Identification of quantitative trait loci in rye introgression lines carrying multiple donor chromosome segments

2012 ◽  
Vol 126 (1) ◽  
pp. 49-58 ◽  
Author(s):  
Gregory S. Mahone ◽  
Matthias Frisch ◽  
Thomas Miedaner ◽  
Peer Wilde ◽  
Heinrich Wortmann ◽  
...  
Keyword(s):  
Quantitative Trait Loci ◽  
Quantitative Trait ◽  
Introgression Lines ◽  
Trait Loci ◽  
Donor Chromosome ◽  
Chromosome Segments

The use of linkage disequilibrium to map quantitative trait loci

2005 ◽  
Vol 45 (8) ◽  
pp. 837 ◽  
Author(s):  
M. E. Goddard ◽  
T. H. E. Meuwissen
Keyword(s):  
Linkage Disequilibrium ◽  
Quantitative Trait Loci ◽  
Statistical Model ◽  
Quantitative Trait ◽  
Linear Models ◽  
Chromosome Segment ◽  
Identical By Descent ◽  
Trait Loci ◽  
Linkage Disequilibrium Information ◽  
Chromosome Segments

This paper reviews the causes of linkage disequilibrium and its use in mapping quantitative trait loci. The many causes of linkage disequilibrium can be understood as due to similarity in the coalescence tree of different loci. Consideration of the way this comes about allows us to divide linkage disequilibrium into 2 types: linkage disequilibrium between any 2 loci, even if they are unlinked, caused by variation in the relatedness of pairs of animals; and linkage disequilibrium due to the inheritance of chromosome segments that are identical by descent from a common ancestor. The extent of linkage disequilibrium due to the latter cause can be logically measured by the chromosome segment homozygosity which is the probability that chromosome segments taken at random from the population are identical by descent. This latter cause of linkage disequilibrium allows us to map quantitative trait loci to chromosome regions. The former cause of linkage disequilibrium can cause artefactual quantitative trait loci at any position in the genome. These artefacts can be avoided by fitting the relatedness of animals in the statistical model used to map quantitative trait loci. In the future it may be convenient to estimate this degree of relatedness between individuals from markers covering the whole genome. The statistical model for mapping quantitative trait loci also requires us to estimate the probability that 2 animals share quantitative trait loci alleles at a particular position because they have inherited a chromosome segment containing the quantitative trait loci identical by descent. Current methods to do this all involve approximations. Methods based on concepts of coalescence and chromosome segment homozygosity are useful, but improvements are needed for practical analysis of large datasets. Once these probabilities are estimated they can be used in flexible linear models that conveniently combine linkage and linkage disequilibrium information.

scholarly journals Less-Than-Additive Epistatic Interactions of Quantitative Trait Loci in Tomato

Genetics ◽  
1996 ◽  
Vol 143 (4) ◽  
pp. 1807-1817 ◽  
Author(s):  
Yuval Eshed ◽  
Dani Zamir
Keyword(s):  
Quantitative Trait Loci ◽  
Quantitative Trait ◽  
Soluble Solids ◽  
Apparent Contradiction ◽  
Epistatic Interactions ◽  
Lycopersicon Pennellii ◽  
Trait Loci ◽  
Chromosome Segments ◽  
Fruit Mass ◽  
Qtl Effects

Abstract Epistasis plays a role in determining the phenotype, yet quantitative trait loci (QTL) mapping has uncovered little evidence for it. To address this apparent contradiction, we analyzed interactions between individual Lycopersicon pennellii chromosome segments introgressed into an otherwise homogeneous genetic background of L. esculentum (cv. M82). Ten different homozygous introgression lines, each containing from 4 to 58 cM of introgressed DNA, were crossed in a half diallele scheme. The 45 derived double heterozygotes were evaluated in the field for four yield-associated traits, along with the 10 single heterozygotes and M82. Of 180 (45 × 4) tested interactions, 28% were epistatic (P < 0.05) on both linear and geometric scales. The detected epistasis was predominately less-than-additive, i.e., the effect of the double heterozygotes was smaller than the sum of the effects of the corresponding single heterozygotes. Epistasis was also found for homozygous linked QTL affecting fruit mass and total soluble solids. Although the frequency of epistasis was high, additivity was the major component in the interaction of pairs of QTL. We propose that the diminishing additivity of QTL effects is amplified when more loci are involved; this mode of epistasis may be an important factor in phenotype canalization and in breeding.

Background-Independent Quantitative Trait Loci for Drought Tolerance Identified Using Advanced Backcross Introgression Lines in Rice

Crop Science ◽  
2013 ◽  
Vol 53 (2) ◽  
pp. 430-441 ◽  
Author(s):  
Yun Wang ◽  
Jinping Zang ◽  
Yong Sun ◽  
Jahuar Ali ◽  
Jianlong Xu ◽  
...  
Keyword(s):  
Quantitative Trait Loci ◽  
Drought Tolerance ◽  
Quantitative Trait ◽  
Introgression Lines ◽  
Advanced Backcross ◽  
Trait Loci
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