Nicholas C. Wheeler

Association genetics in Pinus taeda L. I. wood property traits

Genetic association is a powerful method for dissecting complex adaptive traits due to (i) fine-scale mapping resulting from historical recombination, (ii) wide coverage of phenotypic and genotypic variation within a single experiment, and (iii) the simultaneous discovery of loci and alleles. In this article, genetic association among single nucleotide polymorphisms (58 SNPs) from 20 wood- and drought-related candidate genes and an array of wood property traits with evolutionary and commercial importance, namely, earlywood and latewood specific gravity, percentage of latewood, earlywood microfibril angle, and wood chemistry (lignin and cellulose content), was tested using mixed linear models (MLMs) that account for relatedness among individuals by using a pairwise kinship matrix. Population structure, a common systematic bias in association studies, was assessed using 22 nuclear microsatellites. Different phenotype:genotype associations were found, some of them confirming previous evidence from collocation of QTL and genes in linkage maps (for example, 4cl and percentage of latewood) and two that involve nonsynonymous polymorphisms (cad SNP M28 with earlywood specific gravity and 4cl SNP M7 with percentage of latewood). The strongest genetic association found in this study was between allelic variation in α-tubulin, a gene involved in the formation of cortical microtubules, and earlywood microfibril angle. Intragenic LD decays rapidly in conifers; thus SNPs showing genetic association are likely to be located in close proximity to the causative polymorphisms. This first multigene association genetic study in forest trees has shown the feasibility of candidate gene strategies for dissecting complex adaptive traits, provided that genes belonging to key pathways and appropriate statistical tools are used. This approach is of particular utility in species such as conifers, where genomewide strategies are limited by their large genomes.

Mapping of quantitative trait loci controlling adaptive traits in coastal Douglas-fir. I. Timing of vegetative bud flush

Abstract Thirty three unique quantitative trait loci (QTLs) affecting the timing of spring bud flush have been identified in an intraspecific mapping population of coastal Douglas-fir [Pseudotsuga menziesii (Mirb.) Franco var. menziesii]. Both terminal and lateral bud flush were measured over a 4-year period on clonal replicates at two test sites, allowing for the repeated estimation of QTLs. QTLs were detected on 12 linkage groups and, in general, each explained a small proportion of the total phenotypic variance and were additive in effect. Several QTLs influence the timing of bud flush over multiple years, supporting earlier evidence that the timing of bud flush through developmental stages is under moderate to strong genetic control by the same suite of genes through developmental stages. However, only a few QTLs controlling the timing of bud flush were detected at both test sites, suggesting that geographic location plays a major role in the phenology of spring growth. A small number of QTLs with year and site interactions were also estimated.

Mapping of quantitative trait loci controlling adaptive traits in coastal Douglas-fir. II. Spring and fall cold-hardiness

Abstract Quantitative trait loci (QTLs) affecting fall and spring cold-hardiness were identified in a three-generation outbred pedigree of coastal Douglas-fir [Pseudotsuga meniziesii (Mirb.) Franco var. menziesii]. Eleven QTLs controlling fall cold-hardiness were detected on four linkage groups, and 15 QTLs controlling spring cold-hardiness were detected on four linkage groups. Only one linkage group contained QTLs for both spring and fall cold-hardiness, and these QTLs tended to map in close proximity to one another. Several QTLs were associated with hardiness in all three shoot tissues assayed in the spring, supporting previous reports that there is synchronization of plant tissues during de-acclimatization. For fall cold-hardiness, co-location of QTLs was not observed for the different tissues assayed, which is consistent with previous reports of less synchronization of hardening in the fall. In several cases, QTLs for spring or fall cold-hardiness mapped to the same location as QTLs controlling spring bud flush. QTL estimations, relative magnitudes of heritabilities, and genetic correlations based on clonal data in this single full-sib family, supports conclusions about the genetic control and relationships among cold-hardiness traits observed in population samples of Douglas-fir in previous studies.

Chestnut resistance to the blight disease: insights from transcriptome analysis

BackgroundA century ago, Chestnut Blight Disease (CBD) devastated the American chestnut. Backcross breeding has been underway to introgress resistance from Chinese chestnut into surviving American chestnut genotypes. Development of genomic resources for the family Fagaceae, has focused in this project on Castanea mollissima Blume (Chinese chestnut) and Castaneadentata (Marsh.) Borkh (American chestnut) to aid in the backcross breeding effort and in the eventual identification of blight resistance genes through genomic sequencing and map based cloning. A previous study reported partial characterization of the transcriptomes from these two species. Here, further analyses of a larger dataset and assemblies including both 454 and capillary sequences were performed and defense related genes with differential transcript abundance (GDTA) in canker versus healthy stem tissues were identified.ResultsOver one and a half million cDNA reads were assembled into 34,800 transcript contigs from American chestnut and 48,335 transcript contigs from Chinese chestnut. Chestnut cDNA showed higher coding sequence similarity to genes in other woody plants than in herbaceous species. The number of genes tagged, the length of coding sequences, and the numbers of tagged members within gene families showed that the cDNA dataset provides a good resource for studying the American and Chinese chestnut transcriptomes. In silico analysis of transcript abundance identified hundreds of GDTA in canker versus healthy stem tissues. A significant number of additional DTA genes involved in the defense-response not reported in a previous study were identified here. These DTA genes belong to various pathways involving cell wall biosynthesis, reactive oxygen species (ROS), salicylic acid (SA), ethylene, jasmonic acid (JA), abscissic acid (ABA), and hormone signalling. DTA genes were also identified in the hypersensitive response and programmed cell death (PCD) pathways. These DTA genes are candidates for host resistance to the chestnut blight fungus, Cryphonectria parasitica.ConclusionsOur data allowed the identification of many genes and gene network candidates for host resistance to the chestnut blight fungus, Cryphonectria parasitica. The similar set of GDTAs in American chestnut and Chinese chestnut suggests that the variation in sensitivity to this pathogen between these species may be the result of different timing and amplitude of the response of the two to the pathogen infection. Resources developed in this study are useful for functional genomics, comparative genomics, resistance breeding and phylogenetics in the Fagaceae.

Role of genomics in the potential restoration of the American chestnut

The development of genomic tools will enhance traditional tree breeding technologies leading to more certain and timely recovery of the American chestnut, a keystone heritage tree of the eastern United States. Major efforts are being made in gene discovery, genetic marker development, construction of a BAC-based physical map, and DNA transformation technology. A strategy of map-based cloning, association genetics, and genetic engineering, combined with traditional and marker-assisted backcross breeding is proposed for the long-term genetic restoration of this iconic tree species.

A physical map of the Chinese chestnut (Castanea mollissima) genome and its integration with the genetic map

Three Chinese chestnut bacterial artificial chromosome (BAC) libraries were developed and used for physical map construction. Specifically, high information content fingerprinting was used to assemble 126,445 BAC clones into 1,377 contigs and 12,919 singletons. Integration of the dense Chinese chestnut genetic map with the physical map was achieved via high-throughput hybridization using overgo probes derived from sequence-based genetic markers. A total of 1,026 probes were anchored to the physical map including 831 probes corresponding to 878 expressed sequence tag-based markers. Within the physical map, three BAC contigs were anchored to the three major fungal blight-resistant quantitative trait loci on chestnut linkage groups B, F, and G. A subset of probes corresponding to orthologous genes in poplar showed only a limited amount of conserved gene order between the poplar and chestnut genomes. The integrated genetic and physical map of Chinese chestnut is available at www.fagaceae.org/physical_maps.

Polymix breeding with paternity analysis in Populus: a test for differential reproductive success (DRS) among pollen donors

Polymix breeding with paternity analysis (PMX/WPA) has been proposed as an alternative to traditional full-sib breeding and testing schemes. To fully capture the benefits of PMX/WPA, differential reproductive success (DRS) of pollen parents used in the polymix must be modest. DRS was evaluated in an operational test of PMX/WPA for a hybrid poplar breeding program. A 16-parent pollen polymix (Populus nigra L.) was used to pollinate seven clones of Populus deltoides (Bartr. ex. Marshall) under greenhouse breeding conditions. Progeny were grown out briefly and randomly sampled (357) prior to out-planting in field trials. Twenty-eight simple sequence repeat (SSR) loci were evaluated and 15 were selected for genetic characterization in small populations of three Populus spp (P. nigra, P. deltoides, and P. balsamifera spp trichocarpa Torr. & Gray). Seven loci were ultimately selected for paternity analysis of progeny. The average exclusion probability of the seven loci in P. nigra was 0.604; combined, the theoretical exclusion probability was 0.9999. However, only 95% of sampled progeny were unambiguously assigned a single paternal parent. Missing data likely accounted for most of the ambiguity. DRS was statistically significant though not prohibitive for practical utility of PMX/WPA as a breeding system. Of the 112 potential crosses in this study, 92 were represented. Eight of the 16 pollen parents contributed 83% of the progeny. Good pollen vigor, as measured by germination percent, did not ensure paternal success, but poor vigor was associated with lack of paternal success. PMX/WPA appears to be logistically and economically attractive for hybrid poplar breeding and testing.

Genomics of forest and ecosystem health in the Fagaceae: meeting report

A summary of 35 keynote, invited and volunteer papers delivered at a recent international conference is provided along with web links to PDFs of those presentations. Major conference themes targeted Genomic Tool Development for the Fagaceae and Application of Genomic Resources. The meeting provided a venue for reviewing the rapidly expanding knowledge base on Fagaceae genomics and for developing collaborations between scientists from Europe and North America.