Mapping and KASP marker development for wheat curl mite resistance in “TAM 112” wheat using linkage and association analysis
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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.
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