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| Identification and Expression Analysis of PIN Gene Family in Different Tree Architectures of Peach (Prunus persica) |
| TAN Bin1,2, YANG Li-Ping1, CHEN Li-Chuan1, FENG Mei-Qiao1, LIAN Xiao-Dong1, WEI Peng-Cheng1, CHENG Jun1,2, WANG Xiao-Bei1,2, FENG Jian-Can1,2,* |
1 College of Horticulture, Henan Agricultural University, Zhengzhou 450002, China;
2 Henan Key Laboratory of Fruit and Cucurbit Biology, Zhengzhou 450002, China |
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Abstract The PIN-FORMED (PIN) gene family of trans-membrane proteins as auxin efflux carriers plays a crucial role in polar auxin transport and then influences the growth and development of plants. The objective of this study is to understand the distribution, structure and evolution of PIN protein genes in peach (Prunus persica) genome, to study the expression characteristics of PIN family members in different tree architectures of peach. In this study, PpPIN family was identified from the whole peach genome according to the reported 8 PINs of Arabidopsis thaliana and Mem_trans (PF03547) conserved domains of AtPIN proteins. Several bioinformatics softwares, including TBtools v0.6733, GSDS 2.0, MEME 4.9, Protparam V12.1, MEGA 7.0 and PlantCARE were used to identify chromosome location, gene structure, physical and chemical properties of protein, motif analysis, phylogeny analysis and cis-elements of promoters on PpPIN protein family, respectively. Meanwhile, the expression characteristics of PpPIN genes in the shoot tips of different tree architecture of peach were analyzed based on the results of transcriptome sequencing. And the expression characteristics of PpPIN genes were also analyzed by real-time quantitative RT-PCR (qRT-PCR) in different tissues (organs) of different types of peach. Fifteen PpPIN genes were identified and unevenly distributed on 6 chromosomes of peach. Except for PpPIN3 and PpPIN5, all other PpPIN genes contained introns, with the number of introns ranging from 1 to 10. The number of amino acids and the isoelectric point of PpPIN proteins which were hydrophilic proteins were 357~678 and 4.97~9.40, respectively. Phylogenetic analysis results indicated the PIN proteins of 8 species, including peach, apple (Malus×domestica), Arabidopsis (Arabidopsis thaliana), rice (Oryza sativa), Populus (Populus trichocarpa), potato (Solanum tuberosum), maize (Zea mays) and soybean (Glycine max), were divided into 3 groups (canonical type, noncanonical type 1 and noncanonical type 2). According to the results of evolutionary analysis, 15 PpPIN proteins were divided into 3 groups. Canonical type, Noncanonical type1 and Noncanonical type 2 included 6, 2 and 7 PIN proteins, respectively. The number of conserved motifs of 8 PpPIN proteins of Canonical type and Noncanonical type 1 was 10, and the order of 10 motifs in these 2 types was all the same. While the number of conserved motifs of 7 PpPIN proteins of noncanonical type 2 was 8~11, and the arrangement of conserved motifs was not the same. The cis-element analysis of 15 PpPIN gene promoters showed that the members of PpPIN gene family were affected by light, temperature, drought stress and other environmental conditions, as well as abscisic acid, gibberellin and other hormones. Fifteen PpPIN genes were differentially expressed in different tree architecture of peach. According to the transcriptome analyses, the expression level of PpPIN12 (the homologous gene of AtPIN5) in the shoot tip of 'Fenhuashouxingtao' (dwarf type) was significantly higher than that of 'Qiumihong' (standard type), while the expression level of PpPIN12 in the shoot tip of 'Sahonglongzhu' (pillar type) was significantly lower than that of 'Okuba' (standard type). The expression level of PpPIN2 (the homologous gene of OsPIN2) in the upper phloem of the branch junctions of 'Okubo' (standard type) was obviously higher than that of 'Sahonglongzhu' (pillar type), while the expression level of PpPIN13 gene (the homologous gene of OsPIN13) was opposite to PpPIN2. The 3 candidate genes, including PpPIN12, PpPIN2 and PpPIN13, may play an important role in regulating the formation of plant height and branch angle of peach trees.
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Received: 20 March 2020
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Corresponding Authors:
* jcfeng@henau.edu.cn
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[1] 李明. 2017. 不同生长型桃树体结构特性及调控分枝角度关键基因LAZY1表达特性研究[D]. 硕士学位论文,河南农业大学, 导师: 郑先波. pp. 28-29.
(Li M.2017. Research of tree structure characteristics and the key of gene LAZY1 regulating branch angle of the different growth habits of peach[D]. Thesis for M.S., Henan Agricultural University, Supervisor: Zheng X B. pp. 28-29.)
[2] 连晓东, 谭彬, 郑先波, 等. 2018. 桃主要性状的分子标记与功能基因定位研究进展[J]. 果树学报, 35(3): 334-346.
(Lian X D, Tan B, Zheng X B, et al.2018. Progress in molecular markers and localization of functional genes of main traits in peach[J]. Acta Horticulturae Sinica, 35(3): 334-346.)
[3] 刘小杰, 樊胜, 李国防, et al.2017. 苹果全基因组PIN成员鉴定及MdPIN15的克隆和在腋芽萌发中的表达分析[J]. 园艺学报, (11): 6-19.
(Liu X J, Fan S, Li G F, et al. 2017. Genome-wide identification of PIN gene family, cloning and expression analysis of MdPIN15 during axillary bud burst in Malus[J]. Acta Horticulturae Sinica, (11): 6-19.)
[4] 谭彬, 程钧, 郑先波, 等. 2020. 桃树树型及其关键基因研究进展[J]. 果树学报, 37(4): 600-606.
(Tan B, Cheng J, Zheng X B, et al.2020. Progress on tree architecture and key genes of its regulation in peach[J]. Acta Horticulturae Sinica, 37(4): 600-606.)
[5] Aida M, Vernoux T, Furutani M, et al.2002. Roles of PIN-FORMED1 and MONOPTEROS in pattern formation of the apical region of the Arabidopsis embryo[J]. Development, 129(17): 3965-3974.
[6] Alam M M, Hammer G L, Van O, et al.2014. A physiological framework to explain genetic and environmental regulation of tillering in sorghum[J]. New Phytologist, 203(1): 155-167.
[7] Bennett T A, Liu M M, Aoyama T, et al.2014. Plasma membrane-targeted PIN proteins drive shoot development in a moss[J]. Current Biology, 24(23): 2776-2785.
[8] Blilou I, Xu J, Wildwater M, et al.2005. The PIN auxin efflux facilitator network controls growth and patterning in Arabidopsis roots[J]. Nature, 433(7021): 39-44.
[9] Chen C J, Hao C, Yi Z, et al.2020. TBtools: an integrative toolkit developed for interactive analyses of big biological data[J]. Molecular Plant, 13(8):1194-1202.
[10] Chen Y N, Fan X R, Song W J, et al.2012. Over-expression of OsPIN2 leads to increased tiller numbers, angle and shorter plant height through suppression of OsLAZY1[J]. Plant Biotechnology Journal, 10(2): 139-149.
[11] Cheng J, Zhang M M, Tan B, et al.2019. A single nucleotide mutation in GID1c disrupts its interaction with DELLA1 and causes a GA-insensitive dwarf phenotype in peach[J]. Plant Biotechnology Journal, 17(9): 1723-1735.
[12] Dong Z B, Jiang C, Chen X Y, et al.2013. Maize LAZY1 mediates shoot gravitropism and inflorescence development through regulating auxin transport, auxin signaling, and light response[J]. Plant Physiology, 163(3): 1306-1322.
[13] Estelle M.1998. Polar auxin transport new support for an old model[J]. Plant Cell, 10(11): 1775-1778.
[14] Forestan C, Farinati S, Varotto S.2012. The maize PIN gene family of auxin transporters[J]. Frontiers in Plant Science, 3: 16.
[15] Forestan C, Varotto S.2012. The role of PIN auxin efflux carriers in polar auxin transport and accumulation and their effect on shaping maize development[J]. Molecular plant, 5(4): 787-798.
[16] Hollender C A, Dardick C.2015. Molecular basis of angiosperm tree architecture[J]. New Phytologist, 206(2): 541-556.
[17] Hill J L, Hollender C A.2019. Branching out: New insights into the genetic regulation of shoot architecture in trees[J]. Current Opinion in Plant Biology, 47: 73-80.
[18] Kramer E M.2004. PIN and AUX/LAX proteins: Their role in auxin accumulation[J]. Trends in Plant Science, 9(12): 578-582.
[19] Křeček P, Skupa P, Libus J, et al.2009. The PIN-FORMED (PIN) protein family of auxin transporters[J]. Genome Biology, 10(12): 249.
[20] Mravec J, Skupa P, Bailly A, et al.2009. Subcellular homeostasis of phytohormone auxin is mediated by the ER-localized PIN5 transporter[J]. Nature, 459(7250): 1136-1140.
[21] Muller A, Guan C, Galweiler L, et al.1998. AtPIN2 defines a locus of Arabidopsis for root gravitropism control[J]. EMBO Journal, 17(23): 6903-6911.
[22] Nakamura A, Goda H, Shimada Y, et al.2004. Brassinosteroid selectively regulates PIN gene expression in Arabidopsis[J]. Bioscience Biotechnology and Biochemistry, 68(4): 952-954.
[23] Nicola C, Elizabeth T O T, Matthew C R, et al.2012. Diversification and expression of the PIN, AUX/LAX, and ABCB families of putative auxin transporters in Populus[J]. Frontiers in Plant Science, 3:17.
[24] Palme K, Galweiler L.1999. PIN-pointing the molecular basis of auxin transport[J]. Current Opinion Plant Biology, 2(5): 375-381.
[25] Paponov I A, Teale W D, Trebar M, et al.2005. The PIN auxin efflux facilitators: evolutionary and functional perspectives[J]. Trends in Plant Science, 10(4): 170-177.
[26] Pattison R J, Catala C.2012. Evaluating auxin distribution in tomato (Solanum lycopersicum) through an analysis of the PIN and AUX/LAX gene families[J]. The Plant Journal, 70(4): 585-598.
[27] Peer W A, Bandyopadhyay A, Blakeslee J J, et al.2004. Variation in expression and protein localization of the PIN family of auxin efflux facilitator proteins in flavonoid mutants with altered auxin transport in Arabidopsis thaliana[J]. Plant Cell, 16(7): 1898-1911.
[28] Robert S, Chary S N, Drakakaki G, et al.2008. Endosidin1 defines a compartment involved in endocytosis of the brassinosteroid receptor BRI1 and the auxin transporters PIN2 and AUX1[J]. Proceedings of the National Academy of Sciences of the USA, 105(24): 8464-8469.
[29] Roumeliotis E, Kloosterman B, Oortwijn M, et al.2013. The PIN family of proteins in potato and their putative role in tuberization[J]. Frontiers in Plant Science, 4: 524.
[30] Sassi M, Lu Y, Zhang Y, et al.2012. COP1 mediates the coordination of root and shoot growth by light through modulation of PIN1- and PIN2-dependent auxin transport in Arabidopsis[J]. Development, 139(18): 3402-3412.
[31] Shen C J, Bai Y H, Wang S K, et al.2010. Expression profile of PIN, AUX/LAX and PGP auxin transporter gene families in Sorghum bicolor under phytohormone and abiotic stress[J]. Federation of European Biochemical Societies Journal, 277(14): 2954-2969.
[32] Sukumar P, Maloney G S, Muday G K.2013. Localized induction of the ATP-binding cassette B19 auxin transporter enhances adventitious root formation in Arabidopsis[J]. Plant Physiology, 162(3): 1392-1405.
[33] Tiwari S B, Hagen G, Guilfoyle T J.2004. Aux/IAA proteins contain a potent transcriptional repression domain[J]. Plant Cell, 16(2): 533-543.
[34] Tworkoski T, Scorza R.2001. Root and shoot characteristics of peach trees with different growth habits[J]. Journal of the American Society for Horticultural Science, 126(6):785-790.
[35] Tworkoski T, Miller S, & Scorza R.2006. Relationship of pruning and growth morphology with hormone ratios in shoots of pillar and standard peach trees[J]. Journal of Plant Growth Regulation, 25(2): 145-155.
[36] Viaene T, Delwiche C F, Rensing S A, et al.2013. Origin and evolution of PIN auxin transporters in the green lineage[J]. Trends in Plant Science, 18(1): 5-10.
[37] Wang J R, Hu H, Wang G H, et al.2009. Expression of PIN genes in rice (Oryza sativa L.): Tissue specificity and regulation by hormones[J]. Molecular plant, 2(4): 823-831.
[38] Wang F, Deng Y, Zhou Y, et al.2015. Genome-wide analysis and expression profiling of the phospholipase C gene family in soybean (Glycine max)[J]. PLOS ONE, 10(9): e0138467.
[39] Woodward A W, & Bartel B.2005. Auxin: Regulation, action, and interaction[J]. Annals of Botany, 95(5): 707-735.
[40] Xie X, Qin G, Si P, et al.2017. Analysis of Nicotiana tabacum PIN genes identifies NtPIN4 as a key regulator of axillary bud growth[J]. Physiologia Plantarum, 160(2): 222-239.
[41] Xu K J, Sun F L, Wang Y F, et al.2016. The PIN1 family gene PvPIN1 is involved in auxin-dependent root emergence and tillering in switchgrass[J]. Genetics and Molecular Biology, 39(1): 62-72.
[42] Xu M, Zhu L, Shou H X, et al.2005. A PIN1 family gene, OsPIN1, involved in auxin-dependent adventitious root emergence and tillering in rice[J]. Plant Cell Physiology, 46(10): 1674-1681.
[43] Yang C, Wang D, Zhang C, et al.2019. Comparative analysis of the PIN auxin transporter gene family in different plant species: A focus on structural and expression profiling of PINs in Solanum tuberosum[J]. International Journal of Molecular Sciences, 20(13): 3270-3286.
[44] Yoshihara T, Spalding E P, Iino M.2013. AtLAZY1 is a signaling component required for gravitropism of the Arabidopsis thaliana inflorescence[J]. The Plant Journal, 74(2): 267-279.
[45] Zazimalova E, Krecek P, Skupa P, et al.2007. Polar transport of the plant hormone auxin - the role of PIN-FORMED (PIN) proteins[J]. Cellular and Molecular Life Sciences, 64(13): 1621-1637.
[46] Zhang H, An H S, Wang Y, et al.2015. Low expression of PIN gene family members is involved in triggering the dwarfing effect in M9 interstem but not in M9 rootstock apple trees[J]. Acta Physiologiae Plantarum, 37(104):1-18.
[47] Zhang N, Yu H, Yu H, et al.2018. A core regulatory pathway controlling rice tiller angle mediated by the LAZY1-dependent asymmetric distribution of auxin[J]. The Plant Cell, 30(7): 1461-1475. |
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