Pear genetics: Recent advances, new prospects, and a roadmap for the future

doi:10.1093/hr/uhab040

. 2022 Jan 5:9:uhab040.

doi: 10.1093/hr/uhab040.

Pear genetics: Recent advances, new prospects, and a roadmap for the future

Jiaming Li¹, Mingyue Zhang², Xiaolong Li¹, Awais Khan³, Satish Kumar⁴, Andrew Charles Allan⁵, Kui Lin-Wang⁵, Richard Victor Espley⁵, Caihong Wang⁶, Runze Wang¹, Cheng Xue², Gaifang Yao⁷, Mengfan Qin¹, Manyi Sun¹, Richard Tegtmeier³, Hainan Liu¹, Weilin Wei¹, Meiling Ming¹, Shaoling Zhang¹, Kejiao Zhao¹, Bobo Song¹, Jiangping Ni¹, Jianping An², Schuyler S Korban⁸, Jun Wu¹

Affiliations

¹ Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China.
² State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong 271018, China.
³ Plant Pathology & Plant-Microbe Biology Section, Cornell University, Geneva, NY 14456, USA.
⁴ Hawke's Bay Research Centre, The New Zealand Institute for Plant and Food Research Limited, Havelock North 4157, New Zealand.
⁵ The New Zealand Institute for Plant and Food Research Limited, Auckland 1142, New Zealand.
⁶ College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, China.
⁷ School of Food and Biological Engineering, Hefei University of Technology, 230009 Hefei, China.
⁸ Department of Natural Resources & Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.

PMID: 35031796
PMCID: PMC8778596
DOI: 10.1093/hr/uhab040

Pear genetics: Recent advances, new prospects, and a roadmap for the future

Jiaming Li et al. Hortic Res. 2022.

. 2022 Jan 5:9:uhab040.

doi: 10.1093/hr/uhab040.

Authors

Affiliations

¹ Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China.
² State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong 271018, China.
³ Plant Pathology & Plant-Microbe Biology Section, Cornell University, Geneva, NY 14456, USA.
⁴ Hawke's Bay Research Centre, The New Zealand Institute for Plant and Food Research Limited, Havelock North 4157, New Zealand.
⁵ The New Zealand Institute for Plant and Food Research Limited, Auckland 1142, New Zealand.
⁶ College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, China.
⁷ School of Food and Biological Engineering, Hefei University of Technology, 230009 Hefei, China.
⁸ Department of Natural Resources & Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.

PMID: 35031796
PMCID: PMC8778596
DOI: 10.1093/hr/uhab040

Abstract

Pear, belonging to the genus Pyrus, is one of the most economically important temperate fruit crops. Pyrus is an important genus of the Rosaceae family, subfamily Maloideae, and has at least 22 different species with over 5000 accessions maintained or identified worldwide. With the release of draft whole-genome sequences for Pyrus, opportunities for pursuing studies on the evolution, domestication, and molecular breeding of pear, as well as for conducting comparative genomics analyses within the Rosaceae family, have been greatly expanded. In this review, we highlight key advances in pear genetics, genomics, and breeding driven by the availability of whole-genome sequences, including whole-genome resequencing efforts, pear domestication, and evolution. We cover updates on new resources for undertaking gene identification and molecular breeding, as well as for pursuing functional validation of genes associated with desirable economic traits. We also explore future directions for "pear-omics".

PubMed Disclaimer

Figures

**Figure 1**
A schematic diagram of divergence time and an evolutionary model of multiple plant species, including Pyrus, as well as a model of the domestication of Asian and European pears. (A) Divergence time of nine species, including Vitis vinifera, Malus × domestica, Pyrus communis, Pyrus bretschneideri, Prunus persica, Fragaria vesca, Populus trichocarpa, Carica papaya, and Arabidopsis thaliana. The estimated divergence times (MYA) are inferred based on single-copy orthologous groups and shown at each node. WGD, whole genome duplication. (B) An evolutionary model of wild and cultivated pear species [28]. (C) A schematic representation of the independent domestication process of Asian and European pears along with subsequent modern breeding efforts for cultivar improvement. The domestication process of pear has experienced a weak bottleneck resulting in slightly reduced diversity, while the improvement process shows significantly reduced diversity; thus, new efforts for restoring diversity are extremely urgent in the genetic improvement of pear cultivars.

**Figure 2**
A pipeline for genomic selection

**Figure 3**
A proposed mechanism of stone cell development in pear fruit 4CL: 4-coumarate CoA ligase; C3H: p-coumaroyl shikimate 3’-hydroxylase; C4H: cinnamate 4-hydroxylase; CAD: cinnamyl alcohol dehydrogenase; CCOMT: caffeoyl CoA O-methyltransferase; CCR: cinnamoyl CoA reductase; COMT: caffeic acid O-methyltransferase; F5H: ferulic 5-hydroxylase; HCT: hydroxycinnamoyl transferase; LAC: laccase; PAL: phenylalanine ammonia lyase; POD: peroxidase; SCW: second cell wall.

**Figure 4**
A proposed mechanism for fruit skin color development in pear ANS: anthocyanidin synthase; bZIP: basic region/leucine zipper; 4CL: 4-coumarate coenzyme A ligase; ABC: ATP-binding cassette transporter; ANR: anthocyanidin reductase; AP2/ERF: ethylene response factor/pathogenesis-related transcription factor; BAN: BANYULS; BBX: B-Box; bHLH: basic-helix-loop-helix; C4H: cinnamate 4-hydroxylase; CAD: cinnamyl alcohol dehydrogenase; CCR: cinnamoyl Co A reductase; CHI: chalcone isomerase; CHS: chalcone synthase; COP1: CONSTITUTIVE PHOTOMORPHOGENIC 1; CRY: cryptochrome; DFR: dihydroflavonol 4-reductase; F3H: flavanone 3-hydroxylase; FLS: flavonol synthase; GST: glutathione S- transferase; HY5: ELONGATED HYPOCOTYL 5; LAR: leucoanthocyanidin reductase; MATE: multidrug and toxic compound extrusion; MYB: v-myb avian myeloblastosis viral oncogene homolog; PAL: phenylalanine ammonialyase; POD: peroxidase; UFGT: UDP-glucose; flavonoid-3-O-glucosyltransferase; WD40: WD repeat protein; and WRKY: WRKYGQK domain.

**Figure 5**
A proposed mechanism of sugar accumulation in pear fruit ADPase: ADP-glucose pyrophosphorylase; ADPG: ADP-glucose; FRK: fructokinase; Fru: fructose; G1P: glucose-1-phosphate; G6P: glucose-6-phosphate; Glu: glucose; HXK: hexokinase; HT: hexose transporter; Ivr: invertase; PGM: phosphoglucomutase; SBE: starch branching enzyme; SDE: starch debranching enzyme; Sor: sorbitol; SOT: sorbitol transporter; SOX: sorbitol oxidase; SPS: sucrose phosphate synthase; SUS: sucrose synthase; SS: starch synthase; Suc: sucrose; SUT: sucrose transporter; tMT: tonoplast monosaccharide transporter; UDP: uridine diphosphate; and UDPG: UDP-glucose.

See this image and copyright information in PMC

Cited by

An identical-by-descent segment harbors a 12-bp insertion determining fruit softening during domestication and speciation in Pyrus.
Song B, Li X, Cao B, Zhang M, Korban SS, Yu L, Yang W, Zhao K, Li J, Wu J. Song B, et al. BMC Biol. 2022 Oct 1;20(1):215. doi: 10.1186/s12915-022-01409-w. BMC Biol. 2022. PMID: 36183077 Free PMC article.
Telomere-to-telomere pear (Pyrus pyrifolia) reference genome reveals segmental and whole genome duplication driving genome evolution.
Sun M, Yao C, Shu Q, He Y, Chen G, Yang G, Xu S, Liu Y, Xue Z, Wu J. Sun M, et al. Hortic Res. 2023 Oct 12;10(11):uhad201. doi: 10.1093/hr/uhad201. eCollection 2023 Nov. Hortic Res. 2023. PMID: 38023478 Free PMC article.
Telomere-to-telomere Genome Assembly of two representative Asian and European pear cultivars.
Qi Y, Shan D, Cao Y, Ma N, Lu L, Tian L, Feng Z, Ke F, Jian J, Gao Z, Xu Y. Qi Y, et al. Sci Data. 2024 Oct 26;11(1):1170. doi: 10.1038/s41597-024-04015-3. Sci Data. 2024. PMID: 39461942 Free PMC article.
Integrated Methylome and Transcriptome Analysis between Wizened and Normal Flower Buds in Pyrus pyrifolia Cultivar 'Sucui 1'.
Li H, Liu C, Kan J, Lin J, Li X. Li H, et al. Int J Mol Sci. 2024 Jun 29;25(13):7180. doi: 10.3390/ijms25137180. Int J Mol Sci. 2024. PMID: 39000285 Free PMC article.
The pear genomics database (PGDB): a comprehensive multi-omics research platform for Pyrus spp.
Chen S, Sun M, Xu S, Xue C, Wei S, Zheng P, Gu K, Qiao Z, Liu Z, Zhang M, Wu J. Chen S, et al. BMC Plant Biol. 2023 Sep 15;23(1):430. doi: 10.1186/s12870-023-04406-5. BMC Plant Biol. 2023. PMID: 37710163 Free PMC article.

See all "Cited by" articles

References

1. Potter D, Li J, Sun Jet al. . Phylogeny and classification of Rosaceae. Plant Syst Evol. 2007;266:5–43. 10.1007/s00606-007-0539-9. - DOI
1. Cao YF, Tian LM, Liu-Lin LIet al. . Comparison studies on the stone cell content in flesh of pear cultivars. Acta Hortic Sinica. 2010;22:417–33. 10.16420/j.issn.0513-353x.2010.08.016. - DOI
1. Yao GF, Zhang SL, Cao YFet al. . Characteristics of components and contents of soluble sugars in pear fruits from different species. Scient Agric Sinica. 2010;43:4229–37. 10.3864/j.issn.0578-1752.2010.20.014. - DOI
1. Quinet M, Wesel JP. Botany and taxonomy of pear. In: Korban SS, ed. The Pear Genome. Cham, Switzerland: Springer International Publishing, 2019,1–33.
1. Wu J, Wang Z, Shi Zet al. . The genome of the pear (Pyrus bretschneideri Rehd.). Genome Res. 2013;23:396–408. 10.1101/gr.144311.112. - DOI - PMC - PubMed

LinkOut - more resources

Full Text Sources

[1] Potter D, Li J, Sun Jet al. . Phylogeny and classification of Rosaceae. Plant Syst Evol. 2007;266:5–43. 10.1007/s00606-007-0539-9. - DOI

[2] Potter D, Li J, Sun Jet al. . Phylogeny and classification of Rosaceae. Plant Syst Evol. 2007;266:5–43. 10.1007/s00606-007-0539-9. - DOI

[3] Cao YF, Tian LM, Liu-Lin LIet al. . Comparison studies on the stone cell content in flesh of pear cultivars. Acta Hortic Sinica. 2010;22:417–33. 10.16420/j.issn.0513-353x.2010.08.016. - DOI

[4] Cao YF, Tian LM, Liu-Lin LIet al. . Comparison studies on the stone cell content in flesh of pear cultivars. Acta Hortic Sinica. 2010;22:417–33. 10.16420/j.issn.0513-353x.2010.08.016. - DOI

[5] Yao GF, Zhang SL, Cao YFet al. . Characteristics of components and contents of soluble sugars in pear fruits from different species. Scient Agric Sinica. 2010;43:4229–37. 10.3864/j.issn.0578-1752.2010.20.014. - DOI

[6] Yao GF, Zhang SL, Cao YFet al. . Characteristics of components and contents of soluble sugars in pear fruits from different species. Scient Agric Sinica. 2010;43:4229–37. 10.3864/j.issn.0578-1752.2010.20.014. - DOI

[7] Quinet M, Wesel JP. Botany and taxonomy of pear. In: Korban SS, ed. The Pear Genome. Cham, Switzerland: Springer International Publishing, 2019,1–33.

[8] Quinet M, Wesel JP. Botany and taxonomy of pear. In: Korban SS, ed. The Pear Genome. Cham, Switzerland: Springer International Publishing, 2019,1–33.

[9] Wu J, Wang Z, Shi Zet al. . The genome of the pear (Pyrus bretschneideri Rehd.). Genome Res. 2013;23:396–408. 10.1101/gr.144311.112. - DOI - PMC - PubMed

[10] Wu J, Wang Z, Shi Zet al. . The genome of the pear (Pyrus bretschneideri Rehd.). Genome Res. 2013;23:396–408. 10.1101/gr.144311.112. - DOI - PMC - PubMed

Save citation to file

Email citation

Add to Collections

Add to My Bibliography

Your saved search

Create a file for external citation management software

Your RSS Feed

Pear genetics: Recent advances, new prospects, and a roadmap for the future

Affiliations

Pear genetics: Recent advances, new prospects, and a roadmap for the future

Authors

Affiliations

Abstract

Figures

Similar articles

Cited by

References

LinkOut - more resources

Full Text Sources