A quantitative genetics model for viability selection

Luo, Lijun; Zhang, Yuan-Ming; Xu, Shutu

doi:10.1038/sj.hdy.6800615

Cited by 68 publications

(53 citation statements)

References 23 publications

(25 reference statements)

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“…These traits are vulnerable to environments and the criterion of sterility level is not consistent among different researchers. Some methods have been developed to map sterile genes or segregation distortion loci (Vogl and Xu, 2000;Luo and Xu, 2003;Luo et al, 2004;Wang et al, 2005;Chen and Walsh, 2009). These approaches take advantage of using the distorted segregating molecular markers linked to sterile genes, which circumvents the problems with seed set, rate of aborted pollen or embryo-sac morphology, but none of them took into account the existence of epistasis among sterile loci.…”

Section: Discussionmentioning

confidence: 99%

Genetic mapping of sterile genes with epistasis in backcross designs

2013

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The mapping of sterile genes is an essential issue, which should be solved for the investigation of sterility mechanism in wide hybridization of plants. However, the methods formerly developed cannot address the problem of mapping sterile loci with epistasis. In this study, we developed a new method to map sterile genes with epistasis in wide hybridizations of plants using a backcross design. The maximum likelihood method was used to estimate the parameters of recombination fractions and effects of sterile genes, and the convergent results of these parameters were obtained using the expectation maximization (EM) algorithm. The application and efficiency of this method were tested and demonstrated by a set of simulated data and real data analysis. Results from the simulation experiments showed that the method works well for simultaneously estimating the positions and effects of sterile genes, as well as the epistasis between sterile genes. A real data set of a backcross (BC) population from an interspecific hybrid between cultivated rice, Oryza sativa, and its wild African relative, Oryza longistaminata, was analyzed using the new method. Five sterile genes were detected on the chromosomes of 1, 3, 6, 8 and 10, and significant epistatic effects were found among the four pairs of sterile genes.

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Section: Discussionmentioning

confidence: 99%

Genetic mapping of sterile genes with epistasis in backcross designs

2013

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“…Such a QTL mapping study provides information on genetic architecture of complex traits, albeit some of the QTL may not be useful for breeding purposes. Segregation distortion analysis, however, only requires a few dozens of genotyped individuals (Luo et al, 2005). The detected SDLs provide information on the loci that are targeted by phenotypic selection.…”

Section: Introductionmentioning

confidence: 99%

“…Luo and Xu (2003) first developed an EM (expectation and maximization) algorithm for mapping viability selection loci (the same as SDLs). Luo et al (2005) further developed a quantitative genetic model to map these loci. The above authors postulated a hidden underlying liability for each individual.…”

Section: Introductionmentioning

confidence: 99%

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Mapping quantitative trait loci in selected breeding populations: A segregation distortion approach

Cui

Zhang

et al. 2015

Heredity

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Quantitative trait locus (QTL) mapping is often conducted in line-crossing experiments where a sample of individuals is randomly selected from a pool of all potential progeny. QTLs detected from such an experiment are important for us to understand the genetic mechanisms governing a complex trait, but may not be directly relevant to plant breeding if they are not detected from the breeding population where selection is targeting for. QTLs segregating in one population may not necessarily segregate in another population. To facilitate marker-assisted selection, QTLs must be detected from the very population which the selection is targeting. However, selected breeding populations often have depleted genetic variation with small population sizes, resulting in low power in detecting useful QTLs. On the other hand, if selection is effective, loci controlling the selected trait will deviate from the expected Mendelian segregation ratio. In this study, we proposed to detect QTLs in selected breeding populations via the detection of marker segregation distortion in either a single population or multiple populations using the same selection scheme. Simulation studies showed that QTL can be detected in strong selected populations with selected population sizes as small as 25 plants. We applied the new method to detect QTLs in two breeding populations of rice selected for high grain yield. Seven QTLs were identified, four of which have been validated in advanced generations in a follow-up study. Cloned genes in the vicinity of the four QTLs were also reported in the literatures. This mapping-by-selection approach provides a new avenue for breeders to improve breeding progress. The new method can be applied to breeding programs not only in rice but also in other agricultural species including crops, trees and animals. Heredity (2015) 115, 538-546; doi:10.1038/hdy.2015.56; published online 1 July 2015 INTRODUCTIONOver a century of breeding efforts has produced numerous varieties of domestic plants and animals to provide ample food resources for human. The great successes in plant and animal breeding have largely been achieved by exploiting within-species genetic variation for traits of interest through phenotypic selection. Although appropriate phenotypic selection is effective to exploit useful genetic variation of complex traits in breeding populations, the rich sources of naturally occurring genetic variation in plants and animals are largely hidden at the phenotypic levels and remain uncharacterized at the genomic and molecular levels. As a result, they are very much under-utilized in the past breeding programs. Meanwhile, the past decades have witnessed tremendous progress in genetic dissections of complex traits in plants and animals using DNA markers and genomic technologies (Francia et al., 2005;Collard and Mackill, 2008;Miah et al., 2013). During this period of time, thousands of quantitative trait locus (QTL) affecting a wide range of complex traits have been identified in different plant and animal species. These ...

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“…Compared with the traditional method, this approach leads to more precise linkage groups, and new software, named MapDisto, is available (Lorieux, 2012). Recently, Zhu et al (2007) further extended the multi-point method suitable for distorted, dominant and missing markers under the framework of a quantitative genetics model for viability selection (Luo et al, 2005). However, epistatic distorted markers have been not considered in the above methods.…”

Section: Introductionmentioning

confidence: 99%

Linkage group correction using epistatic distorted markers in F2 and backcross populations

Zhang

2014

Heredity

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Epistasis has been frequently observed in all types of mapping populations. However, relatively little is known about the effect of epistatic distorted markers on linkage group construction. In this study, a new approach was proposed to correct the recombination fraction between epistatic distorted markers in backcross and F 2 populations under the framework of fitness and liability models. The information for three or four markers flanking with an epistatic segregation distortion locus was used to estimate the recombination fraction by the maximum likelihood method, implemented via an expectation-maximisation algorithm. A set of Monte Carlo simulation experiments along with a real data analysis in rice was performed to validate the new method. The results showed that the estimates from the new method are unbiased. In addition, five statistical properties for the new method in a backcross were summarised and confirmed by theoretical, simulated and real data analyses.

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A quantitative genetics model for viability selection

Cited by 68 publications

References 23 publications

Genetic mapping of sterile genes with epistasis in backcross designs

Genetic mapping of sterile genes with epistasis in backcross designs

Mapping quantitative trait loci in selected breeding populations: A segregation distortion approach

Linkage group correction using epistatic distorted markers in F2 and backcross populations

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