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..., Overall goal: 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 in a common garden, and how these two sources of genetic variation contributed to microbe heritability.
Breeding design: We used seeds derived from a cross by Campitelli and Stinchcombe (2013), where individuals from the two alternate homozygous leaf shape phenotypes (i.e., fully lobed or whole) were collected from North Carolina, USA, selfed for seven generations to generate homozygous parents (P1), and then crossed with each other (Figure 1). A single F1 was allowed to self-fertilize, producing F2 progeny. We scored F2 plants for leaf shape, and allowed them to self-fertilize; we refer to all the selfed progeny of an individual F2 plant as a “matriline.”  We used F3 see..., , # Genetic architecture of heritable leaf microbes

This repository includes code and data for analyzing *Ipomoea hederacea*'s leaf microbiome and identifying heritable microbes. Access this dataset on Dryad [https://doi.org/10.5061/dryad.rbnzs7hjz](https://doi.org/10.5061/dryad.rbnzs7hjz)

## 1. Background

**Overall goal:** 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 in a common garden, and how these two sources of genetic variation contributed to microbe heritability.

**Breeding design:** We used seeds derived from a cross by Campitelli and Stinchcombe (2013), where individuals from the two alternate homozygous leaf shape phenotypes (i.e., fully lobed or whole) were collected from North Carolina, USA, selfed for seven gener...