Detecting the genetic basis of local adaptation in loblolly pine (Pinus taeda L.) using whole exome-wide genotyping and an integrative landscape genomics analysis approach

In the Southern United States, the widely distributed loblolly pine contributes greatly to lumber and pulp production, as well as providing many important ecosystem services. Climate change may affect the productivity and range of loblolly pine. Nevertheless, we have insufficient knowledge of the adaptive potential and the genetics underlying the adaptability of loblolly pine. To address this, we tested the association of 2.8 million whole exome-based single nucleotide polymorphisms (SNPs) with climate and geographic variables, including temperature, precipitation, latitude, longitude and elevation data. Using an integrative landscape genomics approach by combining multiple environmental association and outlier detection analyses, we identified 611 SNPs associated with 56 climate and geographic variables. Longitude, maximum temperature of the warm months and monthly precipitation associated with most SNPs, indicating their importance and complexity in shaping the genetic variation in loblolly pine. Functions of candidate genes related to terpenoid synthesis, pathogen defense, transcription factors and abiotic stress response. We provided evidence that environment-associated SNPs also composed the genetic structure of adaptive phenotypic traits including height, diameter, metabolite levels and expression of genes. Our study promotes understanding of the genetic basis of local adaptation in loblolly pine, and provides promising tools for selecting genotypes adapted to local environments in a changing climate

Exploring the genetic basis of gene transcript abundance and metabolite level in loblolly pine (Pinus taeda L.) using association mapping and network construction

Gene transcripts and metabolites are important regulatory checkpoints between genetic variation and complex biological processes such as wood development and drought response in conifers. Loblolly pine (Pinus taeda L.) is one of the most commonly planted forest tree species in the southern U.S. In this study, we tested for associations between 2.8 million exome-derived SNPs and the transcript abundance of 110 wood development genes, 88 disease or drought related genes as well as levels of 82 known metabolites. We identified 1841 SNPs associated with 191 gene expression phenotypes and 524 SNPs associated with 53 metabolite level phenotypes. The identified SNPs reside in genes with a wide variety of functions. We further integrated the identified SNPs and their associated expressed genes and metabolites into networks. We described the SNP-SNP interactions that significantly impacted the gene transcript abundance and metabolite level in the networks. The key loci and genes in the wood development and drought response networks were identified and analyzed. This work provides candidate genes for research on the genetic basis of gene expression and metabolism linked to wood development and drought response in loblolly pine, and highlights the efficiency of using association-mapping-based networks to discover candidate genes with important roles in complex biological processes

The mitogenome of Elaphe bimaculata (Reptilia: Colubridae) has never been published: a case with the complete mitochondrial genome of E. dione

The steppes ratsnake, Elaphe dione (Pallas, 1773), is widely distributed across Eurasia, but the systematics and phylogeography of this species remain poorly studied. Sequencing of the full mitochondrial genome of this species provides a reference for its further study. Here, we report the full mitochondrial genome of an E. dione specimen from Krasnoyarsk Krai (East Siberia, Russia). We found that it is highly similar to the previously reported mitochondrial genome of the sister species, E. bimaculata. Both species misidentification by the authors of E. bimaculata mitogenome and the introgressive hybridization between these taxa can possibly explain this observation

Genetic variation of introduced red oak (Quercus rubra) stands in Germany compared to North American populations

Although Northern red oak (Quercus rubra L.) is the most important introduced deciduous tree species in Germany, only little is known about its genetic variation. For the frst time, we describe patterns of neutral and potentially adaptive nuclear genetic variation in Northern red oak stands across Germany. For this purpose, 792 trees were genotyped including 611 trees from 12 stands in Germany of unknown origin and 181 trees from four populations within the natural distribution area in North America. Our marker set included 12 potentially adaptive (expressed sequence tag-derived simple sequence repeat=EST SSR) and 8 putatively selectively neutral nuclear microsatellite (nSSR) markers. Our results showed that German stands retain comparatively high levels of genetic variation at both EST-SSRs and nSSRs, but are more similar to each other than to North American populations. These fndings are in agreement with earlier chloroplast DNA analyses which suggested that German populations originated from a limited geographic area in North America. The comparison between potentially adaptive and neutral microsatellite markers did not reveal diferences in the analyzed diversity and diferentiation measures for most markers. However, locus FIR013 was identifed as a potential outlier locus. Due to the absence of signatures of selection in German stands, we suggest that introduced populations were established with material from provenances that were adapted to environmental conditions similar to those in Germany. However, we analyzed only a limited number of loci which are unlikely to be representative of adaptive genetic diferences among German stands. Our results suggest that the apparent introduction from a limited geographic range in North America may go along with a reduced adaptive potential

Exome Genotyping, Linkage Disequilibrium and Population Structure in Loblolly Pine (\u3cem\u3ePinus taeda\u3c/em\u3e L.)

Background: Loblolly pine (Pinus taeda L.) is one of the most widely planted and commercially important forest tree species in the USA and worldwide, and is an object of intense genomic research. However, whole genome resequencing in loblolly pine is hampered by its large size and complexity and a lack of a good reference. As a valid and more feasible alternative, entire exome sequencing was hence employed to identify the gene-associated single nucleotide polymorphisms (SNPs) and to genotype the sampled trees. Results: The exons were captured in the ADEPT2 association mapping population of 375 clonally-propagated loblolly pine trees using NimbleGen oligonucleotide hybridization probes, and then exome-enriched genomic DNA fragments were sequenced using the Illumina HiSeq 2500 platform. Oligonucleotide probes were designed based on 199,723 exons (≈49 Mbp) partitioned from the loblolly pine reference genome (PineRefSeq v. 1.01). The probes covered 90.2 % of the target regions. Capture efficiency was high; on average, 67 % of the sequence reads generated for each tree could be mapped to the capture target regions, and more than 70 % of the captured target bases had at least 10X sequencing depth per tree. A total of 972,720 high quality SNPs were identified after filtering. Among them, 53 % were located in coding regions (CDS), 5 % in 5’ or 3’ untranslated regions (UTRs) and 42 % in non-target and non-coding regions, such as introns and adjacent intergenic regions collaterally captured. We found that linkage disequilibrium (LD) decayed very rapidly, with the correlation coefficient (r 2) between pairs of SNPs linked within single scaffolds decaying to half maximum (r 2 = 0.22) within 55 bp, to r 2 = 0.1 within 192 bp, and to r 2 = 0.05 within 451 bp. Population structure analysis using unlinked SNPs demonstrated the presence of two main distinct clusters representing western and eastern parts of the loblolly pine range included in our sample of trees. Conclusions: The obtained results demonstrated the efficiency of exome capture for genotyping species such as loblolly pine with a large and complex genome. The highly diverse genetic variation reported in this study will be a valuable resource for future genetic and genomic research in loblolly pine

An annotated genetic map of loblolly pine based on microsatellite and cDNA markers

BACKGROUND: Previous loblolly pine (Pinus taeda L.) genetic linkage maps have been based on a variety of DNA polymorphisms, such as AFLPs, RAPDs, RFLPs, and ESTPs, but only a few SSRs (simple sequence repeats), also known as simple tandem repeats or microsatellites, have been mapped in P. taeda. The objective of this study was to integrate a large set of SSR markers from a variety of sources and published cDNA markers into a composite P. taeda genetic map constructed from two reference mapping pedigrees. A dense genetic map that incorporates SSR loci will benefit complete pine genome sequencing, pine population genetics studies, and pine breeding programs. Careful marker annotation using a variety of references further enhances the utility of the integrated SSR map. RESULTS: The updated P. taeda genetic map, with an estimated genome coverage of 1,515 cM((Kosambi)) across 12 linkage groups, incorporated 170 new SSR markers and 290 previously reported SSR, RFLP, and ESTP markers. The average marker interval was 3.1 cM. Of 233 mapped SSR loci, 84 were from cDNA-derived sequences (EST-SSRs) and 149 were from non-transcribed genomic sequences (genomic-SSRs). Of all 311 mapped cDNA-derived markers, 77% were associated with NCBI Pta UniGene clusters, 67% with RefSeq proteins, and 62% with functional Gene Ontology (GO) terms. Duplicate (i.e., redundant accessory) and paralogous markers were tentatively identified by evaluating marker sequences by their UniGene cluster IDs, clone IDs, and relative map positions. The average gene diversity, H(e), among polymorphic SSR loci, including those that were not mapped, was 0.43 for 94 EST-SSRs and 0.72 for 83 genomic-SSRs. The genetic map can be viewed and queried at http://www.conifergdb.org/pinemap. CONCLUSIONS: Many polymorphic and genetically mapped SSR markers are now available for use in P. taeda population genetics, studies of adaptive traits, and various germplasm management applications. Annotating mapped genes with UniGene clusters and GO terms allowed assessment of redundant and paralogous EST markers and further improved the quality and utility of the genetic map for P. taeda

Phylogenetic Relationships, Pathogenic Traits, and Wood-Destroying Properties of Porodaedalea niemelaei M. Fischer Isolated in the Northern Forest Limit of Larix gmelinii Open Woodlands in the Permafrost Area

The phytopathogenic and wood destroying traits were studied in a basidiomycete fungus, Porodaedalea niemelaei M. Fischer, widespread in Siberian permafrost woodlands of Gmelinii larch, Larix gmelinii (Rupr.) Rupr. Numerous stands of dying out and fallen larch trees with white-rot („corrosion rot“) were found in the study area. Butt rot incidence varied from 63 to 100 % depending on the stand age and raised up to 0.5-1.5 m above root collar on average or up to 9 m maximum. Root rot was also widespread, including larch undergrowth. The biodiversity of xylotrophic fungi was low, with a pronounced dominance of P. niemelaei. The main factors of dying out of L. gmelinii were infection by P. niemelaei promoted by mechanical damage of roots by reindeers during migration and climate anomalies. The cultures isolated from the fruiting bodies were identified as Porodaedalea niemelaei M. Fischer based on the combination of morphological, culture, and molecular genetic methods. Under laboratory conditions, the strains were characterized as psychrotolerant (temperature limit from 6 to 22 °C) and preferred cultural media based mostly on natural and plant substrates. The most active biodegradation occurred on the broadleaf wood substrates causing up to 50 % of the biomass loss accompanied by active decomposing of the lignocellulosic complex and increasing the amount of water-soluble substances. The phylogenetic analysis demonstrated that P. niemelaei is clearly different from other well-studied Porodaedalea species, such as P. chrysoloma, P. pini, and P. cancriformans, and is very close to a group of unclassified fungi isolated in Norway and Finland. The phylogenetic analysis included 43 isolates and was based on four genetic markers – ITS, nLSU, rpb2, and tef1, commonly used in fungal phylogenetic