Wheat stripe rust is one of the main diseases that seriously threaten wheat production safety. In this study, the genetic analysis of stripe rust resistance was carried out on resistant wheat variety KFA/2*KACHU. The whole F5 RIL population were tested with Chinese Pst CYR33 at the seedling stage and a novel stripe rust resistance gene was identified, temporary named as YrK. In addition, a total of four APR QTLs were identified, however, we did not detect the effect of YrK on stripe rust at the adult plant stage, which may be due to the different Pst races used for inoculation at both seedling and adult plant stages. Closely-linked molecular markers of several stripe rust resistance loci were converted into KASP markers for the MAS in breeding program.
In the present study, YrK was derived from KFA/2*KACHU and showed moderate seedling resistance to YR. The physical location of YrK was mapped at 497–520 Mb on wheat chromosome 5BL based on Chinese spring reference genome (IWGSC 2018). So far, several stripe rust resistance genes/loci have been detected on chromosome 5BL, such as YrExp2 (Lin and Chen 2008), QYr.tem-5B.1 (Feng et al. 2011), QYr.tem-5B.2 (Feng et al. 2011), YrSD (Feng et al. 2013) and Yr74 (Dracatos et al. 2016). YrExp2 was flanked by molecular marker Xgwm639 and the physical position of Xgwm639 was at 504 Mb, which overlapped with YrK, however, YrExp2 was susceptible to Chinese Pst races CYR31, CYR32, CYR33, V26/CH42 and V26/Gui (Lin and Chen 2008). Therefore, it should be different from YrK; QYr.tem-5B.1 and QYr.tem-5B.2 derived from wheat cultivar “Flinor” were two temperature-sensitive seedling resistance QTL and they only provided resistance under high temperature conditions with 166 Mb and 78 Mb away from YrK, respectively, based on the Chinese spring reference genome (Feng et al. 2011). Thus, YrK should be different from both QYr.tem-5B.1 and QYr.tem-5B.2. Although YrSD was mapped at wheat chromosome 5BL and showed moderated resistance to CYR33, it was at least 150Mb away from YrK according to the Chinese spring reference genome, indicating that YrSD and YrK were not identical (Feng et al. 2013). Yr74 was confirmed to be required to co-exist with another rust resistance gene Yr73 in order to provide the resistance of YrA from Avocet, while Yr74 did not exhibit seedling resistance when present alone (Dracatos et al. 2016). Therefore, YrK should be a new race-specific seedling resistance gene of stripe rust.
Among the cloned stripe rust resistance genes, Yr36 belongs to kinase class, and it can provide resistance for wheat stripe rust during both seedling and adult plant stages at a relative high temperature (Fu et al. 2009). In this study, TraesCS5B02G330700 is one of YrK’s candidate genes and belongs to the kinase family as well, while the temperate sensitivity of YrK might need to confirm further.
QYr.hazu-1BL was detected on chromosome 1BL and can explain 12.42–34.20% for stripe rust severity variations. It was flanked by molecular markers 1122155|F|0–53:C > G-53:C > G, 2266964|F|0–57:A > G-57:A > G, 1132278|F|0–20:C > T-20:C > T and KASP_Yr29, while the last marker was designed based on the BSR-seq sequence results and could be directly used for MAS in wheat breeding program. We also used molecular markers cslv46G22 that was closely link to the known pleiotropic APR gene Lr46/Yr29/Pm39 to genotype the parents and RILs and confirmed it should be the same as QYr.hazu-1BL based on the physical position and single maker analysis on the phenotype. Lr46/Yr29/Pm39 was identified in CIMMYT wheat variety “Pavon 76”, conferring slow rusting resistance more than 40 years (Singh et al. 1998). Lan et al. (2014) found that the average disease severity of stripe rust can be reduced by 20% when lines only carried Lr46/Yr29/Pm39. Recently, Ye et al. (2021) also found that RILs carrying gene Yr29 was significantly reduced by 11% of stripe rust severity, while it can be reduced by 45% if lines combing both Yr29 and Yr30.
QYr.hazu-2AS was located on wheat chromosome 2AS, explaining 9.60 to 21.10% of the phenotypic variation. The known stripe rust resistance gene Yr17 was also located the same chromosome and was originated from Aegilops ventricosa (Helguera et al. 2003). The close-linked molecular marker of Yr17, csVrgal3, was used to genotype the two parents and the whole RIL population and it was co-segregated with flanking molecular of QYr.hazu-2AS. Thus, QYr.hazu-2AS was most likely Yr17 in the present study. It showed significant additive effect with other resistance genes resulting in wildly utilization in wheat breeding program in recently (Ye et al. 2021; Gao et al. 2021; Wu et al. 2021; Coriton et al. 2020). We would like to suggest wheat breeders use Yr17 in combination with other genes to improve durable stripe rust resistance in wheat breeding.
A minor QTL for APR, QYr.hzau-2BS, was detected on the short arm of chromosome 2B, accounting for 8.46–17.43% of the phenotypic variation. So far, several stripe rust resistance genes and QTLs were mapped on this chromosome, such as Yr27, Yr31, Yr41 and YrF (Athiyannan et al. 2022; Luo et al. 2008; Zeng et al. 2015; Lan et al. 2014). QYr.hzau-2BS should be different from them given that they were all seedling resistance genes based on the chromosome positions and stripe rust reaction. Wu et al. (2021) mapped an APR locus Qyrnap.nwafu-2BS in CIMMYT wheat line “Napo 63” and its closely-linked molecular marker AX-109302096 was 11.3Mb away from QYr.hazu-2BS based on the Chinese Spring genome. Therefore, the relationship between QYr.hazu-2BS and the reported QTL need to further verify.
Screening germplasm resources for resistance, mining and locating new resistance loci and increasing the genetic diversity of resistance can be conductive to the lasting stability of resistance in wheat stripe rust resistance breeding. MAS based on gene level can accurately aggregate resistance genes and accelerate the breeding process significantly. In this study, the new all-stage resistance gene YrK located on chromosome 5BL can provide moderate resistance to wheat stripe rust in some wheat plant area where seedling stripe rust undermine, the corresponding co-segregated KASP marker designed will be helpful for the application of this gene in wheat breeding program.
In addition, CIMMYT produced a large number of durable resistant wheat lines that are near to immune by accumulation 3–5 APR genes. In order to ensure the stability of stripe rust resistance, the pyramiding and utilization of APR gene should be further strengthened. In this study, QYr.hazu-2AS should be the known gene Yr17 and QYr.hazu-2BS was confirmed most likely a new stripe rust locus. According to the distribution of QYr.hazu-2BS and QYr.hazu-2AS in 153 international wheat collections in the present study, indicating that both resistance loci are mainly distributed in CIMMYT and their utilization rate is very low of in Chinese breeding materials. Thus, the two KASP markers designed in this study will be benefit to speed the application of these two loci in Chinese wheat breeding.