scholarly journals Genome-wide association identifies candidate genes for drought tolerance in coast redwood and giant sequoia

2021 ◽  
Author(s):  
Amanda De La Torre ◽  
Manoj K Sekhwal ◽  
Daniela Puiu ◽  
Steven Salzberg ◽  
Alison Dawn Scott ◽  
...  
Keyword(s):  
Drought Tolerance ◽  
Candidate Genes ◽  
Metabolic Stress ◽  
Population Level ◽  
Severe Drought ◽  
Physiological Basis ◽  
Coast Redwood ◽  
Genome Wide ◽  
Giant Sequoia ◽  
Multivariate Gwas

Drought is a major limitation for survival and growth in plants. With more frequent and severe drought episodes occurring due to climate change, it is imperative to understand the genomic and physiological basis of drought tolerance to be able to predict how species will respond in the future. In this study, univariate and multitrait multivariate GWAS methods were used to identify candidate genes in two iconic and ecosystem-dominating species of the western US, coast redwood and giant sequoia, using ten drought-related physiological and anatomical traits and genome wide sequence-capture SNPs. Population level phenotypic variation was found in carbon isotope discrimination, osmotic pressure at full turgor, xylem hydraulic diameter and total area of transporting fibers in both species. Our study identified new 78 new marker x trait associations in coast redwood and six in giant sequoia, with genes involved in a range of metabolic, stress and signaling pathways, among other functions. This study contributes to a better understanding of the genomic basis of drought tolerance in long-generation conifers and helps guide current and future conservation efforts in the species.

scholarly journals Genome‐wide association identifies candidate genes for drought tolerance in coast redwood and giant sequoia

2021 ◽  
Author(s):  
Amanda R. De La Torre ◽  
Manoj K. Sekhwal ◽  
Daniela Puiu ◽  
Steven L. Salzberg ◽  
Alison Dawn Scott ◽  
...  
Keyword(s):  
Drought Tolerance ◽  
Candidate Genes ◽  
Genome Wide Association ◽  
Coast Redwood ◽  
Genome Wide ◽  
Giant Sequoia

Genome-wide association mapping reveals putative candidate genes for drought tolerance in barley

2020 ◽  
Vol 180 ◽  
pp. 104237
Author(s):  
Rasha A. Tarawneh ◽  
Ahmad M. Alqudah ◽  
Manuela Nagel ◽  
Andreas Börner
Keyword(s):  
Drought Tolerance ◽  
Association Mapping ◽  
Candidate Genes ◽  
Genome Wide Association ◽  
Genome Wide

scholarly journals Spatiotemporal patterns of desiccation tolerance in natural populations of Drosophila melanogaster

2016 ◽  
Author(s):  
Subhash Rajpurohit ◽  
Eran Gefen ◽  
Alan Bergland ◽  
Dmitri Petrov ◽  
Allen G Gibbs ◽  
...  
Keyword(s):  
Drosophila Melanogaster ◽  
Drought Tolerance ◽  
North American ◽  
Desiccation Tolerance ◽  
Experimental Evolution ◽  
Association Studies ◽  
Natural Populations ◽  
Genome Wide Association Studies ◽  
Physiological Basis ◽  
Genome Wide

AbstractWater availability is a major environmental challenge to a variety of terrestrial organisms. In insects, desiccation tolerance varies predictably over various spatial and temporal scales and is an important physiological basis of fitness variation among natural populations. Here, we examine the dynamics of desiccation tolerance in North American populations of Drosophila melanogaster using: 1) natural populations sampled across latitudes and seasons in the eastern USA; 2) experimental evolution in the field in response to changing seasonal environments; 3) a sequenced panel of inbred lines (DGRP) to perform genome wide associations and examine whether SNPs/genes associated with variation in desiccation tolerance exhibit patterns of clinal and/or seasonal enrichment in pooled sequencing of populations. In natural populations we observed a shallow cline in desiccation tolerance, for which tolerance exhibited a positive association with latitude; the steepness of this cline increased with decreasing culture temperature, demonstrating a significant degree of thermal plasticity. No differences in desiccation tolerance were observed between spring and autumn collections from three mid-to-northern latitude populations, or as a function of experimental evolution to seasonality. Similarly, water loss rates did not vary significantly among latitudinal, seasonal or experimental evolution populations. However, changes in metabolic rates during prolonged exposure to dry conditions indicate increased tolerance in higher latitude populations. Genome wide association studies identified thirty-six SNPs in twenty-eight genes associated with sex-averaged drought tolerance. Among North American populations, genes associated with drought tolerance do not show increased signatures of spatially varying selection relative to the rest of the genome, whereas among Australian populations they do.

scholarly journals The Genetic Architecture of Ovariole Number in Drosophila melanogaster: Genes with Major, Quantitative, and Pleiotropic Effects

2017 ◽  
Vol 7 (7) ◽  
pp. 2391-2403 ◽  
Author(s):  
Amanda S Lobell ◽  
Rachel R Kaspari ◽  
Yazmin L Serrano Negron ◽  
Susan T Harbison
Keyword(s):  
Candidate Genes ◽  
Genome Wide Association Study ◽  
Natural Populations ◽  
Direct Role ◽  
Genome Wide ◽  
A Genome ◽  
Fitness Trait ◽  
Sleep Parameters ◽  
Activity Behavior ◽  
Ovariole Number

Abstract Ovariole number has a direct role in the number of eggs produced by an insect, suggesting that it is a key morphological fitness trait. Many studies have documented the variability of ovariole number and its relationship to other fitness and life-history traits in natural populations of Drosophila. However, the genes contributing to this variability are largely unknown. Here, we conducted a genome-wide association study of ovariole number in a natural population of flies. Using mutations and RNAi-mediated knockdown, we confirmed the effects of 24 candidate genes on ovariole number, including a novel gene, anneboleyn (formerly CG32000), that impacts both ovariole morphology and numbers of offspring produced. We also identified pleiotropic genes between ovariole number traits and sleep and activity behavior. While few polymorphisms overlapped between sleep parameters and ovariole number, 39 candidate genes were nevertheless in common. We verified the effects of seven genes on both ovariole number and sleep: bin3, blot, CG42389, kirre, slim, VAChT, and zfh1. Linkage disequilibrium among the polymorphisms in these common genes was low, suggesting that these polymorphisms may evolve independently.

scholarly journals Exogenously Used 24-Epibrassinolide Promotes Drought Tolerance in Maize Hybrids by Improving Plant and Water Productivity in an Arid Environment

Plants ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 354
Author(s):  
El-Sayed M. Desoky ◽  
Elsayed Mansour ◽  
Mohamed M. A. Ali ◽  
Mohamed A. T. Yasin ◽  
Mohamed I. E. Abdul-Hamid ◽  
...  
Keyword(s):  
Drought Tolerance ◽  
Agronomic Traits ◽  
Water Productivity ◽  
Positive Association ◽  
Net Photosynthesis ◽  
Antioxidant Enzyme Activities ◽  
Severe Drought ◽  
Arid Environments ◽  
Maize Hybrids ◽  
Semi Arid

The influence of 24-epibrassinolide (EBR24), applied to leaves at a concentration of 5 μM, on plant physio-biochemistry and its reflection on crop water productivity (CWP) and other agronomic traits of six maize hybrids was field-evaluated under semi-arid conditions. Two levels of irrigation water deficiency (IWD) (moderate and severe droughts; 6000 and 3000 m3 water ha−1, respectively) were applied versus a control (well-watering; 9000 m3 water ha−1). IWD reduced the relative water content, membrane stability index, photosynthetic efficiency, stomatal conductance, and rates of transpiration and net photosynthesis. Conversely, antioxidant enzyme activities and osmolyte contents were significantly increased as a result of the increased malondialdehyde content and electrolyte leakage compared to the control. These negative influences of IWD led to a reduction in CWP and grain yield-related traits. However, EBR24 detoxified the IWD stress effects and enhanced all the above-mentioned parameters. The evaluated hybrids varied in drought tolerance; Giza-168 was the best under moderate drought, while Fine-276 was the best under severe drought. Under IWD, certain physiological traits exhibited a highly positive association with yield and yield-contributing traits or CWP. Thus, exogenously using EBR24 for these hybrids could be an effective approach to improve plant and water productivity under reduced available water in semi-arid environments.

scholarly journals Genome-Wide Association Analysis of Growth Curve Parameters in Chinese Simmental Beef Cattle

Animals ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 192
Author(s):  
Xinghai Duan ◽  
Bingxing An ◽  
Lili Du ◽  
Tianpeng Chang ◽  
Mang Liang ◽  
...  
Keyword(s):  
Beef Cattle ◽  
Candidate Genes ◽  
Growth Curve ◽  
Growth And Development ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Coefficient Of Determination ◽  
Nucleotide Polymorphisms ◽  
Genome Wide ◽  
A Genome

The objective of the present study was to perform a genome-wide association study (GWAS) for growth curve parameters using nonlinear models that fit original weight–age records. In this study, data from 808 Chinese Simmental beef cattle that were weighed at 0, 6, 12, and 18 months of age were used to fit the growth curve. The Gompertz model showed the highest coefficient of determination (R2 = 0.954). The parameters’ mature body weight (A), time-scale parameter (b), and maturity rate (K) were treated as phenotypes for single-trait GWAS and multi-trait GWAS. In total, 9, 49, and 7 significant SNPs associated with A, b, and K were identified by single-trait GWAS; 22 significant single nucleotide polymorphisms (SNPs) were identified by multi-trait GWAS. Among them, we observed several candidate genes, including PLIN3, KCNS3, TMCO1, PRKAG3, ANGPTL2, IGF-1, SHISA9, and STK3, which were previously reported to associate with growth and development. Further research for these candidate genes may be useful for exploring the full genetic architecture underlying growth and development traits in livestock.

scholarly journals A meta-analysis of genome-wide association studies for average daily gain and lean meat percentage in two Duroc pig populations

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Shenping Zhou ◽  
Rongrong Ding ◽  
Fanming Meng ◽  
Xingwang Wang ◽  
Zhanwei Zhuang ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Growth And Development ◽  
Genetic Architecture ◽  
Association Studies ◽  
Meta Analysis ◽  
Average Daily Gain ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Genome Wide ◽  
Daily Gain

Abstract Background Average daily gain (ADG) and lean meat percentage (LMP) are the main production performance indicators of pigs. Nevertheless, the genetic architecture of ADG and LMP is still elusive. Here, we conducted genome-wide association studies (GWAS) and meta-analysis for ADG and LMP in 3770 American and 2090 Canadian Duroc pigs. Results In the American Duroc pigs, one novel pleiotropic quantitative trait locus (QTL) on Sus scrofa chromosome 1 (SSC1) was identified to be associated with ADG and LMP, which spans 2.53 Mb (from 159.66 to 162.19 Mb). In the Canadian Duroc pigs, two novel QTLs on SSC1 were detected for LMP, which were situated in 3.86 Mb (from 157.99 to 161.85 Mb) and 555 kb (from 37.63 to 38.19 Mb) regions. The meta-analysis identified ten and 20 additional SNPs for ADG and LMP, respectively. Finally, four genes (PHLPP1, STC1, DYRK1B, and PIK3C2A) were detected to be associated with ADG and/or LMP. Further bioinformatics analysis showed that the candidate genes for ADG are mainly involved in bone growth and development, whereas the candidate genes for LMP mainly participated in adipose tissue and muscle tissue growth and development. Conclusions We performed GWAS and meta-analysis for ADG and LMP based on a large sample size consisting of two Duroc pig populations. One pleiotropic QTL that shared a 2.19 Mb haplotype block from 159.66 to 161.85 Mb on SSC1 was found to affect ADG and LMP in the two Duroc pig populations. Furthermore, the combination of single-population and meta-analysis of GWAS improved the efficiency of detecting additional SNPs for the analyzed traits. Our results provide new insights into the genetic architecture of ADG and LMP traits in pigs. Moreover, some significant SNPs associated with ADG and/or LMP in this study may be useful for marker-assisted selection in pig breeding.

Sign in / Sign up

Export Citation Format

Share Document