Unconventional R proteins in the botanical tribe Triticeae

Genome-wide identification and characterization of NAC transcription factor-derived microsatellites in wheat (Triticum aestivum L.)

Bread wheat (Triticum aestivum L.) is one of the widely consumed staple foods, providing 20% of the total protein and calories in human nutrition. Seeing its importance in the global food supply, the enrichment of functional genomic resources is vital for meeting future demands and ensuring sustainable production. In addition to the presence of functional domains, the presence of microsatellites within transcription factors makes them valuable candidates for enriching functional marker resources. The NAC transcription factor family regulates a variety of physiological processes in cereal crops. Hence, the present study aims to develop and characterize Triticum aestivum NAC MicroSatellites (TaNACMS) to enrich functional marker resources for genetic diversity analysis, marker-assisted selection, and evolutionary studies. In total, 520 SSRs were identified from 451 TaNAC sequences, and a set of 66 TaNACMS was used for cross-transferability in wild/related wheat species. The cross-transferability rate of 90.22% revealed high locus conservation. Further, 16 TaNACMS were utilized for the characterization of genetic diversity in Indian wheat varieties. These TaNACMS produced 40 alleles (2.5 alleles per locus) with an average observed heterozygosity (Ho), expected heterozygosity (He), and polymorphic information content (PIC) of 0.392, 0.417, and 0.380, respectively. The genetic analysis of wheat genotypes, using principal coordinates analysis (PCoA), neighbor-joining (NJ) clustering, and Bayesian-based STRUCTURE, has revealed three distinct genetic clusters. Two of these clusters consist of Indian wheat varieties, while the third cluster comprises wild/related wheat species. In conclusion, the high rate of transferability of TaNACMS can be effectively utilized for gene flow both within and between species, highlighting evolutionary connections between cultivated wheat and related species. Additionally, these SSRs will aid the marker repository and benefit the wheat improvement programs through marker-assisted selection (MAS).

A single NLR gene confers resistance to leaf and stripe rust in wheat

Nucleotide-binding leucine-rich repeat (NLR) disease resistance genes typically confer resistance against races of a single pathogen. Here, we report that Yr87/Lr85, an NLR gene from Aegilops sharonensis and Aegilops longissima, confers resistance against both P. striiformis tritici (Pst) and Puccinia triticina (Pt) that cause stripe and leaf rust, respectively. Yr87/Lr85 confers resistance against Pst and Pt in wheat introgression as well as transgenic lines. Comparative analysis of Yr87/Lr85 and the cloned Triticeae NLR disease resistance genes shows that Yr87/Lr85 contains two distinct LRR domains and that the gene is only found in Ae. sharonensis and Ae. longissima. Allele mining and phylogenetic analysis indicate multiple events of Yr87/Lr85 gene flow between the two species and presence/absence variation explaining the majority of resistance to wheat leaf rust in both species. The confinement of Yr87/Lr85 to Ae. sharonensis and Ae. longissima and the resistance in wheat against Pst and Pt highlight the potential of these species as valuable sources of disease resistance genes for wheat improvement.

The unconventional resistance protein PTR recognizes the Magnaporthe oryzae effector AVR-Pita in an allele-specific manner

Blast disease caused by the fungus Magnaporthe oryzae is one of the most devastating rice diseases. Disease resistance genes such as Pi-ta or Pi-ta2 are critical in protecting rice production from blast. Published work reports that Pi-ta codes for a nucleotide-binding and leucine-rich repeat domain protein (NLR) that recognizes the fungal protease-like effector AVR-Pita by direct binding. However, this model was challenged by the recent discovery that Pi-ta2 resistance, which also relies on AVR-Pita detection, is conferred by the unconventional resistance gene Ptr, which codes for a membrane protein with a cytoplasmic armadillo repeat domain. Here, using NLR Pi-ta and Ptr RNAi knockdown and CRISPR/Cas9 knockout mutant rice lines, we found that AVR-Pita recognition relies solely on Ptr and that the NLR Pi-ta has no role in it, indicating that it is not the Pi-ta resistance gene. Different alleles of Ptr confer different recognition specificities. The A allele of Ptr (PtrA) detects all natural sequence variants of the effector and confers Pi-ta2 resistance, while the B allele of Ptr (PtrB) recognizes a restricted set of AVR-Pita alleles and, thereby, confers Pi-ta resistance. Analysis of the natural diversity in AVR-Pita and of mutant and transgenic strains identified one specific polymorphism in the effector sequence that controls escape from PtrB-mediated resistance. Taken together, our work establishes that the M. oryzae effector AVR-Pita is detected in an allele-specific manner by the unconventional rice resistance protein Ptr and that the NLR Pi-ta has no function in Pi-ta resistance and the recognition of AVR-Pita.

A diverse panel of 755 bread wheat accessions harbors untapped genetic diversity in landraces and reveals novel genetic regions conferring powdery mildew resistance

KEY MESSAGE

A bread wheat panel reveals rich genetic diversity in Turkish, Pakistani and Iranian landraces and novel resistance loci to diverse powdery mildew isolates via subsetting approaches in association studies. Wheat breeding for disease resistance relies on the availability and use of diverse genetic resources. More than 800,000 wheat accessions are globally conserved in gene banks, but they are mostly uncharacterized for the presence of resistance genes and their potential for agriculture. Based on the selective reduction of previously assembled collections for allele mining for disease resistance, we assembled a trait-customized panel of 755 geographically diverse bread wheat accessions with a focus on landraces, called the LandracePLUS panel. Population structure analysis of this panel based on the TaBW35K SNP array revealed an increased genetic diversity compared to 632 landraces genotyped in an earlier study and 17 high-quality sequenced wheat accessions. The additional genetic diversity found here mostly originated from Turkish, Iranian and Pakistani landraces. We characterized the LandracePLUS panel for resistance to ten diverse isolates of the fungal pathogen powdery mildew. Performing genome-wide association studies and dividing the panel further by a targeted subsetting approach for accessions of distinct geographical origin, we detected several known and already cloned genes, including the Pm2a gene. In addition, we identified 22 putatively novel powdery mildew resistance loci that represent useful sources for resistance breeding and for research on the mildew-wheat pathosystem. Our study shows the value of assembling trait-customized collections and utilizing a diverse range of pathogen races to detect novel loci. It further highlights the importance of integrating landraces of different geographical origins into future diversity studies.

Pathogen perception and deception in plant immunity by kinase fusion proteins

Two studies describe kinase fusion proteins (KFPs) that regulate the perception and deception of wheat pathogens. These highlight the emergence of KFPs as plant immune regulators and emphasize the importance of crop wild relatives as a reservoir for resistance breeding and global food security.