Chromosomes I and X Harbor Consistent Genetic Factors Associated with the Anthocyanin Variation in Potato

Potatoes are an important staple food worldwide and are the third main source of antioxidants in the human diet. One of the most important antioxidant compounds in potatoes is the anthocyanin pigments. Some reports indicate a high positive correlation between color intensity, anthocyanins content, and antioxidant level in potato tubers. The variation in anthocyanins composition and content in potato tubers among diverse germplasm sources has important nutritional and health implications and constitutes an interesting trait for potato breeding programs focused on enhancing the anthocyanin and antioxidant contents of potato materials. We identified and quantified five anthocyanidins (delphinidin, cyanidin, petunidin, pelargonidin, and peonidin) on tubers from the Colombian germplasm collection of Solanum tuberosum L. Group Phureja. The phenotypic data were merged into a genome-wide association study in order to identify genomic regions associated with the nutritional compounds’ variation in potatoes. The association was conducted using a 7520 single nucleotide polymorphisms markers matrix. Seven quantitative trait loci were identified. Chromosomes I and X harbored the most stable quantitative trait loci (QTL). Three quantitative trait loci were identified close to previously reported genes involved in the regulation of anthocyanins in potato tubers. The genomic regions of these QTL reveal presumptive candidate genes as genetic factors that are the basis for a better understanding of the genetic architecture of the regulation of nutritional compounds in potatoes.

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

Genetics ◽

10.1093/genetics/162.4.1863 ◽

2002 ◽

Vol 162 (4) ◽

pp. 1863-1873 ◽

Cited By ~ 3

Author(s):

J Slate ◽

P M Visscher ◽

S MacGregor ◽

D Stevens ◽

M L Tate ◽

...

Keyword(s):

Quantitative Trait Loci ◽

Cervus Elaphus ◽

Quantitative Trait ◽

Red Deer ◽

Wild Population ◽

Additive Genetic Variance ◽

Model Organisms ◽

A Genome ◽

Trait Loci ◽

In The Wild

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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Empirical Nonparametric Bootstrap Strategies in Quantitative Trait Loci Mapping: Conditioning on the Genetic Model

Genetics ◽

10.1093/genetics/148.1.525 ◽

1998 ◽

Vol 148 (1) ◽

pp. 525-535

Author(s):

Claude M Lebreton ◽

Peter M Visscher

Keyword(s):

Quantitative Trait Loci ◽

Confidence Interval ◽

Confidence Intervals ◽

Quantitative Trait ◽

Genetic Factors ◽

Genetic Model ◽

Original Data ◽

Nonparametric Bootstrap ◽

Test Protocol ◽

Trait Loci

AbstractSeveral nonparametric bootstrap methods are tested to obtain better confidence intervals for the quantitative trait loci (QTL) positions, i.e., with minimal width and unbiased coverage probability. Two selective resampling schemes are proposed as a means of conditioning the bootstrap on the number of genetic factors in our model inferred from the original data. The selection is based on criteria related to the estimated number of genetic factors, and only the retained bootstrapped samples will contribute a value to the empirically estimated distribution of the QTL position estimate. These schemes are compared with a nonselective scheme across a range of simple configurations of one QTL on a one-chromosome genome. In particular, the effect of the chromosome length and the relative position of the QTL are examined for a given experimental power, which determines the confidence interval size. With the test protocol used, it appears that the selective resampling schemes are either unbiased or least biased when the QTL is situated near the middle of the chromosome. When the QTL is closer to one end, the likelihood curve of its position along the chromosome becomes truncated, and the nonselective scheme then performs better inasmuch as the percentage of estimated confidence intervals that actually contain the real QTL's position is closer to expectation. The nonselective method, however, produces larger confidence intervals. Hence, we advocate use of the selective methods, regardless of the QTL position along the chromosome (to reduce confidence interval sizes), but we leave the problem open as to how the method should be altered to take into account the bias of the original estimate of the QTL's position.

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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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Identification of quantitative trait loci associated with canopy temperature in soybean

Scientific Reports ◽

10.1038/s41598-020-74614-8 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Sumandeep K. Bazzer ◽

Larry C. Purcell

Keyword(s):

Quantitative Trait Loci ◽

Phenotypic Variation ◽

Quantitative Trait ◽

Recombinant Inbred Lines ◽

Canopy Temperature ◽

Growth And Yield ◽

Indirect Measure ◽

Trait Loci ◽

Genomic Regions ◽

The Impact

Abstract A consistent risk for soybean (Glycine max L.) production is the impact of drought on growth and yield. Canopy temperature (CT) is an indirect measure of transpiration rate and stomatal conductance and may be valuable in distinguishing differences among genotypes in response to drought. The objective of this study was to map quantitative trait loci (QTLs) associated with CT using thermal infrared imaging in a population of recombinant inbred lines developed from a cross between KS4895 and Jackson. Heritability of CT was 35% when estimated across environments. QTL analysis identified 11 loci for CT distributed on eight chromosomes that individually explained between 4.6 and 12.3% of the phenotypic variation. The locus on Gm11 was identified in two individual environments and across environments and explained the highest proportion of phenotypic variation (9.3% to 11.5%) in CT. Several of these CT loci coincided with the genomic regions from previous studies associated with canopy wilting, canopy temperature, water use efficiency, and other morpho-physiological traits related with drought tolerance. Candidate genes with biological function related to transpiration, root development, and signal transduction underlie these putative CT loci. These genomic regions may be important resources in soybean breeding programs to improve tolerance to drought.

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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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