Sequencing trait-associated mutations to clone wheat rust-resistance gene YrNAM

Abstract

Stripe (yellow) rust, caused by Puccinia striiformis f. sp. tritici (Pst), can significantly affect wheat production. Cloning resistance genes is critical for efficient and effective breeding of stripe rust resistant wheat cultivars. One resistance gene (Yr10CG) underlying the Pst resistance locus Yr10 has been cloned. However, following haplotype and linkage analyses indicate the presence of additional Pst resistance gene(s) underlying/near Yr10 locus. Here, we report the cloning of the Pst resistance gene YrNAM in this region using the method of sequencing trait-associated mutations (STAM). YrNAM encodes a non-canonical resistance protein with a NAM domain and a ZnF-BED domain. We show that both domains are required for resistance. Transgenic wheat harboring YrNAM gene driven by its endogenous promoter confers resistance to stripe rust races CYR32 and CYR33. YrNAM is an ancient gene and present in wild wheat species Aegilops longissima and Ae. sharonensis; however, it is absent in most wheat cultivars, which indicates its breeding value.

The wheat stripe rust resistance gene YrNAM is Yr10

“…The G193E mutation occurs at a very highly conserved amino acid, G193 (Fig. 1d ), with 97.2% conservation across the set of 6282 homologs, and this together with the independent generation of loss-of-function mutations in the study by Ni et al 5 for this residue indicate that G193 plays a critical role in NAM domain function.

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“…Moro and a Moro-derived near isogenic line (NIL) Avocet S + Yr10 (Avocet S*6/Moro) 3 were globally distributed and continue to be included in differential sets for phenotyping Pst in Australasia, Europe, India and North America. Two publications reported the putative cloning of Yr10 as homologs of two closely linked genes, TraesCS1B03G0000200 , an NLR designated Yr10 CG , Genbank accession AF149112 4 , and more recently homologs of TraesCS1B03G0003600 LC.1 and TraesCS1B03G0003500 LC.1 , Genbank accession OP490604, was designated YrNAM 5 . We believe this situation is untenable and that one of these linked genes cannot be Yr10 .…”

“…More recently, Ni et al 5 generated 12 putative YrNAM mutants in two homozygous lines identified in a cross of Moro and a susceptible line. Seven of these mutants were subjected to RNA-seq and transcriptome analysis, and mutations were identified in a gene designated YrNAM , which was located 1.2 cM from the Yr10 CG sequence.…”

“…Seven of these mutants were subjected to RNA-seq and transcriptome analysis, and mutations were identified in a gene designated YrNAM , which was located 1.2 cM from the Yr10 CG sequence. YrNAM encodes a non-canonical resistance protein with a NAM (No Apical Meristem) domain and a ZnF (Zinc Finger)-BED domain at the N and C termini, respectively 5 . It is structurally similar to Rph7 , a leaf rust resistance gene in barley containing NAC transcription factor (TF) and ZnF-BED domains 8 .…”

Mapping and characterization of rust resistance genes Lr53 and Yr35 introgressed from Aegilops species

“…Most of these Lr and Yr genes are ASR genes, which exhibit efficacy in both seedling and adult-plant stages. However, owing to the size and complexity of wheat genomes, only 11 Lr genes ( Lr1 , Lr9 / Lr58 , Lr10 , Lr13 , Lr14a , Lr21 , Lr22a , Lr34 , Lr42 , Lr47 , and Lr67 ) and ten Yr genes ( Yr5 / YrSP , Yr7 , Yr27 , Yr15 , Yr18 , Yr36 , Yr46 , Yr28 , YrU1 , and Yr10 / YrNAM ) have been cloned to date (Li et al 2023 ; Ni et al 2023 ) either by map-based cloning or by rapid gene-cloning methods, including MutChromSeq, MutRenSeq, MutIsoSeq, and STAM (Ni et al 2023 ; Sánchez-Martín et al 2016 ; Steuernagel et al 2016 ; Wang et al 2023b ). Among the cloned Lr and Yr genes, Lr34 / Yr18 / Sr57 / Pm38 , Lr67 / Yr46 / Sr55 / Pm46 , and Yr36 are APR genes encoding a putative ATP-binding cassette transporter, a hexose transporter, and a kinase-START protein, respectively (Krattinger et al 2009 ; Moore et al 2015 ; Fu et al 2009 ).…”