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Background: Single nucleotide polymorphisms (SNPs) are the most abundant source of genetic variation among individuals of a species. New genotyping technologies allow examining hundreds to thousands of SNPs in a single reaction for a wide range of applications such as genetic diversity analysis, linkage mapping, fine QTL mapping, association studies, marker-assisted or genome-wide selection. In this paper, we evaluated the potential of highly-multiplexed SNP genotyping for genetic mapping in maritime pine (Pinus pinaster Ait.), the main conifer used for commercial plantation in southwestern Europe.
Results: We designed a custom GoldenGate assay for 1,536 SNPs detected through the resequencing of gene fragments (707 in vitro SNPs/Indels) and from Sanger-derived Expressed Sequenced Tags assembled into a unigene set (829 in silico SNPs/Indels). Offspring from three-generation outbred (G2) and inbred (F2) pedigrees were genotyped. The success rate of the assay was 63.6% and 74.8% for in silico and in vitro SNPs, respectively. A genotyping error rate of 0.4% was further estimated from segregating data of SNPs belonging to the same gene. Overall, 394 SNPs were available for mapping. A total of 287 SNPs were integrated with previously mapped markers in the G2 parental maps, while 179 SNPs were localized on the map generated from the analysis of the F2 progeny. Based on 98 markers segregating in both pedigrees, we were able to generate a consensus map comprising 357 SNPs from 292 different loci. Finally, the analysis of sequence homology between mapped markers and their orthologs in a Pinus taeda linkage map, made it possible to align the 12 linkage groups of both species.
Conclusions: Our results show that the GoldenGate assay can be used successfully for high-throughput SNP genotyping in maritime pine, a conifer species that has a genome seven times the size of the human genome. This SNP-array will be extended thanks to recent sequencing effort using new generation sequencing technologies and will include SNPs from comparative orthologous sequences that were identified in the present study, providing a wider collection of anchor points for comparative genomics among the conifers.
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http://dx.doi.org/10.1186/1471-2164-12-368 | DOI Listing |
Chem Sci
December 2024
Institutes of Physical Science and Information Technology, Key Laboratory of Structure and Functional Regulation of Hybrid Material (Ministry of Education), Anhui University Hefei 230601 China
Lithium metal batteries (LMBs) promise high-energy-density storage but face safety issues due to dendrite-induced lithium deposition, irreversible electrolyte consumption, and large volume changes, which hinder their practical applications. To address these issues, tuning lithium deposition by structuring a host for the lithium metal anode has been recognized as an efficient method. Herein, we report a supercritical water molecular scissor-controlled strategy to form a carbon framework derived from biomass wood.
View Article and Find Full Text PDFPlant Cell Environ
December 2024
Biological Sciences, School of Natural Sciences, University of Tasmania, Hobart, Tasmania, Australia.
Vapour pressure deficit (VPD) is a primary determinant of stomatal behaviour and water balance in plants. With increasing global temperature, the accompanying rise in VPD is likely to have a significant impact on the performance of plant species in the future. However, the plasticity of stomatal response to VPD remains largely unexplored.
View Article and Find Full Text PDFPeerJ
December 2024
Instituto de Silvicultura e Industria de la Madera, Universidad Juárez del Estado de Durango, Durango, Durango, Mexico.
Background: Seedling growth and survival depend on seedling quality. However, there is no experimental evidence showing that the seedling dimensions of the abundant, economically important and widely distributed tree species , , , , and and their hybrids effectively improve survival and growth in reforestations and plantations in Mexico. Therefore, the aim was to evaluate the influence of initial morphological parameters of 2,007 nursery seedlings of these species and their hybrids on their growth and survival 44 months after planting in the Sierra Madre Occidental, Mexico.
View Article and Find Full Text PDFAm J Bot
December 2024
ETH-Zürich, Institute for Integrative Biology, Plant Ecology Group, Zürich, Switzerland.
Premise: Tree structure and function are constrained by and acclimate to climatic conditions. Drought limits plant growth and carbon acquisition and can result in "legacy" effects that last beyond the period of water stress. Leaf and twig-level legacy effects of past water abundance, such as that experienced by trees that established under wetter conditions are unknown.
View Article and Find Full Text PDFBull Math Biol
December 2024
Department of Biology, University of Victoria, Victoria, BC, Canada.
Insects, especially forest pests, are frequently characterized by eruptive dynamics. These types of species can stay at low, endemic population densities for extended periods of time before erupting in large-scale outbreaks. We here present a mechanistic model of these dynamics for mountain pine beetle.
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