scholarly journals Identification of Trait-Improving Quantitative Trait Loci Alleles From a Wild Rice Relative, Oryza rufipogon

Genetics ◽  
1998 ◽  
Vol 150 (2) ◽  
pp. 899-909 ◽  
Author(s):  
Jinhua Xiao ◽  
Jiming Li ◽  
Silvana Grandillo ◽  
Sang Nag Ahn ◽  
Longping Yuan ◽  
...  
Keyword(s):  
Quantitative Trait Loci ◽  
Quantitative Trait ◽  
Quantitative Traits ◽  
Oryza Rufipogon ◽  
Cultivated Rice ◽  
Trait Loci ◽  
Hybrid Variety ◽  
Transgressive Segregants ◽  
Unique Source ◽  
Genetic Diversity Study

Abstract Wild species are valued as a unique source of genetic variation, but they have rarely been used for the genetic improvement of quantitative traits. To identify trait-improving quantitative trait loci (QTL) alleles from exotic species, an accession of Oryza rufipogon, a relative of cultivated rice, was chosen on the basis of a genetic diversity study. An interspecific BC2 testcross population (V20A/O. rufipogon//V20B///V20B////Ce64) consisting of 300 families was evaluated for 12 agronomically important quantitative traits. The O. rufipogon accession was phenotypically inferior for all 12 traits. However, transgressive segregants that outperformed the original elite hybrid variety, V20A/Ce64, were observed for all traits examined. A set of 122 RFLP and microsatellite markers was used to identify QTL. A total of 68 significant QTL were identified, and of these, 35 (51%) had beneficial alleles derived from the phenotypically inferior O. rufipogon parent. Nineteen (54%) of these beneficial QTL alleles were free of deleterious effects on other characters. O. rufipogon alleles at two QTL on chromosomes 1 and 2 were associated with an 18 and 17% increase in grain yield per plant, respectively, without delaying maturity or increasing plant height. This discovery suggests that the innovative use of molecular maps and markers can alter the way geneticists utilize wild and exotic germplasm.

Quantitative trait loci underlying domestication- and yield-related traits in an Oryza sativa × Oryza rufipogon advanced backcross population

Genome ◽  
2008 ◽  
Vol 51 (9) ◽  
pp. 692-704 ◽  
Author(s):  
Lubin Tan ◽  
Peijiang Zhang ◽  
Fengxia Liu ◽  
Guijuan Wang ◽  
Sheng Ye ◽  
...  
Keyword(s):  
Oryza Sativa ◽  
Quantitative Trait Loci ◽  
Quantitative Trait ◽  
Morphological Traits ◽  
Oryza Rufipogon ◽  
Cultivated Rice ◽  
Backcross Population ◽  
Genetic Characteristics ◽  
Significant Qtls ◽  
Trait Loci

To understand the genetic characteristics of the traits related to differentiation between cultivated rice and its wild progenitor, genetic factors controlling domestication- and yield-related traits were identified using a BC3F2 population derived from an accession of common wild rice (donor, Oryza rufipogon Griff.) collected from Yuanjiang, Yunnan province, China, and an indica cultivar, Teqing (recipient, Oryza sativa L.). A genetic linkage map consisting of 125 simple sequence repeat (SSR) markers was constructed. Based on the phenotypes of the 383 BC3F2 families evaluated in two environments, two domestication-related morphological traits, panicle shape and growth habit, were found to be controlled by single Mendelian factors. This implies that the recessive mutations of single genes controlling some morphological traits could have been easily selected during early domestication. By single-point analysis and interval mapping, 59 putative quantitative trait loci (QTLs) that influence 11 quantitative traits were detected at two sites, and 37.5% of the QTL alleles originating from O. rufipogon had a beneficial effect for yield-related traits in the Teqing background. Regions with significant QTLs for domestication- and yield-related traits were detected on chromosomes 1, 4, 5, 7, 8, and 12. Fine mapping and cloning of these domestication-related genes and QTLs will be useful in elucidating the origin and differentiation of Asian cultivated rice in the future.

Impact of the D genome and quantitative trait loci on quantitative traits in a spring durum by spring bread wheat cross

2015 ◽  
Vol 128 (9) ◽  
pp. 1799-1811 ◽  
Author(s):  
J. R. Kalous ◽  
J. M. Martin ◽  
J. D. Sherman ◽  
H.-Y. Heo ◽  
N. K. Blake ◽  
...  
Keyword(s):  
Quantitative Trait Loci ◽  
Bread Wheat ◽  
Quantitative Trait ◽  
Quantitative Traits ◽  
Spring Bread Wheat ◽  
D Genome ◽  
Trait Loci ◽  
Wheat Cross

scholarly journals The contribution of quantitative trait loci and neutral marker loci to the genetic variances and covariances among quantitative traits in random mating populations.

Genetics ◽  
1995 ◽  
Vol 139 (1) ◽  
pp. 445-455 ◽  
Author(s):  
A Ruiz ◽  
A Barbadilla
Keyword(s):  
Quantitative Trait Loci ◽  
Quantitative Trait ◽  
Quantitative Traits ◽  
Random Mating ◽  
Unbiased Estimation ◽  
Limited Information ◽  
Trait Loci ◽  
Marker Loci ◽  
Neutral Marker ◽  
Variance Explained

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.

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

Genetics ◽  
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.

Interaction and quantitative trait loci

2004 ◽  
Vol 44 (11) ◽  
pp. 1135 ◽  
Author(s):  
O. Mayo
Keyword(s):  
Quantitative Trait Loci ◽  
Quantitative Trait ◽  
Quantitative Traits ◽  
Trait Loci ◽  
Different Populations ◽  
Initial Results

Parallel searches for quantitative trait loci (QTL) for growth-related traits in different populations frequently detect sets of QTL that hardly overlap. Thus, many QTL potentially exist. Tools for the detection of QTL that interact are available and are currently being tested. Initial results suggest that epistasis is widespread. Modelling of the first recognised interaction, dominance, continues to be developed. Multigenic interaction appears to be a necessary part of any explanation. This paper covers an attempt to link some of these studies and to draw inferences about useful approaches to understanding and using the genes that influence quantitative traits.

scholarly journals Mapping quantitative trait loci with epistatic effects

2002 ◽  
Vol 79 (2) ◽  
pp. 185-198 ◽  
Author(s):  
NENGJUN YI ◽  
SHIZHONG XU
Keyword(s):  
Quantitative Trait Loci ◽  
Quantitative Trait ◽  
Complex Traits ◽  
Quantitative Traits ◽  
Threshold Model ◽  
Monte Carlo Algorithm ◽  
Epistatic Effects ◽  
Trait Loci ◽  
Robust Statistical Methods ◽  
Qtl Effects

Epistatic variance can be an important source of variation for complex traits. However, detecting epistatic effects is difficult primarily due to insufficient sample sizes and lack of robust statistical methods. In this paper, we develop a Bayesian method to map multiple quantitative trait loci (QTLs) with epistatic effects. The method can map QTLs in complicated mating designs derived from the cross of two inbred lines. In addition to mapping QTLs for quantitative traits, the proposed method can even map genes underlying binary traits such as disease susceptibility using the threshold model. The parameters of interest are various QTL effects, including additive, dominance and epistatic effects of QTLs, the locations of identified QTLs and even the number of QTLs. When the number of QTLs is treated as an unknown parameter, the dimension of the model becomes a variable. This requires the reversible jump Markov chain Monte Carlo algorithm. The utility of the proposed method is demonstrated through analysis of simulation data.

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