Comparative transcriptomics of soybean genotypes with partial resistance towards Phytophthora sojae, Conrad, and M92-220, to moderately susceptible fast neutron mutant soybeans and Sloan.

The breeding of disease-resistant soybeans cultivars to manage Phytophthora root and stem rot caused by the pathogen Phytophthora sojae involves combining quantitative disease resistance (QDR) and Rps gene-mediated resistance. To identify and confirm potential mechanisms of QDR towards P. sojae, we conducted a time course study comparing changes in gene expression among Conrad and M92-220 with high QDR to susceptible genotypes, Sloan and 3 mutants derived from fast neutron (FN) irradiation of M92-220. Differentially expressed genes from Conrad and M92-220 indicated several shared defense-related pathways at the transcriptomic level, but also defense pathways unique to each cultivar such as stilbenoid, diarylheptanoid and gingerol biosynthesis, and monobactam biosynthesis. Gene Ontology pathway analysis showed that the susceptible FN mutants lacked enrichment of three terpenoid related-pathways and two cell wall-related pathways at either one or both timepoints, in contrast to M92-220. The susceptible mutants also lacked enrichment of potentially important KEGG pathways at either one or both timepoints, including sesquiterpenoid and triterpenoid biosynthesis, thiamine metabolism, arachidonic acid, stilbenoid, diarylheptanoid and gingerol biosynthesis, and monobactam biosynthesis. Additionally, thirty-one genes which were differentially expressed in M92-220 following P. sojae infection were not expressed in the mutants. These 31 genes have annotations related to unknown proteins, valine, leucine, and isoleucine biosynthesis and protein and lipid metabolic processes. The results of this study confirm previously proposed mechanisms of QDR, provide evidence for potential novel QDR pathways in M92-220, and furthers our understanding of the complex network associated with QDR mechanisms in soybean towards P. sojae.

Molecular mechanisms underpinning quantitative resistance to Phytophthora sojae in Glycine max using a systems genomics approach.

Expression of quantitative disease resistance in many host-pathogen systems is controlled by genes at multiple loci, each contributing a small effect to the overall response. We used a systems genomics approach to study the molecular underpinnings of quantitative disease resistance in the soybean-Phytophthora sojae pathosystem, incorporating expression quantitative trait loci (eQTL) mapping and gene co-expression network analysis to identify the genes putatively regulating transcriptional changes in response to inoculation. These findings were compared to previously mapped phenotypic (phQTL) to identify the molecular mechanisms contributing to the expression of this resistance. A subset of 93 recombinant inbred lines (RILs) from a Conrad × Sloan population were inoculated with P. sojae isolate 1.S.1.1 using the tray-test method; RNA was extracted, sequenced, and the normalized read counts were genetically mapped from tissue collected at the inoculation site 24 h after inoculation from both mock and inoculated samples. In total, more than 100,000 eQTLs were mapped. There was a switch from predominantly cis-eQTLs in the mock treatment to an almost entirely nonoverlapping set of predominantly trans-eQTLs in the inoculated treatment, where greater than 100-fold more eQTLs were mapped relative to mock, indicating vast transcriptional reprogramming due to P. sojae infection occurred. The eQTLs were organized into 36 hotspots, with the four largest hotspots from the inoculated treatment corresponding to more than 70% of the eQTLs, each enriched for genes within plant-pathogen interaction pathways. Genetic regulation of trans-eQTLs in response to the pathogen was predicted to occur through transcription factors and signaling molecules involved in plant-pathogen interactions, plant hormone signal transduction, and MAPK pathways. Network analysis identified three co-expression modules that were correlated with susceptibility to P. sojae and associated with three eQTL hotspots. Among the eQTLs co-localized with phQTLs, two cis-eQTLs with putative functions in the regulation of root architecture or jasmonic acid, as well as the putative master regulators of an eQTL hotspot nearby a phQTL, represent candidates potentially underpinning the molecular control of these phQTLs for resistance.

Identification of Candidate Genes for a Major Quantitative Disease Resistance Locus From Soybean PI 427105B for Resistance to Phytophthora sojae.

Phytophthora root and stem rot is a yield-limiting soybean disease caused by the soil-borne oomycete Phytophthora sojae. Although multiple quantitative disease resistance loci (QDRL) have been identified, most explain <10% of the phenotypic variation (PV). The major QDRL explaining up to 45% of the PV were previously identified on chromosome 18 and represent a valuable source of resistance for soybean breeding programs. Resistance alleles from plant introductions 427105B and 427106 significantly increase yield in disease-prone fields and result in no significant yield difference in fields with less to no disease pressure. In this study, high-resolution mapping reduced the QDRL interval to 3.1 cm, and RNA-seq analysis of near-isogenic lines (NILs) varying at QDRL-18 pinpointed a single gene of interest which was downregulated in inoculated NILs carrying the resistant allele compared to inoculated NILs with the susceptible allele. This gene of interest putatively encodes a serine-threonine kinase (STK) related to the AtCR4 family and may be acting as a susceptibility factor, based on the specific increase of jasmonic acid concentration in inoculated NILs. This work facilitates further functional analyses and marker-assisted breeding efforts by prioritizing candidate genes and narrowing the targeted region for introgression.

Environment of origin and domestication affect morphological, physiological, and agronomic response to water deficit in chile pepper (Capsicum sp.).

Global climate change is having a significant effect on agriculture by causing greater precipitation variability and an increased risk of drought. To mitigate these effects, it is important to identify specific traits, adaptations, and germplasm that improve tolerance to soil water deficit. Local varieties, known as landraces, have undergone generations of farmer-mediated selection and can serve as sources of variation, specifically for tolerance to abiotic stress. Landraces can possess local adaptations, where accessions adapted to a particular environment will outperform others grown under the same conditions. We explore adaptations to water deficit in chile pepper landraces from across an environmental gradient in Mexico, a center of crop domestication and diversity, as well in improved varieties bred for the US. In the present study, we evaluated 25 US and Mexico accessions in a greenhouse experiment under well-watered and water deficit conditions and measured morphological, physiological, and agronomic traits. Accession and irrigation regime influenced plant biomass and height, while branching, CO2 assimilation, and fruit weight were all influenced by an interaction between accession and irrigation. A priori group contrasts revealed possible adaptations to water deficit for branching, CO2 assimilation, and plant height associated with geographic origin, domestication level, and pepper species. Additionally, within the Mexican landraces, the number of primary branches had a strong relationship with precipitation from the environment of origin. This work provides insight into chile pepper response to water deficit and adaptation to drought and identifies possibly tolerant germplasm.

Two divergent haplotypes from a highly heterozygous lychee genome suggest independent domestication events for early and late-maturing cultivars.

Lychee is an exotic tropical fruit with a distinct flavor. The genome of cultivar 'Feizixiao' was assembled into 15 pseudochromosomes, totaling ~470 Mb. High heterozygosity (2.27%) resulted in two complete haplotypic assemblies. A total of 13,517 allelic genes (42.4%) were differentially expressed in diverse tissues. Analyses of 72 resequenced lychee accessions revealed two independent domestication events. The extremely early maturing cultivars preferentially aligned to one haplotype were domesticated from a wild population in Yunnan, whereas the late-maturing cultivars that mapped mostly to the second haplotype were domesticated independently from a wild population in Hainan. Early maturing cultivars were probably developed in Guangdong via hybridization between extremely early maturing cultivar and late-maturing cultivar individuals. Variable deletions of a 3.7 kb region encompassed by a pair of CONSTANS-like genes probably regulate fruit maturation differences among lychee cultivars. These genomic resources provide insights into the natural history of lychee domestication and will accelerate the improvement of lychee and related crops.

Identification of SNP markers associated with soybean fatty acids contents by genome-wide association analyses.

Composition of fatty acids (FAs) in soybean seed is important for the quality and uses of soybean oil. Using gas chromatography, we have measured soybean FAs profiles of 621 soybean accessions (maturity groups I through IV) grown in five different environments; Columbus, OH (2015), Wooster, OH (2014 and 2015), Plymouth, NC (2015), and Urbana, IL (2015). Using publicly available SoySNP50K genotypic data and the FA profiles from this study, a genome-wide association analysis was completed with a compressed mixed linear model to identify 43 genomic regions significantly associated with a fatty acid at a genome wide significance threshold of 5%. Among these regions, one and three novel genomic regions associated with palmitic acid and stearic acid, respectively, were identified across all five environments. Additionally, nine novel environment-specific FA-related genomic regions were discovered providing new insights into the genetics of soybean FAs. Previously reported FA-related loci, such as FATB1a, SACPD-C, and KASIII, were also confirmed in this study. Our results will be useful for future functional studies and marker-assisted breeding for soybean FAs. Supplementary Information: The online version contains supplementary material available at 10.1007/s11032-021-01216-1.

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.

Germination response of diverse wild and landrace chile peppers (Capsicum spp.) under drought stress simulated with polyethylene glycol.

Responses to drought within a single species may vary based on plant developmental stage, drought severity, and the avoidance or tolerance mechanisms employed. Early drought stress can restrict emergence and seedling growth. Thus, in areas where water availability is limited, rapid germination leading to early plant establishment may be beneficial. Alternatively, germination without sufficient water to support the seedling may lead to early senescence, so reduced germination under low moisture conditions may be adaptive at the level of the population. We studied the germination response to osmotic stress of diverse chile pepper germplasm collected in southern Mexico from varied ecozones, cultivation systems, and of named landraces. Drought stress was simulated using polyethylene glycol solutions. Overall, survival time analysis revealed delayed germination at the 20% concentration of PEG across all ecozones. The effect was most pronounced in the genotypes from hotter, drier ecozones. Additionally, accessions from wetter and cooler ecozones had the fastest rate of germination. Moreover, accessions of the landraces Costeño Rojo and Tusta germinated more slowly and incompletely if sourced from a drier ecozone than a wetter one, indicating that slower, reduced germination under drought stress may be an adaptive avoidance mechanism. Significant differences were also observed between named landraces, with more domesticated types from intensive cultivation systems nearly always germinating faster than small-fruited backyard- or wild-types, perhaps due to the fact that the smaller-fruited accessions may have undergone less selection. Thus, we conclude that there is evidence of local adaptation to both ecozone of origin and source cultivation system in germination characteristics of diverse chile peppers.

Testing methods and statistical models of genomic prediction for quantitative disease resistance to Phytophthora sojae in soybean [Glycine max (L.) Merr] germplasm collections.

KEY MESSAGE: Genomic prediction of quantitative resistance toward Phytophthora sojae indicated that genomic selection may increase breeding efficiency. Statistical model and marker set had minimal effect on genomic prediction with > 1000 markers. Quantitative disease resistance (QDR) toward Phytophthora sojae in soybean is a complex trait controlled by many small-effect loci throughout the genome. Along with the technical and rate-limiting challenges of phenotyping resistance to a root pathogen, the trait complexity can limit breeding efficiency. However, the application of genomic prediction to traits with complex genetic architecture, such as QDR toward P. sojae, is likely to improve breeding efficiency. We provide a novel example of genomic prediction by measuring QDR to P. sojae in two diverse panels of more than 450 plant introductions (PIs) that had previously been genotyped with the SoySNP50K chip. This research was completed in a collection of diverse germplasm and contributes to both an initial assessment of genomic prediction performance and characterization of the soybean germplasm collection. We tested six statistical models used for genomic prediction including Bayesian Ridge Regression; Bayesian LASSO; Bayes A, B, C; and reproducing kernel Hilbert spaces. We also tested how the number and distribution of SNPs included in genomic prediction altered predictive ability by varying the number of markers from less than 50 to more than 34,000 SNPs, including SNPs based on sequential sampling, random sampling, or selections from association analyses. Predictive ability was relatively independent of statistical model and marker distribution, with a diminishing return when more than 1000 SNPs were included in genomic prediction. This work estimated relative efficiency per breeding cycle between 0.57 and 0.83, which may improve the genetic gain for P. sojae QDR in soybean breeding programs.

Workflow for the Quantification of Soluble and Insoluble Carbohydrates in Soybean Seed.

Soybean seed composition has a profound impact on its market value and commercial use as an important commodity. Increases in oil and protein content have been historically pursued by breeders and genetic engineers; consequently, rapid methods for their quantification are well established. The interest in complete carbohydrate profiles in mature seeds, on the other hand, has recently increased due to numerous attempts to redirect carbohydrates into oil and protein or to offer specialty seed with a specific sugar profile to meet animal nutritional requirements. In this work, a sequential protocol for quantifying reserve and structural carbohydrates in soybean seed was developed and validated. Through this procedure, the concentrations of soluble sugars, sugar alcohols, starch, hemicellulose, and crystalline cellulose can be determined in successive steps from the same starting material using colorimetric assays, LC-MS/MS, and GC-MS. The entire workflow was evaluated using internal standards to estimate the recovery efficiency. Finally, it was successfully applied to eight soybean genotypes harvested from two locations, and the resulting correlations of carbohydrate and oil or protein are presented. This methodology has the potential not only to guide soybean cultivar optimization processes but also to be expanded to other crops with only slight modifications.

Genome-wide association analyses of quantitative disease resistance in diverse sets of soybean [Glycine max (L.) Merr.] plant introductions.

Phytophthora sojae is one of the costliest soybean pathogens in the US. Quantitative disease resistance (QDR) is a vital part of Phytophthora disease management. In this study, QDR was measured in 478 and 495 plant introductions (PIs) towards P. sojae isolates OH.121 and C2.S1, respectively, in genome-wide association (GWA) analyses to identify genetic markers linked to QDR loci (QDRL). Populations were generated by sampling PIs from the US, the Republic of Korea, and the full collection of PIs maintained by the USDA. Additionally, a meta-analysis of QDRL reported from bi-parental studies was done to compare past and present findings. Twenty-four significant marker-trait associations were identified from the 478 PIs phenotyped with OH.121, and an additional 24 marker-trait associations were identified from the 495 PIs phenotyped with C2.S1. In total, 48 significant markers were distributed across 16 chromosomes and based on linkage analysis, represent a total of 44 QDRL. The majority of QDRL were identified with only one of the two isolates, and only a region on chromosome 13 was consistently identified. Regions on chromosomes 3, 13, and 17 were identified in previous GWA-analyses and were re-identified in this study. Five QDRL co-localized with P. sojae meta-QDRL identified from QDRL reported in previous biparental mapping studies. The remaining regions represent novel QDRL, in the soybean-P. sojae pathosystem and were primarily identified in germplasm from the Republic of Korea. Overall, the number of loci identified in this study highlights the complexity of QDR to P. sojae.

Hybrid Genome Assembly of a Major Quantitative Disease Resistance Locus in Soybean Toward Fusarium graminearum.

Schwabe [teleomorph: Gibberella zeae (Schweintiz) Petch] has been identified as a pathogen of soybean [ (L.) Merr.] causing seed, seedling damping-off and root rot in North America. A major quantitative disease resistance locus (QDRL) that contributed 38.5% of the phenotypic variance toward in soybean was previously identified through mapping of a recombinant inbred line (RIL) population derived from a cross between 'Wyandot' and PI 567301B. This major QDRL mapped to chromosome 8 to a predicted 305 kb region harboring 36 genes. This locus maps near the locus for soybean cyst nematode (SCN) and the locus contributing to seed coat color. Long-read sequencing of the region was completed and variations in gene sequence and gene order compared with the 'Williams 82' reference were identified. Molecular markers were developed for genes within this region and mapped in the original population, slightly narrowing the region of interest. Analyses of the hybrid genome reassembly using three previously published bacterial artificial chromosome (BAC) sequences (BAC56G2, BAC104J7, and BAC77G7-a) combined with RNA-sequencing narrowed the region making candidate gene identification possible. The markers within this region may be used for marker-assisted selection (MAS). There were 10 differentially expressed genes between resistant and susceptible lines, with four of these candidates also located within the genomic interval defined by the flanking markers. These genes included an actin-related protein 2/3 complex subunit, an unknown protein, a hypothetical protein, and a chalcone synthase 3.

Genome-wide association study of seed protein, oil and amino acid contents in soybean from maturity groups I to IV.

KEY MESSAGE: Genomic regions associated with seed protein, oil and amino acid contents were identified by genome-wide association analyses. Geographic distributions of haplotypes indicate scope of improvement of these traits. Soybean [Glycine max (L.) Merr.] protein and oil are used worldwide in feed, food and industrial materials. Increasing seed protein and oil contents is important; however, protein content is generally negatively correlated with oil content. We conducted a genome-wide association study using phenotypic data collected from five environments for 621 accessions in maturity groups I-IV and 34,014 markers to identify quantitative trait loci (QTL) for seed content of protein, oil and several essential amino acids. Three and five genomic regions were associated with seed protein and oil contents, respectively. One, three, one and four genomic regions were associated with cysteine, methionine, lysine and threonine content (g kg-1 crude protein), respectively. As previously shown, QTL on chromosomes 15 and 20 were associated with seed protein and oil contents, with both exhibiting opposite effects on the two traits, and the chromosome 20 QTL having the most significant effect. A multi-trait mixed model identified trait-specific QTL. A QTL on chromosome 5 increased oil with no effect on protein content, and a QTL on chromosome 10 increased protein content with little effect on oil content. The chromosome 10 QTL co-localized with maturity gene E2/GmGIa. Identification of trait-specific QTL indicates feasibility to reduce the negative correlation between protein and oil contents. Haplotype blocks were defined at the QTL identified on chromosomes 5, 10, 15 and 20. Frequencies of positive effect haplotypes varied across maturity groups and geographic regions, providing guidance on which alleles have potential to contribute to soybean improvement for specific regions.

Changes to the core and flanking sequences of G-box elements lead to increases and decreases in gene expression in both native and synthetic soybean promoters.

Cis-regulatory elements in promoters are major determinants of binding specificity of transcription factors (TFs) for transcriptional regulation. To improve our understanding of how these short DNA sequences regulate gene expression, synthetic promoters consisting of both classical (CACGTG) and variant G-box core sequences along with different flanking sequences derived from the promoters of three different highly expressing soybean genes, were constructed and used to regulate a green fluorescent protein (gfp) gene. Use of the classical 6-bp G-box provided information on the base level of GFP expression while modifications to the 2-4 flanking bases on either side of the G-box influenced the intensity of gene expression in both transiently transformed lima bean cotyledons and stably transformed soybean hairy roots. The proximal 2-bp sequences on either flank of the G-box significantly affected G-box activity, while the distal 2-bp flanking nucleotides also influenced gene expression albeit with a decreasing effect. Manipulation of the upstream 2- to 4-bp flanking sequence of a G-box variant (GACGTG), found in the proximal region of a relatively weak soybean glycinin promoter, significantly enhanced promoter activity using both transient and stable expression assays, if the G-box variant was first converted into a classical G-box (CACGTG). In addition to increasing our understanding of regulatory element composition and structure, this study shows that minimal targeted changes in native promoter sequences can lead to enhanced gene expression, and suggests that genome editing of the promoter region can result in useful and predictable changes in native gene expression.

Impact of Environment on the Biomass Composition of Soybean (Glycine max) seeds.

Factors including genetics, fertilization, and climatic conditions, can alter the biomass composition of soybean seeds, consequently impacting their market value and usage. This study specifically determined the content of protein and oil, as well as the composition of proteinogenic amino acids and fatty acids in seeds from 10 diverse soybean cultivars grown in four different sites. The results highlighted that different environments produce a different composition for the 10 cultivars under investigation. Specifically, the levels of oleic and linoleic acids, important contributors to oil stability, were negatively correlated. Although the protein and oil contents were higher in some locations, their "quality" was lower in terms of composition of essential amino acids and oleic acid, respectively. Finally, proteinogenic histidine and glutamate were the main contributors to the separation between Central and Northern growing sites. Taken together, these results can guide future breeding and engineering efforts aiming to develop specialized soybean lines.

Meta-Analyses of QTLs Associated with Protein and Oil Contents and Compositions in Soybean [Glycine max (L.) Merr.] Seed.

Soybean [Glycine max (L.) Merr.] is a valuable and nutritious crop in part due to the high protein meal and vegetable oil produced from its seed. Soybean producers desire cultivars with both elevated seed protein and oil concentrations as well as specific amino acid and fatty acid profiles. Numerous studies have identified quantitative trait loci (QTLs) associated with seed composition traits, but validation of these QTLs has rarely been carried out. In this study, we have collected information, including genetic location and additive effects, on each QTL for seed contents of protein and oil, as well as amino acid and fatty acid compositions from over 80 studies. Using BioMercator V. 4.2, a meta-QTL analysis was performed with genetic information comprised of 175 QTLs for protein, 205 QTLs for oil, 156 QTLs for amino acids, and 113 QTLs for fatty acids. A total of 55 meta-QTL for seed composition were detected on 6 out of 20 chromosomes. Meta-QTL possessed narrower confidence intervals than the original QTL and candidate genes were identified within each meta-QTL. These candidate genes elucidate potential natural genetic variation in genes contributing to protein and oil biosynthesis and accumulation, providing meaningful information to further soybean breeding programs.

A Leader Intron of a Soybean Elongation Factor 1A (eEF1A) Gene Interacts with Proximal Promoter Elements to Regulate Gene Expression in Synthetic Promoters.

Introns, especially the first intron in the 5' untranslated region (5'UTR), can significantly impact gene expression via intron-mediated enhancement (IME). In this study, we demonstrate the leader intron of a soybean elongation factor 1A (eEF1A) gene (GmScreamM8) was essential for the high activity of the native promoter. Furthermore, the interaction of the GmScreamM8 leader intron with regulatory element sequences from several soybean eEF1A promoters was studied using synthetic promoters, which consisted of element tetramers upstream of a core promoter used to regulate a green fluorescent protein (gfp) reporter gene. Element tetramers, placed upstream of a GmScreamM8 core promoter, showed very high activity using both transient expression in lima bean cotyledons and stable expression in soybean hairy roots, only if the native leader intron was included, suggesting an interaction between intronic sequences and promoter elements. Partial deletions of the leader intron showed that a 222 bp intronic sequence significantly contributed to very high levels of GFP expression. Generation of synthetic intron variants with a monomeric or trimeric repeat of the 222 bp intronic sequence, yielded almost two-fold higher expression compared to the original intron, while partial deletion of the 222 bp intronic repeated sequence significantly decreased gene expression, indicating that this intronic sequence was essential for the intron-element interaction enhancement.

Genome-wide association mapping of partial resistance to Phytophthora sojae in soybean plant introductions from the Republic of Korea.

BACKGROUND: Phytophthora root and stem rot is one of the most yield-limiting diseases of soybean [Glycine max (L.) Merr], caused by the oomycete Phytophthora sojae. Partial resistance is controlled by several genes and, compared to single gene (Rps gene) resistance to P. sojae, places less selection pressure on P. sojae populations. Thus, partial resistance provides a more durable resistance against the pathogen. In previous work, plant introductions (PIs) originating from the Republic of Korea (S. Korea) have shown to be excellent sources for high levels of partial resistance against P. sojae. RESULTS: Resistance to two highly virulent P. sojae isolates was assessed in 1395 PIs from S. Korea via a greenhouse layer test. Lines exhibiting possible Rps gene immunity or rot due to other pathogens were removed and the remaining 800 lines were used to identify regions of quantitative resistance using genome-wide association mapping. Sixteen SNP markers on chromosomes 3, 13 and 19 were significantly associated with partial resistance to P. sojae and were grouped into seven quantitative trait loci (QTL) by linkage disequilibrium blocks. Two QTL on chromosome 3 and three QTL on chromosome 19 represent possible novel loci for partial resistance to P. sojae. While candidate genes at QTL varied in their predicted functions, the coincidence of QTLs 3-2 and 13-1 on chromosomes 3 and 13, respectively, with Rps genes and resistance gene analogs provided support for the hypothesized mechanism of partial resistance involving weak R-genes. CONCLUSIONS: QTL contributing to partial resistance towards P. sojae in soybean germplasm originating from S. Korea were identified. The QTL identified in this study coincide with previously reported QTL, Rps genes, as well as novel loci for partial resistance. Molecular markers associated with these QTL can be used in the marker-assisted introgression of these alleles into elite cultivars. Annotations of genes within QTL allow hypotheses on the possible mechanisms of partial resistance to P. sojae.

Isolation and characterization of "GmScream" promoters that regulate highly expressing soybean (Glycine max Merr.) genes.

To increase our understanding of the regulatory components that control gene expression, it is important to identify, isolate and characterize new promoters. In this study, a group of highly expressed soybean (Glycine max Merr.) genes, which we have named "GmScream", were first identified from RNA-Seq data. The promoter regions were then identified, cloned and fused with the coding region of the green fluorescent protein (gfp) gene, for introduction and analysis in different tissues using 3 tools for validation. Approximately half of the GmScream promoters identified showed levels of GFP expression comparable to or higher than the Cauliflower Mosaic Virus 35S (35S) promoter. Using transient expression in lima bean cotyledonary tissues, the strongest GmScream promoters gave over 6-fold higher expression than the 35S promoter while several other GmScream promoters showed 2- to 3-fold higher expression. The two highest expressing promoters, GmScreamM4 and GmScreamM8, regulated two different elongation factor 1A genes in soybean. In stably transformed soybean tissues, GFP driven by the GmScreamM4 or GmScreamM8 promoter exhibited constitutive high expression in most tissues with preferentially higher expression in proliferative embryogenic tissues, procambium, vascular tissues, root tips and young embryos. Using deletion analysis of the promoter, two proximal regions of the GmScreamM8 promoter were identified as contributing significantly to high levels of gene expression.

Genome-Wide Architecture of Disease Resistance Genes in Lettuce.

Genome-wide motif searches identified 1134 genes in the lettuce reference genome of cv. Salinas that are potentially involved in pathogen recognition, of which 385 were predicted to encode nucleotide binding-leucine rich repeat receptor (NLR) proteins. Using a maximum-likelihood approach, we grouped the NLRs into 25 multigene families and 17 singletons. Forty-one percent of these NLR-encoding genes belong to three families, the largest being RGC16 with 62 genes in cv. Salinas. The majority of NLR-encoding genes are located in five major resistance clusters (MRCs) on chromosomes 1, 2, 3, 4, and 8 and cosegregate with multiple disease resistance phenotypes. Most MRCs contain primarily members of a single NLR gene family but a few are more complex. MRC2 spans 73 Mb and contains 61 NLRs of six different gene families that cosegregate with nine disease resistance phenotypes. MRC3, which is 25 Mb, contains 22 RGC21 genes and colocates with Dm13. A library of 33 transgenic RNA interference tester stocks was generated for functional analysis of NLR-encoding genes that cosegregated with disease resistance phenotypes in each of the MRCs. Members of four NLR-encoding families, RGC1, RGC2, RGC21, and RGC12 were shown to be required for 16 disease resistance phenotypes in lettuce. The general composition of MRCs is conserved across different genotypes; however, the specific repertoire of NLR-encoding genes varied particularly of the rapidly evolving Type I genes. These tester stocks are valuable resources for future analyses of additional resistance phenotypes.