Linkage between Quantitative Trait Loci and Marker Loci: Resolution Power of Three Statistical Approaches in Single Marker Analysis

Abstract Using Cockerham's approach of orthogonal scales, we develop genetic models for the effect of an arbitrary number of multiallelic quantitative trait loci (QTLs) or neutral marker loci (NMLs) upon any number of quantitative traits. These models allow the unbiased estimation of the contributions of a set of marker loci to the additive and dominance variances and covariances among traits in a random mating population. The method has been applied to an analysis of allozyme and quantitative data from the European oyster. The contribution of a set marker loci may either be real, when the markers are actually QTLs, or apparent, when they are NMLs that are in linkage disequilibrium with hidden QTLs. Our results show that the additive and dominance variances contributed by a set of NMLs are always minimum estimates of the corresponding variances contributed by the associated QTLs. In contrast, the apparent contribution of the NMLs to the additive and dominance covariances between two traits may be larger than, equal to or lower than the actual contributions of the QTLs. We also derive an expression for the expected variance explained by the correlation between a quantitative trait and multilocus heterozygosity. This correlation explains only a part of the genetic variance contributed by the markers, i.e., in general, a combination of additive and dominance variances and, thus, provides only very limited information relative to the method supplied here.

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Quantitative trait loci and candidate genes associated with freezing tolerance of winter triticale (× Triticosecale Wittmack)

Journal of Applied Genetics ◽

10.1007/s13353-021-00660-1 ◽

2021 ◽

Author(s):

I. Wąsek ◽

M. Dyda ◽

G. Gołębiowska ◽

M. Tyrka ◽

M. Rapacz ◽

...

Keyword(s):

Chlorophyll Fluorescence ◽

Quantitative Trait Loci ◽

Freezing Tolerance ◽

Quantitative Trait ◽

Electrolyte Leakage ◽

Interval Mapping ◽

Single Marker Analysis ◽

Chlorophyll Fluorescence Parameters ◽

Fluorescence Parameters ◽

Trait Loci

Abstract Freezing tolerance of triticale is a major trait contributing to its winter hardiness. The identification of genomic regions — quantitative trait loci (QTL) and molecular markers associated with freezing tolerance in winter hexaploid triticale — was the aim of this study. For that purpose, a new genetic linkage map was developed for the population of 92 doubled haploid lines derived from ‘Hewo’ × ‘Magnat’ F1 hybrid. Those lines, together with parents were subjected to freezing tolerance test three times during two winter seasons. Plants were grown and cold-hardened under natural fall/winter conditions and then subjected to freezing in controlled conditions. Freezing tolerance was assessed as the plants recovery (REC), the electrolyte leakage (EL) from leaves and chlorophyll fluorescence parameters (JIP) after freezing. Three consistent QTL for several fluorescence parameters, electrolyte leakage, and the percentage of the survived plants were identified with composite interval mapping (CIM) and single marker analysis (SMA). The first locus Qfr.hm-7A.1 explained 9% of variation of both electrolyte leakage and plants recovery after freezing. Two QTL explaining up to 12% of variation in plants recovery and shared by selected chlorophyll fluorescence parameters were found on 4R and 5R chromosomes. Finally, main locus Qchl.hm-5A.1 was detected for chlorophyll fluorescence parameters that explained up to 19.6% of phenotypic variation. The co-located QTL on chromosomes 7A.1, 4R and 5R, clearly indicated physiological and genetic relationship of the plant survival after freezing with the ability to maintain optimal photochemical activity of the photosystem II and preservation of the cell membranes integrity. The genes located in silico within the identified QTL include those encoding BTR1-like protein, transmembrane helix proteins like potassium channel, and phosphoric ester hydrolase involved in response to osmotic stress as well as proteins involved in the regulation of the gene expression, chloroplast RNA processing, and pyrimidine salvage pathway. Additionally, our results confirm that the JIP test is a valuable tool to evaluate freezing tolerance of triticale under unstable winter environments.

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Molecular-Marker-Facilitated Investigations of Quantitative-Trait Loci in Maize. I. Numbers, Genomic Distribution and Types of Gene Action

Genetics ◽

10.1093/genetics/116.1.113 ◽

1987 ◽

Vol 116 (1) ◽

pp. 113-125

Author(s):

M D Edwards ◽

C W Stuber ◽

J F Wendel

Keyword(s):

Quantitative Trait Loci ◽

Phenotypic Variation ◽

Quantitative Trait ◽

Quantitative Traits ◽

Gene Action ◽

Individual Plant ◽

Gene Effects ◽

Individual Gene ◽

Trait Loci ◽

Marker Loci

ABSTRACT Individual genetic factors which underlie variation in quantitative traits of maize were investigated in each of two F2 populations by examining the mean trait expressions of genotypic classes at each of 17–20 segregating marker loci. It was demonstrated that the trait expression of marker locus classes could be interpreted in terms of genetic behavior at linked quantitative trait loci (QTLs). For each of 82 traits evaluated, QTLs were detected and located to genomic sites. The numbers of detected factors varied according to trait, with the average trait significantly influenced by almost two-thirds of the marked genomic sites. Most of the detected associations between marker loci and quantitative traits were highly significant, and could have been detected with fewer than the 1800–1900 plants evaluated in each population. The cumulative, simple effects of marker-linked regions of the genome explained between 8 and 40% of the phenotypic variation for a subset of 25 traits evaluated. Single marker loci accounted for between 0.3% and 16% of the phenotypic variation of traits. Individual plant heterozygosity, as measured by marker loci, was significantly associated with variation in many traits. The apparent types of gene action at the QTLs varied both among traits and between loci for given traits, although overdominance appeared frequently, especially for yield-related traits. The prevalence of apparent overdominance may reflect the effects of multiple QTLs within individual marker-linked regions, a situation which would tend to result in overestimation of dominance. Digenic epistasis did not appear to be important in determining the expression of the quantitative traits evaluated. Examination of the effects of marked regions on the expression of pairs of traits suggests that genomic regions vary in the direction and magnitudes of their effects on trait correlations, perhaps providing a means of selecting to dissociate some correlated traits. Marker-facilitated investigations appear to provide a powerful means of examining aspects of the genetic control of quantitative traits. Modifications of the methods employed herein will allow examination of the stability of individual gene effects in varying genetic backgrounds and environments.

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Quantitative Trait Loci Analysis of Folate Content in Dry Beans,Phaseolus vulgarisL.

International Journal of Agronomy ◽

10.1155/2013/983641 ◽

2013 ◽

Vol 2013 ◽

pp. 1-9 ◽

Cited By ~ 4

Author(s):

S. Khanal ◽

J. Xue ◽

R. Khanal ◽

W. Xie ◽

J. Shi ◽

...

Keyword(s):

Quantitative Trait Loci ◽

Quantitative Trait ◽

Time Interval ◽

Phenotypic Variance ◽

Dry Beans ◽

Total Phenotypic Variance ◽

Dry Bean ◽

Trait Loci ◽

Single Marker ◽

Variance Explained

Dry beans (Phaseolus vulgarisL.) contain high levels of folates, yet the level of folate may vary among different genotypes. Folates are essential vitamins and folate deficiencies may lead to a number of health problems. Among the different forms of folates, 5-methyltetrahydrofolate (5MTHF) comprises more than 80% of the total folate in dry beans. The objectives of this paper were to compare selected genotypes of dry beans for the folate content of the dry seeds and to identify quantitative trait loci (QTL) associated with the folate content in a population derived from an inter-gene-pool cross of dry beans. The folate content was examined in three large-seeded (AC Elk, Redhawk, and Taylor) and one medium-seeded (Othello) dry bean genotypes, their six F1(i.e., one-way diallel crosses), and the F2of Othello/Redhawk that were evaluated in the field in 2009. Total folate and 5MTHF contents were measured twice with one-hour time interval. The significant variation (P<0.05) in the folate content was observed among the parental genotypes, their F1progeny, and members of the F2population, ranging from 147 to 345 μg/100 g. There was a reduction in the 5MTHF and total folate contents in the second compared to the first measurement. Dark red kidney variety Redhawk consistently had the highest and pinto Othello had the lowest total folate and 5MTHF contents in both measurements. A single marker QTL analysis identified three QTL for total folate and 5MTHF contents in the first measurement and one marker for the total folate in the second measurement in the F2. These QTL had significant dominance effects and individually accounted for 7.7% to 10.5% of the total phenotypic variance. The total phenotypic variance explained by the four QTL was 18% for 5MTHF and 19% for total folate in the first measurement, but only 8% for total folate in the second measurement.

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Sequential sampling in determining linkage between marker loci and quantitative trait loci

Theoretical and Applied Genetics ◽

10.1007/bf00225002 ◽

1993 ◽

Vol 85-85 (6-7) ◽

pp. 658-664 ◽

Cited By ~ 7

Author(s):

U. Motro ◽

M. Soller

Keyword(s):

Quantitative Trait Loci ◽

Quantitative Trait ◽

Sequential Sampling ◽

Trait Loci ◽

Marker Loci

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Detection of Quantitative Trait Loci in Outbred Populations With Incomplete Marker Data

Genetics ◽

10.1093/genetics/151.1.409 ◽

1999 ◽

Vol 151 (1) ◽

pp. 409-420 ◽

Cited By ~ 4

Author(s):

Marco C A M Bink ◽

Johan A M Van Arendonk

Keyword(s):

Quantitative Trait Loci ◽

Bayesian Approach ◽

Quantitative Trait ◽

Simulated Data ◽

Residual Variance ◽

Monte Carlo Techniques ◽

Marker Data ◽

Trait Loci ◽

Marker Loci ◽

Outbred Populations

Abstract Augmentation of marker genotypes for ungenotyped individuals is implemented in a Bayesian approach via the use of Markov chain Monte Carlo techniques. Marker data on relatives and phenotypes are combined to compute conditional posterior probabilities for marker genotypes of ungenotyped individuals. The presented procedure allows the analysis of complex pedigrees with ungenotyped individuals to detect segregating quantitative trait loci (QTL). Allelic effects at the QTL were assumed to follow a normal distribution with a covariance matrix based on known QTL position and identity by descent probabilities derived from flanking markers. The Bayesian approach estimates variance due to the single QTL, together with polygenic and residual variance. The method was empirically tested through analyzing simulated data from a complex granddaughter design. Ungenotyped dams were related to one or more sons or grandsires in the design. Heterozygosity of the marker loci and size of QTL were varied. Simulation results indicated a significant increase in power when ungenotyped dams were included in the analysis.

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A comparison between methods for linkage disequilibrium fine mapping of quantitative trait loci

Genetics Research ◽

10.1017/s0016672303006554 ◽

2004 ◽

Vol 83 (1) ◽

pp. 41-47 ◽

Cited By ~ 8

Author(s):

JIHAD M. ABDALLAH ◽

BRIGITTE MANGIN ◽

BRUNO GOFFINET ◽

CHRISTINE CIERCO-AYROLLES ◽

MIGUEL PÉREZ-ENCISO

Keyword(s):

Linkage Disequilibrium ◽

Quantitative Trait Loci ◽

Quantitative Trait ◽

Simulated Data ◽

Likelihood Method ◽

Trait Loci ◽

Single Marker ◽

Linkage Disequilibrium Information ◽

Marker Regression ◽

Trait Locus

We present a maximum likelihood method for mapping quantitative trait loci that uses linkage disequilibrium information from single and multiple markers. We made paired comparisons between analyses using a single marker, two markers and six markers. We also compared the method to single marker regression analysis under several scenarios using simulated data. In general, our method outperformed regression (smaller mean square error and confidence intervals of location estimate) for quantitative trait loci with dominance effects. In addition, the method provides estimates of the frequency and additive and dominance effects of the quantitative trait locus.

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Use of Molecular Markers to Locate Quantitative Trait Loci Linked to High Soluble Solids Content in a Hybrid of Lycopersicon cheesmanii

Journal of the American Society for Horticultural Science ◽

10.21273/jashs.117.3.497 ◽

1992 ◽

Vol 117 (3) ◽

pp. 497-499 ◽

Cited By ~ 3

Author(s):

T. Casey Garvey ◽

John D. Hewitt

Keyword(s):

Quantitative Trait Loci ◽

Quantitative Trait ◽

Soluble Solids ◽

Starch Gel Electrophoresis ◽

Soluble Solids Content ◽

Morphological Marker ◽

Trait Loci ◽

Marker Loci ◽

Solids Content ◽

Lycopersicon Cheesmanii

An interspecific hybrid was made between an accession of Lycopersicon cheesmanii f. minor Riley (LA 1508) from the Galapagos Islands, Ecuador, and L. pennellii (Corr.) D'Arcy (LA 716). LA 1508 was used because of its high soluble solids content (SSC). It was crossed with LA 716 to test for linkage between isozymes and morphological markers and loci conditioning high SSC. For both accessions, chromosome numbers are equal and there are large differences between SSC and no barriers to crossing. Modified BC1 populations derived from the hybridization were assayed for isozyme markers using starch gel electrophoresis. Associations between marker loci and quantitative-trait loci (QTL) conditioning high SSC were determined using analysis of variance. Six isozymes located on five chromosomes and one morphological marker had significant associations with SSC, indicating linkage to QTL. Digenic epistatic interactions between pairs of independent markers did not appear to play an important role in the interactions between QTL that condition SSC.

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Molecular Markers Linked to Quantitative Trait Loci for Anthracnose Resistance in Tomato

HortScience ◽

10.21273/hortsci.33.3.515a ◽

1998 ◽

Vol 33 (3) ◽

pp. 515a-515 ◽

Cited By ~ 5

Author(s):

John R. Stommel ◽

Yiping Zhang

Keyword(s):

Quantitative Trait Loci ◽

Quantitative Trait ◽

Rapd Markers ◽

Random Amplified Polymorphic Dna ◽

Marker Assisted Breeding ◽

Anthracnose Resistance ◽

Trait Loci ◽

Marker Loci ◽

Single Factor Analysis ◽

Potential Use

Random amplified polymorphic DNA (RAPD) and amplified fragment length polymorphism (AFLP) markers linked to quantitative trait loci (QTL) involved in tomato anthracnose resistance were identified in an F2 population of tomato (Lycopersicon esculentum) segregating for anthracnose resistance. The F2 population was developed from the cross of an unadapted and small-fruited, but highly anthracnose-resistant L. esculentum accession and an adapted, but anthracnose-susceptible processing type tomato. Resistance to anthracnose caused by the fungal pathogen Colletotrichum coccodes is estimated to be controlled by at least three genes or chromosomal regions in this cross. One-thousand RAPD random primers and 64 AFLP primer pairs were screened for polymorphisms between the parental lines. Primers or primer pairs which differentiated the anthracnose resistant and susceptible parents were utilized to screen the F2 population for detection of QTL. Using single-factor analysis of variance, a number of markers, including six unmapped RAPD markers were identified that were significantly associated with resistance. Mapping of marker loci and their potential use in marker assisted breeding will be discussed.

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