NBS-LRR PacBio sequencing from a Glycine max diversity panel

Numerous sources of putative novel resistance genes towards Phytophthora
sojae (Rps genes) have been identified and loci mapped in soybeans
(Glycine max L. Merr.) but cloning has remained elusive. We utilized
resistance gene enrichment sequencing (RenSeq) to identify the putative
resistance genes in 20 plant introductions (PIs) and differentials of the
cultivar Williams with rps, Rps1c, Rps3a, and Rps8. The DNA from these
genotypes was enriched and sequenced using more than 25,000 80 nt baits
designed for nucleotide-binding leucine-rich repeat (NLR) encoding
sequences. Overall, there were greater numbers of variants in the
NLR-encoding genes in Rps loci, on Chrs 3, 7, 13, and 18 for the 20 plant
introductions as compared to the Williams differentials for rps, Rps1c,
Rps1k, Rps3a, and Rps8. Genes encoding Rps1c, Rps3a, and Rps8 were
proposed based on sequence differences among the differentials. Among the
20 PIs, there may be additional alleles on Chrs 3, 13, and 18, and PI
399079 may have two new alleles, at Chrs 3 and 7 loci. A unique NLR on Chr
8 was identified in PI 200553. New alleles were also identified on Chrs 3
and 18 when the PI and resistant bulks were compared to susceptible
RILs.  This study demonstrates the utility of RenSeq as an
efficient method to identify and predict specific novel NLR genes in
landrace soybean germplasm, which confer resistance to P. sojae and obtain
gene-specific markers to facilitate their introgression into modern
cultivars.