in the way RAPD and RFLP markers are recruited.Key words: sugar beet, linkage map, RAPD, RFLP, clustering.
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513
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MacKay JJ, O'Malley DM, Presnell T, Booker FL, Campbell MM, Whetten RW, Sederoff RR. Inheritance, gene expression, and lignin characterization in a mutant pine deficient in cinnamyl alcohol dehydrogenase. Proc Natl Acad Sci U S A 1997; 94:8255-60. [PMID: 9223348 PMCID: PMC21590 DOI: 10.1073/pnas.94.15.8255] [Citation(s) in RCA: 148] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
We have discovered a mutant loblolly pine (Pinus taeda L.) in which expression of the gene encoding cinnamyl alcohol dehydrogenase (CAD; EC 1.1.1.195) is severely reduced. The products of CAD, cinnamyl alcohols, are the precursors of lignin, a major cell wall polymer of plant vascular tissues. Lignin composition in this mutant shows dramatic modifications, including increased incorporation of the substrate of CAD (coniferaldehyde), indicating that CAD may modulate lignin composition in pine. The recessive cad-n1 allele, which causes this phenotype, was discovered in a tree heterozygous for this mutant allele. It is inherited as a simple Mendelian locus that maps to the same genomic region as the cad locus. In mutant plants, CAD activity and abundance of cad RNA transcript are low, and free CAD substrate accumulates to a high level. The wood of the mutant is brown, whereas the wood in wild types is nearly white. The wood phenotype resembles that of brown midrib (bm) mutants and some transgenic plants in which xylem is red-brown due to a reduction in CAD activity. However, unlike transgenics with reduced CAD, the pine mutant has decreased lignin content. Wood in which the composition of lignin varies beyond previous expectations still provides vascular function and mechanical support.
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Affiliation(s)
- J J MacKay
- Department of Forestry, North Carolina State University, Raleigh, NC 27695, USA
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514
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Detection of genomic regions differentiating two closely related oak species Quercus petraea (Matt.) Liebl. and Quercus robur L. Heredity (Edinb) 1997. [DOI: 10.1038/hdy.1997.67] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
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515
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Machado LDOR, de Andrade GM, Barrueto Cid LP, Penchel RM, Brasileiro ACM. Agrobacterium strain specificity and shooty tumour formation in eucalypt (Eucalyptus grandis ×E. urophylla). PLANT CELL REPORTS 1997; 16:299-303. [PMID: 30727667 DOI: 10.1007/bf01088285] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/1995] [Revised: 07/02/1996] [Indexed: 06/09/2023]
Abstract
To develop a successful protocol forAgrobacterium-mediated transformation in plants it is essential to determine the most efficient bacterial strain/plant genotype interaction. In the present work, we evaluated the susceptibility ofEucalyptus grandis ×E. urophylla to fiveAgrobacterium rhizogenes and twelveA. tumefaciens wildtype strains. The results showed different degrees of virulence, according to the strain tested, indicating that transformation of this eucalypt hybrid by Agrobacterium-derived vectors is possible. All developed tumours showed an autonomous growth when transferred to a hormone-free medium. Some of these tumours formed shoots spontaneously, with a normal phenotype. Polymerase Chain Reaction (PCR) and Southern blot analyses were performed to confirm the absence of the oncogenic T-DNA in plants derived from these shooty tumours.
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Affiliation(s)
| | - Gisele M de Andrade
- Área de Biologia Celular, CENARGEN/EMBRAPA. C.P. 02372, 70.849-970, Brasilia, DF, Brazil
| | | | - Ricardo M Penchel
- Aracruz Celulose, S. A. Rua Prof. Lobo, 1128, 29.190-000, Aracruz, ES, Brazil
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516
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517
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Dean JF, LaFayette PR, Eriksson KE, Merkle SA. Forest tree biotechnology. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 1997; 57:1-44. [PMID: 9204750 DOI: 10.1007/bfb0102071] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The forest products industry has traditionally viewed trees as merely a raw, and more or less immutable, natural resource. However, unlike such inanimate resources as metallic ores, trees have the potential to be modified genetically, essentially transmuting lead into gold. Increasingly, modern alchemists are applying the tools of biotechnology in efforts to reduce the biological constraints on forest productivity. Several new methodologies being used to address problems in forest biology are described with respect to their potential impact on forest tree improvement. In addition to addressing problems inherent to the current use of trees for production of pulp and paper or solid wood products, genetic manipulation of trees brings with it the potential to create new industries based on the novel characteristics of transgenic trees, e.g. trees containing transgenes to detoxify specific pollutants could be used in the remediation of sites contaminated with hazardous wastes. Efforts to modify trees through biotechnology are in their infancy, and this review seeks to outline the underpinnings of what will undoubtedly be an area of increased emphasis in the next millennium.
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Affiliation(s)
- J F Dean
- Daniel B. Warnell School of Forest Resources, University of Georgia, Athens 30602, USA
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518
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Verhaegen D, Plomion C. Genetic mapping inEucalyptus urophyllaandEucalyptus grandisusing RAPD markers. Genome 1996; 39:1051-61. [DOI: 10.1139/g96-132] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Two single-tree linkage maps were constructed for Eucalyptus urophylla and Eucalyptus grandis, based on the segregation of 480 random amplified polymorphic DNA (RAPD) markers in a F1interspecific progeny. A mixture of three types of single-locus segregations were observed: 244 1:1 female, 211 1:1 male, and 25 markers common to both, segregating 3:1. Markers segregating in the 1:1 ratio (testcross loci) were used to establish separate maternal and paternal maps, while markers segregating in the 3:1 ratio were used to identify homology between linkage groups of the two species maps. An average of 2.8 polymorphic loci were mapped for each arbitrary decamer primer used in the polymerase chain reaction. The mean interval size beween framework markers on the maps was 14 cM. The maps comprised 269 markers covering 1331 cM and 236 markers covering 1415 cM, in 11 linkage groups, for E. urophylla (2n = 2x = 22) and E. grandis (2n = 2x = 22), respectively. A comparative mapping analysis with two other E. urophylla and E. grandis linkage maps showed that RAPDs could be reliable markers for establishing a consensus species map. RAPD markers were automatically and quantitatively scored with an imaging analyzer. They were classified into four categories based on their optical density. A fragment intensity threshold is proposed to optimize the selection of reliable RAPD markers for future mapping experiments. Key words : genetic linkage map, Eucalyptus urophylla, Eucalyptus grandis, random amplified polymorphic DNA, RAPD, automated data collection.
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519
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Plomion C, Liu BH, O'Malley DM. Genetic analysis using trans-dominant linked markers in an F2 family. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 1996; 93:1083-1089. [PMID: 24162485 DOI: 10.1007/bf00230129] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/1996] [Accepted: 08/02/1996] [Indexed: 06/02/2023]
Abstract
Trans-dominant linked markers pairs (trans referring to the repulsion linkage phase) provide a model for inferring the F2 progeny genotype based upon both the conditional probabilities of F2 genotypes, given the F2 phenotype, and prior information on marker arrangement. Prior information of marker arrangement can be readily obtained from a linkage analysis performed on marker segregation data in a family resulting by crossing the F1 individual to a "tester" parent or else can be obtained directly from the gametes of the F1, or from recombinant inbred lines. We showed that a trans-dominant linked marker (TDLM) pair can be recoded as a "co-dominant megalocus" when the recombination fraction, r1, for apair of TDLMs is less than 0.05. We obtained a maximum-likelihood estimator (MLE) of the recombination frequency, r2, between a TDLM pair and a co-dominant marker in an F2 family using the EM algorithm. The MLE was biased. Mean bias increased as r1 and r2 increased, and decreased as sample size increased. The information content for r2 was compared to the information content of dominant and co-dominant markers segregating in an F2 family. It was almost identical with two co-dominant markers when r1≤0.01 and r2≥0.05. For larger values of r1, (0.05≤r1≤0.15) a TDLM pair provided 75%-66% of the information content of two co-dominant markers. Although dominant markers can be converted to co-dominant markers by a laborious process of cloning, sequencing, and PCR, TDLM pairs could easily substitute for co-dominant markers in order to detect quantitative trait loci (QTLs) and estimate gene action in an F2 family.
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Affiliation(s)
- C Plomion
- INRA, Laboratoire de Génétique et Amélioration des Arbres Forestiers, BP45, F-33610, Cestas, France
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520
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Grattapaglia D, Bertolucci FL, Penchel R, Sederoff RR. Genetic mapping of quantitative trait loci controlling growth and wood quality traits in Eucalyptus grandis using a maternal half-sib family and RAPD markers. Genetics 1996; 144:1205-14. [PMID: 8913761 PMCID: PMC1207612 DOI: 10.1093/genetics/144.3.1205] [Citation(s) in RCA: 104] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Quantitative trait loci (QTL) mapping of forest productivity traits was performed using an open pollinated half-sib family of Eucalyptus grandis. For volume growth, a sequential QTL mapping approach was applied using bulk segregant analysis (BSA), selective genotyping (SG) and cosegregation analysis (CSA). Despite the low heritability of this trait and the heterogeneous genetic background employed for mapping, BSA detected one putative QTL and SG two out of the three later found by CSA. The three putative QTL for volume growth were found to control 13.7% of the phenotypic variation, corresponding to an estimated 43.7% of the genetic variation. For wood specific gravity five QTL were identified controlling 24.7% of the phenotypic variation corresponding to 49% of the genetic variation. Overlapping QTL for CBH, WSG and percentage dry weight of bark were observed. A significant case of digenic epistasis was found, involving unlinked QTL for volume. Our results demonstrate the applicability of the within half-sib design for QTL mapping in forest trees and indicate the existence of major genes involved in the expression of economically important traits related to forest productivity in Eucalyptus grandis. These findings have important implications for marker-assisted tree breeding.
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Affiliation(s)
- D Grattapaglia
- Plant Genetics Laboratory, Centro Nacional de Pesquisa de Recursos Genéticos e Biotecnologia, Empresa Brasileira de Pesquisa Agropecuária, Brazil.
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521
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Garcia GM, Stalker HT, Shroeder E, Kochert G. Identification of RAPD, SCAR, and RFLP markers tightly linked to nematode resistance genes introgressed from Arachis cardenasii into Arachis hypogaea. Genome 1996; 39:836-45. [PMID: 8890516 DOI: 10.1139/g96-106] [Citation(s) in RCA: 109] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Two dominant genes conditioning resistance to the root-knot nematode Meloidogyne arenaria were identified in a segregating F2 population derived from the cross of 4x (Arachis hypogaea x Arachis cardenasii)-GA 6 and PI 261942. Mae is proposed as the designation for the dominant gene restricting egg number and Mag is proposed as the designation for the dominant gene restricting galling. The high levels of resistance in GA 6 were introgressed from A. cardenasii and, therefore, a search to identify A. cardenasii specific RAPD markers that are tightly linked to these resistance genes was conducted utilizing bulked segregant analysis. One RAPD marker (Z3/265) was linked at 10 +/- 2.5 (SE) and 14 +/- 2.9 cM from Mag and Mae, respectively. The marker was mapped to linkage group 1 at 5 cM from Xuga.cr239 in the backcross map in an area where introgression from A. cardenasii had previously been reported. This fragment was cloned and used to generate a pair of primers that specifically amplified this locus (sequence characterized amplified region, SCAR) and as a RFLP probe. Their close linkage with the resistance genes will be useful in marker-based selection while transferring nematode resistance from introgression lines into elite breeding lines and cultivars. The Z3/265 marker associated with the genes Mae or Mag was not found in other highly resistant Arachis species (Arachis batizocoi or Arachis stenosperma), in progenies of interspecific crosses with A. cardenasii that were moderately resistant, or in the resistant A. hypogaea lines PI 259634 and PI 259572. These represent the first molecular markers linked with a resistant gene in peanut and the first report of two physiological responses to nematode attack associated with two genetic factors.
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Affiliation(s)
- G M Garcia
- Department of Crop Science, North Carolina State University, Raleigh, 27695-7629, USA
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522
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Dirlewanger E, Pascal T, Zuger C, Kervella J. Analysis of molecular markers associated with powdery mildew resistance genes in peach (Prunus persica (L.) Batsch)xPrunus davidiana hybrids. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 1996; 93:909-19. [PMID: 24162425 DOI: 10.1007/bf00224093] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/1995] [Accepted: 04/19/1996] [Indexed: 05/10/2023]
Abstract
A progeny of 77 hybrids issued from a cross between two heterozygous Prunus, peach [P. persica (L.) Batsch] (variety 'Summergrand') and a related species, P. davidiana (clone 1908), was analysed for powdery mildew resistance in five independent experiments. This population was also analysed for its genotype with isoenzyme and RAPD markers in order to map the genes responsible for resistance. A genetic linkage map was generated for each parent. The 'Summergrand' linkage map is composed of only four linkage groups including 15 RAPD markers and covering 83.1 centiMorgans (cM) of the peach nuclear genome, whereas the P. davidiana linkage map contains 84 RAPD markers and one isoenzyme assigned to ten linkage groups and covering 536 cM. Significant associations between molecular markers and powdery mildew resistance were found in each parent. For P. davidiana, one major QTL with a very strong effect and five other QTLs with minor effects were located in different linkage groups. For 'Summergrand', three QTLs for powdery mildew resistance, with minor effects, were also detected. Consequently, evidence is given here that the powdery mildew resistance of P. davidiana clone 1908 and P. persica variety 'Summergrand' is not a monogenic character but is controlled by at least one major gene and several minor genes.
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Affiliation(s)
- E Dirlewanger
- Centre de Recherches de Bordeaux, INRA, Unité de Recherches sur les Espèces Fruitières et la Vigne, BP 81, 33883, Villenave d'Ornon Cedex, France
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523
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Lu R, Rank GH. Use of RAPD analyses to estimate population genetic parameters in the alfalfa leaf-cutting bee,Megachile rotundata. Genome 1996; 39:655-63. [DOI: 10.1139/g96-083] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
RAPD analyses were performed on five geographically isolated populations of Megachile rotundata. We used haploid males of the alfalfa leaf-cutting bee, M. rotundata, to overcome the limitation of the dominance of RAPD markers in the determination of population genetic parameters. Sixteen primers gave rise to 130 polymorphic and 31 monomorphic bands. The unbiased estimators calculated in this study include within- and between-population heterozygosity, nucleotide divergence, and genetic distance. The genetic diversity (H = 0.32–0.35) was found to be about 10 times that of previous estimates (H = 0.033) based on allozyme data. Contrary to the data obtained at the protein level, our results suggest that Hymenoptera do not have a lower level of genetic variability at the DNA level compared with other insect species. Regardless of the different assumptions underlying the calculation of heterozygosity, divergence, and genetic distance, all five populations showed a parallel interrelationship for the three parameters. We conclude that RAPD markers are a convenient tool to estimate population genetic variation in haploid M. rotundata and that with an adequate sample size the technique is applicable to the evaluation of divergence in diploid populations. Key words : Megachile rotundata, RAPD, heterozygosity, genetic distance, nucleotide divergence.
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524
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Antolin MF, Bosio CF, Cotton J, Sweeney W, Strand MR, Black WC. Intensive linkage mapping in a wasp (Bracon hebetor) and a mosquito (Aedes aegypti) with single-strand conformation polymorphism analysis of random amplified polymorphic DNA markers. Genetics 1996; 143:1727-38. [PMID: 8844159 PMCID: PMC1207434 DOI: 10.1093/genetics/143.4.1727] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The use of random amplified polymorphic DNA from the polymerase chain reaction (RAPD-PCR) allows efficient construction of saturated linkage maps. However, when analyzed by agarose gel electrophoresis, most RAPD-PCR markers segregate as dominant alleles, reducing the amount of linkage information obtained. We describe the use of single strand conformation polymorphism (SSCP) analysis of RAPD markers to generate linkage maps in a haplodiploid parasitic wasp Bracon (Habrobracon) hebetor and a diploid mosquito. Aedes aegypti. RAPD-SSCP analysis revealed segregation of codominant alleles at markers that appeared to segregate as dominant (band presence/band absence) markers or appeared invariant on agarose gels. Our SSCP protocol uses silver staining to detect DNA fractionated on large thin polyacrylamide gels and reveals more polymorphic markers than agarose gel electrophoresis. In B. hebetor, 79 markers were mapped with 12 RAPD primers in six weeks; in A aygpti, 94 markers were mapped with 10 RAPD primers in five weeks. Forty-five percent of markers segregated as codominant loci in B. hebetor, while 11% segregated as codominant loci in A. aegypti. SSCP analysis of RAPD-PCR markers offers a rapid and inexpensive means of constructing intensive linkage maps of many species.
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Affiliation(s)
- M F Antolin
- Department of Biology, Colorado State University, Fort Collins 80523, USA.
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525
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Crouzillat D, Lerceteau E, Petiard V, Morera J, Rodriguez H, Walker D, Phillips W, Ronning C, Schnell R, Osei J, Fritz P. Theobroma cacao L.: a genetic linkage map and quantitative trait loci analysis. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 1996; 93:205-214. [PMID: 24162219 DOI: 10.1007/bf00225747] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/1995] [Accepted: 02/02/1996] [Indexed: 06/02/2023]
Abstract
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 1∶1 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.
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Affiliation(s)
- D Crouzillat
- Centre de Recherche Nestlé Tours, 101 Avenue Gustave Eiffel, Notre Dame-d'Oé, B.P. 9716, 2, Tours Cedex
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526
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Devey ME, Bell JC, Smith DN, Neale DB, Moran GF. A genetic linkage map for Pinus radiata based on RFLP, RAPD, and microsatellite markers. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 1996; 92:673-9. [PMID: 24166390 DOI: 10.1007/bf00226088] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/1995] [Accepted: 09/22/1995] [Indexed: 05/13/2023]
Abstract
A genetic linkage map for radiata pine (Pinus radiata D. Don) has been constructed using segregation data from a three-generation outbred pedigree. A total of 208 loci were analyzed including 165 restriction fragment length polymorphism (RFLP), 41 random amplified polymorphic DNA (RAPD) and 2 microsatellite markers. The markers were assembled into 22 linkage groups of 2 or more loci and covered a total distance of 1382 cM. Thirteen loci were unlinked to any other marker. Of the RFLP loci that were mapped, 93 were detected by loblolly pine (P. taeda L.) cDNA probes that had been previously mapped or evaluated in that species. The remaining 72 RFLP loci were detected by radiata pine probes from a PstI genomic DNA library. Two hundred and eighty RAPD primers were evaluated, and 41 loci which were segregating in a 1∶1 ratio were mapped. Two microsatellite markers were also placed on the map. This map and the markers derived from it will have wide applicability to genetic studies in P. radiata and other pine species.
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Affiliation(s)
- M E Devey
- CSIRO Forestry and Forest Products, Queen Victoria Terrace, P.O. Box 4008, 2600, Australian Capital Territory, Australia
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527
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Wilcox PL, Amerson HV, Kuhlman EG, Liu BH, O'Malley DM, Sederoff RR. Detection of a major gene for resistance to fusiform rust disease in loblolly pine by genomic mapping. Proc Natl Acad Sci U S A 1996; 93:3859-64. [PMID: 8632980 PMCID: PMC39449 DOI: 10.1073/pnas.93.9.3859] [Citation(s) in RCA: 111] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Genomic mapping has been used to identify a region of the host genome that determines resistance to fusiform rust disease in loblolly pine where no discrete, simply inherited resistance factors had been previously found by conventional genetic analysis over four decades. A resistance locus, behaving as a single dominant gene, was mapped by association with genetic markers, even though the disease phenotype deviated from the expected Mendelian ratio. The complexity of forest pathosystems and the limitations of genetic analysis, based solely on phenotype, had led to an assumption that effective long-term disease resistance in trees should be polygenic. However, our data show that effective long-term resistance can be obtained from a single qualitative resistance gene, despite the presence of virulence in the pathogen population. Therefore, disease resistance in this endemic coevolved forest pathosystem is not exclusively polygenic. Genomic mapping now provides a powerful tool for characterizing the genetic basis of host pathogen interactions in forest trees and other undomesticated, organisms, where conventional genetic analysis often is limited or not feasible.
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Affiliation(s)
- P L Wilcox
- Department of Forestry, North Carolina State University, Raleigh 37695, USA
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528
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Molecular Markers, Forest Genetics, and Tree Breeding. ACTA ACUST UNITED AC 1996. [DOI: 10.1007/978-1-4899-0280-1_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/24/2023]
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529
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Hamelin RC, Beaulieu J, Plourde A. Genetic diversity in populations of Cronartium ribicola in plantations and natural stands of Pinus strobus. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 1995; 91:1214-1221. [PMID: 24170049 DOI: 10.1007/bf00220932] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/1995] [Accepted: 05/25/1995] [Indexed: 06/02/2023]
Abstract
Genetic diversity was studied in 22 populations of the white pine blister rust fungus Cronartium ribicola from natural stands and plantations of eastern white pine, Pinus strobus. Pseudo-allelic frequencies were estimated at each of 7 putative RAPD loci by scoring for presence or absence of amplified fragments in dikaryotic aecidiospores. Analysis of genetic distance between all pairs of populations did not reveal any trend with regard to geographic origin or type of white pine stand. In addition, when hierarchical population structure was analysed, total genetic diversity (H s =0.214) was mostly attributable to diversity within populations (H s =0.199; AMOVA φ st =0.121, P<0.01). Genetic diversity of populations relative to region of origin (east, centre, and west) or type of stand (natural stands vs plantations) was not significantly different from zero (P>0.10) Nevertheless, a significant proportion of genetic differentiation was found between populations within region or stand type (F st =0.114; φ sc =0.132, P<0.001). This result indicates that some population structure exists but that it appears to be independent of region of origin or type of stand. At least for 2 populations from white pine plantations, it appears possible that a recent introduction of a limited number of propagules was responsible for low levels of genetic diversity. We interpret these results as meaning that either long-distance dispersal is taking place between populations more than 1000 km apart or that these populations share a common recent ancestor. In addition, we suggest that C. ribicola may still be expanding its distribution by colonizing new plantations.
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Affiliation(s)
- R C Hamelin
- Natural Resources Canada, Canadian Forest Service, Quebec Region, 1055 du PEPS, PO Box 3800, G1V 4C7, Sainte-Foy, Quebec, Canada
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530
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Viruel MA, Messeguer R, de Vicente MC, Garcia-Mas J, Puigdomènech P, Vargas F, Arús P. A linkage map with RFLP and isozyme markers for almond. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 1995; 91:964-71. [PMID: 24169984 DOI: 10.1007/bf00223907] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/1994] [Accepted: 04/21/1995] [Indexed: 05/20/2023]
Abstract
Inheritance and linkage studies were conducted with seven isozyme genes and 120 RFLPs in the F1 progeny of a cross between almond cultivars 'Ferragnes' and 'Tuono'. RFLPs were detected using 57 genomic and 43 cDNA almond clones. Eight of the cDNA probes corresponded to known genes (extensin, prunin (2), α-tubulin, endopolygalacturonase, oleosin, actin depolymerizing factor and phosphoglyceromutase). Single-copy clones were found more frequently in the cDNA (65%) than in the genomic libraries (26%). Two maps were elaborated, one with the 93 loci heterozygous in 'Ferragnes' and another with the 69 loci heterozygous in 'Tuono'. Thirty-five loci were heterozygous in both parents and were used as bridges between both maps. Most of the segregations (91%) were of the 1∶1 or 1∶1∶1∶1 types, and data were analyzed as if they derived from two backcross populations. Eight linkage groups covering 393 cM in 'Ferragnes' and 394 in 'Tuono' were found for each map. None of the loci examined in either map was found to be unlinked. Distorted segregation ratios were mainly concentrated in two linkage groups of the 'Ferragnes' map.
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Affiliation(s)
- M A Viruel
- Departament de Genètica Vegetal, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Carretera de Cabrils s/n, 08348, Cabrils (Barcelona), Spain
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531
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Byrne M, Murrell JC, Allen B, Moran GF. An integrated genetic linkage map for eucalypts using RFLP, RAPD and isozyme markers. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 1995; 91:869-875. [PMID: 24169971 DOI: 10.1007/bf00223894] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/1995] [Accepted: 02/03/1995] [Indexed: 05/28/2023]
Abstract
An integrated genetic linkage map for E. nitens was constructed in an outbred three-generation pedigree. Analysis of 210 RFLP, 125 RAPD and 4 isozyme loci resulted in 330 markers linked in 12 linkage groups covering 1462 cM (n=11 in eucalypts). The 12th linkage group is comprised of only 5 markers and will probably coalesce with another linkage group when further linked loci are located. Co-dominant RFLP loci segregating in both parents were used to integrate linkages identified in the male and female parents. Differences in recombination frequencies in the two parents were observed for a number of pairs of loci, and duplication of sequences was identified both within and between linkage groups. The markers were distributed randomly across the genome except for the RFLPs in linkage group 10 and for some loci showing segregation distortion, which were clustered into three regions of the map. The use of a large number of co-dominant RFLP loci in this map enables it to be used in other pedigrees of E. nitens and forms a basis for the detection and location of QTL in E. nitens and other eucalypt species.
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Affiliation(s)
- M Byrne
- Division of Forestry, CSIRO, Queen Victoria Terrace, PO Box 4008, ACT 2600, Canberra, Australia
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532
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Benet H, Guries RP, Boury S, Smalley EB. Identification of RAPD markers linked to a black leaf spot resistance gene in Chinese elm. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 1995; 90:1068-1073. [PMID: 24173064 DOI: 10.1007/bf00222923] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/1994] [Accepted: 11/22/1994] [Indexed: 06/02/2023]
Abstract
Black leaf spot (Stegophora ulmea) is a common foliage disease on Chinese (Ulmus parvifolia) and Siberian elms (U. pumila), two species which have been widely used as sources of Dutch-elm disease-resistance genes for interspecific elm hybrids. A dominant gene controlling resistance to black leaf spot was identified in a population derived from self-pollination of a single U. parvifolia tree. Using RAPD markers, in combination with bulked segregant analysis, we have identified three markers linked to this resistance gene. A survey of Chinese-elm hybrids revealed that the same gene is likely to confer a high level of resistance to black leaf spot in interspecific elm hybrids, although other genetic factors may also be involved in the determination of a disease phenotype.
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Affiliation(s)
- H Benet
- Centre d'Etudes Océanographiques et de Biologie Marine, CNRS, UPR 4601, F-29680, Roscoff, France
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533
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Plomion C, O'Malley DM, Durel CE. Genomic analysis in maritime pine (Pinus pinaster). Comparison of two RAPD maps using selfed and open-pollinated seeds of the same individual. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 1995; 90:1028-1034. [PMID: 24173058 DOI: 10.1007/bf00222917] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/1994] [Accepted: 12/08/1994] [Indexed: 06/02/2023]
Abstract
Two genomic maps were constructed for one individual tree of maritime pine, Pinus pinaster Ait., using a common set of 263 RAPD markers (random amplified polymorphic DNA). The RAPD markers were chosen from a larger number of polymorphic RAPD fragments on the basis of repeatability and inheritance in a three-generation pedigree. The maps were constructed from two independent mapping samples of 62 megagametophytes (In) from a self cross and from an open-pollinated cross. The markers were grouped (LOD≥4; θ≤0.25) and assigned to 13 major and 5 minor linkage groups. Two framework maps were constructed using the ordering criterion of interval support≥3. Comparison of the two framework maps suggested that the locus order was incorrect for 2% of the framework markers. A bootstrap analysis showed that this error rate was representative for our data set. The results showed that framework maps constructed using RAPD markers were repeatable and that differences in locus order for maps of different genotypes or species could result from chance. The total map distance was 1380 cM, and the map provided coverage of approximately 90% of the genome.
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Affiliation(s)
- C Plomion
- INRA, Station de Recherches Forestières, 33610, Cestas, France
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534
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Grattapaglia D, Bertolucci FL, Sederoff RR. Genetic mapping of QTLs controlling vegetative propagation in Eucalyptus grandis and E. urophylla using a pseudo-testcross strategy and RAPD markers. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 1995; 90:933-47. [PMID: 24173047 DOI: 10.1007/bf00222906] [Citation(s) in RCA: 53] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/1994] [Accepted: 12/08/1994] [Indexed: 05/07/2023]
Abstract
We have extended the combined use of the "pseudo-testcross" mapping strategy and RAPD markers to map quantitative trait loci (QTLs) controlling traits related to vegetative propagation in Eucalyptus. QTL analyses were performed using two different interval mapping approaches, MAPMAKER-QTL (maximum likelihood) and QTL-STAT (non-linear least squares). A total of ten QTLs were detected for micropropagation response (measured as fresh weight of shoots, FWS), six for stump sprouting ability (measured as # stump sprout cuttings, #Cutt) and four for rooting ability (measured as % rooting of cuttings, %Root). With the exception of three QTLs, both interval-mapping methods yielded similar results in terms of QTL detection. Discrepancies in the most likely QTL location were observed between the two methods. In 75% of the cases the most likely position was in the same, or in an adjacent, interval. Standardized gene substitution effects for the QTLs detected were typically between 0.46 and 2.1 phenotypic standard deviations (σp), while differences between the family mean and the favorable QTL genotype were between 0.25 and 1.07 (σp). Multipoint estimates of the total genetic variation explained by the QTLs (89.0% for FWS, 67.1 % for#Cutt, 62.7% for %Root) indicate that a large proportion of the variation in these traits is controlled by a relatively small number of major-effect QTLs. In this cross, E. grandis is responsible for most of the inherited variation in the ability to form shoots, while E. urophylla contributes most of the ability in rooting. QTL mapping in the pseudo-testcross configuration relies on withinfamily linkage disequilibrium to establish marker/trait associations. With this approach QTL analysis is possible in any available full-sib family generated from undomesticated and highly heterozygous organisms such as forest trees. QTL mapping on two-generation pedigrees opens the possibility of using already existing families in retrospective QTL analyses to gather the quantitative data necessary for marker-assisted tree breeding.
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Affiliation(s)
- D Grattapaglia
- Forest Biotechnology Group, Departments of Genetics and Foresty, North Carolina State University, Box 8008, 27695, Raleigh, NC, USA
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535
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Nesbitt KA, Potts BM, Vaillancourt RE, West AK, Reid JB. Partitioning and distribution of RAPD variation in a forest tree species, Eucalyptus globulus (Myrtaceae). Heredity (Edinb) 1995. [DOI: 10.1038/hdy.1995.86] [Citation(s) in RCA: 79] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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536
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Genomic mapping in Pinus pinaster (maritime pine) using RAPD and protein markers. Heredity (Edinb) 1995. [DOI: 10.1038/hdy.1995.90] [Citation(s) in RCA: 52] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
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