Pan-transcriptome analysis provides insights into resistance and fruit quality breeding of pear (Pyrus pyrifolia)

Pyrus pyrifolia, commonly known as sand pear, is a key economic fruit tree in temperate regions that possesses highly diverse germplasm resources for pear quality improvement. However, research on the relationship between resistance and fruit quality traits in the breeding of fruit species like pear is limited. Pan-transcriptomes effectively capture genetic information from coding regions and reflect variations in gene expression between individuals. Here, we constructed a pan-transcriptome based on 506 samples from different tissues of sand pear, and explored the intrinsic relationships among phenotypes and the selection for disease resistance during improvement based on expression presence/absence variations (ePAVs). The pan-transcriptome in this study contains 156,744 transcripts, among which the novel transcripts showed significant enrichment in the defense response. Interestingly, disease resistance genes are highly expressed in landraces of pear but have been selected against during the improvement of this perennial tree species. We found that the genetically diverse landraces can be divided into two subgroups and inferred that they have undergone different dispersal processes. Through co-expression network analysis, we confirmed that the formation of stone cells in pears, the synthesis of fruit anthocyanins, and the ability to resist stress are interrelated. They are jointly regulated by several modules, and the expression of regulatory genes has significant correlations with these three processes. Moreover, we identified candidate genes such as HKL1 that may affect sugar content and are missing from the reference genome. This study provides insights into the associations between complex fruit traits, while providing a database resource for pear disease resistance and fruit quality breeding.