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Mosca E, Eckert AJ, Di Pierro EA, Rocchini D, La Porta N, Belletti P, Neale DB. The geographical and environmental determinants of genetic diversity for four alpine conifers of the European Alps. Mol Ecol 2012; 21:5530-45. [PMID: 23058000 DOI: 10.1111/mec.12043] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2012] [Revised: 08/10/2012] [Accepted: 08/21/2012] [Indexed: 12/11/2022]
Abstract
Climate is one of the most important drivers of local adaptation in forest tree species. Standing levels of genetic diversity and structure within and among natural populations of forest trees are determined by the interplay between climatic heterogeneity and the balance between selection and gene flow. To investigate this interplay, single nucleotide polymorphisms (SNPs) were genotyped in 24 to 37 populations from four subalpine conifers, Abies alba Mill., Larix decidua Mill., Pinus cembra L. and Pinus mugo Turra, across their natural ranges in the Italian Alps and Apennines. Patterns of population structure were apparent using a Bayesian clustering program, STRUCTURE, which identified three to five genetic groups per species. Geographical correlates with these patterns, however, were only apparent for P. cembra. Multivariate environmental variables [i.e. principal components (PCs)] were subsequently tested for association with SNPs using a Bayesian generalized linear mixed model. The majority of the SNPs, ranging from six in L. decidua to 18 in P. mugo, were associated with PC1, corresponding to winter precipitation and seasonal minimum temperature. In A. alba, four SNPs were associated with PC2, corresponding to the seasonal minimum temperature. Functional annotation of those genes with the orthologs in Arabidopsis revealed several genes involved in abiotic stress response. This study provides a detailed assessment of population structure and its association with environment and geography in four coniferous species in the Italian mountains.
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Affiliation(s)
- E Mosca
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
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2
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Neale DB, Marshall KA, Sederoff RR. Chloroplast and mitochondrial DNA are paternally inherited in Sequoia sempervirens D. Don Endl. Proc Natl Acad Sci U S A 2010; 86:9347-9. [PMID: 16594091 PMCID: PMC298492 DOI: 10.1073/pnas.86.23.9347] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Restriction fragment length polymorphisms in controlled crosses were used to infer the mode of inheritance of chloroplast DNA and mitochondrial DNA in coast redwood (Sequoia sempervirens D. Don Endl.). Chloroplast DNA was paternally inherited, as is true for all other conifers studied thus far. Surprisingly, a restriction fragment length polymorphism detected by a mitochondrial probe was paternally inherited as well. This polymorphism could not be detected in hybridizations with chloroplast probes covering the entire chloroplast genome, thus providing evidence that the mitochondrial probe had not hybridized to chloroplast DNA on the blot. We conclude that mitochondrial DNA is paternally inherited in coast redwood. To our knowledge, paternal inheritance of mitochondrial DNA in sexual crosses of a multicellular eukaryotic organism has not been previously reported.
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Affiliation(s)
- D B Neale
- Institute of Forest Genetics, Pacific Southwest Forest and Range Experiment Station, Forest Service, U.S. Department of Agriculture, Berkeley, CA 94701
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Komulainen P, Brown GR, Mikkonen M, Karhu A, García-Gil MR, O'Malley D, Lee B, Neale DB, Savolainen O. Comparing EST-based genetic maps between Pinus sylvestris and Pinus taeda. Theor Appl Genet 2003; 107:667-678. [PMID: 12827250 DOI: 10.1007/s00122-003-1312-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2002] [Accepted: 03/10/2003] [Indexed: 05/24/2023]
Abstract
A genetic map of Pinus sylvestris was constructed using ESTP (expressed sequence tag polymorphism) markers and other gene-based markers, AFLP markers and microsatellites. Part of the ESTP markers (40) were developed and mapped earlier in Pinus taeda, and additional markers were generated based on P. sylvestris sequences or sequences from other pine species. The mapping in P. sylvestris was based on 94 F(1) progeny from a cross between plus-tree parents E635C and E1101. AFLP framework maps for the parent trees were first constructed. The ESTP and other gene sequence-based markers were added to the framework maps, as well as five published microsatellite loci. The separate maps were then integrated with the aid of AFLPs segregating in both trees (dominant segregation ratios 3:1) as well as gene markers and microsatellites segregating in both parent trees (segregation ratios 1:1:1:1 or 1:2:1). The integrated map consisted of 12 groups corresponding to the P. taeda linkage groups, and additionally three and six smaller groups for E1101 and E635C, respectively. The number of framework AFLP markers in the integrated map is altogether 194 and the number of gene markers 61. The total length of the integrated map was 1,314 cM. The set of markers developed for P. sylvestris was also added to existing maps of two P. taeda pedigrees. Starting with a mapped marker from one pedigree in the source species resulted in a mapped marker in a pedigree of the other species in more than 40% of the cases, with about equal success in both directions. The maps of the two species are largely colinear, even if the species have diverged more than 70 MYA. Most cases of different locations were probably due to problems in identifying the orthologous members of gene families. These data provide a first ESTP-containing map of P. sylvestris, which can also be used for comparing this species to additional species mapped with the same markers.
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Affiliation(s)
- P Komulainen
- Department of Biology, University of Oulu, FIN-90014 University of Oulu, Finland
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4
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Sewell MM, Davis MF, Tuskan GA, Wheeler NC, Elam CC, Bassoni DL, Neale DB. Identification of QTLs influencing wood property traits in loblolly pine ( Pinus taeda L.). II. Chemical wood properties. Theor Appl Genet 2002; 104:214-222. [PMID: 12582689 DOI: 10.1007/s001220100697] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Chemical wood property traits were analyzed for the presence of quantitative trait loci (QTLs) in a three-generation outbred pedigree of loblolly pine ( Pinus taeda L.). These traits were assayed using pyrolysis molecular beam mass spectrometry and include mass spectrum peak intensities associated with carbohydrates, alpha-cellulose and hemicellulose sugars, and lignin. Models for projection to latent structures (PLS) were used to also estimate the chemical composition of cell walls (i.e., alpha-cellulose, galactan and lignin) from mass spectrum data using multivariate regression. Both earlywood and latewood fractions from the fifth annual ring were analyzed for each trait. An interval mapping approach designed for an outbred pedigree was used to estimate the number of QTLs, the magnitude of QTL effects, and their genomic position. Eight unique QTLs influencing cell wall chemistry were detected from multiple peak intensities and/or PLS estimates using the one- and two-QTL models. Significant differences in chemical contents were observed among the populations from North Carolina vs Oklahoma, and results from QTLxenvironment analyses suggest that QTLs interact with environmental location. QTLs should be verified in larger experiments and in different genetic and environmental backgrounds. QTL mapping will help towards eventually identifying genes having a major effect on chemical wood properties.
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Affiliation(s)
- M. M. Sewell
- Environmental Sciences Division, Oak Ridge National Laboratory, P.O. Box 2088, MS-6422, Bldg 1059, Rm 103, Oak Ridge, TN 37831-2008, USA
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5
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Brown GR, Kadel EE, Bassoni DL, Kiehne KL, Temesgen B, van Buijtenen JP, Sewell MM, Marshall KA, Neale DB. Anchored reference loci in loblolly pine (Pinus taeda L.) for integrating pine genomics. Genetics 2001; 159:799-809. [PMID: 11606554 PMCID: PMC1461821 DOI: 10.1093/genetics/159.2.799] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Anchored reference loci provide a framework for comparative mapping. They are landmarks to denote conserved chromosomal segments, allowing the synthesis of genetic maps from multiple sources. We evaluated 90 expressed sequence tag polymorphisms (ESTPs) from loblolly pine (Pinus taeda L.) for this function. Primer sets were assayed for amplification and polymorphism in six pedigrees, representing two subgenera of Pinus and a distant member of the Pinaceae, Douglas-fir (Pseudotsuga menziesii [Mirb.] Franco). On average, 89% of primer sets amplified in four species of subgenus Pinus, 49% in one species of subgenus Strobus, and 22% in Douglas-fir. Polymorphisms were detected for 37-61% of the ESTPs within each pedigree. Comparative mapping in loblolly and slash pine (P. elliottii Englm.) revealed that ESTPs mapped to the same location. Disrupted synteny or significant disruptions in colinearity were not detected. Thirty-five ESTPs met criteria established for anchor loci. The majority of those that did not meet these criteria were excluded when map location was known in only a single species. Anchor loci provide a unifying tool for the community, facilitating the creation of a "generic" pine map and serving as a foundation for studies on genome organization and evolution.
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Affiliation(s)
- G R Brown
- Institute of Forest Genetics, Pacific Southwest Research Station, U.S. Department of Agriculture Forest Service, Davis, California 95616, USA
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6
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Temesgen B, Neale DB, Harry DE. Use of haploid mixtures and heteroduplex analysis enhance polymorphisms revealed by denaturing gradient gel electrophoresis. Biotechniques 2000; 28:114-6, 118, 120, passim. [PMID: 10649781 DOI: 10.2144/00281st08] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
PCR-based codominant genetic markers were developed by using primer sequences designed from cDNA clones of loblolly pine (Pinus taeda L.). Such markers offer certain advantages relative to simple-sequence repeat (SSR), also known as short-tandem repeat (STR) markers, and include the ability to quantify and map DNA polymorphisms in expressed genes. However, detecting these DNA polymorphisms is more problematic because many DNA polymorphisms in genes involve base substitutions rather than insertions or deletions. Denaturing gradient gel electrophoresis (DGGE) is a sensitive and efficient method for detecting sequence differences among PCR fragments. This paper demonstrates the application of DGGE to genetically map expressed genes in loblolly pine. Also, heteroduplex DNA fragments, formed during the amplification of DNA from heterozygotes and from mixes of haploid DNAs from megagametophytes, enhanced and strengthened genetic interpretations and genotypic classifications.
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Affiliation(s)
- B Temesgen
- USDA Forest Service, University of California, Davis, USA
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Devey ME, Sewell MM, Uren TL, Neale DB. Comparative mapping in loblolly and radiata pine using RFLP and microsatellite markers. Theor Appl Genet 1999; 99:656-662. [PMID: 22665202 DOI: 10.1007/s001220051281] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Genetic linkage maps were constructed for loblolly pine (Pinus taeda L.) and radiata pine (P. radiata D. Don) using a common set of RFLP and microsatellite markers. The map for loblolly pine combined data from two full-sib families and consisted of 20 linkage groups covering 1281 cM. The map for radiata pine had 14 linkage groups and covered 1223 cM. All of the RFLP probes readily hybridise between loblolly and radiata pine often producing similar hybridisation patterns. There were in total 60 homologous RFLP loci mapped in both species which could be used for comparative purposes. A set of 20 microsatellite markers derived from radiata pine were also assayed; however, only 9 amplified and revealed polymorphic loci in both species. Single-locus RFLP and microsatellite markers were used to match up linkage groups and compare order between species. Twelve syntenic groups were obtained each consisting of from 3 to 9 homologous loci. The order of homologous loci was colinear in most cases, suggesting no major chromosomal rearrangements in the evolution of these species. Comparative mapping between loblolly and radiata pine should facilitate genetic research in both species and provide a framework for mapping in other pine species.
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Affiliation(s)
- M E Devey
- CSIRO Forestry and Forest Products, E4008, Kingston, Australia, AU,
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8
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Sewell MM, Sherman BK, Neale DB. A consensus map for loblolly pine (Pinus taeda L.). I. Construction and integration of individual linkage maps from two outbred three-generation pedigrees. Genetics 1999; 151:321-30. [PMID: 9872970 PMCID: PMC1460451 DOI: 10.1093/genetics/151.1.321] [Citation(s) in RCA: 98] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
A consensus map for loblolly pine (Pinus taeda L.) was constructed from the integration of linkage data from two unrelated three-generation outbred pedigrees. The progeny segregation data from restriction fragment length polymorphism, random amplified polymorphic DNA, and isozyme genetic markers from each pedigree were recoded to reflect the two independent populations of parental meioses, and genetic maps were constructed to represent each parent. The rate of meiotic recombination was significantly greater for males than females, as was the average estimate of genome length for males (1983.7 cM [Kosambi mapping function (K)]) and females [1339.5 cM(K)]. The integration of individual maps allows for the synthesis of genetic information from independent sources onto a single consensus map and facilitates the consolidation of linkage groups to represent the chromosomes n = 12 of loblolly pine. The resulting consensus map consists of 357 unique molecular markers and covers approximately 1300 cM(K).
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Affiliation(s)
- M M Sewell
- Institute of Forest Genetics, USDA Forest Service, Pacific Southwest Research Station, Placerville, California 95667, USA
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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. Theor Appl Genet 1996; 92:673-9. [PMID: 24166390 DOI: 10.1007/bf00226088] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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10
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Lehner A, Campbell MA, Wheeler NC, Pöykkö T, Glössl J, Kreike J, Neale DB. Identification of a RAPD marker linked to the pendula gene in Norway spruce (Picea abies (L.) Karst. f. pendula). Theor Appl Genet 1995; 91:1092-1094. [PMID: 24170001 DOI: 10.1007/bf00223924] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/1995] [Accepted: 05/12/1995] [Indexed: 06/02/2023]
Abstract
The pendula phenotype of Norway spruce [Picea abies (L.) Karst f. pendula] is characterized by narrow crowns and strong apical dominance and is controlled by a single dominant gene (P). This defined genetic control presents one of the few opportunities to map a single gene controlling a morphological trait in a forest tree. We used random amplified polymorphic DNA (RAPD) markers and bulked segregant analysis to identify one locus OPH10_720, linked to the pendula gene. The estimated recombination frequency (r) between OPH10_720 and P was 0.046 (SE r =0.032). Mapping of the pendula gene is an important first step towards the ultimate identification and cloning of this gene.
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Affiliation(s)
- A Lehner
- Institute of Forensic Medicine, Sensengasse 2, A-1090, Vienna, Austria
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Hipkins VD, Marshall KA, Neale DB, Rottmann WH, Strauss SH. A mutation hotspot in the chloroplast genome of a conifer (Douglas-fir: Pseudotsuga) is caused by variability in the number of direct repeats derived from a partially duplicated tRNA gene. Curr Genet 1995; 27:572-9. [PMID: 7553944 DOI: 10.1007/bf00314450] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
We determined the DNA sequence of a 2.7-kb cpDNA XbaI fragment from douglas-fir [Pseudotsuga menziesii (Mirb.) Franco]. RFLPs revealed by the 2.7-kb XbaI clone were observed to vary up to 1 kb among species within the genus Pseudotsuga and up to 200 bp among trees of P. menziesii. The polymerase chain reaction (PCR) allowed the locus of polymorphism to be identified, and the variable region was then sequenced in a second Douglas-fir tree, a single tree of a related species, Japanese Douglas-fir (P. japonica), and in a species lacking a mutation hotspot in the region, Pinus radiata (Monterey pine). The locus of polymorphism is characterized by hundreds of base pairs of imperfect, tandem direct repeats flanked by a partially duplicated and an intact trn Y-GUA gene. The duplication is direct in orientation and consists of 43 bp of the 3' end of trnY and 25 bp of its 3' flanking sequence. Tandem repeats show high sequence similarity to a 27-bp region of the trnY gene that overlaps one end of the duplication. The two trees of Douglas-fir sequenced differed by a single tandem repeat unit, whereas these trees differed from the Japanese Douglas-fir sequenced by approximately 34 repeat units. Repetitive DNA in the Pseudotsuga cpDNA hotspot was most likely generated at the time of the partial trnY gene duplication and these sequences expanded by slipped-strand mispairing and unequal crossing-over.
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Affiliation(s)
- V D Hipkins
- National Forest Genetic Electrophoresis Laboratory, USDA Forest Service, Camino, CA 95709, USA
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12
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Devey ME, Delfino-Mix A, Kinloch BB, Neale DB. Random amplified polymorphic DNA markers tightly linked to a gene for resistance to white pine blister rust in sugar pine. Proc Natl Acad Sci U S A 1995; 92:2066-70. [PMID: 11607517 PMCID: PMC42424 DOI: 10.1073/pnas.92.6.2066] [Citation(s) in RCA: 72] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We have genetically mapped a gene for resistance to white pine blister rust (Cronartium ribicola Fisch.) in sugar pine (Pinus lambertiana Dougl.) by using an approach which relies on three factors: (i) the ability to assay for genetic markers in the haploid stage of the host's life cycle, using megagametophyte seed tissue; (ii) a simple and clearly defined pathosystem; and (iii) the use of random amplified polymorphic DNA (RAPD) markers that can be quickly and efficiently evaluated. Resistance to white pine blister rust in sugar pine is known to be controlled by a single dominant gene (R). Maternal segregation of R and dominant RAPD markers were scored simultaneously following collection of megagametophytes for DNA assays and seedling inoculation with C. ribicola. Bulked samples of haploid megagametophyte DNA from resistant and susceptible offspring of segregating full-sib and half-sib families were used to evaluate 800 random decanucleotide primers. Ten loci linked with the gene for resistance to white pine blister rust were identified and segregation data were obtained from five families. Six of the linked markers were within 5 centimorgans of the gene, and one marker was 0.9 centimorgan from R. These and other markers derived by this approach may provide starting points for map-based cloning of this important gene.
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Affiliation(s)
- M E Devey
- Commonwealth Scientific and Industrial Research Organization/Division of Forestry, Australian Capital Territory, Australia
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Jermstad KD, Reem AM, Henifin JR, Wheeler NC, Neale DB. Inheritance of restriction fragment length polymorphisms and random amplified polymorphic DNAs in coastal Douglas-fir. Theor Appl Genet 1994; 89:758-766. [PMID: 24178022 DOI: 10.1007/bf00223716] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/1994] [Accepted: 04/29/1994] [Indexed: 06/02/2023]
Abstract
A total of 225 new genetic loci [151 restriction fragment length polymorphisms (RFLP) and 74 random amplified polymorphic DNAs (RAPD)] in coastal Douglas-fir [Pseudotsuga menziesii (Mirb.) Franco var. menziesii] have been identified using a three-generation outbred pedigree. The Mendelian inheritance of 16 RFLP loci and 29 RAPD loci was demonstrated based on single-locus segregation in a sample of F2 progeny. One RFLP locus, PtIFG2025, showed segregation distortion. Probe pPtIFG2025 is a loblolly pine cDNA probe encoding for rbcS. The 16 RFLP loci and 23 allozyme loci were also assayed in a sample of 16 Douglas-fir seed-orchard clones. Allelism was determined at 11 of the 16 RFLP loci. RFLPs were able to detect slightly more variation (4.0 alleles per locus) than allozymes (3.1 alleles per locus). The inheritance of an additional 80 RAPD loci was determined based on haploid segregation analysis of megagametophytes from parent tree 013-1. Once 200-300 markers are identified and placed on a genetic map, quantitative trait loci affecting bud phenology will be mapped.
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Affiliation(s)
- K D Jermstad
- Pacific Southwest Research Station, USDA Forest Service, Institute of Forest Genetics, 2480 Carson Road, 95667, Placerville, CA, USA
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Devey ME, Fiddler TA, Liu BH, Knapp SJ, Neale DB. An RFLP linkage map for loblolly pine based on a three-generation outbred pedigree. Theor Appl Genet 1994; 88:273-278. [PMID: 24186005 DOI: 10.1007/bf00223631] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/1993] [Accepted: 09/09/1993] [Indexed: 06/02/2023]
Abstract
A genetic linkage map for loblolly pine (Pinus taeda L.) was constructed using segregation data from a three-generation outbred pedigree consisting of four grandparents, two parents, and 95 F2 progeny. The map was based predominantly on restriction fragment length polymorphism (RFLP) loci detected by cDNA probes. Sixty-five cDNA and three genomic DNA probes revealed 90 RFLP loci. Six polymorphic isozyme loci were also scored. One-fourth (24%) of the cDNA probes detected more than 1 segregating locus, an indication that multigene families are common in pines. As many as six alleles were observed at a single segregating locus among grandparents and it was not unusual for the progeny to segregate for three or four alleles per locus. Multipoint linkage analysis placed 73 RFLP and 2 isozyme loci into 20 linkage groups; the remaining 17 RFLP and 4 isozyme loci were unlinked. The mapped RFLP probes provide a new set of codominant markers for genetic analyses in loblolly pine.
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Affiliation(s)
- M E Devey
- Division of Forestry/CSIRO, Queen Victoria Terrace, P.O. Box 4008, 2600, Canberra, ACT, Australia
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Ahuja MR, Devey ME, Groover AT, Jermstad KD, Neale DB. Mapped DNA probes from loblolly pine can be used for restriction fragment length polymorphism mapping in other conifers. Theor Appl Genet 1994; 88:279-282. [PMID: 24186006 DOI: 10.1007/bf00223632] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/1993] [Accepted: 09/09/1993] [Indexed: 06/02/2023]
Abstract
A high-density genetic map based on restriction fragment length polymorphisms (RFLPs) is being constructed for loblolly pine (Pinus taeda L.). Consequently, a large number of DNA probes from loblolly pine are potentially available for use in other species. We have used some of these DNA probes to detect RFLPs in 12 conifers and an angiosperm. Thirty complementary DNA and two genomic DNA probes from loblolly pine were hybridized to Southern blots containing DNA from five species of Pinus (P. elliottii, P. lambertiana, P. radiata, P. sylvestris, and P. taeda), one species from each of four other genera of Pinaceae (Abies concolor, Larix laricina, Picea abies, and Pseudotsuga menziesii), one species from each of three other families of Coniferales [Sequoia sempervirens (Taxodiaceae), Torreya californica (Taxaceae) and Calocedrus decurrens (Cupressaceae)], and to one angiosperm species (Populus nigra). Results showed that mapped DNA probes from lobolly pine will cross-hybridize to genomic DNA of other species of Pinus and some other genera of the Pinaceae. Only a small proportion of the probes hybridized to genomic DNA from three other families of the Coniferales and the one angiosperm examined. This study demonstrates that mapped DNA probes from loblolly pine can be used to construct RFLP maps for related species, thus enabling the opportunity for comparative genome mapping in conifers.
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Affiliation(s)
- M R Ahuja
- Institute of Forest Genetics, Pacific Southwest Research Station, USDA Forest Service, 2480 Carson Road, 95667, Placerville, CA, USA
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Abstract
Associations among alleles at nine nuclear loci and three chloroplast DNA (cpDNA) genotypes were assessed in a sample of 247 accessions of the wild barley, Hordeum vulgare ssp. spontaneum. Alleles at two of the nine nuclear loci are marked by length variations in the intergenic spacer region of ribosomal DNA (rDNA), and those of the other seven loci are well characterized allozymes. The three chloroplast DNA (cpDNA) genotypes are marked by restriction fragment length polymorphisms resulting from three polymorphic restriction sites detected by Southern blot hybridization. The analyses were performed by dividing the nine nuclear loci into a series of two-locus subsets and constructing log-linear models to characterize associations between the subsets of two nuclear loci and the cpDNA genotypes. Statistically significant associations were detected between six of the nine nuclear loci and the cpDNA genotypes, either individually as pairwise correlations, or through interaction with another nuclear locus to form three-variate complexes. Although the sample size of the present study was inadequate for statistical evaluation of higher order interactions, the results suggest the existence of interactions in which more than two nuclear loci are involved in associations with cpDNA genotypes. The observed cytonuclear associations appear to result from interplay among a number of evolutionary forces including a mating system of predominant selfing, differentiation among gene pools of local populations, and adaptation of barley genotypes to specific environmental conditions.
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Affiliation(s)
- M A Maroof
- Department of Crop and Soil Environmental Sciences, Virginia Polytechnic Institute and State University, Blacksburg 24061
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Devey ME, Jermstad KD, Tauer CG, Neale DB. Inheritance of RFLP loci in a loblolly pine three-generation pedigree. Theor Appl Genet 1991; 83:238-242. [PMID: 24202364 DOI: 10.1007/bf00226257] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/1991] [Accepted: 04/18/1991] [Indexed: 06/02/2023]
Abstract
A high-density restriction fragment length polymorphism (RFLP) linkage map is being constructed for loblolly pine (Pinus taeda L.). Loblolly pine cDNA and genomic DNA clones were used as probes in hybridizations to genomic DNAs prepared from grandparents, parents, and progeny of a three-generation outbred pedigree. Approximately 200 probes were evaluated for their ability to detect polymorphic loci between DNAs prepared from the two parent trees, 20-1010 and 11-1060, and cut with four different restriction enzymes: BamHI, DraI, EcoRI, and HindIII. More than half of the probes detecting single- or low-copy number sequences (56%) revealed polymorphisms between the two parents with at least one restriction enzyme. If necessary, an additional hybridization to DNAs prepared from the four grandparent trees was conducted to determine the zygosity of parent trees. Ten of these probes were hybridized to progeny DNAs from this cross and, as expected, the markers were inherited as simple codominant Mendelian alleles. Four of the ten probes detected segregation of three alleles at one locus, and four probes detected more than one independently segregating locus. RFLPs can be used immediately to assess genetic diversity in conifer populations and to "efingerprint" genotypes in tree improvement programs.
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Affiliation(s)
- M E Devey
- Institute of Forest Genetics, Pacific Southwest Research Station, USDA Forest Service, 2480 Carson Rd., 95667, Placerville, CA, USA
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Ali IF, Neale DB, Marshall KA. Chloroplast DNA restriction fragment length polymorphism in Sequoia sempervirens D. Don Endl., Pseudotsuga menziesii (Mirb.) Franco, Calocedrus decurrens (Torr.), and Pinus taeda L. Theor Appl Genet 1991; 81:83-89. [PMID: 24221163 DOI: 10.1007/bf00226116] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/1990] [Accepted: 07/13/1990] [Indexed: 06/02/2023]
Abstract
The extent and type of chloroplast DNA restriction fragment length polymorphism was determined among individual tree samples of coast redwood, Douglas fir, incense-cedar, and loblolly pine. A total of 107 trees was surveyed for three restriction enzymes (BamHI, EcoRI, HindIII) and six chloroplast DNA probes from petunia (P3, P4, P6, P8, P10, S8). The probes comprise 64% of the petunia chloroplast genome. Polymorphisms were detected in all species but loblolly pine. Coast redwood and incense-cedar had a small number of rare variants, whereas Douglas fir had one highly polymorphic region of insertions/deletions in sequences revealed by the P6 probe from petunia. The mutation hotspot is currently being studied by DNA sequence analysis.
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Affiliation(s)
- I F Ali
- U.S. Department of Agriculture, Institute of Forest Genetics, Pacific Southwest Forest and Range Experiment Station, Forest Service, Box 245, 94701, Berkeley, CA, USA
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Abstract
Dark-grown Douglas-fir (Pseudotsuga menziesii [Mirb.] Franco) seedlings had approximately 30% of the major polypeptide of the light-harvesting chlorophyll a/b binding protein, 30% of cab mRNA, 54% of psbA mRNA, and 14% of total chlorophyll, in comparison with amounts in light-grown seedlings. Seedlings entrained under a 24-hour photoperiod of light and dark showed small diurnal fluctuations in cab and psbA mRNA levels and, when transferred to continuous conditions, no circadian rhythms in mRNA levels were apparent. These results suggest that regulation of cab gene expression in Douglas-fir differs from regulation in angiosperms, because in the latter, both light and circadian factors strongly influence the expression of cab genes.
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Affiliation(s)
- M C Alosi
- Institute of Forest Genetics, Pacific Southwest Forest and Range Experiment Station, Berkeley, California 94701
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Neale DB, Sederoff RR. Paternal inheritance of chloroplast DNA and maternal inheritance of mitochondrial DNA in loblolly pine. Theor Appl Genet 1989; 77:212-216. [PMID: 24232531 DOI: 10.1007/bf00266189] [Citation(s) in RCA: 127] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/1988] [Accepted: 06/29/1988] [Indexed: 06/02/2023]
Abstract
The inheritance of organelle DNAs in loblolly pine was studied by using restriction fragment length polymorphisms. Chloroplast DNA from loblolly pine is paternally inherited in pitch pine x loblolly pine hybrids. Mitochondrial DNA is maternally inherited in loblolly pine crosses. The uniparental inheritance of organelle genomes from opposite sexes within the same plant appears to be unique among those higher plants that have been tested and indicates that loblolly pine, and possibly other conifers, must have special mechanisms for organelle exclusion or degradation or both. This genetic system creates an exceptional opportunity for the study of maternal and paternal genetic lineages within a single species.
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Affiliation(s)
- D B Neale
- U.S. Department of Agriculture, Institute of Forest Genetics, Pacific Southwest Forest and Range Experiment Station, Forest Service, Box 245, 94701, Berkely, CA, USA
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Abstract
Chloroplast DNA (cpDNA) diversity was found within and among populations (245 accessions total) of wild barley, Hordeum vulgare L. ssp. spontaneum Koch from Israel and Iran. Three polymorphic restriction sites (HindIII, EcoRI, BclI) which define three distinct cpDNA lineages were detected. One lineage is common to populations in the Hule Valley and Kinneret of northern Israel, and in Iran. The second lineage is found predominantly in the Lower Jordan Valley and Negev. The distribution of the third lineage is scattered but widespread throughout Israel. Sixty two accessions of cultivated barleys, H. vulgare L., were found, with two exceptions, to belong to just one cpDNA lineage of wild barley, indicating that the cpDNA of cultivated barley is less variable than its wild ancestor. These results demonstrate the need for assessing intraspecific cpDNA variability prior to choosing single accessions for phylogenetic constructions at the species level and higher.
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Affiliation(s)
- D B Neale
- Department of Genetics, University of California, Davis 95616
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Neale DB, Adams WT. Allozyme and mating-system variation in balsam fir (Abies balsamea) across a continuous elevational transect. ACTA ACUST UNITED AC 1985. [DOI: 10.1139/b85-350] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Genetic structure and the mating system of a continuous balsam fir (Abies balsamea (L.) Mill.) population spanning a 610-m elevational gradient on the southeast slope of Mt. Moosilauke, New Hampshire, were investigated by assaying eight polymorphic isozyme loci. In contrast to steep elevational clines for seedling quantitative traits found in an earlier study on the same slope, no significant differences (P > 0.05) in allelic frequencies were found among four subpopulations sampled at 854, 1159, 1312, and 1464 m above sea level. Estimates of the proportion of progeny due to outcrossing [Formula: see text] ranged from 0.78 to 0.99 (mean = 0.89) and were significantly different (P < 0.05) from [Formula: see text] in three of the four subpopulations. At timberline (1464 m), [Formula: see text] was lowest, yet the mean fixation index among adult trees was −0.149, suggesting that selection favors heterozygotes in this marginal environment. Despite the potential for extensive pollen dispersion along the slope, gene flow appears somewhat restricted because of substantial self-fertilization in some subpopulations, localized outcrossing within stands, and asynchrony of flower production among adjacent stands.
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Abstract
Mating systems in two pairs of old-growth uncut and adjacent shelterwood stands of Douglas-fir (Pseudotsuga menziesii var. 'menziesii') were compared by estimating the proportions of viable progenies due to outcrossing (t) with both single-locus and multilocus techniques. Single-locus population estimates (ťs), ranging from 0.41 to 1.16, were significantly (P<0.05) heterogeneous among loci in three of four stands; mean single-locus estimates for shelterwoods were not significantly different from those for uncut stands. Multilocus population estimates (ťm) ranged from 0.94 to 1.00; again, estimates for shelterwoods were not significantly different from those for uncut stands. Multilocus estimates were slightly higher than mean single-locus estimates for uncut stands but were nearly equivalent for shelterwoods, suggesting that related matings other than selfs may be associated with uncut stands, but not shelterwoods. Individual-tree outcrossing rates (ťm i), estimated for six trees in each shelterwood, ranged from 0.90 to 1.10 and were significantly heterogeneous among trees at one of the two shelterwoods. Outcrossing was high (> 0.90) in both uncult and shelterwood stands, and no evidence indicated that low parent-tree density had affected stand outcrossing rates.
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Affiliation(s)
- D B Neale
- Department of Forest Science, College of Forestry, Oregon State University, 97331, Corvallis, OR, USA
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Abstract
Methods for resolving electrophoretic variants from extracts of needle tissue of coastal Douglas-fir (Pseudotsuga menziesii var. menziesii (Mirb.) Franco) are described, and the inheritance of 12 of at least 15 loci that control allozymes from 11 enzyme systems are established. Evidence for the inheritance of allozyme variants was obtained in three ways: (i) comparison in seed orchard clones of allozyme genotypes determined from both megagametophyte and needle tissue; (ii) analysis of segregating full-sib progenies of seed orchard clones; and (iii) comparison of needle allozyme pattern phenotypes to previously reported embryo phenotypes. Ten of the 12 loci (coding phosphoglucomutase, PGM(1) and PGM(2); glycerate dehydrogenase, GLYDH; phosphoglucose isomerase, PG1(2); glutamate dehydrogenase, GDH; glucose-6-phosphate dehydrogenase, G-6PD; 6-phosphogluconate dehydrogenase, 6-PGD(1); isocitrate dehydrogenase, IDH; diaphorase, DIA(2); malate dehydrogenase, MDH(1)) produce clear bands in seed tissue; however, glutamate oxaloacetate transaminase GOT(3) (N) was not found in seeds and shikimic dehydrogenase (SDH) could only be clearly resolved in needles (N). Several enzymes active in seed tissue could not be detected in needle tissues.Key words: Douglas-fir, needle tissue isozymes, inheritance.
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Abstract
Evidence for the inheritance of isozymes in megagametophyte (1N) and embryo (2N) seed tissues of balsam fir (Abies balsamea (Linn.) Mill.) is presented. Segregation of isozymes in megagametophytes of heterozygous mother trees and comparison of banding patterns with those of other conifers indicate that a minimum of 14 loci code isozymes in the enzyme systems studied. Isozymes coded by 13 of these loci are detectable in both seed tissues; one locus is apparently active only in haploid tissue. Two loci segregation data were available for 20 of the 28 possible pairwise combinations of eight polymorphic loci. Chi-square tests of independence revealed that five of these pairs are linked. Genes similar to those in two of the pairs are linked in other Pinus species.
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