We report the draft genome of the black cottonwood tree, Populus trichocarpa . Integration of shotgun sequence assembly with genetic mapping enabled chromosome-scale reconstruction of the genome. More than 45,000 putative protein-coding genes were identified. Analysis of the assembled genome revealed a whole-genome duplication event; about 8000 pairs of duplicated genes from that event survived in the Populus genome. A second, older duplication event is indistinguishably coincident with the divergence of the Populus and Arabidopsis lineages. Nucleotide substitution, tandem gene duplication, and gross chromosomal rearrangement appear to proceed substantially more slowly in Populus than in Arabidopsis. Populus has more protein-coding genes than Arabidopsis , ranging on average from 1.4 to 1.6 putative Populus homologs for each Arabidopsis gene. However, the relative frequency of protein domains in the two genomes is similar. Overrepresented exceptions in Populus include genes associated with lignocellulosic wall biosynthesis, meristem development, disease resistance, and metabolite transport.

BackgroundThe 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.ResultsWe 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.ConclusionsIn 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.

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.

Summary• Herbivore-induced plant volatiles (HIPVs), in addition to attracting natural enemies of herbivores, can serve a signaling function within plants to induce or prime defenses. However, it is largely unknown, particularly in woody plants, which volatile compounds within HIPV blends can act as signaling molecules.• Leaves of hybrid poplar saplings were exposed in vivo to naturally wound-emitted concentrations of the green leaf volatile (GLV) cis-3-hexenyl acetate (z3HAC) and then subsequently fed upon by gypsy moth larvae. Volatiles were collected throughout the experiments, and leaf tissue was collected to measure phytohormone concentrations and expression of defense-related genes.• Relative to controls, z3HAC-exposed leaves had higher concentrations of jasmonic acid and linolenic acid following gypsy moth feeding. Furthermore, z3HAC primed transcripts of genes that mediate oxylipin signaling and direct defenses, as determined by both qRT-PCR and microarray analysis using the AspenDB 7 K expressed sequence tags (EST) microarray containing c. 5400 unique gene models. Moreover, z3HAC primed the release of terpene volatiles.• The widespread priming response suggests an adaptive benefit to detecting z3HAC as a wound signal. Thus, woody plants can detect and use z3HAC as a signal to prime defenses before actually experiencing damage. GLVs may therefore have important ecological functions in arboreal ecosystems.

Summary• Genomic selection is increasingly considered vital to accelerate genetic improvement. However, it is unknown how accurate genomic selection prediction models remain when used across environments and ages. This knowledge is critical for breeders to apply this strategy in genetic improvement.• Here, we evaluated the utility of genomic selection in a Pinus taeda population of c. 800 individuals clonally replicated and grown on four sites, and genotyped for 4825 singlenucleotide polymorphism (SNP) markers. Prediction models were estimated for diameter and height at multiple ages using genomic random regression best linear unbiased predictor (BLUP).• Accuracies of prediction models ranged from 0.65 to 0.75 for diameter, and 0.63 to 0.74 for height. The selection efficiency per unit time was estimated as 53-112% higher using genomic selection compared with phenotypic selection, assuming a reduction of 50% in the breeding cycle. Accuracies remained high across environments as long as they were used within the same breeding zone. However, models generated at early ages did not perform well to predict phenotypes at age 6 yr.• These results demonstrate the feasibility and remarkable gain that can be achieved by incorporating genomic selection in breeding programs, as long as models are used at the relevant selection age and within the breeding zone in which they were estimated.

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food supply. Curry et al. (1995) predicted decreased soybean yields in the southeastern USA associated with Climate change due to increased [CO 2 ] and elevated temperature a 5ЊC increase in temperature predicted by several may impact the composition of crop seed. This study was conducted to determine the potential effects of climate change on composition global climate change models. Allen and Boote (2000) and gene expression of soybean [Glycine max (L.) Merr. cv. 'Bragg'] reviewed the documented impacts of climate change on seed. Soybean plants were grown in sunlit, controlled environment soybean, including decreased yield and quality due to chambers under diel, sinusoidal temperatures of 28/18, 32/22, 36/26, higher growth temperature. Sunlit, controlled environ-40/30, and 44/34؇C (day/night, maximum/minimum), and two levels ment chambers have been used to examine the effects of [CO 2 ], 350 and 700 mol mol Ϫ1 , imposed during the entire life and interactions of increased [CO 2 ] and temperature cycle. The effect of temperature on mature seed composition and on plants (Pickering et al., 1994), revealing important transcripts in developing seed was pronounced, but there was no effect alterations of physiology, growth, and seed yield (Baker of [CO 2 ]. Total oil concentration was highest at 32/22؇C and decreased and Allen, 1993; Allen and Boote, 2000). with further increase in temperature. Oleic acid concentration in-The unique chemical composition of soybean has creased with increasing temperature whereas linolenic acid decreased. Concentrations of N and P increased with temperature to 40/30؇C, made it one of the most valuable agronomic crops worldthen decreased. Total nonstructural carbohydrates (TNC) decreased wide. Consumed for thousands of years in Asia, soybean as temperatures increased, and the proportion of soluble sugars to has steadily gained importance as food in the USA, and starch decreased. Transcripts of a gene that is downregulated by auxin many new products have been developed using soybean (ADR12) were dramatically downregulated by elevated temperature, seed as raw material (Liu, 1997). Oil and protein compossibly reflecting the altered course of seed development under enviprise ≈20 and 40%, respectively, of the dry weight of ronmental stress. Transcripts of ␤-glucosidase, a gene expressed dursoybean seed, and approximate values of other compoing normal soybean seed development, were detected in seed grownnents include carbohydrates (30%), crude fiber (5%), at 28/18؇C but not in seed grown at 40/30؇C, which also suggests and ash (5%) (Hymowitz et al., 1972). In addition, soythat normal programs affecting seed composition were perturbed by bean contains minerals such as Fe, Cu, Mn, Ca, Mg, elevated temperature. These results confirm previous studies indicating that high temperature alters soybean seed composition, and sug-Zn, Co, P, and K. Vitamins B 1 , B 2 , and B 6 , as well as gest possible mechanisms by which climate change may affect soybean isoflavones, are also available in soybean (A...

Until very recently, complete characterization of the megagenomes of conifers has remained elusive. The diploid genome of sugar pine (Pinus lambertiana Dougl.) has a highly repetitive, 31 billion bp genome. It is the largest genome sequenced and assembled to date, and the first from the subgenus Strobus, or white pines, a group that is notable for having the largest genomes among the pines. The genome represents a unique opportunity to investigate genome "obesity" in conifers and white pines. Comparative analysis of P. lambertiana and P. taeda L. reveals new insights on the conservation, age, and diversity of the highly abundant transposable elements, the primary factor determining genome size. Like most North American white pines, the principal pathogen of P. lambertiana is white pine blister rust (Cronartium ribicola J.C. Fischer ex Raben.). Identification of candidate genes for resistance to this pathogen is of great ecological importance. The genome sequence afforded us the opportunity to make substantial progress on locating the major dominant gene for simple resistance hypersensitive response, Cr1. We describe new markers and gene annotation that are both tightly linked to Cr1 in a mapping population, and associated with Cr1 in unrelated sugar pine individuals sampled throughout the species' range, creating a solid foundation for future mapping. This genomic variation and annotated candidate genes characterized in our study of the Cr1 region are resources for future marker-assisted breeding efforts as well as for investigations of fundamental mechanisms of invasive disease and evolutionary response.KEYWORDS conifer genome; transposable elements; white pine blister rust T HE gymnosperm genus Pinus is diverse and ubiquitous in temperate zones (Critchfield and Little 1966;Farjon and Filer 2013). Pines are often the keystone trees of terrestrial ecosystems (Richardson and Rundel 1998;Keane et al. 2012, and citations therein). Typical of conifers, pines have megagenomes that vary greatly in size among species, yet their karyotype is highly conserved. Pinus is divided into two large, ancient monophyletic subgenera, Strobus and Pinus, "white pines" and "yellow pines," respectively (Critchfield and Little 1966;Gernandt et al. 2005). The first Pinus genome sequence (22 Gbp) was recently reported for Pinus taeda L. ), a yellow pine commonly known as loblolly pine. The genomes of white pines are larger and more variable in size (Tomback 1982). Fossils allied with Strobus are known from the early Tertiary and late Cretaceous (Millar 1998) et al. 2006), the discovery of the underlying genes, and of markers serviceable for genetic improvement in reforestation, may be greatly accelerated by the genome sequence itself. P. lambertiana, commonly known as sugar pine, is a white pine native to western North America that is distributed from northern Oregon to Baja California at a wide span of altitudes. It is currently the tallest pine species, with heights reaching 76 m. The female cones of sugar pine are also gigan...