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Number of genes controlling a quantitative trait in a hybrid zone of the aposematic frog Ranitomeya imitator.

ABSTRACT: The number of genes controlling mimetic traits has been a topic of much research and discussion. In this paper, we examine a mimetic, dendrobatid frog Ranitomeya imitator, which harbours extensive phenotypic variation with multiple mimetic morphs, not unlike the celebrated Heliconius system. However, the genetic basis for this polymorphism is unknown, and not easy to determine using standard experimental approaches, for this hard-to-breed species. To circumvent this problem, we first develop a new protocol for automatic quantification of complex colour pattern phenotypes from images. Using this method, which has the potential to be applied in many other systems, we define a phenotype associated with differences in colour pattern between different mimetic morphs. We then proceed to develop a maximum-likelihood method for estimating the number of genes affecting a quantitative trait segregating in a hybrid zone. This method takes advantage of estimates of admixture proportions obtained using genetic data, such as microsatellite markers, and is applicable to any other system where a phenotype has been quantified in an admixture/introgression zone. We evaluate the method using extensive simulations and apply it to the R. imitator system. We show that probably one or two, or at most three genes, control the mimetic phenotype segregating in a R. imitator hybrid zone identified using image analyses.

SUBMITTER: Vestergaard JS

PROVIDER: S-EPMC4424634 | biostudies-literature | 2015 May

REPOSITORIES: biostudies-literature

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Number of genes controlling a quantitative trait in a hybrid zone of the aposematic frog Ranitomeya imitator.

Vestergaard Jacob S JS Twomey Evan E Larsen Rasmus R Summers Kyle K Nielsen Rasmus R

Proceedings. Biological sciences 20150501 1807

The number of genes controlling mimetic traits has been a topic of much research and discussion. In this paper, we examine a mimetic, dendrobatid frog Ranitomeya imitator, which harbours extensive phenotypic variation with multiple mimetic morphs, not unlike the celebrated Heliconius system. However, the genetic basis for this polymorphism is unknown, and not easy to determine using standard experimental approaches, for this hard-to-breed species. To circumvent this problem, we first develop a n ...[more]

PMID: 25925096

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Project description:A new mixed-model method was developed for mapping quantitative trait loci (QTL) by incorporating multiple polygenic covariance structures. First, we used genome-wide markers to calculate six different kinship matrices. We then partitioned the total genetic variance into six variance components, one corresponding to each kinship matrix, including the additive, dominance, additive × additive, dominance × dominance, additive × dominance, and dominance × additive variances. The six different kinship matrices along with the six estimated polygenic variances were used to control the genetic background of a QTL mapping model. Simulation studies showed that incorporating epistatic polygenic covariance structure can improve QTL mapping resolution. The method was applied to yield component traits of rice. We analyzed four traits (yield, tiller number, grain number, and grain weight) using 278 immortal F2 crosses (crosses between recombinant inbred lines) and 1619 markers. We found that the relative importance of each type of genetic variance varies across different traits. The total genetic variance of yield is contributed by additive × additive (18%), dominance × dominance (14%), additive × dominance (48%), and dominance × additive (15%) variances. Tiller number is contributed by additive (17%), additive × additive (22%), and dominance × additive (43%) variances. Grain number is mainly contributed by additive (42%), additive × additive (19%), and additive × dominance (31%) variances. Grain weight is almost exclusively contributed by the additive (73%) variance plus a small contribution from the additive × additive (10%) variance. Using the estimated genetic variance components to capture the polygenic covariance structure, we detected 39 effects for yield, 39 effects for tiller number, 24 for grain number, and 15 for grain weight. The new method can be directly applied to polygenic-effect-adjusted genome-wide association studies (GWAS) in human and other species.

Dataset Information

Number of genes controlling a quantitative trait in a hybrid zone of the aposematic frog Ranitomeya imitator.

Publications

Number of genes controlling a quantitative trait in a hybrid zone of the aposematic frog Ranitomeya imitator.

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