QTL-seq and marker development for resistance to Fusarium oxysporum f. sp. niveum race 1 in cultivated watermelon
Tóm tắt
Fusarium wilt, caused by the fungus Fusarium oxysporum f. sp. niveum (Fon), is one of the predominant diseases of watermelon. Resistance to Fon race 1 is conferred by a single major quantitative trait locus (QTL), Fo-1.1, but resolution of this region has been poor due to low marker density. In this study, a combination of whole genome resequencing of bulked segregants (QTL-seq analysis) followed by QTL mapping with kompetitive allele specific PCR (KASP) markers developed across Fo-1.1 successfully increased the resolution from 2.03 to 1.56 Mb and 315 kb, respectively. The linkage of the KASP markers to Fon race 1 resistance across a wide range of watermelon germplasm was validated in a set of elite watermelon cultivars. The linked markers described here provide a breeder-friendly toolkit immediately available for high-throughput genotyping in large-scale breeding programs for fine mapping and incorporation of Fon race 1 resistance in watermelon.
Tài liệu tham khảo
Antoniw JF, Ritter CE, Pierpoint WS, Van Loon LC (1980) Comparison of three pathogenesis-related proteins from plants of two cultivars of tobacco infected with TMV. J Gen Virol 47(1):79–87
Berrocal-Lobo M, Molina A (2004) Ethylene response factor 1 mediates Arabidopsis resistance to the soilborne fungus Fusarium oxysporum. Mol Plant-Microbe Interact 17(7):763–770
Branham SE, Levi A, Farnham MW, Patrick Wechter W (2017) A GBS-SNP-based linkage map and quantitative trait loci (QTL) associated with resistance to Fusarium oxysporum f. sp. niveum race 2 identified in Citrullus lanatus var. citroides. Theor Appl Genet 130:319–330. https://doi.org/10.1007/s00122-016-2813-0
Broman KW, Sen S (2009) A guide to QTL mapping with R/qtl (Vol. 46). Springer, New York
Broman KW, Speed T (2002) A model selection approach for the identification of quantitative trait loci in experimental crosses (with discussion). J R Stat Soc B 64(641–656):731–775
Broman KW, Wu H, Sen S, Churchill GA (2003) R/qtl: QTL mapping in experimental crosses. Bioinformatics 19:889–890. https://doi.org/10.1093/bioinformatics/btg112
Catanzariti AM, Lim GTT, Jones DA (2015) The tomato I-3 gene: a novel gene for resistance to fusarium wilt disease. New Phytol 207:106–118. https://doi.org/10.1111/nph.13348
Chambers JM, Freeny A, Heiberger RM (1992) Analysis of variance; designed experiments. Chapter 5 of Statistical models in S, eds J. M. Chambers and T. J. Hastie, Wadsworth & Brooks/Cole
Cole SJ, Diener AC (2013) Diversity in receptor-like kinase genes is a major determinant of quantitative resistance to Fusarium oxysporum f.sp matthioli. New Phytol 200:172–184. https://doi.org/10.1111/nph.12368
Collard BCY, Mackill DJ (2008) Marker-assisted selection: an approach for precision plant breeding in the twenty-first century. Philos Trans R Soc B Biol Sci 363:557–572. https://doi.org/10.1098/rstb.2007.2170
Elshire RJ, Glaubitz JC, Sun Q et al (2011) A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS One 6:e19379. https://doi.org/10.1371/journal.pone.0019379
FAOSTAT: Food and Agriculture Organization of the United Nations (2017) http://www.fao.org/faostat/en/#search/watermelon. Accessed 7/2/2018
Girhepuje PV, Shinde GB (2011) Transgenic tomato plants expressing a wheat endochitinase gene demonstrate enhanced resistance to Fusarium oxysporum f. sp. lycopersici. Plant Cell Tiss Org Cult 105(2):243–251
Guo S, Zhang J, Sun H et al (2013) The draft genome of watermelon (Citrullus lanatus) and resequencing of 20 diverse accessions. Nat Genet 45:51–58. https://doi.org/10.1038/ng.2470
Jabeen N, Chaudhary Z, Gulfraz M, Rashid H, Mirza B (2015) Expression of rice chitinase gene in genetically engineered tomato confers enhanced resistance to fusarium wilt and early blight. Plant Pathol J 31(3):252–258
Keinath AP, Hassell RL, Everts KL, Zhou XG (2010) Cover crops of hybrid common vetch reduce fusarium wilt of seedless watermelon in the eastern United States. Plant Health Progress Online publication doi:https://doi.org/10.1094/PHP-2010-0914-01-RS
Kosambi DD (1943) The estimation of map distances from recombination values. Ann Eugenics 12:172–175. https://doi.org/10.1111/j.1469-1809.1943.tb02321.x
Kosugi S, Natsume S, Yoshida K et al (2013) Coval: improving alignment quality and variant calling accuracy for next-generation sequencing data. PLoS One. https://doi.org/10.1371/journal.pone.0075402
Lambel S, Lanini B, Vivoda E et al (2014) A major QTL associated with Fusarium oxysporum race 1 resistance identified in genetic populations derived from closely related watermelon lines using selective genotyping and genotyping-by-sequencing for SNP discovery. Theor Appl Genet 127:2105–2115. https://doi.org/10.1007/s00122-014-2363-2
Levi A, Thomas CE, Wehner TC, Zhang X (2001) Low genetic diversity indicates the need to broaden the genetic base of cultivated watermelon. HortScience 36:1096–1101.
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
Li H, Handsaker B, Wysoker A et al (2009) The sequence alignment/map format and SAMtools. Bioinformatics 25:2078–2079. https://doi.org/10.1093/bioinformatics/btp352
Li N, Wang J, Shang J, Li N, Xu Y, Ma S (2017) Fine-mapping of QTL and development of InDel markers for Fusarium oxysporum race 1 resistance in watermelon. Sci Agric Sin 50:131–141. https://doi.org/10.3864/j.issn.0578-1752.2017.01.012
Manichaikul A, Moon JY, Sen Ś et al (2009) A model selection approach for the identification of quantitative trait loci in experimental crosses, allowing epistasis. Genetics 181:1077–1086. https://doi.org/10.1534/genetics.108.094565
Marchler-Bauer A, Bryant SH (2004) CD-search: protein domain annotations on the fly. Nucleic Acids Res 32:327–331. https://doi.org/10.1093/nar/gkh454
Marchler-Bauer A, Bo Y, Han L et al (2017) CDD/SPARCLE: functional classification of proteins via subfamily domain architectures. Nucleic Acids Res 45:D200–D203. https://doi.org/10.1093/nar/gkw1129
Martyn RD, Bruton BD (1989) An initial survey of the United States for races of Fusarium oxysporum f. sp. niveum. HortSci 24:696–698
Martyn RD, Netzer D (1991) Resistance to races 0, 1, and 2 of fusarium wilt of watermelon in Citrullus sp. PI-296341-FR. HortSci 26:429–432
Meru G, McGregor C (2016) Genotyping by sequencing for SNP discovery and genetic mapping of resistance to race 1 of Fusarium oxysporum in watermelon. Sci Hortic 209:31–40. https://doi.org/10.1016/j.scienta.2016.06.005
Michelmore RW, Paran I, Kesseli RV (1991) 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 88:9828–9832. https://doi.org/10.1073/pnas.88.21.9828
Moosa A, Farzand A, Sahi ST, Khan SA (2017) Transgenic expression of antifungal pathogenesis-related proteins against phytopathogenic fungi–15 years of success. Israel J Plant Sci. https://doi.org/10.1080/07929978.2017.1288407
Mundt CC (2014) Durable resistance: a key to sustainable management of pathogens and pests. Infect Genet Evol 27:446–455. https://doi.org/10.1016/j.meegid.2014.01.011
Netzer D, Weintall CH (1980) Inheritance of resistance in watermelon to race 1 of Fusarium oxysporum f. sp. niveum. Plant Dis 64:853–854
Nimmakayala P, Levi A, Abburi L, Abburi VL, Tomason YR, Saminathan T, Vajja VG, Malkaram S, Reddy R, Wehner TC, Mitchell SE, Reddy UK (2014) Single nucleotide polymorphisms generated by genotyping by sequencing to characterize genome-wide diversity, linkage disequilibrium, and selective sweeps in cultivated watermelon. BMC Genomics 15:767. https://doi.org/10.1186/1471-2164-15-767
R Core Team (2017) R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria
Ren Y, Jiao D, Gong G et al (2015) Genetic analysis and chromosome mapping of resistance to Fusarium oxysporum f. sp. niveum (FON) race 1 and race 2 in watermelon (Citrullus lanatus L.). Mol Breed 35:1–9. https://doi.org/10.1007/s11032-015-0375-5
Sekhwal M, Li P, Lam I et al (2015) Disease resistance gene analogs (RGAs) in plants. Int J Mol Sci 16:19248–19290. https://doi.org/10.3390/ijms160819248
Sen S, Churchill GA (2001) A statistical framework for quantitative trait mapping. Genetics 159:371–387. https://doi.org/10.1126/science.1242429
Singh D, Haicour R, Sihachakr D, Rajam MV (2015) Expression of rice chitinase gene in transgenic eggplant confers resistance to fungal wilts. Indian J Biotechnol 14:233–240
Takagi H, Abe A, Yoshida K et al (2013) QTL-seq: rapid mapping of quantitative trait loci in rice by whole genome resequencing of DNA from two bulked populations. Plant J 74:174–183. https://doi.org/10.1111/tpj.12105
United States Environmental Protection Agency (2017) International Actions - The Montreal Protocol on Substances that Deplete the Ozone Layer. https://www.epa.gov/ozone-layer-protection/international-actions-montreal-protocol-substances-deplete-ozone-layer
Van Loon LC, Van Strien EA (1999) The families of pathogenesis-related proteins, their activities, and comparative analysis of PR-1 type proteins. Physiol Mol Plant Pathol 55(2):85–97
Van Loon LC, Pierpoint WS, Boller TH, Conejero V (1994) Recommendations for naming plant pathogenesis-related proteins. Plant Mol Biol Report 12(3):245–264
Wechter WP, Kousik C, McMillan M, Levi A (2012) Identification of resistance to Fusarium oxysporum f. sp. niveum race 2 in Citrullus lanatus var. citroides plant introductions. HortSci 47:334–338. https://doi.org/10.1002/ird.1717
Xu Y (2014) SNP loci linked with blight resistant gene Fon-1 in watermelon, and markers thereof. Patent CN103146691B. 02 April 2014
Zeng ZB, Kao CH, Basten CJ (1999) Estimating the genetic architecture of quantitative traits. Genet Res 74:279–289. https://doi.org/10.1017/S0016672399004255
Zhou XG, Everts KL, Bruton BD (2010) Race 3, a new and highly virulent race of Fusarium oxysporum f. sp. niveum causing fusarium wilt in watermelon. Plant Dis 94:92–98