Development and Validation of KASP Markers for Wheat Streak Mosaic Virus Resistance Gene Wsm 2

Wheat streak mosaic virus (WSMV) can cause significant yield loss in wheat (Triticum aestivum L.) in the Great plains of North America. A recently identified WSMV resistance gene, Wsm2, was mapped to chromosome 3BS in germplasm line ‘Co960293–2’. Effective genetic markers tightly linked to the gene will enhance the selection of WSMV-resistant lines through marker-assisted selection. We have mapped Wsm2 using a highdensity map developed from the wheat 90K Infinium iSelect single-nucleotide polymorphism (SNp) array with recombinant inbred lines from the cross between Co960293–2 and susceptible cultivar ‘TAM 111’. Array-based SNps that mapped within 4 cM of Wsm2 on chromosome 3BS were converted to Kompetitive Allele Specific polymerase Chain reaction (KASp) assays in this study. Six KASp SNps were validated in two doubled haploid populations developed from crosses of ‘ronL’ ́ ‘ripper’ and ‘Snowmass’ ́ ‘Antero’. ronL and Snowmass possess the Wsm2 gene from Co960293–2. Three closely linked KASp SNps, converted from IAAV6442, BS00018764_51, and wsnp_ ra_c16264_24873670, showed high sensitivity and specificity (0.83 £ sensitivity £ 0.97, 0.89 £ specificity £ 0.99). The latter two were also validated in six F2 breeding populations. These three KASp SNps were effective in differentiating resistant and susceptible genotypes. Comparative mapping was performed using sequences of SNps flanking Wsm2 and identified candidate genes and regions in Brachypodium and rice (Oryza sativa L. ssp. japonica). The KASp SNps developed in this study should be useful for marker-assisted selection of Wsm2 in wheat breeding programs, and the newly constructed map will also facilitate map based cloning of Wsm2. C-T. Tan, S. Assanga, J.C. Rudd, Q. Xue, M.P. Fuentealba, S.-Y. Liu, Texas A&M AgriLife Research, 6500 Amarillo Blvd. W, Amarillo, TX 79106; S. Assanga, A. Ibrahim, Dep. of Soil and Crop Sciences, Texas A&M Univ., College Station, TX 77843; G. Zhang, X. Zhang, Agricultural Research Center–Hays, Kansas State Univ., Hays, KS 67601; S.D. Haley, P. Byrne, Soil and Crop Sciences Dep., Colorado State Univ., Fort Collins, CO 80523; G. Bai, USDA–ARS Central Genotyping Center, Manhattan, KS 66506. Received 15 Apr. 2016. Accepted 22 Sept. 2016. *Corresponding author (SLiu@ag.tamu.edu). Assigned to Associate Editor Toi Tsilo. Abbreviations: BAC, bacterial artificial chromosome; BLASTN, nucleotide–nucleotide basic local alignment search tool; DH, doubled haploid; EST, expressed sequence tag; IWGSC, International Wheat Genome Sequencing Consortium; KASP, Kompetitive Allele Specific Polymerase Chain Reaction; LOD, logarithm of odds; MAS, markerassisted selection; RILs, recombinant inbred lines; RR, ‘RonL’ ́ ‘Ripper’; SA, ‘Snowmass’ ́ ‘Antero’; SNP, single-nucleotide polymorphism; SSR, simple sequence repeat; WSMV, wheat streak mosaic virus. Published in Crop Sci. 57:340–349 (2017). doi: 10.2135/cropsci2016.04.0234 © Crop Science Society of America | 5585 Guilford Rd., Madison, WI 53711 USA This is an open access article distributed under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/). Published November 1, 2016

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