Evaluation of Genetic Diversity and Host Resistance to Stem Rust in USDA NSGC Durum Wheat Accessions

Abstract

The USDA-ARS National Small Grains Collection (NSGC) maintains germplasm representing global diversity of small grains and their wild relatives. To evaluate the utility of the NSGC durum wheat (Triticum turgidum L. ssp. durum) accessions, we assessed genetic diversity and linkage disequilibrium (LD) patterns in a durum core subset containing 429 lines with spring growth habit originating from 64 countries worldwide. Genetic diversity estimated using wheat single-nucleotide polymorphism (SNP) markers showed considerable diversity captured in this collection. Average LD decayed over a genetic distance to within 3 cM at r 2 = 0.2, with a fast LD decay for markers linked at >5 cM. We evaluated accessions for resistance to wheat stem rust, caused by a fungal pathogen, Puccinia graminis Pers. Pers. f. sp. tritici Eriks. and E. Henn (Pgt), using races from both eastern Africa and North America, at seedling and adult plant stages. Five accessions were identified as resistant to all stem rust pathogen races evaluated. Genome-wide association analysis detected 17 significant associations at the seedling stage with nine likely corresponding to Sr7, Sr12, and Sr13 and the remaining potentially being novel genes located on six chromosomes. A higher frequency of resistant accessions was found at the adult plant stage than at the seedling stage. However, few significant associations were detected possibly a result of strong G  E interactions not properly accounted for in the mixed model. Nonetheless, the resistant accessions identified in this study should provide wheat breeders with valuable resources for improving stem rust resistance.

A Genome-Wide Association Study of Highly Heritable Agronomic Traits in Durum Wheat

“…Population structure might bring false positive or negative marker-trait associations (MTAs) which should be considered as covariates in GWAS analysis. The population structure of the durum wheat panel based on the full set of informative SNPs has been previously described (Aoun et al, 2016; Chao et al, 2017). Due to the possible impact of linkage on the inference of genetic relationships, the genetic stratification issue was revisited by running an analysis using a sub-set of unlinked markers (pairwise LD < 0.2).…”

“…The line information and genotype data of the 493 durum wheat entries were reserved in the T3/Wheat database 2 . This panel has previously been exploited to identify the genetic basis of resistance against certain foliar pathogens (Aoun et al, 2016; Chao et al, 2017). In addition, genotypic data from a domesticated emmer wheat (Sun, 2015) and a bread wheat (Cavanagh et al, 2013) diversity panel was used to infer the genetic divergence of identified quantitative trait loci (QTL).…”

“…However, the extent of this effort in durum wheat has been much more limited (e.g., Maccaferri et al, 2008; Peleg et al, 2009; Golabadi et al, 2011; Roncallo et al, 2017). The USDA-ARS National Small Grain Collection (NSGC, Aberdeen, ID, United States) conserves over 8,000 entries and represents the global diversity of durum wheat (Chao et al, 2017). A core subset has been assembled from this collection, comprising 493 entries with spring growth habit, of which 235 are classed as landraces, 77 as breeding lines, 55 as released cultivars, leaving 126 of unknown breeding status (Aoun et al, 2016; Chao et al, 2017).…”

“…The USDA-ARS National Small Grain Collection (NSGC, Aberdeen, ID, United States) conserves over 8,000 entries and represents the global diversity of durum wheat (Chao et al, 2017). A core subset has been assembled from this collection, comprising 493 entries with spring growth habit, of which 235 are classed as landraces, 77 as breeding lines, 55 as released cultivars, leaving 126 of unknown breeding status (Aoun et al, 2016; Chao et al, 2017). The size of this panel is appropriate for conducting genome-wide association studies (GWAS), a method which has been applied with some success to reveal the genetic basis of some key agronomic traits in bread wheat (e.g., Liu Y. et al, 2017; Sun et al, 2017; Würschum et al, 2017, 2018).…”

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

“…Though several studies have evaluated seedling and/or field response of wheat association mapping panels to Pgt isolates (Yu et al, 2011 , 2012 ; Letta et al, 2014 ; Zhang et al, 2014 ; Gao et al, 2017 ; Mihalyov et al, 2017 ; Muleta et al, 2017 ), only one has evaluated field response of the wheat population studied to more than one Pgt race (Chao et al, 2017 ). In that study, field response of a bulk of six Pgt isolates in Minnesota was compared to response to a bulk of Pgt isolates in Ethiopia, and differences between these datasets could be due to environment and/or race.…”