SMRT-AgRenSeq-d in potato (Solanum tuberosum) as a method to identify candidates for the nematode resistance Gpa5

Potato is the thirdmost important food crop in theworld.Diverse pathogens threaten sustainable crop production but can be controlled,in many cases,through the deployment of disease resistance genes belonging to the family of nucleotide-binding,leucine-rich-repeat(NLR)genes.To identify effective disease resistance genes in established varieties,we have successfully established SMRT-AgRenSeq in tetraploid potatoes and have further enhanced the methodology by including dRenSeq in an approach that we term SMR-AgRenSeq-d.The inclusion of dRenSeq enables the filtering of candidates after the association analysis by establishing a presence/absence matrix across resistant and susceptible varieties that is translated into an F1 score.Using a SMRT-RenSeq-based sequence representation of the NLRome from the cultivar Innovator,SMRT-AgRenSeq-d analyses reliably identified the late blight resistance benchmark genes Rpi-R1,Rpi-R2-like,Rpi-R3a,and Rpi-R3b in a panel of 117 varieties with variable phenotype penetrations.All benchmark genes were identified with an F1 score of 1,which indicates absolute linkage in the panel.This method also identified nine strong candidates for Gpa5 that controls the potato cyst nematode(PCN)species Globodera pallida(pathotypes Pa2/3).Assuming that NLRs are involved in controlling many types of resistances,SMRT-AgRenSeq-d can readily be applied to diverse crops and pathogen systems.

Identification and mapping of Rpi-blb4 in diploid wild potato species Solanum bulbocastanum

More than 170 years after causing the potato famine in Ireland,late blight is still considered one of the most devastating crop diseases.Commercial potato breeding efforts depend on natural sources of resistance to protect crops from the rapidly evolving late blight pathogen,Phytophthora infestans.We have identified and mapped a novel broad-spectrum disease resistance gene effective against P.infestans from the wild,diploid potato species Solanum bulbocastanum.Diagnostic resistance gene enrichment sequencing(dRenSeq)was used to confirm the uniqueness of the identified resistance.RenSeq and GenSeq-based mapping of the resistance,referred to as Rpi-blb4,alongside recombinant screening,positioned the locus responsible for the resistance to potato chromosome 5.The interval spans approximately 2.3 Mb and corresponds to the DM reference genome positions of 11.25 and 13.56 Mb.