Long-read genome sequencing of bread wheat facilitates disease resistance gene cloning

Naveenkumar Athiyannan,Nathalie Rodde,Stéphane Cauet,Kirsty S Botha,Rod A Wing,David Kudrna,Shannon S Derman,Nahed Mohammed,Jan Bettgenhaeuser,Willem H P Boshoff,Michael Abrouk,Simon G Krattinger,Renée Prins

doi:10.1038/s41588-022-01022-1

Abstract

The cloning of agronomically important genes from large, complex crop genomes remains challenging. Here we generate a 14.7 gigabase chromosome-scale assembly of the South African bread wheat (Triticum aestivum) cultivar Kariega by combining high-fidelity long reads, optical mapping and chromosome conformation capture. The resulting assembly is an order of magnitude more contiguous than previous wheat assemblies. Kariega shows durable resistance to the devastating fungal stripe rust disease1. We identified the race-specific disease resistance gene Yr27, which encodes an intracellular immune receptor, to be a major contributor to this resistance. Yr27 is allelic to the leaf rust resistance gene Lr13; the Yr27 and Lr13 proteins show 97% sequence identity2,3. Our results demonstrate the feasibility of generating chromosome-scale wheat assemblies to clone genes, and exemplify that highly similar alleles of a single-copy gene can confer resistance to different pathogens, which might provide a basis for engineering Yr27 alleles with multiple recognition specificities in the future.

Highlights

Circular consensus sequencing (CCS)[4] represents a recent technological breakthrough in DNA sequencing that circumvents the hitherto negative relationship between read length and accuracy, enabling the production of genome assemblies with greatly improved completeness and contiguity[5,6]
Of the 83 yellow rust resistance (Yr) genes described in the wheat gene pool, only nine have been cloned so far[10], precluding knowledge-guided global deployment of Yr genes based on sequences and molecular mechanisms
The resistance of Kariega to stripe rust is conferred by three quantitative trait loci (QTLs): QYr.sgi-2B.1 on chromosome arm 2BS; QYr.sgi-4A.1 on chromosome arm 4AL; and the durable stripe rust resistance gene Yr18 on chromosome arm 7DS, which encodes an ATP-binding cassette (ABC) transporter[1,11]

Summary

Introduction

Circular consensus sequencing (CCS)[4] represents a recent technological breakthrough in DNA sequencing that circumvents the hitherto negative relationship between read length and accuracy, enabling the production of genome assemblies with greatly improved completeness and contiguity[5,6]. A South African spring bread wheat cultivar released in 1993, shows high levels of adult plant stripe rust resistance (Fig. 1a). To facilitate the cloning of the remaining stripe rust resistance genes from Kariega, we generated a de novo genome assembly.

Results

Conclusion