Wheat stripe rust is a highly contagious disease caused by the fungal pathogen Puccinia striiformis f. sp. tritici (Pst). The pathogen is capable of spreading rapidly over long distances and causing large-scale epidemics (Wellings 2011; Chen 2020). When wheat crops in a large geographic region are affected by stripe rust, the grain yield can be reduced by 5% − 20% (Wellings 2021). In an individual field grown with a highly susceptible wheat cultivar, severe stripe rust can cause a complete loss of grain yield (Chen 2014; Zhou et al. 2022). The most effective approach for controlling stripe rust is to breed resistant cultivars. Unfortunately, many wheat varieties that were once resistant to the disease have become susceptible in China and many other countries (Chen et al. 2009; Kang et al. 2015). It is urgent to identify wheat germplasm and genes for resistance to be used in developing wheat cultivars with effective and durable resistance to stripe rust (Zhou et al. 2015b).
There are two types of stripe rust resistance genes, all-stage resistance (ASR) and adult-plant resistance (APR). ASR refers resistance to the disease throughout all growth stages, whereas plants with only adult-plant resistance (APR) are susceptible at the seedling stage, but become resistant after the seedling stage and the resistance level can increase as plants grow older and often when the weather becomes warmer (Chen 2005, 2013). ASR can be easily detected in the seedling stage and easily transferred into new cultivars. When effective, an ASR gene can provide complete control for the cultivar or cultivars carrying the gene, but the gene can be circumvented by new virulent races of the pathogen. In contrast, APR is usually non-race specific and therefore durable. However, APR is usually partial, and some APR genes may not provide adequate resistance if stripe rust starts early in the plant growth season and the weather is not warm enough for the full expression of the resistance genes (Chen 2013, 2014). The best approach is to combine both effective ASR and APR genes in wheat cultivars to achieve adequate and durable resistance for control of stripe rust (Chen 2013).
To date, 86 officially named Yr genes (Klymiuk et al. 2022; Feng et al. 2023; Zhu et al. 2023) and more than 300 provisionally named genes or quantitative trait loci (QTL) in wheat and its wild relatives have been identified for resistance to stripe rust (Wang and Chen 2017; Pakeerathan et al. 2019; Li et al. 2020). Of the 86 permanently designated genes, about 30 genes confer APR, including Yr11, Yr12, Yr13, Yr14, Yr16, Yr18, Yr29, Yr30, Yr34, Yr36, Yr39, Yr46, Yr48, Yr49, Yr52, Yr54, Yr56, Yr58, Yr59, Yr60, Yr62, Yr68, Yr71, Yr75, Yr77, Yr78, Yr79, Yr80, Yr83 and Yr86; and the others confer ASR. Six ASR genes (Yr5, Yr7, Yr15, YrAS2388, YrSP and YrU1) (Klymiuk et al. 2018; Marchal et al. 2018; Wang et al. 2020; Zhang et al. 2020) and three APR genes (Yr18, Yr36 and Yr46) (Fu et al. 2009; Krattinger et al. 2009; Moore et al. 2015) have been cloned. Although the number of reported stripe rust resistance genes is quite large, many of the race-specific ASR genes are no longer effective. It is still needed to identify more effective genes and develop molecular markers for more efficiently breeding stripe rust resistant wheat cultivars.
The utilization of marker-assisted selection (MAS) enables breeders to incorporate multiple resistance genes into new cultivars (Zhou et al. 2015a). With the advancing high-throughput sequencing and molecular marker technologies, more effective and user-friendly markers have been developed for various traits, including stripe rust resistance and used in breeding programs through MAS (Barendse et al. 2009; Kump et al. 2011). Simple nucleotide polymorphisms (SNPs) offer an extremely promising approach for exploring genetic variations in crop germplasms and permit the identification of markers closely linked to the target genes or QTL (Wu et al. 2018). By converting SNPs into Kompetitive Allele Specific PCR (KASP) markers, individual markers can be used to screening breeding lines for the specific traits (Rasheed et al. 2016).
Spring wheat PI 660072 was developed by the Wheat Health, Genetics and Quality Research Unit of the US Department of Agriculture, Agricultural Research Service (USDA-ARS) and Washington State University and deposited in the USDA-ARS National Small Grains Collection (Wang et al. 2012). The line was selected from the progeny from a cross of stripe rust susceptible spring wheat Avocet S (AvS) and resistant spring wheat line PI 180957 originally from India. In the previous study, PI 660072 was resistant to US Pst races PST-114 and PST-127 and moderately resistant to PST-43 and PST-100 in the seedling tests and highly resistant in the fields under natural Pst infection in Washington State before its registration, and it was thus concluded to have both ASR and high-temperature adult-plant resistance (Wang et al. 2012). PI 660072 has continually shown high resistance to stripe rust in the United States (Wang MN and Chen XM, unpublished data). In China, PI 660072 was also highly resistant to the predominant Pst races in both greenhouse seedling and field adult-plant tests (Zhou et al. 2015b). However, the genetic basis of the stripe rust resistance in PI 660072 was not clear. The objectives of this study were to: 1) genetically characterize the stripe rust resistance in PI 660072 and map its resistance genes using a whole-genome QTL mapping approach, 2) assess the stability of the resistance genes across different environments, 3) determine if the genes confer ASR and APR and 4) to develop KASP markers to be used in MAS.