scholarly journals Population genomics of Populus trichocarpa identifies signatures of selection and adaptive trait associations

2014 ◽  
Vol 46 (10) ◽  
pp. 1089-1096 ◽  
Author(s):  
Luke M Evans ◽  
Gancho T Slavov ◽  
Eli Rodgers-Melnick ◽  
Joel Martin ◽  
Priya Ranjan ◽  
...  
Keyword(s):  
Population Genomics ◽  
Populus Trichocarpa ◽  
Adaptive Trait ◽  
Signatures Of Selection ◽  
Trait Associations

scholarly journals Evolutionary quantitative genomics of Populus trichocarpa

2015 ◽  
Author(s):  
Ilga Porth ◽  
Jaroslav Klapste ◽  
Athena D McKown ◽  
Jonathan La Mantia ◽  
Robert D Guy ◽  
...  
Keyword(s):  
Disease Resistance ◽  
Molecular Basis ◽  
Population Genomics ◽  
Populus Trichocarpa ◽  
Detection Methods ◽  
Forest Trees ◽  
Adaptive Traits ◽  
Trait Variation ◽  
Adaptive Trait ◽  
Quantitative Genomics

Forest trees generally show high levels of local adaptation and efforts focusing on understanding adaptation to climate will be crucial for species survival and management. Merging quantitative genetics and population genomics, we studied the molecular basis of climate adaptation in 433 Populus trichocarpa (black cottonwood) genotypes originating across western North America. Variation in 74 field-assessed traits (growth, ecophysiology, phenology, leaf stomata, wood, and disease resistance) was investigated for signatures of selection (comparing QST -FST) using clustering of individuals by climate of origin. 29,354 SNPs were investigated employing three different outlier detection methods. Narrow-sense QST for 53% of distinct field traits was significantly divergent from expectations of neutrality (indicating adaptive trait variation); 2,855 SNPs showed signals of diversifying selection, and of these, 118 SNPs (within 81 genes) were associated with adaptive traits (based on significant QST). Many SNPs were putatively pleiotropic for functionally uncorrelated adaptive traits, such as autumn phenology, height, and disease resistance. Evolutionary quantitative genomics in P. trichocarpa provides an enhanced understanding regarding the molecular basis of climate-driven selection in forest trees. We highlight that important loci underlying adaptive trait variation also show relationship to climate of origin.

Amazing grass: developmental genetics of maize domestication

2005 ◽  
Vol 33 (6) ◽  
pp. 1502-1506 ◽  
Author(s):  
E. Vollbrecht ◽  
B. Sigmon
Keyword(s):  
Reverse Genetics ◽  
Population Genomics ◽  
Evolutionary Developmental Biology ◽  
Developmental Genetics ◽  
Crop Domestication ◽  
Modern Maize ◽  
Signatures Of Selection ◽  
Maize Domestication ◽  
Plant Form ◽  
Evo Devo

Crop plants were domesticated by prehistoric farmers through artificial selection to provide a means of feeding the human population. This article discusses the developmental genetics of crop domestication and improvement, including the historical framework and recent approaches in maize and other grasses. In many cases, selecting for a plant form that correlates with productivity involves controlling meristem activity. In the domestication of modern maize from its progenitor Zea mays ssp. parviglumis, QTL (quantitative trait loci) mapping, genetics and population genomics approaches have identified several genes that contain signatures of selection. Only a few genes involved in the derivation of the highly productive maize ear have been identified, including teosinte glume architecture1 and ramosa1. Future prospects hinge on forward and reverse genetics, as well as on other approaches from the developing discipline of evo-devo (evolutionary developmental biology).

scholarly journals A Whole Genome Re-Sequencing Based GWA Analysis Reveals Candidate Genes Associated with Ivermectin Resistance in Haemonchus contortus

Genes ◽  
2020 ◽  
Vol 11 (4) ◽  
pp. 367 ◽  
Author(s):  
Sawar Khan ◽  
Ayesha Nisar ◽  
Jianqi Yuan ◽  
Xiaoping Luo ◽  
Xueqin Dou ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Haemonchus Contortus ◽  
Population Genomics ◽  
Small Ruminants ◽  
Track Record ◽  
Genome Wide ◽  
Signatures Of Selection ◽  
Parasitic Worms ◽  
Important Parasite

The most important and broad-spectrum drug used to control the parasitic worms to date is ivermectin (IVM). Resistance against IVM has emerged in parasites, and preserving its efficacy is now becoming a serious issue. The parasitic nematode Haemonchus contortus (Rudolphi, 1803) is economically an important parasite of small ruminants across the globe, which has a successful track record in IVM resistance. There are growing evidences regarding the multigenic nature of IVM resistance, and although some genes have been proposed as candidates of IVM resistance using lower magnification of genome, the genetic basis of IVM resistance still remains poorly resolved. Using the full magnification of genome, we herein applied a population genomics approach to characterize genome-wide signatures of selection among pooled worms from two susceptible and six ivermectin-resistant isolates of H. contortus, and revealed candidate genes under selection in relation to IVM resistance. These candidates also included a previously known IVM-resistance-associated candidate gene HCON_00148840, glc-3. Finally, an RNA-interference-based functional validation assay revealed the HCON_00143950 as IVM-tolerance-associated gene in H. contortus. The possible role of this gene in IVM resistance could be detoxification of xenobiotic in phase I of xenobiotic metabolism. The results of this study further enhance our understanding on the IVM resistance and continue to provide further evidence in favor of multigenic nature of IVM resistance.

scholarly journals Signatures of selection underpinning rapid coral adaptation to the world’s warmest reefs

2022 ◽  
Vol 8 (2) ◽  
Author(s):  
Edward G. Smith ◽  
Khaled M. Hazzouri ◽  
Jae Young Choi ◽  
Patrice Delaney ◽  
Mohammed Al-Kharafi ◽  
...  
Keyword(s):  
Population Genomics ◽  
Signatures Of Selection

Population genomics reveals loci associated with coral adaptation to thermally extreme reefs.

scholarly journals Genome Scans for Selection and Introgression based on k-nearest Neighbor Techniques

2019 ◽  
Author(s):  
Bastian Pfeifer ◽  
Nikolaos Alachiotis ◽  
Pavlos Pavlidis ◽  
Michael G. Schimek
Keyword(s):  
Nearest Neighbor ◽  
Population Genomics ◽  
Nearest Neighbors ◽  
Genome Scan ◽  
R Package ◽  
Fixation Index ◽  
K Nearest Neighbor ◽  
Recombination Rates ◽  
Genome Scans ◽  
Signatures Of Selection

AbstractIn recent years, genome-scan methods have been extensively used to detect local signatures of selection and introgression. Here, we introduce a series of versatile genome-scan methods that are based on non-parametric k-nearest neighbors (kNN) techniques, while incorporating pairwise Fixation Index (FST) estimates and pairwise nucleotide differences (dxy) as features. Simulations were performed for both positive directional selection and introgression, with varying parameters, such as recombination rates, population background histories, the proportion of introgression, and the time of gene flow. We find that kNN-based methods perform remarkably well while yielding stable results almost over the entire range of k. We provide a GitHub repository (pievos101/kNN-Genome-Scans) containing R source code to demonstrate how to apply the proposed methods to real-world genomic data using the population genomics R-package PopGenome.

scholarly journals Population genomics identifies the origin and signatures of selection of Korean weedy rice

2016 ◽  
Vol 15 (3) ◽  
pp. 357-366 ◽  
Author(s):  
Qiang He ◽  
Kyu-Won Kim ◽  
Yong-Jin Park
Keyword(s):  
Population Genomics ◽  
Weedy Rice ◽  
Signatures Of Selection ◽  
Selection Of

The population genomics of rapid adaptation: disentangling signatures of selection and demography in white sands lizards

2015 ◽  
Vol 25 (1) ◽  
pp. 306-323 ◽  
Author(s):  
Stefan Laurent ◽  
Susanne P. Pfeifer ◽  
Matthew L. Settles ◽  
Samuel S. Hunter ◽  
Kayla M. Hardwick ◽  
...  
Keyword(s):  
Population Genomics ◽  
Rapid Adaptation ◽  
Signatures Of Selection ◽  
White Sands

Betaines and free amino acids in salt stressed vitroplants and winter resting buds of Populus trichocarpa x deltoides

1991 ◽  
Vol 83 (1) ◽  
pp. 136-143 ◽  
Author(s):  
L. Bray ◽  
D. Chriqui ◽  
K. Gloux ◽  
D. Le Rudulier ◽  
M. Meyer ◽  
...  
Keyword(s):  
Amino Acids ◽  
Free Amino Acids ◽  
Free Amino ◽  
Populus Trichocarpa

Adaptive trait variation in the federally endangered Lindera melissifolia (Lauraceae), as it relates to genotype and genotype-environment interaction1

2019 ◽  
Vol 146 (3) ◽  
pp. 166
Author(s):  
Tracy S. Hawkins ◽  
Craig S. Echt ◽  
Margaret S. Devall ◽  
Paul B. Hamel ◽  
A. Dan Wilson ◽  
...  
Keyword(s):  
Trait Variation ◽  
Adaptive Trait
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