Identification of Unique Genetic Sources of Soybean Rust Resistance from the USDA Soybean Germplasm Collection

Abstract

Soybean [Glycine max (L.) Merr.] rust is caused by the fungal pathogen Phakopsora pachyrhizi. Six rust resistance loci (Rpp1, 2, 3, 4, 5, and 6) have been reported. Crosses were made between 75 resistant plant introductions (PIs) and a susceptible elite line or cultivar. Bulked segregant analysis (BSA) was used to determine if the PI resistance genes mapped to a previously identified locus or to an unreported locus. Fifty‐two PIs had resistance genes that mapped to the Rpp3 region on chromosome 6 of the soybean genome. A set of P. pachyrhizi isolates was used to further characterize the resistance of these PIs. Forty‐two of the PIs exhibited the same reaction profiles as either PI 462312 (Rpp3) or ‘Hyuuga’ (Rpp3 and Rpp5) to the panel of isolates. The fine mapping of Rpp1, Rpp3, and Rpp4 and the availability of the SoySNP50K Infinium Chip data on the USDA Soybean Germplasm Collection made it possible to use BSA and isolate data on these PIs to determine in retrospect how effective haplotype analysis would be in narrowing down the PIs to those likely to have a unique source of resistance. Thirty‐seven of the 52 PIs (71%) mapping to the Rpp3 region had a haplotype identical to that of PI 462312. A combination of these analyses could prove useful in more rapidly narrowing down resistant PIs to those likely to carry a unique resistance gene.

Asian soybean rust in Brazil: past, present, and future

“…Furthermore, another technique, the latest next-generation sequencing platforms, has improved the capacity to assess genetic variability at the genomic level in soybean accessions. It revealed important polymorphisms and haplotypes among individuals that responded differently to different isolates of the pathogen, improving the capacity of marker selection based on single polymorphism nucleotides (Kim et al, 2012;Harris et al, 2015;Yu et al, 2015).…”

Molecular Characterization of Resistance to Soybean Rust (Phakopsora pachyrhizi Syd. & Syd.) in Soybean Cultivar DT 2000 (PI 635999)

“…pachyrhizi population. Thus, further investigation is needed to determine whether the SBR resistance of DT 2000 is controlled by the same genes/alleles as those previously reported [13,17,18,47,53]. Moreover, it is worth noting that a number of the USDA germplasm accessions that have shown resistance to P .…”

“…An Rpp gene associated with lesion type was mapped to the genomic location of the Rpp3 locus [47], but it is not yet known whether DT 2000 carries the same allele as PI 462312, the source of the original Rpp3 gene. Other studies have shown that numerous SBR-resistant soybean germplasm accessions carry a resistance gene at the Rpp3 locus [13,17,18,47]. …”

“…Chakraborty et al [15] identified Rpp1-b , a different dominant resistance allele at the Rpp1 locus in PI 594538A, Ray et al [16] discovered additional resistance alleles at the Rpp1 locus in PI 587886 and PI 587880A, and Hossain et al [17] also reported other alleles at the Rpp1 locus in PI 594767A and PI 587905. Harris et al [18] found that 52 out of 75 resistant PIs had a resistance gene mapping to the Rpp3 locus. While the original Rpp1 gene from PI 200492 has provided high levels of resistance to U.S. P .…”

Registration of Four Near‐Isogenic Soybean Lines of G00‐3213 for Resistance to Asian Soybean Rust

“…(Hyuuga) (chr 6; PI 506764) was initially believed to be a novel allele at the Rpp3 locus (Monteros et al, 2007); however, a subsequent study showed that PI 506764 actually has a natural pyramid of genes at the Rpp3 and Rpp5 loci (Kendrick et al, 2011). Additionally, many other resistance sources have been documented representing what appears to be many different plant introductions with resistance genes at the same loci, or novel resistance alleles (Harris et al, 2015).…”