Paternal inheritance of chloroplast DNA and maternal inheritance of mitochondrial DNA in loblolly pine

Summary 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.     

Inconsistencies in Neanderthal genomic DNA sequences

Two recently published papers describe nuclear DNA sequences that were obtained from the same Neanderthal fossil. Our reanalyses of the data from these studies show that they are not consistent with each other and point to serious problems with the data quality in one of the studies, possibly due to modern human DNA contaminants and/or a high rate of sequencing errors.     

Characterization of EST-SSRs in loblolly pine and spruce

In the first large study of conifer expressed sequence tag-simple sequence repeats (EST-SSRs), two large conifer EST databases were characterized for EST-SSRs. One database was from “interior spruce” (white and Engelmann spruce in Southern British Columbia) and Sitka spruce, while the other was from loblolly pine. We found 475 and 629 unique EST-SSRs in loblolly pine and spruce, respectively. 3′ ESTs contained 14% more SSRs than 5′ EST reads in loblolly pine and 41% more in spruce. Conifer EST-SSRs differed conspicuously from angiosperm EST-SSRs in several aspects. EST-SSRs were considerably less frequent in conifers (one EST-SSR every ∼50 kb) than in angiosperms (one EST-SSR every ∼20 kb). Dinucleotide repeats were the most abundant repeat class in conifers, while in angiosperms, trinucleotides were most common. Finally, the AT motif was the dominant motif recovered in both conifer species, whereas AG was the most common dinucleotide repeat in angiosperms. Also, as these EST-SSRs in conifers could be developed into useful genetic markers, our work demonstrates the value of large-scale EST sequencing projects for in-silico approaches for marker development.     

Gas exchange and canopy structure of 9-year-old loblolly pine,pitch pine and pitch x loblolly hybrids

Summary Seasonal gas exchange and canopy structure were compared among 9-year-old loblolly pine (Pinus taeda L.), pitch pine (Pinus rigida Mill.), and pitch x loblolly hybrids (Pinus rigida x taeda) growing in an F2 plantation located in Critz, Va., USA. Leaf net photosynthesis, conductance, internal CO₂ concentration (c_i), water use efficiency (WUE; photosynthesis/conductance), dark respiration and the ratio of net photosynthesis/respiration did not vary among or within the three taxa. Significant differences in volume production, crown length, total crown leaf surface area and the silhouette area of shade shoots among the taxa were observed. The loblolly-South Carolina source had greater volume and crown surface area than the pitch pine, and the hybrid taxa were intermediate between the two. Although the silhouette area ratio of shade foliage varied among taxa, it was not related to volume. A strong relationship between total leaf surface area and volume was observed. Leaf conductance, c_i, WUE and leaf water potential were the physiological parameters significantly and positively correlated with volume. This study suggests that the amount of needle surface in the canopy is more important in early stand volume growth than the leaf carbon exchange rate and the degree of needle self-shading in the lower canopy.     

Magnesium uptake kinetics in loblolly pine seedlings

Recent studies have suggested that the growth of loblolly pine (Pinus taeda L.) has declined in the southern United States and it has been hypothesized that foliar Mg deficiency may play an important role in the perceived decline. Quantitative nutrient uptake models such as the Barber-Cushman model have been used successfully to investigate nutrient uptake by crop species under a variety of field and experimental conditions and may provide one approach to evaluating this question. However, in order to use this approach it is necessary to develop, for the plant species and nutrient of interest, values for maximal nutrient influx rate at high solution concentrations (I_max), the solution concentration where net influx is 0.5 I_max (K_m), and the nutrient concentration below which influx ceases (C_min). As a first step in evaluating the potential of such an approach, two sets of experiments using established solution nutrient depletion techniques were used to define these values for loblolly pine seedlings 180, 240, 365, and 425 days in age. Observed I_max values for Mg range from 7.90E-8 to 1.29E-7 mol cm^–2 s^–1 with younger seedlings having higher values. Values of K_m for all seedling ages were quite similar ranging from 8.69 to 8.58E-3 mol cm^–3. Most importantly, the results of both experiments indicate that during a growth flush, seedlings will withdraw Mg from solution until the concentration is essentially zero (C_min=0). During non-flush periods uptake rates appear to be greatly reduced. Therefore, efforts to model Mg uptake will need to take these differences as well as seedling age influences into consideration.     

Decoding the massive genome of loblolly pine using haploid DNA and novel assembly strategies

Background

The size and complexity of conifer genomes has, until now, prevented full genome sequencing and assembly. The large research community and economic importance of loblolly pine, Pinus taeda L., made it an early candidate for reference sequence determination.

Results

We develop a novel strategy to sequence the genome of loblolly pine that combines unique aspects of pine reproductive biology and genome assembly methodology. We use a whole genome shotgun approach relying primarily on next generation sequence generated from a single haploid seed megagametophyte from a loblolly pine tree, 20-1010, that has been used in industrial forest tree breeding. The resulting sequence and assembly was used to generate a draft genome spanning 23.2 Gbp and containing 20.1 Gbp with an N50 scaffold size of 66.9 kbp, making it a significant improvement over available conifer genomes. The long scaffold lengths allow the annotation of 50,172 gene models with intron lengths averaging over 2.7 kbp and sometimes exceeding 100 kbp in length. Analysis of orthologous gene sets identifies gene families that may be unique to conifers. We further characterize and expand the existing repeat library based on the de novo analysis of the repetitive content, estimated to encompass 82% of the genome.

Conclusions

In addition to its value as a resource for researchers and breeders, the loblolly pine genome sequence and assembly reported here demonstrates a novel approach to sequencing the large and complex genomes of this important group of plants that can now be widely applied.     

Carbon cycling in a loblolly pine plantation

Summary The carbon cycle of a loblolly pine plantation in North Carolina was examined during its 12th through 16th years from planting. Net primary production during the study period averaged 2056 g C m^-2 year^-1. With autotrophic respiration equal to 2068 g C, the calculated gross production was 4124 g C m^-2 year^-1. Heterotrophic respiration of 694 g C m^-2 year^-1 resulted in net ecosystem production of 1362 g C m^-2 year^-1. In carbon cycle comparisons between forest ecosystems, autotrophic respiration rates were found to be closely coupled to regional temperature.     

Development of DNA methylation-based epigenetic age predictors in loblolly pine (Pinus taeda)

Biological ageing is connected to life history variation across ecological scales and informs a basic understanding of age-related declines in organismal function. Altered DNA methylation dynamics are a conserved aspect of biological ageing and have recently been modelled to predict chronological age among vertebrate species. In addition to their utility in estimating individual age, differences between chronological and predicted ages arise due to acceleration or deceleration of epigenetic ageing, and these discrepancies are linked to disease risk and multiple life history traits. Although evidence suggests that patterns of DNA methylation can describe ageing in plants, predictions with epigenetic clocks have yet to be performed. Here, we resolve the DNA methylome across CpG, CHG, and CHH-methylation contexts in the loblolly pine tree (Pinus taeda) and construct epigenetic clocks capable of predicting ages in this species within 6% of its maximum lifespan. Although patterns of CHH-methylation showed little association with age, both CpG and CHG-methylation contexts were strongly associated with ageing, largely becoming hypomethylated with age. Among age-associated loci were those in close proximity to malate dehydrogenase, NADH dehydrogenase, and 18S and 26S ribosomal RNA genes. This study reports one of the first epigenetic clocks in plants and demonstrates the universality of age-associated DNA methylation dynamics which can inform conservation and management practices, as well as our ecological and evolutionary understanding of biological ageing in plants.     

Nutrient proportions in foliage of semi-mature loblolly pine

Summary Nitrogen and phosphorus limitations to growth are common in many loblolly pine (Pinus taeda) stands. Interactions of these nutrients may complicate interpretation of foliar nutrient analysis for predicting response to forest fertilization. Proportions of foliar nutrient concentrations (and the changes in these proportions following fertilization) were examined in 36 semi-mature loblolly pine plantations in the southeastern United States. Mean proportions of nutrient concentrations (NPKCaMg) for non-fertilized stands were 1009.336.517.29.2. Potassium and phosphorus were higher. Nitrogen fertilization generally decreased the PN ratio and enhanced growth, indicating a nitrogen deficiency in most stands under study. Additions of nitrogen and phosphorus together yielded a significant increase in the PN ratio. Effects of fertilization effects on other nutrient concentration ratios were also examined.Paper No. 9401 of the Journal Series of the North Carolina Agricultural Research Service, Raleigh, NC 27695.     

Patterns of saproxylic beetle succession in loblolly pine

• 1 Patterns of insect succession in dead wood remain unclear, particularly beyond the first several years of decay. In the present study, saproxylic beetles were sampled from loblolly pine (Pinus taeda L.) logs aged between 1 month and 9 years old using both emergence traps attached to logs in the field and rearing bags in the laboratory.
• 2 Species richness peaked within the first year as a result of a diverse assemblage of bark beetles, wood‐borers and predators associated with young logs. After the phloem phase, there were no significant differences in species richness among decay classes.
• 3 Beetle communities differed significantly among decay classes, with 25 and seven species being significantly associated with young and old logs, respectively.

     

Microarray-based survey of repetitive genomic sequences in Vicia spp.

A modified DNA microarray-based technique was devised for preliminary screening of short fragment genomic DNA libraries from three Vicia species (V. melanops, V. narbonensis, and V. sativa) to isolate representative highly abundant DNA sequences that show different distribution patterns among related legume species. The microarrays were sequentially hybridized with labeled genomic DNAs of thirteen Vicia and seven other Fabaceae species and scored for hybridization signals of individual clones. The clones were then assigned to one of the following groups characterized by hybridization to: (1) all tested species, (2) most of the Vicia and Pisum species, (3) only a few Vicia species, and (4) preferentially a single Vicia species. Several clones from each group, 65 in total, were sequenced. All Group I clones were identified as rDNA genes or fragments of chloroplast genome, whereas the majority of Group II clones showed significant homologies to retroelement sequences. Clones in Groups III and IV contained novel dispersed repeats with copy numbers 10²–10⁶/1C and two genus-specific tandem repeats. One of these belongs to the VicTR-B repeat family, and the other clone (S12) contains an amplified portion of the rDNA intergenic spacer. In situ hybridization using V. sativa metaphase chromosomes revealed the presence of the S12 sequences not only within rDNA genes, but also at several additional loci. The newly identified repeats, as well as the retroelement-like sequences, were characterized with respect to their abundance within individual genomes. Correlations between the repeat distributions and the current taxonomic classification of these species are discussed.     

Accuracy of genomic selection methods in a standard data set of loblolly pine (Pinus taeda L.)

Genomic selection can increase genetic gain per generation through early selection. Genomic selection is expected to be particularly valuable for traits that are costly to phenotype and expressed late in the life cycle of long-lived species. Alternative approaches to genomic selection prediction models may perform differently for traits with distinct genetic properties. Here the performance of four different original methods of genomic selection that differ with respect to assumptions regarding distribution of marker effects, including (i) ridge regression-best linear unbiased prediction (RR-BLUP), (ii) Bayes A, (iii) Bayes Cπ, and (iv) Bayesian LASSO are presented. In addition, a modified RR-BLUP (RR-BLUP B) that utilizes a selected subset of markers was evaluated. The accuracy of these methods was compared across 17 traits with distinct heritabilities and genetic architectures, including growth, development, and disease-resistance properties, measured in a Pinus taeda (loblolly pine) training population of 951 individuals genotyped with 4853 SNPs. The predictive ability of the methods was evaluated using a 10-fold, cross-validation approach, and differed only marginally for most method/trait combinations. Interestingly, for fusiform rust disease-resistance traits, Bayes Cπ, Bayes A, and RR-BLUB B had higher predictive ability than RR-BLUP and Bayesian LASSO. Fusiform rust is controlled by few genes of large effect. A limitation of RR-BLUP is the assumption of equal contribution of all markers to the observed variation. However, RR-BLUP B performed equally well as the Bayesian approaches.The genotypic and phenotypic data used in this study are publically available for comparative analysis of genomic selection prediction models.     

In vitro regeneration of loblolly pine and random amplified polymorphic DNA analyses of regenerated plantlets

 Adventitious buds were induced from organogenic callus derived from mature zygotic embryos of three lines (E-311, E-440, and E-822) of loblolly pine (Pinus taeda L.) within 27 weeks of culture. The influence of cytokinins, silver nitrate, and low-temperature treatment on the differentiation of adventitious buds was analyzed. Elongation of adventitious buds was achieved on TE medium supplemented with 0.5 mg/l indole-3-butyric acid (IBA) and 1 mg/l 6-benzyladenine (BA). After adventitious shoots had rooted on TE medium supplemented with 0.5 mg/l IBA, 2 mg/l BA, and 0.5 mg/l gibberellic acid, 498 regenerated plantlets were transferred to a perlite:peatmoss:vermiculite (1 :>: 1) soil mixture; 351 of these survived in the field. Total DNA was extracted from 21 regenerated plantlets randomly chosen from the 151 regenerated plantlets of line E-822. Random amplified polymorphic DNA (RAPD) analysis using 80 arbitrary oligonucleotide 10-mers showed that 21 primers gave 107 clear reproducible bands, with the amplification products being monomorphic for all of the plantlets of line E-822 tested. A total of 2,247 bands obtained from these studies exhibited no aberration in RAPD banding patterns among the tested plantlets. These results suggest that somatic organogenesis can be used for clonal micropropagation of some lines of loblolly pine without the fear of the appearance of unwanted somaclonal variants. Received: 5 August 2000 / Revision received: 5 September 2000 / Accepted: 10 October 2000     

Winter nitrogen fertilization of loblolly pine seedlings

Loblolly pine (Pinus taeda L.) seedlings were nitrogen fertilized during winter in a bare root forest tree nursery located in the coastal plain of the southeastern United States. Total application rates were 0, 50, 100, and 200 kg/N/ha applied in split applications 4 weeks apart in January and February. Seedlings were lifted and outplanted in March, 4 weeks after the second fertilization and measured at 3 and 6 months after outplanting. No seedling morphological differences were encountered at the time of lifting and outplanting although seedling shoot nitrogen content was 28% greater in the highest fertilization treatment compared to the check. Shoot nitrogen concentrations fell after outplanting regardless of treatment, decreasing from an average of 1.51% across all treatments at the time of planting to 0.64% at 6 months after planting. When measured at 6 months after outplanting, seedling dry weight and height growth after planting was shown to increase by 12% and 24%, respectively, for the high nitrogen treatment. This and other studies across a variety of sites have found positive post-outplanting seedling growth response after nutrient loading in the nursery.     

Functional genomics and cell wall biosynthesis in loblolly pine

Loblolly pine (Pinus taeda L.) is the most widely planted tree species in the USA and an important tree in commercial forestry world-wide. The large genome size and long generation time of this species present obstacles to both breeding and molecular genetic analysis. Gene discovery by partial DNA sequence determination of cDNA clones is an effective means of building a knowledge base for molecular investigations of mechanisms governing aspects of pine growth and development, including the commercially relevant properties of secondary cell walls in wood. Microarray experiments utilizing pine cDNA clones can be used to gain additional information about the potential roles of expressed genes in wood formation. Different methods have been used to analyze data from first-generation pine microarrays, with differing degrees of success. Disparities in predictions of differential gene expression between cDNA sequencing experiments and microarray experiments arise from differences in the nature of the respective analyses, but both approaches provide lists of candidate genes which should be further investigated for potential roles in cell wall formation in differentiating pine secondary xylem. Some of these genes seem to be specific to pine, while others also occur in model plants such as Arabidopsis, where they could be more efficiently investigated.     

Three separate mitochondrial DNA sequences are contiguous in human genomic DNA

We isolated from a HeLa genomic library 38 plaques that hybridized to total mitochondrial (mt) DNA isolated from human placenta. One clone (HLmt-17.8) hybridized to a 740 base-pair (12 S ribosomal RNA gene and displacement loop) mtDNA probe and was characterized in more detail. Within its 17.8 x 10(3) base-pair insert a 1.6 x 10(3) base-pair mtDNA fragment was similar to three non-sequential coding genes of human mtDNA, including a part of the 12 S ribosomal RNA (684-971), the cytochrome oxidase I (6553-7302), and two NADH dehydrogenase [ND4L/ND4] (10,606-11,159). The similarity to human mtDNA sequences was 92.0%, 92.3% and 92.4%, respectively, the highest degree of similarity to human mtDNA so far reported. This is also the first report of several adjacent mtDNA-like sequences in cellular chromosomes. The mtDNA-like sequences in HLmt-17.8 was found in the DNAs of human placenta, freshly isolated human leukocytes, foreskin and several human cell lines; but it was not present in other primates or lower organisms. The HLmt-17.8 mtDNA-like region appears to be a pseudogene that transferred into the nucleus in humans more recently than nine million years ago.     

Identifying potential tRNA genes in genomic DNA sequences.

We have developed an algorithm that automatically and reproducibly identifies potential tRNA genes in genomic DNA sequences, and we present a general strategy for testing the sensitivity of such algorithms. This algorithm is useful for the flagging and characterization of long genomic sequences that have not been experimentally analyzed for identification of functional regions, and for the scanning of nucleotide sequence databases for errors in the sequences and the functional assignments associated with them. In an exhaustive scan of the GenBank database, 97.5% of the 744 known tRNA genes were correctly identified (true-positives), and 42 previously unidentified sequences were predicted to be tRNAs. A detailed analysis of these latter predictions reveals that 16 of the 42 are very similar to known tRNA genes, and we predict that they do, in fact, code for tRNA, yielding a false-positive rate for the algorithm of 0.003%. The new algorithm and testing strategy are a considerable improvement over any previously described strategies for recognizing tRNA genes, and they allow detections of genes (including introns) embedded in long genomic sequences.     

Phenylalanine ammonia-lyase from loblolly pine : purification of the enzyme and isolation of complementary DNA clones

Phenylalanine ammonia-lyase (EC 4.3.1.5) has been purified from differentiating secondary xylem of loblolly pine (Pinus taeda L.). Native molecular weight of the enzyme was estimated to be 280,000, with a subunit molecular weight of 74,000; isoelectric point, 5.8; and Michaelis constant for i-phenylalanine, 27 micromolar. No evidence was obtained for the existence of isoforms of the enzyme, nor for negative cooperativity of substrate binding. Polyclonal antibodies were raised against the phenylalanine ammonia-lyase subunit and used to identify a pal clone in an expression library of xylem complementary DNA (cDNA). Polymerase chain reaction, using oligonucleotide primers made from N-terminal amino acid sequence and from the 5′ end of the clone isolated from the expression library, was also used to isolate cDNA clones. These methods yielded cDNA clones covering the protein coding region of the pal messenger RNA. Comparisons of nucleotide sequence of pal cDNAs from pine, bean, sweet potato, and rice showed 60 to 62% identity between the pine clone and the angiosperm clones.