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Journal of Integrative Agriculture  2024, Vol. 23 Issue (12): 3953-3965    DOI: 10.1016/j.jia.2023.09.014
Special Issue: 小麦遗传育种Wheat Genetics · Breeding · Germplasm Resources
Crop Science Advanced Online Publication | Current Issue | Archive | Adv Search |
Karyotype establishment and development of specific molecular markers of Aegilops geniculata Roth based on SLAF-seq 

Yongfu Wang1, Jianzhong Fan1, Hong Zhang1, 2, 3, Pingchuan Deng1, 2, 3, Tingdong Li1, 2, 3, Chunhuan Chen1, 2, 3, Wanquan Ji1, 2, 3#, Yajuan Wang1, 2, 3#

1 College of Agronomy, Northwest A&F University, Yangling 712100, China

2 State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling 712100, China

3 Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs, Yangling 712100, China

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摘要  

病原菌的不断进化对小麦的抗病能力构成威胁,危及粮食安全。因此,培育抗病小麦品种是规避这一问题最经济有效的途径。卵穗山羊草SY159是小麦近缘种,包含有许多优异的基因资源。在这项研究中,我们利用寡核苷酸探针Oligo-pTa535Oligo-pSc119.2,参考了一整套小麦-卵穗山羊草(TA2899)附加系的荧光原位杂交(FISH)结果,构建了SY159染色体核型。利用SLAF-seq技术,开发400对特异标记对SY159染色体进行筛选,检测效率达81.5%。同时,以一整套小麦-卵穗山羊草(TA2899)附加系为参考,对特异性标记进行同源群归属的分类,并以源于SY1597Mg附加系进行验证,证实了利用该技术开发卵穗山羊草SY159不同染色体特异标记的适用性。这为加快卵穗山羊草在小麦遗传育种中的应用奠定了坚实的基础。



Abstract  

The constant evolution of pathogens poses a threat to wheat resistance against diseases, endangering food security.  Developing resistant wheat varieties is the most practical approach for circumventing this problem.  As a close relative of wheat, Aegilops geniculata, particularly accession SY159, has evolved numerous beneficial traits that could be applied to improve wheat.  In this study, we established the karyotype of SY159 by fluorescence in situ hybridization (FISH) using the oligonucleotide probes Oligo-pTa535 and Oligo-pSc119.2 and a complete set of wheat–Ae. geniculata accession TA2899 addition lines as a reference.  Using specific-locus amplified fragment sequencing (SLAF-seq) technology, 400 specific markers were established for detecting the SY159 chromosomes with efficiencies reaching 81.5%.  The SY159-specific markers were used to classify the different homologous groups of SY159 against the wheat–Ae. geniculata addition lines.  We used these specific markers on the 7Mg chromosome after classification, and successfully confirmed their suitability for studying the different chromosomes of SY159.  This study provides a foundation for accelerating the application of SY159 in genetic breeding programs designed to improve wheat. 

Keywords:  Aegilops geniculata Roth       chromosome karyotype analysis       FISH       SLAF-seq       specific molecular marker  
Received: 05 May 2023   Accepted: 09 August 2023
Fund: 
This work was funded by the National Natural Science Foundation of China (31471481) and the Project of Science and Technology of Shaanxi Province of China (2021NY-081 and 2023YBNY-033).  

About author:  Yongfu Wang, E-mail: wyf063575@163.com; #Correspondence Wanquan Ji, E-mail: jiwanquan2008@126.com; Yajuan Wang, E-mail: wangyj7604@163.com

Cite this article: 

Yongfu Wang, Jianzhong Fan, Hong Zhang, Pingchuan Deng, Tingdong Li, Chunhuan Chen, Wanquan Ji, Yajuan Wang. 2024. Karyotype establishment and development of specific molecular markers of Aegilops geniculata Roth based on SLAF-seq . Journal of Integrative Agriculture, 23(12): 3953-3965.

An D G, Han G H, Wang J, Yan H W, Zhou Y L, Cao L J, Jin Y L, Zhang X T. 2022. Cytological and genetic analyses of a wheat–rye 2RL ditelosomic addition line with adult plant resistance to powdery mildew. The Crop Journal10, 911–916.

Badaeva E D, Amosova A V, Muravenko O V, Samatadze T E, Chikida N N, Zelenin A V, Friebe B, Gill B S. 2002. Genome differentiation in Aegilops. 3. Evolution of the D-genome cluster. Plant Systematics and Evolution231, 163–190.

Badaeva E D, Amosova A V, Samatadze T E, Zoshchuk S A, Shostak N G, Chikida N N, Zelenin A V, Raupp W J, Friebe B, Gill B S. 2004. Genome differentiation in Aegilops. 4. Evolution of the U-genome cluster. Plant Systematics and Evolution246, 45–76.

Bie T D, Zhao R H, Zhu S Y, Chen S L, Cen B, Zhang B Q, Gao D R, Jiang Z N, Chen T T, Wang L, Wu R L, He H G. 2015. Development and characterization of marker MBH1 simultaneously tagging genes Pm21 and PmV conferring resistance to powdery mildew in wheat. Molecular Breeding35, 189.

Chaves M S, Martinelli J A, Wesp-Guterres C, Graichen F A S, Brammer S P, Scagliusi S M, da Silva P R, Wietholter P, Torres G A M, Lau E Y, Consoli L, Chaves A L S. 2013. The importance for food security of maintaining rust resistance in wheat. Food Security5, 157–176.

Chen P D, You C F, Hu Y, Chen S W, Zhou B, Cao A Z, Wang X. 2012. Radiation-induced translocations with reduced Haynaldia villosa chromatin at the Pm21 locus for powdery mildew resistance in wheat. Molecular Breeding31, 477–484.

Chen S Q, Huang Z F, Dai Y, Qin S W, Gao Y Y, Zhang L L, Gao Y, Chen J M. 2013. The development of 7E chromosome-specific molecular markers for Thinopyrum elongatum based on SLAF-seq technology. PLoS ONE8, e65122.

Danilova T V, Akhunova A R, Akhunov E D, Friebe B, Gill B S. 2017. Major structural genomic alterations can be associated with hybrid speciation in Aegilops markgrafii (Triticeae). The Plant Journal92, 317–330.

Danilova T V, Friebe B, Gill B S. 2014. Development of a wheat single gene FISH map for analyzing homoeologous relationship and chromosomal rearrangements within the Triticeae. Theoretical and Applied Genetics127, 715–730.

Drader T, Johnson K, Brueggeman R, Kudrna D, Kleinhofs A. 2009. Genetic and physical mapping of a high recombination region on chromosome 7H (1) in barley. Theoretical and Applied Genetics118, 811–820.

Friebe B, Jiang J, Raupp W J, McIntosh R A, Gill B S. 1996. Characterization of wheat–alien translocations conferring resistance to diseases and pests: Current status. Euphytica91, 59–87.

Friebe B R, Tuleen N A, Gill B S. 1999. Development and identification of a complete set of Triticum aestivum Aegilops geniculata chromosome addition lines. Genome42, 374–380.

Gill B S, Sharma H C, Raupp W J, Browder L E, Waines J G. 1985. Evaluation of Aegilops species for resistance to wheat powdery mildew, wheat leaf rust, Hessian Fly, and Greenbug. Plant Disease69, 314–316.

Gong W P, Li G R, Zhou J P, Li G Y, Liu C, Huang C Y, Zhao Z D, Yang Z J. 2014. Cytogenetic and molecular markers for detecting Aegilops uniaristata chromosomes in a wheat background. Genome57, 489–497.

Han F P, Liu B, Fedak G, Liu Z H. 2004. Genomic constitution and variation in five partial amphiploids of wheat–Thinopyrum intermedium as revealed by GISH, multicolor GISH and seed storage protein analysis. Theoretical and Applied Genetics109, 1070–1076.

Hao M, Liu M, Luo J T, Fan C L, Yi Y J, Zhang L Q, Yuan Z W, Ning S Z, Zheng Y L, Liu D C. 2018. Introgression of powdery mildew resistance gene Pm56 on rye chromosome arm 6RS into wheat. Front Plant Science9, 1040.

He H G, Liu R K, Ma P T, Du H N, Zhang H H, Wu Q H, Yang L J, Gong S J, Liu T L, Huo N X, Gu Y Q, Zhu S Y. 2021. Characterization of Pm68, a new powdery mildew resistance gene on chromosome 2BS of Greek durum wheat TRI 1796. Theoretical and Applied Genetics134, 53–62.

Jia Q J, Tan C, Wang J M, Zhang X Q, Zhu J H, Luo H, Yang J M, Westcott S, Broughton S, Moody D, Li C D. 2016. Marker development using SLAF-seq and whole-genome shotgun strategy to fine-map the semi-dwarf gene ari-e in barley. BMC Genomics17, 911.

Jiang Y, Wang D L, Hao M, Zhang J, Liu D C. 2023. Development and characterization of wheat–Aegilops kotschyi 1Uk(1A) substitution line with positive dough quality parameters. Journal of Integrative Agriculture22, 999–1008.

Jin Y L, Guo T T, Liu H, An D G. 2022. Research progress on the wheat powdery mildew resistance gene Pm2Chinese Journal of Eco-Agriculture30, 779–786. (in Chinese)

Kent W J. 2002. BLAT - The BLAST-like alignment tool. Genome Research12, 656–664.

Kozich J J, Westcott S L, Baxter N T, Highlander S K, Schloss P D. 2013. Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform. Applied and Environmental Microbiology79, 5112–5120.

Kuraparthy V, Chhuneja P, Dhaliwal H S, Kaur S, Bowden R L, Gill B S. 2007. Characterization and mapping of cryptic alien introgression from Aegilops geniculata with new leaf rust and stripe rust resistance genes Lr57 and Yr40 in wheat. Theoretical and Applied Genetics114, 1379–1389.

Landjeva S P, Ganeva G D. 2000. Chromosome N-banding polymorphism in Aegilops geniculata Roth. Genetic Resources and Crop Evolution47, 35–42.

Li H, Durbin R. 2009. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics25, 1754–1760.

Li H H, Jiang B, Wang J C, Lu Y Q, Zhang J P, Pan C L, Yang X M, Li X Q, Liu W H, Li L H. 2017. Mapping of novel powdery mildew resistance gene(s) from Agropyron cristatum chromosome 2P. Theoretical and Applied Genetics130, 109–121.

Li X, Yang W X, Li Y N, Liu D Q, Yan H F, Meng Q F, Zhang T. 2007. Identification of AFLP markers linked to Lr19 resistance to wheat leaf rust. Agricultural Sciences in China6, 311–315.

Li X J, Hu X G, Hu T Z, Li G, Ru Z G, Zhang L L, Lang Y M. 2015. Identification of a novel wheat–Thinopyrum ponticumaddition line revealed with cytology, SSR, EST-SSR, EST-STS and PLUG markers. Cereal Research Communications43, 544–553.

Linc G, Sepsi A, Molnar-Lang M. 2012. A FISH karyotype to study chromosome polymorphisms for the Elytrigia elongata E genome. Cytogenet Genome Research136, 138–144.

Liu L Q, Luo Q L, Teng W, Li B, Li H W, Li Y W, Li Z S, Zheng Q. 2018. Development of Thinopyrum ponticum-specific molecular markers and FISH probes based on SLAF-seq technology. Planta247, 1099–1108.

Liu W X, Rouse M, Friebe B, Jin Y, Gill B, Pumphrey M O. 2011. Discovery and molecular mapping of a new gene conferring resistance to stem rust, Sr53, derived from Aegilops geniculata and characterization of spontaneous translocation stocks with reduced alien chromatin. Chromosome Research19, 669–682.

Liu Y B, Pan X B, Li J S. 2014. Current agricultural practices threaten future global food production. Journal of Agricultural and Environmental Ethics28, 203–216.

Luan Y, Wang X G, Liu W H, Li C Y, Zhang J P, Gao A N, Wang Y D, Yang X M, Li L H. 2010. Production and identification of wheat–Agropyron cristatum 6P translocation lines. Planta232, 501–510.

Luo C, Shu B, Yao Q S, Wu H X, Xu W T, Wang S B. 2016. Construction of a high-density genetic map based on large-scale marker development in mango using specific-locus amplified fragment sequencing (SLAF-seq). Front Plant Science7, 1310.

Mahjoub A, Abdellaoui R, Ben N M, Ben B N. 2010 Genetic diversity of Tunisian accessions of Aegilops geniculata Roth and durum wheats (Triticum durum Desf.) using RAPD markers. Acta Botanica Gallica157, 3–12.

Mahjoub A, Rouaissi M, Mguis K, Gharbi M S E, Gazzah M E, Brahim N B. 2008. Agromorphological variation in spontaneous Aegilops geniculata Roth populations suitable for mediterranean conditions. World Journal of Agricultural Sciences4, 737–744.

Molnar I, Cifuentes M, Schneider A, Benavente E, Molnar-Lang M. 2011. Association between simple sequence repeat-rich chromosome regions and intergenomic translocation breakpoints in natural populations of allopolyploid wild wheats. Annals of Botany107, 65–76.

Molnar I, Simkova H, Leverington-Waite M, Goram R, Cseh A, Vrana J, Farkas A, Dolezel J, Molnar-Lang M, Griffiths S. 2013. Syntenic relationships between the U and M genomes of Aegilops, wheat and the model species Brachypodium and rice as revealed by COS markers. PLoS ONE8, e70844.

Mukai Y, Endo T R, Gill B S. 1990. Physical mapping of the 5 SrRNA multigene family in common wheat. Journal of Heredity81, 290–295.

Nagy E D, Molnar I, Schneider A, Kovacs G, Molnar-Lang M. 2006. Characterization of chromosome-specific S-SAP markers and their use in studying genetic diversity in Aegilops species. Genome49, 289–296.

Petersen S, Lyerly J H, Worthington M L, Parks W R, Cowger C, Marshall D S, Brown-Guedira G, Murphy J P. 2015. Mapping of powdery mildew resistance gene Pm53 introgressed from Aegilops speltoides into soft red winter wheat. Theoretical and Applied Genetics, 128, 303–312.

Prabhu K V, Gupta S K, Charpe A, Koul S. 2004. SCAR marker tagged to the alien leaf rust resistance gene Lr19 uniquely marking the Agropyron elongatum-derived gene Lr24 in wheat: A revision. Plant Breeding123, 417–420.

Said M, Capal P, Farkas A, Gaal E, Ivanizs L, Friebe B, Dolezel J, Molnar I. 2022. Flow karyotyping of wheat–Aegilops additions facilitate dissecting the genomes of Aebiuncialis and Aegeniculata into individual chromosomes. Front Plant Science13, 1017958.

Said M, Holusova K, Farkas A, Ivanizs L, Gaal E, Capal P, Abrouk M, Martis-Thiele M M, Kalapos B, Bartos J, Friebe B, Dolezel J, Molnar I. 2021. Development of DNA markers from physically mapped loci in Aegilops comosa and Aegilops umbellulata using single-gene FISH and chromosome sequences. Front Plant Science12, 689031.

Said M, Hribova E, Danilova T V, Karafiatova M, Cizkova J, Friebe B, Dolezel J, Gill B S, Vrana J. 2018. The Agropyron cristatum karyotype, chromosome structure and cross-genome homoeology as revealed by fluorescence in situ hybridization with tandem repeats and wheat single-gene probes. Theoretical and Applied Genetics131, 2213–2227.

Schneider A, Molnar I, Molnar-Lang M. 2010. Selection of U and M genome-specific wheat SSR markers using wheat–Aegilops biuncialis and wheat–Aegeniculata addition lines. Euphytica175, 357–364.

Schneider A, Molnar-Lang M. 2012. Detection of various U and M chromosomes in wheat–Aegilops biuncialis hybrids and derivatives using fluorescence in situ hybridisation and molecular markers. Czech Journal of Genetics and Plant Breeding48, 169–177.

Song L Q, Zhao H, Zhang Z, Zhang S, Liu J J, Zhang W, Zhang N, Ji J, Li L H, Li J M. 2020. Molecular cytogenetic identification of wheat–Aegilops biuncialis 5Mb disomic addition line with tenacious and black glumes. International Journal of Molecular Sciences21, 4053.

Song Z P, Zuo Y Y, Xiang Q, Li W J, Li J, Liu G, Dai S F, Yan Z H. 2023. Investigation of Aegilops umbellulata for stripe rust resistance, heading date, and the contents of iron, zinc, and gluten protein. Journal of Integrative Agriculture22, 1258–1265.

Stoilova T, Spetsov P. 2006. Chromosome 6U from Aegilops geniculata Roth carrying powdery mildew resistance in bread wheat. Breeding Science56, 351–357.

Sun X W, Liu D Y, Zhang X F, Li W B, Liu H, Hong W G, Jiang C B, Guan N, Ma C X, Zeng H P, Xu C H, Song J, Huang L, Wang C M, Shi J J, Wang R, Zheng X H, Lu C Y, Wang X W, Zheng H K. 2013. SLAF-seq: An efficient method of large-scale de novo SNP discovery and genotyping using high-throughput sequencing. PLoS ONE8, e58700.

Tang Z X, Li M, Chen L, Wang Y Y, Ren Z L, Fu S L. 2014a. New types of wheat chromosomal structural variations in derivatives of wheat–rye hybrids. PLoS ONE9, e110282.

Tang Z X, Yang Z J, Fu S L. 2014b. Oligonucleotides replacing the roles of repetitive sequences pAs1, pSc119.2, pTa-535, pTa71, CCS1, and pAWRC.1 for FISH analysis. Theoretical and Applied Genetics55, 313–318.

Tilman D, Cassman K G, Matson P A, Naylor R, Polasky S. 2002. Agricultural sustainability and intensive production practices. Nature418, 671–677.

Wang H W, Sun S L, Ge W Y, Zhao L F, Hou B Q, Wang K, Lyu Z F, Chen L Y, Xu S S, Guo J, Li M, Su P S, Li X F, Wang G P, Bo C Y, Fang X J, Zhuang W W, Cheng X X, Wu J W, Dong L H, et al. 2020. Horizontal gene transfer of Fhb7 from fungus underlies Fusarium head blight resistance in wheat. Science368, 6493.

Wang Y F, Cheng X F, Yang X Y, Wang C C, Zhang H, Deng P C, Liu X L, Chen C H, Ji W Q, Wang Y J. 2021. Molecular cytogenetics for a wheat–Aegilops geniculata 3Mg alien addition line with resistance to stripe rust and powdery mildew. BMC Plant Biology21, 575.

Wang Y J, Quan W, Peng N N, Wang C C, Yang X F, Liu X L, Zhang H, Chen C H, Ji W Q. 2016. Molecular cytogenetic identification of a wheat–Aegilops geniculata Roth 7Mg disomic addition line with powdery mildew resistance. Molecular Breeding36, 40.

Wang Y J, Wang C Y, Zhang H, Li H, Liu X L, Ji W Q. 2015. Identification and evaluation of disease resistance and HMW-GS composition of Aegilops geniculata Roth. Genetic Resources and Crop Evolution62, 1085–1093.

Wang Y Z, Cao Q, Zhang J J, Wang S W, Chen C H, Wang C Y, Zhang H, Wang Y J, Ji W Q. 2020. Cytogenetic analysis and molecular marker development for a new wheat–Thinopyrum ponticum 1Js (1D) disomic substitution line with resistance to stripe rust and powdery mildew. Front Plant Science11, 1282.

Wu M, Zhang J P, Wang J C, Yang X M, Gao A N, Zhang X K, Liu W H, Li L H. 2009. Cloning and characterization of repetitive sequences and development of SCAR markers specific for the P genome of Agropyron cristatumEuphytica172, 363–372.

Yang G T, Boshoff W H P, Li H W, Pretorius Z A, Luo Q L, Li B, Li Z S, Zheng Q. 2021. Chromosomal composition analysis and molecular marker development for the novel Ug99-resistant wheat–Thinopyrum ponticum translocation line WTT34. Theoretical and Applied Genetics134, 1587–1599.

Yang X Y, Xu M R, Wang Y F, Cheng X F, Huang C X, Zhang H, Li T D, Wang C C, Chen C H, Wang Y J, Ji W Q. 2022. Development and molecular cytogenetic identification of two wheat–Aegilops geniculata Roth 7Mg chromosome substitution lines with resistance to Fusarium head blight, powdery mildew and stripe rust. International Journal of Molecular Sciences23, 7056.

Zaharieva M, Monneveux P, Henry M, Rivoal R, Valkoun J, Nachit M M. 2001. Evaluation of a collection of wild wheat relative Aegilops geniculata Roth and identification of potential sources for useful traits. Euphytica119, 33–38.

Zeller F J, Kong L, Hartl L, Mohler V, Hsam S L K. 2002. Chromosomal location of genes for resistance to powdery mildew in common wheat (Triticum aestivum L. em Thell.). Euphytica123, 187–194.

Zhang R Q, Xiong C X, Mu H Q, Yao R N, Meng X R, Kong L N, Xing L P, Wu J Z, Feng Y G, Cao A Z. 2021. Pm67, a new powdery mildew resistance gene transferred from Dasypyrum villosum chromosome 1V to common wheat (Triticum aestivum L.). The Crop Journal9, 882–888.

Zhang Y, Zhang J P, Huang L, Gao A N, Zhang J, Yang X M, Liu W H, Li X Q, Li L H. 2015. A high-density genetic map for P genome of Agropyron Gaertn. based on specific-locus amplified fragment sequencing (SLAF-seq). Planta242, 1335–1347.

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