Title Genetic Relationship of Stripe Rust Resistance Genes Yr 34 and Yr 48 in Wheat and Identification of Linked KASP Markers Permalink

The Australian continent was free from wheat stripe rust caused by Puccinia striiformis f. sp. tritici until exotic incursions occurred in 1979 and 2002. The 2002 incursion enabled the identification of a new stripe rust resistance gene (Yr34) in the advanced breeding line WAWHT2046. In this study,we developed and validatedmarkers closely linkedwithYr34, which is located in the distal region in the long arm of chromosome 5A. Four kompetitive allele-specific polymerase chain reaction (KASP) and three sequencetagged site (STS) markers derived from the International Wheat Genome Sequencing Consortium RefSeq v1.0 scaffold-77836 cosegregated with Yr34. Markers sun711, sun712, sun725, sunKASP_109, and sunKASP_112 were shown to be suitable for marker-assisted selection in a validation panel of 71 Australian spring wheat genotypes, with the exception of cultivar Orion that carried the Yr34-linked alleles for sunKASP_109 and sunKASP_112. Markers previously reported to be linked with adult plant stripe rust resistance gene Yr48 also cosegregated with Yr34. Wheat genotypes carrying Yr34 and Yr48 produced identical haplotypes for the Yr34-linked markers identified in this study and those previously reported to be linkedwithYr48. Phenotypic testing of genotypes carrying Yr34 and Yr48 showed that both genes conferred similar seedling responses to pre-2002 and post-2002 P. striiformis f. sp. tritici pathotypes. Further testing of 600 F2 plants from a cross between WAWHT2046 and RIL143 (Yr48) with P. striiformis f. sp. tritici pathotype 134 E16A+Yr17+Yr27+ failed to reveal any susceptible segregants. Our results strongly suggest that Yr34 and Yr48 are the same gene, and that Yr48 should be considered a synonym of Yr34. Stripe rust is a widely distributed disease of wheat, occurring in almost all continents, except Antarctica (Chen 2005). It is relatively new in Australia, with the first incursion of Puccinia striiformis f. sp. tritici pathotype 104 E137A− occurring in 1979 in eastern Australia (O’Brien et al. 1980). Since then, 21 variants of the original pathotype have been reported, through acquisition of virulence for stripe rust resistance genes YrA, Yr6, Yr7, and Yr17 either individually or sequentially in different combinations. In 2002, another incursion occurred in Western Australia (WA). It was pathotyped as 134 E16A+ and named as the “WA pathotype”. This pathotype differed from the eastern Australian pathotypes and appeared to be similar to those reported by Chen (2005) in the United States and Hovmøller and Bayles (2005) in Europe. The key feature of this pathotype compared with the earlier group was its combined virulence for genes Yr8 and Yr9 and avirulence for Yr3, Yr4, and Yr34 (Bariana et al. 2006; Wellings et al. 2003). Since the original incursion, several new variants from the WA pathotype involving virulence for Yr10, Yr17, Yr24/Yr26, YrJ, YrT, and Yr27 have been detected (Singh et al. 2010; Wellings 2007). The incursion of the WA pathotype in Australia resulted in high yield losses and increased expenditure on chemical control (AU$40 to 90 million) during the crop seasons of 2003 to 2005 (Wellings 2007). Several Australian cultivars that carried resistance to pre-2002 pathotypes were susceptible to theWA pathotype, while cultivar Rubric and the advanced breeding line WAWHT2046 from the Department of Primary Industries and Regional Development, WA expressed higher levels of resistance (Bariana et al. 2006). Rubric was shown to carry Yr4 (Bansal et al. 2010), whereas the resistance gene carried by WAWHT2046 was mapped 12.2 centimorgans (cM) distal to the awn inhibitor locus B1 in the long arm of chromosome 5A and was formally named Yr34 by Bariana et al. (2006) using a WAWHT2046/Carnamah doubled-haploid (DH) population. Yr34 remains effective against all variants of the WA pathotype detected thus far in Australia. The advent of next-generation DNA sequencing and highthroughput marker genotyping has played a significant role in speeding up the process of developing trait-linked markers and identifying causal genes for trait variation. Several technologies now exist for high-density genotyping, including Diversity Array Technology (DArT; www.diversityarrays.com), Illumina iSelect single-nucleotide polymorphism (SNP) array (Wang et al. 2014), and genotyping by sequencing (He et al. 2014). Such technologies, in combination with the International Wheat Genome Sequencing Consortium (IWGSC) assembly for common wheat variety Chinese Spring and the more recent release of the annotation for the wheat genome (https://wheat-urgi. versailles.inra.fr/About-us/News/IWGSC-RefSeq-v1.0-annotation-isnow-available), now make it possible to physically localize traitlinked polymorphism in the wheat genome to develop new markers to saturate a genomic region of interest, and to prioritize candidate genes for functional analysis. For example, markers linked with Sr56 and Lr52/Yr47were developed using these genomic resources (Bansal et al. 2014; Qureshi et al. 2017). Despite the effectiveness of Yr34 against all post-2002 pathotypes, this gene has not been widely used in Australian breeding programs, presumably due to expression of high seedling infection type (IT) 23C-33C and the unavailability of closely linked molecular markers. Adult plant stripe rust resistance gene Yr48 was located in chromosome 5AL by Lowe et al. (2011), and these workers placed it distal to Yr34 based on a comparison of their map with that presented by Bariana et al. (2006). This studywas planned to produce a detailedmap of the Yr34 region on the long arm of chromosome 5A using various genomic resources to identify closely linked markers for effective pyramiding of this gene with other marker-tagged rust resistance genes, and to study the relationship between Yr34 and Yr48. Material and Methods Plant material. The WAWHT2046/Carnamah DH population of 106 lines from Bariana et al. (2006) was used in this study. Another WAWHT2046/Avocet S-derived recombinant inbred line (RIL) population (68 lines) was used to validate the association of Yr34-linked Corresponding author: U. K. Bansal; E-mail: urmil.bansal@sydney.edu. au Accepted for publication 18 September 2017. © 2017 The American Phytopathological Society 1 Plant Disease • XXXX • XXX:X-X • https://doi.org/10.1094/PDIS-08-17-1144-RE