Signatures of Dobzhansky–Muller Incompatibilities in the Genomes of Recombinant Inbred Lines

Abstract

In the construction of recombinant inbred lines (RILs) from two divergent inbred parents certain genotype (or epigenotype) combinations may be functionally "incompatible" when brought together in the genomes of the progeny, thus resulting in sterility or lower fertility. Natural selection against these epistatic combinations during inbreeding can change haplotype frequencies and distort linkage disequilibrium (LD) relations between loci on the same or on different chromosomes. These LD distortions have received increased experimental attention, because they point to genomic regions that may drive a Dobzhansky-Muller type of reproductive isolation and, ultimately, speciation in the wild. Here we study the selection signatures of two-locus epistatic incompatibility models and quantify their impact on the genetic composition of the genomes of two-way RILs obtained by selfing. We also consider the biases introduced by breeders when trying to counteract the loss of lines by selectively propagating only viable seeds. Building on our theoretical results, we develop model-based maximum-likelihood (ML) tests that can be applied to multilocus RIL genotype data to infer the precise mode of incompatibility as well as the relative fitness of incompatible loci. We illustrate this ML approach in the context of two published Arabidopsis thaliana RIL panels. Our work lays the theoretical foundation for studying more complex systems such as RILs obtained by sibling mating and/or from multiparental crosses.KEYWORDS genetic incompatibility; RIL; long-range LD; selection; epistasis; recombination; complex traits; Dobzhansky-Muller; inbreeding H YBRIDS from crosses between two divergent parental lines sometimes display low fertility and phenotypic abnormalities (Presgraves 2010). These effects are often attributable to combinations of parental genotypes (or epigenotypes) at two or more loci that are functionally incompatible when brought together into a single genome. This form of negative epistasis was originally invoked by Dobzhansky (1937) and Muller (1942) as a model for speciation. In the classical Dobzhansky-Muller (DM) model, a population splits into two subpopulations that become reproductively isolated through geographic or temporal mechanisms (i.e., prezygotically). Once separated, the two subpopulations acquire independent mutations that are incompatible upon hybridization, thus resulting in sterility or reduced fertility among offspring. This process prevents further mixing and reinforces the existing (prezygotic) reproductive isolation genetically (i.e., postzygotically). Additional independent mutations accumulate over time, causing further divergence between subpopulations and ultimately speciation. Empirical examples of interspecific genetic incompatibilities are well documented in the literature (Presgraves 2010) and have motivated extensive theoretical work in evolutionary genetics (e.g., Nei et al. 1983;Orr and Orr 1996;Turelli and Orr 2000;Barton 2001;Orr and Turelli 2001;Turelli et al. 2001;Welch 2004;Fi...

AlphaBeta: computational inference of epimutation rates and spectra from high-throughput DNA methylation data in plants

“…For example, with selection in favor of epiallele u (model ABuu), the fitness of epihomozygote m/m and epiheterozygote m/u are reduced by a factor of w and (w + 1)/2, respectively. We incorporate this fitness loss directly into the transition matrix by weighing the transition probabilities to these epigenotypes accordingly [33]. Similar arguments hold for the case where selection is for epiallele m. As a reference, we define model ABnull as the null model of no accumulation, with α = 0, β = 0, and w = 1.…”

Genomic mechanisms and consequences of diverse postzygotic barriers between monkeyflower species

“…In plants, TRD at individual loci has many documented sources, including environmental selection (Yin et al 2004), meiotic drive by chromosomes (Fishman and Saunders 2008), exposure of suppressed gamete killers (Koide et al 2008a), pollen competition , and Dobzhansky-Muller incompatibilities that kill gametes or zygotes (Leppälä et al 2008;Kerwin and Sweigart 2017). In some cases, strong Dobzhansky-Muller incompatibilities (e.g., gametic or gametophytic lethals) can generate both local distortion and linkage disequilibrium between physically unlinked loci if they kill a given multi-locus genotypic class (Colomé-Tatché and Johannes 2016). Although differentiating among multiple mechanisms of hybrid TRD can be challenging, joint mapping of fitness traits and TRD in multiple generations increases power and precision to characterize intrinsic postzygotic barriers.…”

Detecting Epistatic Selection with Partially Observed Genotype Data by Using Copula Graphical Models

“…Recently, Colomé‐Tatché and Johannes () studied two‐loci epistatic selection in RILs. The reconstruction of multiloci epistatic selection networks, however, has received little attention by experimentalists.…”