Validation of CAPS marker WR003 for the leaf rust resistance gene Lr1 and the molecular evolution of Lr1 in wheat

https://doi.org/10.17221/119/2021-CJGPBCitation:

Liu X.J., Liu X.C., Sun H.Y., Hao C.Y., Wang X.X., Rong Z.J., Feng Z.Y. (2022): Validation of CAPS marker WR003 for the leaf rust resistance gene Lr1 and the molecular evolution of Lr1 in wheat. Czech J. Genet. Plant Breed., 58: 223–232.

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The wheat leaf rust resistance gene Lr1 encodes a typical coiled-coil nucleotide-binding site leucine-rich repeat (CC-NBS-LRR) of resistance protein containing 1 344 amino acids. WR003, a cleaved amplified polymorphic sequence (CAPS) marker is derived from the LRR regions of Lr1. In this study, a worldwide collection of 120 Aegilops tauschii accessions and 282 hexaploid wheat varieties was screened for Lr1 alleles using WR003, and the specificity of WR003 for Lr1 was confirmed by pathogenicity tests and genotype analysis. The sequence alignment and phylogenetic tree analysis of 38 Lr1 haplotypes provided a further view of the molecular evolution of Lr1. The results showed that there were very few polymorphisms between the Lr1 alleles from Ae. tauschii and hexaploid wheat with the same resistance phenotype. The polymorphisms of the Lr1 haplotypes were mainly between the different resistance lines, rather than between the different ploidy levels. These results indicate that Lr1 originated from Ae. tauschii and differentiated into resistant and susceptible genotypes before its introgression into hexaploid wheat. Therefore, it is likely that wheat Lr1 has at least two major variants for disease resistance and susceptibility, and except for certain point mutations, few gene conversions and genetic re-combinations occurred during the hexaploid wheat domestication.

References:
Ausemus E.R., Harrington J.B., Reitz L.P., Worzella W.W. (1946): A summary of genetic studies in hexaploid and tetraploid wheats. Journal of the American Society of Agronomy, 38: 1083–1099.
 
Avni R., Nave M., Barad O., Baruch K., Twardziok S.O., Gundlach H., Hale I., Mascher M., Spannagl M., Wiebe K. et al. (2017): Wild emmer genome architecture and diversity elucidate wheat evolution and domestication. Science, 357: 93–97. https://doi.org/10.1126/science.aan0032
 
Chen Z., Shen Z.J., Zhao D., Xu L., Zhang L.J., Zou Q. (2020): Genome-wide analysis of LysM-containing gene family in wheat: Structural and phylogenetic analysis during development and defense. Genes (Basel), 12: 31.  https://doi.org/10.3390/genes12010031
 
Cloutier S., McCallum B.D., Loutre C., Banks T.W., Wic-ker T., Feuillet C., Keller B., Jordan M.C. (2007): Leaf rust resistance gene Lr1, isolated from bread wheat (Triticum aestivum L.) is a member of the large psr567 gene family. Plant Molecular Biology, 65: 93–106. https://doi.org/10.1007/s11103-007-9201-8
 
El Baidouri M., Murat F., Veyssiere M., Molinier M., Flores R., Burlot L., Alaux M., Quesneville H., Pont C., Salse J. (2017): Reconciling the evolutionary origin of bread wheat (Triticum aestivum). New Phytologist, 213: 1477–1486. https://doi.org/10.1111/nph.14113
 
Froger A., Hall J.E. (2007): Transformation of plasmid DNA into E. coli using the heat shock method. Jove-Journal of Visualized Experiments, 6: 253. https://doi.org/10.3791/253
 
Garnault M., Duplaix C., Leroux P., Couleaud G., David O., Walker A.S., Carpentier F. (2021): Large-scale study validates that regional fungicide applications are major determinants of resistance evolution in the wheat pathogen Zymoseptoria tritici in France. New Phytologist, 229: 3508–3521. https://doi.org/10.1111/nph.17107
 
Gebrewahid T.W., Zhang P.P., Yao Z.J., Li Z.F., Liu D.Q. (2020): Identification of leaf rust resistance genes in bread wheat cultivars from Ethiopia. Plant Disease, 104: 2354–2361.  https://doi.org/10.1094/PDIS-12-19-2606-RE
 
Graner A., Siedler H., Jahoor A., Hermann R.G., Wenzel G. (1990): Assessment of the degree and the type of restriction fragment length polymorphism in barley (Hordeum vulgare). Theoretical and Applied Genetics, 80: 826–832. https://doi.org/10.1007/BF00224200
 
Haas M., Schreiber M., Mascher M. (2019): Domestication and crop evolution of wheat and barley: Genes, genomics, and future directions. Journal of Integrative Plant Biology, 61: 204–225. https://doi.org/10.1111/jipb.12737
 
Juliana P., Singh R.P., Singh P.K., Poland J.A., Bergstrom G.C., Huerta-Espino J., Bhavani S., Crossa J., Sorrells M.E. (2018): Genome-wide association mapping for resistance to leaf rust, stripe rust and tan spot in wheat reveals potential candidate genes. Theoretical and Applied Genetics, 131: 1405–1422. https://doi.org/10.1007/s00122-018-3086-6
 
Keller B., Wicker T., Krattinger S.G. (2018): Advances in wheat and pathogen genomics: implications for disease control. Annual Review of Phytopathology, 56: 67–87. https://doi.org/10.1146/annurev-phyto-080516-035419
 
Krattinger S.G., Keller B. (2016): Molecular genetics and evolution of disease resistance in cereals. New Phytologist, 212: 320–332. https://doi.org/10.1111/nph.14097
 
Kthiri D., Loladze A., N’Diaye A., Nilsen K.T., Walkowiak S., Dreisigacker S., Ammar K., Pozniak C.J. (2019): Mapping of genetic loci conferring resistance to leaf rust from three globally resistant durum wheat sources. Frontiers in Plant Science, 10: 1247.  https://doi.org/10.3389/fpls.2019.01247
 
Kumar S., Stecher G., Tamura K. (2016): MEGA7: Molecular evolutionary genetics analysis version 7.0 for bigger datasets. Molecular Biology and Evolution, 33: 1870–1874. https://doi.org/10.1093/molbev/msw054
 
Larkin M.A., Blackshields G., Brown N.P., Chenna R., McGettigan P.A., McWilliam H., Valentin F., Wallace I.M., Wilm A., Lopez R., Thompson J.D., Gibson T.J., Higgins D.G. (2007): Clustal W and Clustal X version 2.0. Bioinformatics, 23: 2947–2948. https://doi.org/10.1093/bioinformatics/btm404
 
Ling H.Q., Zhu Y., Keller B. (2003): High-resolution mapping of the leaf rust disease resistance gene Lr1 in wheat and characterization of BAC clones from the Lr1 locus. Theoretical and Applied Genetics, 106: 875–882. https://doi.org/10.1007/s00122-002-1139-2
 
Ling H.Q., Qiu J., Singh R.P., Keller B. (2004): Identification and genetic characterization of an Aegilops tauschii ortholog of the wheat leaf rust disease resistance gene Lr1. Theoretical and Applied Genetics, 109: 1133–1138. https://doi.org/10.1007/s00122-004-1734-5
 
Manjunatha C., Sharma S., Kulshreshtha D., Gupta S., Singh K., Bhardwaj S.C., Aggarwal R. (2018): Rapid detection of Puccinia triticina causing leaf rust of wheat by PCR and loop mediated isothermal amplification. PLoS ONE, 13: e0196409. https://doi.org/10.1371/journal.pone.0196409
 
Matuszczak M., Spasibionek S., Gacek K., Bartkowiak-Broda I. (2020): Cleaved amplified polymorphic sequences (CAPS) marker for identification of two mutant alleles of the rapeseed BnaA.FAD2 gene. Molecular Biology Reports, 47: 7607–7621. https://doi.org/10.1007/s11033-020-05828-2
 
Michikawa A., Yoshida K., Okada M., Sato K., Takumi S. (2019): Genome-wide polymorphisms from RNA sequencing assembly of leaf transcripts facilitate phylogenetic analysis and molecular marker development in wild einkorn wheat. Molecular Genetics and Genomics, 294: 1327–1341. https://doi.org/10.1007/s00438-019-01581-9
 
Pasam R.K., Bansal U., Daetwyler H.D., Forrest K.L., Wong D., Petkowski J., Willey N., Randhawa M., Chhetri M., Miah H., Tibbits J., Bariana H., Hayden M.J. (2017): Detection and validation of genomic regions associated with resistance to rust diseases in a worldwide hexaploid wheat landrace collection using BayesR and mixed linear model approaches. Theoretical and Applied Genetics, 130: 777–793. https://doi.org/10.1007/s00122-016-2851-7
 
Prasad P., Savadi S., Bhardwaj S.C., Gupta P.K. (2020): The progress of leaf rust research in wheat. Fungal Biology, 124: 537–550. https://doi.org/10.1016/j.funbio.2020.02.013
 
Qiu J.W., Schürch A.C., Yahiaoui N., Dong L.L., Fan H.J., Zhang Z.J., Keller B., Ling H.Q. (2007): Physical mapping and identification of a candidate for the leaf rust resistance gene Lr1 of wheat. Theoretical and Applied Genetics, 115: 159–168. https://doi.org/10.1007/s00122-007-0551-z
 
Rani R., Singh R., Yadav N.R. (2019): Evaluating stripe rust resistance in Indian wheat genotypes and breeding lines using molecular markers. Comptes Rendus Biologies, 342: 154–174. https://doi.org/10.1016/j.crvi.2019.04.002
 
Sarkar C., Saklani B.K., Singh P.K., Asthana R.K., Sharma T.R. (2019): Variation in the LRR region of Pi54 protein alters its interaction with the AvrPi54 protein revealed by in silico analysis. PLoS ONE, 14: e0224088. https://doi.org/10.1371/journal.pone.0224088
 
Saucet S.B., Esmenjaud D., Van Ghelder C. (2021): Integrity of the Post-LRR domain is required for TIR-NB-LRR function. Molecular Plant-Microbe Interactions, 34: 286–296. https://doi.org/10.1094/MPMI-06-20-0156-R
 
Segura D.M., Masuelli R.W., Sanchez-Puerta M.V. (2017): Dissimilar evolutionary histories of two resistance gene families in the genus Solanum. Genome, 60: 17–25. https://doi.org/10.1139/gen-2016-0101
 
Wu H., Kang Z., Li X., Li Y., Li Y., Wang S., Liu D. (2020a): Identification of wheat leaf rust resistance genes in Chinese wheat cultivars and the improved germplasms. Plant Disease, 104: 2669–2680. https://doi.org/10.1094/PDIS-12-19-2619-RE
 
Wu X., Bian Q., Lin Q., Sun Q., Ni X., Xu X., Qiu Y., Xuan Y., Cao Y., Li T. (2020b): Sensitivity of Puccinia graminis f.sp. tritici isolates from China to triadimefon and cross-resistance against diverse fungicides. Plant Disease, 104: 2082–2085.  https://doi.org/10.1094/PDIS-01-20-0009-RE
 
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