Whole-genome resequencing of 495 Pyrus accessions provides insights into the genetics of agronomic traits and evolutionary history of pear

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.

Acknowledgements

This research was supported by the China Agriculture Research System of MOF and MARA (CARS-28-01), the Science and Technology Innovation Program of the Chinese Academy of Agricultural Sciences (CAAS-ASTIP-2021-RIP-01), and the Agricultural Variety Improvement Project of Shandong Province (2022LZGC011). We thank Z.X. Tian from the Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, and H. Xie from the Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, for constructive discussions regarding this manuscript. We thank Robert McKenzie, PhD, from Liwen Bianji (Edanz) (www.liwenbianji.cn) for editing the English text of a draft of this manuscript.

Author contributions

Y.F.C. conceived and designed the research. Y.Z., L.M.T., X.G.D., D.Q., H.L.H., C.L., X.Y., and C.X.X. performed the field experiments and phenotyping analysis. J.P.B. and R.Q.P. performed the sequencing experiments and analyzed the genomic variants and data. Y.F.C., Y.Z., J.P.B., and Y.Y. analyzed the population structure and demographic history. J.Y.X., J.P.B., and S.M.Z. analyzed the genome-wide selection of domestication traits. S.M.Z., J.P.B., Y.Z., R.Q.P., and J.Y.X. performed the GWAS analysis. W.H performed the analysis of malic acid and aroma metabolites. Y.F.C., S.M.Z., Y.Z., J.B.B., J.Y.X., Y.Y., and W.H. wrote the manuscript. Y.F.C. and Y.Y. revised the manuscript. All authors read and approved the final manuscript.

Data availability

The short-read genomic resequencing data for 495 Pyrus accessions generated in this study have been deposited with the NCBI under BioProject ID PRJNA1102892.

Conflicts of interest statement

The authors declare no conflicts of interest.

Supplementary material

Supplementary material is available at Horticulture Research online.

References

[1] Bailey LH . Pyrus stand cyclopedia Hort . 1917; 5: 2865-78

[2] Rubtsov GA . Geographical distribution of the genus Pyrus and trends and factors in its evolution . Am Nat. 1944; 78: 358-66

[3] Pu FS, Wang YL . Pomology of China: Pears . Shanghai, China: Shanghai Scientific and Technical Publishers, 1963

[4] Cao YF, Zhang SL . Pear genetic resource in China . Beijing, China: China Agriculture Press, 2020

[5] Challice JS, Westwood MN . Numerical taxonomic studies of the genus Pyrus using both chemical and botanical characters . Bot J Linn Soc. 1973; 67: 121-48

[6] Wu J, Wang YT, Xu JB, et al. Diversification and independent domestication of Asian and European pears. Genome Biol . 2018; 19: 77

[7] Li JM, Wang Y, Zhang SL, et al. Pear genetics: recent advances, new prospects, and a roadmap for the future. Hortic Res. 2022; 9: uhab040

[8] Jin ZT, Lin XH, Ma DK, et al. Unravelling the web of life: incomplete lineage sorting and hybridisation as primary mechanisms over polyploidisation in the evolutionary dynamics of pear species. Mol Ecol Resour. 2025; 25: e70029

[9] Müller JV . Domestication of wild pears in Europe, with specific emphasis on the Caucasian endemic pear Pyrus communis subsp. caucasica (Fed.) Browicz . Hortic Sci Biotechnol. 2024; 99: 1-8

[10] Vidaković A, Šatović Z, Liber Z, et al. Genetic diversity of Pyrus pyraster (L.) Burgsd. and P. spinosa Forssk.: evidence of introgression from cultivated into wild pear populations . Trees. 2024; 38: 1297-314

[11] Xue L, Liu Q, Hu H, et al. The southwestern origin and eastward dispersal of pear (Pyrus pyrifolia) in East Asia revealed by comprehensive genetic structure analysis with SSR markers . Tree Genet Genomes. 2018; 14: 48

[12] Chen XN, Li JM, Zhang SL . Genome-wide genetic diversity and IBD analysis reveals historic dissemination routes of pear in China. Tree Genet Genomes . 2022; 18: 1

[13] Yue XY, Zheng XC, Li JM, et al. Combined analyses of chloroplast DNA haplotypes and microsatellite markers reveal new insights into the origin and dissemination route of cultivated pears native to East Asia. Front Plant Sci. 2018; 9: 591

[14] Rehder A . Manual of Cultivated Trees and Shrubs (2nd Ed) . London, UK: Macmillan, 1940

[15] Kikuchi A . Assessment of China pear species and cultivars. Collect Rec Hort Res Fac Agri Kyoto Univ . 1946; 3: 1-11

[16] Kikuchi A . Horticulture of Fruit Trees . Tokyo, Japan: Yokendo, 1948

[17] Zhang MY, Xue C, Hu H, et al. Genome-wide association studies provide insights into the genetic determination of fruit traits of pear. Nat Commun. 2021; 12: 1144

[18] Cao YF, Liu FZ, Hu HJ, et al. Descriptors and data standard for pear (Pyrus spp.) . Beijing, China: China Agriculture Press, 2006

[19] Zhang Y, Cao YF, Huo HL, et al. Diversity of pear germplasm resources based on twig and leaf phenotypic traits. Sci Agric Sin . 2018; 51: 3353-69

[20] Yamamoto T, Terakami S, Takada N, et al. Identification of QTLs controlling harvest time and fruit skin color in Japanese pear (Pyrus pyrifolia Nakai) . Breed Sci. 2014; 64: 351-61

[21] Wu J, Li LT, Li M, et al. High-density genetic linkage map construction and identification of fruit-related QTLs in pear using SNP and SSR markers. J Exp Bot. 2014; 65: 5771-81

[22] Iwata H, Hayashi T, Terakami S, et al. Potential assessment of genome-wide association study and genomic selection in Japanese pear Pyrus pyrifolia . Breed Sci. 2013; 63: 125-40

[23] Dong XG, Wang Z, Tian LM, et al. De novo assembly of a wild pear (Pyrus betuleafolia) genome . Plant Biotechnol J. 2020; 18: 581-95

[24] Wu J, Wang ZW, Shi ZB, et al. The genome of the pear (Pyrus bretschneideri Rehd) . Genome Res. 2013; 23: 396-408

[25] Jing DL, Liu XY, He Q, et al. Genome assembly of wild loquat (Eriobotrya japonica) and resequencing provide new insights into the genomic evolution and fruit domestication in loquat . Hortic Res. 2023; 10: uhac265

[26] Huang ZY, Shen F, Chen Y, et al. Chromosome-scale genome assembly and population genomics provide insights into the adaptation, domestication, and flavonoid metabolism of Chinese plum. Plant J. 2021; 108: 1174-92

[27] Xu JJ, Fang X, Li CY, et al. General and specialized tyrosine metabolism pathways in plants. Abiotech. 2020; 1: 97-105

[28] Luo DL, Wang XG, Chen JY, et al. Analysis of α-linolenic acid metabolism in ‘Fengtang’ plum across different maturity stages. Sci Hortic. 2025; 346: 114173

[29] Pang LL, Wu Y, Pan YF, et al. Insights into exogenous melatonin associated with phenylalanine metabolism in postharvest strawberry. Postharvest Biol Technol. 2020; 168: 111244

[30] Harada T, Torii Y, Morita S, et al. Cloning, characterization, and expression of xyloglucan endotransglucosylase/hydrolase and expansin genes associated with petal growth and development during carnation flower opening. J Exp Bot. 2011; 62: 815-23

[31] Groppi A, Liu S, Cornille A, et al. Population genomics of apricots unravels domestication history and adaptive events. Nat Commun. 2021; 12: 3956

[32] Fang C, Ma YM, Wu SW, et al. Genome-wide association studies dissect the genetic networks underlying agronomical traits in soybean. Genome Biol. 2017; 18: 161

[33] Rodríguez-Leal D, Lemmon ZH, Man J, et al. Engineering quantitative trait variation for crop improvement by genome editing. Cell. 2017; 171: 470-80

[34] Cheng X, Xiong Y, Li DH, et al. Bioinformatic and expression analysis of the OMT gene family in Pyrus bretschneideri cv. Dangshan Su . Genet Mol Res. 2016; 15:gmr.15038664

[35] Martínez-Rivas FJ, Blanco-Portales R, Moyano E, et al. Strawberry fruit FanCXE1 carboxylesterase is involved in the catabolism of volatile esters during the ripening process. Hortic Res. 2022; 9: uhac095

[36] Wu ZJ, Liang GD, Li YY, et al. Transcriptome and metabolome analyses provide insights into the composition and biosynthesis of grassy aroma volatiles in white-fleshed pitaya. ACS Omega. 2022; 7: 6518-30

[37] Li YZ, He LL, Song YH, et al. Comprehensive study of volatile compounds and transcriptome data providing genes for grape aroma. BMC Plant Biol . 2023; 23: 171

[38] Zhang Y, Cao YF, Huo HL, et al. An assessment of the genetic diversity of pear (Pyrus L.) germplasm resources based on the fruit phenotypic traits . J Integr Agric. 2022; 21: 2275-90

[39] Purugganan MD, Rounsley SD, Schmidt RJ, et al. Molecular evolution of flower development: diversification of the plant MADS-box regulatory gene family. Genetics. 1995; 140: 345-56

[40] Han SW, Laura G , Danny JS . The signal peptide peptidase is required for pollen function in Arabidopsis . Plant Physiol. 2009; 149: 1289-301

[41] Zhang Y, Cao YF, Huo HL, et al. Research on diversity of pear germplasm resources based on flowers phenotype traits. Acta Hortic Sin . 2016; 43: 1245-56

[42] Jiang B, Chen LJ, Duan SM, et al. Transcriptomic analysis identifies differentially expressed genes in purple tender shoots and green mature leaves of Zijuan tea. Czech J Food Sci. 2022; 40: 210-20

[43] Liu YL, Zhang XJ, Zhao ZY . Effects of fruit bagging on anthocyanins, sugars, organic acids, and color properties of ‘Granny Smith’ and ‘Golden Delicious’ during fruit maturation. Eur Food Res Technol. 2013; 236: 329-39

[44] Ellis CM, Nagpal P, Young JC, et al. Auxin response factor 1 and auxin response factor 2 regulate senescence and floral organ abscission in Arabidopsis thaliana . Development. 2005; 132: 4563-74

[45] He M, Tian HL, Luo XW, et al. Molecular progress in research on fruit astringency. Molecules. 2015; 20: 1434-51

[46] Guo XY, Lv YQ, Ye Y, et al. Polyphenol oxidase dominates the conversions of flavonol glycosides in tea leaves. Food Chem . 2021; 339: 128088

[47] Cao K, Zhou ZK, Wang Q, et al. Genome-wide association study of 12 agronomic traits in peach. Nat Commun. 2016; 7: 13246

[48] Suwanagul A, Richardson G . Identification of headspace volatile compounds from different pear (Pyrus communis L.) varieties . Acta Hortic. 1998; 475: 605-24

[49] Souleyre E, Marshall S, Oakeshott J, et al. Biochemical characterisation of MdCXE1, a carboxylesterase from apple that is expressed during fruit ripening. Phytochemistry. 2011; 72: 564-71

[50] Félix JMR , Rosario BP , Enriqueta M , et al. Strawberry fruit FanCXE1 carboxylesterase is involved in the catabolism of volatile esters during the ripening process. Hortic Res. 2022; 9: uhac095

[51] Wang XH, Chen YY, Zhang JJ, et al. Comparative analysis of volatile aromatic compounds from a wide range of pear (Pyrus L.) germplasm resources based on HS-SPME with GC-MS . Food Chem. 2023; 418: 135963

[52] Zhang ZM, Zeng DD, Li GK . The study of the aroma profile characteristics of durian pulp during storage by the combination sampling method coupled with GC-MS. Flavour Fragr J . 2007; 22: 71-7

[53] Chen JQ, Lü JH, He ZS, et al. Investigations into the production of volatile compounds in Korla fragrant pears (Pyrus sinkiangensis Yu) . Food Chem. 2020; 302: 125337

[54] Zhang LJ, Zhou K, Wang MH, et al. The functional characterization of carboxylesterases involved in the degradation of volatile esters produced in strawberry fruits. Int J Mol Sci. 2022; 24: 383

[55] Versini G, Franco MA, Moser S, et al. Characterisation of pear distillates from wild and cultivated varieties in Sardinia. Int J Food Sci Technol . 2012; 47: 2519-31

[56] Qi LY, Li XJ, Zang NN, et al. Genome-wide identification of CXE and PuCXE15 functions in the catabolism of volatile ester in ‘Nanguo’ pear fruit. Plant Physiol Biochem. 2023; 203: 107996

[57] Oba T, Kato M, Kitazato H, et al. Paleoenvironmental changes in the Japan Sea during the last 85,000 years. Paleoceanography . 1991; 6: 499-518

[58] Li JM, Zhang MY, Li XL, et al. Pear genetics: recent advances, new prospects, and a roadmap for the future. Hortic Res. 2022; 9: uhab040

[59] Wu GA, Prochnik S, Jenkins J, et al. Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication. Nat Biotechnol. 2014; 32: 656-62

[60] Soomro T, Jordan M, Watts S, et al. Genomic insights into apple aroma diversity. Fruit Res. 2023; 3: 27

[61] Cao XM, Su YK, Zhao T, et al. Multi-omics analysis unravels chemical roadmap and genetic basis for peach fruit aroma improvement. Cell Rep . 2024; 43: 114623

[62] He WJ, Laaksonen O, Tian Y, et al. Chemical composition of juices made from cultivars and breeding selections of European pear (Pyrus communis L.) . J Agric Food Chem. 2022; 70: 5137-50

[63] Kumar S, Deng CH, Molloy C, et al. Extreme-phenotype GWAS unravels a complex nexus between apple (Malus domestica) red-flesh colour and internal flesh browning . Fruit Res. 2022; 2: 1-14

[64] Nagamine T . The descriptors for characterization and evaluation in plant genetic resource. National Inst Agrobiological Resources of Jap . 1999; 1: 1-406

[65] Murray MG, Thompson WF . Rapid isolation of high molecular weight plant DNA. Nucleic Acids Res. 1980; 8: 4321-5

[66] Li H, Durbin R . Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009; 25: 1754-60

[67] McKenna A, Hanna M, Banks E, et al. The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010; 20: 1297-303

[68] Danecek P, Auton A, Abecasis G, et al. The variant call format and VCFtools. Bioinformatics. 2011; 27: 2156-8

[69] Wang K, Li MY, Hakonarson H . Annovar: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res. 2010; 38: e164

[70] Lippert C, Listgarten J, Liu Y, et al. FaST linear mixed models for genome-wide association studies. Nat Methods. 2011; 8: 833-5

[71] Li MX, Yeung JMY, Cherny SS, et al. Evaluating the effective numbers of independent tests and significant p-value thresholds in commercial genotyping arrays and public imputation reference datasets. Hum Genet. 2012; 131: 747-56

[72] Pfaffl MW . A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Res. 2001; 29: e45

[73] Stamatakis A . RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 2014; 30: 1312-3

[74] Purcell S, Neale B, Todd-Brown K, et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet. 2007; 81: 559-75

[75] Yang J, Lee SH, Goddard ME, et al. GCTA: a tool for genome-wide complex trait analysis. Am J Hum Genet . 2011; 88: 76-82

[76] Alexander DH , Novembre J , Lange K . Fast model-based estimation of ancestry in unrelated individuals. Genome Res. 2009; 19: 1655-64

[77] Zhang C, Dong SS, Xu JY, et al. PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format files. Bioinformatics. 2019; 35: 1786-8

[78] Schiffels S, Durbin R . Inferring human population size and separation history from multiple genome sequences. Nat Genet. 2014; 46: 919-25

[79] Korunes KL, Samuk K . Pixy: unbiased estimation of nucleotide diversity and divergence in the presence of missing data. Mol Ecol Resour. 2021; 21: 1359-68

[80] Chen H, Patterson N, Reich D . Population differentiation as a test for selective sweeps. Genome Res. 2010; 20: 393-402

[81] Pickrell J, Pritchard J . Inference of population splits and mixtures from genome-wide allele frequency data. Nat Preced. 2012; 1: 1

[82] Fitak RR . OptM: estimating the optimal number of migration edges on population trees using TreeMix. Biol Methods Protoc. 2021; 6: bpab017

[83] Durand EY, Patterson N, Reich D, et al. Testing for ancient admixture between closely related populations. Mol Biol Evol. 2011; 28: 2239-52

[84] Emms DM, Kelly S . OrthoFinder: phylogenetic orthology inference for comparative genomics. Genome Biol. 2019; 20: 238