Identification of QTLs influencing wood property traits in loblolly pine ( Pinus taeda L.). II. Chemical wood properties

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, α-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., α-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 QTL×environment 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. Received: 19 January 2001 / Accepted: 31 May 2001     

Identification of quantitative trait loci influencing annual height- and diameter-increment growth in loblolly pine (Pinus taeda L.)

 Quantitative trait loci (QTLs) for annual height- and diameter-increment growth were estimated in each of two three-generation loblolly pine pedigrees. Annual height-increment was measured in three consecutive years in the BASE pedigree and in four consecutive years in the QTL pedigree. Annual diameter-increment was measured only in the QTL pedigree for two consecutive years. An interval mapping-approach was used to estimate the number of QTLs, the magnitude of QTL effects, and their position on genetic linkage maps. Thirteen different height-increment and eight different diameter-increment QTLs were detected, suggesting that the these traits are, at least in part, controlled by a few genes of large effect. Little evidence was found for the expression of individual QTLs in multiple years or in multiple genetic backgrounds. These results were discussed in terms of the power of the experiment and their consequences for marker-assisted breeding. Received: 12 July 1998/Accepted: 5 August 1998     

Agrobacterium-mediated transformation and assessment of factors influ-encing transgene expression in loblolly pine (Pinus taeda L.)

INTRODUCTIONRecombinant DNA technology is a powerful toolfor the introduction of foreign genes into longlivedperennials and fOr fundamelltal studies of gene expression. Using such techniques, we can overcomethe difficulties associated with the breeding of a long-lived perennial. At present, although considerablereseaxch effort has been devoted to the genetic en-gineering of fOrest trees, it has lagged behind ad-vances made in herbaceous crops due both to eco-nomics and the recalcitrant n…     

Genotype by environment interaction for index traits that combine growth and wood density in loblolly pine

 Genotype×environment interactions of individual traits have been assessed in numerous experiments with forest trees. However, since breeding programs rarely aim at the improvement of a single trait, the impact of G×E on index or composite traits must also be assessed. In a study with 12-year-old loblolly pine families in the southeastern U.S., G×E variance was of relatively little importance compared to genetic variance for wood density but was of greater significance for several growth traits. An index that combined stem volume and wood density to improve dry weight but maintain wood density constant (restricted selection index) resulted in substantially greater G×E variance compared to either of the component traits. The interaction variance of an index trait is shown to be a function of the index coefficients and the G×E variances and covariances for its constituent traits. As a result, for some conditions it surpasses the magnitude of G×E variance for each component trait. Received: 5 September 1996 / Accepted: 25 October 1996     

Identification of quantitative trait loci influencing wood property traits in loblolly pine (Pinus taeda L.). III. QTL Verification and candidate gene mapping

A long-term series of experiments to map QTL influencing wood property traits in loblolly pine has been completed. These experiments were designed to identify and subsequently verify QTL in multiple genetic backgrounds, environments, and growing seasons. Verification of QTL is necessary to substantiate a biological basis for observed marker-trait associations, to provide precise estimates of the magnitude of QTL effects, and to predict QTL expression at a given age or in a particular environment. Verification was based on the repeated detection of QTL among populations, as well as among multiple growing seasons for each population. Temporal stability of QTL was moderate, with approximately half being detected in multiple seasons. Fewer QTL were common to different populations, but the results are nonetheless encouraging for restricted applications of marker-assisted selection. QTL from larger populations accounted for less phenotypic variation than QTL detected in smaller populations, emphasizing the need for experiments employing much larger families. Additionally, 18 candidate genes related to lignin biosynthesis and cell wall structure were mapped genetically. Several candidate genes colocated with wood property QTL; however, these relationships must be verified in future experiments.     

Genetic mapping of expressed sequence tag polymorphism (ESTP) markers in loblolly pine (Pinus taeda L.)

The development and mapping of genetic markers based upon expressed sequence tag polymorphisms (ESTPs) in loblolly pine (Pinus taeda L.) are reported. The new markers were generated by PCR-amplification of loblolly pine genomic DNAs with primers designed from sequenced cDNAs. The cDNA libraries were constructed from RNAs expressed in the needles of loblolly pine seedlings or in the xylem from young trees. DNA polymorphisms were identified by analyzing the amplified products for differences in fragment size or restriction sites, or by examining mobility differences using denaturing gradient gel electrophoresis (DGGE). DGGE revealed more DNA polymorphisms than the other two methods. Fifty six ESTPs were mapped using either of two mapping populations and positioned onto a loblolly pine consensus genetic map. Unlike many other markers commonly used in forestry, ESTPs can be used as orthologous markers for comparative mapping, to map genes of known function, or to identify candidate genes affecting important traits in loblolly pine. Received: 10 April 2000 / Accepted: 13 July 2000     

Wood properties and ring width responses to long-term atmospheric CO2 enrichment in field-grown loblolly pine (Pinus taeda L.)

Loblolly pine (Pinus taeda L.) were grown in the field, under non-limiting nutrient conditions, in open-top chambers for 4 years at ambient CO₂ partial pressures (pCO₂) and with a CO₂-enriched atmosphere (+ 30 Pa pCO₂ compared to ambient concentration). A third replicate of trees were grown without chambers at ambient pCO₂. Wood anatomy, wood density and tree ring width were analysed using stem wood samples. No significant differences were observed in the cell wall to cell lumen ratio within the latewood of the third growth ring formed in 1994. No significant differences were observed in the density of resin canals or in the ratio of resin canal cross-sectional area to xylem area within the same growth ring. Ring widths were significantly wider in the CO₂-enrichment treatment for 3 of 4 years compared to the ambient chamber control treatment. Latewood in the 1995 growth ring was significantly wider than that in the ambient control and represented a larger percentage of the total growth-ring width. Carbon dioxide enrichment also significantly increased the total wood specific gravity (determined by displacement). However, when determined as total sample wood density by X-ray densitometry, the density of enriched samples was not significantly higher than that of the ambient chamber controls. Only the 1993 growth ring of enriched trees had a significantly higher maximum latewood density than that of trees grown on non-chambered plots or ambient chambered controls. No significant differences were observed in the minimum earlywood density of individual growth rings between chambered treatments. These results show that the most significant effect of CO₂ enrichment on wood production in loblolly pine is its influence on radial growth, measured as annual tree ring widths. This influence is most pronounced in the first year of growth and decreases with age.     

Water status and growth of loblolly pine (Pinus taeda L.) callus

Water status of Pinus taeda L. callus supported on Murashige and Skoog (MS) liquid medium was characterized over an 8 week period using thermocouple psychrometry. Medium with 30 gl⁻¹ sucrose was used to produce a high water potential (Ψ_w) of −0.4 MPa (H), and the same medium was used to create a moderate Ψ_w of −0.7 MPa (M) by the addition of 10% polyethylene glycol (PEG, w/v, MW=8000). Calli were produced from cotyledon explants on H medium for 2 weeks and then transferred to either M or H medium. Callus absorption of PEG accounted for 40% of the callus dry weight and less than 7% of the callus fresh weight. Callus dry weight (without the PEG fraction) on M medium was 40% of that observed on H medium. Fresh weight on M medium was only 15% of that observed on H medium. The Ψ_w of both H and M media remained constant throughout the culture period. On H medium, callus Ψ_w and osmotic potential (Ψ_s) both increased 0.05 MPa/week with the callus Ψ_w approaching that of the external medium. On M medium, callus Ψ_w and Ψ_s both decreased more than 0.1 MPa/week with the callus Ψ_w decreasing greatly below that of the external medium. The latter was attributed to a rapidly produced osmotic shock induced upon callus transfer and/or PEG which caused less callus hydration and resulted in reduced growth. Callus turgor potential (Ψ_p) was estimated to be +0.02 to +0.09 MPa and turgor was maintained as callus Ψ_w increased or decreased. After 8 weeks, cell volumes from callus on M medium were 50 to 60% less than on H medium, suggesting that reduced cell volumes were related to turgor maintenance.     

Correlation between infection by ophiostomatoid fungi and the presence of subterranean termites in loblolly pine (Pinus taeda L.) roots

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High-throughput genotyping and mapping of single nucleotide polymorphisms in loblolly pine (Pinus taeda L.)

The development and application of genomic tools to loblolly pine (Pinus taeda L.) offer promising insights into the organization and structure of conifer genomes. The application of a high-throughput genotyping assay across diverse forest tree species, however, is currently limited taxonomically. This is despite the ongoing development of genome-scale projects aiming at the construction of expressed sequence tag (EST) libraries and the resequencing of EST-derived unigenes for a diverse array of forest tree species. In this paper, we report on the application of Illumina’s high-throughput GoldenGate™ SNP genotyping assay to a loblolly pine mapping population. Single nucleotide polymorphisms (SNPs) were identified through resequencing of previously identified wood quality, drought tolerance, and disease resistance candidate genes prior to genotyping. From that effort, a 384 multiplexed SNP assay was developed for high-throughput genotyping. Approximately 67% of the 384 SNPs queried converted into high-quality genotypes for the 48 progeny samples. Of those 257 successfully genotyped SNPs, 70 were segregating within the mapping population. A total of 27 candidate genes were subsequently mapped onto the existing loblolly pine consensus map, which consists of 12 linkage groups spanning a total map distance of 1,227.6 cM. The ability of SNPs to be mapped to the same position as fragment-based markers previously developed within the same candidate genes, as well as the pivotal role that SNPs currently play in the dissection of complex phenotypic traits, illustrate the usefulness of high-throughput SNP genotyping technologies to the continued development of pine genomics. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Identification of QTLs for grain yield and grain-related traits of maize (Zeamays L.) using an AFLP map, different testers, and cofactor analysis

We exploited the AFLP®¹(AFLP® is a registered trademark of Keygene, N.V.) technique to map and characterise quantitative trait loci (QTLs) for grain yield and two grain-related traits of a maize segregating population. Two maize elite inbred lines were crossed to produce 229 F₂ individuals which were genotyped with 66 RFLP and 246 AFLP marker loci. By selfing the F₂ plants 229 F₃ lines were produced and subsequently crossed to two inbred testers (T1 and T2). Each series of testcrosses was evaluated in field trials for grain yield, dry matter concentration, and test weight. The efficiency of generating AFLP markers was substantially higher relative to RFLP markers in the same population, and the speed at which they were generated showed a great potential for application in marker-assisted selection. AFLP markers covered linkage group regions left uncovered by RFLPs; in particular at telomeric regions, previously almost devoided of markers. This increase of genome coverage afforded by the inclusion of the AFLPs revealed new QTL locations for all the traits investigated and allowed us to map telomeric QTLs with higher precision. The present study has also provided an opportunity to compare simple (SIM) and composite interval mapping (CIM) for QTL analysis. Our results indicated that the method of CIM employed in this study has greater power in the detection of QTLs, and provided more precise and accurate estimates of QTL positions and effects than SIM. For all traits and both testers we detected a total of 36 QTLs, of which only two were in common between testers. This suggested that the choice of a tester for identifying QTL alleles for use in improving an inbred is critical and that the expression of QTL alleles identified may be tester-specific.     

Seasonal response of photosynthesis to elevated CO2 in loblolly pine (Pinus taeda L.) over two growing seasons

Trees growing in natural systems undergo seasonal changes in environmental factors that generate seasonal differences in net photosynthetic rates. To examine how seasonal changes in the environment affect the response of net photosynthetic rates to elevated CO₂, we grew Pinus taeda L. seedlings for three growing seasons in open-top chambers continuously maintained at either ambient or ambient + 30 Pa CO₂. Seedlings were grown in the ground, under natural conditions of light, temperature nd nutrient and water availability. Photosynthetic capacity was measured bimonthly using net photosynthetic rate vs. intercellular CO₂ partial pressure (A-C_i) curves. Maximum Rubisco activity (Vc_max) and ribulose 1,5-bisphosphate regeneration capacity mediated by electron transport (J_max) and phosphate regeneration (PiRC) were calculated from A-C_i curves using a biochemically based model. Rubisco activity, activation state and content, and leaf carbohydrate, chlorophyll and nitrogen concentrations were measured concurrently with photosynthesis measurements. This paper presents results from the second and third years of treatment. Mean leaf nitrogen concentrations ranged from 13.7 to 23.8 mg g^?1, indicating that seedlings were not nitrogen deficient. Relative to ambient CO₂ seedlings, elevated CO₂ increased light-saturated net photosynthetic rates 60–110% during the summer, but < 30% during the winter. A relatively strong correlation between leaf temperature and the relative response of net photosynthetic rates to elevated CO₂ suggests a strong effect of leaf temperature. During the third growing season, elevated CO₂ reduced Rubisco activity 30% relative to ambient CO₂ seedlings, nearly completely balancing Rubisco and RuBP-regeneration regulation of photosynthesis. However, reductions in Rubisco activity did not eliminate the seasonal pattern in the relative response of net photosynthetic rates to elevated CO₂. These results indicate that seasonal differences in the relative response of net photosynthetic rates to elevated CO₂ are likely to occur in natural systems.     

Adventitious root formation in cuttings of loblolly pine (Pinus taeda L .): developmental sequence and effects of maturation

 Adventitious root formation in cuttings from fascicular shoots in loblolly pine (Pinus taeda L.) consists of four more or less discontinuous stages: (1) proliferation of cells at the base of the cutting, (2) differentiation of wound vascular tissue and periderm, (3) dedifferentiation of a zone near the wound cambium and wound phloem to form a root initial, and (4) formation of a root meristem. Anatomical changes during adventitious root initiation are described in cuttings from donors of different types and ages. Cuttings from seedlings and 3- to 7-year-old hedged stock plants rooted better than cuttings from 3-year-old tree form donors. It is concluded that the loss of rooting capacity in loblolly pine can be arrested by shearing loblolly pine stock plants to low hedges. The process of root initiation, however, was similar in cuttings from all sources and is apparently not the cause for the rapid decline of rooting potential with increasing age of the donor plant. Received: 3 June 1997 / Accepted: 15 August 1997     

AFLP mapping of QTLs for in vitro organogenesis traits using recombinant inbred lines in sunflower (Helianthus annuus L.)

Genetic control for two in vitro organogenesis traits, the number of shoots per explant plated (S/E) and the number of shoots per regenerating explant (S/RE), was investigated in 75 recombinant inbred lines (RILs) of sunflower and their two parents (PAC-2 and RHA-266). Genetic variability was observed among the 75 RILs for the organogenesis traits studied. Some RILs presented significant differences when compared with the best parental line (RHA-266). Genetic gain, in terms of the percentage of the best parent, for 32% of the selected RILs was significant. A set of 99RILs from the same cross including the 75 mentioned above was screened with 333 AFLP markers and a linkage map was constructed based on 264 linked loci. Six putative QTLs for the S/RE (tentatively named osr) and seven QTLs for the S/E (ose) trait were detected using composite interval mapping. For each trait, the QTLs explained 52% (ose) and 67% (osr) of the total phenotypic variance. These results suggested that additive gene effects predominate in explaining a large proportion of the observed genetic variation associated with regeneration ability. The coincidental location of QTLs for S/E and S/RE is discussed. Received: 20 September 1999 / Accepted: 16 May 2000     

Variations in maturation strains and root shape in root systems of Maritime pine (Pinus pinaster Ait.)

 In order to determine if different types of wood were being laid down in the root system of Maritime pine (Pinus pinaster Ait), in response to wind loading, longitudinal residual maturation strains (LRMS), indicating the existence of mechanical stress in developing wood cells, were measured in the trunk and lateral roots. Two age groups of trees (5- and 13-year- old) were compared. LRMS were greater in the trunk and roots of 13-year-old trees than in 5-year-old trees. This phenomenon may be due to increased competition between older trees. LRMS in leeward roots of both age-groups were positive i.e. the wood cells had developed under compression, as also occurs in reaction wood of gymnosperms. As leeward roots are placed under compression during tree sway, an abnormal type of wood may form in the roots in order to counteract the increased stress. In other roots, the strains were negative i.e. the cells had developed under tension, as occurs in normal wood. In the roots of younger trees, LRMS were also positive nearer the stem, thus indicating that wood formation may also be influenced by bending stresses experienced in this zone. In addition to LRMS measurements, radial growth in roots was examined in order to determine the influence of mechanical loading on secondary growth. In older trees, there was a significant increase of 34% in woody growth below the biological centre, compared to that above. This eccentricity is unlike that found in most other tree species, where secondary growth is usually greater on the upper side of the root. However, Maritime pine has a tap root, which will alter the pattern of stress within the root system. Under wind loading, a concentration of mechanical stress will develop at the bases of the stem, lateral roots and tap root. Received: 7 July 1997 / Accepted: 11 December 1997