Targeted capture and cloning of Rps6 reveal redundancy in soybean resistance genes

Effective management of Phytophthora root rot in soybean is compromised by the rapid loss of efficacy of the most widely deployed resistance genes to Phytophthora sojae (Rps). However, some genes such as Rps3a and Rps6 are still offering a strong protection but are nonetheless rare in elite material, probably owing to the fact that they have never been properly characterized. In this study, we have employed RenSeq, and whole genome sequencing to unravel the nature of Rps6 as a complex locus composed of 10 NLR genes. In a cell death assay using soybean protoplasts, we show that one of the candidates from the cluster interacts robustly with Avr6. Transfer of the candidate gene into a susceptible root system confirmed its function and status as the bona fide Rps6. Through sequence comparison with other Rps differentials, we further discovered that Rps3c and Rps4, originally thought to be distinct genes on different chromosomes, are, in fact, the exact same resistance gene as Rps6, mediating recognition to the same effector, Avr6. These results clarify a long-standing confusion regarding the identity of some elusive Rps genes and offer the precise sequence and position of Rps6. At the same time, along with the recently exposed homology between Rps3b and Rps11, these findings raise some concerns about the apparent multiplicity of Rps genes. Indeed, there may be fewer sources of resistance than assumed, which should instill caution in using current Rps genes to ensure durable management of Phytophthora root rot.