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Title: Molecular Responses to Climate and Resource Availability: Emerging Evidence from Systems Biology Research in Populus.

Abstract

The emergence of Populus as a model system for tree biology continues to be driven by a community of scientists dedicated to developing the resources needed to undertake genetic and functional genomic studies in this genus. As a result, understanding the molecular processes that underpin the growth and development of cottonwood, aspen, and hybrid poplar has steadily increased over the last several decades. Recently, our ability to examine the basic mechanisms whereby trees respond to a changing climate and resource limitations has benefitted greatly from the sequencing of the P. trichocarpa genome. This landmark event has laid a solid foundation upon which tree biologists can now explore the genome-wide effects of temperature, water and nutrient limitations on processes that govern the growth and development of some of the longest living and tallest growing organisms on Earth. Although the challenges likely to be encountered by scientists who work with trees are many, recent literature provides a number of examples whereby a systems approach, one that focuses on transcriptomic, proteomic, and metabolomic analyses is beginning to provide insights into the molecular-scale response of poplars to their climatic and edaphic environment.

Authors:
 [1];  [1];  [2]
  1. ORNL
  2. University of Florida
Publication Date:
Research Org.:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
966738
DOE Contract Number:
DE-AC05-00OR22725
Resource Type:
Journal Article
Resource Relation:
Journal Name: Critical Reviews in Plant Science; Journal Volume: 28
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; AVAILABILITY; BIOLOGY; CLIMATES; FUNCTIONALS; GENETICS; NUTRIENTS; POPLARS; TREES; WATER; Genomics; molecular biology; poplar; populus; trees

Citation Formats

Wullschleger, Stan D, Weston, David, and Davis, John M. Molecular Responses to Climate and Resource Availability: Emerging Evidence from Systems Biology Research in Populus.. United States: N. p., 2009. Web. doi:10.1080/07352680903241246.
Wullschleger, Stan D, Weston, David, & Davis, John M. Molecular Responses to Climate and Resource Availability: Emerging Evidence from Systems Biology Research in Populus.. United States. doi:10.1080/07352680903241246.
Wullschleger, Stan D, Weston, David, and Davis, John M. 2009. "Molecular Responses to Climate and Resource Availability: Emerging Evidence from Systems Biology Research in Populus.". United States. doi:10.1080/07352680903241246.
@article{osti_966738,
title = {Molecular Responses to Climate and Resource Availability: Emerging Evidence from Systems Biology Research in Populus.},
author = {Wullschleger, Stan D and Weston, David and Davis, John M},
abstractNote = {The emergence of Populus as a model system for tree biology continues to be driven by a community of scientists dedicated to developing the resources needed to undertake genetic and functional genomic studies in this genus. As a result, understanding the molecular processes that underpin the growth and development of cottonwood, aspen, and hybrid poplar has steadily increased over the last several decades. Recently, our ability to examine the basic mechanisms whereby trees respond to a changing climate and resource limitations has benefitted greatly from the sequencing of the P. trichocarpa genome. This landmark event has laid a solid foundation upon which tree biologists can now explore the genome-wide effects of temperature, water and nutrient limitations on processes that govern the growth and development of some of the longest living and tallest growing organisms on Earth. Although the challenges likely to be encountered by scientists who work with trees are many, recent literature provides a number of examples whereby a systems approach, one that focuses on transcriptomic, proteomic, and metabolomic analyses is beginning to provide insights into the molecular-scale response of poplars to their climatic and edaphic environment.},
doi = {10.1080/07352680903241246},
journal = {Critical Reviews in Plant Science},
number = ,
volume = 28,
place = {United States},
year = 2009,
month = 1
}
  • The emergence of Populus as a model system for tree biology continues to be driven by a community of scientists dedicated to developing the resources needed to undertake genetic and functional genomic studies in this genus. As a result, understanding the molecular processes that underpin the growth and development of cottonwood, aspen, and hybrid poplar has steadily increased over the last several decades. Recently, our ability to examine the basic mechanisms whereby trees respond to a changing climate and resource limitations has benefited greatly from the sequencing of the P. trichocarpa genome. This landmark event has laid a solid foundationmore » upon which biologists can now quantify, in breathtaking and unprecedented detail, the diversity of genes, proteins, and metabolites that govern the growth and development of some of the longest living and tallest growing organisms on Earth. Although the challenges likely to be encountered by scientists who work with trees are many, recent literature provides a few examples where a systems approach, one that focuses on integrating transcriptomic, proteomic, and metabolomic analyses, is beginning to provide insights into the molecular-scale response of poplars to their climatic and edaphic environment. In this review, our objectives are to look at evidence from studies that examine the molecular response of poplar to edaphic and climatic cues and highlight instances where two or more omic-scale measurements confirm and hopefully expand our inferences about mechanisms contributing to observed patterns of response. Based on conclusions drawn from these studies, we propose that three requirements will be essential as systems biology in poplar moves to reveal unique insights. These include use of genetically-defined individuals (e.g., pedigrees or transgenics) in studies; incorporation of modeling as a complement to transcriptomic, proteomic and metabolomic data; and inclusion of whole-tree and stand-level phenotypes to place molecular-scale insights into a real-world context.« less
  • The genus Populus consists of dioecious woody species with largely unknown genetic mechanisms for gender determination. We have discovered genetic and genomic features in the peritelomeric region of chromosome XIX that suggest this region of the Populus genome is in the process of developing characteristics of a sex chromosome. We have identified a gender-associated locus that consistently maps to this region. Furthermore, comparison of genetic maps across multiple Populus families reveals consistently distorted segregation within this region. We have intensively characterized this region using an F1 interspecific cross involving the female genotype that was used for genome sequencing. This regionmore » shows suppressed recombination and high divergence between the alternate haplotypes, as revealed by dense map-based genome assembly using microsatellite markers. The suppressed recombination, distorted segregation, and haplotype divergence were observed only for the maternal parent in this cross. Furthermore, the progeny of this cross showed a strongly male-biased sex ratio, in agreement with Haldane's rule that postulates that the heterogametic sex is more likely to be absent, rare, or sterile in interspecific crosses. Together, these results support the role of chromosome XIX in sex determination and suggest that sex determination in Populus occurs through a ZW system in which the female is the heterogametic gender.« less
  • The rate of generation of molecular sequence data is forcing the use of computers as a central tool in molecular biology. Current use of computers is limited largely to data management and sequence comparisons, but rapid growth in the volume of data is generating pressure for the development of high-speed analytical methods for deciphering the codes connecting nucleotide sequence with protein structure and function.
  • In this study, 148 428 simple sequence repeat (SSR) primer pairs were designed from the unambiguously mapped sequence scaffolds of the Nisqually-1 genome. The physical position of the priming sites were identified along each of the 19 Populus chromosomes, and it was specified whether the priming sequences belong to intronic, intergenic, exonic or UTR regions. A subset of 150 SSR loci were amplified and a high amplification success rate (72%) was obtained in P. tremuloides, which belongs to a divergent subgenus of Populus relative to Nisqually-1. PCR reactions showed that the amplification success rate of exonic primer pairs was muchmore » higher than that of the intronic/intergenic primer pairs. Applying ANOVA and regression analyses to the flanking sequences of microsatellites, the repeat lengths, the GC contents of the repeats, the repeat motif numbers, the repeat motif length and the base composition of the repeat motif, it was determined that only the base composition of the repeat motif and the repeat motif length significantly affect the microsatellite variability in P. tremuloides samples. The SSR primer resource developed in this study provides a database for selecting highly transferable SSR markers with known physical position in the Populus genome and provides a comprehensive genetic tool to extend the genome sequence of Nisqually-1 to genetic studies in different Populus species.« less