基于转录组测序筛选与柚裂果相关的基因

doi:10.3864/j.issn.0578-1752.2023.20.013

Abstract

Abstract:

【Objective】Fruit cracking is a universal physiological disorder that occurs during growth in citrus fruits. However, the molecular mechanisms that regulate cracking in citrus fruits remain unclear. The aim of this study was to screen genes that were related to resistance to fruit cracking. 【Method】 Normal fruits from a pomelo (Citrus grandis (L). Osbeck) cultivar (Duxin 1) resistant to cracking, as well as normal and cracked fruits from Duwei, a cultivar sensitive to cracking, were collected on August 3, 2021 and August 20, 2021, respectively. The pericarp surrounding blossom ends of the fruits (the blossom end was considered the center, approximate 30 millimeters radius) were sampled for RNA-seq. 【Result】 The differentially expressed genes (DEGs) in each stage were screened based on the comparisons of a transcriptome between cracked fruits from the cracking-sensitive cultivar and normal fruits from both cultivars. In the stage A, 1 660 DEGs were obtained, and 104 DEGs were common between the comparison. A total of 1 972 DEGs were screened in stage B, and 82 were common in the comparison. All the DEGs screened at both stages were used for a Gene Ontology enrichment analysis. In the classification of biological process, the major common sub-classifications, including ‘metabolic process’, ‘cellular process’, ‘single-organism process’, ‘biological regulation’, ‘response to stimulus’, and ‘signaling’ were identified in both stages. All the screened DEGs were also analyzed using Kyoto Encyclopedia of Genes and Genomes enrichment. Many genes were enriched in several metabolic pathways, including ‘carbon metabolism’, ‘MAPK signaling pathway-plant’, ‘plant hormone signal transduction’ and ‘protein processing in endoplasmic reticulum’. In addition, these pathways were identified in both stages. Several genes related to resistance to fruit cracking were identified in this study. The levels of transcription of Expansin-A1 were significantly higher in the pericarp of normal fruits from the two cultivars than that in the pericarp of cracked fruits from the sensitive cultivar. Calcineurin B-like protein gene was highly expressed in the pericarp of normal fruits from both cultivars when compared with the pericarp of cracked fruits from the sensitive cultivar. However, this difference disappeared at the stage B. The genes for heat stress transcription factor, serine/threonine-protein kinase, auxin-responsive protein, and dehydration-responsive element-binding protein were upregulated in the pericarp of cracked fruits from the sensitive cultivar compared with the pericarp of normal fruits from the two cultivars in both stages. 【Conclusion】These findings suggested that the genes related to strength of pericarp, water movement, and responsing to high temperature and water deficiency stresses were critical to regulating resistance to fruit cracking.

Key words: pummelo (Citrus grandis L. Osbeck), fruit cracking, pericarp, transcriptome, cracking-resistant gene

LU YanQing, LIN YanJin, WANG XianDa, LU XinKun. A Transcriptome Analysis Identifies Candidate Genes Related to Fruit Cracking in Pomelo Fruits[J].Scientia Agricultura Sinica, 2023, 56(20): 4087-4101.

0
/ / Recommend

Add to citation manager EndNote|Reference Manager|ProCite|BibTeX|RefWorks

URL: https://www.chinaagrisci.com/EN/10.3864/j.issn.0578-1752.2023.20.013

https://www.chinaagrisci.com/EN/Y2023/V56/I20/4087

Figures/Tables 14

Fig. 1

Table 1

Table 2

Table 3

Table 4

Fig. 2

Fig. 3

Fig. 4

Table 5

Common KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways for all differentially expressed genes screened on the base of comparisons"

代谢途径 Pathway	代谢途径编号 Ko ID	差异基因数量 DEG number
代谢途径 Pathway	代谢途径编号 Ko ID	A1 vs A3	B1 vs B3	A2 vs A3	B2 vs B3
植物病原菌互作Plant-pathogen interaction	ko04626	34	95	48	7
植物激素信号转导Plant hormone signal transduction	ko04075	15	43	37	5
碳代谢Carbon metabolism	ko01200	14	40	8	1
植物MAPK信号途径MAPK signaling pathway - plant	ko04016	12	32	27	2
内质网蛋白加工Protein processing in endoplasmic reticulum	ko04141	12	32	10	1
糖酵解/糖异生Glycolysis / Gluconeogenesis	ko00010	7	21	6	2
磷酸戊糖途径Pentose phosphate pathway	ko00030	3	7	1	1
果糖和甘露糖代谢Fructose and mannose metabolism	ko00051	3	7	1	1
半乳糖代谢Galactose metabolism	ko00052	4	18	6	1
抗坏血酸和醛酸代谢Ascorbate and aldarate metabolism	ko00053	3	9	1	1
类固醇代谢Steroid biosynthesis	ko00100	1	6	1	2
氰基氨基酸代谢Cyanoamino acid metabolism	ko00460	1	9	1	2
谷胱甘肽代谢Glutathione metabolism	ko00480	4	11	6	1
磷酸肌醇代谢Inositol phosphate metabolism	ko00562	4	16	3	2
甘油磷脂代谢Glycerophospholipid metabolism	ko00564	2	12	5	2
亚油酸代谢Linoleic acid metabolism	ko00591	2	3	4	2
ɑ-亚油酸代谢alpha-Linolenic acid metabolism	ko00592	5	11	8	2
丙酮酸代谢Pyruvate metabolism	ko00620	5	11	3	1
光合组织碳固定Carbon fixation in photosynthetic organisms	ko00710	1	10	2	1
类倍半萜烯和三萜烯合成Sesquiterpenoid and triterpenoid biosynthesis	ko00909	2	10	4	1
苯丙烷类生物合成Phenylpropanoid biosynthesis	ko00940	17	28	6	4
类黄酮合成Flavonoid biosynthesis	ko00941	9	12	1	2
异黄酮合成Isoflavonoid biosynthesis	ko00943	2	2	1	1
芪类化合物、二芳基庚烷和姜辣素合成 Stilbenoid, diarylheptanoid and gingerol biosynthesis	ko00945	7	12	1	2
ABC转运体ABC transporters	ko02010	6	12	6	1
剪接体Spliceosome	ko03040	5	11	6	1
玉米素合成Zeatin biosynthesis	ko00908	1	9	4	1
泛素介导的蛋白质降解过程Ubiquitin mediated proteolysis	ko04120	9	12	7	1
吞噬体Phagosome	ko04145	1	5	2	1
植物昼夜节律Circadian rhythm-plant	ko04712	2	17	5	3

Table 5

Table 6

Table 7

Table 8

Table 9

Fig. 5

References 57

[1]	芮文婧, 王晓敏, 张倩男, 胡学义, 胡新华, 付金军, 高艳明, 李建设. 番茄353份种质资源表型性状遗传多样性分析. 园艺学报, 2018, 45(3): 561-570.
	RUI W J, WANG X M, ZHANG Q N, HU X Y, HU X H, FU J J, GAO Y M, LI J S. Genetic diversity analysis of 353 tomato germplasm resources by phenotypic traits. Acta Horticulturae Sinica, 2018, 45(3): 561-570. (in Chinese) doi: 10.16420/j.issn.0513-353x.2017-0274
[2]	MITRA S K, PATHAK P K, DEBNATH S, SARKAR A, MONDAL D. Elucidation of the factors responsible for cracking and sunburn in litchi and integrated management to minimize the disorders. Acta Horticulturae, 2010, 863: 225-234.
[3]	MUTHOO A K, RAINA B L, NATHU B L. Fruit cracking studies in some commerical cultivars of litchi (Litchi chinensis Sonn). Advances in Plant Sciences, 1999, 12(2): 543-547.
[4]	叶正文, 叶兰香, 张学英. “朋娜” 等脐橙的裂果规律及赤霉素防裂效果. 上海农业学报, 2002, 18(4): 52-57.
	YE Z W, YE L X, ZHANG X Y. The fruit cracking rules of navel orange varieties such as “pengna” and the effect of gibberellin (ga) preventing fruits from cracking. Acta Agriculturae Shanghai, 2002, 18(4): 52-57. (in Chinese)
[5]	李娟, 陈杰忠. 柑桔裂果发生类型、过程及预防对策. 广东农业科学, 2011, 38(10): 32-33, 37.
	LI J, CHEN J Z. The style, process and control of cracking fruit in citrus. Guangdong Agricultural Sciences, 2011, 38(10): 32-33, 37. (in Chinese)
[6]	郗鑫, 刘晨筱, 陈虹, 白晋华, 郭红彦. 不同枣品种果实性状与裂果的相关性. 山西农业科学, 2016, 44(10): 1476-1478, 1507.
	XI X, LIU C X, CHEN H, BAI J H, GUO H Y. Correlation analysis of fruit characters and cracking in different varieties of jujube. Journal of Shanxi Agricultural Sciences, 2016, 44(10): 1476-1478, 1507. (in Chinese)
[7]	栗现芳, 陈晓龙, 问徐鹏, 赵怡, 马辉. 枣易裂品种和抗裂品种间各糖组分含量与裂果的相关性分析. 分子植物育种, 2020, 18(18): 6180-6186.
	LI X F, CHEN X L, WEN X P, ZHAO Y, MA H. Correlation analysis between the sugar components and fruit cracking in easily cracked and resistant jujube. Molecular Plant Breeding, 2020, 18(18): 6180-6186. (in Chinese)
[8]	李建国, 黄辉白. 荔枝果实理化特性及果皮形态学与裂果易感性的关系. 华南农业大学学报, 1995, 16(1): 84-89.
	LI J G, HUANG H B. Phybico- chemical properties and peel morphology in relation to fruit-cracking susceptibility in litchi fruit. Journal of South China Agricultural University, 1995, 16(1): 84-89. (in Chinese)
[9]	YU J, ZHU M T, WANG M J, TANG W Y, WU S, ZHANG K, YANG G S. Effect of nordihydroguaiaretic acid on grape berry cracking. Scientia Horticulturae, 2020, 261: 108979. doi: 10.1016/j.scienta.2019.108979
[10]	BEYER M, KNOCHE M. Studies on water transport through the sweet cherry fruit surface: V. conductance for water uptake. Journal of the American Society for Horticultural Science, 2002, 127(3): 325-332. doi: 10.21273/JASHS.127.3.325
[11]	LI N, FU L J, SONG Y Q, LI J, XUE X F, LI S R, LI L L. Water entry in jujube fruit and its relationship with cracking. Acta Physiologiae Plantarum, 2019, 41(9): 162. doi: 10.1007/s11738-019-2954-2
[12]	SONG Y Q, LI J, FU L J, LI N, LI L L. Change of fruit surface characteristics and its relationship with water absorption and fruit cracking in Ziziphus jujuba ‘Huping’. Scientia Silvae Sinicae, 2018, 54(12): 52-59.
[13]	PESCHEL S, KNOCHE M. Characterization of microcracks in the cuticle of developing sweet cherry fruit. Journal of the American Society for Horticultural Science, 2005, 130(4): 487-495. doi: 10.21273/JASHS.130.4.487
[14]	HUANG X M, YUAN W Q, WANG H C, LI J G, HUANG H B, SHI L, YIN J H. Linking cracking resistance and fruit desiccation rate to pericarp structure in Litchi (Litchi chinensisSonn.). The Journal of Horticultural Science and Biotechnology, 2004, 79(6): 897-905. doi: 10.1080/14620316.2004.11511863
[15]	HUANG X M, WANG H C, GAO F F, HUANG H B. A comparative study of the pericarp of litchi cultivars susceptible and resistant to fruit cracking. The Journal of Horticultural Science and Biotechnology, 1999, 74(3): 351-354. doi: 10.1080/14620316.1999.11511120
[16]	张鹏飞, 张燕, 巩磊, 纪薇, 高美英, 刘亚令, 郝晓娟. 植物生长调节剂对枣果皮细胞壁多糖的影响研究. 山西农业大学学报(自然科学版), 2014, 34(2): 174-178.
	ZHANG P F, ZHANG Y, GONG L, JI W, GAO M Y, LIU Y L, HAO X J. Effects of plant growth regulators on pericarp cell wall polysaccharide of Chinese jujube. Journal of Shanxi Agricultural University (Natural Science Edition), 2014, 34(2): 174-178. (in Chinese)
[17]	YANG Z E, WU Z, ZHANG C, HU E M, ZHOU R, JIANG F L. The composition of pericarp, cell aging, and changes in water absorption in two tomato genotypes: mechanism, factors, and potential role in fruit cracking. Acta Physiologiae Plantarum, 2016, 38(9): 215. doi: 10.1007/s11738-016-2228-1
[18]	CHOI J H, LEE B, GU M M, LEE U Y, KIM M S, JUNG S K, CHOI H S. Course of fruit cracking in ‘Whansan’ pears. Horticulture, Environment, and Biotechnology, 2020, 61(1): 51-59. doi: 10.1007/s13580-019-00200-1
[19]	杨磊, 冯贝贝, 靳娟, 樊丁宇, 刘晶, 克里木∙伊明, 郝庆. 新疆6个大果红枣裂果性差异及其内在原因分析. 西北植物学报, 2021, 41(8)1364-1370.
	YANG L, FENG B B, JIN J, FAN D Y, LIU J, KELIMU∙YIMIN, HAO Q. Differences in fruit cracking of six big fruit type jujube cultivars from Xinjiang and its internal causes. Acta Botanica Boreali- Occidentalia Sinica, 2021, 41(8): 1364-1370. (in Chinese)
[20]	CHOI D, KIM J H, LEE Y. Expansins in plant development// Advances in Botanical Research. Amsterdam: Elsevier, 2008: 47-97.
[21]	SEKI Y, KIKUCHI Y, YOSHIMOTO R, ABURAI K, KANAI Y, RUIKE T, IWABATA K, GOITSUKA R, SUGAWARA F, ABE M, SAKAGUCHI K. Promotion of crystalline cellulose degradation by expansins from Oryza sativa. Planta, 2015, 241(1): 83-93. doi: 10.1007/s00425-014-2163-6
[22]	MINOIA S, BOUALEM A, MARCEL F, TROADEC C, QUEMENER B, CELLINI F, PETROZZA A, VIGOUROUX J, LAHAYE M, CARRIERO F, BENDAHMANE A. Induced mutations in tomato SlExp1 alter cell wall metabolism and delay fruit softening. Plant Science, 2016, 242: 195-202. doi: 10.1016/j.plantsci.2015.07.001
[23]	KASAI S, HAYAMA H, KASHIMURA Y, KUDO S, OSANAI Y. Relationship between fruit cracking and expression of the expansin gene MdEXPA3 in ‘Fuji’ apples (Malus domestica Borkh.). Scientia Horticulturae, 2008, 116(2): 194-198. doi: 10.1016/j.scienta.2007.12.002
[24]	WANG Y, LU W J, LI J G, JIANG Y M. Differential expression of two expansin genes in developing fruit of cracking-susceptible and-resistant Litchi cultivars. Journal of the American Society for Horticultural Science, 2006, 131(1): 118-121. doi: 10.21273/JASHS.131.1.118
[25]	辛海青, 周军永, 孙耀星, 穆文磊, 杨健, 马福利, 孙俊, 薛峥嵘, 陆丽娟, 孙其宝. 枣易裂与抗裂品种灌水后果皮结构和扩张蛋白基因表达差异研究. 园艺学报, 2021, 48(9): 1785-1793. doi: 10.16420/j.issn.0513-353x.2020-0903
	XIN H Q, ZHOU J Y, SUN Y X, MU W L, YANG J, MA F L, SUN J, XUE Z R, LU L J, SUN Q B. Differences in the pericarp structure and the expression of expansin genes after irrigation between easily cracked and resistant jujube. Acta Horticulturae Sinica, 2021, 48(9): 1785-1793. (in Chinese) doi: 10.16420/j.issn.0513-353x.2020-0903
[26]	GRABHERR M G, HAAS B J, YASSOUR M, LEVIN J Z, THOMPSON D A, AMIT I, ADICONIS X, FAN L, RAYCHOWDHURY R, ZENG Q D, CHEN Z H, MAUCELI E, HACOHEN N, GNIRKE A, RHIND N, DI PALMA F, BIRREN B W, NUSBAUM C, LINDBLAD-TOH K, FRIEDMAN N, REGEV A. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nature Biotechnology, 2011, 29(7): 644-652. doi: 10.1038/nbt.1883 pmid: 21572440
[27]	BUCHFINK B, XIE C, HUSON D H. Fast and sensitive protein alignment using DIAMOND. Nature Methods, 2015, 12(1): 59-60. doi: 10.1038/nmeth.3176 pmid: 25402007
[28]	邓泱泱, 荔建琦, 吴松锋, 朱云平, 陈耀文, 贺福初. nr数据库分析及其本地化. 计算机工程, 2006, 32(5): 71-73, 76.
	DENG Y Y, LI J Q, WU S F, ZHU Y P, CHEN Y W, HE F C.Integrated nr database in protein annotation system and its localization. Computer Engineering, 2006, 32(5): 71-73, 76. (in Chinese)
[29]	APWEILER R, BAIROCH A, WU C H, BARKER W C, BOECKMANN B, FERRO S, GASTEIGER E, HUANG H Z, LOPEZ R, MAGRANE M, MARTIN M J, NATALE D A, O'DONOVAN C, REDASCHI N, YEH L S L. UniProt: The universal protein knowledgebase. Nucleic Acids Research, 2004, 32: D115-D119.
[30]	TATUSOV R L, GALPERIN M Y, NATALE D A, KOONIN E V.The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Research, 2000, 28(1): 33-36.
[31]	KOONIN E V, FEDOROVA N D, JACKSON J D, JACOBS A R, KRYLOV D M, MAKAROVA K S, MAZUMDER R, MEKHEDOV S L, NIKOLSKAYA A N, RAO B S, ROGOZIN I B, SMIRNOV S, SOROKIN A V, SVERDLOV A V, VASUDEVAN S, WOLF Y I, YIN J J, NATALE D A. A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes. Genome Biology, 2004, 5(2): R7. doi: 10.1186/gb-2004-5-2-r7 pmid: 14759257
[32]	HUERTA-CEPAS J, SZKLARCZYK D, FORSLUND K, COOK H, HELLER D, WALTER M C, RATTEI T, MENDE D R, SUNAGAWA S, KUHN M, JENSEN L J, VON MERING C, BORK P. eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences. Nucleic Acids Research, 2016, 44: D286-D293.
[33]	KANEHISA M, GOTO S, KAWASHIMA S, OKUNO Y, HATTORI M. The KEGG resource for deciphering the genome. Nucleic Acids Research, 2004, 32(Suppl_1): D277-D280.
[34]	XIE C, MAO X Z, HUANG J J, DING Y, WU J M, DONG S, KONG L, GAO G, LI C Y, WEI L P. KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases. Nucleic Acids Research, 2011, 39(Suppl_2): W316-W322.
[35]	JONES P, BINNS D, CHANG H Y, FRASER M, LI W Z, MCANULLA C, MCWILLIAM H, MASLEN J, MITCHELL A, NUKA G, PESSEAT S, QUINN A F, SANGRADOR-VEGAS A, SCHEREMETJEW M, YONG S Y, LOPEZ R, HUNTER S. InterProScan 5: Genome-scale protein function classification. Bioinformatics, 2014, 30(9): 1236-1240. doi: 10.1093/bioinformatics/btu031 pmid: 24451626
[36]	EDDY S R. Profile hidden Markov models. Bioinformatics, 1998, 14(9): 755-763. doi: 10.1093/bioinformatics/14.9.755 pmid: 9918945
[37]	FINN R D, TATE J, MISTRY J, COGGILL P C, SAMMUT S J, HOTZ H R, CERIC G, FORSLUND K, EDDY S R, SONNHAMMER E L L, BATEMAN A.The Pfam protein families database. Nucleic Acids Research, 2008, 36: D281-D288.
[38]	LOVE M I, HUBER W, ANDERS S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biology, 2014, 15(12): 550. doi: 10.1186/s13059-014-0550-8
[39]	张锐, 周开兵. 荔枝果实膨大期果皮总RNA提取方法的筛选. 中国南方果树, 2013, 42(5): 11-14.
	ZHANG R, ZHOU K B. Screening of the methods for extraction of total RNA from Litchi pericarp at the swollen stage. South China Fruits, 2013, 42(5): 11-14. (in Chinese)
[40]	SCHMITTGEN T D, LIVAK K J. Analyzing real-time PCR data by the comparative C_T method. Nature Protocols, 2008, 3(6): 1101-1108. doi: 10.1038/nprot.2008.73
[41]	WEI W, YANG C, LUO J, LU C M, WU Y J, YUAN S. Synergism between cucumber α-expansin, fungal endoglucanase and pectin lyase. Journal of Plant Physiology, 2010, 167(14): 1204-1210. doi: 10.1016/j.jplph.2010.03.017
[42]	COSGROVE D J. Loosening of plant cell walls by expansins. Nature, 2000, 407(6802): 321-326. doi: 10.1038/35030000
[43]	WANG X Y, HUANG B R. Lipid- and calcium-signaling regulation of HsfA2c-mediated heat tolerance in tall fescue. Environmental and Experimental Botany, 2017, 136: 59-67. doi: 10.1016/j.envexpbot.2017.01.008
[44]	GAI W X, MA X, LI Y, XIAO J J, KHAN A, LI Q H, GONG Z H. CaHsfA1d improves plant thermotolerance via regulating the expression of stress- and antioxidant-related genes. International Journal of Molecular Sciences, 2020, 21(21): 8374. doi: 10.3390/ijms21218374
[45]	ZHAO Y, YU W G, HU X Y, SHI Y H, LIU Y, ZHONG Y F, WANG P, DENG S Y, NIU J, YU X D. Physiological and transcriptomic analysis revealed the involvement of crucial factors in heat stress response of Rhododendron hainanense. Gene, 2018, 660: 109-119. doi: 10.1016/j.gene.2018.03.082
[46]	CHO J H, CHOI M N, YOON K H, KIM K N.Ectopic expression of SjCBL1, calcineurin B-like 1 gene from Sedirea japonica, rescues the salt and osmotic stress hypersensitivity in Arabidopsis cbl1 mutant. Frontiers in Plant Science, 2018, 9: 1188.
[47]	XU G Y, LI M J, ZHANG H, CHEN Q S, JIN L F, ZHENG Q X, LIU P P, CAO P J, CHEN X, ZHAI N, ZHOU H N. NtRLK5, a novel RLK-like protein kinase from Nitotiana tobacum, positively regulates drought tolerance in transgenic Arabidopsis. Biochemical and Biophysical Research Communications, 2018, 503(3): 1235-1240. doi: 10.1016/j.bbrc.2018.07.030
[48]	XU M, LI H, LIU Z N, WANG X H, XU P, DAI S J, CAO X, CUI X Y. The soybean CBL-interacting protein kinase, GmCIPK2, positively regulates drought tolerance and ABA signaling. Plant Physiology and Biochemistry, 2021, 167: 980-989. doi: 10.1016/j.plaphy.2021.09.026 pmid: 34583133
[49]	LI C X, ZHANG W L, YUAN M, JIANG L N, SUN B, ZHANG D J, SHAO Y, LIU A Q, LIU X Q, MA J H. Transcriptome analysis of osmotic-responsive genes in ABA-dependent and-independent pathways in wheat (Triticum aestivum L.) roots. PeerJ, 2019, 7: e6519.
[50]	REDILLAS M C F R, JEONG J S, KIM Y S, JUNG H, BANG S W, CHOI Y D, HA S H, REUZEAU C, KIM J K. The overexpression ofOsNAC9alters the root architecture of rice plants enhancing drought resistance and grain yield under field conditions. Plant Biotechnology Journal, 2012, 10(7): 792-805. doi: 10.1111/pbi.2012.10.issue-7
[51]	SUN X L, SUN M Z, LUO X, DING X D, JI W, CAI H, BAI X, LIU X F, ZHU Y M. A Glycine soja ABA-responsive receptor-like cytoplasmic kinase, GsRLCK, positively controls plant tolerance to salt and drought stresses. Planta, 2013, 237(6): 1527-1545. doi: 10.1007/s00425-013-1864-6
[52]	DAS A, BASU P, KUMAR M, ANSARI J, SHUKLA A, THAKUR S, SINGH P, DATTA S, CHATURVEDI S, SHESHSHAYEE M, BANSAL K, SINGH N. Transgenic chickpea (Cicer arietinum L.) harbouring AtDREB1a are physiologically better adapted to water deficit. BMC Plant Biology, 2021, 21: 39. doi: 10.1186/s12870-020-02815-4
[53]	HU W, LV Y Y, LEI W R, LI X, CHEN Y H, ZHENG L Q, XIA Y, SHEN Z G. Cloning and characterization of the Oryza sativa wall-associated kinase gene OsWAK11 and its transcriptional response to abiotic stresses. Plant and Soil, 2014, 384(1/2): 335-346. doi: 10.1007/s11104-014-2204-8
[54]	ZANDALINAS S I, RIVERO R M, MARTÍNEZ V, GÓMEZ- CADENAS A, ARBONA V. Tolerance of citrus plants to the combination of high temperatures and drought is associated to the increase in transpiration modulated by a reduction in abscisic acid levels. BMC Plant Biology, 2016, 16: 105. doi: 10.1186/s12870-016-0791-7 pmid: 27121193
[55]	HASANUZZAMAN M, NAHAR K, ALAM M M, FUJITA M. Modulation of antioxidant machinery and the methylglyoxal detoxification system in selenium-supplemented Brassica napus seedlings confers tolerance to high temperature stress. Biological Trace Element Research, 2014, 161(3): 297-307. doi: 10.1007/s12011-014-0120-7
[56]	BATCHO A A, SARWAR M B, RASHID B, HASSAN S, HUSNAIN T. Heat shock protein gene identified from Agave sisalana (AsHSP70) confers heat stress tolerance in transgenic cotton (Gossypium hirsutum). Theoretical and Experimental Plant Physiology, 2021, 33(2): 141-156. doi: 10.1007/s40626-021-00200-6
[57]	CONTRAN N, TONELLI M, CROSTI P, CERANA R, MALERBA M. Antioxidant system in programmed cell death of sycamore (Acer pseudoplatanus L.) cultured cells. Acta Physiologiae Plantarum, 2012, 34(2): 617-629. doi: 10.1007/s11738-011-0862-1

Metrics

Viewed

Full text

Abstract

Cited

Shared

Discussed

Comments

Recommended 0

No Suggested Reading articles found!

基因号 Gene ID	功能注释 Functional annotation	正向和反向引物序列 Forward and reverse primer sequences (5'-3')
c22288.graph_c0	脱水响应元件结合蛋白 Dehydration-responsive element-binding protein	F: AGGTAAAGGAGGACCGGAGA
c22288.graph_c0	脱水响应元件结合蛋白 Dehydration-responsive element-binding protein	R: ATTAAGCCGTGCACAAGGAC
c39020.graph_c1	未知蛋白 Uncharacterized protein	F: CGTTTGAACCGTAGGAGCAT
c39020.graph_c1	未知蛋白 Uncharacterized protein	R: GGCATAGGGCTGTGTTTGTT
c35353.graph_c1	扩张蛋白-A10 Expansin-A10	F: TAAGGTCACCACAAGCGATG
c35353.graph_c1	扩张蛋白-A10 Expansin-A10	R: GTGGCTCTAGCGGAATTGAG
c35353.graph_c0	扩张蛋白-A1 Expansin-A1	F: AGTTTTGGCCCCAGTTTCTT
c35353.graph_c0	扩张蛋白-A1 Expansin-A1	R: GGAGGCATCAGGTTCACAAT
c19677.graph_c0	扩张蛋白-A1 Expansin-A1	F: AGGAAGGGAGGCATCAGATT
c19677.graph_c0	扩张蛋白-A1 Expansin-A1	R: AGTTCCTTGACATGGGTTGC
c17406.graph_c1	生长素响应蛋白IAA30 Auxin-responsive protein IAA30	F: AGCCAGAGCTGCAAGTTGTT
c17406.graph_c1	生长素响应蛋白IAA30 Auxin-responsive protein IAA30	R: ATCATCCCCCACACTTGGTA
c37618.graph_c0	生长素响应蛋白IAA26 Auxin-responsive protein IAA26	F: GCAGGAGCAGTCCTTTTCTG
c37618.graph_c0	生长素响应蛋白IAA26 Auxin-responsive protein IAA26	R: CTCACAGCCCTGTTGCACTA
c36022.graph_c0	丝氨酸/苏氨酸蛋白激酶 Probable serine/threonine-protein kinase	F: TCCCGAAAATCTCCATCTTG
c36022.graph_c0	丝氨酸/苏氨酸蛋白激酶 Probable serine/threonine-protein kinase	R: ATTGGAAAGGCACTGACCAC
c28883.graph_c0	丝氨酸/苏氨酸蛋白激酶 Serine/threonine-protein kinase	F: TGGTCACTTTTGGGGAAGAG
c28883.graph_c0	丝氨酸/苏氨酸蛋白激酶 Serine/threonine-protein kinase	R: TGTCACCATCTCCCAAATCA
c17721.graph_c0	热激响应转录因子A-4b Heat stress transcription factor A-4b	F: TGCTGTCTCATCCTCAGTGG
c17721.graph_c0	热激响应转录因子A-4b Heat stress transcription factor A-4b	R: GGGTATTGCGACCAGTGTCT
c34836.graph_c0	热激响应转录因子A-8 Heat stress transcription factor A-8	F: AAAAAGCCAGCAGCAGATGT
c34836.graph_c0	热激响应转录因子A-8 Heat stress transcription factor A-8	R: CCATGCGCCAGTTATTTTCT
GQ389668.1	肌动蛋白 Actin	F: AGAGCATCCGGTTCTTCTCA
GQ389668.1	肌动蛋白 Actin	R: TTGCACAGCAAAGAATCAGG

序列长度 Length range (bp)	转录本Transcript		Unigene
序列长度 Length range (bp)	数量 Total number	比例 Percentage (%)	数量 Total number	比例 Percentage (%)
200-300	21084	6.90	17974	33.87
300-500	17482	5.72	11546	21.75
500-1000	26848	8.78	8780	16.54
1000-2000	64480	21.09	6155	11.60
2000+	175863	57.52	8620	16.24
总数量 Total number	305757		53075
总长度 Total Length	783171572		54363867
N50长度 N50 Length	3486		2329
平均长度 Mean Length	2561		1024

比较组 Comparison	所有差异基因数量 All DEG number	上调基因 Up-regulated DEG	下调基因 Down-regulated DEG
A1 vs A3	752	441	311
A2 vs A3	908	665	243
A1 vs A2	1650	848	802
B1 vs B3	1875	1074	801
B2 vs B3	97	71	26
B1 vs B2	1073	565	508

时期 Stage	基因号 Gene ID	基因表达量 FPKM			错误发现率 FDR			功能注释 Functional annotation
时期 Stage	基因号 Gene ID	1	2	3	1 vs 3	1 vs 2	2 vs 3	功能注释 Functional annotation
A	c35353.graph_c0	723.06	1041.65	280.40	4.30E-02	-	2.87E-07	扩张蛋白-A1 Expansin-A1
B	c19677.graph_c0	1472.25	1252.20	542.02	2.37E-12	-	6.02E-10	扩张蛋白-A1 Expansin-A1

时期Stage	基因号 Gene ID	基因表达量 FPKM			错误发现率 FDR			功能注释 Functional annotation
时期Stage	基因号 Gene ID	1	2	3	1 vs 3	1 vs 2	2 vs 3	功能注释 Functional annotation
A	c17406.graph_c1	4.44	7.73	14.15	1.49E-02	-	2.45E-02	生长素响应蛋白Auxin-responsive protein IAA30
B	c37618.graph_c0	16.51	15.89	29.42	1.34E-02	-	8.54E-03	生长素响应蛋白Auxin-responsive protein IAA26

A Transcriptome Analysis Identifies Candidate Genes Related to Fruit Cracking in Pomelo Fruits

RichHTML

PDF

Abstract

Cite this article

share this article

Figures/Tables 14

References 57

Related Articles 15

Metrics

Comments

Recommended 0

[1]	XIAO Tao, LI Hui, LUO Wei, YE Tao, YU Huan, CHEN YouBo, SHI YuShi, ZHAO DePeng, WU Yun. Screening of Candidate Genes for Green Shell Egg Shell Color Traits in Chishui Black Bone Chicken Based on Transcriptome Sequencing [J]. Scientia Agricultura Sinica, 2023, 56(8): 1594-1605.
[2]	LI Hui, ZHANG YuFeng, LI XiaoGang, WANG ZhongHua, LIN Jing, CHANG YouHong. Identification of Salt-Tolerant Transcription Factors in the Roots of Pyrus betulaefolia by the Association Analysis of Genome-Wide DNA Methylation and Transcriptome [J]. Scientia Agricultura Sinica, 2023, 56(7): 1377-1390.
[3]	LI YiPu, TONG LiXiu, LIN YaNan, SU ZhiJun, BAO HaiZhu, WANG FuGui, LIU Jian, QU JiaWei, HU ShuPing, SUN JiYing, WANG ZhiGang, YU XiaoFang, XU MingLiang, GAO JuLin. Investigation of Low Nitrogen Tolerance of ZmCCT10 in Maize [J]. Scientia Agricultura Sinica, 2023, 56(6): 1035-1044.
[4]	QU Qing, LIU Ning, ZOU JinPeng, ZHANG YaXuan, JIA Hui, SUN ManLi, CAO ZhiYan, DONG JinGao. Screening of Differential Genes and Analysis of Metabolic Pathways in the Interaction Between Fusarium verticillioides and Maize Kernels [J]. Scientia Agricultura Sinica, 2023, 56(6): 1086-1101.
[5]	WANG JianFeng, CHENG JiaXin, SHU WeiXue, ZHANG YanRu, WANG XiaoJie, KANG ZhenSheng, TANG ChunLei. Functional Analysis of Effector Hasp83 in the Pathogenicity of Puccinia striiformis f. sp. tritici [J]. Scientia Agricultura Sinica, 2023, 56(5): 866-878.
[6]	ZHANG Xin, YANG XingYu, ZHANG ChaoRan, ZHANG Chong, ZHENG HaiXia, ZHANG XianHong. Identification and Expression Analysis of Heat Shock Protein Superfamily Genes in Callosobruchus chinensis [J]. Scientia Agricultura Sinica, 2023, 56(19): 3814-3828.
[7]	YOU YuWan,ZHANG Yu,SUN JiaYi,ZHANG Wei. Genome-Wide Identification of NAC Family and Screening of Its Members Related to Prickle Development in Rosa chinensis Old Blush [J]. Scientia Agricultura Sinica, 2022, 55(24): 4895-4911.
[8]	YOU JiaLing,LI YouMei,SUN MengHao,XIE ZhaoSen. Analysis Reveals the Differential Expression of Genes Related to Starch Accumulation in Chloroplast of Leaf with Different Ages in Pinot Noir Grape [J]. Scientia Agricultura Sinica, 2022, 55(21): 4265-4278.
[9]	SUN BaoJuan,WANG Rui,SUN GuangWen,WANG YiKui,LI Tao,GONG Chao,HENG Zhou,YOU Qian,LI ZhiLiang. Transcriptome and Metabolome Integrated Analysis of Epistatic Genetics Effects on Eggplant Peel Color [J]. Scientia Agricultura Sinica, 2022, 55(20): 3997-4010.
[10]	LIU Xin,ZHANG YaHong,YUAN Miao,DANG ShiZhuo,ZHOU Juan. Transcriptome Analysis During Flower Bud Differentiation of Red Globe Grape [J]. Scientia Agricultura Sinica, 2022, 55(20): 4020-4035.
[11]	GUO YongChun, WANG PengJie, JIN Shan, HOU Binghao, WANG ShuYan, ZHAO Feng, YE NaiXing. Identification of Co-Expression Gene Related to Tea Plant Response to Glyphosate Based on WGCNA [J]. Scientia Agricultura Sinica, 2022, 55(1): 152-166.
[12]	HuaZhi CHEN,YuanChan FAN,HaiBin JIANG,Jie WANG,XiaoXue FAN,ZhiWei ZHU,Qi LONG,ZongBing CAI,YanZhen ZHENG,ZhongMin FU,GuoJun XU,DaFu CHEN,Rui GUO. Improvement of Nosema ceranae Genome Annotation Based on Nanopore Full-Length Transcriptome Data [J]. Scientia Agricultura Sinica, 2021, 54(6): 1288-1300.
[13]	DU Yu,ZHU ZhiWei,WANG Jie,WANG XiuNa,JIANG HaiBin,FAN YuanChan,FAN XiaoXue,CHEN HuaZhi,LONG Qi,CAI ZongBing,XIONG CuiLing,ZHENG YanZhen,FU ZhongMin,CHEN DaFu,GUO Rui. Construction and Annotation of Ascosphaera apis Full-Length Transcriptome Utilizing Nanopore Third-Generation Long-Read Sequencing Technology [J]. Scientia Agricultura Sinica, 2021, 54(4): 864-876.
[14]	ZHAO WeiSong,GUO QingGang,DONG LiHong,WANG PeiPei,SU ZhenHe,ZHANG XiaoYun,LU XiuYun,LI SheZeng,MA Ping. Transcriptome and Proteome Analysis of Bacillus subtilis NCD-2 Response to L-proline from Cotton Root Exudates [J]. Scientia Agricultura Sinica, 2021, 54(21): 4585-4600.
[15]	LIU Lian,TANG ZhiPeng,LI FeiFei,XIONG Jiang,LÜ BiWen,MA XiaoChuan,TANG ChaoLan,LI ZeHang,ZHOU Tie,SHENG Ling,LU XiaoPeng. Fruit Quality in Storage, Storability and Peel Transcriptome Analysis of Rong’an Kumquat, Huapi Kumquat and Cuimi Kumquat [J]. Scientia Agricultura Sinica, 2021, 54(20): 4421-4433.

时期Stage	基因号 Gene ID	基因表达量 FPKM			错误发现率 FDR			功能注释 Functional annotation
时期Stage	基因号 Gene ID	1	2	3	1 vs 3	1 vs 2	2 vs 3	功能注释 Functional annotation
A	c36022.graph_c0	29.16	31.34	60.97	3.14E-02	-	3.14E-02	丝氨酸/苏氨酸蛋白激酶 Probable serine/threonine-protein kinase
A	c38468.graph_c0	8.28	15.26	4.44	2.60E-02	4.83E-03	2.49E-08	类受体蛋白激酶Receptor-like protein kinase
A	c14973.graph_c0	1.25	1.50	4.75	1.73E-02	-	1.61E-02	钙结合蛋白Calcium-binding protein
A	c36157.graph_c0	11.00	5.92	23.33	1.42E-02	4.43E-02	8.86E-12	钙转运蛋白ATP酶12 Calcium-transporting ATPase 12
A	c21280.graph_c0	118.37	96.38	227.39	1.72E-02	-	3.40E-06	小磷酸酶样蛋白 Small phosphatase-like protein 2
A	c36839.graph_c1	127.36	83.10	51.02	3.37E-10	-	1.72E-04	类钙调磷酸酶B亚基Calcineurin B-like protein 9
B	c28883.graph_c0	2.56	4.54	9.12	1.48E-08	2.33E-02	1.81E-02	丝氨酸/苏氨酸蛋白激酶 Serine/threonine-protein kinase
B	c39163.graph_c0	0.79	2.90	6.61	3.09E-28	2.59E-09	3.48E-02	酪氨酸、丝氨酸/苏氨酸激酶 Tyrosine and serine/threonine kinase
B	c34263.graph_c0	4.91	5.32	9.33	8.58E-05	-	4.67E-03	类受体蛋白激酶Receptor-like protein kinase
B	c38550.graph_c0	1.14	1.39	6.23	2.78E-08	-	2.05E-04	细胞壁相关受体激酶5 Wall-associated receptor kinase 5

时期Stage	基因号 Gene ID	基因表达量 FPKM			错误发现率 FDR			功能注释 Functional annotation
时期Stage	基因号 Gene ID	1	2	3	1 vs 3	1 vs 2	2 vs 3	功能注释 Functional annotation
A	c17721.graph_c0	17.77	23.18	45.26	1.29E-05	-	2.67E-03	热激响应转录因子A-4b Heat stress transcription factor A-4b
A	c22288.graph_c0	6.71	5.62	19.10	2.29E-03	-	2.53E-03	脱水响应元件结合蛋白2C Dehydration-responsive element-binding protein 2C
A	c26460.graph_c0	1.54	2.93	11.17	9.95E-03	-	1.77E-04	bHLH25转录因子 Transcription factor bHLH25
A	c34522.graph_c0	3.74	3.85	1.85	3.97E-03	-	3.47E-02	bHLH25转录因子 Transcription factor bHLH155
A	c38390.graph_c5	18.11	20.61	47.19	8.50E-06	-	8.14E-04	MYC2转录因子Transcription factor MYC2
A	c29615.graph_c0	644.08	683.09	1201.43	2.26E-02	-	1.23E-04	MYC2转录因子Transcription factor MYC2
B	c34836.graph_c0	11.68	15.18	23.71	7.70E-05	-	6.15E-04	热激响应转录因子A-8 Heat stress transcription factor A-8
B	c22288.graph_c0	17.66	11.87	41.93	4.18E-02	-	7.88E-20	脱水响应元件结合蛋白2C Dehydration-responsive element-binding protein 2C
B	c37500.graph_c2	12.51	13.93	25.75	2.47E-03	-	2.11E-03	SRM1转录因子Transcription factor SRM1
B	c21303.graph_c0	0.70	1.19	2.85	5.24E-04	-	2.97E-02	BOA转录因子Transcription factor BOA
B	c31054.graph_c0	24.26	25.08	12.52	6.39E-04	-	1.24E-02	BIM1转录因子Transcription factor BIM1