-
Flower scent is a highly valued quality trait in ornamental plants. In the natural environment, numerous plant species release floral scents to attract a diverse range of animal pollinators, predominantly insects, to facilitate their reproductive cycle. The metabolism of floral scent components, comprising small molecules and volatile chemicals, entails a complex interplay of physiological and biochemical processes. Understanding this intricate mechanism is crucial for unraveling the intricate biology behind floral scents in ornamental plants[29]. With further research on plant secondary metabolism, floral scent components and biosynthesis have been continuously elucidated[30]. Mei stands out among other Prunus species due to its ability to produce strong floral scents. Thus, the study of flower fragrance in Mei has drawn plenty of attention recently. A study conducted in Wakayama Prefecture, Japan, identified 22 components of Mei floral scents through methanol extraction under reflux[31]. However, it was noted that the components extracted by the solvent might not fully reflect the actual aroma components released by Mei. To overcome this limitation, researchers employed headspace solid-phase microextraction combined with gas chromatography-mass spectrometry (HS-SPME-GC-MS) to identify the floral scent components of selected Mei cultivates[32], and the results showed that benzaldehyde and benzyl acetate were the key components affecting the aroma intensity of Mei, with their relative contents are 75% and 90.36%, respectively. The relative content of benzyl acetate in P. sibirica was only 0.06%, indicating that benzyl acetate is a characteristic volatile component of Mei. Except for benzaldehyde and benzyl acetate, many unique components, including eugenol, benzyl alcohol, cinnamyl alcohol, cinnamyl acetate were discovered in various Mei cultivars[11,33]. Generally, the different types and contents of compounds released by Mei are the fundamental reasons for the difference in flower scents of Mei cultivars. In one example, benzyl acetate and eugenol made up the majority of the floral volatiles in cultivars with white flowers[34], like 'Fuban Lve', 'Zaohua Lve', 'Subai Taige' and 'Zao Yudie', whereas only 'Fenpi Gongfen', 'Jiangsha Gongfen', and 'Fenhong Zhusha' (pink flowers) synthesized cinnamyl alcohol and cinnamyl acetate. The endogenous extract of the interspecific hybrids in Mei contained less benzyl alcohol, but more benzyl benzoate, which had a competitive inhibition on the production of benzyl acetate, which may result in the difference in characteristic scent between Mei and its interspecific hybrids[33]. The complex biosynthesis of scents compounds from Mei resulted in a wide variety of volatile chemicals with various levels of concentrations. There were notable variations in the endogenous content and volatilization of main components of 'Sanlun Yudie' during the whole flowering stage. In the bud stage, all volatiles were low, and no eugenol was detected. Benzaldehyde had the highest volatility at the end of flowering, benzyl alcohol and benzyl acetate had the highest volatility at full flowering stage, and eugenol had the highest volatility at fading stage. The content of benzaldehyde was the highest at bud stage, benzyl alcohol and eugenol at fading stage, and benzaldehyde acetate at full flowering stage[32]. In addition, previous studies indicated that mostly emit benzenoid chemicals[35]. Subsequent studies further divided the stamens into anthers and filaments and found that filaments primarily emitted benzyl acetate, while anthers primarily released benzaldehyde[36].
Based on genome-wide analysis and RNA sequencing, a substantial number of flower scent-related genes have been discovered (Table 1). A comparison of gene expression differences between the two flowering periods (developed bud and squaring flower) of the 'Sanlun Yudie' revealed 6,954 DEGs and 595 transcriptional regulators included (TFs) of 76 TF families. Under the influence of phenylalanine ammonia-lyase (PAL), the essential protein in the synthesis of phenylpropane and the benzene ring, phenylalanine produces trans-cinnamic acid[37]. The P. mume genome contained three PmPALs, and PmPAL2 might contribute to synthetic aroma compounds[38]. P450 proteins were found to be particularly abundant during Mei's blooming stage, and two P450 genes were prominently shown in the DEGs that were upregulated[38]. The short-chain dehydrogenases/reductases (SDR) family was closely related with the formation of benzyl alcohol. A total of 147 SDR genes were identified in P. mume genome, and nine candidate genes were significantly expressed in flowers[38,39], suggesting that they might be associated with the synthesis of benzaldehyde and benzyl alcohol in Mei. The MYB family gathered the most 50 TF, followed by 42 basic helix loop-helix (bHLH), and 35 NAC. A total of 36 TFs specifically expressed in flowers were dispersed over 18 TF families[40], including six MYB-related, six MYB, three NAC, and so on. The MYB family was found during the synthesis of flower scent. At present, four MYB TFs (MYB1/2/3/4) from Mei have been identified and described, and the expression levels of three of them increased with the blooming of flowers[18]. In addition, yeast two-hybrid (Y2HGold) and bimolecular fluorescence complementation (BiFC) assays verified that the metabolism regulation processes involved in floral scents, which affected the expression of downstream genes like 3-deoxy-7-phosphoheptulonate synthase (PmDAHPS), arogenate dehydratases (PmADT), PmPAL, CoA ligase/acyl activating enzyme (PmCNL/AAE). Fourty four PmBEATs genes were found in the P. mume genome[11]. PmBEAT34/36/37 were highly expressed in flowers and their highest expression was observed at the blooming stage. Mei flower cell ability to synthesize benzyl acetate could be influenced by the expression levels of PmBEAT36/37. PmBEAT34/3/37 all had benzyl alcohol acetyltransferase activity in vitro[11]. Coniferyl alcohol acetyltransferase (CFAT) is a crucial substrate for the synthesis of eugenol, which catalyzes the conversion of coniferyl alcohol into coniferyl acetate. The 90 PmBAHD (including 44 PmBEAT family) genes were screened from the whole genome and phylogenetically divided into five major groups. PmBAHD67-69 might have a role in the metabolism of floral scents[41]. Two CFAT genes (PmCFAT1 and PmCFAT2) were cloned, and bioinformatics analysis and expression profiling suggest that PmCFAT1 may be crucial for eugenol biosynthesis but not PmCFAT2[34]. DNA methylation is a frequent epigenetic modification and differentially methylated genes (DMGs) were shown to have essential functions in controlling the floral fragrance production of Mei, for instance PmCFAT1a/1c, PmBEAT36/37, PmPAAS3, PmBAR8/9/10, and PmCNL1/3/5/6/14/17/20[11,32,34,42]. O-methyltransferase (PmOMT) may regulate the formation of methyl eugenol and is highly expressed in flower organs in Mei. Three eugenol synthase genes were cloned by RT-PCR from the blooming flowers of 'Sanlun Yudie', named PmEGSI/PmEGS2/PmEGS3 (eugenol synthase genes), respectively. The most significantly expressed PmEGS2 was introduced into petunia (Petunia hybrida 'W115'), which proved that PmEGS2 gene plays a role in the eugenol pathway and participates in eugenol biosynthesis and metabolism[43]. One hundred and thirty ATP-binding cassette (ABC) genes have been found in Mei, classified into eight subfamilies, including 55 PmABCG genes, which were specifically expressed in the flowers[44]. Volatilization of benzaldehyde and benzyl alcohol was substantially connected with PmABCG2/18/26, but negatively correlated with phenylmethyl acetate, and volatilization of benzyl acetate was highly correlated with PmABCG9/13/23. Besides, the study found that PmIAA2/12/15/16 was also involved in the synthesis of benzyl acetate and cinnamyl acetate[45]. These genes, exhibiting high expression levels in various floral organ parts, are believed to have a significant impact on the transmembrane transport of floral components[44]. Through transcriptome analysis and enzyme activity assays, it was demonstrated that PmCAD1 (cinnamyl alcohol dehydrogenase) was identified as having a crucial part in the biosynthesis of cinnamyl alcohol in vitro. These findings shed light on the specific enzymatic pathway responsible for the production of this aromatic compound in Mei[46].
Table 1. Functional validation information of flower scent.
Flower scent Gene ID Function description Validation methods Reference PmPAL2 Pm030127 Involved in phenylpropanoids/
benzenoids biosynthesisHS-SPME-GC-MS Methods [32] PmBEAT36/37 Pm011009/Pm011010 Performs a key part in the biosynthesis
of benzyl acetateBioinformatics analysis, expression pattern analysis, plasmid construction, subcellular localization, enzyme activity analysis, GC-MS analysis [11] PmBAR Pm012335/Pm013777/
Pm013782Performs a key part in the biosynthesis
of benzyl acetate, as the key genes responsible for BAR activityIntegrative metabolite, enzyme activity, and transcriptome analysis, plasmid construction, qPCR validation [42] PmBAHD16/25 Pm010996/Pm011009 Plays an important role in promoting
the production of benzyl acetateGC-MS analysis, bioinformatics analysis, expression pattern and WGCNA analysis, validation of transgenic Arabidopsis plants [41] PmIAA2/12/15/16 Pm003529/Pm013416/
Pm013597/Pm020225Involved in the synthesis of benzyl
acetate and cinnamyl acetateBioinformatics analysis, expression pattern analysis [45] PmMYB Pm015692/Pm021211/
Pm025253Engaged in floral fragrance metabolic control via influencing the expression
of downstream genesGC-MS analysis, bioinformatics analysis, expression pattern analysis, subcellular localization, vector construction [18] PmEGS Pm012360 Involved in eugenol biosynthesis Bioinformatics analysis, expression pattern analysis, subcellular localization [43] PmCFAT1 Pm030674 Involved in floral scent metabolism GC-MS analysis, bioinformatics analysis, expression pattern analysis, subcellular localization [34] PmABCG2/18/26 Pm001070/Pm022014/
Pm029602Positively linked with benzaldehyde and benzyl alcohol volatilization rates Bioinformatics analysis, expression pattern analysis, GC-MS analysis of volatile components [44] PmABCG9/13/23 Pm011453/Pm012323/
Pm026080Positively linked with benzaldehyde and benzyl alcohol volatilization rates Bioinformatics analysis, expression pattern analysis, GC-MS analysis of volatile components [44] PmCAD1/2 Pm021215/Pm021214 Play roles in cinnamyl alcohol synthesis GC-MS analysis, bioinformatics analysis, expression pattern analysis, real-time fluorescence quantitative PCR, vector construction [46] -
Mei originated in southwest China and the Yangtze River basin, is a subtropical tree species. However, in the northern region of China, low temperature has seriously limited the growth of Mei, and few varieties can be applied. The selection and breeding of cold-resistant cultivars of Mei has been an important direction of breeding. Over the years, the cultivation of cold-resistant cultivars mainly focused on the conventional breeding methods such as introduction and domestication, distant cross breeding[5]. Since the 1950s, Chen et al.[2] cultivated a group of cold-resistant of Mei cultivars, such as 'Fenghou', 'Danfenghou' and 'Meimei', by using the introduction and domestication experiments in northern China, and successively carried out regional experiments of different cultivars in Inner Mongolia, Liaoning, Shanxi, Qinghai and Gansu[2,79]. Zhang[5] bred cold-resistant cultivars of Mei such as 'Yanxing' and 'Huahudie', through distant crossbreeding with strong cold resistance Mei relatives, which can withstand low temperatures from −35°C to −25°C. Subsequently, a series of cold-resistant cultivars such as 'Yutaizhaoshui', 'Songchun', 'Zhongshanxing' and 'Shantaobai' were selected and bred through several decades of selection, domestication, cross breeding and distant crossing etc. Most of these cultivars are Apricot Mei Group, which laid the material foundation for the concept of 'Transferring Mei from South to North'. Chen et al.[79] used Apricot Mei Group and Mei cultivars to breed a cold resistant cultivar 'Xiangruibai' with the characteristic scent of Mei, which achieved an enormous advance in cold-resistant fragrant flower breeding of Mei. It is worth mentioning that the broad field cultivation region occupied by Mei has spread 2,000 km from the Yangtze River Basin through many years of multi-point comparative experiments.
The comparison of physiological changes of Mei can analyze the difference of cold resistance of different cultivars. The cold resistance of 38 Mei cultivars was analyzed, and it turned out this the cold hardiness of apricot Mei series is higher than that of true Mei series[80]. Similarly, the physiological indexes of Mei growing in different dimensions and seasons were analyzed, and it was found that the 'Yanapricot' cultivar had the strongest cold resistance[39].
With the conclusion of Mei's entire gene sequencing, it is now possible to investigate resistance genes and establish the groundwork for Mei molecular breeding. A vital phase in the upper life cycle of plants, dormancy is an adaptive reaction that allows plants to withstand harsh environments, like cold temperatures[81]. The reaction to cold stress and dormancy was modeled molecularly[82] using the interaction between PmDAM and PmCBF. It was discovered that low temperatures triggered the production of PmCBF, and the build-up of CBF encouraged the development of PmDAM, causing flower buds to go into dormancy[82]. Candidate TFs and target genes that can control Mei dormancy by adjusting endogenous hormone content in response to environmental cues were effectively screened in the coexpression network of genes linked to flower bud dormancy[83]. Among them, ABRE binding factor PmABF2, PmABF4, and PmSVP changed Abscisic acid (ABA) content to govern bud dormancy[83]. Furthermore, it was shown that PmSOC1-2, which interacts with PmDAM, regulates floral bud dormancy via ABA regulation[84]. At present, the research on the molecular mechanism of Mei blossom cold resistance mainly focuses on CBF (C-repeat binding factors), ICE1 (Inducer of CBF expression1), ERF (ethylene responsive transcription factor), LEA, DAM, WRKY and other gene families[7,82,85−87]. Cold stress, which includes chilling (cold temperatures of above 0 °C) and freezing (below 0 °C) stress, is a significant factor limiting plant growth, development, and geographical distribution[88]. Cold acclimation is a protective strategy promoting plant tolerance and resistance to cold stress that is controlled through both CBF-dependent and CBF-independent pathways[89]. Six PmCBFs genes were cloned from Mei, and all of them have been shown to be triggered by cold stress, and the function of transgenic plants was verified[90]. CBF and DAM are the key genes in Mei that respond to cold and dormancy respectively, and the possible interrelationships surrounding the CBF and DAM genes, as cold acclimation and dormancy are closely linked. In particular, the interaction among PmCBFs with PmDAM reveals the molecular mechanism behind cold-response pathway and dormancy regulation in Mei growth[82]. ICE1, a member of the bHLH transcription factor family, might activate AtCBF3 and AtCOR genes in reaction to low temperature[85,91]. Overexpression of PmICE1 increased cold resistance in Arabidopsis compared with control[92]. Meanwhile, other bHLH transcription factors may influence cold tolerance of Mei. There were 95 PmbHLH genes found in the P. mume entire genome, which were grouped into 23 subfamilies. Through investigation of transcriptome and qRT-PCR data, PmbHLH4/6/25/28/38/40/57 was discovered playing a major part in resisting low-temperature stress[93,94]. The overexpression of PmBBX32 gene reduced the damage to Arabidopsis and may improve transgenic plant cold resistance by increasing antioxidant enzyme activity and proline content[95]. Validation of transgenic tobacco showed that overexpression of PmPUB1, PmPUB3 (Plant U-Box E3 ligases) and PmWRKY18 genes increased cold resistance[87,96]. A total of 30 late embryogenesis abundant (LEA) genes were identified on a genome-wide level using the Hidden Markov Model (HMM), four (PmLEA10/19/20/29) of these genes were involved in plant responses to cold[86]. In addition, PmWRKY18 and PmLEA8/19/20 were induced to be expressed by Atco exogenous ABA and may be involved in ABA-dependent cold signaling regulatory pathways[86,87]. Freezing tolerance genes have been discovered in Mei by RNA-seq and ATAC-seq (assay for transposase-accessible chromatin using sequencing) analysis. Cold-shock protein CS120-like (PmCSL) expression also considerably significantly up-regulated, meanwhile the chromatin opening of PmCSL was markedly increased[97]. The freezing resistance of transgenic Arabidopsis plants was markedly enhanced by overexpressing PmCSL. Afterward, a large number of genes associated with cold resistance were found in P. mume genome, like 13 HDACs (histone deacetylases)[98], 49 bZIP (basic leucine zipper) transcription factors[99], 113 NAC transcription factor genes[100], 17 SWEET (sugars will eventually be exported transporter)[101], 58 WRKYs[87,102], 16 CIPKs (serine/threonine protein kinase)[103], 11 MAP kinases (mitogen-activated protein kinase, MPKs) and seven MAPK kinases (MKKs)[104], and Table 2 contains additional functional genes and information[105−109]. Gene structures, phylogenetic relationships, cis-acting elements, and expression patterns in reactions to cold treatment were all intensively investigated in order to obtain insights into the mechanisms underlying cold response in woody plants. These investigations have significantly enhanced our comprehension of the roles of gene families involved in cold tolerance. By elucidating the genetic basis of cold response, these studies have provided valuable information for the development of molecular breeding programs in woody plants.
Table 2. Functional validation information of cold resistance.
Cold resistance Gene ID Function description Validation Methods Reference PmCBF1/2/3/4/5/6 Pm023769/Pm023772/
Pm023773/Pm023775/
Pm023777/Pm027913/Key TF that responses to cold signal qRT-PCR, gene cloning and Yeast 2 Hybrid assays, BiFC assays, promoter cloning and Yeast 1 Hybrid assays [82] PmICE1 − PmCBF express levels are increased in response to a low temperature signal Bioinformatics analysis, expression pattern analysis, subcellular localization, vector construction, Arabidopsis transformation, and low-temperature stress experiments [92] PmLEA10/29 Pm026684/Pm006114 Besponse to cold stress Gene expression analysis, Tobacco transformation and stress tolerance analysis, Relative Water Content (RWC), protein assay and analysis, statistical approach for MDA and REL [86] PmLEA19/20 Pm020945/Pm021811 Response to cold stress; participate in ABA-dependent pathway Gene expression analysis, Tobacco transformation and stress tolerance analysis, Relative Water Content (RWC), protein assay and analysis, statistical approach for MDA and REL [86] PmRS Pm027594/Pm025896 Diminish the negative effects of cold Gene cloning, expression pattern analysis, subcellular localization, transformation of Arabidopsis thaliana, cold resistance analysis, transformation of Mei [107] PmBBX32 Pm013051 Diminish the negative effects of cold Expression pattern analysis, transformed Arabidopsis thaliana, low-temperature stress treatment, physiological index determination [95] PmCIPK5/6/13 Pm001690/Pm018300/
Pm008498Modulating the stress response to cold Bioinformatics analysis, expression pattern analysis, qRT-PCR [103] PmNAC11/20/23/40/
42/48/57/59/60/61/
66/82/85/86/107Pm001403/Pm005783/ Pm006470/Pm011234/
Pm011603/Pm012630/
Pm015876/Pm017550/
Pm018292/Pm018442/
Pm019659/Pm024558/
Pm025184/Pm025307/
Pm025184/Pm025307/
Pm028721Involved in the cold-stress response Bioinformatics analysis, expression pattern analysis, qRT-PCR [100] PmbHLH4/6/25/28/ 38/40/57 Pm002111/Pm002283/
Pm008898/Pm016406/ Pm018355/Pm023237Play a critical part in the resistance to low temperature stress Bioinformatics analysis, expression pattern analysis, qRT-PCR [93,94] PmPUB1/3 Pm006753/Pm009248 Play a significant part in the regulatory network connected to low temperature stress Bioinformatics analysis, expression pattern analysis, qRT-PCR, overexpression of tobacco, low-temperature treatment, physiological index measurement [87] PmWRKY18 Pm005698 Play a significant part in the regulatory network connected to low temperature stress, sensitive to ABA treatment Bioinformatics analysis, expression pattern analysis, qRT-PCR, overexpression of tobacco, low-temperature treatment, physiological index measurement [87] PmWRKY57 LOC103321497 Function in improving cold tolerance of plants Cloning and sequence analysis, subcellular localization, transformation of A. thaliana, determination of plant physiological index, expression analysis of genes [102] PmSOD3 Pm003436 Had important regulatory roles in cold acclimation process Physiological index determination, section observation, tissue browning, ion leakage rate, infrared thermal imaging technology, and freeze thaw detection sensors [109] PmPOD2/19 Pm000967/Pm022119 Had important regulatory roles in cold acclimation process Physiological index determination, section observation, tissue browning, ion leakage rate, infrared thermal imaging technology, and freeze thaw detection sensors [109] PmNCED3/8/9 Pm005153/Pm011164/
Pm016267Significant role in the plant's response to cold stress Bioinformatics analysis, expression pattern analysis, qRT-PCR [108] PmCSL − Significantly improved the freezing tolerance of transgenic plants Bioinformatics analysis, expression pattern analysis, ATAC sequencing, gene cloning and gene expression analysis, plant transformation and low temperature treatment [97] PmHDAC1/6/14 Pm020717/Pm024325/
Pm012683Significantly respond to cold stress Bioinformatics analysis, expression pattern analysis, qRT-PCR [98] PmbZIP 12/31/36/41/48 Pm005288/Pm020080/
Pm021804/Pm025001/
Pm029028Responses to low-temperature stress Bioinformatics analysis, expression pattern analysis, qRT-PCR [99] PmSWEET1/12/13/14 Pm007697/Pm022696/
Pm024167/Pm024554Responses to cold stress Bioinformatics analysis, expression pattern analysis, qRT-PCR [101] PmCDPK14 Pm026757 Play an essential role in resisting low temperature stress Bioinformatics analysis, expression pattern analysis, qRT-PCR, compare between two genomes of Mei [105] PmMAPK3/5/6/20 Pm000966/Pm023935/
Pm027774/Pm014593Significantly respond to cold stress Bioinformatics analysis, expression pattern analysis, qRT-PCR, compare between two genome databases of Mei [104] PmMAPKK2/3/6 Pm027015/Pm015648/
Pm027289Significantly respond to cold stress Bioinformatics analysis, expression pattern analysis, qRT-PCR, compare between two genome databases of Mei [104] PmRCI2s Pm027750/Pm003262/
Pm003263Significantly induced by low temperature Bioinformatics analysis, expression pattern analysis, qRT-PCR [106] -
Data sharing not applicable to this article as no datasets were generated or analyzed during the current study.
-
About this article
Cite this article
Fan D, Miao R, Lv W, Wen Z, Meng J, et al. 2024. Prunus mume genome research: current status and prospects. Ornamental Plant Research 4: e006 doi: 10.48130/opr-0024-0004
Prunus mume genome research: current status and prospects
- Received: 25 October 2023
- Accepted: 05 January 2024
- Published online: 04 March 2024
Abstract: Mei (Prunus mume) is an excellent garden tree highly praised in China, possessing both ornamental and cultural values. Breeding Mei with distinctive characteristics and high resistance has become a long-term goal to meet the visual and spiritual demands in the new era. With the rapid development of biotechnology, researchers have successively completed the whole genome sequence and resequencing of Mei, and continue to employ advanced techniques to investigate the formation mechanisms of important ornamental traits and stress resistance traits in Mei. Thus, the groundwork has been established for achieving the breeding objectives. In this article, we provide an overview of the development and expansion of genome projects over the past decade, including whole-genome sequencing, resequencing, and genetic mapping. We further present a concise summary of the research progress made in understanding major ornamental traits and cold resistance traits. These accomplishments hold great promise for significantly enhancing the efficiency of Mei and further realizing breeding goals.
-
Key words:
- Genome mapping /
- Resequencing /
- Functional genomics /
- Mei /
- Breeding