Bartaula et al. BMC Plant Biology (2019) 19:319 https://doi.org/10.1186/s12870-019-1893-9 RESEARCH ARTICLE Open Access Mapping non-host resistance to the stem rust pathogen in an interspecific barberry hybrid Radhika Bartaula1, Arthur T. O. Melo2, Sarah Kingan3, Yue Jin4 and Iago Hale2* Abstract Background: Non-host resistance (NHR) presents a compelling long-term plant protection strategy for global food security, yet the genetic basis of NHR remains poorly understood. For many diseases, including stem rust of wheat [causal organism Puccinia graminis (Pg)], NHR is largely unexplored due to the inherent challenge of developing a genetically tractable system within which the resistance segregates. The present study turns to the pathogen’salternate host, barberry (Berberis spp.), to overcome this challenge. Results: In this study, an interspecific mapping population derived from a cross between Pg-resistant Berberis thunbergii (Bt)andPg-susceptible B. vulgaris was developed to investigate the Pg-NHR exhibited by Bt. To facilitate QTL analysis and subsequent trait dissection, the first genetic linkage maps for the two parental species were constructed and a chromosome-scale reference genome for Bt was assembled (PacBio + Hi-C). QTL analysis resulted in the identification of a single 13 cM region (~ 5.1 Mbp spanning 13 physical contigs) on the short arm of Bt chromosome 3. Differential gene expression analysis, combined with sequence variation analysis between the two parental species, led to the prioritization of several candidate genes within the QTL region, some of which belong to gene families previously implicated in disease resistance. Conclusions: Foundational genetic and genomic resources developed for Berberis spp. enabled the identification and annotation of a QTL associated with Pg-NHR. Although subsequent validation and fine mapping studies are needed, this study demonstrates the feasibility of and lays the groundwork for dissecting Pg-NHR in the alternate host of one of agriculture’s most devastating pathogens. Keywords: Wheat, Stem rust, Barberry, Non-host resistance, Durable resistance, Reference genome Background detected in East Africa in 1998, more than 80% of the Stem rust, caused by the fungal pathogen Puccinia graminis world’s wheat germplasm was estimated to be vulnerable to (Pg), has for millennia been one of the most destructive its unprecedented virulence on the widely-deployed resist- diseases of wheat and related small grains [1–3]. Effective ance gene Sr31 [7]. The rapid distribution and continued control of the disease was realized in the middle of the evolution of the Ug99 family of races, combined with recent twentieth century through the concerted development of stem rust outbreaks in Europe [8], underscore the need for resistant wheat varieties and the removal of Pg’salternate new sources of resistance [9]. Traditionally, such new host, common barberry (Berberis vulgaris L.), from major sources have been sought almost entirely from within the wheat growing areas [3, 4]. In the last 20 years, however, diverse Triticum genepool. Although translatability to the emergence of new virulent stem rust races has rendered wheat improvement may be less straightforward, or poten- some long-used resistance genes ineffective [5, 6]. For tially even unachievable, a complementary approach may to example, when the wheat stem rust race Ug99 was first look beyond this genepool for potential mechanisms of non-host resistance (NHR) to the complex Pg pathogen. * Correspondence: [email protected] NHR is a form of resistance in which all individuals of 2Department of Agriculture, Nutrition, and Food Systems, University of New Hampshire, Durham, NH 03824, USA a potential host species exhibit immunity to all indivi- Full list of author information is available at the end of the article duals (e.g. races) of a potential pathogen [10]. As the © The Author(s). 2019 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Bartaula et al. BMC Plant Biology (2019) 19:319 Page 2 of 17 most common form of disease resistance and one that barberries may have played an important role in the evo- possesses intrinsic durability, NHR presents a compel- lution of the rust fungi. First, Berberis spp. host a wide ling strategy for achieving broad-spectrum, durable pro- diversity of rusts, including numerous macrocyclic, hete- tection against many plant pathogens, including the roecious species of Puccinia (e.g. Pg, P. striiformis, P. causal organism of wheat stem rust [11, 12]. The genetic montanensis, P. brachypodii, P. pigmea, P. koeleriae,and mechanisms underlying Pg-NHR remain largely unknown, P. arrhenatheri), a number of autoecious rusts (e.g. especially in comparison to the relatively well-studied Cumminsiella spp., belonging to Pucciniaceae; Edythea mechanisms of race specific and quantitative, race non- spp., belonging to Uropyxidaceae; and Pucciniosira spp., specific host resistance. Over the past decade, however, belonging to Pucciniosiraceae), and even some ana- efforts have mounted to understand NHR to rust pathogens morphic rusts (e.g. Acedidium and Uredo spp.). Second, using various model and non-model plants. Many plant only slight morphological differences exist among the te- species, including Arabidopsis thaliana, Brachypodium liospores of the various macrocyclic rusts [35], suggesting distachyon, rice, barley, and cowpea [13–18], have been a single evolutionary origin of these pathogens. Third, a used to study NHR to P. striiformis f. sp. tritici, the causal recent palaeobotanical finding of B. wuyunensis from a organism of wheat stripe rust. In contrast, NHR to the sediment layer between 55 to 65 million years ago in wheat stem rust pathogen Pg has thus far been studied only northeastern China suggests that the barberries are one of in rice [13], as distinct from the studies of intermediate Pg the earliest groups of angiosperms [36]. resistance conducted in barley and B. distachyon [19, 20]. More specific to the grass rusts, there are eight known As the only globally important small grain immune to Puccinia spp. that complete their sexual (aecial) stage on all known rust diseases, rice (Oryza spp.) presents a barberry and their asexual (uredinial and telial) stages on logical potential source of Pg-NHR genes. Genetic stud- graminaceous plants from the Poaceae family. This rela- ies of Pg-NHR in rice are difficult, however, precisely tionship, in combination with the relative ages of these because populations of non-hosts fail, by definition, to two plant families, suggests that Puccinia spp. likely segregate for resistance. Although some limited progres- parasitized the Berberidaceae prior to their host expan- sion of Pg infection has been shown in rice, thus raising sion to the grasses. Today, the genus Puccinia is com- the possibility of dissecting Pg-NHR in that system, the prised of more than 2000 species; and within that infection process exhibits little variation, requires te- diverse genus, host jump rather than co-speciation is be- dious microscopic studies to characterize, and ultimately lieved to be the primary means of speciation [37]. As fails to complete [13]. As an alternative to rice, the more recent examples, a host jump from Poaceae to Berberis-Pg system was recently proposed as a tractable Ranunculaceae likely produced the P. recondita complex pathosystem for studying the genetics of Pg-NHR [21]. and its aligned species, a jump to Liliaceae likely pro- Numerous species within the highly diverse Berberis,or duced P. hordei and its aligned species, and a jump to barberry, genus are susceptible to Pg infection (e.g. Euro- Oxalidaceae likely produced P. sorghi and its aligned pean barberry B. vulgaris L., the target of massive eradi- species. Because the relationship between barberries and cation efforts from wheat-growing regions in the the rusts likely predates such speciation (Fig. 1), it is of twentieth century) [22, 23]. Others, however, are consi- fundamental interest to probe the mechanism(s) of NHR dered non-hosts. Japanese barberry B. thunbergii DC., exhibited by some contemporary species of barberry. for example, is considered a non-host of Pg due to two In this study, an interspecific B. ×ottawensis mapping lines of evidence: 1) Over nearly a century of extensive population was created to study the inheritance of the testing at the USDA Cereal Disease Lab, no Pg infection gene(s) underlying the putative Pg-NHR of B. thunbergii. has ever been observed in the species [24–33], and 2) To support this work, necessary genetic and genomic re- No Pg infection has been observed on B. thunbergii sources were developed, including genetic linkage maps for under natural conditions, despite rampant proliferation the two parental species (B. thunbergii and B. vulgaris)and of the species in the landscape. Because hybridization a chromosome-scale reference genome for B. thunbergii. between such host and non-host species are known to This study not only establishes foundational resources for occur in nature (e.g. B. ×ottawensis C.K. Scheid) [34], the Berberis-Pg pathosystem but also demonstrates their populations of interspecific barberry hybrids present a use in an initial dissection of Pg-NHR, with the long-term potential means of mapping and dissecting the genetic hope of contributing insight into possible novel mecha- basis of Pg-NHR. nisms of durable resistance to the stem rust pathogen. The barberries are a compelling model for other reasons as well. Unlike rice, which has no known co-evolutionary Results relationship with Pg, barberries are thought to be one of Variant detection and linkage map construction the first eudicots parasitized by the rusts (Fig.