Genome-wide Mapping for Stripe Rust Resistance Loci in Common Wheat Cultivar

Stripe rust caused by Puccinia striiformis f. sp. tritici threatens worldwide wheat production. Growing resistant cultivars is the best way to control this disease. Chinese wheat cultivar Qinnong 142 (QN142) has a high level of adult-plant resistance to stripe rust. To identify quantitative trait loci (QTLs) related to stripe rust resistance, we developed a recombinant inbred line (RIL) population from a cross betweenQN142 and susceptible cultivar Avocet S. The parents and 165 F6 RILs were evaluated in terms of their stripe rust infection type and disease severity in replicated field tests with six site-year environments. The parents and RILs were genotyped with single-nucleotide polymorphism (SNP) markers. Four stable QTLs were identified in QN142 and mapped to chromosome arms 1BL, 2AL, 2BL, and 6BS. The 1BL QTL was probably the known resistance gene Yr29, the 2BL QTL was in a resistance gene-rich region, and the 2AL and 6BS QTLs might be new. Kompetitive allele specific polymerase chain reactionmarkers developed from the SNPmarkers flanking theseQTLs were highly polymorphic in a panel of 150 wheat cultivars and breeding lines. These markers could be used in marker-assisted selection for incorporating the stripe rust resistance QTL into new wheat cultivars. Wheat (Triticum aestivum L.) is a major crop throughout the world. Stripe rust (yellow rust) caused by Puccinia striiformisWestend. f. sp. tritici Erikss. occurs in almost all wheat-producing regions. This disease causes significant economic losses in terms of reduced grain production and the expenses incurred for disease management (Beddow et al. 2015; Hovmøller et al. 2010; McIntosh et al. 1995). In general, stripe rust causes yield losses of 5 to 25% in susceptible wheat cultivars, but it may cause complete yield losses in severe epidemics (Chen 2005; Wellings 2011). As the largest stripe rust epidemic region throughout the world, China frequently suffers severe yield losses (Chen 2014; Li and Zeng 2002; Wan et al. 2007). Growing resistant cultivars is an economical, effective, and environmentally friendly way to control this disease (Li and Zeng 2002; McIntosh et al. 1995; Wiesner-Hanks and Nelson 2016). Both all-stage resistance (ASR) and adult-plant resistance (APR) have been used for breedingwheat cultivars with resistance to stripe rust (Chen 2013). ASR often confers complete resistance during all growth stages and is easy to select during the breeding process, but it is mostly race-specific and not durable (Johnson 1981; McDonald and Linde 2002). By contrast, APR usually confers partial resistance during the adult-plant stage, and it is mostly race-nonspecific and more durable. However, APR can be relatively difficult to incorporate into new cultivars compared with ASR (Chen 2013; Park and McIntosh 1994). Many wheat cultivars that exhibit durable resistance possess APR (Boyd 2005; Chen 2013; McIntosh 1992; Navabi et al. 2005; Singh et al. 2005). Over 300 genes or quantitative trait loci (QTLs) for either ASR or APR to P. striiformis f. sp. tritici in various wheat genotypes have been mapped to all 21 chromosomes (Maccaferri et al. 2015; McIntosh et al. 2016, 2017; Rosewarne et al. 2013; Wang and Chen 2017). However, many of the ASR genes are no longer effective against the current P. striiformis f. sp. tritici populations, and many of the APR QTLs have only small effects. Moreover, not all of these genes or QTLs have molecular markers that can be used for marker-assisted selection (MAS) in breeding programs. Therefore, more resistance genes or QTLs and suitable user-friendly markers should be identified. It is important to map QTLs and to identify closely linked markers to combine with resistance QTLs in wheat cultivars. During the last 20 years, different types of molecular markers have been developed, such as simple sequence repeat (SSR) (Röder et al. 1998) and resistance gene analog polymorphism (Chen et al. 1998), and used for mapping wheat genes (Ren et al. 2012a, b; Rosewarne et al. 2013; Zhou et al. 2014). These polymerase chain reaction (PCR) markers have been applied successfully in MAS, but the densities of these types of markers are about 10–20 cM per marker (Semagn et al. 2010; Yan et al. 2006). Thus, more cost-effective markers and high-throughput genotyping platforms are still required for MAS (St. Clair 2010; Yang et al. 2015). More recently, single nucleotide polymorphism (SNP) markers have been developed, which are abundant, mostly codominant, and distributed throughout the genome, and applied in studies of wheat genetics (Allen et al. 2013; Rasheed et al. 2016; Wu et al. 2017, 2018). SNP markers have many advantages for high-throughput genotyping, including their low cost, allele specificity, and high efficiency (Colasuonno et al. 2014; Gupta et al. 2008; Long et al. 2017; Semagn et al. 2014). SNP chips containing different numbers of markers, including 9K, 15K, 35K, 50K, 55K, 90K, 660K, and 820K, are commercially available, and some of these chips have been used widely to identify genes for various traits in wheat (Allen et al. 2017; Cavanagh et al. 2013; Jia and Zhao 2016; Muqaddasi et al. 2017; Wang et al. 2014; Winfield et al. 2016). Wheat cultivar Qinnong 142 (QN142) developed from the cross of Zhengmai 8329/87135-2-1-2-9 by the Baoji Academy of Agricultural Sciences, Shaanxi, China, is a high-yielding cultivar with resistance to stripe rust. This cultivar has been grown in the Yellow and Huai River Valley wheat zone of China since 2005, and it has been widely used as a parent in breeding programs.We have tested QN142 Corresponding authors: Dejun Han; E-mail: handj@nwsuaf.edu. cn and Zhensheng Kang; E-mail: kangzs@nwsuaf.edu. cn Qingdong Zeng and Jianhui Wu contributed equally to this work. Funding:This study was financially supported by the National Science Foundation for Young Scientists of China (grant no. 31701421), China Postdoctoral Science Foundation funding (2017M623260), Earmarked Fund for Modern Agro-industry Technology Research System (No. CARS-3-1-11), and National Natural Science Foundation of China (31371924). *The e-Xtra logo stands for “electronic extra” and indicates that seven supplementary tables are published online. Accepted for publication 28 August 2018. © 2018 The American Phytopathological Society Plant Disease /March 2019 439 Plant Disease • 2019 • 103:439-447 • https://doi.org/10.1094/PDIS-05-18-0846-RE