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.

Mapping of quantitative trait loci for gibberellic acid response at rice (Oryza sativa L.) seedling stage

Plant Science ◽  
2006 ◽  
Vol 170 (1) ◽  
pp. 12-17 ◽  
Author(s):  
Yanjun Dong ◽  
H. Kamiuten ◽  
Zhongnan Yang ◽  
Dongzhi Lin ◽  
T. Ogawa ◽  
...  
Keyword(s):  
Oryza Sativa ◽  
Quantitative Trait Loci ◽  
Gibberellic Acid ◽  
Quantitative Trait ◽  
Oryza Sativa L ◽  
Seedling Stage ◽  
Trait Loci

scholarly journals A Genome-Wide Association Study for Fumonisin Contamination Resistance in Tropical Maize

2021 ◽  
Author(s):  
KARLA Jorge Silva ◽  
Claudia Teixeira Guimarães ◽  
Sylvia Morais de Sousa Tinoco ◽  
Karine da Costa Bernardino ◽  
Roberto dos Santos Trindade ◽  
...  
Keyword(s):  
Quantitative Trait Loci ◽  
Candidate Genes ◽  
Quantitative Trait ◽  
Genome Wide Association Study ◽  
Fungal Infections ◽  
Selection Process ◽  
Tropical Maize ◽  
Safe Alternative ◽  
A Genome ◽  
Trait Loci

Abstract Native genetic resistance has been considered an effective and environmentally safe alternative to control fungal infections and to reduce mycotoxins accumulation in maize grains. Marker-assisted breeding can be used to accelerate the genetic gains for fumonisin contamination resistance. Thus, the objective of this study was to identify quantitative trait loci (QTLs) and candidate genes for resistance to fumonisin contamination in an Embrapa’s tropical maize panel. Two-hundred and five inbreed lines were evaluated in three field trials Brazil in order to quantify fumonisin contamination in maize grains. The lines were genotyped-by-sequencing (GBS), generating 385,654 high-quality polymorphic SNPs. Mycotoxins in the grain samples were isolated using commercial immunoaffinity columns and its concentrations were evaluated by fluorometric technique. Nine quantitative trait loci (QTL) were found associated with fumonisin concentration resistance in maize. Seven candidate genes with annotated functions associated with biosynthetic pathways of pathogen resistance and four genes have not been previously described as related to fumonisins contamination resistance. These findings will be important to better understand the fumonisin contamination resistance and to support the development of SNP markers to accelerate the selection process in tropical maize breeding programs.

Quantitative trait loci analysis of root traits under phosphorus deficiency at the seedling stage in wheat

Genome ◽  
2018 ◽  
Vol 61 (3) ◽  
pp. 209-215 ◽  
Author(s):  
Xilan Yang ◽  
Yaxi Liu ◽  
Fangkun Wu ◽  
Xiaojun Jiang ◽  
Yu Lin ◽  
...  
Keyword(s):  
Quantitative Trait Loci ◽  
Quantitative Trait ◽  
Phosphorus Deficiency ◽  
Root Traits ◽  
Seedling Stage ◽  
Available Phosphorus ◽  
Phenotypic Variance ◽  
P Efficiency ◽  
P Deficiency ◽  
Trait Loci

Deficiency of available phosphorus (P) in soil limits wheat production and creates a need to develop P-deficiency-tolerant cultivars. Plant roots, important organs for absorbing nutrients and synthesizing growth regulators, are good candidates for P-efficiency screening. In this study, we evaluated five root traits under hydroponic culture conditions either with (AP) or without (NP) applied P in a recombinant inbred line population (H461/CM107) of Triticum aestivum L. at the seedling stage. Four significant quantitative trait loci (QTL) were detected, on chromosomes 1D, 2D, 3D, and 7D in NP-treated plants, explaining up to 13.0%, 11.0%, 14.4%, and 12.8% of the phenotypic variance, respectively. Among these QTL, Qrt.sicau-3D and Qrt.sicau-7D showed pleiotropic and additive effects. All QTL were found to be novel. The diversity array technology markers flanking the QTL were converted to simple sequence repeat markers that can be deployed in future genetic studies of P deficiency. These QTL lead to an increase in root biomass and respond to P-deficiency stress; these characteristics are crucial to improve root traits for breeding or further investigation of the gene(s) involved in P-deficiency tolerance.

scholarly journals Detection of quantitative trait loci for resistance/susceptibility to pseudorabies virus in swine

2002 ◽  
Vol 83 (1) ◽  
pp. 167-172 ◽  
Author(s):  
Gerald Reiner ◽  
Elke Melchinger ◽  
Marcela Kramarova ◽  
Eberhardt Pfaff ◽  
Matthias Büttner ◽  
...  
Keyword(s):  
Quantitative Trait Loci ◽  
Quantitative Trait ◽  
Pseudorabies Virus ◽  
Neurological Symptoms ◽  
Pseudoautosomal Region ◽  
Phenotypic Variance ◽  
Large White ◽  
Genome Wide ◽  
A Genome ◽  
Trait Loci

This study describes genetic differences in resistance/susceptibility to pseudorabies virus (PrV) between European Large White and Chinese Meishan pigs, with a mapping of quantitative trait loci (QTL) obtained from a genome-wide scan in F2 animals. Eighty-nine F2 pigs were challenged intranasally at 12 weeks with 105 p.f.u. of the wild-type PrV strain NIA-3. For QTL analysis, 85 microsatellite markers, evenly spaced on the 18 porcine autosomes and on the pseudoautosomal region of the X chromosome, were genotyped. All pigs developed clinical signs, i.e. fever, from 3 to 7 days p.i. The pure-bred Large White pigs, the F1 and three-quarters of the F2 animals, but none of the Meishan pigs, developed neurological symptoms and died or were euthanized. QTLs for appearance/non-appearance of neurological symptoms were found on chromosomes 9, 5, 6 and 13. They explained 10·6–17·9% of F2 phenotypic variance. QTL effects for rectal temperature after PrV challenge were found on chromosomes 2, 4, 8, 10, 11 and 16. Effects on chromosomes 9, 10 and 11 were significant on a genome-wide level. The results present chromosomal regions that are associated with presence/absence of neurological symptoms as well as temperature course after intranasal challenge with NIA-3. The QTLs are in proximity to important candidate genes that are assumed to play crucial roles in host defence against PrV.

scholarly journals Variance-quantitative trait loci enable systematic discovery of gene-environment interactions for cardiometabolic serum biomarkers

2021 ◽  
Author(s):  
Kenneth E Westerman ◽  
Timothy D Majarian ◽  
Franco Giulianini ◽  
Dong-Keun Jang ◽  
Jose C Florez ◽  
...  
Keyword(s):  
Quantitative Trait Loci ◽  
Quantitative Trait ◽  
Meta Analysis ◽  
Health Study ◽  
Small Subset ◽  
Phenotypic Variance ◽  
Gene Environment ◽  
Genome Wide ◽  
Trait Loci ◽  
The Uk

Gene-environment interactions (GEIs) represent the modification of genetic effects by environmental exposures and are critical for understanding disease and informing personalized medicine. GEIs often induce differential phenotypic variance across genotypes; these variance-quantitative trait loci (vQTLs) can be prioritized in a two-stage GEI detection strategy to greatly reduce the computational and statistical burden and enable testing of a broader range of exposures. We performed genome-wide vQTL analysis for 20 serum cardiometabolic biomarkers by multi-ancestry meta-analysis of 350,016 unrelated participants in the UK Biobank, identifying 182 independent locus-biomarker pairs (p < 4.5x10-9). Most vQTLs were concentrated in a small subset (4%) of loci with genome-wide significant main effects, and 44% replicated (p < 0.05) in the Women's Genome Health Study (N = 23,294). Next, we tested each vQTL for interaction across 2,380 exposures, identifying 846 significant GEIs (p < 2.4x10-7). Specific examples demonstrated interaction of triglyceride-associated variants with distinct body mass- versus body fat-related exposures as well as genotype-specific associations between alcohol consumption and liver stress at the ADH1B gene. Our catalog of vQTLs and GEIs is publicly available in an online portal.

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