Low genetic diversity, high inbreeding and limited gene flow in the endangered species Linaria flava subsp. sardoa revealed by genome-wide analysis of polymorphisms

Linaria flava subsp. sardoa is a critically endangered plant endemic to the coastal sand dunes of Sardinia (Italy) and Corsica (France), and is recognized under European frameworks for biodiversity conservation and strict protection actions. However, despite its conservation status, little is known about its genomic landscape. Investigating its population genetic structure is essential to assess levels of genetic diversity, and detect potential inbreeding or isolation among populations. Such information provides a critical basis for the development of effective management and conservation strategies. In this study a genotyping-by-sequencing approach was used to identify 24,312 Single Nucleotide Polymorphisms and to investigate genomic diversity and population structure in 96 samples of L. sardoa, belonging to eight populations. Our results evidenced high levels of inbreeding (mean inbreeding coefficient = 0.87), low levels of genetic diversity within population (mean He = 0.05), coupled with high genetic differentiation between populations of L. sardoa (mean pairwise FST=0.57). These patterns suggest a lack of genetic diversity, long-term isolation and limited gene flow, raising concerns about the species' resilience to environmental change and stochastic events, and calling for immediate conservation actions. Only some individuals from the MOL population showed significantly lower levels of inbreeding and higher levels of heterozygosity. All these findings provide valuable insights to inform both current and future conservation strategies for the species. A possible conservation action for L. sardoa could therefore be the reinforcement of existing populations including in the donor pool at least a small proportion of individuals from other populations, in particular from populations, like MOL, showing higher genetic diversity.