Searching for novel sources of field resistance to Ug99 and Ethiopian stem rust races in durum wheat via association mapping

Abstract

Puccinia graminis f. sp. tritici, the causative agent of stem rust in wheat, is a devastating disease of durum wheat. While more than 50 stem rust resistance (Sr) loci have been identified in wheat, only a few of them have remained effective against Ug99 (TTKSK race) and other durum-specific Ethiopian races. An association mapping (AM) approach based on 183 diverse durum wheat accessions was utilized to identify resistance loci for stem rust response in Ethiopia over four field-evaluation seasons and artificial inoculation with Ug99 and a mixture of durum-specific races. The panel was profiled with simple sequence repeat, Diversity Arrays Technology and sequence-tagged site markers (1,253 in total). The resistance turned out to be oligogenic, with twelve QTL-tagging markers that were significant (P < 0.05) across three or four seasons. R (2) values ranged from 1.1 to 11.3 %.Twenty-four additional single-marker/QTL regions were found to be significant over two seasons. The AM results confirmed the role of Sr13, previously described in bi-parental mapping studies, and the role of chromosome regions putatively harbouring Sr9, Sr14, Sr17 and Sr28. Three minor QTLs were coincident with those reported in hexaploid wheat and five overlapped with those recently reported in the Sebatel × Kristal durum mapping population. Thirteen single-marker/QTL regions were located in chromosome regions where no Sr genes/QTLs have been previously reported. The allelic variation identified in this study is readily available and can be exploited for marker-assisted selection, thus providing additional opportunities for a more durable stem rust resistance under field conditions.

A consensus map for Ug99 stem rust resistance loci in wheat

“…Seven QTL were found on 1B (three on the short arm, three on the long arm and one is still in an undetermined arm location). Four were mapped using bi-parental crosses (PBW343/Crossbill, PBW343/Kenya Nyangumi: CIMMYT unpublished; Avocet/Pavon76: Njau et al 2013; Bhavani et al 2011) and three using association mapping (ESWYT: Crossa et al 2007; LD-SRRSN (spring): Yu et al 2011 and the AM durum panel: Letta et al 2013). Four of these QTL are represented in Fig.…”

“…Stem rust resistance loci data were collected from 21 recent studies, for a total of 24 biparental mapping populations, 3 association panels, 2 BC 2 populations, and two from resistance gene cloning (Bansal et al 2008; Bhavani et al 2011; Crossa et al 2007; Ghazvini et al 2012; Haile et al 2012; Hiebert et al 2010, 2011; Kaur et al 2009; Letta et al 2013; Olson et al 2013; Njau et al 2013; Periyannan et al 2013; Rouse et al 2012, 2014; Saintenac et al 2013; Singh et al 2013a, b, c; CIMMYT unpublished, Yu et al 2011, 2012) (Table 1). The details of the reports, including the chromosome positions of stem rust resistance loci, their LOD (log (Odds)) scores and p values, parents used to develop the population as well as stem rust pathotypes for disease reaction are presented in Table 1.…”

Genetic architecture of main effect QTL for heading date in European winter wheat

“…The method is based on the meiotic events which occurred during the entire development of the lines and which results in an increased genetic resolution determined by the extent of linkage disequilibrium (LD) of the species under investigation (Hamblin et al, 2011). Whole-genome association mapping was applied in wheat for ear emergence (Le Gouis et al, 2012), as well as for yield and agronomic traits (Neumann et al, 2011; Reif et al, 2011; Wang et al, 2012) and resistance to pathogens (Crossa et al, 2007; Maccaferri et al, 2010; Miedaner et al, 2011; Yu et al, 2011, 2013; Letta et al, 2013; Kollers et al, 2013a,b). …”

Genome-wide association analysis identified SNPs closely linked to a gene resistant to Soil-borne wheat mosaic virus

“…9.1.2; SAS Institute Inc., Cary, NC). A threshold of P < 10 -6 was obtained using the experiment-wise association significance probability obtained through 10,000 permutation tests implemented in TASSEL to claim alleles that were significantly associated with SBWMV resistance (Letta et al 2013). …”

“…Reported yield losses due to SBWMV infection range from 10% to 30% and, in extreme cases up to 80% in seriously infected fields in the U. S. and 50% in Brazil ( (Malosetti et al 2007). In wheat, association analysis has also been successfully used to identify new genes for resistance to stem rust and pre-harvest sprouting, and for quality traits (Letta et al 2013;Kulwal et al 2012; Reif et al 2011). Previously, we have identified a SSR marker, Xgwm469 that was associated with the SBWMV resistance gene on 5DL after analyzing 282 SSR markers across 205 wheat accessions (Zhang et al 2011).…”