高通量转录组在园艺植物色素代谢中的研究进展

doi:10.13560/j.cnki.biotech.bull.1985.2017-0018

摘要/Abstract

摘要： 色素代谢是园艺植物中最为重要的研究领域之一，目前相关研究主要集中在花青素代谢和类胡萝卜素代谢上，其决定园艺植物的品质性状和观赏性状。利用转录组学技术，可以从转录组水平上揭示园艺植物色素代谢的分子机理。综述了转录组学在主要果树、蔬菜和观赏植物的色素节点分离、分支代谢、新基因分离、调控机制及环境对色素代谢影响方面的主要研究进展，分析了目前应用中存在的问题，并展望了转录组学在园艺植物色素代谢中的发展前景，以期为利用高通量测序技术分析色素代谢机制、分离关键基因并应用于园艺作物品质定向育种提供参考。

关键词: 转录组学, 生物信息学, 色素代谢

Abstract: Pigments mechanism is one of the most important research fields in horticultural plants. Related researches mainly include anthocyanin and carotenoid biosynthesis，which decide the quality and ornamental character of horticultural plants. Using transcriptomic technology，the transcriptional regulation mechanism of horticulture plants can be investigated at the transcriptome level. This paper summarized the recent reports about the isolation of code genes，branch mechanism，new genes isolation，regulatory mechanism，and environment- pigments interaction of fruit trees，vegetables and ornamental plants. The current problems in application were analyzed. The development prospect of transcriptomics in horticultural plants pigments metabolism was also prospected. We hope that it will provide useful information for the regulation mechanism study，important gene isolation and quality orientation breeding of horticulture plants by using transcriptomic technology.

Key words: transcriptomics, bioinformatics, pigment metabolism

李霞,王顺利. 高通量转录组在园艺植物色素代谢中的研究进展[J]. 生物技术通报, 2017, 33(7): 7-14.

LI Xia, WANG Shun-li. Research Advances of Transcriptomics in Horticulture Plants Pigments Metabolism[J]. Biotechnology Bulletin, 2017, 33(7): 7-14.

参考文献

[1] Tanaka Y, Sasaki N, Ohmiya A. Biosynthesis of plant pigments：anthocyanins, betalains and carotenoids[J] . The Plant Journal, 2008, 54（4）：733-749.
[2] Liu L, Shao Z, Zhang M, et al. Regulation of carotenoid metabolism in tomato[J] . Molecular Plant, 2015, 8：28-39.
[3] 高慧君, 明家琪, 张雅娟, 等. 园艺植物中类胡萝卜素合成与调控的研究进展. 园艺学报[J] . 2015, 42：1633-1648.
[4] Jaakola L. New insights into the regulation of anthocyanin biosynthesis in fruits[J] . Trends in Plant Science, 2013, 18（9）：477-483.
[5] Li W, Liu Y, Zeng S, et al. Gene expression profiling of development and anthocyanin accumulation in kiwifruit（Actinidia chinensis）based on transcriptome sequencing[J] . PLoS One, 2015, 10（8）：e0136439.
[6] Liu Y, Zeng S, Sun W, et al. Comparative analysis of carotenoid accumulation in two goji（Lycium barbarum L. and L. ruthenicum Murr.）fruits[J] . BMC Plant Biology, 2014, 14（1）：269.
[7] Ma J, Li J, Zhao J, et al. Inactivation of a gene encoding carotenoid cleavage dioxygenase（CCD4）leads to carotenoid-based yellow coloration of fruit flesh and leaf midvein in peach[J] . Plant Molecular Biology Reporter, 2014, 32（1）：246-257.
[8] Ohmiya A, Kishimoto S, Aida R, et al. Carotenoid cleavage Dioxygenase（CmCCD4a）contributes to white color formation in chrysanthemum petals[J] . Plant Physiology, 2006, 142：1193-1201.
[9] Zhang B, Liu C, Wang YQ, et al. Disruption of a CAROTENOID CLEAVAGE DIOXYGENASE 4 gene converts flower colour from white to yellow in Brassica species[J] . New Phytologist, 2015, 206（4）：1513-1526.
[10] Ahn JH, Kim JS, Kim S, et al. De novo transcriptome analysis to identify anthocyanin biosynthesis genes responsible for tissue-specific pigmentation in zoysiagrass（Zoysia japonica Steud.）[J] . PLoS One, 2015, 10（4）：e0124497.
[11] Liu Y, Linwang K, Deng C, et al. Comparative transcriptome analysis of white and purple potato to identify genes involved in anthocyanin biosynthesis[J] . PLoS One, 2015, 10（6）：e0129148.
[12] Fukushima A, Nakamura M, Suzuki H, et al. High-throughput sequencing and de novo assembly of red and green forms of the Perilla frutescens var. crispa transcriptome[J] . PLoS One, 2015, 10（6）：e0129154.
[13] Hong Y, Tang X, Huang H, et al. Transcriptomic analyses reveal species-specific light-induced anthocyanin biosynthesis in chrysanthemum[J] . BMC Genomics, 2015, 16（1）：1-18.
[14] Wu ZG, Jiang W, Mantri N, et al. Transciptome analysis reveals flavonoid biosynthesis regulation and simple sequence repeats in yam（Dioscorea alata L.）tubers[J] . BMC Genomics, 2015, 16（1）：346.
[15] Casimiro-Soriguer I, Narbona E, Buide M, et al. Transcriptome and biochemical analysis of a flower color polymorphism in Silene littorea（Caryophyllaceae）[J] . Frontiers in PlantScience, 2016, 7（939）：204.
[16] Mushtaq MA, Pan Q, Chen D, et al. Comparative leaves transcriptome analysis emphasizing on accumulation of anthocyanins in brassica：molecular regulation and potential interaction with photosynthesis[J] . Frontiers in Plant Science, 2016, 7：311.
[17] Lou Q, Liu Y, Qi Y, et al. Transcriptome sequencing and metabolite analysis reveals the role of delphinidin metabolism in flower colour in grape hyacinth[J] . Journal of Experimental Botany, 2014, 65（12）：3157-3164.
[18] Jin X, Huang H, Wang L, et al. Transcriptomics and metabolite analysis reveals the molecular mechanism of anthocyanin biosynthesis branch pathway in different senecio cruentus cultivars[J] . Frontiers in Plant Science, 2016, 7（107）：1307.
[19] 宿福园, 姚延兴, 李长林, 等. 中国园艺学会2015年学术年会论文摘要集：黑柿花青苷累积的转录组和表达谱分析[C] . 北京：中国林业出版社, 2015.
[20] Yamagishi M, Toda S, Tasaki K. The novel allele of the LhMYB12 gene is involved in splatter-type spot formation on the flower tepals of Asiatic hybrid lilies（Lilium spp.）[J] . New Phytologist, 2014, 201（3）：1009-1020.
[21] Yuan YW, Sagawa JM, Frost L, et al. Transcriptional control of floral anthocyanin pigmentation in monkeyflowers（Mimulus）[J] . New Phytologist, 2014, 204（4）：1013-1027.
[22] Lee JM, Joung JG, Mcquinn R, et al. Combined transcriptome, genetic diversity and metabolite profiling in tomato fruit reveals that the ethylene response factor SlERF6 plays an important role in ripening and carotenoid accumulation[J] . Plant Journal, 2012, 70（2）：191-204.
[23] Bashandy H, Pieti?inen M, Carvalho E, et al. Anthocyanin biosynthesis in gerbera cultivar ‘Estelle’ and its acyanic sport ‘Ivory’[J] . Planta, 2015, 242（3）：601-611.
[24] EI-Sharkawy I, Liang D, Xu K. Transcriptome analysis of an apple（Malus×domestica）yellow fruit somatic mutation identifies a gene network module highly associated with anthocyanin and epigenetic regulation[J] . Journal of Experimental Botany, 2015, 47 Suppl 1（22）：218-225.
[25] Xu Y, Feng S, Jiao Q, et al. Comparison of MdMYB1 sequences and expression of anthocyanin biosynthetic and regulatory genes between Malus domestica Borkh. cultivar ‘Ralls’ and its blushed sport. [J] . Euphytica, 2012, 185（2）：157-170.
[26] Saminathan T, Bodunrin A, Singh NV. Genome-wide identification of microRNAs in pomegranate（Punica granatum L.）by high-throughput sequencing[J] . BMC Plant Biology, 2016, 16（1）：1-16.
[27] Xu Q, Liu Y, Zhu A, et al. Discovery and comparative profiling of microRNAs in a sweet orange red-flesh mutant and its wild type[J] . BMC Genomics, 2010, 11（1）：1-17.
[28] Tzuri G, Zhou X, Chayut N, et al. A ‘golden’ SNP in CmOr governs the fruit flesh color of melon（Cucumis melo）[J] . Plant Journal for Cell & Molecular Biology, 2015, 82（2）：267-279.
[29] Sagawa JM, Stanley LE, Lafountain AM, et al. An R2R3-MYB transcription factor regulates carotenoid pigmentation in Mimulus lewisii flowers[J] . New Phytologist, 2016, 209（3）：1049-1057.
[30] Zhou Y, Zhou H, Linwang K, et al. Transcriptome analysis and transient transformation suggest an ancient duplicated MYB transcription factor as a candidate gene for leaf red coloration in peach[J] . BMC Plant Biology, 2014, 14（1）：1-13.
[31] Zhou H, Linwang K, Wang H, et al. Molecular genetics of blood-fleshed peach reveals activation of anthocyanin biosynthesis by NAC transcription factors[J] . Plant Journal, 2015, 82（1）：105-121.
[32] 朱满兰, 王亮生, 张会金, 等. 耐寒睡莲花瓣中花青素苷组成及其与花色的关系[J] . 植物学报, 2012, 47（5）：437-453.
[33] Wu Q, Wu J, Li SS, et al. Transcriptome sequencing and metabolite analysis for revealing the blue flower formation in waterlily[J] . BMC Genomics, 2016, 17（1）：897.
[34] Weiss D. Regulation of flower pigmentation and growth：Multiple signaling pathways control anthocyanin synthesis in expanding petals[J] . Physiologia Plantarum, 2000, 110（2）：152-157.
[35] 胡可, 韩科厅, 戴思兰. 环境因子调控植物花青素苷合成及呈色的机理[J] . 植物学报, 2010, 45（3）：307-317.
[36] Zhang HN, Li WC, Wang HC, et al. Transcriptome profiling of light-regulated anthocyanin biosynthesis in the pericarp of litchi[J] . Frontiers in Plant Science, 2016, 07（225）.
[37] Wu BH, Cao YG, Guan L, et al. Genome-wide transcriptional profiles of the berry skin of two red grape cultivars（Vitis vinifera）in which anthocyanin synthesis is sunlight-dependent or -independent[J] . PLoS One, 2014, 9（9）：e105959.
[38] Li P, Li YJ, Zhang FJ, et al. The Arabidopsis UDP-glycosyltransfe-rases UGT79B2 and UGT79B3, contribute to cold, salt and drought stress tolerance via modulating anthocyanin accumulation[J] . The Plant Journal, 2017, 89（1）：85-103.
[39] Qiu Z, Wang X, Gao J, et al. The tomato hoffman’s anthocyaninless gene encodes a bHLH transcription factor involved in anthocyanin biosynthesis that is developmentally regulated and induced by low temperatures[J] . PLoS One, 2016, 11（3）：e0151067.
[40] Movahed N, Pastore C, Cellini A, et al. The grapevine VviPrx31 peroxidase as a candidate gene involved in anthocyanin degradation in ripening berries under high temperature[J] . Journal of Plant Research, 2016, 129（3）：513-526.
[41] Loreti E, Povero G, Novi G, et al. Gibberellins, jasmonate and abscisic acid modulate the sucrose-induced expression of anthocyanin biosynthetic genes in Arabidopsis[J] . New Phytologist, 2008, 179（4）：1004-1016.
[42] Ji XH, Zhang R, Wang N, et al. Transcriptome profiling reveals auxin suppressed anthocyanin biosynthesis in red-fleshed apple callus（Malus sieversii f. niedzwetzkyana）[J] . Plant Cell, Tissue and Organ Culture（PCTOC）, 2015, 123（2）：389-404.
[43] Ito S, Nozoye T, Sasaki E, et al. Strigolactone regulates anthocyanin accumulation, acid phosphatases production and plant growth under low phosphate condition in arabidopsis[J] . PLoS One, 2015, 10 （3）：e0119724.
［44］ Hsieh L-C, Lin S-I, Shih AC-C, et al. Uncovering small RNA-mediated responses to phosphate deficiency in Arabidopsis by deep sequencing［J］. Plant Physiology, 2009, 151（4）：2120-2132.
［45］ Mardis ER. The impact of next-generation sequencing technology on genetics［J］. Trends in Genetics, 2008, 24（3）：133-141.
［46］王云生. 基于高通量测序的植物群体基因组学研究进展［J］. 遗传, 2016, 38（8）：688-699.
［47］ Craig DW, Pearson JV, Szelinger S, et al. Identification of genetic variants using bar-coded multiplexed sequencing［J］. Nature Methods, 2008, 5（10）：887-893.
［48］ Ming R, Vanburen R, Wai CM, et al. The pineapple genome and the evolution of CAM photosynthesis［J］. Nature Genetics, 2015, 47（12）：1435-1442.
［49］ Huang S, Li R, Zhang Z, et al. The genome of the cucumber, Cucumis sativus L.［J］. Nature Genetics, 2009, 41（12）：1275-1281.
［50］ Bolger A, Scossa F, Bolger ME, et al. The genome of the stress-tolerant wild tomato species Solanum pennellii［J］. Nature Genetics, 2014, 46（9）：1034-1038.
［51］ Zhang Q, Chen W, Sun L, et al. The genome of Prunus mume［J］. Nature Communications, 2011, 3（4）：187-190.
［52］ Velasco R, Zharkikh A, Affourtit J, et al. The genome of the domesticated apple（Malus × domestica Borkh.）［J］. Nature Genetics, 2010, 42（10）：833-839.
［53］ Qi JJ, Liu X, Shen D, et al. A genomic variation map provides insights into the genetic basis of cucumber domestication and diversity［J］. Nature Genetics, 2013, 45（12）：1510-1515.
［54］ Lin T, Zhu G, Zhang J, et al. Genomic analyses provide insights into the history of tomato breeding［J］. Nature Genetics, 2014, 46（11）：1220-1226.
［55］ Iorizzo M, Ellison S, Senalik D, et al. A high-quality carrot genome assembly provides new insights into carotenoid accumulation and asterid genome evolution［J］. Nature Genetics, 2016, 48（6）：657.