Genetic architecture of phenotypic differences between endangered hybridizing Arabis floodplain species
. .
This repository contains the appendix of my thesis, structured into three chapters. It includes supporting materials such as tables, R scripts, Python codes, and other relevant files. The content is organized for ease of understanding and reproducibility of the analyses presented in the thesis.
Chapter 2: Genetic architecture of phenotypic differences between endangered hybridizing Arabis floodplain species
. .
Deciphering the genetic basis of ecological differences among hybridizing species is essential for predicting their adaptive responses to climate change and human activities. Previous studies identified a hybridization hotspot on the Rhine River, highlighting episodic gene flow between Arabis nemorensis and A. sagittata. I quantified interspecific differences in 22 phenotypic traits between these closely related species. To investigate the genetic architecture underlying these differences, I constructed a genetic map for A. nemorensis and A. sagittata using an interspecific F2 population of 742 individuals derived from reciprocal crosses of sympatric parents. The genetic map, comprising 2,082 SNPs across eight linkage groups, provided a genetically validated genome assembly for both species. Using this map, I identified the genetic basis of 20 phenotypic traits, uncovering 58 quantitative trait loci (QTLs) distributed across the genome. Analysis of fertility variation and segregation distortions revealed six large-effect QTLs associated with significant fitness loss in hybrids. While F2 hybrids generally exhibited lower seed production than parental lines, some hybrids displayed extreme trait values and patterns of transgressive segregation. Incompatibility QTLs had a simple genetic basis, and several ecologically relevant QTLs were independent of incompatibility loci, indicating potential for hybrid offspring to combine novel trait combinations absent in either parent. Fine mapping of the largest-effect QTL, associated with flowering time and explaining 23% of phenotypic variation, conducted on 410 F3 individuals, identified TFL1 as a regulator close to age pathway, excluding FLC and CO as contributors within this QTL region. Lastly, contrary to our expectations, A. nemorensis showed a larger biomass. Also unexpectedly, the root-to-shoot ratio did not differ significantly between the species. These observations suggest potential genetic similarities in their nutrient allocation strategies. However, I recommend further experiments under varying soil conditions to validate these findings.