Identification and map-based cloning of an EMS-induced mutation in wheat gene TaSP1 related to spike architecture.
Journal
TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik
ISSN: 1432-2242
Titre abrégé: Theor Appl Genet
Pays: Germany
ID NLM: 0145600
Informations de publication
Date de publication:
06 May 2024
06 May 2024
Historique:
received:
08
02
2024
accepted:
10
04
2024
medline:
6
5
2024
pubmed:
6
5
2024
entrez:
6
5
2024
Statut:
epublish
Résumé
A candidate gene TaSP1 related to spike shape was cloned, and the gene-specific marker was developed to efficiently track the superior haplotype in common wheat. Spike shape, an important factor that affects wheat grain yield, is mainly defined by spike length (SPL), spikelet number (SPN), and compactness. Zhoumai32 mutant 1160 (ZM1160), a mutant obtained from ethyl methane sulfonate (EMS) treatment of hexaploid wheat variety Zhoumai32, was used to identify and clone the candidate gene that conditioned the spike shape. Genetic analysis of an F
Identifiants
pubmed: 38709271
doi: 10.1007/s00122-024-04621-0
pii: 10.1007/s00122-024-04621-0
doi:
Substances chimiques
Ethyl Methanesulfonate
9H154DI0UP
Genetic Markers
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
119Subventions
Organisme : Key Technology R&D Program of Henan Province of China
ID : 225200810024
Organisme : Key Technology R&D Program of Henan Province of China
ID : 231111112900
Informations de copyright
© 2024. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.
Références
Abe A, Kosugi S, Yoshida K, Natsume S, Takagi H, Kanzaki H, Matsumura H, Yoshida K, Mitsuoka C, Tamiru M, Innan H, Cano L, Kamoun S, Terauchi R (2012) Genome sequencing reveals agronomically important loci in rice using MutMap. Nat Biotechnol 30:174–178. https://doi.org/10.1038/nbt.2095
doi: 10.1038/nbt.2095
pubmed: 22267009
Beales J, Turner A, Griffiths S, Snape JW, Laurie DA (2007) A Pseudo-Response Regulator is misexpressed in the photoperiod insensitive Ppd-D1a mutant of wheat (Triticum aestivum L.). Theor Appl Genet 115:721–733. https://doi.org/10.1007/s00122-007-0603-4
doi: 10.1007/s00122-007-0603-4
pubmed: 17634915
Boden SA, Cavanagh C, Cullis BR, Ramm K, Greenwood J, Finnegan EJ, Trevaskis B, Swain SM (2015) Ppd-1 is a key regulator of inflorescence architecture and paired spikelet development in wheat. Nat Plants 1:14016. https://doi.org/10.1038/nplants.2014.16
doi: 10.1038/nplants.2014.16
pubmed: 27246757
Cao SH, Xu DG, Hanif M, Xia XC, He ZH (2020) Genetic architecture underpinning yield component traits in wheat. Theor Appl Genet 133:1811–1823. https://doi.org/10.1007/s00122-020-03562-8
doi: 10.1007/s00122-020-03562-8
pubmed: 32062676
Cao J, Liu KY, Song WJ, Zhang JN, Yao YY, Xin MM, Hu ZR, Peng HR, Ni ZF, Sun QX, Du JK (2021) Pleiotropic function of the SQUAMOSA PROMOTER-BINDING PROTEIN-LIKE gene TaSPL14 in wheat plant architecture. Planta 253:44. https://doi.org/10.1007/s00425-020-03531-x
doi: 10.1007/s00425-020-03531-x
pubmed: 33481116
pmcid: 7822796
Chen YX, Chen YS, Shi CM, Huang ZB, Zhang Y, Li SK, Li Y, Ye J, Yu C, Li Z, Zhang XQ, Wang J, Yang HM, Fang L, Chen Q (2018) SOAPnuke: a MapReduce acceleration-supported software for integrated quality control and preprocessing of high-throughput sequencing data. GigaScience 7:1–6. https://doi.org/10.1093/gigascience/gix120
doi: 10.1093/gigascience/gix120
pubmed: 29659813
pmcid: 5827348
Chen Z, Cheng X, Chai L, Wang Z, Bian R, Li J, Zhao A, Xin M, Guo W, Hu Z, Peng H, Yao Y, Sun Q, Ni Z (2020a) Dissection of genetic factors underlying grain size and fine mapping of QTgw.cau-7D in common wheat (Triticum aestivum L.). Theor Appl Genet 133(1):149–162. https://doi.org/10.1007/s00122-019-03447-5
doi: 10.1007/s00122-019-03447-5
pubmed: 31570967
Chen ZY, Cheng XJ, Chai LL, Wang ZH, Du DJ, Wang ZH, Bian RL, Zhao AJ, Xin MM, Guo WL, Hu ZR, Peng HR, Yao YY, Sun QX, Ni ZF (2020b) Pleiotropic QTL influencing spikelet number and heading date in common wheat (Triticum aestivum L.). Theor Appl Genet 133:1825–1838. https://doi.org/10.1007/s00122-020-03556-6
doi: 10.1007/s00122-020-03556-6
pubmed: 32016554
Cheng XJ, Xin MM, Xu RB, Chen ZY, Cai WL, Chai LL, Xu HW, Jia L, Feng ZY, Wang ZH, Peng HR, Yao YY, Hu ZR, Guo WL, Ni ZF, Sun QX (2020) A single amino acid substitution in STKc_GSK3 kinase conferring semispherical grains and its implications for the origin of Triticum sphaerococcum. Plant Cell 32:923–934. https://doi.org/10.1105/tpc.19.00580
doi: 10.1105/tpc.19.00580
pubmed: 32060175
pmcid: 7145488
Deng QY, Kong ZX, Wu XX, Ma SW, Yuan Y, Jia HY, Ma ZQ (2019) Cloning of a COBL gene determining brittleness in diploid wheat using a MapRseq approach. Plant Sci 285:141–150. https://doi.org/10.1016/j.plantsci.2019.05.011
doi: 10.1016/j.plantsci.2019.05.011
pubmed: 31203879
Ding PY, Mo ZQ, Tang HP, MU Y, Deng M, Jiang QT, Liu YX, Chen GD, Chen GY, Wang JR, Li W, Qi PF, Jiang YF, Kang HY, Yan GJ, Wei YM, Zheng YL, Lan XJ, Ma J, (2022) A major and stable QTL for wheat spikelet number per spike validated in different genetic backgrounds. J Integr Agr 21:1551–1562. https://doi.org/10.1016/S2095-3119(20)63602-4
doi: 10.1016/S2095-3119(20)63602-4
Dixon LE, Farre A, Finnegan EJ, Orford S, Griffiths S, Boden SA (2018) Developmental responses of bread wheat to changes in ambient temperature following deletion of a locus that includes FLOWERING LOCUS T1. Plant Cell Environ 41:1715–1725. https://doi.org/10.1111/pce.13130
doi: 10.1111/pce.13130
pubmed: 29314053
pmcid: 6033019
Dobrovolskaya O, Pont C, Sibout R, Martinek P, Badaeva E, Murat F, Chosson A, Watanabe N, Prat E, Gautier N, Gautier V, Poncet C, Orlov YL, Krasnikov AA, Bergès H, Salina E, Laikova L, Salse J (2015) FRIZZY PANICLE drives supernumerary spikelets in bread wheat. Plant Physiol 167:189–199. https://doi.org/10.1104/pp.114.250043
doi: 10.1104/pp.114.250043
pubmed: 25398545
Fu DL, Szücs P, Yan LL, Helguera M, Skinner JS, Zitzewitz JV, Hayes PM, Dubcovsky J (2005) Large deletions within the first intron in VRN-1 are associated with spring growth habit in barley and wheat. Mol Genet Genomics 273:54–65. https://doi.org/10.1007/s00438-004-1095-4
doi: 10.1007/s00438-004-1095-4
pubmed: 15690172
Gao CX (2021) Genome engineering for crop improvement and future agriculture. Cell 184:1621–1635. https://doi.org/10.1016/j.cell.2021.01.005
doi: 10.1016/j.cell.2021.01.005
pubmed: 33581057
Gao F, Wen W, Liu J, Rasheed A, Yin G, Xia X, Wu X, He Z (2015) Genome-wide linkage mapping of QTL for yield components, plant height and yield-related physiological traits in the Chinese wheat cross Zhou 8425B/Chinese Spring. Front Plant Sci 6:1099. https://doi.org/10.3389/fpls.2015.01099
doi: 10.3389/fpls.2015.01099
pubmed: 26734019
pmcid: 4683206
Gao XQ, Wang N, Wang XL, Zhang XS (2019) Architecture of Wheat Inflorescence: Insights from Rice. Trends Plant Sci 24:802–809. https://doi.org/10.1016/j.tplants.2019.06.002
doi: 10.1016/j.tplants.2019.06.002
pubmed: 31257155
Greenwood JR, Finnegan EJ, Watanabe N, Trevaskis B, Swain SM (2017) New alleles of the wheat domestication gene Q reveal multiple roles in growth and reproductive development. Development 144:1959–1965. https://doi.org/10.1242/dev.146407
doi: 10.1242/dev.146407
pubmed: 28455374
Guo J, Shi W, Zhang Z, Cheng J, Sun D, Yu J, Li X, Guo P, Hao C (2018) Association of yield-related traits in founder genotypes and derivatives of common wheat (Triticum aestivum L.). BMC Plant Biol 18:38. https://doi.org/10.1186/s12870-018-1234-4
doi: 10.1186/s12870-018-1234-4
pubmed: 29458339
pmcid: 5819277
Hu WJ, Gao DR, Liao S, Cheng SH, Jia JZ, Xu WG (2023) Identification of a pleiotropic QTL cluster for Fusarium head blight resistance, spikelet compactness, grain number per spike and thousand-grain weight in common wheat. Crop J 11:672–677. https://doi.org/10.1016/j.cj.2022.09.007
doi: 10.1016/j.cj.2022.09.007
International Wheat Genome Sequencing Consortium (IWGSC) (2018) Shifting the limits in wheat research and breeding using a fully annotated reference genome. Science 361:eaar719. https://doi.org/10.1126/science.aar7191
doi: 10.1126/science.aar7191
Karkute SG, Kumar V, Tasleem M, Mishra DC, Chaturvedi KK, Rai A, Sevanthi AM, Gaikwad K, Sharma TR, Solanke AU (2022) Genome-wide analysis of von Willebrand factor A gene family in rice for its role in imparting biotic stress resistance with emphasis on rice blast disease. Rice Sci 29:375–384. https://doi.org/10.1016/j.rsci.2021.11.007
doi: 10.1016/j.rsci.2021.11.007
Kippes N, Zhu J, Chen A, Vanzetti L, Lukaszewski A, Nishida H, Kato K, Dvorak J, Dubcovsky J (2014) Fine mapping and epistatic interactions of the vernalization gene VRN-D4 in hexaploid wheat. Mol Genet Genomics 289:47–62. https://doi.org/10.1007/s00438-013-0788-y
doi: 10.1007/s00438-013-0788-y
pubmed: 24213553
Kong XC, Wang F, Geng SF, Guan JT, Tao S, Jia ML, Sun JL, Wang ZY, Wang K, Ye XG, Ma J, Liu DC, Wei YM, Zheng YL, Fu XD, Mao L, Lan XJ, Li AL (2022) The wheat AGL6-like MADS-box gene is a master regulator for floral organ identity and a target for spikelet meristem development manipulation. Plant Biotechnol J 20:75–88. https://doi.org/10.1111/pbi.13696
doi: 10.1111/pbi.13696
pubmed: 34487615
Kuzay S, Lin H, Li C, Chen S, Woods DP, Zhang J, Lan TY, Korff M, Dubcovsky J (2022) WAPO-A1 is the causal gene of the 7AL QTL for spikelet number per spike in wheat. PLoS Genet 18:e1009747. https://doi.org/10.1371/journal.pgen.1009747
doi: 10.1371/journal.pgen.1009747
pubmed: 35025863
pmcid: 8791482
Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23:2947–2948. https://doi.org/10.1093/bioinformatics/btm404
doi: 10.1093/bioinformatics/btm404
pubmed: 17846036
Li CX, Dubcovsky J (2008) Wheat FT protein regulates VRN1 transcription through interactions with FDL2. Plant J 55:543–554. https://doi.org/10.1111/j.1365-313X.2008.03526.x
doi: 10.1111/j.1365-313X.2008.03526.x
pubmed: 18433437
pmcid: 4739743
Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25:1754–1760. https://doi.org/10.1093/bioinformatics/btp324
doi: 10.1093/bioinformatics/btp324
pubmed: 19451168
pmcid: 2705234
Li YG, Liang HH, Bai SL, Zhou Y, Sun GL, Su YR, Gao AL, Zhang DL, Li SP (2017) Molecular characterization and variation of the celiac disease epitope domains among α-gliadin genes in Aegilops tauschii. J Agric Food Chem 65:3422–3429. https://doi.org/10.1021/acs.jafc.7b00338
doi: 10.1021/acs.jafc.7b00338
pubmed: 28391694
Li FJ, Wen WE, He ZH, Liu JD, Jin H, Cao SH, Geng HW, Yan J, Zhang PZ, Wang YX, Xia XC (2018) Genome-wide linkage mapping of yield-related traits in three Chinese bread wheat populations using high-density SNP markers. Theor Appl Genet 131:1903–1924. https://doi.org/10.1007/s00122-018-3122-6
doi: 10.1007/s00122-018-3122-6
pubmed: 29858949
Li K, Debernardi JM, Li CX, Lin HQ, Zhang CZ, Jernstedt J, Korff MV, Zhong JS, Dubcovsky J (2021a) Interactions between SQUAMOSA and SHORT VEGETATIVE PHASE MADS-box proteins regulate meristem transitions during wheat spike development. Plant Cell 33:3621–3644. https://doi.org/10.1093/plcell/koab243
doi: 10.1093/plcell/koab243
pubmed: 34726755
pmcid: 8643710
Li T, Deng GB, Tang YY, Su Y, Wang JH, Cheng J, Yang Z, Qiu XB, Pu X, Zhang HL, Liang JJ, Yu MQ, Wei YM, Long H (2021b) Identification and validation of a novel locus controlling spikelet number in bread wheat (Triticum aestivum L.). Front Plant Sci 12:611106. https://doi.org/10.3389/fpls.2021.611106
doi: 10.3389/fpls.2021.611106
pubmed: 33719283
pmcid: 7952655
Livak KJ, Schmittgen T (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2
doi: 10.1006/meth.2001.1262
pubmed: 11846609
Long L, Guo DD, Gao W, Yang WW, Hou LP, Ma XN, Miao YC, Botella JR, Song CP (2018) Optimization of CRISPR/Cas9 genome editing in cotton by improved sgRNA expression. Plant Methods 14:85. https://doi.org/10.1186/s13007-018-0353-0
doi: 10.1186/s13007-018-0353-0
pubmed: 30305839
pmcid: 6169012
Ma ZQ, Zhao DM, Zhang CQ, Zhang ZZ, Xue SL, Lin F, Kong ZX, Tian DG, Luo QY (2007) Molecular genetic analysis of five spike-related traits in wheat using RIL and immortalized F2 populations. Mol Genet Genomics 277:31–42. https://doi.org/10.1007/s00438-006-0166-0
doi: 10.1007/s00438-006-0166-0
pubmed: 17033810
Ma FF, Xu YF, Ma ZQ, Li LH, An DG (2018) Genome-wide association and validation of key loci for yield-related traits in wheat founder parent Xiaoyan 6. Mol Breeding 38:91. https://doi.org/10.1007/s11032-018-0837-7
doi: 10.1007/s11032-018-0837-7
Ma J, Ding PY, Liu JJ, Li T, Zou YY, Habib A, Mu Y, Tang HP, Jiang QT, Liu YX, Chen GY, Wang JR, Deng M, Qi PF, Li W, Pu ZE, Zheng YL, Wei YM, Lan XJ (2019) Identification and validation of a major and stably expressed QTL for spikelet number per spike in bread wheat. Theor Appl Genet 132:3155–3167. https://doi.org/10.1007/s00122-019-03415-z
doi: 10.1007/s00122-019-03415-z
pubmed: 31435704
McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA (2010) The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 20:1297–1303. https://doi.org/10.1101/gr.107524.110
doi: 10.1101/gr.107524.110
pubmed: 20644199
pmcid: 2928508
Meng L, Li HH, Zhang LY, Wang JK (2015) QTL IciMapping: Integrated software for genetic linkage map construction and quantitative trait locus mapping in biparental populations. Crop J 3:269–283. https://doi.org/10.1016/j.cj.2015.01.001
doi: 10.1016/j.cj.2015.01.001
Panda D, Sahu N, Behera PK, Lenka K (2020) Genetic variability of panicle architecture in indigenous rice landraces of Koraput region of Eastern Ghats of India for crop improvement. Physiol Mol Biol Plants 26:1961–1971. https://doi.org/10.1007/s12298-020-00871-6
doi: 10.1007/s12298-020-00871-6
pubmed: 33088042
pmcid: 7548273
Sakuma S, Pourkheirandish M, Hensel G, Jochen Kumlehn J, Stein N, Tagiri A, Yamaji N, Ma JF, Sassa H, Koba T, Komatsuda T (2013) Divergence of expression pattern contributed to neofunctionalization of duplicated HD-Zip I transcription factor in barley. New Phytol 197:939–948. https://doi.org/10.1111/nph.12068
doi: 10.1111/nph.12068
pubmed: 23293955
Sakuma S, Golan G, Guo ZF, Ogawa T, Tagiri A, Sugimoto K, Bernhardt N, Brassac J, Mascher M, Hensel G, Ohnishi S, Jinno H, Yamashita Y, Ayalon I, Peleg Z, Schnurbusch T, Komatsuda T (2019) Unleashing floret fertility in wheat through the mutation of a homeobox gene. Proc Natl Acad Sci USA 116:5182–5187. https://doi.org/10.1073/pnas.1815465116
doi: 10.1073/pnas.1815465116
pubmed: 30792353
pmcid: 6421441
Si YQ, Tian SQ, Niu JQ, Yu ZQ, Ma SW, Lu Q, Wu HL, Ling HQ, Zheng SS (2023) Dissection and validation of a promising QTL controlling spikelet number on 5B in bread wheat. Theor Appl Genet 136:240. https://doi.org/10.1007/s00122-023-04488-7
doi: 10.1007/s00122-023-04488-7
pubmed: 37930446
Takagi H, Tamiru M, Abe A, Yoshida K, Uemura A, Yaegashi H, Obara T, Oikawa K, Utsushi H, Kanzaki E, Mitsuoka C, Natsume S, Kosugi S, Kanzaki H, Matsumura H, Urasaki N, Kamoun S, Terauchi R (2015) MutMap accelerates breeding of a salt-tolerant rice cultivar. Nat Biotechnol 33:445–449. https://doi.org/10.1038/nbt.3188
doi: 10.1038/nbt.3188
pubmed: 25798936
Wang R, Liu YX, Isham K, Zhao WD, Wheeler J, Klassen N, Hu YG, Bonman JM, Chen JL (2018) QTL identification and KASP marker development for productive tiller and fertile spikelet numbers in two high-yielding hard white spring wheat cultivars. Mol Breeding 38:135–146. https://doi.org/10.1007/s11032-018-0894-y
doi: 10.1007/s11032-018-0894-y
Wang YJ, Abrouk M, Gourdoupis S, Koo DH, Karafiátová M, Molnár I, Holušová K, Doležel J, Athiyannan N, Cavalet-Giorsa E, Jaremko Ł, Poland J, Krattinger SG (2023) An unusual tandem kinase fusion protein confers leaf rust resistance in wheat. Nat Genet 55:914–920. https://doi.org/10.1038/s41588-023-01401-2
doi: 10.1038/s41588-023-01401-2
pubmed: 37217716
pmcid: 10260399
Xiong HC, Li YT, Guo HJ, Xie YD, Zhao LS, Gu JY, Zhao SR, Ding YP, Liu LX (2021) Genetic maping by integration of 55K SNP array and KASP markers reveals candidate genes for important agronomic traits in hexaploid wheat. Front Plant Sci 12:628478. https://doi.org/10.3389/fpls.2021.628478
doi: 10.3389/fpls.2021.628478
pubmed: 33708233
pmcid: 7942297
Xu HW, Zhang RQ, Wang MM, Li LH, Yan L, Wang Z, Zhu J, Chen XY, Zhao AJ, Su ZQ, Xing JW, Sun QX, Ni ZF (2022) Identification and characterization of QTL for spike morphological traits, plant height and heading date derived from the D genome of natural and resynthetic allohexaploid wheat. Theor Appl Genet 135:389–403. https://doi.org/10.1007/s00122-021-03971-3
doi: 10.1007/s00122-021-03971-3
pubmed: 34674009
Xue SL, Hu SS, Chen X, Ma YY, Lu MX, Bai SL, Wang XT, Sun TP, Wang YX, Wan HS, An X, Li SP (2022) Fine mapping of Pm58 from Aegilops tauschii conferring powdery mildew resistance. Theor Appl Genet 135:1657–1669. https://doi.org/10.1007/s00122-022-04061-8
doi: 10.1007/s00122-022-04061-8
pubmed: 35234985
Yan LL, Loukoianov A, Blechl A, Blechl A, Tranquilli G, Ramakrishna W, Sanmiguel P, Bennetzen JL, Echenique V, Dubcovsky J (2004) The wheat VRN2 gene is a flowering repressor down-regulated by vernalization. Science 303:1640–1644. https://doi.org/10.1126/science.1094305
doi: 10.1126/science.1094305
pubmed: 15016992
pmcid: 4737501
Yan LL, Fu DL, Li C, Blechl A, Tranquilli G, Bonafede M, Sanchez A, Valarik M, Yasuda S, Dubcovsky J (2006) The wheat and barley vernalization gene VRN3 is an orthologue of FT. Proc Natl Acad Sci 103:19581–19586. https://doi.org/10.1073/pnas.0607142103
doi: 10.1073/pnas.0607142103
pubmed: 17158798
pmcid: 1748268
Zhang ZC, Belcram H, Gornicki P, Charles M, Just J, Huneau C, Magdelenat G, Couloux A, Samain S, Samain S, Gill SB, Rasmussen JB, Barbe V, Faris JD (2011) Duplication and partitioning in evolution and function of homoeologous Q loci governing domestication characters in polyploid wheat. Proc Natl Acad Sci USA 108:18737–18742. https://doi.org/10.1073/pnas.1110552108
doi: 10.1073/pnas.1110552108
pubmed: 22042872
pmcid: 3219148
Zhang ZC, Li AL, Song GY, Geng SF, Gill BS, Faris JD, Mao L (2020) Comprehensive analysis of Q gene near-isogenic lines reveals key molecular pathways for wheat domestication and improvement. Plant J 102:299–310. https://doi.org/10.1111/tpj.14624
doi: 10.1111/tpj.14624
pubmed: 31778224
Zhang XY, Jia HY, Li T, Wu JZ, Nagarajan R, Lei L, Powers C, Kan CC, Hua W, Liu ZY, Chen C, Carver BF, Yan LL (2022) TaCol-B5 modifies spike architecture and enhances grain yield in wheat. Science 376:180–183. https://doi.org/10.1126/science.abm0717
doi: 10.1126/science.abm0717
pubmed: 35389775
Zhou CY, Xiong HC, Li YT, Guo HJ, Xie YD, Zhao LS, Gu JY, Zhao SR, Ding YP, Song XY, Liu LX (2020) Genetic analysis and QTL mapping of a novel reduced height gene in common wheat (Triticum aestivum L.). J Integr Agr 19:1721–1730. https://doi.org/10.1016/s2095-3119(20)63224-5
doi: 10.1016/s2095-3119(20)63224-5