Genetic interactions regulating seed phytate and oligosaccharides in soybean (Glycine max L.).

Two low-phytate soybean (Glycine max (L.) Merr.) mutant lines- V99-5089 (mips mutation on chromosome 11) and CX-1834 (mrp-l and mrp-n mutations on chromosomes 19 and 3, respectively) have proven to be valuable resources for breeding of low-phytate, high-sucrose, and low-raffinosaccharide soybeans, traits that are highly desirable from a nutritional and environmental standpoint. A recombinant inbred population derived from the cross CX1834 x V99-5089 provides an opportunity to study the effect of different combinations of these three mutations on soybean phytate and oligosaccharides levels. Of the 173 recombinant inbred lines tested, 163 lines were homozygous for various combinations of MIPS and two MRP loci alleles. These individuals were grouped into eight genotypic classes based on the combination of SNP alleles at the three mutant loci. The two genotypic classes that were homozygous mrp-l/mrp-n and either homozygous wild-type or mutant at the mips locus (MIPS/mrp-l/mrp-n or mips/mrp-l/mrp-n) displayed relatively similar ~55% reductions in seed phytate, 6.94 mg g -1 and 6.70 mg g-1 respectively, as compared with 15.2 mg g-1 in the wild-type MIPS/MRP-L/MRP-N seed. Therefore, in the presence of the double mutant mrp-l/mrp-n, the mips mutation did not cause a substantially greater decrease in seed phytate level. However, the nutritionally-desirable high-sucrose/low-stachyose/low-raffinose seed phenotype originally observed in soybeans homozygous for the mips allele was reversed in the presence of mrp-l/mrp-n mutations: homozygous mips/mrp-l/mrp-n seed displayed low-sucrose (7.70%), high-stachyose (4.18%), and the highest observed raffinose (0.94%) contents per gram of dry seed. Perhaps the block in phytic acid transport from its cytoplasmic synthesis site to its storage site, conditioned by mrp-l/mrp-n, alters myo-inositol flux in mips seeds in a way that restores to wild-type levels the mips conditioned reductions in raffinosaccharides. Overall this study determined the combinatorial effects of three low phytic acid causing mutations on regulation of seed phytate and oligosaccharides in soybean

Additional file 3: of Genome-wide transcriptome analyses of developing seeds from low and normal phytic acid soybean lines

Defense related genes differentially expressed in early stages of seed development. Column ‘S’ reports the stages of development in which the gene is differentially expressed. Genes down-regulated in 3mlpa mutant are indicated by negative values of log 2 ratio. Adjusted P-values are only reported for the stages in which the gene is differentially expressed. (XLSX 60 kb

Additional file 2: Figure S1. of Genome-wide transcriptome analyses of developing seeds from low and normal phytic acid soybean lines

Relative gene expression of MIPS1, MRP-L, MRP-N. Fold change between 3mlpa and 3MWT at respective seed developmental stages for genes encoding (a) MIPS1, (b) MRP-L and (c) MRP-N. Green and orange bars indicate mean fold change values from RNA-Seq and qPCR experiments, respectively. There was no significant difference in the gene expression profiles estimated using qPCR and RNA-Seq analyses at significance level of 0.01 (See Additional file 7 for more information) (PDF 27 kb

Additional file 7: of Genome-wide transcriptome analyses of developing seeds from low and normal phytic acid soybean lines

Primers used for quantitative real-time PCR. Gene ID for MIPS1 was not available for the first reference soybean assembly; therefore it is indicated as ‘NA’. Published primer sequences were obtained for MIPS1 [18], RS2 [60] and housekeeping gene, UBQ10 [71] (XLSX 45 kb

Identification of Quantitative Disease Resistance Loci Toward Four Pythium Species in Soybean

In this study, four recombinant inbred line (RIL) soybean populations were screened for their response to infection by Pythium sylvaticum, Pythium irregulare, Pythium oopapillum, and Pythium torulosum. The parents, PI 424237A, PI 424237B, PI 408097, and PI 408029, had higher levels of resistance to these species in a preliminary screening and were crossed with “Williams,” a susceptible cultivar. A modified seed rot assay was used to evaluate RIL populations for their response to specific Pythium species selected for a particular population based on preliminary screenings. Over 2500 single-nucleotide polymorphism (SNP) markers were used to construct chromosomal maps to identify regions associated with resistance to Pythium species. Several minor and large effect quantitative disease resistance loci (QDRL) were identified including one large effect QDRL on chromosome 8 in the population of PI 408097 × Williams. It was identified by two different disease reaction traits in P. sylvaticum, P. irregulare, and P. torulosum. Another large effect QDRL was identified on chromosome 6 in the population of PI 408029 × Williams, and conferred resistance to P. sylvaticum and P. irregulare. These large effect QDRL will contribute toward the development of improved soybean cultivars with higher levels of resistance to these common soil-borne pathogens.This article is published as Clevinger EM, Biyashev R, Lerch-Olson E, Yu H, Quigley C, Song Q, Dorrance AE, Robertson AE and Saghai Maroof MA (2021) Identification of Quantitative Disease Resistance Loci Toward Four Pythium Species in Soybean. Front. Plant Sci. 12:644746. doi:10.3389/fpls.2021.644746.</p

Mining germplasm panels and phenotypic datasets to identify loci for resistance to Phytophthora sojae in soybean

Phytophthora sojae causes Phytophthora root and stem rot of soybean and has been primarily managed through deployment of qualitative Resistance to P. sojae genes (Rps genes). The effectiveness of each individual or combination of Rps gene(s) depends on the diversity and pathotypes of the P. sojae populations present. Due to the complex nature of P. sojae populations, identification of more novel Rps genes is needed. In this study, phenotypic data from previous studies of 16 panels of plant introductions (PIs) were analyzed. Panels 1 and 2 consisted of 448 Glycine max and 520 G. soja, which had been evaluated for Rps gene response with a combination of P. sojae isolates. Panels 3 and 4 consisted of 429 and 460 G. max PIs, respectively, which had been evaluated using individual P. sojae isolates with complex virulence pathotypes. Finally, Panels 5–16 (376 G. max PIs) consisted of data deposited in the USDA Soybean Germplasm Collection from evaluations with 12 races of P. sojae. Using these panels, genome-wide association (GWA) analyses were carried out by combining phenotypic and SoySNP50K genotypic data. GWA models identified two, two, six, and seven novel Rps loci with Panels 1, 2, 3, and 4, respectively. A total of 58 novel Rps loci were identified using Panels 5–16. Genetic and phenotypic dissection of these loci may lead to the characterization of novel Rps genes that can be effectively deployed in new soybean cultivars against diverse P. sojae populations.This article is published as Van, Kyujung, William Rolling, Ruslan M. Biyashev, Rashelle L. Matthiesen, Nilwala S. Abeysekara, Alison E. Robertson, Deloris J. Veney, Anne E. Dorrance, Leah K. McHale, and M. A. Saghai Maroof. "Mining germplasm panels and phenotypic datasets to identify loci for resistance to Phytophthora sojae in soybean." The Plant Genome 14, no. 1 (2021): e20063. doi:10.1002/tpg2.20063.</p