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

Ecology and Evolution
Mengmeng LuKonstantin V Krutovsky

Abstract

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...Continue Reading

References

Jul 2, 2003·The Plant Journal : for Cell and Molecular Biology·Bao-Cai TanDonald R McCarty
May 25, 2005·Proceedings of the National Academy of Sciences of the United States of America·Dae-Kyun RoJörg Bohlmann
Jun 26, 2007·Bioinformatics·Peter J BradburyEdward S Buckler
Jul 9, 2009·Nature Reviews. Genetics·Trudy F C MackayJulien F Ayroles
Feb 25, 2010·Current Biology : CB·Jonathan K PritchardGraham Coop
Aug 21, 2010·Molecular Ecology·Andrew J EckertDavid B Neale
Sep 15, 2010·Nature Reviews. Genetics·Jonathan K Pritchard, Anna Di Rienzo
Jun 10, 2011·Bioinformatics·Petr DanecekUNKNOWN 1000 Genomes Project Analysis Group
Dec 2, 2011·The New Phytologist·Andrew J EckertDavid B Neale
Jan 10, 2012·Evolution; International Journal of Organic Evolution·Matthew V Rockman
Feb 16, 2012·Molecular Ecology·Valérie Le Corre, Antoine Kremer
May 23, 2012·Nature Genetics·Wen-Yun YangEran Halperin
Jun 21, 2012·Genetics·Pavlos PavlidisWolfgang Stephan
Aug 8, 2014·PLoS Genetics·Jeremy J Berg, Graham Coop
Jul 18, 2015·Molecular Ecology·Christian RellstabRolf Holderegger
Dec 15, 2015·The American Naturalist·Sam Yeaman
Mar 30, 2018·American Journal of Speech-language Pathology·Charles R GreenwoodJudith J Carta

❮ Previous
Next ❯

Methods Mentioned

BETA
exome sequencing
dissection

Software Mentioned

RDA
Samβada
VCFtools
Diva
R Core
OutFLANK
R package vegan
GIS
TASSEL
blastx

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.