Evaluating the accuracy of variant calling methods using the frequency of parent-offspring genotype mismatch

The use of NGS datasets has increased dramatically over the last decade, however, there have been few systematic analyses quantifying the accuracy of the commonly used variant caller programs. Here we used a familial design consisting of diploid tissue from a single Pinus contorta parent and the maternally derived haploid tissue from 106 full-sibling offspring, where mismatches could only arise due to mutation or bioinformatic error. Given the rarity of mutation, we used the rate of mismatches between parent and offspring genotype calls to infer the SNP genotyping error rates of FreeBayes, HaplotypeCaller, SAMtools, UnifiedGenotyper, and VarScan. With baseline filtering HaplotypeCaller and UnifiedGenotyper yielded one to two orders of magnitude larger numbers of SNPs and error rates, whereas FreeBayes, SAMtools and VarScan yielded lower numbers of SNPs and more modest error rates. To facilitate comparison between variant callers we standardized each SNP set to the same number of SNPs using additional filtering, where UnifiedGenotyper consistently produced the smallest proportion of genotype errors, followed by HaplotypeCaller, VarScan, SAMtools, and FreeBayes. Additionally, we found that error rates were minimized for SNPs called by more than one variant caller. Finally, we evaluated the performance of various commonly used filtering metrics on SNP calling. Our analysis provides a quantitative assessment of the accuracy of five widely used variant calling programs and offers valuable insights into both the choice of variant caller program and the choice of filtering metrics, especially for researchers using non-model study systems.

Evaluating the accuracy of variant calling methods using the frequency of parent-offspring genotype mismatch

The use of NGS datasets has increased dramatically over the last decade, however, there have been few systematic analyses quantifying the accuracy of the commonly used variant caller programs. Here we used a familial design consisting of diploid tissue from a single Pinus contorta parent and the maternally derived haploid tissue from 106 full-sibling offspring, where mismatches could only arise due to mutation or bioinformatic error. Given the rarity of mutation, we used the rate of mismatches between parent and offspring genotype calls to infer the SNP genotyping error rates of FreeBayes, HaplotypeCaller, SAMtools, UnifiedGenotyper, and VarScan. With baseline filtering HaplotypeCaller and UnifiedGenotyper yielded one to two orders of magnitude larger numbers of SNPs and error rates, whereas FreeBayes, SAMtools and VarScan yielded lower numbers of SNPs and more modest error rates. To facilitate comparison between variant callers we standardized each SNP set to the same number of SNPs using additional filtering, where UnifiedGenotyper consistently produced the smallest proportion of genotype errors, followed by HaplotypeCaller, VarScan, SAMtools, and FreeBayes. Additionally, we found that error rates were minimized for SNPs called by more than one variant caller. Finally, we evaluated the performance of various commonly used filtering metrics on SNP calling. Our analysis provides a quantitative assessment of the accuracy of five widely used variant calling programs and offers valuable insights into both the choice of variant caller program and the choice of filtering metrics, especially for researchers using non-model study systems.

Biochar Stability in a Highly Weathered Sandy Soil under Four Years of Continuous Corn Production

Biochar is being considered a climate change mitigation tool by increasing soil organic carbon contents (SOC), however, questions remain concerning its longevity in soil. We applied 30,000 kg ha−1 of biochars to plots containing a Goldsboro sandy loam (Fine-loamy, siliceous, sub-active, thermic Aquic Paleudults) and then physically disked all plots. Thereafter, the plots were agronomically managed under 4 years (Y) of continuous corn (Zea Mays, L.) planting. Annually, incremental soil along with corresponding bulk density samples were collected and SOC concentrations were measured in topsoil (down to 23-cm). The biochars were produced from Lodgepole pine (Pinus contorta) chip (PC) and Poultry litter (PL) feedstocks. An untreated Goldsboro soil (0 biochar) served as a control. After four years, SOC contents in the biochar treated plots were highest in the top 0–5 and 5–10 cm depth suggesting minimal deeper movement. Declines in SOC contents varied with depth and biochar type. After correction for SOC declines in controls, PL biochar treated soil had a similar decline in SOC (7.9 to 10.3%) contents. In contrast, the largest % SOC content decline (20.2%) occurred in 0–5 cm deep topsoil treated with PC biochar. Our results suggest that PC biochar had less stability in the Goldsboro soil than PL biochar after 4 years of corn grain production.

Preference and Performance of the Pine-Tree Lappet Dendrolimus pini on Various Pine Species

Global commercial and recreational transport may lead to the unintentional invasion of insect species, which in turn may pose a threat to native organisms. In this study, we aimed to assess whether the economically important pest of Pinus sylvestris L., moth Dendrolimus pini L. (DP), is able to feed on nine other pine species, and how this will affect its survival, performance, growth, and development. We carried out food choice tests and a no-choice laboratory feeding experiment. We found that this insect mostly preferred its prime host, but also Pinus cembra L., Pinus contorta Douglas ex Loudon, Pinus nigra J.F.Arnold, and Pinus ponderosa Douglas ex C.Lawson. The performance test revealed a host-specific response of DP to the host plant. This response was manifested in a large variation in body mass as well as in a decrease or increase in life-history traits, such as fecundity, and wing morphology parameters. However, the larvae’s choice of particular hosts corresponded to the results of the performance test. Larvae more willingly selected food allowing better results in their performance. Larvae achieved better values of growth and development when fed on European and North American pine species or on species with two- and three-needle fascicles. In addition, attractants and repellents in needles of different pine species were chemically analyzed. Variations in the secondary metabolite composition as well as the specific leaf area of different pine species effectively explained the results found in the insects, but the content of sugars and nitrogen remains to be elucidated. We speculate that DP poses a serious threat to large areas of pine forests, if transferred, as it can survive and develop on many economically important tree species in North America and Europe.

Economic potential of adopting genomic technology in Alberta’s tree improvement sector

The adoption of genomic technology and the use of improved seeds are expected to improve timber productivity in Alberta. However, this improvement will need to take place within the confines of the public-private nature of the sector where 93% of the total forest area is publicly owned. The purpose of this study is to explore the extent to which a timber harvest policy known as the allowable cut effect can affect the welfare outcomes of adopting genomics-assisted tree breeding. Using the forest industry of Alberta as the empirical setting, the economic returns to the adoption of this new breeding technology in lodgepole pine (Pinus contorta Dougl. ex Loud. var. latifolia Engelm.) and white spruce (Picea glauca (Moench) Voss) are calculated by estimating a timber supply model and a spatial equilibrium model. Under certain policy and technology improvement scenarios, the economic returns are negative, which would result in non-adoption of the technology. However, under other feasible conditions, the payoffs of genomics-assisted tree breeding research are large and positive. These results illustrate the important role that government policies can have on the returns to adopting new technologies.

Economic potential of adopting genomic technology in Alberta’s tree improvement sector

The adoption of genomic technology and the use of improved seeds are expected to improve timber productivity in Alberta. However, this improvement will need to take place within the confines of the public-private nature of the sector where 93% of the total forest area is publicly owned. The purpose of this study is to explore the extent to which a timber harvest policy known as the allowable cut effect can affect the welfare outcomes of adopting genomics-assisted tree breeding. Using the forest industry of Alberta as the empirical setting, the economic returns to the adoption of this new breeding technology in lodgepole pine (Pinus contorta Dougl. ex Loud. var. latifolia Engelm.) and white spruce (Picea glauca (Moench) Voss) are calculated by estimating a timber supply model and a spatial equilibrium model. Under certain policy and technology improvement scenarios, the economic returns are negative, which would result in non-adoption of the technology. However, under other feasible conditions, the payoffs of genomics-assisted tree breeding research are large and positive. These results illustrate the important role that government policies can have on the returns to adopting new technologies.

Representatives of thePine Family (Pinaceae Lindl.) of the North American Flora in the Collection of the Dendrological Garden named after V.N. Nilov (NRIF)

The article presents the results of the introduction of the North American flora woody species of the pine family (Pinaceae Lindl.) to the European North of Russia. The research purpose is to select the most valuable specimens for introduction into northern conditions from the tree species collection. The research has involved experimental, calculation, analytical, and comparative methods. The conclusion on the result of the introduction of a particular plant was based on the materials of long-term phenological observations, which were carried out according to the method of botanical gardens improved for the conditions of the European North of Russia. As a result of the introduction of North American species of the Pinaceae Lindl. family to the region, a large-scale test of foreign conifers was carried out for the first time; a collection of 2 species of fir, 4 species and 3 forms of spruce, 2 species of pine, and 1 species of Douglas fir was created. Most attention was paid to the introduction of species of the genus Pinus. Positive results of cultivation of Pinus contorta Loud. var. latifolia S. Wats. in the Dendrological garden allowed us to select it for further introduction testing in experimental plantations of the region. On plantations located in the Arkhangelsk and Vologda regions and the Komi Republic, 104.2 ths seedlings were grown from the seed samples, mostly from the northern natural range of this pine. Unfortunately, not all of the breeding material for the North American pine species tested was derived from natural growth sites, which puts into question some of the unsatisfactory results. Therefore, for Jack pine and Weymouth pine, it is advisable to use in testing additional samples from the most northern regions of their natural ranges in Canada. Many of these species are of both scientific and practical interest for forestry. To assess the economic value of those introduced species, adaptive capabilities of which in the conditions of the European North according to the results of studies are not in doubt, it is advisable to lay out pilot plantations in the region, similar to the already created plantings of North American lodgepole pine (Pinus contorta Loud. var. latifolia S. Wats.). The concentration of different species like balsam fir (Abies balsamea Mill.), Fraser fir (Abies fraseri (Pursch.) Poir.), American larch (Larix laricina (Du Roi) K.Koch.), Canadian spruce (Picea glauca Voss.), Engelmann’s spruce (Picea engelmannii Engelm.), black spruce (Picea mariana Britt.), Jack pine (Pinus banksiana Lamb.), lodgepole pine (Pinus contorta Loud. var. latifolia S. Wats.), and Douglas fir (Pseudotsuga menziesii Mirb.), involving several seed origins from the most northern regions of its natural range for each, in 2-3 forest areas will allow creating a valuable introduction object; scientific and practical importance of those mentioned cannot be overestimated.

Análisis de un sistema silvopastoral con Pinus contorta (Dougl. ex Loud) en la Región de Aysén, Chile = Analysis of a silvopastoral system with Pinus contorta (Dougl. ex Loud) in the Region of Aysén, Chile

En el año 2003 se estableció una investigación para evaluar la potencialidad de los sistemas silvopastorales con Pinus contorta (Dougl. ex Loud), en la zona intermedia de la provincia de Coyhaique, Región de Aysén, Patagonia chilena. Para su evaluación se comparan dos diseños silvopastorales con la especie, uno sin manejo y el otro con manejo, versus usos tradicionales de la tierra en Aysén, como es el manejo ganadero con bovinos sobre una pradera naturalizada. Los resultados del estudio arrojan que los sistemas silvopastorales mostraron ser una alternativa para los productores de la Patagonia, dado que les permite obtener ingresos intermedios por la venta de carne y madera proveniente de raleos, mientras que obtendrán un ingreso final por la venta de madera por el componente forestal. La producción de carne en peso vivo indicó que estos sistemas son apropiados para la zona, ya que la producción fue similar a la del sistema ganadero en los primeros dos años de evaluación, aunque el área efectiva del pastoreo se redujo, mostrando la influencia beneficiosa de los árboles en los factores climáticos como viento y temperatura.