scholarly journals Dissecting the Polygenic Basis of Cold Adaptation Using Genome-Wide Association of Traits and Environmental Data in Douglas-fir

Genes ◽  
2021 ◽  
Vol 12 (1) ◽  
pp. 110
Author(s):  
Amanda R. De La Torre ◽  
Benjamin Wilhite ◽  
Daniela Puiu ◽  
John Bradley St. Clair ◽  
Marc W. Crepeau ◽  
...  
Keyword(s):  
Cold Adaptation ◽  
Cold Hardiness ◽  
Douglas Fir ◽  
Environmental Data ◽  
Genome Wide Association ◽  
Trait Variation ◽  
Genome Wide ◽  
Primary And Secondary Metabolism ◽  
Natural Range ◽  
Whole Genome Resequencing

Understanding the genomic and environmental basis of cold adaptation is key to understand how plants survive and adapt to different environmental conditions across their natural range. Univariate and multivariate genome-wide association (GWAS) and genotype-environment association (GEA) analyses were used to test associations among genome-wide SNPs obtained from whole-genome resequencing, measures of growth, phenology, emergence, cold hardiness, and range-wide environmental variation in coastal Douglas-fir (Pseudotsuga menziesii). Results suggest a complex genomic architecture of cold adaptation, in which traits are either highly polygenic or controlled by both large and small effect genes. Newly discovered associations for cold adaptation in Douglas-fir included 130 genes involved in many important biological functions such as primary and secondary metabolism, growth and reproductive development, transcription regulation, stress and signaling, and DNA processes. These genes were related to growth, phenology and cold hardiness and strongly depend on variation in environmental variables such degree days below 0c, precipitation, elevation and distance from the coast. This study is a step forward in our understanding of the complex interconnection between environment and genomics and their role in cold-associated trait variation in boreal tree species, providing a baseline for the species’ predictions under climate change.

Genome-wide association implicates numerous genes underlying ecological trait variation in natural populations ofPopulus trichocarpa

2014 ◽  
Vol 203 (2) ◽  
pp. 535-553 ◽  
Author(s):  
Athena D. McKown ◽  
Jaroslav Klápště ◽  
Robert D. Guy ◽  
Armando Geraldes ◽  
Ilga Porth ◽  
...  
Keyword(s):  
Natural Populations ◽  
Genome Wide Association ◽  
Trait Variation ◽  
Genome Wide

Comparative study on freezing resistance of conifers with special reference to cold adaptation and its evolutive aspects

1983 ◽  
Vol 61 (9) ◽  
pp. 2323-2332 ◽  
Author(s):  
A. Sakai
Keyword(s):  
Comparative Study ◽  
Special Reference ◽  
Cold Adaptation ◽  
Cold Hardiness ◽  
Winter Hardiness ◽  
Freezing Resistance ◽  
Flower Primordia ◽  
The World ◽  
Natural Range ◽  
Different Parts

From extensive winter hardiness studies of conifers growing in different parts of the world, large differences in winter hardiness are evident among families and genera. Very hardy conifers have evolved from four northern genera of Pinaceae: Pinus, Picea, Larix, and Abies. Winter hardiness of conifers varies with the minimum winter temperature of their natural range. The freezing resistance of most conifers is characterized by the relative susceptibility of the shoot and flower primordia of buds to freezing. The shoot and flower primordia of conifers, except the genus Pinus, survive freezing by extraorgan freezing. The results are discussed with reference to evolution of cold hardiness of conifers.

scholarly journals A Y-linked anti-Müllerian hormone type-II receptor is the sex-determining gene in ayu, Plecoglossus altivelis

PLoS Genetics ◽  
2021 ◽  
Vol 17 (8) ◽  
pp. e1009705
Author(s):  
Masatoshi Nakamoto ◽  
Tsubasa Uchino ◽  
Eriko Koshimizu ◽  
Yudai Kuchiishi ◽  
Ryota Sekiguchi ◽  
...  
Keyword(s):  
Genotyping By Sequencing ◽  
Genome Wide Association ◽  
Whole Genome ◽  
Type Ii ◽  
Genome Resequencing ◽  
Plecoglossus Altivelis ◽  
Genome Wide ◽  
Males And Females ◽  
Whole Genome Resequencing ◽  
Male Specific

Whole-genome duplication and genome compaction are thought to have played important roles in teleost fish evolution. Ayu (or sweetfish), Plecoglossus altivelis, belongs to the superorder Stomiati, order Osmeriformes. Stomiati is phylogenetically classified as sister taxa of Neoteleostei. Thus, ayu holds an important position in the fish tree of life. Although ayu is economically important for the food industry and recreational fishing in Japan, few genomic resources are available for this species. To address this problem, we produced a draft genome sequence of ayu by whole-genome shotgun sequencing and constructed linkage maps using a genotyping-by-sequencing approach. Syntenic analyses of ayu and other teleost fish provided information about chromosomal rearrangements during the divergence of Stomiati, Protacanthopterygii and Neoteleostei. The size of the ayu genome indicates that genome compaction occurred after the divergence of the family Osmeridae. Ayu has an XX/XY sex-determination system for which we identified sex-associated loci by a genome-wide association study by genotyping-by-sequencing and whole-genome resequencing using wild populations. Genome-wide association mapping using wild ayu populations revealed three sex-linked scaffolds (total, 2.03 Mb). Comparison of whole-genome resequencing mapping coverage between males and females identified male-specific regions in sex-linked scaffolds. A duplicate copy of the anti-Müllerian hormone type-II receptor gene (amhr2bY) was found within these male-specific regions, distinct from the autosomal copy of amhr2. Expression of the Y-linked amhr2 gene was male-specific in sox9b-positive somatic cells surrounding germ cells in undifferentiated gonads, whereas autosomal amhr2 transcripts were detected in somatic cells in sexually undifferentiated gonads of both genetic males and females. Loss-of-function mutation for amhr2bY induced male to female sex reversal. Taken together with the known role of Amh and Amhr2 in sex differentiation, these results indicate that the paralog of amhr2 on the ayu Y chromosome determines genetic sex, and the male-specific amh-amhr2 pathway is critical for testicular differentiation in ayu.

Genetic variation in cold hardiness of Douglas-fir in relation to parent tree environment

1999 ◽  
Vol 29 (1) ◽  
pp. 62-72 ◽  
Author(s):  
L M Balduman ◽  
S N Aitken ◽  
M Harmon ◽  
W T Adams
Keyword(s):  
Principal Components ◽  
Cold Hardiness ◽  
Breeding Population ◽  
Douglas Fir ◽  
Trait Variation ◽  
Spring Phenology ◽  
Parent Tree ◽  
Geographic Patterns ◽  
Moisture Regimes ◽  
Components Analysis

The extent to which parent trees within breeding zones of coastal Douglas-fir (Pseudotsuga menziesii var. menziesii (Mirb.) Franco) are locally adapted to their native environments was evaluated. Forty families from each of one Coastal and one Cascade breeding population in Oregon were assessed for cold hardiness and growth phenology, and family means for traits were summarized using principal components analysis (PCA). Composition of the first two principal components (PCs) was consistent between breeding zones, years, and test sites. PC-1, describing 39-46% of trait variation, represents a suite of traits related to spring phenology and spring cold hardiness. PC-2, describing 20-22% of trait variation, consists of cold-hardiness traits not associated with phenology. The first two PCs from each population, as well as univariate traits, were regressed on parent tree location variables and modeled climatic indices separately. In the Coastal zone, PC-1 was weakly but significantly related to temperature and moisture regimes (0.176 [Formula: see text] r2 [Formula: see text] 0.235), varying with elevation and distance from the ocean. PC-2 was related to temperature and moisture regimes in both populations (0.087 [Formula: see text] r2 [Formula: see text] 0.249). These relatively weak geographic patterns for adaptive traits within breeding zones suggest that current zone size is not excessive and could likely be increased north or south.

scholarly journals Mapping of susceptible variants for cold medicine-related Stevens–Johnson syndrome by whole-genome resequencing

2021 ◽  
Vol 6 (1) ◽  
Author(s):  
Yosuke Kawai ◽  
Yuki Hitomi ◽  
Mayumi Ueta ◽  
Seik-Soon Khor ◽  
Ken Nakatani ◽  
...  
Keyword(s):  
Rare Variants ◽  
Genetic Variations ◽  
Genome Wide Association ◽  
Stevens Johnson Syndrome ◽  
Whole Genome ◽  
Nucleotide Polymorphisms ◽  
Severe Condition ◽  
Genome Wide ◽  
Johnson Syndrome ◽  
Whole Genome Resequencing

AbstractStevens–Johnson syndrome (SJS) and its severe condition with extensive skin detachment and a poor prognosis, toxic epidermal necrolysis (TEN), are immunologically mediated severe cutaneous reactions of the skin and mucous membranes such as the ocular surface. Genetic variations on theHLA-Aand other autosomal genes have been identified as risk factors for cold medicine-related SJS/TEN with severe ocular complications (CM-SJS/TEN with SOC). Using a whole-genome sequencing (WGS) approach, we explored other susceptible variants of CM-SJS/TEN with SOC, especially among rare variants and structural variants (SVs). WGS was performed on samples from 133 patients with CM-SJS/TEN with SOC and 418 healthy controls to obtain single nucleotide polymorphisms (SNPs) and SVs. Genome-wide association tests were performed with these variants. Our genome-wide association test reproduced the associations of the common variants ofHLA-Aand loci on chromosome 16q12.1. We also identified novel associations of SVs on these loci and an aggregation of rare coding variants on theTPRM8gene. In silico gene expression analysis on theHLA-Alocus revealed that the SNP (rs12202296), which was significantly associated with susceptibility to CM-SJS/TEN with SOC, was correlated to an increase inHLA-Aexpression levels in the whole blood (P = 2.9 × 10−17), from the GTEx database. The majority of variants that were significantly associated with CM-SJS/TEN with SOC were found in non-coding regions, indicating the regulatory role of genetic variations in the pathogenesis of CM-SJS/TEN with SOC.

Genome wide association study on memory in schizophrenia patients and unaffected probands

2009 ◽  
Vol 42 (05) ◽  
Author(s):  
B Konte ◽  
I Giegling ◽  
AM Hartmann ◽  
H Konnerth ◽  
P Muglia ◽  
...  
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Genome Wide
Sign in / Sign up

Export Citation Format

Share Document