A Genome Scan for Quantitative Trait Loci in a Wild Population of Red Deer (Cervus elaphus)

Abstract Recent empirical evidence indicates that although fitness and fitness components tend to have low heritability in natural populations, they may nonetheless have relatively large components of additive genetic variance. The molecular basis of additive genetic variation has been investigated in model organisms but never in the wild. In this article we describe an attempt to map quantitative trait loci (QTL) for birth weight (a trait positively associated with overall fitness) in an unmanipulated, wild population of red deer (Cervus elaphus). Two approaches were used: interval mapping by linear regression within half-sib families and a variance components analysis of a six-generation pedigree of >350 animals. Evidence for segregating QTL was found on three linkage groups, one of which was significant at the genome-wide suggestive linkage threshold. To our knowledge this is the first time that a QTL for any trait has been mapped in a wild mammal population. It is hoped that this study will stimulate further investigations of the genetic architecture of fitness traits in the wild.

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A Genome-Wide Association Study Identifies Protein Quantitative Trait Loci (pQTLs)

PLoS Genetics ◽

10.1371/journal.pgen.1000072 ◽

2008 ◽

Vol 4 (5) ◽

pp. e1000072 ◽

Cited By ~ 294

Author(s):

David Melzer ◽

John R. B. Perry ◽

Dena Hernandez ◽

Anna-Maria Corsi ◽

Kara Stevens ◽

...

Keyword(s):

Quantitative Trait Loci ◽

Association Study ◽

Quantitative Trait ◽

Genome Wide Association Study ◽

Genome Wide Association ◽

Genome Wide ◽

A Genome ◽

Trait Loci

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

Plants ◽

10.3390/plants8020033 ◽

2019 ◽

Vol 8 (2) ◽

pp. 33 ◽

Cited By ~ 6

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.

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A genome-wide scan for quantitative trait loci affecting serum glucose and lipids in a White Duroc × Erhualian intercross F2 population

Mammalian Genome ◽

10.1007/s00335-009-9190-9 ◽

2009 ◽

Vol 20 (6) ◽

pp. 386-392 ◽

Cited By ~ 14

Author(s):

Rongrong Chen ◽

Jun Ren ◽

Wanbo Li ◽

Xiang Huang ◽

Xueming Yan ◽

...

Keyword(s):

Quantitative Trait Loci ◽

Quantitative Trait ◽

Serum Glucose ◽

F2 Population ◽

Genome Wide ◽

A Genome ◽

Trait Loci ◽

Genome Wide Scan

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ADDO: a comprehensive toolkit to detect, classify and visualize additive and non-additive quantitative trait loci

Bioinformatics ◽

10.1093/bioinformatics/btz786 ◽

2019 ◽

Vol 36 (5) ◽

pp. 1517-1521

Author(s):

Leilei Cui ◽

Bin Yang ◽

Nikolas Pontikos ◽

Richard Mott ◽

Lusheng Huang

Keyword(s):

Quantitative Trait Loci ◽

Quantitative Trait ◽

Association Studies ◽

Genetic Effects ◽

Supplementary Information ◽

Genome Wide Association Studies ◽

Additive Effects ◽

A Genome ◽

Trait Loci ◽

Additive Genetic Effects

Abstract Motivation During the past decade, genome-wide association studies (GWAS) have been used to map quantitative trait loci (QTLs) underlying complex traits. However, most GWAS focus on additive genetic effects while ignoring non-additive effects, on the assumption that most QTL act additively. Consequently, QTLs driven by dominance and other non-additive effects could be overlooked. Results We developed ADDO, a highly efficient tool to detect, classify and visualize QTLs with additive and non-additive effects. ADDO implements a mixed-model transformation to control for population structure and unequal relatedness that accounts for both additive and dominant genetic covariance among individuals, and decomposes single-nucleotide polymorphism effects as either additive, partial dominant, dominant or over-dominant. A matrix multiplication approach is used to accelerate the computation: a genome scan on 13 million markers from 900 individuals takes about 5 h with 10 CPUs. Analysis of simulated data confirms ADDO’s performance on traits with different additive and dominance genetic variance components. We showed two real examples in outbred rat where ADDO identified significant dominant QTL that were not detectable by an additive model. ADDO provides a systematic pipeline to characterize additive and non-additive QTL in whole genome sequence data, which complements current mainstream GWAS software for additive genetic effects. Availability and implementation ADDO is customizable and convenient to install and provides extensive analytics and visualizations. The package is freely available online at https://github.com/LeileiCui/ADDO. Supplementary information Supplementary data are available at Bioinformatics online.

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Detection of quantitative trait loci for locomotion and osteochondrosis-related traits in Large White ✕ Meishan pigs

Animal Science ◽

10.1017/s1357729800053418 ◽

2003 ◽

Vol 76 (2) ◽

pp. 155-165 ◽

Cited By ~ 18

Author(s):

G.J. Lee ◽

A.L. Archibald ◽

G.B. Garth ◽

A.S. Law ◽

D. Nicholson ◽

...

Keyword(s):

Quantitative Trait Loci ◽

Quantitative Trait ◽

Chromosome 1 ◽

Chromosome 15 ◽

Large White ◽

Chromosome 13 ◽

Genome Wide ◽

A Genome ◽

Trait Loci ◽

Gait Score

AbstractData from the F2 generation of a Large White (LW) ✕ Meishan (MS) crossbred population were analysed to detect quantitative trait loci (QTL) for leg and gait scores, osteochondrosis and physis scores. Legs, feet and gait score were assessed in 308 F2 animals at 85 ( + 5) kg and osteochondrosis and physis scores were recorded for the right foreleg after slaughter. A genome scan was performed using 111 genetic markers chosen to span the genome that were genotyped on the F2 animals and their F1 parents and purebred grandparents. A QTL on chromosome 1 affecting gait score was significant at the genome-wide significance level. Additional QTL significant at the chromosome-wide 5% threshold level (approx. equivalent to the genome-wide suggestive level) were detected on chromosome 1 for front feet and back legs scores, on chromosome 13 for front legs and front feet scores, on chromosome 14 for front legs, front feet and back legs scores and on chromosome 15 for back feet score. None of the QTL for osteochondrosis score exceeded the chromosome-wide suggestive level, but one chromosome-wide QTL for physis score was found on chromosome 7. On chromosome 1, gait and front feet scores mapped to the middle of the chromosome and showed additive effects in favour of the LW alleles and no dominance effects. The QTL for back legs score mapped to the distal end of the chromosome and showed a dominant effect and no additive effect. On chromosomes 14 and 15, the LW allele was again superior to the MS allele. On chromosome 13, there were both additive and dominance effects in favour of the MS allele. The MS alleles on chromosome 13 may have potential for introgression into a commercial LW population. The other putative QTLs identified may have value in marker-assisted selection in LW or MS-synthetic populations.

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Chromosomal segments underlying quantitative trait loci for mohair production in Angora goats

Animal Genetic Resources Information ◽

10.1017/s1014233909990423 ◽

2009 ◽

Vol 45 ◽

pp. 107-112 ◽

Cited By ~ 1

Author(s):

E.M. Cano ◽

S. Debenedetti ◽

M. Abad ◽

D. Allain ◽

H.R. Taddeo ◽

...

Keyword(s):

Molecular Markers ◽

Quantitative Trait Loci ◽

Quantitative Trait ◽

Fibre Diameter ◽

Average Fibre Diameter ◽

A Genome ◽

Argentinean Patagonia ◽

Trait Loci ◽

Average Fibre ◽

Angora Goats

SummaryThis study reports the results obtained in the search of chromosomal regions affecting fleece traits in a population of Angora goats in the Argentinean Patagonia. Six hundred thirty-four offspring from 14 parental half-sib families were used. Nine phenotypic fleece traits were recorded at 4 and 11 months of age. A genome examination using 85 informative molecular markers was conducted. A linkage analysis was performed using a regression interval analysis. Our study identified 10 genomic regions affecting the average fibre diameter, coefficient of variation of the average fibre diameter, percentage of fibres with diameters over 30 µm, greasy fleece weight, staple length, average curvature of fibres, percentage of continuous medullated fibres and percentage of kemp fibres located on five goat chromosomes (1, 2, 5, 13 and 19). These results show that the average size of the quantitative trait loci effect was 1.6 phenotypic standard deviations for different traits and families. The aims of quantitative trait loci detection is the potential use of these molecular markers to increase accuracy in predicting the genetic merit of breeding and its implementation in animal breeding schemes through marker-assisted selection.

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Quantitative trait loci conferring resistance in hybrid poplar to Septoriapopulicola, the cause of leaf spot

Canadian Journal of Forest Research ◽

10.1139/x26-219 ◽

1996 ◽

Vol 26 (11) ◽

pp. 1943-1950 ◽

Cited By ~ 48

Author(s):

G. Newcombe ◽

H.D. Bradshaw Jr.

Keyword(s):

Quantitative Trait Loci ◽

Pacific Northwest ◽

Quantitative Trait ◽

Leaf Spot ◽

Hybrid Poplar ◽

Threshold Value ◽

Black Cottonwood ◽

A Genome ◽

Genome Map ◽

Trait Loci

Leaf spot of native black cottonwood, Populustrichocarpa, and its hybrids, is caused by Septoriapopulicola in the Pacific Northwest. F1 clones of the most common poplar hybrid in the region, P. trichocarpa × Populusdeltoides, are typically intermediate in disease phenotype between their susceptible P. trichocarpa and resistant P. deltoides parents. To uncover the genetic basis of the resistance of these hybrids to S. populicola, a three-generation, P. trichocarpa × P. deltoides pedigree was evaluated for leaf spot by determining the percentage of spotted leaves in a randomized, replicated planting during the 4th and 5th years of tree growth. A genome map-based analysis of quantitative trait loci (QTL) revealed that a two-QTL model explained 68.3% and 61.2%, and 71.9% and 70.3%, of phenotypic and genetic variance, respectively, in the F2 generation over the 2 years. One QTL conditioning resistance was significant (threshold value for the log10 of the odds ratio = 2.9) both years, while the second QTL was different in map position each year. All three QTLs were dominant, inherited from the resistant, non-native P. deltoides parent, and located on linkage groups A, M, and X. The segregation pattern of resistance to S. populicola in the pedigree coupled with the genome map-based analysis suggests that dominant alleles at two to three resistance loci complement each other to produce a highly resistant phenotype.

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A Genome Search Identifies Major Quantitative Trait Loci on Human Chromosomes 3 and 4 That Influence Cholesterol Concentrations in Small LDL Particles

Arteriosclerosis Thrombosis and Vascular Biology ◽

10.1161/01.atv.19.3.777 ◽

1999 ◽

Vol 19 (3) ◽

pp. 777-783 ◽

Cited By ~ 54

Author(s):

David L. Rainwater ◽

Laura Almasy ◽

John Blangero ◽

Shelley A. Cole ◽

John L. VandeBerg ◽

...

Keyword(s):

Quantitative Trait Loci ◽

Quantitative Trait ◽

Human Chromosomes ◽

Ldl Particles ◽

A Genome ◽

Trait Loci ◽

Genome Search

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Identification of Distinct Quantitative Trait Loci Affecting Length or Weight Variability at Birth in Humans

The Journal of Clinical Endocrinology & Metabolism ◽

10.1210/jc.2006-0529 ◽

2006 ◽

Vol 91 (10) ◽

pp. 4164-4170 ◽

Cited By ~ 13

Author(s):

Delphine Fradin ◽

Simon Heath ◽

Jacques Lepercq ◽

Mark Lathrop ◽

Pierre Bougnères

Keyword(s):

Birth Weight ◽

Quantitative Trait Loci ◽

Fetal Growth ◽

Quantitative Trait ◽

Close Correlation ◽

Birth Length ◽

Lod Score ◽

Sibling Pairs ◽

A Genome ◽

Trait Loci

Abstract Context: The variability of human fetal growth is multifactorial. Twin and family studies demonstrate that genetic determinants influence normal fetal growth, but the responsible genetic polymorphisms are unknown. Objective: The objective of the study was the mapping of quantitative trait loci (QTLs) for birth length and weight. Design and Methods: To approach the genetic factors implicated in the normal variation of birth length and weight, we conducted a genome-wide approach of these two quantitative traits in 220 French Caucasian pedigrees (412 sibling pairs) using a variance components method. Results: We observed evidence for several QTLs influencing birth length or birth weight independently. Whereas birth length and weight showed a close correlation (r = 0.76, P < 0.0001), their genetic variability appeared largely determined by distinct genomic loci. Birth length was influenced by two major QTLs located in 2p21 and 2q11 (LOD scores 2.69 and 3.57). The variability of birth weight was linked to another QTL on 7q35 (LOD score 3.1). Several other regions showed more modest evidence for linkage with LOD score values of 1–2 on chromosomes 7, 8, 10, 13, and 17 for birth length and chromosomes 1, 2, 6, 8, 10, 13, 14, 15, 17, and 20 for birth weight. Conclusion: These preliminary QTLs provide a first step toward the identification of the genomic variants involved in the variability of human fetal growth. Our results should, however, be considered preliminary until they are replicated in other studies.

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