Comparative Genomics and Functional Studies of Wheat BED-NLR Loci

Abstract

Nucleotide-binding leucine-rich-repeat (LRR) receptors (NLRs) with non-canonical integrated domains (NLR-IDs) are widespread in plant genomes. Zinc-finger BED (named after the Drosophila proteins Boundary Element-Associated Factor and DNA Replication-related Element binding Factor, named BED hereafter) are among the most frequently found IDs. Five BED-NLRs conferring resistance against bacterial and fungal pathogens have been characterized. However, it is unknown whether BED-NLRs function in a manner similar to other NLR-IDs. Here, we used chromosome-level assemblies of wheat to explore the Yr7 and Yr5a genomic regions and show that, unlike known NLR-ID loci, there is no evidence for a NLR-partner in their vicinity. Using neighbor-network analyses, we observed that BED domains from BED-NLRs share more similarities with BED domains from single-BED proteins and from BED-containing proteins harboring domains that are conserved in transposases. We identified a nuclear localization signal (NLS) in Yr7, Yr5, and the other characterized BED-NLRs. We thus propose that this is a feature of BED-NLRs that confer resistance to plant pathogens. We show that the NLS was functional in truncated versions of the Yr7 protein when expressed in N. benthamiana. We did not observe cell-death upon the overexpression of Yr7 full-length, truncated, and ‘MHD’ variants in N. benthamiana. This suggests that either this system is not suitable to study BED-NLR signaling or that BED-NLRs require additional components to trigger cell death. These results define novel future directions to further understand the role of BED domains in BED-NLR mediated resistance.

Wheat genetic loci conferring resistance to stripe rust in the face of genetically diverse races of the fungus Puccinia striiformis f. sp. tritici

“…Yr5 (represented in the wheat reference genome of cv. Chinese Spring by gene model TraesCS2B01G488700) and Yr7 (for which no equivalent Chinese Spring gene model is thought to be present; Marchal et al 2020) are paralogous BED-NLR genes with ~ 78% DNA identity across their coding regions (Marchal et al 2018). YrSP is a truncated allele of Yr5 resulting in the loss of most of the LRR coding region (Marchal et al 2018).…”

“…Collectively, this indicates that while Yr7 and Yr5/YrSP do not themselves confer resistance at QYr.niab-2B.1, it is possible that different mutations at their underlying genes, or allelic variation at nearby paralogous BED-NLRs in the vicinity, could underly resistance at this locus. Indeed, recent analysis of wheat genome assembly sequences has found copy number variation for BED-NLRs within the vicinity of the Yr5 and Yr7 locus (Marchal et al 2020). Ultimately, further investigation of these, and other, candidates at the QTL is required to narrow down the underlying causative gene and polymorphism.…”

Comparative Study of Zf-BED Encoding Genes in Land Plants and Their Roles in Cotton

“…In these classes, the presence of "Dimer_Tnp_hAT" as a decoy domain was common in all plants, pointing towards their essential roles in plant development [56]. Despite their important functionalities, very few classes of Zf-BED proteins have been reported in literature to date; for instance, zfBED-NB-ARC(NLR) (class XII; ZfBED-NBS and class XIV; ZfBED-NBS-LRR) domain architecture was reported as conferring disease resistance in plants [19,53,57]. These classes were only found in Brachypodium distachyon (Bradi5g22179.1), Oryza sativa (OsR498G0409301900.01.T01), Medicago truncatula (XP_013447741.2), and Populus trichocarpa (Potri.001G404800, Potri.001G405100, Potri.019G002700, Potri.T013632, Potri.T107066).…”

“…For instance, multiple resistance proteins contain a Zf-BED domain, conferring resistance to various biotic stresses [17]. The Zf-BED domains also associate with the Nod-like receptor (NLR) proteins either at the N-or C-termini [18][19][20][21]. As such, NLR proteins play critical roles in plant immune systems [22][23][24].…”

A genome-wide comparative evolutionary analysis of zinc finger-BED transcription factor genes in land plants

“…For instance, multiple resistance proteins contain a Zf-BED domain, conferring immunity to various biotic stresses 18 . The Zf-BED domains also associate with the Nod-like receptor (NLR) proteins either at the N– or C– termini 17 , 19 – 21 . As such, NLR proteins play critical roles in plant immune responses 22 – 24 .…”