Genetic architecture of heritable leaf microbes

Background Host-associated microbiomes are shaped by both their
environment and host genetics, and often impact host performance. The
scale of host genetic variation important to microbes is largely unknown,
yet fundamental to the community assembly of host-associated microbiomes,
and with implications for the eco-evolutionary dynamics of microbes and
hosts. Using Ipomoea hederacea, Ivy-leaved morning glory, we generated
matrilines differing in quantitative genetic variation and leaf shape,
which is controlled by a single Mendelian locus. We then investigated the
relative roles of Mendelian and quantitative genetic variation in
structuring the leaf microbiome, and how these two sources of genetic
variation contributed to microbe heritability. Results We found that
despite large effects of the environment, both Mendelian and quantitative
genetic host variation were important in contributing to microbe
heritability, and that the cumulative small effect genomic differences due
to matriline explained as much or more microbial variation than a single
large effect locus. Furthermore, our results are the first to suggest that
leaf shape itself contributes to variation in the abundances of some
microbes in the leaf microbiome. Conclusions The genetic architecture of
plant-associated microbiomes depends on both quantitative genetic
variation and Mendelian traits, with similar contributions to microbe
heritability. Our results demonstrate the roles of different scales of
host genetic variation in the assembly of a natural microbiome. The
genetic basis and heritability of a host’s microbial phenotype is
important for host evolution and ecology because microbes can affect host
fitness, and because it can influence reciprocal selection between hosts
and microbiomes. Additionally, when host-associated microbiomes have
heritability, then this suggests they have the capacity to evolve as other
host traits might, with potentially adaptive functions.