scholarly journals qtlXplorer: an online systems genetics browser in the Eucalyptus Genome Integrative Explorer (EucGenIE)

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Nanette Christie ◽  
Chanaka Mannapperuma ◽  
Raphael Ployet ◽  
Karen van der Merwe ◽  
Niklas Mähler ◽  
...  
Keyword(s):  
Plant Species ◽  
Large Scale ◽  
Woody Plant ◽  
Population Genomics ◽  
Complex Trait ◽  
Systems Genetics ◽  
Integrative Genomics ◽  
Trait Variation ◽  
Woody Plant Species ◽  
Online Tools

Abstract Background Affordable high-throughput DNA and RNA sequencing technologies are allowing genomic analysis of plant and animal populations and as a result empowering new systems genetics approaches to study complex traits. The availability of intuitive tools to browse and analyze the resulting large-scale genetic and genomic datasets remain a significant challenge. Furthermore, these integrative genomics approaches require innovative methods to dissect the flow and interconnectedness of biological information underlying complex trait variation. The Plant Genome Integrative Explorer (PlantGenIE.org) is a multi-species database and domain that houses online tools for model and woody plant species including Eucalyptus. Since the Eucalyptus Genome Integrative Explorer (EucGenIE) is integrated within PlantGenIE, it shares genome and expression analysis tools previously implemented within the various subdomains (ConGenIE, PopGenIE and AtGenIE). Despite the success in setting up integrative genomics databases, online tools for systems genetics modelling and high-resolution dissection of complex trait variation in plant populations have been lacking. Results We have developed qtlXplorer (https://eucgenie.org/QTLXplorer) for visualizing and exploring systems genetics data from genome-wide association studies including quantitative trait loci (QTLs) and expression-based QTL (eQTL) associations. This module allows users to, for example, find co-located QTLs and eQTLs using an interactive version of Circos, or explore underlying genes using JBrowse. It provides users with a means to build systems genetics models and generate hypotheses from large-scale population genomics data. We also substantially upgraded the EucGenIE resource and show how it enables users to combine genomics and systems genetics approaches to discover candidate genes involved in biotic stress responses and wood formation by focusing on two multigene families, laccases and peroxidases. Conclusions qtlXplorer adds a new dimension, population genomics, to the EucGenIE and PlantGenIE environment. The resource will be of interest to researchers and molecular breeders working in Eucalyptus and other woody plant species. It provides an example of how systems genetics data can be integrated with functional genetics data to provide biological insight and formulate hypotheses. Importantly, integration within PlantGenIE enables novel comparative genomics analyses to be performed from population-scale data.

scholarly journals The distribution of woody species in relation to climate and fire in Yosemite National Park, California, USA

Fire Ecology ◽  
2020 ◽  
Vol 16 (1) ◽  
Author(s):  
Jan W. van Wagtendonk ◽  
Peggy E. Moore ◽  
Julie L. Yee ◽  
James A. Lutz
Keyword(s):  
Plant Species ◽  
Sierra Nevada ◽  
Species Distribution ◽  
National Park ◽  
Woody Plant ◽  
Fire Regime ◽  
Yosemite National Park ◽  
Distribution Models ◽  
Ecological Zones ◽  
Woody Plant Species

Abstract Background The effects of climate on plant species ranges are well appreciated, but the effects of other processes, such as fire, on plant species distribution are less well understood. We used a dataset of 561 plots 0.1 ha in size located throughout Yosemite National Park, in the Sierra Nevada of California, USA, to determine the joint effects of fire and climate on woody plant species. We analyzed the effect of climate (annual actual evapotranspiration [AET], climatic water deficit [Deficit]) and fire characteristics (occurrence [BURN] for all plots, fire return interval departure [FRID] for unburned plots, and severity of the most severe fire [dNBR]) on the distribution of woody plant species. Results Of 43 species that were present on at least two plots, 38 species occurred on five or more plots. Of those 38 species, models for the distribution of 13 species (34%) were significantly improved by including the variable for fire occurrence (BURN). Models for the distribution of 10 species (26%) were significantly improved by including FRID, and two species (5%) were improved by including dNBR. Species for which distribution models were improved by inclusion of fire variables included some of the most areally extensive woody plants. Species and ecological zones were aligned along an AET-Deficit gradient from cool and moist to hot and dry conditions. Conclusions In fire-frequent ecosystems, such as those in most of western North America, species distribution models were improved by including variables related to fire. Models for changing species distributions would also be improved by considering potential changes to the fire regime.

Weight–diameter relationships for 22 woody plant species

1969 ◽  
Vol 47 (12) ◽  
pp. 1851-1855 ◽  
Author(s):  
E. S. Telfer
Keyword(s):  
Plant Species ◽  
Woody Plants ◽  
Woody Plant ◽  
Stem Diameter ◽  
Prediction Equations ◽  
Woody Plant Species ◽  
Leaf Weight ◽  
Ground Line

Prediction equations are presented for use in estimating total aboveground weight and maximum leaf weight for 22 species of woody plants. Stem diameter at the ground line was found to be closely correlated with both total and leaf weights. This diameter was therefore used in the equations as the measurement from which weights were predicted.

scholarly journals Estimation of water stress tolerance of six woody plant species

2021 ◽  
Vol 5 (2) ◽  
pp. 64-72
Author(s):  
Danesha Seth Carley ◽  
Lauren A Gragg ◽  
Matthew J Matthew ◽  
Thomas W Rufty
Keyword(s):  
Water Stress ◽  
Stress Tolerance ◽  
Plant Species ◽  
Woody Plant ◽  
Woody Plant Species ◽  
Water Stress Tolerance
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