Identification of a soybean rust resistance gene in PI 567104B

Phytochemical profiling of soybean genotypes using GC-MS and UHPLC-DAD/MS

Soybean is one of the most economically important crops worldwide. However, soybean yield can be substantially decreased by many diseases. Soybean genotypes could have different reactions to pathogen infection. As a first step toward investigating the biochemical basis of soybean resistance and susceptibility to disease, phytochemicals in the seeds of 52 soybean genotypes previously reported to have different reactions to diseases of soybean rust (SBR), Phomopsis seed decay (PSD), and purple seed stain (PSS) were analyzed. Using GC-MS, a total of 46 compounds were tentatively identified which included 11 chemical groups. Among those, the major group was esters, followed by carboxylic acid, ketone, and sugar moieties. Compounds having reported antioxidant, anti-microbial, and anti-inflammatory activities were also identified. UHPLC-DAD/MS analysis indicated that there were five major isoflavone components presented in the samples, including daidzin, glycitin, genistin, malonyldaidzin, and malonylglycitin. Isoflavones have been reported to play an important role in defense from plant pathogens. Although there was variance in the isoflavone content among soybean genotypes, those with the SBR resistance Rpp6 gene (PI 567102B, PI 567104B, PI 567129) consistently exhibited the highest concentrations of daidzin, glycitin, genistin, and malonyldaidzin. The SBR resistant genotype, PI 230970 (Rpp2) had the greatest amount of genistin. The SBR resistant genotype, PI 200456 (Rpp5) resistant genotype uniquely contained glycitein, a compound that was absent in the other 51 genotypes examined. A PSD-resistant genotype PI 424324B had nearly four times the amount of stigmasterol as PI 556625, which was susceptible to SBR, PSD, and PSS in our previous tests. Results of this study provide useful information for further investigation of the biochemical basis of soybean resistance to diseases. The results may also aid in selection of soybean lines for breeding for resistance to soybean rust and other diseases.

Soybean-Phakopsora pachyrhizi interactions: towards the development of next-generation disease-resistant plants

Soybean rust (SBR), caused by the obligate biotrophic fungus Phakopsora pachyrhizi, is a devastating foliar disease threatening soybean production. To date, no commercial cultivars conferring durable resistance to SBR are available. The development of long-lasting SBR resistance has been hindered by the lack of understanding of this complex pathosystem, encompassing challenges posed by intricate genetic structures in both the host and pathogen, leading to a gap in the knowledge of gene-for-gene interactions between soybean and P. pachyrhizi. In this review, we focus on recent advancements and emerging technologies that can be used to improve our understanding of the P. pachyrhizi-soybean molecular interactions. We further explore approaches used to combat SBR, including conventional breeding, transgenic approaches and RNA interference, and how advances in our understanding of plant immune networks, the availability of new molecular tools, and the recent sequencing of the P. pachyrhizi genome could be used to aid in the development of better genetic resistance against SBR. Lastly, we discuss the research gaps of this pathosystem and how new technologies can be used to shed light on these questions and to develop durable next-generation SBR-resistant soybean plants.

Phenotypic Evaluation of Soybean Genotypes for Their Reaction to a Mississippi Isolate of Phakopsora pachyrhizi Causing Soybean Rust

Soybean rust (SBR) caused by Phakopsora pachyrhizi Syd. and P. Syd. is one of the most important foliar diseases of soybean. SBR has the potential to cause major economic damage to global and U.S. soybean production. Analysis of reactions of soybean genotypes to P. pachyrhizi is an important step towards breeding for resistance to SBR. Fifty-four diverse soybean genotypes with both known and unknown Rpp resistance genes were tested for their reactions to a Mississippi P. pachyrhizi isolate. PI 567102B (Rpp6) had a near-immune reaction with the lowest disease severity score and no sporulation. Among seventeen genotypes with resistant or incomplete resistant reddish-brown (RB) reactions, eight are improved breeding lines that are available to researchers through material transfer agreements (MTAs). Thirty-six genotypes had the susceptible TAN reaction. Four soybean lines (RN06-32-1(7-b, GC 00138-29, G01-PR16, and GC 84051-9-1) had RB reactions and significantly lower SBR severity and sporulation than three of the six resistant checks, PI 230970 (Rpp2), PI 462312 (Rpp3), and PI 459025B (Rpp4). G01-PR16 is a publicly released germplasm. This research provides new information about reactions of different soybean genotypes to a midsouthern USA isolate of P. pachyrhizi and thereby aids in breeding for resistance to SBR.

Mapping QTLs Controlling Soybean Rust Disease Resistance in Chiang Mai 5, an Induced Mutant Cultivar

Soybean rust (SBR) caused by the fungus Phakopsora pachyrhizi is an important folia disease of soybean (Glycine max). In this study, we identified QTLs controlling SBR in Chiang Mai 5 (CM5), an SBR-resistant cultivar developed by induced mutation breeding. A recombinant inbred line (RIL) population of 108 lines developed from a cross between Sukhothai 2 (SKT2, a susceptible cultivar) and CM5 was evaluated for SBR resistance under field conditions in Thailand. QTL analysis for the resistance in the RIL population identified a single QTL, qSBR18.1, for resistance. qSBR18.1 was mapped to a 212-kb region on chromosome 18 between simple sequence repeat markers Satt288 and sc21_3420 and accounted for 21.31-35.09% depending on the traits evaluated for resistance. The qSBR18.1 interval overlapped with genomic regions containing resistance to P. pachyrhizi 4 (Rpp4), a locus for SBR resistance. Three tightly linked genes, Glyma.18G226250, Glyma.18G226300, and Glyma.18G226500, each encoding leucine-rich repeat-containing protein, were identified as candidate genes for SBR resistance at the qSRB18.1. The qSBR18.1 would be useful for breeding of SBR resistance.

Genomic regions associated with resistance to soybean rust (Phakopsora pachyrhizi) under field conditions in soybean germplasm accessions from Japan, Indonesia and Vietnam

Eight soybean genomic regions, including six never before reported, were found to be associated with resistance to soybean rust (Phakopsora pachyrhizi) in the southeastern USA. Soybean rust caused by Phakopsora pachyrhizi is one of the most important foliar diseases of soybean [Glycine max (L.) Merr.]. Although seven Rpp resistance gene loci have been reported, extensive pathotype variation in and among fungal populations increases the importance of identifying additional genes and loci associated with rust resistance. One hundred and ninety-one soybean plant introductions from Japan, Indonesia and Vietnam, and 65 plant introductions from other countries were screened for resistance to P. pachyrhizi under field conditions in the southeastern USA between 2008 and 2015. The results indicated that 84, 69, and 49% of the accessions from southern Japan, Vietnam or central Indonesia, respectively, had negative BLUP values, indicating less disease than the panel mean. A genome-wide association analysis using SoySNP50K Infinium BeadChip data identified eight genomic regions on seven chromosomes associated with SBR resistance, including previously unreported regions of Chromosomes 1, 4, 6, 9, 13, and 15, in addition to the locations of the Rpp3 and Rpp6 loci. The six unreported genomic regions might contain novel Rpp loci. The identification of additional sources of rust resistance and associated genomic regions will further efforts to develop soybean cultivars with broad and durable resistance to soybean rust in the southern USA.

Novel disease resistance gene paralogs created by CRISPR/Cas9 in soy

KEY MESSAGE

Novel disease resistance gene paralogues are generated by targeted chromosome cleavage of tandem duplicated NBS-LRR gene complexes and subsequent DNA repair in soybean. This study demonstrates accelerated diversification of innate immunity of plants using CRISPR. Nucleotide-binding-site-leucine-rich-repeat (NBS-LRR) gene families are key components of effector-triggered immunity. They are often arranged in tandem duplicated arrays in the genome, a configuration that is conducive to recombinations that will lead to new, chimeric genes. These rearrangements have been recognized as major sources of novel disease resistance phenotypes. Targeted chromosome cleavage by CRISPR/Cas9 can conceivably induce rearrangements and thus emergence of new resistance gene paralogues. Two NBS-LRR families of soy have been selected to demonstrate this concept: a four-copy family in the Rpp1 region (Rpp1L) and a large, complex locus, Rps1 with 22 copies. Copy-number variations suggesting large-scale, CRISPR/Cas9-mediated chromosome rearrangements in the Rpp1L and Rps1 complexes were detected in up to 58.8% of progenies of primary transformants using droplet-digital PCR. Sequencing confirmed development of novel, chimeric paralogs with intact open reading frames. These novel paralogs may confer new disease resistance specificities. This method to diversify innate immunity of plants by genome editing is readily applicable to other disease resistance genes or other repetitive loci.

Reactions of Soybean Germplasm Accessions to Six Phakopsora pachyrhizi Isolates from the United States

Soybean rust, caused by Phakopsora pachyrhizi Syd. & P. Syd., is one of the most economically important foliar diseases of soybean. Resistant cultivars could reduce yield losses and management costs but considerable pathogenic diversity exists among populations of the fungus; thus, resistance to a range of pathotypes is essential. Seedling and detached-leaf assays were conducted to characterize the resistance of 55 soybean plant introductions (PIs) to six purified isolates of P. pachyrhizi originating from the southern United States. In the greenhouse resistance assays, the differentials Hyuuga (PI 506764) and PI 471904 and accessions PI 224268, PI 567025A, PI 567039, PI 567046A, and DT 2000 (PI 635999) were resistant to all six isolates, including Florida isolates from 2011 and 2012 that were able to defeat resistance conditioned by the Rpp1 through Rpp4 genes. Twenty-six other PIs were resistant to four or five of the six isolates. In the detached-leaf assays, eight accessions developed reddish-brown reactions to all six isolates, with an average of only 0.23 to 0.55 uredinia/lesion. These included Hyuuga, DT 2000, two differentials with a resistance allele at the Rpp5 locus, and accessions PI 224268, PI 423960B, PI 567025A, and PI 567046A. Many of the resistant accessions have subsequently been reported to have a resistance allele at the Rpp3 locus, and two others have resistance genes at the Rpp4 or Rpp6 locus. This study provided new information about resistance reaction phenotypes that can be useful for understanding mechanisms of resistance, which Rpp genes and alleles could be combined to obtain broader and more durable rust resistance in soybean cultivars, and pathotype diversity among the six isolates used.

Discovery of a seventh Rpp soybean rust resistance locus in soybean accession PI 605823

KEY MESSAGE

A novel Rpp gene from PI 605823 for resistance to Phakopsora pachyrhizi was mapped on chromosome 19. Soybean rust, caused by the obligate biotrophic fungal pathogen Phakopsora pachyrhizi Syd. & P. Syd, is a disease threat to soybean production in regions of the world with mild winters. Host plant resistance conditioned by resistance to P. pachyrhizi (Rpp) genes has been found in numerous soybean accessions, and at least 10 Rpp genes or alleles have been mapped to six genetic loci. Identifying additional disease-resistance genes will facilitate development of soybean cultivars with durable resistance. PI 605823, a plant introduction from Vietnam, was previously identified as resistant to US populations of P. pachyrhizi in greenhouse and field trials. In this study, bulked segregant analysis using an F2 population derived from 'Williams 82' × PI 605823 identified a genomic region associated with resistance to P. pachyrhizi isolate GA12, which had been collected in the US State of Georgia in 2012. To further map the resistance locus, linkage mapping was carried out using single-nucleotide polymorphism markers and phenotypic data from greenhouse assays with an F2:3 population derived from Williams 82 × PI 605823 and an F4:5 population derived from '5601T' × PI 605823. A novel resistance gene, Rpp7, was mapped to a 154-kb interval (Gm19: 39,462,291-39,616,643 Glyma.Wm82.a2) on chromosome 19 that is different from the genomic locations of any previously reported Rpp genes. This new gene could be incorporated into elite breeding lines to help provide more durable resistance to soybean rust.