Analysis of natural allelic variation in
            <i>Arabidopsis</i>
            using a multiparent recombinant inbred line population

Huang, Xueqing; Paulo, Maria João; Boer, Martin P.; Effgen, Sigi; Keizer, Paul; Koornneef, M.; Eeuwijk, Fred van

doi:10.1073/pnas.1100465108

Cited by 152 publications

(135 citation statements)

References 41 publications

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“…It has been suggested that power issues reduce the number of QTL observable with multiparent mapping lines (Keurentjes et al 2011). There were, for example, fewer QTL observed for flowering time using multiparent populations of A. thaliana (Kover et al 2009b;Huang et al 2011) than in studies that used mapping populations from intercrosses of two accessions. However, in this study the number of QTL identified (8 QTL for seed size and 9 QTL for seed number) is comparable to the other QTL studies.…”

Section: Discussionmentioning

confidence: 99%

The Genetic Basis of Natural Variation in Seed Size and Seed Number and Their Trade-Off Using Arabidopsis thaliana MAGIC Lines

Gnan¹,

Priest²,

Kover

2014

Genetics

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Offspring number and size are key traits determining an individual's fitness and a crop's yield. Yet, extensive natural variation within species is observed for these traits. Such variation is typically explained by trade-offs between fecundity and quality, for which an optimal solution is environmentally dependent. Understanding the genetic basis of seed size and number, as well as any possible genetic constraints preventing the maximization of both, is crucial from both an evolutionary and applied perspective. We investigated the genetic basis of natural variation in seed size and number using a set of Arabidopsis thaliana multiparent advanced generation intercross (MAGIC) lines. We also tested whether life history affects seed size, number, and their trade-off. We found that both seed size and seed number are affected by a large number of mostly nonoverlapping QTL, suggesting that seed size and seed number can evolve independently. The allele that increases seed size at most identified QTL is from the same natural accession, indicating past occurrence of directional selection for seed size. Although a significant trade-off between seed size and number is observed, its expression depends on life-history characteristics, and generally explains little variance. We conclude that the trade-off between seed size and number might have a minor role in explaining the maintenance of variation in seed size and number, and that seed size could be a valid target for selection.T HE reproductive output of an organism is a critical lifehistory trait defining its fitness and is the result of both offspring number and quality. In the case of cereal crops, the number and size of seeds are also the main constituents of yield. Thus, understanding the genetic architecture of seed size and number, and any possible genetic constraints to maximizing them, is crucial from both an evolutionary and applied perspective (Sadras 2007;Van Daele et al. 2012;Kesavan et al. 2013). Despite its importance, the genetic basis of natural variation in seed size and number and their interaction with life-history traits remain poorly understood.Previous studies on the genetic basis of seed traits have predominantly used mutant screens and identified genes in key pathways involved in seed development (Garcia et al. 2003;Tzafrir et al. 2004;Adamski et al. 2009;Fang et al. 2012). However, since this approach only allows for the comparison of phenotypic effects of genes that are "on" or "off" (Koornneef et al. 2004), genes' contribution to natural continuous variation in seed size or seed number remain largely uncharacterized. Because the effects of mutants are often dependent on the genetic background (Tonsor et al. 2005;Chou et al. 2011), a QTL mapping approach using multiple parents is ideal to identify genetic factors that can contribute to natural variation in these traits in a heterogeneous genetic background.Identification of genetic factors affecting seed traits is further complicated by potential trade-offs between them. Life-history the...

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Section: Discussionmentioning

confidence: 99%

The Genetic Basis of Natural Variation in Seed Size and Seed Number and Their Trade-Off Using Arabidopsis thaliana MAGIC Lines

Gnan¹,

Priest²,

Kover

2014

Genetics

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“…polyallelism, genetic heterogeneity) by forward genetic approaches is difficult in spite of their suspected importance in human disease (McClellan and King 2010). Indeed, detecting multiallelism requires a multiple-parent QTL scheme, and this has only been recently implemented in a handful of model organisms (Huang et al 2011;Long et al 2014a). Furthermore, GWAS studies typically underestimate the contributions of mixed alleles (Thornton et al 2013).…”

Section: How When and Why Ligand Genes Are Likely Drivers Of Pattermentioning

confidence: 99%

Morphological Evolution Repeatedly Caused by Mutations in Signaling Ligand Genes

Martin

Courtier‐Orgogozo

2017

Diversity and Evolution of Butterfly Wing Patterns

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What types of genetic changes underlie evolution? Secreted signaling molecules (syn. ligands) can induce cells to switch states and thus largely contribute to the emergence of complex forms in multicellular organisms. It has been proposed that morphological evolution should preferentially involve changes in developmental toolkit genes such as signaling pathway components or transcription factors. However, this hypothesis has never been formally confronted to the bulk of accumulated experimental evidence. Here we examine the importance of ligandcoding genes for morphological evolution in animals. We use Gephebase (http:// www.gephebase.org), a database of genotype-phenotype relationships for evolutionary changes, and survey the genetic studies that mapped signaling genes as causative loci of morphological variation. To date, 19 signaling genes represent 20% of the cases where an animal morphological change has been mapped to a gene (80/391). This includes the signaling gene Agouti, which harbors multiple cis-regulatory alleles linked to color variation in vertebrates, contrasting with the effects of coding variation in its target, the melanocortin receptor MC1R. In sticklebacks, genetic mapping approaches have identified 4 signaling genes out of 14 loci associated with lake adaptations. Finally, in butterflies, a total of 18 allelic variants of the WntA Wnt-family ligand cause color pattern adaptations related to wing mimicry, both within and between species. We discuss possible hypotheses explaining these cases of natural replication (genetic parallelism) and conclude that signaling ligand loci are an important source of sequence variation underlying morphological change in nature.

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“…Therefore, the THDC and FHC designs were examined. The THDC design is similar to the Arabidopsis multi-parental RIL design (Paulo et al, 2008;Huang et al, 2011), where the PIs are crossed in pairs to create two-way hybrids, which were then crossed in a diallel. Instead of a diallel cross, the FHC had a second generation of pairwise hybridisations.…”

Section: Comparison Of the Examined Mating Designsmentioning

confidence: 99%

QTL detection power of multi-parental RIL populations in Arabidopsis thaliana

2012

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A major goal of today's biology is to understand the genetic basis of quantitative traits. This can be achieved by statistical methods that evaluate the association between molecular marker variation and phenotypic variation in different types of mapping populations. The objective of this work was to evaluate the statistical power of quantitative trait loci (QTL) detection of various multi-parental mating designs, as well as to assess the reasons for the observed differences. Our study was based on an empirical data of 20 Arabidopsis thaliana accessions, which have been selected to capture the maximum genetic diversity. The examined mating designs differed strongly with respect to the statistical power to detect QTL. We observed the highest power to detect QTL for the diallel cross with random mating design. The results of our study suggested that performing sibling mating within subpopulations of joint-linkage mapping populations has the potential to considerably increase the power for QTL detection. Our results, however, revealed that using designs in which more than two parental alleles segregate in each subpopulation increases the power even more.

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Analysis of natural allelic variation in Arabidopsis using a multiparent recombinant inbred line population

Cited by 152 publications

References 41 publications

The Genetic Basis of Natural Variation in Seed Size and Seed Number and Their Trade-Off Using Arabidopsis thaliana MAGIC Lines

The Genetic Basis of Natural Variation in Seed Size and Seed Number and Their Trade-Off Using Arabidopsis thaliana MAGIC Lines

Morphological Evolution Repeatedly Caused by Mutations in Signaling Ligand Genes

QTL detection power of multi-parental RIL populations in Arabidopsis thaliana

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