scholarly journals The complex genetic and molecular basis of a model quantitative trait

2016 ◽  
Vol 27 (1) ◽  
pp. 209-218 ◽  
Author(s):  
Robert A. Linder ◽  
Fabian Seidl ◽  
Kimberly Ha ◽  
Ian M. Ehrenreich

Quantitative traits are often influenced by many loci with small effects. Identifying most of these loci and resolving them to specific genes or genetic variants is challenging. Yet, achieving such a detailed understanding of quantitative traits is important, as it can improve our knowledge of the genetic and molecular basis of heritable phenotypic variation. In this study, we use a genetic mapping strategy that involves recurrent backcrossing with phenotypic selection to obtain new insights into an ecologically, industrially, and medically relevant quantitative trait—tolerance of oxidative stress, as measured based on resistance to hydrogen peroxide. We examine the genetic basis of hydrogen peroxide resistance in three related yeast crosses and detect 64 distinct genomic loci that likely influence the trait. By precisely resolving or cloning a number of these loci, we demonstrate that a broad spectrum of cellular processes contribute to hydrogen peroxide resistance, including DNA repair, scavenging of reactive oxygen species, stress-induced MAPK signaling, translation, and water transport. Consistent with the complex genetic and molecular basis of hydrogen peroxide resistance, we show two examples where multiple distinct causal genetic variants underlie what appears to be a single locus. Our results improve understanding of the genetic and molecular basis of a highly complex, model quantitative trait.

Genetics ◽  
1996 ◽  
Vol 144 (4) ◽  
pp. 1923-1932 ◽  
Author(s):  
Peter M Visscher ◽  
Chris S Haley ◽  
Robin Thompson

The efficiency of marker-assisted introgression in backcross populations derived from inbred lines was investigated by simulation. Background genotypes were simulated assuming that a genetic model of many genes of small effects in coupling phase explains the observed breed difference and variance in backcross populations. Markers were efficient in introgression backcross programs for simultaneously introgressing an allele and selecting for the desired genomic background. Using a marker spacing of 10–20 cM gave an advantage of one to two backcross generations selection relative to random or phenotypic selection. When the position of the gene to be introgressed is uncertain, for example because its position was estimated from a trait gene mapping experiment, a chromosome segment should be introgressed that is likely to include the allele of interest. Even for relatively precisely mapped quantitative trait loci, flanking markers or marker haplotypes should cover ∼10–20 cM around the estimated position of the gene, to ensure that the allele frequency does not decline in later backcross generations.


Endocrine ◽  
2017 ◽  
Vol 58 (2) ◽  
pp. 386-389 ◽  
Author(s):  
Giovanna Rotondo Dottore ◽  
Riccardo Chiarini ◽  
Maria De Gregorio ◽  
Marenza Leo ◽  
Giamberto Casini ◽  
...  

Endocrine ◽  
2017 ◽  
Vol 58 (2) ◽  
pp. 390-390 ◽  
Author(s):  
Giovanna Rotondo Dottore ◽  
Riccardo Chiarini ◽  
Maria De Gregorio ◽  
Marenza Leo ◽  
Giamberto Casini ◽  
...  

Genetics ◽  
1992 ◽  
Vol 132 (4) ◽  
pp. 1177-1185 ◽  
Author(s):  
M J Mackinnon ◽  
M A Georges

Abstract The effects of within-sample selection on the outcome of analyses detecting linkage between genetic markers and quantitative traits were studied. It was found that selection by truncation for the trait of interest significantly reduces the differences between marker genotype means thus reducing the power to detect linked quantitative trait loci (QTL). The size of this reduction is a function of proportion selected, the magnitude of the QTL effect, recombination rate between the marker locus and the QTL, and the allele frequency of the QTL. Proportion selected was the most influential of these factors on bias, e.g., for an allele substitution effect of one standard deviation unit, selecting the top 80%, 50% or 20% of the population required 2, 6 or 24 times the number of progeny, respectively, to offset the loss of power caused by this selection. The effect on power was approximately linear with respect to the size of gene effect, almost invariant to recombination rate, and a complex function of QTL allele frequency. It was concluded that experimental samples from animal populations which have been subjected to even minor amounts of selection will be inefficient in yielding information on linkage between markers and loci influencing the quantitative trait under selection.


Genetics ◽  
1989 ◽  
Vol 121 (1) ◽  
pp. 185-199 ◽  
Author(s):  
E S Lander ◽  
D Botstein

Abstract The advent of complete genetic linkage maps consisting of codominant DNA markers [typically restriction fragment length polymorphisms (RFLPs)] has stimulated interest in the systematic genetic dissection of discrete Mendelian factors underlying quantitative traits in experimental organisms. We describe here a set of analytical methods that modify and extend the classical theory for mapping such quantitative trait loci (QTLs). These include: (i) a method of identifying promising crosses for QTL mapping by exploiting a classical formula of SEWALL WRIGHT; (ii) a method (interval mapping) for exploiting the full power of RFLP linkage maps by adapting the approach of LOD score analysis used in human genetics, to obtain accurate estimates of the genetic location and phenotypic effect of QTLs; and (iii) a method (selective genotyping) that allows a substantial reduction in the number of progeny that need to be scored with the DNA markers. In addition to the exposition of the methods, explicit graphs are provided that allow experimental geneticists to estimate, in any particular case, the number of progeny required to map QTLs underlying a quantitative trait.


Genetics ◽  
1987 ◽  
Vol 116 (3) ◽  
pp. 479-486
Author(s):  
Alan Hastings

ABSTRACT Allelic substitutions under stabilizing phenotypic selection on quantitative traits are studied in Monte Carlo simulations of 8 and 16 loci. The results are compared and contrasted to analytical models based on work of M. Kimura for two and "infinite" loci. Selection strengths of S = 4Nes approximately four (which correspond to reasonable strengths of selection for quantitative characters) can retard substitution rates tenfold relative to rates under neutrality. An important finding is a strong dependence of per locus substitution rates on the number of loci.


2016 ◽  
Vol 14 (4) ◽  
pp. 149 ◽  
Author(s):  
Sunghwan Bae ◽  
Sungkyoung Choi ◽  
Sung Min Kim ◽  
Taesung Park

2014 ◽  
Author(s):  
Karl W Broman

Every data visualization can be improved with some level of interactivity. Interactive graphics hold particular promise for the exploration of high-dimensional data. R/qtlcharts is an R package to create interactive graphics for experiments to map quantitative trait loci (QTL; genetic loci that influence quantitative traits). R/qtlcharts serves as a companion to the R/qtl package, providing interactive versions of R/qtl's static graphs, as well as additional interactive graphs for the exploration of high-dimensional genotype and phenotype data.


2004 ◽  
Vol 142 (3) ◽  
pp. 289-295 ◽  
Author(s):  
M. A. DI RENZO ◽  
N. C. BONAMICO ◽  
D. G. DÍAZ ◽  
M. A. IBAÑEZ ◽  
M. E. FARICELLI ◽  
...  

‘Mal de Río Cuarto’ (MRC) disease, caused by a member of the family Reoviridae belonging to the genus Fijivirus, is considered to be the most damaging viral disease of maize (Zea mays L.) in Argentina. Resistance to MRC disease is a quantitative trait with moderate heritability ranging from 0·44 to 0·56. The objective of this study was to identify simple sequence repeats (SSR) loci linked to quantitative trait loci (QTL) contributing to MRC disease resistance. Two hundred and twenty-seven F3 derived-lines from a cross between a susceptible inbred line, Mo17, and a partially resistant inbred line, BLS14, were evaluated across four Río Cuarto environments. A disease severity index (DSI) based on disease grades was calculated and used to rate F3 derived-lines for their resistance to MRC disease. A subset of parental F2 plants belonging to susceptible and resistant F3 derived-lines from field assessments was assayed for 180 SSR primer pairs to map resistance genes. Fifty-six maize SSR were employed for the testing of linkage among DNA markers and the mapping of QTL through composite interval mapping. Resistance to MRC disease was affected by two QTL on chromosomes 1 and 8 which showed overdominance and dominant gene action, respectively. A simultaneous fit with these QTL in the joint analyses explained 36·2% of the phenotypic variance. In spite of the fact that relative efficiency of marker-assisted selection (MAS) in comparison to phenotypic selection was close to 1, the mapped QTL could improve the efficiency of efforts in breeding for resistance to MRC disease.


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