scholarly journals Identification of blossom-end rot loci using joint QTL-seq and linkage-based QTL mapping in tomato

2021 ◽  
Author(s):  
Yasin Topcu ◽  
Manoj Sapkota ◽  
Eudald Illa-Berenguer ◽  
Savithri U. Nambeesan ◽  
Esther van der Knaap
Keyword(s):  
Cytochrome P450 ◽  
Environmental Factors ◽  
Qtl Mapping ◽  
Candidate Genes ◽  
Quantitative Trait ◽  
Genetic Basis ◽  
Fruit Weight ◽  
Physiological Disorder ◽  
Support Interval ◽  
Blossom End Rot

Abstract Key message Blossom-End Rot is Quantitatively Inherited and Maps to Four Loci in Tomato. Abstract Blossom-end rot (BER) is a devastating physiological disorder that affects tomato and other vegetables, resulting in significant crop losses. To date, most studies on BER have focused on the environmental factors that affect calcium translocation to the fruit; however, the genetic basis of this disorder remains unknown. To investigate the genetic basis of BER, two F2 and F3:4 populations along with a BC1 population that segregated for BER occurrence were evaluated in the greenhouse. Using the QTL-seq approach, quantitative trait loci (QTL) associated with BER Incidence were identified at the bottom of chromosome (ch) 3 and ch11. Additionally, linkage-based QTL mapping detected another QTL, BER3.1, on ch3 and BER4.1 on ch4. To fine map the QTLs identified by QTL-seq, recombinant screening was performed. BER3.2, the major BER QTL on ch3, was narrowed down from 5.68 to 1.58 Mbp with a 1.5-LOD support interval (SI) corresponding to 209 candidate genes. BER3.2 colocalizes with the fruit weight gene FW3.2/SlKLUH, an ortholog of cytochrome P450 KLUH in Arabidopsis. Further, BER11.1, the major BER QTL on ch11, was narrowed down from 3.99 to 1.13 Mbp with a 1.5-LOD SI interval comprising of 141 candidate genes. Taken together, our results identified and fine mapped the first loci for BER resistance in tomato that will facilitate marker-assistant breeding not only in tomato but also in many other vegetables suffering for BER.

scholarly journals Quantitative Trait Loci for Floral Morphology in Arabidopsis thaliana

Genetics ◽  
2000 ◽  
Vol 156 (3) ◽  
pp. 1379-1392 ◽  
Author(s):  
Thomas Juenger ◽  
Michael Purugganan ◽  
Trudy F C Mackay
Keyword(s):  
Arabidopsis Thaliana ◽  
Genetic Variation ◽  
Qtl Mapping ◽  
Candidate Genes ◽  
Inbred Line ◽  
Recombinant Inbred Line Population ◽  
Quantitative Trait ◽  
Recombinant Inbred ◽  
Genetic Basis ◽  
Genome Wide

Abstract A central question in biology is how genes control the expression of quantitative variation. We used statistical methods to estimate genetic variation in eight Arabidopsis thaliana floral characters (fresh flower mass, petal length, petal width, sepal length, sepal width, long stamen length, short stamen length, and pistil length) in a cosmopolitan sample of 15 ecotypes. In addition, we used genome-wide quantitative trait locus (QTL) mapping to evaluate the genetic basis of variation in these same traits in the Landsberg erecta × Columbia recombinant inbred line population. There was significant genetic variation for all traits in both the sample of naturally occurring ecotypes and in the Ler × Col recombinant inbred line population. In addition, broad-sense genetic correlations among the traits were positive and high. A composite interval mapping (CIM) analysis detected 18 significant QTL affecting at least one floral character. Eleven QTL were associated with several floral traits, supporting either pleiotropy or tight linkage as major determinants of flower morphological integration. We propose several candidate genes that may underlie these QTL on the basis of positional information and functional arguments. Genome-wide QTL mapping is a promising tool for the discovery of candidate genes controlling morphological development, the detection of novel phenotypic effects for known genes, and in generating a more complete understanding of the genetic basis of floral development.

scholarly journals Barcoded Bulk QTL mapping reveals highly polygenic and epistatic architecture of complex traits in yeast

2021 ◽  
Author(s):  
Alex N. Nguyen Ba ◽  
Katherine R. Lawrence ◽  
Artur Rego-Costa ◽  
Shreyas Gopalakrishnan ◽  
Daniel Temko ◽  
...  
Keyword(s):  
Quantitative Trait Locus ◽  
Qtl Mapping ◽  
Quantitative Trait ◽  
Complex Traits ◽  
Large Scale ◽  
Genetic Basis ◽  
Association Studies ◽  
Model Organisms ◽  
Genome Wide Association Studies ◽  
Trait Locus

Mapping the genetic basis of complex traits is critical to uncovering the biological mechanisms that underlie disease and other phenotypes. Genome-wide association studies (GWAS) in humans and quantitative trait locus (QTL) mapping in model organisms can now explain much of the observed heritability in many traits, allowing us to predict phenotype from genotype. However, constraints on power due to statistical confounders in large GWAS and smaller sample sizes in QTL studies still limit our ability to resolve numerous small-effect variants, map them to causal genes, identify pleiotropic effects across multiple traits, and infer non-additive interactions between loci (epistasis). Here, we introduce barcoded bulk quantitative trait locus (BB-QTL) mapping, which allows us to construct, genotype, and phenotype 100,000 offspring of a budding yeast cross, two orders of magnitude larger than the previous state of the art. We use this panel to map the genetic basis of eighteen complex traits, finding that the genetic architecture of these traits involves hundreds of small-effect loci densely spaced throughout the genome, many with widespread pleiotropic effects across multiple traits. Epistasis plays a central role, with thousands of interactions that provide insight into genetic networks. By dramatically increasing sample size, BB-QTL mapping demonstrates the potential of natural variants in high-powered QTL studies to reveal the highly polygenic, pleiotropic, and epistatic architecture of complex traits.Significance statementUnderstanding the genetic basis of important phenotypes is a central goal of genetics. However, the highly polygenic architectures of complex traits inferred by large-scale genome-wide association studies (GWAS) in humans stand in contrast to the results of quantitative trait locus (QTL) mapping studies in model organisms. Here, we use a barcoding approach to conduct QTL mapping in budding yeast at a scale two orders of magnitude larger than the previous state of the art. The resulting increase in power reveals the polygenic nature of complex traits in yeast, and offers insight into widespread patterns of pleiotropy and epistasis. Our data and analysis methods offer opportunities for future work in systems biology, and have implications for large-scale GWAS in human populations.

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.

scholarly journals Genetic architecture of floral traits in bee- and hummingbird-pollinated sister species of Aquilegia (columbine)

2021 ◽  
Author(s):  
Molly B. Edwards ◽  
Gary P. T. Choi ◽  
Nathan J. Derieg ◽  
Ya Min ◽  
Angie C. Diana ◽  
...  
Keyword(s):  
Qtl Mapping ◽  
Candidate Genes ◽  
Genetic Architecture ◽  
Genetic Basis ◽  
Single Locus ◽  
Floral Traits ◽  
Pollination Syndromes ◽  
Evolutionary Consequence ◽  
Floral Color ◽  
Hummingbird Pollination

Interactions with animal pollinators have helped shape the stunning diversity of flower morphologies across the angiosperms. A common evolutionary consequence of these interactions is that some flowers have converged on suites of traits, or pollination syndromes, that attract and reward specific pollinator groups. Determining the genetic basis of these floral pollination syndromes can help us understand the processes that contributed to the diversification of the angiosperms. Here, we characterize the genetic architecture of a bee-to-hummingbird pollination shift in Aquilegia (columbine) using QTL mapping of 17 floral traits encompassing color, nectar composition, and organ morphology. In this system, we find that the genetic architectures underlying differences in floral color are quite complex, and we identify several likely candidate genes involved in anthocyanin and carotenoid floral pigmentation. Most morphological and nectar traits also have complex genetic underpinnings; however, one of the key floral morphological phenotypes, nectar spur curvature, is shaped by a single locus of large effect.

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 CREBBP and WDR 24 Affects Quantitative Variation in Red Colouration in the Chicken

2018 ◽  
Author(s):  
J. Fogelholm ◽  
R. Henriksen ◽  
A. Höglund ◽  
N. Huq ◽  
M. Johnsson ◽  
...  
Keyword(s):  
Qtl Mapping ◽  
Candidate Genes ◽  
Quantitative Trait ◽  
Species Recognition ◽  
Major Effect ◽  
Quantitative Variation ◽  
Wild Populations ◽  
Effect Modifier ◽  
Colour Variation ◽  
Plumage Colouration

AbstractPlumage colouration in birds is important for a plethora of reasons, ranging from camouflage, sexual signaling, and species recognition. The genes underlying colour variation have been vital in understanding how genes can affect a phenotype. Multiple genes have been identified that affect plumage variation, but research has principally focused on major-effect genes (such as those causing albinism, barring, and the like), rather than the smaller effect modifier loci that more subtly influence colour. By utilizing a domestic x wild advanced intercross with a combination of classical QTL mapping of red colouration as a quantitative trait and a targeted genetical genomics approach, we have identified five separate candidate genes (CREBBP, WDR24, ARL8A, PHLDA3, LAD1) that putatively influence quantitative variation in red colouration in chickens. Such small effect loci are potentially far more prevalent in wild populations, and can therefore potentially be highly relevant to colour evolution.

scholarly journals The genetic basis of Drosophila melanogaster defense against Beauveria bassiana explored through evolve and resequence and quantitative trait locus mapping

2021 ◽  
Author(s):  
Parvin Shahrestani ◽  
Elizabeth King ◽  
Reza Ramezan ◽  
Mark Phillips ◽  
Melissa Riddle ◽  
...  
Keyword(s):  
Quantitative Trait Locus ◽  
Drosophila Melanogaster ◽  
Qtl Mapping ◽  
Beauveria Bassiana ◽  
Quantitative Trait ◽  
Genetic Basis ◽  
Immune Defense ◽  
Cross Resistance ◽  
Antifungal Immunity ◽  
Trait Locus

Many of the molecular mechanisms for antifungal immunity in Drosophila melanogaster have been defined, but relatively little is known about the genetic basis for variation in antifungal immunity in natural populations. Using two population genetic approaches, Quantitative Trait Locus (QTL) Mapping and Evolve and Resequence (E&R), we explored the genetics underlying D. melanogaster immune defense against infection with the fungus Beauveria bassiana. Immune defense was highly variable both in the recombinant inbred lines from the Drosophila Synthetic Population Resource used for our QTL Mapping and in the synthetic outbred populations used in our E&R study. Survivorship of infection improved dramatically over just 10 generations in the E&R study, and continued to increase for an additional 9 generations, revealing a trade-off with uninfected longevity. Populations selected for increased defense against B. bassiana evolved cross resistance to a second, distinct B. bassiana strain but not to bacterial pathogens. The QTL mapping study revealed that sexual dimorphism in defense depends on host genotype, and the E&R study indicated that dimorphism also depends on the specific pathogen to which the host is exposed. Both the QTL Mapping and E&R experiments generated lists of potentially causal candidate genes, although these lists were non-overlapping.

scholarly journals Identification of quantitative trait loci and the exploration of candidate genes for the tolerance to Zn deficiency in maize

2019 ◽  
Author(s):  
Jianqin Xu ◽  
Xiaoyang Zhu ◽  
Xiuyi Fu ◽  
Futong Yu
Keyword(s):  
Quantitative Trait Loci ◽  
Candidate Genes ◽  
Quantitative Trait ◽  
Genetic Basis ◽  
Target Genes ◽  
Functional Characterization ◽  
Chromosome 1 ◽  
Zn Deficiency ◽  
Homologous Gene ◽  
Trait Loci

Abstract Background Zn is essential for plants and Zn deficiency leads to great reduction in quality and quantity of crops. Maize, as one of the most important main staple crops worldwide, is more susceptible to Zn deficiency than any other cereal crops. Therefore, understanding the functional mechanisms in tolerance to Zn deficiency in maize is urgent but is still lacking. In this study, quantitative trait loci (QTL) analysis in K22 and By815 RIL population with high-density bin map was conducted to investigate genetic basis of the mechanisms in maize to tolerate Zn deficiency, subsequently some candidate genes were identified and considered as being associated with Zn metabolisms in plants. Results 21 QTLs were detected and accounted for 5.9% - 16.6% of phenotypic variations. Based on the co-localization in this study and the comparisons with previous studies in different RIL and GWAS populations, 223 candidate genes were identified inside the reduced QTL peak intervals on chromosome 1, 2, 6, 7 and 9. Furthermore, 9 genes detected within the peak bins of valuable genomic regions are suggested to be associated with ions transportation and some redox processes affected by Zn deficiency. Additionally, 5 genes, including ZmIRT1, ZmNRAMP6, ZmEIN2 and ZmHMAs, whose homologous gene have been studied and considered to be responsible for metal cations transportation and ethylene-signaling pathway requiring a transition metal were discovered in 5 loci we mapped. Conclusions 14 target genes identified in 9 loci we mapped in this work were explored to elucidate the potential functions in Zn homeostasis and the direct or indirect effects on mechanisms in Zn deficiency tolerance in maize. It is the first time that ZmIRT1, ZmNRAMP6, ZmHMAs were identified using linkage analysis under Zn deficiency in maize, providing genetic evidence and foundation for further gene functional characterization. Our findings have assisted us untangling the genetic basis of possible mechanisms in response to Zn deficiency in maize.

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