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高粱(Sorghum bicolor)是禾本科(Poaceae)一年生草本植物，也是研究C4植物的模式生物。甜高粱相对于普通高粱有其独特的糖代谢积累机理，发掘其糖合成、运输和积累相关的调控基因和代谢途径，有助于糖分和碳源分配的遗传改良设计，又可为其他重要的C4作物提供参考。本研究结合基因组、转录组和代谢组等多组学数据，从蔗糖转运、蔗糖合成相关基因家族以及基因共表达网络等多个角度对甜高粱及高粱的组学数据进行比较分析。结果如下：(1)构建了甜高粱及普通高粱品种的泛基因组，大小为908 Mb,比单个参考基因组增加约24.6%,进行了核心基因、非核心基因以及基因组存在/缺失变异区域相关基因的分类统计及功能富集分析，对多样本多个时期的RNA-seq数据进行差异表达分析，构建基因共表达网络，对基因集进行筛选验证，进一步筛选得到了糖分相关基因；(2)利用12份不同时期的甜高粱(Rio)、高粱(BTx406)以及两者子代(R9188)的RNA-seq数据进行差异表达分析与基因共表达分析，通过与对应时期蔗糖浓度变化数据进行相关性分析，得到与蔗糖代谢相关的基因集。研究成果有助于揭示甜高粱与高粱糖分差异原因，为高粱品种改良及育种相关研究提供借鉴。
Abstract：Sorghum(Sorghum bicolor) is an annual herb of the Poaceae and a model organism for the study of C4 plants. Compared with ordinary sorghum, sweet sorghum has a unique mechanism of sugar metabolism and accumulation. Discovering the regulatory genes and metabolic pathways related to sugar synthesis, transportation and accumulation will not only help the genetic improvement design of its own sugar and carbon source allocation, but also provide a reference for other important C4 crops. In this study, combined with multi-omics data such as genome, transcriptome, and metabolome, the differences between sweet sorghum and sorghum were analyzed from multiple perspectives, such as sucrose transport, sucrose synthesis-related gene families and gene co-expression networks, and the following results were obtained.(1) The pan-genomes of sweet sorghum and common sorghum varieties were constructed with a size of 908 Mb, about 24.6% larger than a single reference genome. The classification statistics and functional enrichment of core and non-core genes, and genes related to the presence/absence variation regions of the genome were performed. The differential expression analysis was performed on RNA-seq data of multiple samples and multiple periods, gene co-expre-ssion network was constructed, gene set was screened and verified, and sugar-related genes were further screened through annotation;(2) 12 RNA-seq data of sweet sorghum(Rio), sorghum(BTx406) and their progeny(R9188) at different periods were used for differential expression analysis and gene co-expression analysis. The gene set related to sucrose metabolism was obtained by correlation analysis with sucrose concentration change data of corresponding period. These results will help to explore the difference in sugar content between sweet sorghum and sorghum, and provide reference for sorghum variety improvement and breeding.
Bihmidine S.,Baker R.F.,Hoffner C.,and Braun D.M.,2015,Sucrose accumulation in sweet sorghum stems occurs by apoplasmic phloem unloading and does not involve differential sucrose transporter expression,BMC Plant Biol.,15:186.
Bihmidine S.,Julius B.T.,Dweikat I.,and Braun D.M.,2016,Tonoplast Sugar Transporters (SbTSTs) putatively control sucrose accumulation in sweet sorghum stems,Plant Signal.Behav.,11:e1117721.
Calviňo M.,and Messing J.,2012,Sweet sorghum as a model system for bioenergy crops,Curr.Opin.Biotechnol.,23(3):323-329.
Chen L.Q.,Qu X.Q.,Hou B.H.,Sosso D.,Osorio S.,Fernie A.R.,and Frommer W.B.,2012,Sucrose efflux mediated by SWEET proteins as a key step for phloem transport,Science,335(6065):207-211.
Cingolani P.,Platts A.,Wang le L.,Coon M.,Nguyen T.,Wang L.,Land S.J.,Lu X.,and Ruden D.M.,2012,A program for annotating and predicting the effects of single nucleotide polymorphisms,SNPEff:SNPs in the genome of Drosophila melanogaster strain w1118;iso-2;iso-3,Fly (Austin),6(2):80-92.
Cooper E.A.,Brenton Z.W.,Flinn B.S.,Jenkins J.,Shu S.,Flowers D.,Luo F.,Wang Y.,Xia P.,Barry K.,Daum C.,Lipzen A.,Yoshinaga Y.,Schmutz J.,Saski C.,Vermerris W.,and Kresovich S.,2019,A new reference genome for Sorghum bicolor reveals high le-vels of sequence similarity between sweet and grain genotypes:implications for the genetics of sugar metabolism,BMC Genomics,20(1):420.
Delcher A.L.,Phillippy A.,Carlton J.,and Salzberg S.L.2002,Fast algorithms for large-scale genome alignment and comparison,Nucleic Acids Res.,30(11):2478-2483.
Emms D.M.,and Kelly S.,2015,OrthoFinder:solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy,Genome Biol.,16(1):157.
Hirsch C.N.,Foerster J.M.,Johnson J.M.,Sekhon R.S.,Muttoni G.,Vaillancourt B.,Peňagaricano F.,Lindquist E.,Pedraza M.A.,Barry K.,de Leon N.,Kaeppler S.M.,and Buell C.R.,2014,Insights into the maize pangenome and pan transcriptome,Plant Cell,26(1):121-135.
Kubo H,and Hayashi K.,2011,Characterization of root cells of anl2 mutant in Arabidopsis thaliana,Plant Sci.,180(5):679-685.
Leach K.A.,Tran T.M.,Slewinski T.L.,Meeley R.B.,and Braun D.M.,2017,Sucrose transporter2 contributes to maize growth,development,and crop yield,J.Integr.Plant Biol.,59(6):390-408.
Li H.,2011,A statistical framework for SNP calling,mutation discovery,association mapping and population genetical parameter estimation from sequencing data,Bioinformatics,27(21):2987-2993.
Li H.,Feng X.W.,and Chu C.,2020,The design and construction of reference pangenome graphs with minigraph,Genome Biol.,21(1):265.
Li Y.,Wang W.Q.,Feng Y.P.,Tu M.,Wittich P.E.,Bate N.J.,and Messing J.,2019,Transcriptome and metabolome reveal distinct carbon allocation patterns during internode sugar accumulation in different sorghum genotypes,Plant Biotechnol.J.,17(2):472-487.
Li Y.H.,Zhou G.,Ma J.,Jiang W.,Jin L.G.,Zhang Z.,Guo Y.,Zhang J.,Sui Y.,Zheng L.,Sui Y.,Zheng L.,Zhang S.S.,Zuo Q.,Shi X.H.,Li Y.F.,Zhang W.K.,Hu Y.,Kong G.,Hong H.L.,Tan B.,Song J.,Liu Z.X.,Wang Y.,Ruan H.,Yeung C.K.,Liu J.,Wang H.,Zhang L.J.,Guan R.X.,Wang K.J.,Li W.B.,Chen S.Y.,Chang R.Z.,Jiang Z.,Jackson S.A.,Li R.,and Qiu L.J.,2014,De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits,Nat.Biotechnol.,32(10):1045-1052.
Lu F.,Romay M.C.,Glaubitz J.C.,Bradbury P.J.,Elshire R.J.,Wang T.,Li Y.,Li Y.,Semagn K.,Zhang X.,Hernandez A.G.,Mikel M.A.,Soifer I.,Barad O.,and Buckler E.S.,2015,High-resolution genetic mapping of maize pan-genome sequence anchors,Nat.Commun.,6:6914.
Lunn J.E.,Delorge I.,Figueroa C.M.,van Dijck P.,and Stitt M.,2014,Trehalose metabolism in plants,Plant J.,79(4):544-567.
McCormick R.F.,Truong S.K.,Sreedasyam A.,Jenkins J.,Shu S.,Sims D.,Kennedy M.,Amirebrahimi M.,Weers B.D.,McKinley B.,Mattison A.,Morishige D.T.,Grimwood J.,Schmutz J.,and Mullet J.E.,2018,The Sorghum bicolor reference genome:improved assembly,gene annotations,a transcriptome atlas,and signatures of genome organization,Plant J.,93(2):338-354.
Milne R.J.,Byrt C.S.,Patrick J.W.,and Grof C.P.,2013,Are sucrose transporter expression profiles linked with patterns of biomass partitioning in Sorghum phenotypes?Front.Plant Sci.,4:223.
Mohamed M.F.M.,Emam M.M.,Salama K.H.A.,and Morsy A.A.,2021,Sorghum under saline conditions:responses,tolerance mechanisms,and management strategies,Planta,254(2):24.
Mullet J.,Morishige D.,McCormick R.,Truong S.,Hilley J.,McKinley B.,Anderson R.,Olson S.N.,and Rooney W.,2014,Energy sorghum—a genetic model for the design of C4 grass bioenergy crops,J.Exp.Bot.,65(13):3479-3489.
Otasek D.,Morris J.H.,Bou?as J.,Pico A.R.,and Demchak B.,2019,Cytoscape Automation:empowering workflow-based network analysis,Genome Biol.,20(1):185.
Paterson A.H.,Bowers J.E.,Bruggmann R.,Dubchak I.,Grimwood J.,Gundlach H.,Haberer G.,Hellsten U.,Mitros T.,Poliakov A.,Schmutz J.,Spannagl M.,Tang H.,Wang X.,Wicker T.,Bharti A.K.,Chapman J.,Feltus F.A.,Gowik U.,Grigoriev I.V.,Lyons E.,Maher C.A.,Martis M.,Narechania A.,Otillar R.P.,Penning B.W.,Salamov A.A.,Wang Y.,Zhang L.,Carpita N.C.,Freeling M.,Gingle A.R.,Hash C.T.,Keller B.,Klein P.,Kresovich S.,McCann M.C.,Ming R.,Peterson D.G.,Mehboob-ur-Rahman,Ware D.,Westhoff P.,Mayer K.F.,Messing J.,and Rokhsar D.S.,2009,The Sorghum bicolor genome and the diversification of grasses,Nature,457(7229):551-556.
Ruperao P.,Thirunavukkarasu N.,Gandham P.,Selvanayagam S.,Govindaraj M.,Nebie B.,Manyasa E.,Gupta R.,Das R.R.,Odeny D.A.,Gandhi H.,Edwards D.,Deshpande S.P.,and Rathore A.,2021,Sorghum pan-genome explores the functional utility for genomic-assisted breeding to accelerate the genetic gain,Front Plant Sci.,12:666342.
Sivitz A.B.,Hermand V.,Curie C.,and Vert G.,2012,Arabidopsis bHLH100 and bHLH101 control iron homeostasis via a FIT-independent pathway,PLoS ONE,7(9):e44843.
Smith O.,Nicholson W.V.,Kistler L.,Mace E.,Clapham A.,Rose P.,Stevens C.,Ware R.,Samavedam S.,Barker G.,Jordan D.,Fuller D.Q.,and Allaby R.G.,2019,A domestication history of dynamic adaptation and genomic deterioration in Sorghum,Nat.Plants,5(4):369-379.
Springer N.M.,Ying K.,Fu Y.,Ji T.,Yeh C.T.,Jia Y.,Wu W.,Richmond T.,Kitzman J.,Rosenbaum H.,Iniguez A.L.,Barbazuk W.B.,Jeddeloh J.A.,Nettleton D.,and Schnable P.S.,2009,Maize inbreds exhibit high levels of copy number variation (CNV) and presence/absence variation (PAV) in genome content,PLoS Genet.,5(11):e1000734.
Tettelin H.,Masignani V.,Cieslewicz M.J.,Donati C.,Medini D.,Ward N.L.,Angiuoli S.V.,Crabtree J.,Jones A.L.,Durkin A.S.,Deboy R.T.,Davidsen T.M.,Mora M.,Scarselli M.,Margarit y Ros I.,Peterson J.D.,Hauser C.R.,Sundaram J.P.,Nelson W.C.,Madupu R.,Brinkac L.M.,Dodson R.J.,Rosovitz M.J.,Sullivan S.A.,Daugherty S.C.,Haft D.H.,Selengut J.,Gwinn M.L.,Zhou L.,Zafar N.,Khouri H.,Radune D.,Dimitrov G.,Watkins K.,O′Connor K.J.,Smith S.,Utterback T.R.,White O.,Rubens C.E.,Grandi G.,Madoff L.C.,Kasper D.L.,Telford J.L.,Wessels M.R.,Rappuoli R.,and Fraser C.M.,2005,Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae:implications for the microbial "pan-genome",Proc.Natl.Acad.Sci.USA,102(39):13950-13955.
Trapnell C.,Hendrickson D.G.,Sauvageau M.,Goff L.,Rinn J.L.,and Pachter,L.,2013,Differential analysis of gene regulation at transcript resolution with RNA-seq,Nat.Biotechnol.,31(1):46-53.
Wang J.,Nayak S.,Koch K.and Ming R.,2013,Carbon partitioning in sugarcane (Saccharum species),Front Plant Sci.,4:201.
Wang L.,Chen J.T.,and Zhang Z.X.,2007,Strategies and progresses on cereal comparative genomics,Hereditas,29(9):1055-1060.(王磊，陈景堂，张祖新，2007,主要禾谷类作物比较基因组学研究策略与进展，遗传，29(9):1055-1060.)
Zhang L.M.,Leng C.Y.,Luo H.,Wu X.Y.,Liu Z.Q.,Zhang Y.M.,Zhang H.,Xia Y.,Shang L.,Liu C.M.,Hao D.Y.,Zhou Y.H.,Chu C.C.,Cai H.W.,and Jing H.C.,2018,Sweet sorghum originated through selection of Dry,a plant-specific NAC transcription factor gene,Plant Cell,30(10):2286-2307.
Zhao Q.,Feng Q.,Lu H.Y.,Li Y.,Wang A.H.,Tian Q.L.,Zhan Q.L.,Lu Y.Q.,Zhang L.,Huang T.,Wang Y.C.,Fan D.L.,Zhao Y.,Wang Z.Q.,Zhou C.C.,Chen J.Y.,Zhu C.R.,Li W.J.,Weng Q.J.,Xu Q.,Wang Z.X.,Wei X.H.,Han B.,and Huang X.H.,2018,Pan-genome analysis highlights the extent of genomic variation in cultivated and wild rice,Nat.Genet.,50(2):278-284.
Zheng L.Y.,Guo X.S.,He B.,Sun L.J.,Peng Y.,Dong S.S.,Liu T.F.,Jiang S.,Ramachandran S.,Liu C.M.,and Jing H.C.,2011,Genome-wide patterns of genetic variation in sweet and grain sorghum (Sorghum bicolor),Genome Biol.,12(11):R114.
基本信息:
DOI：10.13417/j.gab.041.001938
中图分类号:S566.5;S514
引用信息:
[1]王东欣,宋佳明,王令强,等.甜高粱与高粱的多组学比较分析[J].基因组学与应用生物学,2022,41(Z1):1938-1951.DOI:10.13417/j.gab.041.001938.
基金信息:
国家自然科学基金项目(31871269)资助
2022-05-30
2022-05-30
2022-05-30