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Functional Genomics

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The Pear Genome

Part of the book series: Compendium of Plant Genomes ((CPG))

Abstract

Several closely related species of commercial importance in the genus Pyrus are cultivated throughout the world. In eastern Asia, specifically in China, Japan, and Korea, the East Asian pear, including the Chinese white pear (P. pyrifolia white pear group, also referred to as P. × bretschneideri), the Chinese sand pear (P. pyrifolia), the Japanese pear (P. pyrifolia), the Ussurian pear (P. ussuriensis), and the Xingiang pear (P. sinkiangensis), is cultivated, while in the rest of the world, the European pear (P. communis) is more commonly grown. Whole-genome sequences have been released for both P. × bretschneideri cv. Dangshansuli (also known to belong to P. pyrifolia white pear group) and P. communis cv. Bartlett. As a result of these draft pear genome sequences, major advances have been made in pursuing functional genomics studies in pear.

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References

  • Bai S, Sun Y, Qian M, Yang F, Ni J, Tao R, Li L, Shu Q, Zhang D, Teng Y (2017a) Transcriptome analysis of bagging-treated red Chinese sand pear peels reveals light-responsive pathway functions in anthocyanin accumulation. Sci Rep 7(1):63

    Article  PubMed  PubMed Central  Google Scholar 

  • Bai S, Tao R, Tang Y, Yin L, Ma Y, Ni J, Yan X, Yang Q, Wu Z, Zeng Y, Teng Y (2019) BBX16, a B‐box protein, positively regulates light‐induced anthocyanin accumulation by activating MYB10 in red pear. Plant Biotechnol J. https://doi.org/10.1111/pbi.13114

  • Bai S, Tuan PA, Saito T, Ito A, Ubi BE, Ban Y, Moriguchi T (2017b) Repression of TERMINAL FLOWER1 primarily mediates floral induction in pear (Pyrus pyrifolia Nakai) concomitant with change in gene expression of plant hormone-related genes and transcription factors. J Exp Bot 68(17):4899–4914

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bielenberg DG, Wang YE, Li Z, Zhebentyayeva T, Fan S, Reighard GL, Scorza R, Abbott AG (2008) Sequencing and annotation of the evergrowing locus in peach [Prunus persica (L.) Batsch] reveals a cluster of six MADS-box transcription factors as candidate genes for regulation of terminal bud formation. Tree Genet Genomes 4(3):495–507

    Article  Google Scholar 

  • Broun P (2005) Transcriptional control of flavonoid biosynthesis: a complex network of conserved regulators involved in multiple aspects of differentiation in Arabidopsis. Curr Opin Plant Biol 8(3):272–279

    Article  CAS  PubMed  Google Scholar 

  • Chagné D, Crowhurst RN, Pindo M, Thrimawithana A, Deng C, Ireland H, Fiers M, Dzierzon H, Cestaro A, Fontana P, Bianco L, Lu A, Storey R, Knabel M, Saeed M, Montanari S, Kim YK, Nicolini D, Larger S, Stefani E, Allan AC, Bowen J, Harvey I, Johnston J, Malnoy M, Troggio M, Perchepied L, Sawyer G, Wiedow C, Won K, Viola R, Hellens RP, Brewer L, Bus VG, Schaffer RJ, Gardiner SE, Velasco R (2014) The draft genome sequence of European pear (Pyrus communis L. ‘Bartlett’). PLoS ONE 9(4):e92644

    Article  PubMed  PubMed Central  Google Scholar 

  • Dondini L, Pierantoni L, Ancarani V, D’Angelo M, Cho KH, Shin IS, Musacchi S, Kang SJ, Sansavini S (2008) The inheritance of the red colour character in European pear (Pyrus communis) and its map position in the mutated cultivar ‘Max Red Bartlett’. Plant Breed 127(5):524–526

    Article  Google Scholar 

  • Duan XW, Zhang WN, Huang J, Hao L, Wang SN, Wang AD, Meng D, Zhang QL, Chen QJ, Li TZ (2016) PbWoxT1 mRNA from pear (Pyrus betulaefolia) undergoes long-distance transport assisted by a polypyrimidine tract binding protein. New Phytol 210(2):511–524

    Article  CAS  PubMed  Google Scholar 

  • Duan XW, Zhang WN, Huang J, Zhao LM, Ma C, Hao L, Yuan H, Harada T, Li TZ (2015) KNOTTED1 mRNA undergoes long-distance transport and interacts with movement protein binding protein 2C in pear (Pyrus betulaefolia). Plant Cell Tiss Org Cult 121(1):109–119

    Article  Google Scholar 

  • Espley RV, Brendolise C, Chagne D, Kutty-Amma S, Green S, Volz RK, Putterill J, Schouten HJ, Gardiner SE, Hellens RP, Allan AC (2009) Multiple repeats of a promoter segment causes transcription factor autoregulation in red apples. Plant Cell 21(1):168–183

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Faust M, Erez A, Rowland LJ, Wang SY, Norman HA (1997) Bud dormancy in perennial fruit trees: physiological basis for dormancy induction, maintenance, and release. HortScience 32(4):623–629

    Article  Google Scholar 

  • Feng S, Wang Y, Yang S, Xu Y, Chen X (2010) Anthocyanin biosynthesis in pears is regulated by a R2R3-MYB transcription factor PyMYB10. Planta 232(1):245–255

    Article  CAS  PubMed  Google Scholar 

  • Freiman A, Shlizerman L, Golobovitch S, Yablovitz Z, Korchinsky R, Cohen Y, Samach A, Chevreau E, Le Roux P-M, Patocchi A, Flaishman MA (2012) Development of a transgenic early flowering pear (Pyrus communis L.) genotype by RNAi silencing of PcTFL1-1 and PcTFL1-2. Planta 235(6):1239–1251

    Article  PubMed  Google Scholar 

  • Hichri I, Barrieu F, Bogs J, Kappel C, Delrot S, Lauvergeat V (2011) Recent advances in the transcriptional regulation of the flavonoid biosynthetic pathway. J Exp Bot 62(8):2465–2483

    Article  CAS  PubMed  Google Scholar 

  • Hiwasa K, Nakano R, Hashimoto A, Matsuzaki M, Murayama H, Inaba A, Kubo Y (2004) European, Chinese and Japanese pear fruits exhibit differential softening characteristics during ripening. J Exp Bot 55(406):2281–2290

    Article  CAS  PubMed  Google Scholar 

  • Huang X, Li K, Jin C, Zhang S (2015) ICE1 of Pyrus ussuriensis functions in cold tolerance by enhancing PuDREBa transcriptional levels through interacting with PuHHP1. Sci Rep 5:17620. https://doi.org/10.1038/srep17620

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ito A, Yaegaki E, Hayama H, Kusaba S, Yamaguchi I, Yoshioka H (1999) Bending shoots stimulates flowering and influences hormone levels in lateral buds of Japanese pear. Hortscience 34(7):1224–1228

    Article  CAS  Google Scholar 

  • Jin C, Huang XS, Li KQ, Yin H, Li LT, Yao ZH, Zhang SL (2016) Overexpression of a bHLH1 transcription factor of Pyrus ussuriensis confers enhanced cold tolerance and increases expression of stress-responsive genes. Front Plant Sci 7:441

    PubMed  PubMed Central  Google Scholar 

  • Jung S, Ficklin SP, Lee T, Cheng CH, Blenda A, Zheng P, Yu J, Bombarely A, Cho I, Ru S, Evans K, Peace C, Abbott AG, Mueller LA, Olmstead MA, Main D (2014) The genome database for Rosaceae (GDR): year 10 update. Nucl Acids Res 42(Database issue):D1237–1244

    Article  PubMed  PubMed Central  Google Scholar 

  • Kanehisa M, Furumichi M, Tanabe M, Sato Y, Morishima K (2017) KEGG: new perspectives on genomes, pathways, diseases and drugs. Nucl Acids Res 45(D1):D353–D361

    Article  CAS  PubMed  Google Scholar 

  • Kobayashi S, Goto-Yamamoto N, Hirochika H (2004) Retrotransposon-induced mutations in grape skin color. Science 304(5673):982

    Article  PubMed  Google Scholar 

  • Lang GA, Early JD, Martin GC, Darnell RL (1987) Endodormancy, paradormancy, and ecodormancy—physiological terminology and classification for dormancy research. HortScience 22(3):371–377

    Google Scholar 

  • Layne REC, Quamme HA (1975) Pears. In: Janik J, Moore JN (eds) Advances in fruit breeding. Purdue University Press, West Lafayette, IN, pp 38–70

    Google Scholar 

  • Li J, Xu Y, Niu Q, He L, Teng Y, Bai S (2018) Abscisic acid (ABA) promotes the induction and maintenance of pear (Pyrus pyrifolia white pear group) flower bud endodormancy. Int J Mol Sci 19(1):310. https://doi.org/10.3390/ijms19010310

    Article  CAS  PubMed Central  Google Scholar 

  • Li K, Xing C, Yao Z, Huang X (2017a) PbrMYB21, a novel MYB protein of Pyrus betulaefolia, functions in drought tolerance and modulates polyamine levels by regulating arginine decarboxylase gene. Plant Biotechnol J 15(9):1186–1203

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Li L, Deng CH, Knabel M, Chagne D, Kumar S, Sun J, Zhang S, Wu J (2017b) Integrated high-density consensus genetic map of Pyrus and anchoring of the ‘Bartlett’ v1.0 (Pyrus communis) genome. DNA Res 24(3):289–301

    Google Scholar 

  • Medina-Puche L, Cumplido-Laso G, Amil-Ruiz F, Hoffmann T, Ring L, Rodriguez-Franco A, Luis Caballero J, Schwab W, Munoz-Blanco J, Blanco-Portales R (2014) MYB10 plays a major role in the regulation of flavonoid/phenylpropanoid metabolism during ripening of Fragaria ananassa fruits. J Exp Bot 65(2):401–417

    Article  CAS  PubMed  Google Scholar 

  • Murayama H, Sekine D, Yamauchi Y, Gao M, Mitsuhashi W, Toyomasu T (2006) Effect of girdling above the abscission zone of fruit on ‘Bartlett’ pear ripening on the tree. J Exp Bot 57(14):3679–3686

    Article  CAS  PubMed  Google Scholar 

  • Nashima K, Shimizu T, Nishitani C, Yamamoto T, Takahashi H, Nakazono M, Itai A, Isuzugawa K, Hanada T, Takashina T (2013a) Microarray analysis of gene expression patterns during fruit development in European pear (Pyrus communis). Sci Hortic 164:466–473

    Article  CAS  Google Scholar 

  • Nashima K, Takahashi H, Nakazono M, Shimizu T, Nishitani C, Yamamoto T, Itai A, Isuzugawa K, Hanada T, Takashina T, Kato M, Matsumoto S, Oikawa A, Shiratake K (2013b) Transcriptome analysis of giant pear fruit with fruit-specific DNA reduplication on a mutant branch. J Jpn Soc Hortic Sci 82(4):301–311

    Article  CAS  Google Scholar 

  • Nham NT, de Freitas ST, Macnish AJ, Carr KM, Kietikul T, Guilatco AJ, Jiang CZ, Zakharov F, Mitcham EJ (2015) A transcriptome approach towards understanding the development of ripening capacity in ‘Bartlett’ pears (Pyrus communis L.). BMC Genomics 16:762

    Google Scholar 

  • Ni J, Bai S, Zhao Y, Qian M, Tao R, Yin L, Gao L and Teng Y (2019) Ethylene response factors Pp4ERF24 and Pp12ERF96 regulate blue light-induced anthocyanin biosynthesis in ‘Red Zaosu’ pear fruits by interacting with MYB114. Plant Mol Biol 99:67–78

    Article  PubMed  Google Scholar 

  • Niu Q, Li J, Cai D, Qian M, Jia H, Bai S, Hussain S, Liu G, Teng Y, Zheng X (2016) Dormancy-associated MADS-box genes and microRNAs jointly control dormancy transition in pear (Pyrus pyrifolia white pear group) flower bud. J Exp Bot 67(1):239–257

    Article  CAS  PubMed  Google Scholar 

  • Pierantoni L, Dondini L, De Franceschi P, Musacchi S, Winkel BSJ, Sansavini S (2010) Mapping of an anthocyanin-regulating MYB transcription factor and its expression in red and green pear, Pyrus communis. Plant Physiol Biochem 48(12):1020–1026

    Article  CAS  PubMed  Google Scholar 

  • Qian M, Zhang D, Yue X, Wang S, Li X, Teng Y (2013) Analysis of different pigmentation patterns in ‘Mantianhong’ (Pyrus pyrifolia Nakai) and ‘Cascade’ (Pyrus communis L.) under bagging treatment and postharvest UV-B/visible irradiation conditions. Scient Hort 151(2):75–82

    Article  Google Scholar 

  • Qian M, Ni J, Niu Q, Bai S, Bao L, Li J, Sun Y, Zhang D, Teng Y (2017) Response of miR156-SPL module during the red peel coloration of bagging-treated Chinese sand pear (Pyrus pyrifolia Nakai). Front Physiol 8:550

    Article  PubMed  PubMed Central  Google Scholar 

  • Reuscher S, Fukao Y, Morimoto R, Otagaki S, Oikawa A, Isuzugawa K, Shiratake K (2016) Quantitative proteomics-based reconstruction and identification of metabolic pathways and membrane transport proteins related to sugar accumulation in developing fruits of pear (Pyrus communis). Plant Cell Physiol 57(3):505–518

    Article  CAS  PubMed  Google Scholar 

  • Saito T, Bai S, Imai T, Ito A, Nakajima I, Moriguchi T (2015a) Histone modification and signaling cascade of the dormancy-associated MADS-box gene, PpMADS13-1, in Japanese pear (Pyrus pyrifolia) during endodormancy. Plant Cell Environ 38(6):1157–1166

    Article  CAS  PubMed  Google Scholar 

  • Saito T, Bai S, Ito A, Sakamoto D, Saito T, Ubi BE, Imai T, Moriguchi T (2013) Expression and genomic structure of the dormancy-associated MADS box genes MADS13 in Japanese pears (Pyrus pyrifolia Nakai) that differ in their chilling requirement for endodormancy release. Tree Physiol 33(6):654–667

    Article  CAS  PubMed  Google Scholar 

  • Saito T, Tuan PA, Katsumi-Horigane A, Bai SL, Ito A, Sekiyama Y, Ono H, Moriguchi T (2015b) Development of flower buds in the Japanese pear (Pyrus pyrifolia) from late autumn to early spring. Tree Physiol 35(6):653–662

    Article  CAS  PubMed  Google Scholar 

  • Shi DQ, Tang C, Wang RZ, Gu C, Wu X, Hu S, Jiao J, Zhang SL (2017) Transcriptome and phytohormone analysis reveals a comprehensive phytohormone and pathogen defence response in pear self-/cross-pollination. Plant Cell Rep 36(11):1785–1799

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Takos AM, Jaffé FW, Jacob SR, Bogs J, Robinson SP, Walker AR (2006) Light-induced expression of a MYB gene regulates anthocyanin biosynthesis in red apples. Plant Physiol 142(3):1216–1232

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tanaka Y, Sasaki N, Ohmiya A (2008) Biosynthesis of plant pigments: anthocyanins, betalains and carotenoids. Plant J 54(4):733–749

    Article  CAS  PubMed  Google Scholar 

  • Tao R, Bai S, Ni J, Yang Q, Zhao Y, Teng Y (2018) The blue light signal transduction pathway is involved in anthocyanin accumulation in ‘Red Zaosu’ pear. Planta 248(1):37–48

    Article  CAS  PubMed  Google Scholar 

  • Tuan PA, Bai S, Saito T, Ito A, Moriguchi T (2017) Dormancy-associated MADS-box (DAM) and the abscisic acid pathway regulate pear endodormancy through a feedback mechanism. Plant Cell Physiol 58(8):1378–1390

    Article  CAS  PubMed  Google Scholar 

  • Tuan PA, Bai SL, Saito T, Imai T, Ito A, Moriguchi T (2016) Involvement of EARLY BUD-BREAK, an AP2/ERF transcription factor gene, in bud break in Japanese pear (Pyrus pyrifolia Nakai) lateral flower buds: expression, histone modifications and possible target genes. Plant Cell Physiol 57(5):1038–1047

    Article  Google Scholar 

  • Wang YZ, Dai MS, Zhang SJ, Shi ZB (2014) Exploring candidate genes for pericarp russet pigmentation of sand pear (Pyrus pyrifolia) via RNA-seq data in two genotypes contrasting for pericarp color. PLoS ONE 9(1):e83675

    Article  PubMed  PubMed Central  Google Scholar 

  • Wang Z, Meng D, Wang A, Li T, Jiang S, Cong P, Li T (2013) The methylation of the PcMYB10 promoter is associated with green-skinned sport in max red bartlett pear. Plant Physiol 162(2):885–896

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wang ZG, Du H, Zhai R, Song LY, Ma FW, Xu LF (2017) Transcriptome analysis reveals candidate genes related to color fading of ‘Red Bartlett’ (Pyrus communis L.). Front Plant Sci 8:455

    Google Scholar 

  • Wu J, Wang Z, Shi Z, Zhang S, Ming R, Zhu S, Khan M, Tao S, Korban S, Wang H, Chen N, Nishio T, Xu X, Cong L, Qi K, Huang X, Wang Y, Zhao X, Wu J, Deng C, Gou C, Zhou W, Yin H, Qin G, Sha Y, Tao Y, Chen H, Yang Y, Song Y, Zhan D, Wang J, Li L, Dai M, Gu C, Wang Y, Shi D, Wang X, Zhang H, Zeng L, Zheng D, Wang C, Chen M, Wang G, Xie L, Sovero V, Sha S, Huang W, Zhang S, Zhang M, Sun J, Xu L, Li Y, Liu X, Li Q, Shen J, Wang J, Paull R, Bennetzen J, Zhang S (2013a) The genome of the pear (Pyrus bretschneideri Rehd.). Genome Res 23(2):396–408

    Article  PubMed  Google Scholar 

  • Wu J, Zhao G, Yang YN, Le WQ, Khan MA, Zhang SL, Gu C, Huang WJ (2013b) Identification of differentially expressed genes related to coloration in red/green mutant pear (Pyrus communis L.). Tree Genet Genomes 9(1):75–83

    Article  CAS  Google Scholar 

  • Xie M, Huang Y, Zhang YP, Wang X, Yang H, Yu O, Dai WH, Fang CB (2013) Transcriptome profiling of fruit development and maturation in Chinese white pear (Pyrus bretschneideri Rehd). BMC Genom 14:823

    Article  CAS  Google Scholar 

  • Yang YN, Yao GF, Yue WQ, Zhang SL, Wu J (2015) Transcriptome profiling reveals differential gene expression in proanthocyanidin biosynthesis associated with red/green skin color mutant of pear (Pyrus communis L.). Front Plant Sci 6:795

    Google Scholar 

  • Yao G, Ming M, Allan AC, Gu C, Li L, Wu X, Wang R, Chang Y, Qi K, Zhang S, Wu J (2017) Map-based cloning of the pear gene MYB114 identifies an interaction with other transcription factors to coordinately regulate fruit anthocyanin biosynthesis. Plant J 92(3):437–451

    Article  CAS  PubMed  Google Scholar 

  • Zhai R, Wang ZM, Zhang SW, Meng G, Song LY, Wang ZG, Li PM, Ma FW, Xu LF (2016) Two MYB transcription factors regulate flavonoid biosynthesis in pear fruit (Pyrus bretschneideri Rehd.). J Exp Bot 67(5):1275–1284

    Article  PubMed  Google Scholar 

  • Zhang JY, Cheng X, Jin Q, Su XQ, Li ML, Yan CC, Jiao XY, Li DH, Lin Y, Cai YP (2017) Comparison of the transcriptomic analysis between two Chinese white pear (Pyrus bretschneideri Rehd.) genotypes of different stone cells contents. PLoS ONE 12(10):e0187114. https://doi.org/10.1371/journal.pone.0187114

    Article  PubMed  PubMed Central  Google Scholar 

  • Zhang MY, Xue C, Xu LL, Sun HH, Qin MF, Zhang SL, Wu J (2016) Distinct transcriptome profiles reveal gene expression patterns during fruit development and maturation in five main cultivated species of pear (Pyrus L.). Sci Rep 6:28130. https://doi.org/10.1038/srep28130

  • Zhang WN, Duan XW, Ma C, Harada T, Li TZ (2013) Transport of mRNA molecules coding NAC domain protein in grafted pear and transgenic tobacco. Biol Plantarum 57(2):224–230

    Article  CAS  Google Scholar 

  • Zhang WN, Gong L, Ma C, Xu HY, Hu JF, Harada T, Li TZ (2012) Gibberellic acid-insensitive mRNA transport in Pyrus. Plant Mol Biol Rep 30(3):614–623

    Article  Google Scholar 

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Bai, S., Teng, Y. (2019). Functional Genomics. In: Korban, S. (eds) The Pear Genome. Compendium of Plant Genomes. Springer, Cham. https://doi.org/10.1007/978-3-030-11048-2_14

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