A Genome-Wide Association Study of Field and Seedling Response to Individual Stem Rust Pathogen Races Reveals Combinations of Race-Specific Genes in North American Spring Wheat.

Erena A Edae,Matthew N Rouse,Michael O Pumphrey

doi:10.3389/fpls.2018.00052

Abstract

Stem rust of wheat caused by the fungal pathogen Puccinia graminis f. sp. tritici historically caused major yield losses of wheat worldwide. To understand the genetic basis of stem rust resistance in contemporary North American spring wheat, genome-wide association analysis (GWAS) was conducted on an association mapping panel comprised of 250 elite lines. The lines were evaluated in separate nurseries each inoculated with a different P. graminis f. sp. tritici race for 3 years (2013, 2015, and 2016) at Rosemount, Minnesota allowing the evaluation of race-specificity separate from the effect of environment. The lines were also challenged with the same four races at the seedling stage in a greenhouse facility at the USDA-ARS Cereal Disease Laboratory. A total of 22,310 high-quality SNPs obtained from the Infinium 90,000 SNPs chip were used to perform association analysis. We observed often negative and sometimes weak correlations between responses to different races that highlighted the abundance of race-specific resistance and the inability to predict the response of the lines across races. Markers strongly associated with resistance to the four races at seedling and field environments were identified. At the seedling stage, the most significant marker-trait associations were detected in the regions of known major genes (Sr6, Sr7a, and Sr9b) except for race QFCSC where a strong association was detected on chromosome arm 1AL. We postulated the presence of Sr2, Sr6, Sr7a, Sr8a, Sr9b, Sr11, Sr12, Sr24, Sr25, Sr31, and Sr57 (Lr34) in this germplasm based on phenotypic and marker data. We found over half of the panel possessed three or more Sr genes, and most commonly included various combinations of Sr6, Sr7a, Sr8a, Sr9b, Sr11, Sr12, and Sr57. Most of these genes confer resistance to specific P. graminis f. sp. tritici races accounting for the prevalent stem rust resistance in North American spring wheat.

Highlights

Stem rust of wheat (Triticum aestivum L.), caused by Puccinia graminis f. sp. tritici (Pgt) Erikss. & Henning, is potentially a destructive disease of wheat at the global scale (Singh et al, 2011)
(>6) to race QFCSC and about 14% of the lines were susceptible to race QTHJC
The phenotypic correlation coefficients among the four races were in the range of moderate (r = 0.47 between QTHJC and QFCSC) to high (r = 0.7 between TPMKC and RCRSC; Supplemental Figure 2)

Summary

Introduction

Stem rust of wheat (Triticum aestivum L.), caused by Puccinia graminis f. sp. tritici (Pgt) Erikss. & Henning, is potentially a destructive disease of wheat at the global scale (Singh et al, 2011). There was a large decline in the number of Pgt races since 1960, race TPMKC was the most prevalent race in the United States until the late 1980s After this time, the frequency of race TPMKC was low because of the use of resistance cultivars of both hard red winter and spring wheats that carried the stem rust resistance (Sr) gene Sr6 (Kolmer et al, 2007). Based on the reaction of the four races to the wheat stem rust resistance genes in the differential set, race TPMKC is virulent to Sr8a, Sr9e, and SrTmp but avirulent to Sr9a and Sr9b, whereas RCRSC is virulent to Sr9a and Sr9b but avirulent to Sr8a, Sr9e, and SrTmp (Supplemental Table 1). Both phenotypic and genotypic analyses indicated that these races are distinct from each other

Objectives

Methods

Results

Conclusion