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Article|02 Mar 2026|OPEN
Whole-genome resequencing of 495 Pyrus accessions provides insights into the genetics of agronomic traits and evolutionary history of pear
Simeng Zhang1 ,† , Ying Zhang1 ,† , Jinpeng Bi2 ,† , Jiayu Xu1 ,† , Luming Tian1 , Xingguang Dong1 , Yang Yu3 ,† , Wei Heng4 ,† , Dan Qi1 , Hongliang Huo1 , Chao Liu1 , Ruiqing Pan2 , Xiang Yang1 , Chenxi Xu1 and Yufen Cao,1 ,
1Research Institute of Pomology, Chinese Academy of Agricultural Sciences, Xingcheng 125100, China
2Berry Genomics Corporation, Beijing 100015, China
3Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
4School of Horticulture, Anhui Agricultural University, Hefei 230036, China
*Corresponding author. E-mail: caoyufen@caas.cn
†Simeng Zhang,Ying Zhang,Jinpeng Bi,Jiayu Xu,Yang Yu,Wei Heng contributed equally to the study.

Horticulture Research 13,
Article number: uhag042 (2026)
doi: https://doi.org/10.1093/hr/uhag042
Views: 19

Received: 09 Sep 2025
Accepted: 08 Feb 2026
Published online: 02 Mar 2026

Abstract

Pear (Pyrus L.) is a fruit tree of global commercial importance. Its genetic relationships, evolutionary history, dissemination routes, and genetic determinants of most agronomic traits remain to be elucidated. We conducted whole-genome resequencing of 495 Pyrus accessions. Phylogenetic and demographic analyses resolved geographic groupings of the accessions, identifying the Yunnan–Guizhou Plateau as the putative dissemination center for cultivated Pyrus pyrifolia and P. bretschneideri. Identification of two evolutionary bottlenecks provides insights into the population dynamics of pear species. Admixture and introgression analyses revealed both intraspecific and interspecific genetic exchanges, substantiating the complex emergence of cultivated populations. Genome-wide association study (GWAS) identified loci associated with nine crucial agronomic traits, together with eight candidate genes. The GWAS, molecular, and biochemical analyses suggested that PbeMADS25, PbeSPP, PbeDHQ-SDH, PbeARF2, PbePPO, PbePIN3, PbeCXE, and PbeMYB38 participate in the regulation of number of stigmas and number of locules, number of stamens, young leaf color, sepal persistence, astringency, acidity, aroma, and fruit skin color, respectively. Overexpression and metabonomic analysis of PbeCXE indicated that it affects the fruit aroma by affecting the balance between ester biosynthesis and substrate consumption. These findings expand our understanding of Pyrus evolution and provide a genomic foundation for genetic improvement of agronomic traits.