Genomic Analysis and Delineation of the Tan Spot Susceptibility Locus Tsc1 in Wheat

Abstract

The necrotrophic fungal pathogen Pyrenophora tritici-repentis (Ptr) causes the foliar disease tan spot in both bread wheat and durum wheat. Wheat lines carrying the tan spot susceptibility gene Tsc1 are sensitive to the Ptr-produced necrotrophic effector (NE) Ptr ToxC. A compatible interaction results in leaf chlorosis, reducing yield by decreasing the photosynthetic area of leaves. Developing genetically resistant cultivars will effectively reduce disease incidence. Toward that goal, the production of chlorosis in response to inoculation with Ptr ToxC-producing isolates was mapped in two low-resolution biparental populations derived from LMPG-6 × PI 626573 (LP) and Louise × Penawawa (LouPen). In total, 58 genetic markers were developed and mapped, delineating the Tsc1 candidate gene region to a 1.4 centiMorgan (cM) genetic interval spanning 184 kb on the short arm of chromosome 1A. A total of nine candidate genes were identified in the Chinese Spring reference genome, seven with protein domains characteristic of resistance genes. Mapping of the chlorotic phenotype, development of genetic markers, both for genetic mapping and marker-assisted selection (MAS), and the identification of Tsc1 candidate genes provide a foundation for map-based cloning of Tsc1.

Keywords: Ptr ToxC; Pyrenophora tritici-repentis; Triticum; Tsc1; disease resistance; tan spot; wheat.

Figure 1

Leaves of wheat genotypes with Tsc1 (top) and without Tsc1 (bottom) inoculated with a Pyrenophora tritici-repentis (Ptr) ToxC-producing isolate.

Figure 2

Saturation maps of the Tsc1 region developed in Louise × Penawawa (LouPen) and LMPG-6 × PI 626573 (LP) populations. The LouPen genetic map is on the left and the LP genetic map is on the right. Loci mapped are listed on the right of the LouPen genetic map and the left of the LP genetic map. Opposite the loci, the genetic distances are displayed in centiMorgans (cM). Markers in orange are SNP markers from the wheat 9 K iSelect Assay BeadChip. Markers in black are simple sequence repeat (SSR) markers designed in this study. Blue markers were designed in other studies. Dashed lines connect markers mapped in both populations. The black outlined rectangle indicates the loci cosegregating with Tsc1. The pink shaded portion of the chromosome represents the candidate gene region in each population.

Figure 3

Comparison of the physical and genetic order of markers. The LouPen genetic map is on the right and the Chinese Spring v2.1 physical map is on the left. Markers in red font connected by red dashed lines are not colinear. All other markers are colinear.

Figure 4

Tsc1 candidate gene region in Chinese Spring reference genome v2.1. The scale on the top represents the physical position in base pairs. Genetic markers are displayed as vertical gray bars. Genes are displayed as arrows, labeled 1–5, corresponding to the genes in the table below. Genes with nucleotide binding and ARC (NB-ARC), protein kinase (PK) and leucine rich repeat (LRR), LRR, retinal pigment epithelial membrane, and gliadin domains are shown in purple, orange, yellow, green, and blue, respectively. Gene IDs, protein domains, Pfam IDs, and physical positions of each gene are included in the table.

Figure 5

Evaluation of markers cosegregating with Tsc1. The polyacrylamide gel images of markers fcp731 (A) and fcp732 (B) run on lines with known sensitivity statuses (Table 1) are shown. Horizontal brackets in pink and orange denote amplicons in lines with Tsc1 and tsc1, respectively. The primary amplicon was scored for marker fcp732 (B). The amplicons denoted by the purple bracket were scored for marker fcp731 (A).