scholarly journals Three quantitative trait loci explain more than 60% of phenotypic variation for chill coma recovery time in Drosophila ananassae

2019 ◽  
Author(s):  
Annabella Königer ◽  
Saad Arif ◽  
Sonja Grath
Keyword(s):  
Candidate Genes ◽  
Cold Tolerance ◽  
Quantitative Trait ◽  
Recovery Time ◽  
Differentially Expressed ◽  
Drosophila Ananassae ◽  
Phenotypic Variance ◽  
Climatic Fluctuations ◽  
Standard Interval ◽  
Chill Coma

AbstractEctothermic species such as insects are particularly vulnerable to climatic fluctuations. Nevertheless, many insects that evolved and diversified in the tropics have successfully colonized temperate regions all over the globe. To shed light on the genetic basis of cold tolerance in such species, we conducted a quantitative trait locus (QTL) mapping experiment for chill coma recovery time (CCRT) in Drosophila ananassae, a cosmopolitan species that has expanded its range from tropical to temperate regions.We created a mapping population of recombinant inbred advanced intercross lines (RIAILs) from two founder strains with diverging CCRT phenotypes. The RIAILs were phenotyped for their CCRT and, together with the founder strains, genotyped for polymorphic markers with double-digest restriction site-associated DNA (ddRAD) sequencing. Using a hierarchical mapping approach that combined standard interval mapping and a multiple-QTL model, we mapped three QTL which altogether explained 64% of the phenotypic variance. For two of the identified QTL, we found evidence of epistasis. To narrow down the list of cold tolerance candidate genes, we cross-referenced the QTL intervals with genes that we previously identified as differentially expressed in response to cold in D. ananassae, and with thermotolerance candidate genes of D. melanogaster. Among the 58 differentially expressed genes that were contained within the QTL, GF15058 showed a significant interaction of the CCRT phenotype and gene expression. Further, we identified the orthologs of four D. melanogaster thermotolerance candidate genes, MtnA, klarsicht, CG5246 (D.ana/GF17132) and CG10383 (D.ana/GF14829) as candidates for cold tolerance in D. ananassae.

scholarly journals Transcriptome Analysis Reveals Candidate Genes for Cold Tolerance in Drosophila ananassae

Genes ◽  
2018 ◽  
Vol 9 (12) ◽  
pp. 624 ◽  
Author(s):  
Annabella Königer ◽  
Sonja Grath
Keyword(s):  
Candidate Genes ◽  
Cold Tolerance ◽  
Cold Hardiness ◽  
Cold Shock ◽  
Drosophila Ananassae ◽  
Tropical Species ◽  
Seasonal Temperature ◽  
Tropical Regions ◽  
Chill Coma ◽  
Before And After

Coping with daily and seasonal temperature fluctuations is a key adaptive process for species to colonize temperate regions all over the globe. Over the past 18,000 years, the tropical species Drosophila ananassae expanded its home range from tropical regions in Southeast Asia to more temperate regions. Phenotypic assays of chill coma recovery time (CCRT) together with previously published population genetic data suggest that only a small number of genes underlie improved cold hardiness in the cold-adapted populations. We used high-throughput RNA sequencing to analyze differential gene expression before and after exposure to a cold shock in coldtolerant lines (those with fast chill coma recovery, CCR) and cold-sensitive lines (slow CCR) from a population originating from Bangkok, Thailand (the ancestral species range). We identified two candidate genes with a significant interaction between cold tolerance and cold shock treatment: GF14647 and GF15058. Further, our data suggest that selection for increased cold tolerance did not operate through the increased activity of heat shock proteins, but more likely through the stabilization of the actin cytoskeleton and a delayed onset of apoptosis.

scholarly journals Meta-Analysis of Quantitative Trait Loci Associated with Seedling-Stage Salt Tolerance in Rice (Oryza sativa L.)

Plants ◽  
2019 ◽  
Vol 8 (2) ◽  
pp. 33 ◽  
Author(s):  
Md. Islam ◽  
John Ontoy ◽  
Prasanta Subudhi
Keyword(s):  
Quantitative Trait Loci ◽  
Salt Tolerance ◽  
Candidate Genes ◽  
Quantitative Trait ◽  
Oryza Sativa L ◽  
Meta Analysis ◽  
Seedling Stage ◽  
Phenotypic Variance ◽  
A Genome ◽  
Trait Loci

Soil and water salinity is one of the major abiotic stresses that reduce growth and productivity in major food crops including rice. The lack of congruence of salt tolerance quantitative trait loci (QTLs) in multiple genetic backgrounds and multiple environments is a major hindrance for undertaking marker-assisted selection (MAS). A genome-wide meta-analysis of QTLs controlling seedling-stage salt tolerance was conducted in rice using QTL information from 12 studies. Using a consensus map, 11 meta-QTLs for three traits with smaller confidence intervals were localized on chromosomes 1 and 2. The phenotypic variance of 3 meta-QTLs was ≥20%. Based on phenotyping of 56 diverse genotypes and breeding lines, six salt-tolerant genotypes (Bharathy, I Kung Ban 4-2 Mutant, Langmanbi, Fatehpur 3, CT-329, and IARI 5823) were identified. The perusal of the meta-QTL regions revealed several candidate genes associated with salt-tolerance attributes. The lack of association between meta-QTL linked markers and the level of salt tolerance could be due to the low resolution of meta-QTL regions and the genetic complexity of salt tolerance. The meta-QTLs identified in this study will be useful not only for MAS and pyramiding, but will also accelerate the fine mapping and cloning of candidate genes associated with salt-tolerance mechanisms in rice.

Effect of starvation on the cold tolerance of adult Drosophila suzukii (Diptera: Drosophilidae)

2021 ◽  
pp. 1-11
Author(s):  
Madelena De Ro ◽  
Thomas Enriquez ◽  
Jochem Bonte ◽  
Negin Ebrahimi ◽  
Hans Casteels ◽  
...  
Keyword(s):  
Body Composition ◽  
Cold Stress ◽  
Cold Tolerance ◽  
Body Mass ◽  
Food Deprivation ◽  
Recovery Time ◽  
Invasive Pest ◽  
Drosophila Suzukii ◽  
Chill Coma ◽  
Critical Thermal Minimum

Abstract The spotted wing drosophila, Drosophila suzukii, is an invasive pest in Europe and North America. Access to resources may be challenging in late fall, winter and early spring and flies may suffer from food deprivation along with cold stress in these periods. Whereas a plethora of studies have been performed on the overwintering capacity of D. suzukii, the effects of starvation on the fly's cold tolerance have not been addressed. In the present study, young D. suzukii adults (reared at 25°C, LD 12:12 h) were deprived of food for various periods (0, 12, 24 and 36 h), after which chill coma recovery time, critical thermal minimum, as well as acute and chronic cold tolerance were assessed. Additionally, the body composition of adults (body mass, water content, total lipid, glycerol, triglycerides, glucose and proteins) before and after starvation periods was analysed to confirm that starvation had detectable effects. Starved adults had a lower body mass, and both lipid and carbohydrate levels decreased with starvation time. Starvation slightly increased critical thermal minimum and affected chill coma recovery time; however, these changes were not gradual with starvation duration. Starvation promoted acute cold tolerance in both sexes. This effect appeared faster in males than in females. Food deprivation also led to enhanced survival to chronic cold stress. Short-term starvation was thus associated with significant changes in body composition in D. suzukii, and these alterations could alter some ecologically relevant traits related to cold tolerance, particularly in females. Our results suggest that food deprivation during short time (<36 h) can promote cold tolerance (especially survival after a cold stress) of D. suzukii flies. Future studies should address the ecological significance of these findings as short food deprivation may occur in the fields on many occasions and seasons.

scholarly journals Artificial Selection to a Nonlethal Cold Stress in Trogoderma variabile Shows Associations With Chronic Cold Stress and Body Size

2020 ◽  
Vol 49 (2) ◽  
pp. 422-434
Author(s):  
Alison R Gerken ◽  
Shelby R Abts ◽  
Erin D Scully ◽  
James F Campbell
Keyword(s):  
Body Size ◽  
Cold Stress ◽  
Cold Tolerance ◽  
Recovery Time ◽  
Extreme Temperature ◽  
Chill Coma ◽  
Trogoderma Variabile ◽  
Cold Tolerant ◽  
Susceptible Populations ◽  
Seven Generations

Abstract Extreme temperature has been used as an alternative to chemical treatments for stored product pests for years. Resistance to heat or cold treatments has not been documented in stored product insects, but repeated use of ineffective treatments could lead to adaptive tolerance. Trogoderma variabile (Dermestidae) is a common pest of stored products, and the larval stage is highly resistant to cold and destructive. We artificially selected populations by inducing chill coma at four different cold temperature treatments: 3 and 5 h at −10°C and 3 and 5 h at 0°C. Recovery time was highly heritable after selection for seven generations for decreased recovery time (cold tolerance) and increased recovery time (cold susceptibility) at all time and temperature combinations. Three replicate populations for each time and temperature combination varied substantially, suggesting different mutations in each population were probably responsible for selected phenotypes. Body size decreased in populations selected for cold susceptibility compared with those selected for cold tolerance and survivorship to long-term cold stress increased in the cold-tolerant populations compared with the susceptible populations. After the cessation of the selection experiment, cold tolerance dissipated within four generations from the populations at −10°C, but was maintained in populations exposed to 0°C. Our results suggest that warehouse beetles can adapt to cold stress quickly, but in the absence of cold stress, the proportion of cold-tolerant/susceptible individuals is quickly reduced, suggesting that some of the mutations responsible for these phenotypes may be associated with fitness costs under normal conditions.

scholarly journals Linkage mapping and quantitative trait loci analysis of sweetness and other fruit quality traits in papaya

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Usana Nantawan ◽  
Chutchamas Kanchana-udomkan ◽  
Ido Bar ◽  
Rebecca Ford
Keyword(s):  
Quantitative Trait Loci ◽  
Candidate Genes ◽  
Fruit Quality ◽  
Quantitative Trait ◽  
Selective Breeding ◽  
Fruit Weight ◽  
Phenotypic Variance ◽  
Quality Traits ◽  
Fruit Quality Traits ◽  
Trait Loci

Abstract Background The identification and characterisation of quantitative trait loci (QTL) is an important step towards identifying functional sequences underpinning important crop traits and for developing accurate markers for selective breeding strategies. In this study, a genotyping-by-sequencing (GBS) approach detected QTL conditioning desirable fruit quality traits in papaya. Results For this, a linkage map was constructed comprising 219 single nucleotide polymorphism (SNP) loci across 10 linkage groups and covering 509 centiMorgan (cM). In total, 21 QTLs were identified for seven key fruit quality traits, including flesh sweetness, fruit weight, fruit length, fruit width skin freckle, flesh thickness and fruit firmness. Several QTL for flesh sweetness, fruit weight, length, width and firmness were stable across harvest years and individually explained up to 19.8% of the phenotypic variance of a particular trait. Where possible, candidate genes were proposed and explored further for their application to marker-assisted breeding. Conclusions This study has extended knowledge on the inheritance and genetic control for key papaya physiological and fruit quality traits. Candidate genes together with associated SNP markers represent a valuable resource for the future of strategic selective breeding of elite Australian papaya cultivars.

scholarly journals Multiple paths to cold tolerance: the role of environmental cues, morphological traits and the circadian clock gene vrille

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Noora Poikela ◽  
Venera Tyukmaeva ◽  
Anneli Hoikkala ◽  
Maaria Kankare
Keyword(s):  
Circadian Clock ◽  
Cold Acclimation ◽  
Cold Tolerance ◽  
Recovery Time ◽  
Morphological Traits ◽  
Clock Gene ◽  
Circadian Clock Gene ◽  
Chill Coma ◽  
The Impact ◽  
Insect Cold Tolerance

Abstract Background Tracing the association between insect cold tolerance and latitudinally and locally varying environmental conditions, as well as key morphological traits and molecular mechanisms, is essential for understanding the processes involved in adaptation. We explored these issues in two closely-related species, Drosophila montana and Drosophila flavomontana, originating from diverse climatic locations across several latitudes on the coastal and mountainous regions of North America. We also investigated the association between sequence variation in one of the key circadian clock genes, vrille, and cold tolerance in both species. Finally, we studied the impact of vrille on fly cold tolerance and cold acclimation ability by silencing it with RNA interference in D. montana. Results We performed a principal component analysis (PCA) on variables representing bioclimatic conditions on the study sites and used latitude as a proxy of photoperiod. PC1 separated the mountainous continental sites from the coastal ones based on temperature variability and precipitation, while PC2 arranged the sites based on summer and annual mean temperatures. Cold tolerance tests showed D. montana to be more cold-tolerant than D. flavomontana and chill coma resistance (CTmin) of this species showed an association with PC2. Chill coma recovery time (CCRT) of both species improved towards northern latitudes, and in D. flavomontana this trait was also associated with PC1. D. flavomontana flies were darkest in the coast and in the northern mountainous populations, but coloration showed no linkage with cold tolerance. Body size decreased towards cold environments in both species, but only within D. montana populations largest flies showed fastest recovery from cold. Finally, both the sequence analysis and RNAi study on vrille suggested this gene to play an essential role in D. montana cold resistance and acclimation, but not in recovery time. Conclusions Our study demonstrates the complexity of insect cold tolerance and emphasizes the need to trace its association with multiple environmental variables and morphological traits to identify potential agents of natural selection. It also shows that a circadian clock gene vrille is essential both for short- and long-term cold acclimation, potentially elucidating the connection between circadian clock system and cold tolerance.

scholarly journals Lens orientalis Contributes Quantitative Trait Loci and Candidate Genes Associated With Ascochyta Blight Resistance in Lentil

2021 ◽  
Vol 12 ◽  
Author(s):  
Rama Harinath Reddy Dadu ◽  
Ido Bar ◽  
Rebecca Ford ◽  
Prabhakaran Sambasivam ◽  
Janine Croser ◽  
...  
Keyword(s):  
Quantitative Trait Loci ◽  
Candidate Genes ◽  
Quantitative Trait ◽  
Mapping Population ◽  
Ascochyta Blight ◽  
Genotyping By Sequencing ◽  
Defense Responses ◽  
Phenotypic Variance ◽  
Genetic Dissection ◽  
Trait Loci

Australian lentil production is affected by several major biotic constraints including Ascochyta blight (AB), caused by Ascochyta lentis, a devastating fungal disease. Cultivation of AB resistant cultivars, alongside agronomic management including fungicide application, is the current most economically viable control strategy. However, the breakdown of AB resistance in cultivars, such as Northfield and Nipper, suggests the need for introgression of new and diverse resistance genes. Successful introgression entails an understanding of the genetic basis of resistance. In this context, a biparental mapping population derived from a cross between a recently identified AB resistant accession ILWL 180 (Lens orientalis) and a susceptible cultivar ILL 6002 was produced. A genetic linkage map was constructed from single-nucleotide polymorphism markers generated using a genotyping-by-sequencing transcript approach. Genetic dissection of the mapping population revealed a major quantitative trait loci (QTL) region nested with three QTLs on linkage group 5 and explained 9.5–11.5 percent (%) of phenotypic variance for AB resistance. Another QTL was identified on LG2 with phenotypic variance of 9.6%. The identified QTL regions harbored putative candidate genes potentially associated with defense responses to A. lentis infection. The QTL analysis and the candidate gene information are expected to contribute to the development of diagnostic markers and enable marker-assisted resistance selection in lentil breeding programmes.

scholarly journals Association analysis and functional annotation of imputed sequence data within genomic regions influencing resistance to gastro-intestinal parasites detected by an LDLA approach in a nucleus flock of Sarda dairy sheep

2022 ◽  
Vol 54 (1) ◽  
Author(s):  
Sara Casu ◽  
Mario Graziano Usai ◽  
Tiziana Sechi ◽  
Sotero L. Salaris ◽  
Sabrina Miari ◽  
...  
Keyword(s):  
Linkage Disequilibrium ◽  
Candidate Genes ◽  
Association Analysis ◽  
Functional Annotation ◽  
Sequence Data ◽  
Ovis Aries ◽  
Differentially Expressed ◽  
Phenotypic Variance ◽  
Major Health Problem ◽  
Functional Variants

Abstract Background Gastroinestinal nematodes (GIN) are one of the major health problem in grazing sheep. Although genetic variability of the resistance to GIN has been documented, traditional selection is hampered by the difficulty of recording phenotypes, usually fecal egg count (FEC). To identify causative mutations or markers in linkage disequilibrium (LD) to be used for selection, the detection of quantitative trait loci (QTL) for FEC based on linkage disequilibrium-linkage analysis (LDLA) was performed on 4097 ewes (from 181 sires) all genotyped with the OvineSNP50 Beadchip. Identified QTL regions (QTLR) were imputed from whole-genome sequences of 56 target animals of the population. An association analysis and a functional annotation of imputed polymorphisms in the identified QTLR were performed to pinpoint functional variants with potential impact on candidate genes identified from ontological classification or differentially expressed in previous studies. Results After clustering close significant locations, ten QTLR were defined on nine Ovis aries chromosomes (OAR) by LDLA. The ratio between the ANOVA estimators of the QTL variance and the total phenotypic variance ranged from 0.0087 to 0.0176. QTL on OAR4, 12, 19, and 20 were the most significant. The combination of association analysis and functional annotation of sequence data did not highlight any putative causative mutations. None of the most significant SNPs showed a functional effect on genes’ transcript. However, in the most significant QTLR, we identified genes that contained polymorphisms with a high or moderate impact, were differentially expressed in previous studies, contributed to enrich the most represented GO process (regulation of immune system process, defense response). Among these, the most likely candidate genes were: TNFRSF1B and SELE on OAR12, IL5RA on OAR19, IL17A, IL17F, TRIM26, TRIM38, TNFRSF21, LOC101118999, VEGFA, and TNF on OAR20. Conclusions This study performed on a large experimental population provides a list of candidate genes and polymorphisms which could be used in further validation studies. The expected advancements in the quality of the annotation of the ovine genome and the use of experimental designs based on sequence data and phenotypes from multiple breeds that show different LD extents and gametic phases may help to identify causative mutations.

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