[1]梁文化,孙旭超,岳红亮,等.水稻超大籽粒形成的重要基因和调控通路的转录组分析[J].江苏农业学报,2020,(04):801-813.[doi:doi:10.3969/j.issn.1000-4440.2020.04.001]
 LIANG Wen-hua,SUN Xu-chao,YUE Hong-liang,et al.Transcriptome analysis on critical genes and key pathways in extra-large grain development of rice[J].,2020,(04):801-813.[doi:doi:10.3969/j.issn.1000-4440.2020.04.001]
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水稻超大籽粒形成的重要基因和调控通路的转录组分析()
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江苏农业学报[ISSN:1006-6977/CN:61-1281/TN]

卷:
期数:
2020年04期
页码:
801-813
栏目:
遗传育种·生理生化
出版日期:
2020-08-31

文章信息/Info

Title:
Transcriptome analysis on critical genes and key pathways in extra-large grain development of rice
作者:
梁文化孙旭超岳红亮田铮陈涛赵庆勇朱镇赵凌赵春芳姚姝路凯王才林张亚东
(江苏省农业科学院粮食作物研究所/江苏省优质水稻工程技术研究中心/国家水稻改良中心南京分中心,江苏南京210014)
Author(s):
LIANG Wen-huaSUN Xu-chaoYUE Hong-liangTIAN ZhengCHEN TaoZHAO Qing-yongZHU ZhenZHAO LingZHAO Chun-fangYAO ShuLU KaiWANG Cai-linZHANG Ya-dong
(Institute of Food Crops, Jiangsu Academy of Agricultural Sciences/Jiangsu High Quality Rice R&D Center/Nanjing Branch of China National Center for Rice Improvement, Nanjing 210014, China)
关键词:
水稻粒型RNA-Seq幼穗转录组
Keywords:
ricegrain shapeRNA-Seqyoung panicletranscriptome
分类号:
S511.2+101
DOI:
doi:10.3969/j.issn.1000-4440.2020.04.001
文献标志码:
A
摘要:
以特大粒水稻品系TD70和小粒籼稻品种Kasalath不同发育时期的幼穗为材料,进行转录组测序。将获得的干净读长(Clean read)以日本晴(Nipponbare)基因组序列为参考序列进行比对得到唯一读长(即特异比对到参考基因组的read),利用FPKM(Fragments per kilobase of transcript per million fragments mapped)法计算基因的表达水平,用GO和KEGG数据库对差异表达基因(Differentially expressed genes, DEGs)进行功能注释、富集和代谢通路分析。结果表明,在水稻幼穗发育的早、中、后3个时期分别获得3 618个、4 183个和5 254个差异表达基因,共有4 374个差异表达基因得到基因本体(Gene ontology, GO)功能注释,主要涉及DNA结合、细胞进程、信号转导、细胞增殖、物质转运等方面。KEGG数据库分析结果显示,差异表达基因共涉及119条代谢通路,主要包括淀粉和蔗糖代谢通路、内质网中的蛋白质加工通路、激素信号转导通路、细胞周期蛋白通路等。
Abstract:
Using young panicles of extra-large grain rice TD70 and small grain indica rice Kasalath at different growth stages as materials, transcriptome sequencing was conducted. Unique read was acquired by comparing the obtained clean read with reference genome sequences from Nipponbare. Expression levels of genes were counted by fragments per kilobase of transcript per million fragments mapped (FPKM) method. Functional annotation, enrichment and metabolic pathway of the differentially expressed genes (DEGs) were analysed by using GO and KEGG databases. The results showed that 3 618, 4 183 and 5 254 DEGs were obtained in the early, middle and late stages of young panicle development, and a total of 4 374 DEGs were annotated with gene ontology (GO), mainly involving DNA binding, cellular processes, signal transduction, cell proliferation and material transfer, etc. The analysis results of KEGG database analysis indicated that DEGs referred to 119 metabolic pathways, mainly including starch and sucrose metabolism, protein processing in endoplasmic reticulum, hormone signal transduction, cyclin and so on.

参考文献/References:

[1]杨联松,白一松,张培江,等. 谷粒形状与稻米品质相关性研究[J]. 杂交水稻,2001,16(4):48-50, 54.
[2]徐正进,陈温福,马殿荣,等. 稻谷粒形与稻米主要品质性状的关系[J]. 作物学报,2004,30(9):894-900.
[3]FAN C C, XING Y Z, MAO H L, et al. GS3,a major QTL for grain length and weight and minor QTL for grain width and thickness in rice,encodes a putative transmembrane protein[J]. Theoretical and Applied Genetics,2006,112(6): 1164-1171.
[4]QI P, LIN Y S, SONG X J, et al. The novel quantitative trait locus GL3.1 controls rice grain size and yield by regulating Cyclin-T1;3[J]. Cell Research,2012,22(12): 1666-1680.
[5]ZHANG X J, WANG J F, HUANG J, et al. Rare allele of OsPPKL1 associated with grain length causes extra-large grain and a significant yield increase in rice[J]. Proceedings of the National Academy of Sciences,2012,109(52): 21534-21539.
[6]SI L Z, CHEN J Y, HUANG X H, et al. OsSPL13 controls grain size in cultivated rice[J]. Nature Genetics,2016,48(4): 447-456.
[7]YING J Z, MA M, BAI C, et al. TGW3,a major QTL that negatively modulates grain length and weight in rice[J]. Molecular Plant,2018,11(5): 750-753.
[8]LIU Q, HAN R X, WU K, et al. G-protein βγ subunits determine grain size through interaction with MADS-domain transcription factors in rice[J]. Nature Communications,2018,9(1): 1-12.
[9]ZHAO D S, LI Q F, ZHANG C Q, et al. GS9 acts as a transcriptional activator to regulate rice grain shape and appearance quality[J]. Nature Communications,2018,9(1): 1240.
[10]SONG X J, HUANG W, SHI M, et al. A QTL for rice grain width and weight encodes a previously unknown RING-type E3 ubiquitin ligase[J]. Nature Genetics,2007,39(5): 623-630.
[11]SHOMURA A, IZAWA T, EBANA K, et al. Deletion in a gene associated with grain size increased yields during rice domestication[J]. Nature Genetics,2008,40(8): 1023-1028.
[12]WENG J F, GU S H, WAN X Y, et al. Isolation and initial characterization of GW5,a major QTL associated with rice grain width and weight[J]. Cell Research,2008,18(12): 1199-1209.
[13]LI Y B, FAN C C, XING Y Z, et al. Natural variation in GS5 plays an important role in regulating grain size and yield in rice[J]. Nature Genetics,2011,43(12): 1266-1269.
[14]WANG Y X, XIONG G S, HU J, et al. Copy number variation at the GL7 locus contributes to grain size diversity in rice[J]. Nature Genetics,2015,47(8): 944-948.
[15]WANG S K, LI S, LIU Q, et al. The OsSPL16-GW7 regulatory module determines grain shape and simultaneously improves rice yield and grain quality[J]. Nature Genetics,2015,47(8): 949-954.
[16]WANG S K, WU K, YUAN Q B, et al. Control of grain size,shape and quality by OsSPL16 in rice[J]. Nature Genetics,2012,44(8): 950-954.
[17]WANG S S, WU K, QIAN Q, et al. Non-canonical regulation of SPL transcription factors by a human OTUB1-like deubiquitinase defines a new plant type rice associated with higher grain yield[J]. Cell Research,2017,27(9): 1142-1156.
[18]HUANG K, WANG D K, DUAN P G, et al. Wide and thick GRAIN 1,which encodes an otubain-like protease with deubiquitination activity,influences grain size and shape in rice[J]. Plant Journal,2017,91(5): 849-860.
[19]MAO H L, SUN S Y, YAO J L, et al. Linking differential domain functions of the GS3 protein to natural variation of grain size in rice[J]. Proceedings of the National Academy of Sciences, 2010,107(45): 19579-19584.
[20]SUN S Y, WANG L, MAO H L, et al. A G-protein pathway determines grain size in rice[J]. Nature Communications,2018,9(1): 851.
[21]LIU J F, CHEN J, ZHENG X M, et al. GW5 acts in the brassinosteroid signalling pathway to regulate grain width and weight in rice[J]. Nature Plants,2017, 3: 17043.
[22]XU C J, LIU Y, LI Y B, et al. Differential expression of GS5 regulates grain size in rice[J]. Journal of Experimental Botany,2015,66(9): 2611-2623.
[23]丁丹. 水稻5个粒型相关基因的分子标记开发与效应分析[D]. 南京:南京农业大学,2014.
[24]张亚东,张颖慧,董少玲,等. 特大粒水稻材料粒型性状的QTL检测[J]. 中国水稻科学,2013,27(2):122-128.
[25]ZHANG Y D, ZHENG J, LIANG Z K, et al. Verification and evaluation of grain QTLs using RILs from TD70 × Kasalath in rice[J]. Genetics & Molecular Research,2015,14(4): 14882-14892.
[26]ZHANG Y D, ZHAO Q Y, ZHAO C F. Distribution of seven grain genes and evaluation of their genetic effects on grain traits[J]. Pakistan Journal of Botany,2016,48(3): 1073-1079.
[27]WANG L, LI P H, BRUTNELL T P. Exploring plant transcriptomes using ultra high-throughput sequencing[J]. Briefings in Functional Genomics,2010,9(2): 118-128.
[28]GUO H B, MENDRIKAHY J N, XIE L, et al. Transcriptome analysis of neo-tetraploid rice reveals specific differential gene expressions associated with fertility and heterosis[J]. Scientific Reports,2017, 7: 40139.
[29]SHANKAR R, BHATTACHARJEE A, JAIN M. Transcriptome analysis in different rice cultivars provides novel insights into desiccation and salinity stress responses[J]. Scientific Reports, 2016, 6: 23719.
[30]GONZLEZ-SCHAIN N, DRENI L, LAWAS L M F, et al. Genome-wide transcriptome analysis during anthesis reveals new insights into the molecular basis of heat stress tesponses in tolerant and sensitive rice varieties[J]. Plant & Cell Physiology,2016,57(1): 57-68.
[31]WANG J, ZHANG Q, WANG Y, et al. Analysing the rice young panicle transcriptome reveals the gene regulatory network controlled by TRIANGULAR HULL1[J]. Rice,2019,12(1): 6.
[32]ZHANG W H, SUN P Y, HE Q, et al. Transcriptome analysis of near-isogenic line provides novel insights into genes associated with panicle traits regulation in rice[J]. PLoS One, 2018, 13(6): e0199077.
[33]KE S, LIU X J, LUAN X, et al. Genome-wide transcriptome profiling provides insights into panicle development of rice (Oryza sativa L.)[J]. Gene,2018,675: 285-300.
[34]TRAPNELL C, ROBERTS A, GOFF L, et al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks[J]. Nature Protocols,2012, 7(3): 562-578.
[35]KAWAHARA, Y BASTIDE M D L, HAMILTON J P, et al. Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data[J]. Rice,2013,6(1): 1-10.
[36]LI H, HANDSAKER B, WYSOKER A, et al. The sequence alignment/map (SAM) format and SAMtools[J]. Bioinformatics,2009,25(1/2): 1653-1654.
[37]LIVAK K J, SCHMITTGEN T D. Analysis of relative gene expression data using real-time quantitative PCR and the 2-△△Ct method[J]. Methods,2001,25(4): 402-408.
[38]YU J, XIONG H, ZHU X, et al. OsLG3 contributing to rice grain length and yield was mined by Ho-LAMap[J]. BMC Biology,2017,15(1): 28.
[39]LI N, XU R, LI Y H. Molecular networks of seed size control in plants[J]. Annual Review of Plant Biology,2019,70(1): 1-30.
[40]DUBOS C, STRACKE R, GROTEWOLD E, et al. MYB transcription factors in Arabidopsis[J]. Trends in Plant Science,2010,15(10): 573-581.

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备注/Memo

备注/Memo:
收稿日期:2019-12-11基金项目:国家自然科学基金面上项目(31771761);国家自然科学基金项目(31901485);江苏省农业科技自主创新基金项目[CX(18)1001];江苏省农业科学院院基金项目(003116111653);江苏省农业科学院粮食作物研究所所基金项目(LZS17-6);江苏省农业生物学重点实验室开放课题项目(4911707Z201705);江苏省重点研发计划项目(BE2018357);国家现代农业产业技术体系项目(CARS-01-62)作者简介:梁文化(1984-),男,山东临沂人,博士,助理研究员,主要从事水稻遗传育种研究。(E-mail)liangwenhua0228@126.com通讯作者:张亚东,(Tel)025-84390314;(E-mail)zhangyd@ jaas.ac.cn
更新日期/Last Update: 2020-09-08