Location: Cereal Crops Improvement Research
Project Number: 3060-21000-046-012-T
Project Type: Trust Fund Cooperative Agreement
Start Date: Jun 15, 2021
End Date: Dec 30, 2024
Objective:
1) Fine mapping of the major QTL on 7H, QRptm-7H-119-137 (QRptm-7H hereafter).
2) Identification of candidate genes for QRptm-7H.
3) Development of user-friendly markers to assist barley breeding for resistance to SFNB.
4) Field and greenhouse test to confirm if the resistance induced by disruption of QRptm-7H is effective at both seedling and adult stages.
Approach:
1) A total of 200 F2s will be genotyped with flanking markers for the three loci, and the individuals segregating only at the 7H locus will be selected to develop near-isogenic lines (NILs). Meanwhile, 180 RILs will be used to identify heterozygous residuals at the 7H locus for construction of NIL.
2) Fine mapping of QRptm-7H
At least 1000 RILs will be used for genetic mapping. Inoculum isolate preparation and inoculation will follow the methods established by Nepane et al. (2015). Briefly, two-week-old seedlings growing in a greenhouse will be spray-inoculated, followed by incubation for 24 hours in a mist chamber. The inoculated plants will be then transferred to a growth chamber. Ninety-four RILs will be used first for SNP genotyping with the barley 50k iSelect SNP Array. To assisted breeding selection, the linked SNPs will be converted to PCR-based markers, such as semi-thermal asymmetric reverse PCR (STARP) markers.
3) Data Analysis and interpretation
Disease reactions will be evaluated seven days after inoculation using a 1 to 5 scale as described by Neupane et al. (2015), where 1 is highly resistant and 5 is highly susceptible. The average disease severities from three independent replicates of the phenotyping assays will be used for mapping of SFNB resistance/susceptibility. A permutation test with 1000 iterations will be performed to find a LOD threshold for QTL analysis at a significance level of a = 0.05 and 0.01. Linkage analysis and QTL mapping will be conducted using the software program Joinmap.
4) Identification of candidate genes for QRptm-7H.
Gene annotation will be conducted with the genome sequence at the QRptm-7H region, and potential candidate genes will be identified for functional validation. User-friendly markers will be developed for the candidate genes.
5) Field and greenhouse test of QRptm-7H at both seedling and adult stages
Near-isogenic lines will be used for field and greenhouse test to confirm if the 7H locus is effective at both seedling and adult stages. Three replicates with a completely randomized design will be employed.
