Pangenome Analysis of Pyrus Reveals Potential Role of Transcription Factors in Recent Adaptation to Arid Environments

Abstract

Pears (genus Pyrus) are among the most extensively cultivated tree fruits with a wide-reaching economic impact. Despite this, the genetic basis of most pear traits of interest, including abiotic stress tolerance, tree architecture, precocity, parthenocarpy, disease resistance, and fruit ripening, remains poorly understood. Although extensive efforts have been made to identify quantitative trait loci (QTLs) that explain the genetic basis of pear traits, many are poorly transferable, limiting their utility for informing genetic improvement or management of pears across most genetic backgrounds. To provide a whole-genome context and enable the exploration of functional variation in Pyrus, we developed a pangenome graph using 31 accessions representing 23 Pyrus species from the National Clonal Germplasm Repository. Whole-genome sequencing was performed solely with Oxford Nanopore, generating highly contiguous assemblies for pangenome construction, demonstrating the viability of a single-platform approach to pangenomic analysis in Viridiplantae. Exploration of the pangenome graph reveals genes present in some lineages, with potential functional implications. A group of arid-adapted Pyrus species exhibits signs of selective sweeps in regions associated with transcription factors, likely impacting abiotic stress tolerance. With the development of this pangenomic resource, resequencing analysis in Pyrus is now possible without the limitations imposed by single-reference genome assemblies.