A lineage-specific Exo70 is required for receptor kinase-mediated immunity in barley

Abstract

In the evolution of land plants, the plant immune system has experienced expansion in immune receptor and signaling pathways. Lineage-specific expansions have been observed in diverse gene families that are potentially involved in immunity but lack causal association. Here, we show that Rps8-mediated resistance in barley to the pathogen Puccinia striiformis f. sp. tritici (wheat stripe rust) is conferred by a genetic module: Pur1 and Exo70FX12, which are together necessary and sufficient. Pur1 encodes a leucine-rich repeat receptor kinase and is the ortholog of rice Xa21, and Exo70FX12 belongs to the Poales-specific Exo70FX clade. The Exo70FX clade emerged after the divergence of the Bromeliaceae and Poaceae and comprises from 2 to 75 members in sequenced grasses. These results demonstrate the requirement of a lineage-specific Exo70FX12 in Pur1-mediated immunity and suggest that the Exo70FX clade may have evolved a specialized role in receptor kinase signaling.

Fig. 1.. Rps8 is associated with the presence of a 546-kb InDel.

(A) First leaf of SxGP doubled-haploid population accessions indicating the presence (+) or absence (−) of Rps6, Rps7, and Rps8. (B) High-resolution recombination screen mapped Rps8 to a 0.5 cM genetic interval spanning 936 kb in Morex. Genes include DUF4371, DUF1997, ARM, Exo70FX12, LRR-RK (Pur1), two BTB/POZ, fragmented NLR (CC-NB and LRR-DDE), ZnF, Myb, and several unknown and transposon-derived genes. Numbers in the genetic interval are recombinant individuals. (C) Repetitive content of the Rps8 region. Tandem array of the 5′ repeat region of a CACTA DNA transposon interrupted by long-terminal repeat (LTR) retrotransposons (black box). (D) Rps8 functional haplotypes are conserved, encompassing a 546-kb InDel. Genomes include Morex (Rps8), Golden Promise (blue; Rps8), CI16139 (pink; Rps8), and wild barley accessions B1K-04-12 (yellow) and OUH602 (green; rps8). A large (190 kb), repetitive region is a breakpoint in the assembly of the locus in CI16139 and Golden Promise. A 546-kb InDel (light orange) encompasses five nonrepetitive genes: Exo70FX12, Pur1, CC-NB, LRR-DDE, and CC-TM. A second 86-kb deletion is highlighted in a dark orange box. Colored solid lines indicate assembled contigs, whereas black lines indicate flanking or ambiguous sequence (excluding Morex).

Fig. 2.. Expression level polymorphism in Pur1 and Exo70FX12 is correlated with the presence of a functional Rps8 haplotype.

(A and B) Expression level polymorphism in Pur1 and Exo70FX12 is correlated with the presence of a functional Rps8 haplotype. Association of presence or absence of Rps8 in diverse barley accessions and leaf RNAseq for Pur1 (HORVU.MOREX.r3.4HG0407750.1) and Exo70FX12 (HORVU.MOREX.r3.4HG0407730.1). The expression level polymorphism in Exo70FX12 and Pur1 is predictive for Rps8-mediated resistance except in the barley accessions Heils Franken and WBDC247.

Fig. 3.. Rps8-mediated resistance requires both Pur1 and Exo70FX12.

(A) Infection phenotypes of Rps8-mediated resistance mutants using Pst isolate 16/035. Panel shows boxplots, individual data points, and total number of evaluated plants (N) over three biological replicates. (B) Positions of sodium azide–induced mutations and natural variation in barley cv. Heils Franken (rps8.a) within Exo70FX12 and Pur1 primary structure. Subdomain structure of Exo70FX is based on conservation with yeast Exo70. The domain structure of Pur1 is based on InterProScan. (C) Infection phenotypes for independent single-copy transformants of barley cv. SxGP DH-47 expressing Exo70FX12, Pur1, Exo70FX12 and Pur1, and Exo70FX12HF (Heils Franken allele) and Pur1, under their native promoters and terminators. The presence (blue) or absence (orange) of the T-DNA was determined using a quantitative polymerase chain reaction (qPCR)–based assay. When not determined (ND), data points are in black. Inoculations were performed using Pst isolate 16/035 and scored at 14 days after inoculation, N shows the number of evaluated seedlings.

Fig. 4.. Pur1 is the ortholog of Xa21.

Maximum likelihood unrooted phylogenetic tree based on 69 full-length RK proteins from the Xa21/Pur1 clade and putative Xa21 homologs from 24 Poaceae species (data file S5). Color coding on the subtree indicates the tribe origin of branches [Bambusoideae (pink), Oryzoideae (blue), and Pooideae (orange)]. Red dots indicate bootstrap support greater than 80%. The basal branch on the Xa21 subtree indicated by an arrow is supported at 95%. Scale indicates 1.0 substitution per site.

Fig. 5.. Rps8 Exo70 belongs to the Poales-specific Exo70FX subfamily.

(A) Rooted maximum likelihood (ML) phylogenetic tree based on 365 full-length Exo70 proteins from barley (H. vulgare), wheat (Triticum aestivum), purple false brome (Brachypodium distachyon), rice (O. sativa), O. thomaeum, maize (Z. mays), foxtail millet (S. italica), and sorghum (S. bicolor) (data file S7). Structure-guided multiple sequence alignment was performed using MAFFT DASH with yeast, human, mouse, and A. thaliana Exo70A1 proteins. Rooted using yeast, human, and mouse Exo70 as outgroups. The 10 present Exo70 subfamilies (A, B, C, D, E, F, G, H, I, and FX) are distinguished with distinct light gray regions, and the Exo70FX10/11/12/15 clades are further highlighted in dark gray. Rps8 Exo70 encodes HvExo70FX12. Red dots indicate bootstrap support greater than 80%. Scale indicates 1.0 substitution per site. (B) Rooted ML phylogenetic tree using 51 full-length Exo70 proteins from the Exo70FX10/11/12/15 clades and putative Exo70FX homologs from 13 Pooideae species (data file S4). Rooted using the Exo70FX10 clade as an outgroup. Red dots indicate bootstrap support greater than 80%. Scale indicates 0.1 substitutions per site.