Bulked segregant analysis RNA-seq (BSR-Seq) validated a stem resistance locus in Aegilops umbellulata, a wild relative of wheat
Autoři:
Erena A. Edae aff001; Matthew N. Rouse aff001
Působiště autorů:
Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, United States of America
aff001; Cereal Disease Laboratory, United State Department of Agriculture-Agricultural Service, St. Paul, Minnesota, United States of America
aff002
Vyšlo v časopise:
PLoS ONE 14(9)
Kategorie:
Research Article
prolekare.web.journal.doi_sk:
https://doi.org/10.1371/journal.pone.0215492
Souhrn
Many disease resistance genes that have been transferred from wild relatives to cultivated wheat have played a significant role in wheat production worldwide. Ae. umbellulata is one of the species within the genus Aegilops that have been successfully used as sources of resistance genes to leaf rust, stem rust and powdery mildew. The objectives of the current work was to validate the map position of a major QTL that confers resistance to the stem rust pathogen races Ug99 (TTKSK) and TTTTF with an independent bi-parental mapping population and to refine the QTL region with a bulk segregant analysis approach. Two F2 bi-parental mapping populations were developed from stem rust resistant Ae. umbellulata accessions (PI 298905 and PI 5422375) and stem rust susceptible accessions (PI 542369 and PI 554395). Firstly, one of the two populations was used to map the chromosome location of the resistance gene. Later on, the 2nd population was used to validate the chromosome location in combination with a bulk segregant analysis approach. For the bulk segregant analysis, RNA was extracted from a bulk of leaf tissues of 12 homozygous resistant F3 families, and a separate bulk of 11 susceptible homozygous F3 families derived from the PI 5422375 and PI 554395 cross. The RNA samples of the two bulks and the two parents were sequenced for SNPs identification. Stem rust resistance QTL was validated on chromosome 2U of Ae. umbellulata in the same region in both populations. With bulk segregant analysis, the QTL position was delimited within 3.2 Mbp. Although there were a large number of genes in the orthologous region of the detected QTL on chromosome 2D of Ae. tauschii, we detected only two Ae. umbellulata NLR genes which can be considered as a potential candidate genes.
Klíčová slova:
Biology and life sciences – Genetics – Genomics – Genome analysis – Organisms – Eukaryota – Plants – Grasses – Computational biology – Research and analysis methods – Molecular biology – Wheat – Sequence assembly tools – Database and informatics methods – Bioinformatics – Sequence analysis – Sequence alignment – Molecular biology techniques – Gene mapping – Molecular genetics – Molecular biology assays and analysis techniques – Chromosome mapping – Bulked-segregant analysis – Departures from diploidy – Polyploidy – Hexaploidy
Zdroje
1. Singh RP, Hodson DP, Huerta-Espino J, Jin Y, Njau P, Wanyera R, et al. Will stem rust destroy the world’s wheat crop? Adv. Agron. 2008; 98:271–309.
2. Singh RP, Hodson DP, Jin Y, Lagudah ES, Ayliffe MA, Bhavani S, et al. Emergence and spread of new races of wheat stem rust fungus: continued threat to food security and prospects of generic control. Phytopathol. 2015; 105:872–884.
3. Liu W.X., Jin Y., Rouse M., Friebe B., Gill B., and Pumphrey M.O. Development and characterization of wheat-Ae. searsii Robertsonian translocations and a recombinant chromosome conferring resistance to stem rust. Theor Appl Genet. 2011; 122:1537–1545. doi: 10.1007/s00122-011-1553-4 21347655
4. Liu W., Rouse M., Friebe B., Jin Y., Gill B., and Pumphrey M.O. 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 Res. 2011; 19:669–82. doi: 10.1007/s10577-011-9226-3 21728140
5. Olson E. L., Rouse M. N., Pumphrey M. O., Bowden R. L., Gill B. S., and Poland J. A. Simultaneous transfer, introgression, and genomic localization of genes for resistance to stem rust race TTKSK (Ug99) from Aegilops tauschii to wheat. Theor Appl Genet, 2013; 126:1179–1188. doi: 10.1007/s00122-013-2045-5 23377571
6. Olson E. L., Rouse M. N., Pumphrey M. O., Bowden R. L., Gill B. S., and Poland J. A. Introgression of stem rust resistance genes SrTA10187 and SrTA10171 from Aegilops tauschii to wheat. Theor Appl Genet. 2013; 126: 2477–2484. doi: 10.1007/s00122-013-2148-z 23864229
7. Wulf B, Moscou M. Strategies for transferring resistance into wheat: from wide crosses to GM cassettes. Frontiers in Plant Science 2014; 5:1–11. doi: 10.3389/fpls.2014.00692 25538723
8. Gill BS, Sharma HC, Raup WJ, Browder LE, Hatchet JW, Harvey JH, et al. Evaluation of Aegilops species for resistance to wheat powdery mildew, wheat leaf rust and Hessian fly and green bug. Plant Dis.1985; 69:314–316.
9. Friebe B., Jiang J, Raupp WJ, McIntosh RA and Gill BS. Characterization of wheat alien translocations conferring resistance to diseases and pests: current status. Euphytica 1996; 71:59–87.
10. Schneider A., Molnar I, and Molnar-Lang M. Utilization of Aegilops (goat grass) species to widen the genetic diversity of cultivated wheat. Euphytica 2008; 163:1–19.
11. Edae AE, Olivera DP, Jin Y, Poland JA, and Rouse NM. Genotype-by-Sequencing facilitates genetic mapping of a stem rust resistance locus in Aegilops umbellulata, a wild relative of cultivated wheat. BMC Genomics 2016; 17:1039. doi: 10.1186/s12864-016-3370-2 27978816
12. Chepelev I., Wei G, Tang Q and Zhao K. Detection of single nucleotide variations in expressed exons of the human genome using RNA-Seq. Nucl Acids 2009; 37:e106.
13. Canovas A, Rincon G, Islas-Trjo A, Wickamasinghe S and Medrano J. SNP Discovery in the bovine milk transcriptome using RNA-Seq technology. Mamm Genome 2010; 21: 592–598. doi: 10.1007/s00335-010-9297-z 21057797
14. O’Neil S, Emrich S. Assessing De Novo transcriptome assembly metrics for consistency and utility. BMC Genomics 2013; 14:465. doi: 10.1186/1471-2164-14-465 23837739
15. Michelmore RW, Paran I, Kesseli RV. Identification of markers linked to disease-resistance genes by bulked segregant analysis: a rapid method to detect markers in specific genomic regions by using segregating populations. Proc Natl Acad Sci 1991; 88:9828–9832. doi: 10.1073/pnas.88.21.9828 1682921
16. Liu SZ, Yeh CT, Tang HM, Nettleton D, Schnable PS. Gene mapping via bulked segregant RNA-Seq (BSR-Seq). PLoS One 2012; 7:e36406. doi: 10.1371/journal.pone.0036406 22586469
17. Li L., Li D, Liu SZ, Ma XL, Dietrich CR, Hu HC, et al. The maize glossy13 gene, cloned via BSR-Seq and Seq-walking encodes a putative ABC transporter required for the normal accumulation of epicuticular waxes. PLoS One 2013; 8:e82333. doi: 10.1371/journal.pone.0082333 24324772
18. Trick M., Adamski NM, Mugford SG, Jiang CC, Febrer M, et al. Combining SNP discovery from next-generation sequencing data with bulked segregant analysis (BSA) to fine-map genes in polyploid wheat. BMC Plant Biol 2012; 12:14. doi: 10.1186/1471-2229-12-14 22280551
19. Ramirez-Gonzalez RH., Segovia V, Bird N, Fenwick P, Holdgate S, et al. RNA-Seq bulked segregant analysis enables the identification of high-resolution genetic markers for breeding in hexaploid wheat. Plant Biotechnol 2015; 13: 613–624.
20. Zou C, Wang P, Xu Y. Bulked sample analysis in genetics, genomics and crop improvement. Plant Biotechnol 2016; 10:1941–1955. doi: 10.1111/pbi.12559 26990124
21. Rouse NM, Wanyera R, Njau P, Jin Y. Sources of resistance to stem rust race Ug99 in spring wheat germplasm. Plant Dis. 2011; 95:762–766. doi: 10.1094/PDIS-12-10-0940 30731910
22. Stakman EC, Stewart DM, Loegering WQ. Identification of physiologic races of Puccinia graminis var. tritici. U. S. Dep Agric Agric Res Serv. 1962; E-617.
23. Edae AE., Olivera DP, Jin Y, Rouse N M. Genotyping-by-Sequencing facilitates a high density consensus linkage map for Aegilops umbellulata, a wild relative of cultivated wheat. G3: Genes/ Genomics/ Genetics 2017; 7(5): 1551–1561.
24. Bolger AM., Lohse M, Usadel B. Trimmomatic: A flexible trimmer for Illumina sequence data. Bioinformatics 2014; 30(15):2114–20. doi: 10.1093/bioinformatics/btu170 24695404
25. Grabherr M, Haas M, Yassour M, Levin J, Thompson D, Amit I, et al. Trinity: reconstructing a full-length transcriptome without a genome from RNA-Seq data. Nat Biotechnol 2013; 29(7): 644–652. https://trinotate.github.io/ 21572440 Accessed on 05/18/2017.
26. Luo MC., Gu YQ, Puiu D, Wang H, Twardziok SO, Deal KR, et al. Genome sequence of the progenitor of the wheat D genome Aegilops tauschii. Nature 2017; 551:498–502. doi: 10.1038/nature24486 29143815
27. Li H., Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 2009; 25(16): 2078–2079. doi: 10.1093/bioinformatics/btp352 19505943
28. Koboldt D, Chen K, Wylie T, Larson D, McLellan M, Mardis E. et al. VarScan: variant detection in massively parallel sequencing of individual and pooled samples. Bioinformatics 2009; 25(17):2283–2285. doi: 10.1093/bioinformatics/btp373 19542151
29. Finn RD, Clements J, Eddy SR. HMMER web server: interactive sequence similarity searching. Nucleic Acids Research 2011; 39:W29–W37, doi: 10.1093/nar/gkr367 21593126
30. Bailey TL, Boden M, Buske FA, Frith M, Grant CE, Clementi L. et al. MEME SUITE: tools for motif discovery and searching. Nucleic Acids Research 2009; 37:W22–W208.
31. Steuernagel B, Florian J, Kamil W, Jonathan J, Brande W. NLR-parser: rapid annotation of plant NLR complements. Bioinformatics 2015; 31(10):1665–166. doi: 10.1093/bioinformatics/btv005 25586514
32. Jupe F, Pritchard L, Etherington GJ, Mackenzie K, Cock P, Wright F, et al. Identification and localization of the NB-LRR gene family within the potato genome. BMC Genomics 2012; 13:75. doi: 10.1186/1471-2164-13-75 22336098
33. Li W, Godzik A. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 2006; 22(13):1658–1659. doi: 10.1093/bioinformatics/btl158 16731699
34. Sears ER. The transfer of leaf rust resistance from Aegilops umbellulata to wheat. Brookhaven Symp. Biol. 1956; 9: 1–21.
35. Ozgen M, Yildiz M, Ulukan H, Koyuncu N. Association of gliadin protein pattern and rust resistance derived from Aegilops ubmellulata Zhuk. In winter Triticum durum Desf. Breeding Science 2004; 54:287–290.
36. Saintenac C., Zhang W, Salcedo A, Rouse N M, Trick HN, Akhunov E, et al. Identification of wheat gene Sr35 that confers resistance to Ug99 stem rust race group. Science 2013; 341: 783–786. doi: 10.1126/science.1239022 23811222
37. Ellis JG, Lagudah ES, Spielmeyer W, Dodds PN. The past, present and future of breeding rust resistant wheat. Frontiers in Plant Science 2014; 5(641).
38. Zhang W, Chen S, Abate Z, Nirmala N, Rouse NM, Dubcovsky J, et al. Identification and characterization of Sr13, a tetraploid wheat gene that confers resistance to the Ug99 stem rust race group. PNAS 2017; E9483–E9492. doi: 10.1073/pnas.1706277114 29078294
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