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

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

Conflicting genomic signals affect phylogenetic inference in four species of North American pines

Adaptive evolutionary processes in plants may be accompanied by episodes of introgression, parallel evolution and incomplete lineage sorting that pose challenges in untangling species evolutionary history. Genus Pinus (pines) is one of the most abundant and most studied groups among gymnosperms, and a good example of a lineage where these phenomena have been observed. Pines are among the most ecologically and economically important plant species. Some, such as the pines of the southeastern USA (southern pines in subsection Australes), are subjects of intensive breeding programmes. Despite numerous published studies, the evolutionary history of Australes remains ambiguous and often controversial. We studied the phylogeny of four major southern pine species: shortleaf (Pinus echinata), slash (P. elliottii), longleaf (P. palustris) and loblolly (P. taeda), using sequences from 11 nuclear loci and maximum likelihood and Bayesian methods. Our analysis encountered resolution difficulties similar to earlier published studies. Although incomplete lineage sorting and introgression are two phenomena presumptively underlying our results, the phylogenetic inferences seem to be also influenced by the genes examined, with certain topologies supported by sets of genes sharing common putative functionalities. For example, genes involved in wood formation supported the clade echinata–taeda, genes linked to plant defence supported the clade echinata–elliottii and genes linked to water management properties supported the clade echinata–palustris. The support for these clades was very high and consistent across methods. We discuss the potential factors that could underlie these observations, including incomplete lineage sorting, hybridization and parallel or adaptive evolution. Our results likely reflect the relatively short evolutionary history of the subsection that is thought to have begun during the middle Miocene and has been influenced by climate fluctuations

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

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

Exome genotyping, linkage disequilibrium and population structure in loblolly pine (Pinus taeda 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-016-3081-8) contains supplementary material, which is available to authorized users