scholarly journals Genetic variation in heat tolerance of the coral Platygyra daedalea offers the potential for adaptation to ocean warming

2020 ◽  
Author(s):  
Holland Elder ◽  
Virginia Weis ◽  
Jose Montalvo-Proano ◽  
Veronique J.L Mocellin ◽  
Andrew H. Baird ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Heat Stress ◽  
Heat Tolerance ◽  
Nucleotide Polymorphisms ◽  
Narrow Sense Heritability ◽  
Coding Regions ◽  
Genomic Tools ◽  
Coral Reef Ecosystems ◽  
Few Data ◽  
Genomic Regions

AbstractReef-building corals are foundational species in coral reef ecosystems and are threatened by many stressors including rising ocean temperatures. In 2015/16 and 2016/17, corals around the world experienced consecutive bleaching events and most coral populations are projected to experience temperatures above their current bleaching thresholds annually by 2050. Adaptation to higher temperatures is therefore necessary if corals are to persist in a warming future. While many aspects of heat stress have been well studied, few data are available for predicting the capacity for adaptive cross-generational responses in corals. To address this knowledge gap, we quantified the heritability and genetic variation associated with heat tolerance in Platygyra daedalea from the Great Barrier Reef (GBR). We tracked the survival of replicate quantitative genetic crosses (or families) of coral larvae from six parents in a heat stress selection experiment. We also identified allelic shifts in heat-selected survivors versus paired, non-selected controls of the same coral crosses. We estimated narrow sense heritability to be 0.66 and detected a total of 1,069 single nucleotide polymorphisms (SNPs) associated with heat tolerance. An overlap of 148 unique SNPs shared between experimental crosses indicates that specific genomic regions are responsible for heat tolerance of P. daedalea and some of these SNPs fall in coding regions. These findings suggest that this P. daedalea population has the genetic prerequisites for adaptation to increasing temperatures. This study also provides knowledge for the development of high throughput genomic tools to screen for variation within and across populations to harness or enhance adaptation through assisted gene flow and assisted migration.

Assessing genetic variation for heat stress tolerance in Indian bread wheat genotypes using morpho-physiological traits and molecular markers

2016 ◽  
Vol 15 (6) ◽  
pp. 539-547 ◽  
Author(s):  
P. Sharma ◽  
S. Sareen ◽  
M. Saini ◽  
Shefali
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Heat Stress ◽  
Molecular Markers ◽  
Heat Tolerance ◽  
Polymorphic Information Content ◽  
Physiological Traits ◽  
Phenotypic Traits ◽  
Phenotypic Data ◽  
Wheat Genotypes

AbstractHeat stress greatly limits the productivity of wheat in many regions. Knowledge on the degree of genetic diversity of wheat varieties along with their selective traits will facilitate the development of high yielding, stress-tolerant wheat cultivar. The objective of this study were to determine genetic variation in morpho-physiological traits associated with heat tolerance in 30 diverse wheat genotypes and to examine genetic diversity and relationship among the genotypes varying heat tolerance using molecular markers. Phenotypic data of 15 traits were evaluated for heat tolerance under non-stress and stress conditions for two consecutive years. A positive and significant correlation among cell membrane stability, canopy temperature depression, biomass, susceptibility index and grain yield was shown. Genetic diversity assessed by 41 polymorphic simple sequence repeat (SSR) markers was compared with diversity evaluated for 15 phenotypic traits averaged over stress and non-stress field conditions. The mean polymorphic information content for SSR value was 0.38 with range of 0.12–0.75. Based on morpho-physiological traits and genotypic data, three groups were obtained based on their tolerance (HHT, MHT and LHT) levels. Analysis of molecular variance explained 91.7% of the total variation could be due to variance within the heat tolerance genotypes. Genetic diversity among HHT was higher than LHT genotypes and HHT genotypes were distributed among all cluster implied that genetic basis of heat tolerance in these genotypes was different thereby enabling the wheat breeders to combine these diverse sources of genetic variation to improve heat tolerance in wheat breeding programme.

scholarly journals Genetic variation of populations of Citrus psorosis virus

2006 ◽  
Vol 87 (10) ◽  
pp. 3097-3102 ◽  
Author(s):  
Susana Martín ◽  
María Laura García ◽  
Antonella Troisi ◽  
Luis Rubio ◽  
Gonzalo Legarreta ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Type Species ◽  
Protein Gene ◽  
Nucleotide Substitutions ◽  
Coding Regions ◽  
Citrus Psorosis Virus ◽  
Selection For ◽  
Genomic Regions ◽  
Two Populations ◽  
Amino Acid Sequence Conservation

Citrus psorosis virus (CPsV), the type species of genus Ophiovirus, has a segmented, negative-stranded RNA genome. We examined the population structure and genetic variation of CPsV in three coding regions located in RNAs 1, 2 and 3, analysing 22 isolates from Argentina, California, Florida, Italy and Spain. Most isolates contained a predominant sequence and some minor variants. Estimations of the genetic diversity and phylogenetic clustering of isolates disclosed two populations, one comprising isolates from Spain, Italy, Florida and California and the other including the Argentinean isolates. Isolate CPV-4 (from Texas) included for comparison was distant from both groups, suggesting that it belongs to a third group. The low ratio between non-synonymous and synonymous nucleotide substitutions indicated strong selection for amino acid sequence conservation, particularly in the coat protein gene. Incongruent phylogenetic relationships in different genomic regions suggested that exchange of genomic segments may have contributed to CPsV evolution.

scholarly journals The wheat Seven in Absentia gene is associated with increases in biomass and yield in hot climates

2019 ◽  
Author(s):  
Pauline Thomelin ◽  
Julien Bonneau ◽  
Chris Brien ◽  
Radoslaw Suchecki ◽  
Ute Baumann ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Heat Stress ◽  
High Temperature ◽  
Heat Tolerance ◽  
Positional Cloning ◽  
Genomic Region ◽  
Sequence Variant ◽  
Positive Allele ◽  
Breeding Programmes ◽  
Seven In Absentia

AbstractWheat productivity is severely reduced by high temperatures. Breeding of heat tolerant cultivars can be achieved by identifying genes controlling physiological and agronomical traits with high temperature and using these to select superior genotypes, but no gene underlying genetic variation for heat tolerance has previously been described. We completed the positional cloning of qYDH.3BL, a quantitative trait locus (QTL) on bread wheat chromosome 3B associated with increased yield in hot and dry climates. The delimited genomic region contained 12 putative genes and a sequence variant in the promoter region of one gene - seven in absentia, TaSINA. This was associated with the QTL’s effects on early vigour, plant biomass and yield components in two distinct wheat populations grown under various growth conditions. Near isogenic lines carrying the positive allele at qYDH.3BL under-expressed TaSINA and had increased vigour and water use efficiency early in development, as well as increased biomass, grain number and grain weight following heat stress. A survey of worldwide distribution indicated that the positive allele became widespread from the 1950s through the CIMMYT wheat breeding programme but, to date, has been selected only in breeding programmes in Mexico and Australia.Significance statementWheat is the world’s most widely grown crop and a staple of human diet. Even brief episodes of high temperature in the growing season cause severe yield reductions. Finding and deploying genes for heat stress tolerance in new varieties is a priority for food security with climate change. We narrowed a genetic locus to a small genomic region where genetic variation was present only in one gene that showed clear differences of expression and improved yield and physiology under stress in the populations. Using diagnostic markers to track the positive haplotype in nearly 750 accessions, we found many regions where the allele could be used in breeding programmes to increase wheat’s heat tolerance.

Genetics of Thoroughbred Racehorse Performance

2021 ◽  
Vol 10 (1) ◽  
Author(s):  
Ernest Bailey ◽  
Jessica L. Petersen ◽  
Theodore S. Kalbfleisch
Keyword(s):  
Genetic Variation ◽  
Annual Review ◽  
Publication Date ◽  
The Past ◽  
Racing Performance ◽  
Thoroughbred Horses ◽  
Genomic Tools ◽  
Dna Variants ◽  
Different Types ◽  
Genomic Regions

Thoroughbred horses have been selected for racing performance for more than 400 years. Despite continued selection, race times have not improved significantly during the past 60 years, raising the question of whether genetic variation for racing performance still exists. Studies using phenotypes such as race time, money earned, and handicapping, however, demonstrate that there is extensive variation within these traits and that they are heritable. Even so, these are poor measures of racing success since Thoroughbreds race at different ages and distances and on different types of tracks, and some may not race at all. With the advent of genomic tools, DNA variants are being identified that contribute to racing success. Aside from strong associations for myostatin variants with best racing distance, weak to modest associations with racing phenotypes are reported for other genomic regions. These data suggest that diverse genetic strategies have contributed to producing a successful racehorse, and genetic variation contributing to athleticism remains important. Expected final online publication date for the Annual Review of Animal Biosciences, Volume 10 is February 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Genetic characterization and identification of single nucleotide polymorphisms of ATP1A1 gene in Indian humped cattle

2015 ◽  
Author(s):  
A. Barani ◽  
K. P. Ramesha ◽  
M. Basavaraju ◽  
Akhila Rao ◽  
TVL. Narasimha Rao
Keyword(s):  
Heat Stress ◽  
Heat Tolerance ◽  
Direct Sequencing ◽  
Bos Indicus ◽  
Plasma Potassium ◽  
Single Strand Conformation Polymorphism ◽  
Integral Membrane Protein ◽  
Nucleotide Polymorphisms ◽  
Coding Region ◽  
Information Index

Climate change in India is likely to aggravate the heat stress in dairy animals due to rise in temperature coupled with increased precipitation. In animals heat stress affects the alteration of plasma Potassium (K (+)) and Sodium Na (+) ions. ATP1A1 gene belongs to the family of P-type cation transport ATPases, and to the subfamily of Na+/K+ -ATPases. Na+/K+ -ATPase is an integral membrane protein responsible for establishing and maintaining the electrochemical gradients of Na+ and K+ ions across the plasma membrane. The present study is aimed to investigate the polymorphisms in the entire coding region of ATP1A1 gene in Bos indicus (Deoni) cattle by PCR- Single-Strand Conformation Polymorphism (PCR- SSCP) and direct sequencing of variants. Sequence analysis showed 16 SNPs, of which 5 SNPs were in the coding region and the remaining 11 SNPs were detected in the non-coding region of ATP1A1 gene. All the observed variations in the coding regions of ATP1A1 gene were silent mutations. The genotypic, allelic frequencies, c<sup>2</sup> test for Hardy-Weinberg equilibrium and Shannon’s information index were calculated using POPGENE-32. The study revealed a high degree of genetic variability in ATP1A1 gene in the Deoni cattle population which indicated the utility of this gene for further studies for identification of markers associated with heat tolerance in Indian humped cattle for using in marker assisted selection for heat tolerance.

scholarly journals Differential Responses of Amino Acids and Soluble Proteins to Heat Stress Associated with Genetic Variations in Heat Tolerance for Hard Fescue

2018 ◽  
Vol 143 (1) ◽  
pp. 45-55 ◽  
Author(s):  
Jinyu Wang ◽  
Bo Yuan ◽  
Yi Xu ◽  
Bingru Huang
Keyword(s):  
Amino Acids ◽  
Genetic Variation ◽  
Heat Stress ◽  
Amino Acid ◽  
Heat Tolerance ◽  
Amino Acid Content ◽  
Soluble Proteins ◽  
Total Soluble Protein ◽  
Total Amino Acid ◽  
Amino Acid Synthesis

Amino acid and protein metabolism are interrelated and both play important roles in plant adaptation to heat stress. The objective of this study was to identify amino acids and soluble proteins associated with genetic variation in heat tolerance of hard fescue (Festuca trachyphylla). According to a previous screening experiment, the hard fescue cultivars Reliant IV and Predator were selected as heat-tolerant and heat-sensitive cultivars, respectively. Plants of these two hard fescue cultivars were exposed to heat stress at 38/33 °C (day/night) or optimal temperature at 21/18 °C in growth chambers. Each cultivar had four replications under each temperature, and the experimental design was a split-plot design, temperature as the main plots and cultivars as the subplots. Under heat stress, ‘Reliant IV’ exhibited higher turf quality (TQ) and greater membrane stability than ‘Predator’. In response to heat stress, total amino acid content increased, whereas total soluble protein content decreased in both cultivars. The greater accumulation of amino acids in ‘Reliant IV’ was contributed by the greater increase of proteins involved in the glycolysis and the tricarboxylic acid (TCA) cycle that provided carbon skeleton for amino acid synthesis. ‘Reliant IV’ leaves exhibited greater extent of increases in the content of six individual amino acids (histidine, glutamine, proline, threonine, aspartate, and tryptophan) than ‘Predator’ under heat stress. Several soluble proteins were upregulated in response to heat stress, to a greater extent in ‘Reliant IV’ than ‘Predator’, including the proteins involved in photosynthesis, protein folding, redox hemostasis, stress signaling, stress defense, cell organization, and metabolism. These differentially accumulated free amino acids and soluble proteins could be associated with the genetic variation in heat tolerance of hard fescue.

Whole-genome resequencing of Ujumqin sheep to investigate the determinants of the multi-vertebral trait

Genome ◽  
2018 ◽  
Vol 61 (9) ◽  
pp. 653-661 ◽  
Author(s):  
Shuo Li ◽  
Rongsong Luo ◽  
Defang Lai ◽  
Min Ma ◽  
Fei Hao ◽  
...  
Keyword(s):  
Nucleotide Polymorphisms ◽  
Genome Resequencing ◽  
Single Nucleotide ◽  
Frameshift Mutations ◽  
Synonymous Mutations ◽  
Coding Regions ◽  
Homozygous Mutations ◽  
Vertebral Development ◽  
Whole Genome Resequencing ◽  
Genomic Regions

The Ujumqin sheep is one of the most profitable breeds in China, with unique multi-vertebral characteristics. We performed high-throughput genome resequencing of five multi-vertebral and three non-multi-vertebral sheep in an Ujumqin population. We identified the genomic regions that correlated with the germplasm characteristics to establish the cause of the “multi-vertebral” phenotype in this breed. Sequencing generated a total of 314 952 000 000 bp of raw data. The alignment rate of all the samples was between 98.53% and 99.11%, and the mean depth of coverage relative to the reference genome was between 11.58× and 14.92×. After comparing the differences between the two groups, we identified 21 homozygous single nucleotide polymorphisms (SNPs) in the mutant exons of 14 genes. Nineteen loci of 10 genes contained nonsynonymous mutations, while two loci contained synonymous mutations. Resequencing revealed homozygous mutations comprised of 44 indels located within exons of 19 genes. These indels included 37 frameshift mutations, 6 non-frameshift mutations, and 1 stopgain single nucleotide variation (SNV). Finally, comparisons of genotypic variations revealed 17 genes with homozygous mutations in their coding regions, 5 of which have previously been associated with vertebral development and the remaining 12 genes were newly identified in this study.

scholarly journals Discovery of an autoimmunity-associated IL2RA enhancer by unbiased targeting of transcriptional activation

2016 ◽  
Author(s):  
Dimitre R. Simeonov ◽  
Benjamin G. Gowen ◽  
Mandy Boontanrart ◽  
Theodore Roth ◽  
Youjin Lee ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Transcriptional Activation ◽  
Gene Activation ◽  
Interleukin 2 ◽  
General Mechanism ◽  
Enhancer Activity ◽  
Extracellular Signals ◽  
Coding Regions ◽  
Cell Type Specific ◽  
Genomic Regions

The majority of genetic variants associated with common human diseases map to enhancers, non-coding elements that shape cell type-specific transcriptional programs and responses to specific extracellular cues 1-3. In order to understand the mechanisms by which non-coding genetic variation contributes to disease, systematic mapping of functional enhancers and their biological contexts is required. Here, we develop an unbiased discovery platform that can identify enhancers for a target gene without prior knowledge of their native functional context. We used tiled CRISPR activation (CRISPRa) to synthetically recruit transcription factors to sites across large genomic regions (>100 kilobases) surrounding two key autoimmunity risk loci, CD69 and IL2RA (interleukin-2 receptor alpha; CD25). We identified several CRISPRa responsive elements (CaREs) with stimulation-dependent enhancer activity, including an IL2RA enhancer that harbors an autoimmunity risk variant. Using engineered mouse models and genome editing of human primary T cells, we found that sequence perturbation of the disease-associated IL2RA enhancer does not block IL2RA expression, but rather delays the timing of gene activation in response to specific extracellular signals. This work develops an approach to rapidly identify functional enhancers within non-coding regions, decodes a key human autoimmunity association, and suggests a general mechanism by which genetic variation can cause immune dysfunction.

scholarly journals Molecular Mapping of QTLs for Heat Tolerance in Chickpea

2018 ◽  
Vol 19 (8) ◽  
pp. 2166 ◽  
Author(s):  
Pronob Paul ◽  
Srinivasan Samineni ◽  
Mahendar Thudi ◽  
Sobhan Sajja ◽  
Abhishek Rathore ◽  
...  
Keyword(s):  
Heat Stress ◽  
Heat Tolerance ◽  
Molecular Mapping ◽  
Recombinant Inbred Lines ◽  
Interval Mapping ◽  
Snp Markers ◽  
Environment Interaction ◽  
Major Qtls ◽  
Heat Tolerant ◽  
Genomic Regions

Chickpea (Cicer arietinum L.), a cool-season legume, is increasingly affected by heat-stress at reproductive stage due to changes in global climatic conditions and cropping systems. Identifying quantitative trait loci (QTLs) for heat tolerance may facilitate breeding for heat tolerant varieties. The present study was aimed at identifying QTLs associated with heat tolerance in chickpea using 292 F8-9 recombinant inbred lines (RILs) developed from the cross ICC 4567 (heat sensitive) × ICC 15614 (heat tolerant). Phenotyping of RILs was undertaken for two heat-stress (late sown) and one non-stress (normal sown) environments. A genetic map spanning 529.11 cM and comprising 271 genotyping by sequencing (GBS) based single nucleotide polymorphism (SNP) markers was constructed. Composite interval mapping (CIM) analysis revealed two consistent genomic regions harbouring four QTLs each on CaLG05 and CaLG06. Four major QTLs for number of filled pods per plot (FPod), total number of seeds per plot (TS), grain yield per plot (GY) and % pod setting (%PodSet), located in the CaLG05 genomic region, were found to have cumulative phenotypic variation of above 50%. Nineteen pairs of epistatic QTLs showed significant epistatic effect, and non-significant QTL × environment interaction effect, except for harvest index (HI) and biomass (BM). A total of 25 putative candidate genes for heat-stress were identified in the two major genomic regions. This is the first report on QTLs for heat-stress response in chickpea. The markers linked to the above mentioned four major QTLs can facilitate marker-assisted breeding for heat tolerance in chickpea.

scholarly journals Mapping QTLs for phenotypic and morpho-physiological traits related to grain yield under late sown conditions in wheat (Triticum aestivum L.)

2021 ◽  
Author(s):  
Yaswant Kumar Pankaj ◽  
Lalit Pal ◽  
Ragupathi Nagarajan ◽  
Kulvinder Singh Gill ◽  
Vishnu Kumar ◽  
...  
Keyword(s):  
Heat Stress ◽  
Grain Yield ◽  
Heat Tolerance ◽  
Canopy Temperature ◽  
Triticum Aestivum L ◽  
Interval Mapping ◽  
Phenotypic Variance ◽  
Breeding Lines ◽  
Positive Correlations ◽  
Genomic Regions

The elevating temperature makes heat stress one of the major issues for wheat production globally. To elucidate genetic basis and map heat tolerance traits, a set of 166 doubled haploid lines (DHLs) derived from the cross between PBW3438/IC252874 was used. The population was evaluated under Normal sown (NS) and late sown (LS) conditions, by exposing to heat stress during rabi season. The canopy temperature (CT) showed positive correlations with grain yield, whereas Soil plant analysis development (SPAD) was not significantly correlated and associated with GY in both the normal and late sown conditions. Composite interval mapping (CIM) identified total 12 Quantitative trait loci (QTLs) viz., 2 (Normal sown), 10 (late sown) mapped on linkage groups 1A, 1D, 2B, 2D, 3B, 4D, 5B, and 6D, during both the crop seasons 2017-18 and 2018-19. Combining the results of these QTLs revealed a major stable QTL for grain yield (GY) on chromosome 3B with 11.84% to 21.24% explaining phenotypic variance under both sowing conditions. QTL for CT and SPAD was detected on chromosome 1A while QTL for GY on chromosomes 3B and 5B. The identified QTLs in the genomic regions could be targeted for genetic improvement and marker-assisted selection for heat tolerance in wheat. The tools like SPAD and CT could be exploited to screen a large number of breeding lines.

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