Epistasis and genotype-environment interaction for quantitative trait loci affecting flowering time in Arabidopsis thaliana

Juenger, Thomas E.; Sen, Sáunak; Stowe, Kirk A.; Simms, Ellen L.

doi:10.1007/1-4020-3836-4_9

Cited by 98 publications

(154 citation statements)

References 51 publications

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“…For example, Wu (1998) reported that 13 out of 15 QTL for plasticity showed clear indications of gene regulation. Ungerer et al (2003) found that 55-83% of the plasticity QTL colocalized with QTL having an effect on the respective quantitative traits. In the study by Kraakman et al (2004), three of five QTL for plasticity co-located with QTL having an effect on the quantitative trait itself; thus, two of the QTL for plasticity were good candidates for gene regulation.…”

Section: Discussionmentioning

confidence: 98%

“…Thus, environmental canalization and phenotypic plasticity can be viewed as the two possible extremes of response to changes in environment (see Flatt, 2005). Because different genotypes of the same species may display a wide range of variation in the level of their plasticity response (Breitkreutz et al, 2003;Ungerer et al, 2003;Ros et al, 2004;Turner, 2004), there must be a genetic basis of response to environmental change. Alleles at loci that affect variation in a phenotype across environments should therefore be considered as determinants of plasticity and canalization.…”

Section: Introductionmentioning

confidence: 99%

“…Kleibenstein et al (2002) used data from a population of recombinant inbred lines of Arabidopsis thaliana phenotyped in two environments, followed the example of Weber and Scheiner (1992), and used the difference between phenotypic trait scores in two environments as a direct measure of plasticity. Ungerer et al (2003) extended this approach to data from more than two environments. Their measure of phenotypic plasticity was based on quantifying the difference in a phenotypic trait for each genotype across each pair of environments.…”

Section: Introductionmentioning

confidence: 99%

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Genetics of phenotypic plasticity: QTL analysis in barley, Hordeum vulgare

2008

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Phenotypic plasticity is the variation in phenotypic traits produced by a genotype in different environments. In contrast, environmental canalization is defined as the insensitivity of a genotype's phenotype to variation in environments. Despite the extensive literature on the evolutionary significance and potential genetic mechanisms driving plasticity and canalization, few studies tried to unravel the genetic basis of this phenomenon. Using both simulations and real data from barley (Hordeum vulgare), we used QTL mapping to obtain insights into the genetics of phenotypic plasticity. We explored two ways of quantifying phenotypic plasticity, namely the phenotypic variance across environments and the Finlay-Wilkinson's regression slope. Each relates to a different concept of stability. Through QTL detection with real and simulated data, we show that each measure of plasticity detects specific types of plasticity QTL. Most of the plasticity QTLs were detected in the data set with the lowest number of environments. All plasticity QTL co-located with loci showing QTL Â E interaction and there were no QTL that only affected plasticity. The number of environments that are considered and their homogeneity is a key to interpret the genetic control of phenotypic plasticity. Regulatory pathways of plasticity may vary from one set of environments to another due to unique features of each environment. Therefore, with an increasing number of environments, it may become impossible to detect a single 'consistent' regulatory pathway for all environments.

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Section: Discussionmentioning

confidence: 98%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Genetics of phenotypic plasticity: QTL analysis in barley, Hordeum vulgare

2008

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“…If genes are environmentally sensitive, this phenotypic plasticity is expressed at a genetic level in response to environmental variation i.e., a genotype 9 environment (G 9 E) interaction (Maloof 2003;Juenger et al 2005). G 9 E can limit deployment of potential crop improvements since commercially successful cultivars or varieties must be robust under many if not all growing environments.…”

Section: Influence Of Geneticsmentioning

confidence: 99%

Oxidative discolouration in whole-head and cut lettuce: biochemical and environmental influences on a complex phenotype and potential breeding strategies to improve shelf-life

et al. 2017

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Lettuce discolouration is a key post-harvest trait. The major enzyme controlling oxidative discolouration has long been considered to be polyphenol oxidase (PPO) however, levels of PPO and subsequent development of discolouration symptoms have not always correlated. The predominance of a latent state of the enzyme in plant tissues combined with substrate activation and contemporaneous suicide inactivation mechanisms are considered as potential explanations for this phenomenon. Leaf tissue physical properties have been associated with subsequent discolouration and these may be influenced by variation in nutrient availability, especially excess nitrogen and head maturity at harvest. Mild calcium and irrigation stress has also been associated with a reduction in subsequent discolouration, although excess irrigation has been linked to increased discolouration potentially through leaf physical properties. These environmental factors, including high temperature and UV light intensities, often have impacts on levels of phenolic compounds linking the environmental responses to the biochemistry of the PPO pathway. Breeding strategies targeting the PAL and PPO pathway biochemistry and environmental response genes are discussed as a more cost-effective method of mitigating oxidative discolouration then either modified atmosphere packaging or post-harvest treatments, although current understanding of the biochemistry means that such programs are likely to be limited in nature and it is likely that they will need to be deployed alongside other methods for the foreseeable future.Keywords Lettuce Á Discolouration Á Biochemistry Á Environment Á Polyphenols Á Phenylpropanoid pathway Á Review The value of lettuceThe UK processed salad sector was valued at approximately £848 million in

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“…The genetic basis of adaptation to environmental factors is still not understood in detail. Data suggest that variation in stress responsive genes may affect the individual performance under environmentally unfavorable conditions (Gillespie & Turelli, 1989;Quesada et al, 2002;Ungerer et al, 2003) and may therefore be involved in the genetic manifestation of adaptation. A significant proportion of diversity at the molecular level of stress responsive genes appears to be adaptive rather than neutral (Pe`re zdse la Vega, 1996;Favatier et al, 1997;Nevo et al, 1998).…”

Section: Introductionmentioning

confidence: 99%

Correlation between hordatine accumulation, environmental factors and genetic diversity in wild barley (Hordeum spontaneum C. Koch) accessions from the Near East Fertile Crescent

et al. 2006

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Wild barley shows a large morphological and phenotypic variation, which is associated with ecogeographical factors and correlates with genotypic differences. Diversity of defense related genes and their expression in wild barley has been recognized and has led to attempts to exploit genes from H. spontaneum in breeding programs. The aim of this study was to determine the variation in the accumulation of hordatines, which are Hordeum-specific preformed secondary metabolites with strong and broad antimicrobial activity in vitro, in 50 accessions of H. spontaneum from different habitats in Israel. Differences in the accumulation of hordatines in the seedling stage were significant between different H. spontaneum genotypes from different regional locations and micro-sites. Variation in the hordatine accumulation within genotypes was between 9% and 45%, between genotypes from the same location between 13% and 38%, and between genotypes from different locations up to 121%. Principal component analysis showed that water related factors explain 39%, temperature related factors explain 33% and edaphic factors account for 11% of the observed variation between the populations of H. spontaneum. Genetic analysis of the tested accessions with LP-PCR primers that are specific for genes involved in the biosynthetic pathway of hordatines showed tight correlations between hordatine abundance and genetic diversity of these markers. Multiple regression analyses indicated associations between genetic diversity of genes directly involved in hordatine biosynthesis, ecogeographical factors and the accumulation of hordatines.

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Epistasis and genotype-environment interaction for quantitative trait loci affecting flowering time in Arabidopsis thaliana

Cited by 98 publications

References 51 publications

Genetics of phenotypic plasticity: QTL analysis in barley, Hordeum vulgare

Genetics of phenotypic plasticity: QTL analysis in barley, Hordeum vulgare

Oxidative discolouration in whole-head and cut lettuce: biochemical and environmental influences on a complex phenotype and potential breeding strategies to improve shelf-life

Correlation between hordatine accumulation, environmental factors and genetic diversity in wild barley (Hordeum spontaneum C. Koch) accessions from the Near East Fertile Crescent

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