scholarly journals Genetic mapping of metabolic traits in the blind Mexican cavefish reveals sex-dependent quantitative trait loci associated with cave adaptation

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Misty R. Riddle ◽  
Ariel Aspiras ◽  
Fleur Damen ◽  
Suzanne McGaugh ◽  
Julius A. Tabin ◽  
...  
Keyword(s):  
Blood Glucose ◽  
Quantitative Trait Loci ◽  
Blood Sugar ◽  
Body Condition ◽  
Quantitative Trait ◽  
Genetic Basis ◽  
Metabolic Evolution ◽  
Trait Loci ◽  
F2 Hybrids ◽  
Cave Environment

Abstract Background Despite a longstanding interest in understanding how animals adapt to environments with limited nutrients, we have incomplete knowledge of the genetic basis of metabolic evolution. The Mexican tetra, Astyanax mexicanus, is a species of fish that consists of two morphotypes; eyeless cavefish that have adapted to a low-nutrient cave environment, and ancestral river-dwelling surface fish with abundant access to nutrients. Cavefish have evolved altered blood sugar regulation, starvation tolerance, increased fat accumulation, and superior body condition. To investigate the genetic basis of cavefish metabolic evolution we carried out a quantitative trait loci (QTL) analysis in surface/cave F2 hybrids. We genetically mapped seven metabolism-associated traits in hybrids that were challenged with a nutrient restricted diet. Results We found that female F2 hybrids are bigger than males and have a longer hindgut, bigger liver, and heavier gonad, even after correcting for fish size. Although there is no difference between male and female blood sugar level, we found that high blood sugar is associated with weight gain in females and lower body weight and fat level in males. We identified a significant QTL associated with 24-h-fasting blood glucose level with the same effect in males and females. Differently, we identified sex-independent and sex-dependent QTL associated with fish length, body condition, liver size, hindgut length, and gonad weight. We found that some of the genes within the metabolism QTL display evidence of non-neutral evolution and are likely to be under selection. Furthermore, we report predicted nonsynonymous changes to the cavefish coding sequence of these genes. Conclusions Our study reveals previously unappreciated genomic regions associated with blood glucose regulation, body condition, gonad size, and internal organ morphology. In addition, we find an interaction between sex and metabolism-related traits in A. mexicanus. We reveal coding changes in genes that are likely under selection in the low-nutrient cave environment, leading to a better understanding of the genetic basis of metabolic evolution.

Quantitative Trait Loci for Susceptibility to Tapeworm Infection in the Red Flour Beetle

Genetics ◽  
2003 ◽  
Vol 165 (3) ◽  
pp. 1307-1315
Author(s):  
Daibin Zhong ◽  
Aditi Pai ◽  
Guiyun Yan
Keyword(s):  
Quantitative Trait Loci ◽  
Quantitative Trait ◽  
Genetic Basis ◽  
Life Cycles ◽  
Red Flour Beetle ◽  
Phenotypic Variance ◽  
Flour Beetle ◽  
Trait Loci ◽  
Host Ecology ◽  
Tapeworm Infection

Abstract Parasites have profound effects on host ecology and evolution, and the effects of parasites on host ecology are often influenced by the magnitude of host susceptibility to parasites. Many parasites have complex life cycles that require intermediate hosts for their transmission, but little is known about the genetic basis of the intermediate host's susceptibility to these parasites. This study examined the genetic basis of susceptibility to a tapeworm (Hymenolepis diminuta) in the red flour beetle (Tribolium castaneum) that serves as an intermediate host in its transmission. Quantitative trait loci (QTL) mapping experiments were conducted with two independent segregating populations using amplified fragment length polymorphism (AFLP) markers and randomly amplified polymorphic DNA (RAPD) markers. A total of five QTL that significantly affected beetle susceptibility were identified in the two reciprocal crosses. Two common QTL on linkage groups 3 and 6 were identified in both crosses with similar effects on the phenotype, and three QTL were unique to each cross. In one cross, the three main QTL accounted for 29% of the total phenotypic variance and digenic epistasis explained 39% of the variance. In the second cross, the four main QTL explained 62% of the variance and digenic epistasis accounted for only 5% of the variance. The actions of these QTL were either overdominance or underdominance. Our results suggest that the polygenic nature of beetle susceptibility to the parasites and epistasis are important genetic mechanisms for the maintenance of variation within or among beetle strains in susceptibility to tapeworm infection.

scholarly journals Footprints in time: comparative quantitative trait loci mapping of the pitcher-plant mosquito, Wyeomyia smithii

2012 ◽  
Vol 279 (1747) ◽  
pp. 4551-4558 ◽  
Author(s):  
William E. Bradshaw ◽  
Kevin J. Emerson ◽  
Julian M. Catchen ◽  
William A. Cresko ◽  
Christina M. Holzapfel
Keyword(s):  
Quantitative Trait Loci ◽  
Adaptive Evolution ◽  
Quantitative Trait ◽  
Genetic Basis ◽  
Natural Populations ◽  
Cumulative Effect ◽  
Single Species ◽  
Interval Mapping ◽  
Photoperiodic Response ◽  
Trait Loci

Identifying regions of the genome contributing to phenotypic evolution often involves genetic mapping of quantitative traits. The focus then turns to identifying regions of ‘major’ effect, overlooking the observation that traits of ecological or evolutionary relevance usually involve many genes whose individual effects are small but whose cumulative effect is large. Herein, we use the power of fully interfertile natural populations of a single species of mosquito to develop three quantitative trait loci (QTL) maps: one between two post-glacially diverged populations and two between a more ancient and a post-glacial population. All demonstrate that photoperiodic response is genetically a highly complex trait. Furthermore, we show that marker regressions identify apparently ‘non-significant’ regions of the genome not identified by composite interval mapping, that the perception of the genetic basis of adaptive evolution is crucially dependent upon genetic background and that the genetic basis for adaptive evolution of photoperiodic response is highly variable within contemporary populations as well as between anciently diverged populations.

Influence of ethanol on thermoregulation: mapping quantitative trait loci

2001 ◽  
Vol 7 (2) ◽  
pp. 159-169 ◽  
Author(s):  
LARRY I. CRAWSHAW ◽  
HELEN L. WALLACE ◽  
ROBIN CHRISTENSEN ◽  
JOHN C. CRABBE
Keyword(s):  
Quantitative Trait Loci ◽  
Quantitative Trait ◽  
Genetic Basis ◽  
Core Body Temperature ◽  
Inbred Mouse ◽  
Regulatory System ◽  
Mouse Strains ◽  
Trait Loci ◽  
Cyclic Changes ◽  
Core Body

The genetic basis for the effects of ethanol on thermoregulation was investigated by utilizing recombinant inbred mouse strains from C57BL/6J and DBA/2J progenitor strains. Changes in core body temperature (Tc) and the degree of fluctuation of Tc were monitored in male mice following the administration of ethanol in an environment with cyclic changes in ambient temperature (Ta). Changes in Tc were utilized to assess ethanol-induced effects on regulated Tc, whereas fluctuations in Tc were utilized to assess thermoregulatory disruption. Ethanol was administered intraperitoneally at 1.5, 2.5, and 3.5 g/kg for all strains. Change in Tc and increase in tail temperature were also evaluated at 2.5 g/kg ethanol in a constant Ta of 26°C. Associations between the measured physiological responses and previously mapped genetic markers were used to identify quantitative trait loci (QTLs). This established probable chromosome locations for a number of genes for the responses. To our knowledge, this is the first report of QTLs that underlie changes in regulation as well as the disruption of a physiological regulatory system.

scholarly journals Overdominance and Epistasis Are Important for the Genetic Basis of Heterosis in Brassica rapa

HortScience ◽  
2007 ◽  
Vol 42 (5) ◽  
pp. 1207-1211 ◽  
Author(s):  
De-Kun Dong ◽  
Jia-Shu Cao ◽  
Kai Shi ◽  
Le-Cheng Liu
Keyword(s):  
Quantitative Trait Loci ◽  
Brassica Rapa ◽  
Quantitative Trait ◽  
Genetic Basis ◽  
Phenotypic Variance ◽  
Epistasis Analysis ◽  
Main Effect ◽  
Trait Loci ◽  
Component Traits ◽  
The Cross

To investigate the genetic basis of heterosis in Brassica rapa, an F2 population was produced from the cross of B. rapa L. subsp. chinensis (L.) Hanelt and B. rapa L. subsp. rapifera Metzg. Trait performances of the F1 hybrid showed evident mid parent heterosis, which varied from 18.55% to 101.62% for the 11 traits investigated. A total of 23 main effect quantitative trait loci (QTLs) were detected for biomass and its component traits, which could explain 4.38% to 47.80% of the phenotypic variance, respectively. Sixty-five percent of these QTLs showed obvious overdominance. Epistasis analysis detected 444 two-locus interactions for the 11 traits at the threshold of P < 0.005. Some of them remained significant when more stringent threshold were set. These results suggested that overdominance and epistasis might play an important role as the genetic basis of heterosis in B. rapa.

scholarly journals Quantitative Trait Loci (QTLs) for Intumescence Severity in Eucalyptus globulus and Validation of QTL Detection Based on Phenotyping Using Open-Pollinated Families of a Mapping Population

Plant Disease ◽  
2018 ◽  
Vol 102 (8) ◽  
pp. 1566-1573 ◽  
Author(s):  
Hans Ammitzboll ◽  
René E. Vaillancourt ◽  
Brad M. Potts ◽  
Sambavi Singarasa ◽  
Radhika Mani ◽  
...  
Keyword(s):  
Quantitative Trait Loci ◽  
Qtl Analysis ◽  
Quantitative Trait ◽  
Fungal Pathogen ◽  
Eucalyptus Globulus ◽  
Fungal Pathogens ◽  
Genetic Basis ◽  
Physiological Disorder ◽  
Trait Loci ◽  
Qtl Discovery

Intumescence is a nonpathogenic physiological disorder characterized by leaf blistering. This disorder can affect growth and development in glasshouses and growth chambers and may be confused with pathogenic diseases. We used quantitative trait loci (QTL) analysis to examine the genetic basis of variation in intumescence severity in Eucalyptus globulus, and test for colocation with previously detected QTLs for pathogen susceptibility. QTL analysis used the phenotype means of open-pollinated (OP) families of an outcrossed F2 mapping family (OP F3; n = 300) of E. globulus and the linkage map constructed in the F2. We validate this phenotyping approach for QTL analysis by assessing a trait previously used for QTL discovery in the F2 and showing the same major QTL was detected with the OP F3. For intumescence severity, five putative QTLs were detected across four linkage groups. Four of these did not colocate with previously reported QTLs for fungal pathogen susceptibility in Eucalyptus, suggesting the mechanisms underlying susceptibility to intumescence and to the two fungal pathogens are largely independent. This study demonstrates there is a genetic basis for variation in intumescence severity, reports the first QTL for intumescence severity in plants, and provides a robust framework for investigating the potential mechanisms involved.

Comparative Mapping of Quantitative Trait Loci Sculpting the Curd of Brassica oleracea

Genetics ◽  
2000 ◽  
Vol 155 (4) ◽  
pp. 1927-1954 ◽  
Author(s):  
Tien-Hung Lan ◽  
Andrew H Paterson
Keyword(s):  
Quantitative Trait Loci ◽  
Brassica Oleracea ◽  
Quantitative Trait ◽  
Genetic Basis ◽  
Allelic Variation ◽  
Morphological Data ◽  
Human Consumption ◽  
Trait Loci ◽  
Challenges And Opportunities ◽  
Different Populations

Abstract The enlarged inflorescence (curd) of cauliflower and broccoli provide not only a popular vegetable for human consumption, but also a unique opportunity for scientists who seek to understand the genetic basis of plant growth and development. By the comparison of quantitative trait loci (QTL) maps constructed from three different F2 populations, we identified a total of 86 QTL that control eight curd-related traits in Brassica oleracea. The 86 QTL may reflect allelic variation in as few as 67 different genetic loci and 54 ancestral genes. Although the locations of QTL affecting a trait occasionally corresponded between different populations or between different homeologous Brassica chromosomes, our data supported other molecular and morphological data in suggesting that the Brassica genus is rapidly evolving. Comparative data enabled us to identify a number of candidate genes from Arabidopsis that warrant further investigation to determine if some of them might account for Brassica QTL. The Arabidopsis/Brassica system is an important example of both the challenges and opportunities associated with extrapolation of genomic information from facile models to large-genome taxa including major crops.

scholarly journals Spike Density Quantitative Trait Loci Detection and Analysis in Tetraploid and Hexaploid Wheat Recombinant Inbred Line Populations

2021 ◽  
Vol 12 ◽  
Author(s):  
Jianing You ◽  
Hang Liu ◽  
Surong Wang ◽  
Wei Luo ◽  
Lulu Gou ◽  
...  
Keyword(s):  
Quantitative Trait Loci ◽  
Inbred Line ◽  
Recombinant Inbred Line ◽  
Quantitative Trait ◽  
Recombinant Inbred ◽  
Genetic Basis ◽  
Snp Array ◽  
Spike Density ◽  
Kernel Length ◽  
Trait Loci

Spike density (SD) is an agronomically important character in wheat. In addition, an optimized spike structure is a key basis for high yields. Identification of quantitative trait loci (QTL) for SD has provided a genetic basis for constructing ideal spike morphologies in wheat. In this study, two recombinant inbred line (RIL) populations (tetraploid RIL AM and hexaploid RIL 20828/SY95-71 (2SY)) previously genotyped using the wheat55K SNP array were used to identify SD QTL. A total of 18 QTL were detected, and three were major and one was stably expressed (QSd.sau-2SY-7A.2, QSd.sau-AM-5A.2, QSd.sau-AM-7B, and QSd.sau-2SY-2D). They can explain up to 23.14, 19.97, 12.00, and 9.44% of phenotypic variation, respectively. QTL × environment and epistatic interactions for SD were further analyzed. In addition, pyramiding analysis further revealed that there were additive effects between QSd.sau-2SY-2D and QSd.sau-2SY-7A.2 in 2SY, and QSd.sau-AM-5A.2 and QSd.sau-AM-7B in AM. Pearson’s correlation between SD and other agronomic traits, and effects of major or stable QTL on yield related traits indicated SD significantly impacted spike length (SL), spikelet number per spike (SNS) and kernel length (KL). Several genes related to spike development within the physical intervals of major or stable QTL were predicted and discussed. Collectively, our research identified QTL with potential applications for modern wheat breeding and broadening the genetic basis of SD.

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