Dearth of polymorphism associated with a sustained response to selection for flowering time in maize

Abstract

BackgroundLong term selection experiments bring unique insights on the genetic architecture of quantitative traits and their evolvability. Indeed, they are utilized to (i) monitor changes in allele frequencies and assess the effects of genomic regions involved traits determinism; (ii) evaluate the role of standing variation versus new mutations during adaptation; (iii) investigate the contribution of non allelic interactions. Here we describe genetic and phenotypic evolution of two independent Divergent Selection Experiments (DSEs) for flowering time conducted during 16 years from two early maize inbred lines.ResultsOur experimental design uses selfing as the mating system and small population sizes, so that two independent families evolved within each population, Late and Early. Observed patterns are strikingly similar between the two DSEs. We observed a significant response to selection in both directions during the first 7 generations of selection. Within Early families, the response is linear through 16 generations, consistent with the maintenance of genetic variance. Within Late families and despite maintenance of significant genetic variation across 17 generations, the response to selection reached a plateau after 7 generations. This plateau is likely caused by physiological limits. Residual heterozygosity in the initial inbreds can partly explain the observed responses as evidenced by 42 markers derived from both Methyl-Sensitive Amplification- and Amplified Fragment Length- Polymorphisms. Among the 42, a subset of 13 markers most of which are in high linkage disequilibrium, display a strong association with flowering time variation. Their fast fixation throughout DSEs’ pedigrees results in strong genetic differentiation between populations and families.ConclusionsOur results reveal a paradox between the sustainability of the response to selection and the associated dearth of polymorphisms. Among other hypotheses, we discuss the maintenance of heritable variation by few mutations with strong epistatic interactions whose effects are modified by continuous changes of the genetic background through time.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-015-0382-5) contains supplementary material, which is available to authorized users.

Transcriptomic response to divergent selection for flowering times reveals convergence and key players of the underlying gene regulatory network

“…The dynamics of the response to selection in Saclay divergent selection experiments is consistent with a continuous input of new mutations (Durand, et al 2010). The use of markers also revealed the contribution of complete sweeps from standing genetic variation (Durand, et al 2015). The contribution of both, new mutations and standing variants, to the response to selection to flowering time is consistent with the known complexity of this trait -its high mutation target, i.e.…”

“…This is particularly intriguing for the two Saclay divergent selection experiments that were conducted independently in two genetic backgrounds (two inbred lines) with limited standing variation (<1.9% residual heterozygosity) and very small population size. In these experiments, by applying divergent selection over 16 generations, we generated considerable phenotypic response with up to three-weeks difference between early and late flowering populations (Durand, et al 2015), a range comparable to what is observed among the maize European Nested Association Mapping panel when evaluated across multiple environments (Lehermeier, et al 2014). The dynamics of the response to selection in Saclay divergent selection experiments is consistent with a continuous input of new mutations (Durand, et al 2010).…”

“…We created a unique genetic material by applying divergent selection for flowering time independently to two maize inbred lines (F252 and MBS847-thereafter MBS) (Durand, et al 2015). This material is used to investigate evolutionary responses to selection of a complex trait and to dissect its genetic architecture.…”

“…This material is used to investigate evolutionary responses to selection of a complex trait and to dissect its genetic architecture. After 13 generations of selection, phenotypic responses revealed roughly two weeks difference between Early and VeryLate F252 populations, and between Early and Late MBS populations (data extracted from Durand, et al (2015), Figure 1). Starting from nearly-fixed commercial inbreds, this difference is striking.…”

Quantifying natural seasonal variation in mutation parameters with mutation accumulation lines

“…Explanations for this observation include selective removal of deleterious mutations in native environments or epigenetic differences among the MA lines (Becker et al., 2011). Notably, similar differences between the amount of genetic and phenotypic variation were also found in a selection experiment with maize (Durand et al., 2015). …”