A Transcriptional Regulatory Network of \u3cem\u3eRsv3\u3c/em\u3e-Mediated Extreme Resistance against \u3cem\u3eSoybean Mosaic Virus\u3c/em\u3e

Resistance genes are an effective means for disease control in plants. They predominantly function by inducing a hypersensitive reaction, which results in localized cell death restricting pathogen spread. Some resistance genes elicit an atypical response, termed extreme resistance, where resistance is not associated with a hypersensitive reaction and its standard defense responses. Unlike hypersensitive reaction, the molecular regulatory mechanism(s) underlying extreme resistance is largely unexplored. One of the few known, naturally occurring, instances of extreme resistance is resistance derived from the soybean Rsv3 gene, which confers resistance against the most virulent Soybean mosaic virus strains. To discern the regulatory mechanism underlying Rsv3-mediated extreme resistance, we generated a gene regulatory network using transcriptomic data from time course comparisons of Soybean mosaic virus-G7-inoculated resistant (L29, Rsv3-genotype) and susceptible (Williams82, rsv3-genotype) soybean cultivars. Our results show Rsv3 begins mounting a defense by 6 hpi via a complex phytohormone network, where abscisic acid, cytokinin, jasmonic acid, and salicylic acid pathways are suppressed. We identified putative regulatory interactions between transcription factors and genes in phytohormone regulatory pathways, which is consistent with the demonstrated involvement of these pathways in Rsv3-mediated resistance. One such transcription factor identified as a putative transcriptional regulator was MYC2 encoded by Glyma.07G051500. Known as a master regulator of abscisic acid and jasmonic acid signaling, MYC2 specifically recognizes the G-box motif (“CACGTG”), which was significantly enriched in our data among differentially expressed genes implicated in abscisic acid- and jasmonic acid-related activities. This suggests an important role for Glyma.07G051500 in abscisic acid- and jasmonic acid-derived defense signaling in Rsv3. Resultantly, the findings from our network offer insights into genes and biological pathways underlying the molecular defense mechanism of Rsv3-mediated extreme resistance against Soybean mosaic virus. The computational pipeline used to reconstruct the gene regulatory network in this study is freely available at https://github.com/LiLabAtVT/rsv3-network

Soybean mosaic virus: A successful potyvirus with a wide distribution but restricted natural host range

Taxonomy. Soybean mosaic virus (SMV) is a species within the genus Potyvirus, family Potyviridae that includes almost a quarter of all known plant RNA viruses affecting agriculturally important plants. The Potyvirus genus is the largest of all genera of plant RNA viruses with 160 species. Particle. The filamentous particles of SMV, typical of potyviruses, are about 7,500 Å long and 120 Å in diameter with a central hole of about 15 Å in diameter. Coat protein residues are arranged in helice of about 34 Å pitch having slightly less than 9 subunits per turn. Genome. The SMV genome consists of a single-stranded positive-sense polyadenylated RNA of approximately 9.6 kb with a virus-encoded protein (VPg) linked at the 5\u27 terminus. The genomic RNA contains a single large open reading frame (ORF). The polypeptide produced from the large ORF is processed proteolytically by three viral-encoded proteinases to yield about 10 functional proteins. A small ORF, partially overlapping the P3 cistron, pipo, is encoded as a fusion protein in the N-terminus of P3 (P3N+PIPO). Biological properties. SMV’s host range is restricted mostly to two plant species of a single genus; Glycine max (cultivated soybean) and G. soja (wild soybean). SMV is transmitted by aphids non-persistently and by seeds. Variability of SMV is recognized by reactions on cultivars with dominant resistance (R) genes. Recessive resistance genes are not known. Geographical distribution and economic importance. As a consequence of its seed transmissibility, SMV is present in all soybean growing areas of the world. SMV infections can reduce significantly seed quantity and quality (e.g., mottled seed coats, reduced seed size and viability, and altered chemical composition). Control. The most effective means of managing losses from SMV are planting virus-free seeds and cultivars containing single or multiple R genes. Key attractions. The interactions of SMV with soybean genotypes containing different dominant R genes and understanding functional role(s) of SMV-encoded proteins in virulence, transmission and pathogenicity have been intensively investigated. The SMV-soybean pathosystem has become an excellent model for examining the genetics and genomics of uniquely complex gene-for-gene resistance model in a crop of worldwide importance

A Method for Combining Isolates of Phytophthora sojae to Screen for Novel Sources of Resistance to Phytophthora Stem and Root Rot in Soybean

Soybean cultivars with specific single resistance genes (Rps) are grown to reduce yield loss due to Phytophthora stem and root rot caused by the oomycete pathogen Phytophthora sojae. To identify novel Rps loci, soybean lines are often screened several times, each time with an isolate of P. sojae that differs in virulence on various Rps genes. The goal of this study was to determine whether several isolates of P. sojae that differ in virulence on Rpsgenes could be combined into a single source of inoculum and used to screen soybean lines for novel Rps genes. A set of 14 soybean differential lines, each carrying a specific Rps gene, was inoculated with three isolates of P. sojae, which differed in virulence on 6 to 10 Rps genes, individually or in a 1:1:1 mixture. Inoculum containing the 1:1:1 mixture of isolates was virulent on 13 Rps genes. The mixed-inoculum method was used to screen 1,019 soybean accessions in a blind assay for novel sources of resistance. In all, 17% of Glycine max accessions and 11% of G. soja accessions were resistant (≤30% dead plants), suggesting that these accessions may carry a novel Rps gene or genes. Advantages of combining isolates into a single source of inoculum include reduced cost, ability to screen soybean germplasm with inoculum virulent on all known Rps genes, and ease of identifying novel sources of resistance. This study is a precursor to identifying novel sources of resistance to P. sojae in soybean using RXLR effectors

Infection and genotype remodel the entire soybean transcriptome

<p>Abstract</p> <p>Background</p> <p>High throughput methods, such as high density oligonucleotide microarray measurements of mRNA levels, are popular and critical to genome scale analysis and systems biology. However understanding the results of these analyses and in particular understanding the very wide range of levels of transcriptional changes observed is still a significant challenge. Many researchers still use an arbitrary cut off such as two-fold in order to identify changes that may be biologically significant. We have used a very large-scale microarray experiment involving 72 biological replicates to analyze the response of soybean plants to infection by the pathogen <it>Phytophthora sojae </it>and to analyze transcriptional modulation as a result of genotypic variation.</p> <p>Results</p> <p>With the unprecedented level of statistical sensitivity provided by the high degree of replication, we show unambiguously that almost the entire plant genome (97 to 99% of all detectable genes) undergoes transcriptional modulation in response to infection and genetic variation. The majority of the transcriptional differences are less than two-fold in magnitude. We show that low amplitude modulation of gene expression (less than two-fold changes) is highly statistically significant and consistent across biological replicates, even for modulations of less than 20%. Our results are consistent through two different normalization methods and two different statistical analysis procedures.</p> <p>Conclusion</p> <p>Our findings demonstrate that the entire plant genome undergoes transcriptional modulation in response to infection and genetic variation. The pervasive low-magnitude remodeling of the transcriptome may be an integral component of physiological adaptation in soybean, and in all eukaryotes.</p

Combined use of gliadins and SSRs to analyse the genetic variability of the Spanish collection of cultivated diploid wheat (Triticum monococcum L. ssp. monococcum)

This work studied the combined use of gliadins and SSRs to analyse inter- and intra-accession variability of the Spanish collection of cultivated einkorn (Triticum monococcum L. ssp. monococcum) maintained at the CRF-INIA. In general, gliadin loci presented higher discrimination power than SSRs, reflecting the high variability of the gliadins. The loci on chromosome 6A were the most polymorphic with similar PIC values for both marker systems, showing that these markers are very useful for genetic variability studies in wheat. The gliadin results indicated that the Spanish einkorn collection possessed high genetic diversity, being the differentiation large between varieties and small within them. Some associations between gliadin alleles and geographical and agro-morphological data were found. Agro-morphological relations were also observed in the clusters of the SSRs dendrogram. A high concordance was found between gliadins and SSRs for genotype identification. In addition, both systems provide complementary information to resolve the different cases of intra-accession variability not detected at the agro-morphological level, and to identify separately all the genotypes analysed. The combined use of both genetic markers is an excellent tool for genetic resource evaluation in addition to agro-morphological evaluation

Restriction fragment length polymorphisms distinguish among accessions of Ceratopteris thalictroides and C. richardii ( Parkeriaceae )

We have used cDNA clones as probes on Southern blots to detect restriction fragment length polymorphisms among seven Ceratopteris thalictroides accessions, three C. richardii accessions, and one putative interspecific hybrid. We found that the stringency of post-hybridization washes was a critical parameter affecting the quality of our blots; even with homologous cDNA sequences low stringency conditions resulted in a smear of signal, but high stringency washes gave blots with distinct bands. Most probes showed hybridization with four or more genomic fragments. Similarities in the number and size of fragments between and within species indicated that (i) C. richardii shows limited polymorphism among accessions tested, (ii) C. thalictroides is highly polymorphic, and (iii) Hawaiian accessions of C. thalictroides are divergent relative to their continental cohorts and among themselves. The putative interspecific hybrid did not group closely with either of these species.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/41637/1/606_2004_Article_BF00939725.pd

Infuence of the year and HMW glutenin subunits on end-use quality predictors if bread wheat waxy lines

The effects of environment and the high molecular weight glutenins on some quality properties (sedimentation volume, % protein content, and starch pasting viscosity) of bread wheat mutant waxy lines were evaluated. Thirty-eight 100% amylose-free F 2 derived F 6 and F 7 lines were used. The results indicated that the environment did not influence sedimentation volume, mixograph parameters and starch viscosity parameters of waxy flour. Variation in the % protein content was determined mainly by the environment. The sedimentation volume and the mixograph peak development time were influenced by the variation at over expression of Bx7 and the mixograph peak development time was influenced by the Glu-D1 locus. One starch viscosity parameter, time to peak viscosity, was influenced by variation at the Glu-A1 locus. This parameter is significantly lower in the waxy lines than the parent line, which shows the influence of the waxy loci. No significant correlation was observed for sedimentation volume, mixograph parameters, protein content and viscosity parameters of waxy line

The Genomic Signature of Crop-Wild Introgression in Maize

The evolutionary significance of hybridization and subsequent introgression has long been appreciated, but evaluation of the genome-wide effects of these phenomena has only recently become possible. Crop-wild study systems represent ideal opportunities to examine evolution through hybridization. For example, maize and the conspecific wild teosinte Zea mays ssp. mexicana, (hereafter, mexicana) are known to hybridize in the fields of highland Mexico. Despite widespread evidence of gene flow, maize and mexicana maintain distinct morphologies and have done so in sympatry for thousands of years. Neither the genomic extent nor the evolutionary importance of introgression between these taxa is understood. In this study we assessed patterns of genome-wide introgression based on 39,029 single nucleotide polymorphisms genotyped in 189 individuals from nine sympatric maize-mexicana populations and reference allopatric populations. While portions of the maize and mexicana genomes were particularly resistant to introgression (notably near known cross-incompatibility and domestication loci), we detected widespread evidence for introgression in both directions of gene flow. Through further characterization of these regions and preliminary growth chamber experiments, we found evidence suggestive of the incorporation of adaptive mexicana alleles into maize during its expansion to the highlands of central Mexico. In contrast, very little evidence was found for adaptive introgression from maize to mexicana. The methods we have applied here can be replicated widely, and such analyses have the potential to greatly informing our understanding of evolution through introgressive hybridization. Crop species, due to their exceptional genomic resources and frequent histories of spread into sympatry with relatives, should be particularly influential in these studies

Genetic differentiation and geographical Relationship of Asian barley landraces using SSRs

Genetic diversity in 403 morphologically distinct landraces of barley (Hordeum vulgare L. subsp. vulgare) originating from seven geographical zones of Asia was studied using simple sequence repeat (SSR) markers from regions of medium to high recombination in the barley genome. The seven polymorphic SSR markers representing each of the chromosomes chosen for the study revealed a high level of allelic diversity among the landraces. Genetic richness was highest in those from India, followed by Pakistan while it was lowest for Uzbekistan and Turkmenistan. Out of the 50 alleles detected, 15 were unique to a geographic region. Genetic diversity was highest for landraces from Pakistan (0.70 ± 0.06) and lowest for those from Uzbekistan (0.18 ± 0.17). Likewise, polymorphic information content (PIC) was highest for Pakistan (0.67 ± 0.06) and lowest for Uzbekistan (0.15 ± 0.17). Diversity among groups was 40% compared to 60% within groups. Principal component analysis clustered the barley landraces into three groups to predict their domestication patterns. In total 51.58% of the variation was explained by the first two principal components of the barley germplasm. Pakistan landraces were clustered separately from those of India, Iran, Nepal and Iraq, whereas those from Turkmenistan and Uzbekistan were clustered together into a separate group