Mapping and KASP marker development for wheat curl mite resistance in “TAM 112” wheat using linkage and association analysis
Wheat curl mite (WCM, Aceria tosichella Keifer) and WCM-transmitted wheat streak mosaic virus (WSMV, genus Tritimovirus) are devastating production constraints for wheat in the US Great Plains. Breeding wheat cultivars with genetic resistance to WCM and WSMV is a viable and economically feasible way to reduce yield loss. The objectives of this study were to (a) identify tightly linked markers for WCM resistance in the wheat cultivar TAM 112 (PI 643143) using linkage and association analysis with the 90K Infinium iSelect SNP array and genotyping-by-sequencing, respectively and (b) develop and test kompetitive allele specific PCR (KASP) single-nucleotide polymorphisms (SNPs) for marker-assisted selection (MAS) of WCM resistance. We tested 124 F5:7 recombinant inbred lines (RILs) derived from the cross of TAM 112 and the WCM-susceptible cultivar TAM 111 (PI 631352). All lines were infested with a Texas WCM collection 2 (TWCMC2) that is virulent to resistance found on the wheat-rye 1AL.1RS translocation at the two-leaf stage and were rated for symptoms on the first and second week after infestation. Linkage maps were constructed with 4890 markers, including SNPs, simple sequence repeats (SSRs), and sequence-tagged site (STS) markers covering 21 chromosomes. A WCM resistance gene present in TAM 112 (CmcTAM112) was mapped onto chromosome arm 6DS. A genome-wide association study of wheat streak mosaic (WSM) symptoms from a separate experiment in Colorado showed significant marker-trait associations at the target regions on 6DS where CmcTAM112 was located, which demonstrated the effectiveness of this gene to reduce symptom severity. Four SNPs flanking CmcTAM112 were mapped within 3.6 cM in the biparental mapping population. We developed two KASP markers that are within 1.3 cM distal to CmcTAM112 and tested in diverse germplasm. These two markers can be used in MAS for improving WCM resistance in some wheat genetic backgrounds.
Keywords90K SNP array Genome-wide association study (GWAS) Genotyping-by-sequencing (GBS) Kompetitive allele specific PCR (KASP) Marker-assisted selection (MAS) Wheat curl mite (WCM)
The authors acknowledge Jason Baker at Texas A&M AgriLife Research Center in Amarillo for technical help and development of the population. We acknowledge Dr. Chenggen Chu and Dev R. Poudel for their critical review and suggestions. We also thank Dr. Charlie Rush for providing access to the ABI 7500 instrument for running KASP assays.
Author contribution statement
S. Dhakal conducted phenotyping experiments for WCM, performed all aspects of data analysis and wrote the manuscript; C.-T. Tan confirmed KASP markers and ran the analysis; H. Yu performed KASP assays and rephenotyped some heterogeneous lines; L. Garza prepared the WCM experiments; J.C. Rudd, Q. Xue and A.M.H. Ibrahim provided overall support and help with data interpretation; R.N. Devkota coordinated advancement of the mapping population; V. Anderson and S.D. Haley conducted the GWAS for the breeding nursery lines, analyzed related data, interpreted the results, and provided editorial input on the draft manuscript; S. Liu designed the experiments and provided suggestions for data analysis, interpretation and writing of the manuscript.
This research was partially supported by the Texas Wheat Producers Board, Texas A&M AgriLife Research and the National Research Initiative Competitive Grants 2017-67007-25939 from the USDA National Institute of Food and Agriculture.
Compliance with ethical standards
Conflict of interest
The authors declare that they have no conflict of interest.
The experiments comply with the ethical standards in the country in which they were performed.
- Andrews JE, Slykhuis JT (1956) Reaction of winter wheat varieties and Triticum × Agropyron hybrids when inoculated with wheat streak mosaic virus by the mite vector Aceria tulipae Keifer. Plant Dis Rep 40:513–516Google Scholar
- Appel JA, DeWolf E, Bockus W, Todd T (2012) Preliminary 2011 Kansas wheat disease loss estimates. Kansas Dep. Of Agric., Topeka, KS. http://agriculture.ks.gov/docs/default-source/pp-disease-reports-2012/2012-ks-wheat-disease-loss-estimates.pdf. Accessed 24 Jan 2018
- Butler D (2009) asreml: asreml() fits the linear mixed model. R package version 3.0. https://www.vsni.co.uk/downloads/asreml-r/. Accessed 5 Jan 2018
- Chapman JA, Mascher M, Buluç A, Barry K, Georganas E, Session A, Strnadova V, Jenkins J, Sehgal S, Oliker L, Schmutz J, Yelick KA, Scholz U, Waugh R, Poland JA, Muehlbauer GJ, Stein N, Rokhsar DS (2015) A whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome. Genome Biol 16:26Google Scholar
- Gill BS, Wilson DL, Raupp WJ, Hatchett JH, Harvey TL, Cox TS, Sears RG (1991b) Registration of KS89WGRC4 hard red winter wheat germplasm with resistance to Hessian fly, greenbug, and soil-borne mosaic virus. Crop Sci 31:246Google Scholar
- Goff KE, Ramonell KM (2007) The role and regulation of receptor-like kinases in plant defense. Gene Regul and Syst Bio 1:167–175Google Scholar
- Harvey TL, Martin TJ, Seifers DL (1994) Importance of plant resistance to insect and mite vectors in controlling virus diseases of plants: resistance to the wheat curl mite (Acari: Eriophyidae). J Agric Entomol 11:271–277Google Scholar
- Harvey TL, Martin TJ, Seifers DL (1995) Survival of five wheat curl mites, Aceria tosichella Keifer (Acari: Eriophyidae) strains on mite resistant wheat. Exp and Appl Acarol 19:459–463Google Scholar
- Harvey TL, Martin TJ, Seifers DL (2000) Effect of nonviruliferous wheat curl mites on yield of winter wheat. J. Agric. Urban Entomol. 17:9–13Google Scholar
- Harvey TL, Martin TJ, Seifers DL (2002) Wheat yield reduction due to wheat curl mite (Acari: Eriophyidae) infestations. J Agric Urban Entomol 19:9–13Google Scholar
- Larson RI, Atkinson TG (1973) Wheat-Agropyron chromosome substitution lines as sources of resistance to wheat streak mosaic virus and its vector, Aceria tulipae. In: Sears ER, Sears LM (eds) Proc. 4th Int. Wheat Genetics Symposium. Columbia, Missouri, 6–11 August 1972. University of Missouri, Columbia, pp 173–177Google Scholar
- LGC Genomics (2017) KASP genotyping chemistry: user guide and manual. https://www.lgcgroup.com/LGCGroup/media/PDFs/Products/Genotyping/KASP-genotyping-chemistry-User-guide.pdf. Accessed 5 Jan 2018
- Ribaut JM, Banziger M, Betran J, Jiang C, Edmeades GO, Dreher K, Hoisington D (2002) Use of molecular markers in plant breeding: drought tolerance improvement in tropical maize. In: Kang MS (ed) Quantitative genetics, genomics, and plant breeding. CABI Publishing, Wallingford, UK, pp 85–100Google Scholar
- Rozen S, Skaletsky HJ (1998) Primer3: WWW primer tool. http://biotools.umassmed.edu/bioapps/primer3_www.cgi. Accessed 5 Jan 2018
- Slykhuis JT (1955) Aceria tulipae Keifer (Acarina: Eriophidae) in relation to spread of wheat streak mosaic. Phytopathology 45:116–128Google Scholar
- Turner SD (2014) qqman: an R package for visualizing GWAS results using Q-Q and manhattan plots. biorXiv. https://www.r-project.org/nosvn/pandoc/qqman.html. Accessed 5 Jan 2018
- Wang S, Wong D, Forrest K, Allen A, Chao S, Huang BE, Maccaferri M, Salvi S, Milner SG, Cattivelli L, Mastrangelo AM, Whan A, Stephen S, Barker G, Wieseke R, Plieske J, International Wheat Genome Sequencing Consortium, Lillemo M, Mather D, Appels R, Dolferus R, Brown-Guedira G, Korol A, Akhunova AR, Feuillet C, Salse J, Morgante M, Pozniak C, Luo MC, Dvorak J, Morell M, Dubcovsky J, Ganal M, Tuberosa R, Lawley C, Mikoulitch I, Cavanagh C, Edwards KJ, Hayden M, Akhunov E (2014) Characterization of polyploidy wheat genomic diversity using a high-density 90,000 single nucleotide polymorphism array. Plant Biotechnol 12:787–796CrossRefGoogle Scholar
- Wang H, Zhang H, Du R, Chen G, Liu B, Yang Y, Qin L, Cheng E et al (2016) Identification and validation of QTLs controlling multiple traits in sorghum. Crop Pasture Sci 67:193–203Google Scholar
- Wilkinson PA, Winfield MO, Barker GLA, Allen AM, Burridge A, Coghill JA, Burridge A, Edwards KJ (2012) CerealsDB 2.0: an integrated resource for plant breeders and scientists. BMC Bioinf 13:219. http://www.cerealsdb.uk.net//cerealgenomics/CerealsDB/blast_WGS.php. Accessed 24 Jan 2018CrossRefGoogle Scholar