DOI: 10.15482/usda.adc/1528703
title: Data from: Mapping the Quantitative Field Resistance to Stripe Rust in a Hard Winter Wheat Population ‘Overley’ × ‘Overland’

description: Data reported in research published in Crop Science, “Mapping the quantitative field resistance to stripe rust in a hard winter wheat population ‘Overley’ × ‘Overland.’”  Authors are Wardah Mustahsan, Mary J. Guttieri, Robert L. Bowden, Kimberley Garland-Campbell, Katherine Jordan, Guihua Bai, Guorong Zhang from USDA Agricultural Research Service and Kansas State University. This study was conducted to identify quantitative trait loci (QTL) associated with field resistance to stripe rust, also known as yellow rust (YR), in hard winter wheat. Stripe rust infection type and severity were rated in recombinant inbred lines (RILs, n=204) derived from a cross between hard red winter wheat cultivars ‘Overley’ and ‘Overland’ in replicated field trials in the Great Plains and Pacific Northwest. RILs (n=184) were genotyped with reduced representation sequencing to produce SNP markers from alignment to the ‘Chinese Spring’ reference sequence, IWGSC v2.1, and from alignment to the reference sequence for ‘Jagger’, which is a parent of Overley. Genetic linkage maps were developed independently from each set of SNP markers. QTL analysis identified genomic regions on chromosome arms 2AS, 2BS, 2BL, and 2DL that were associated with stripe rust resistance using multi-environment best linear unbiased predictors for stripe rust infection type and severity. Results for the two linkage maps were very similar. PCR-based SNP marker assays associated with the QTL regions were developed to efficiently identify these genomic regions in breeding populations.
Field response to YR was evaluated in seven trials: Rossville, KS (2018 and 2019), Hays, KS (2019), Pullman, WA (2019 and 2020) and Central Ferry, WA (2019 and 2020). An augmented experimental design was used at Rossville, KS with highly replicated checks and two full replications of RILs (n=187 in 2018; n=204 in 2019). The field experiment at Hays was arranged in a partially replicated augmented design with one or two replications of each RIL (n=194). The parental checks (Overley and Overland) were represented in three blocks for each of the two field replications at Hays, and RILs were distributed among blocks; not all RILs were present in each replication. RILs were arranged in an augmented design with two replications at Pullman (n=204 RILs) and Central Ferry (n=155 RILs in 2019; n=204 in 2020). At Pullman and Central Ferry.
The trials at Rossville, KS were inoculated using an inoculum consisting of equal parts of four isolates that were all virulent to Yr9. Two isolates were collected in Kansas in 2010 and had virulence to Yr17 but not QYr.tamu-2B. The other two isolates were from Kansas in 2012 and had virulence to QYr.tamu-2B, but not Yr17. Susceptible spreader rows (KS89180B, carrying Yr9) were inoculated several times during the tillering stage in the evenings with an ultra-low volume sprayer using a suspension of 2 mL of fresh urediniospores in 1 L of Soltrol 170 isoparaffin oil. Trials at Pullman, WA and Central Ferry, WA were evaluated under natural inoculum supplemented by a mixture of isolates collected in the previous field season. The trial at Hays, KS was evaluated under natural infection.
Data collection at Rossville, KS began once the susceptible check (KS89180B) had an infection severity coverage of ~10% and continued until senescence. In Rossville, disease ratings (IT and SEV) were collected on 16, 22, and 28th of May 2019. Most ratings in Rossville were taken some time after heading from Zadoks stages 55 to 70. In Pullman, disease ratings were collected on July 1 and 12. In Central Ferry, disease ratings were taken on 12th and 18th of June 2019. The second rating date was used for subsequent statistical analysis. In Hays, disease ratings were taken on June 1, 2019, when the plants were in early booting or heading stages (Zadoks 31-41). Stripe rust evaluations were measured using two disease rating scales: IT (0-9; from no infection to highly susceptible, Line and Qayoum, 1992) and SEV based on visual estimation of the percent flag leaf area affected by the pathogen including associated chlorosis and necrosis (0-100%).
DNA was extracted from seedlings, and genotyping-by-sequencing was conducted as described previously (Guttieri, 2020) on a subset of 189 lines (187 RILS and 2 parents) of which 23 RILs were F6-derived and 164 RILs were F9-derived. Single nucleotide polymorphisms (SNPs) were identified in parallel using reference-based calling in the TASSEL pipeline (Bradbury et al., 2007) using both the IWGSC v2.1 reference genome (Zhu et al., 2021) and the Jagger reference sequence (Wheat Genomes Project (http://www.10wheatgenomes.com/10-wheat-genomes-project-and-the-wheat-ini...). The TASSEL pipeline was executed with the following parameters: minimum read count = 1, minimum quality score = 0, minimum locus coverage = 0.19, and minimum minor allele frequency = 0.005, minimum heterozygous proportion = 0, and removal of minor SNP states. The resulting SNP datasets from each reference sequence were filtered in TASSEL by taxa (RILs) and sites (SNPs). The RILs were filtered to include those RILs for which at least 20% sites were present. The sites were filtered to include sites for which &gt; 60% of RILs were called, minor allele frequency (MAF) &gt; 0.25, maximum allele frequency &lt; 0.75, maximum heterozygous proportion = 0.25, and removal of minor SNP states. The ABH plugin in TASSEL was applied to this reduced dataset to identify parental genotypes.
Resources in this dataset:


Resource Title: Multilocation Stripe Rust Data
File Name: MultiLocRawData_Yr.xslx


Resource Title: OvOv_CS_TasselSNPCalls
File Name: KSM17-OvOv-parents_merge1.hmp_.txt
Resource Description: Output of TASSEL GBS SNP calling pipeline using Chinese Spring v2 refseq. Starting point for map construction pipeline.


Resource Title: OvOv GBS SNP Calls Jagger RefSeq
File Name: KSM17-OvOv-Jagger_pmerge1.hmp_.txt
Resource Description: TASSEL output from reference-based SNP calling using the Jagger reference sequence


Resource Title: QTL-Associated KASP Markers with IT and SEV BLUPs
File Name: KASP_Data_IT_SEV.xlsx
Resource Description: Multilocation best linear unbiased predictors (BLUPs) for stripe rust infection type and severity of recombinant inbred lines. KASP assay results for QTL-associated SNPs, coded Overley = 2, Overland = 0, Het = 1, Missing = "."