Deleterious phenotypes in wild Arabidopsis arenosa populations are common and linked to runs of homozygosity

Abstract

In this study, we aimed to systematically assess the frequency at which potentially deleterious phenotypes appear in natural populations of the outcrossing model plant Arabidopsis arenosa, and to establish their underlying genetics. For this purpose, we collected seeds from wild A. arenosa populations and screened over 2,500 plants for unusual phenotypes in the greenhouse. We repeatedly found plants with obvious phenotypic defects, such as small stature and necrotic or chlorotic leaves, among first-generation progeny of wild A. arenosa plants. Such abnormal plants were present in about 10% of maternal sibships, with multiple plants with similar phenotypes in each of these sibships, pointing to a genetic basis of the observed defects. A combination of transcriptome profiling, linkage mapping and genome-wide runs of homozygosity patterns using a newly assembled reference genome indicated a range of underlying genetic architectures associated with phenotypic abnormalities. This included evidence for homozygosity of certain genomic regions, consistent with alleles that are identical by descent being responsible for these defects. Our observations suggest that deleterious alleles with different genetic architectures are segregating at appreciable frequencies in wild A. arenosa populations.

Runs of homozygosity reveal contrasting histories of inbreeding across global lineages of the edible porcini mushroom, Boletus edulis

“…To summarise variation in the antiquity of ROH among lineages, we converted the length of each ROH into the estimated number of generations since the most recent common ancestor (TMRCA) according to Howrigan et al (2011) using a recombination rate estimate from another agarycomycete species (Gao et al, 2018;Larraya et al, 2000). We found a diversity of ROH 2023), the application of to plants has been more limited (Barragan et al, 2024;Kumar et al, 2021;Pavan et al, 2021) and we are not aware of any ROH studies in fungi. We therefore conducted the first genomic survey to our knowledge of ROHs in a wild, globally distributed fungus.…”

“…Despite the many advantages of ROHs, their potential has not yet been fully realised in plants and fungi. In particular, while a handful of studies have used ROHs to investigate phenotypic traits and inbreeding in plants ( Barragan et al, 2024;Kumar et al, 2021;Pavan et al, 2021) we are not aware of any studies of ROHs in fungi. Such studies are urgently needed to improve our understanding of the dynamics of forest ecosystems in an era of environmental change.…”