Development and Validation of SNP and InDel Markers for Pod-Shattering Tolerance in Soybean.

Pod-shattering causes a significant yield loss in many soybean cultivars. Shattering-tolerant cultivars provide the most effective approach to minimizing this loss. We developed molecular markers for pod-shattering and validated them in soybeans with diverse genetic backgrounds. The genes Glyma.16g141200, Glyma.16g141500, and Glyma.16g076600, identified in our previous study by quantitative trait locus (QTL) mapping and whole-genome resequencing, were selected for marker development. The whole-genome resequencing of three parental lines (one shattering-tolerant and two shattering-susceptible) identified single nucleotide polymorphism (SNP) and/or insertion/deletion (InDel) regions within or near the selected genes. Two SNPs and one InDel were converted to Kompetitive Allele-Specific PCR (KASP) and InDel markers, respectively. The accuracy of the markers was examined in the two recombinant inbred line populations used for the QTL mapping, as well as the 120 varieties and elite lines, through allelic discrimination and phenotyping by the oven-drying method. Both types of markers successfully discriminated the pod shattering-tolerant and shattering-susceptible genotypes. The prediction accuracy, which was as high as 90.9% for the RILs and was 100% for the varieties and elite lines, also supported the accuracy and usefulness of these markers. Thus, the markers can be used effectively for genetic and genomic studies and the marker-assisted selection for pod-shattering tolerance in soybean.

A Large Root Phenome Dataset Wide-Opened the Potential for Underground Breeding in Soybean.

The root is the most critical plant organ for water and nutrient acquisition. Although the root is vital for water and nutrient uptake, the diverse root characters of soybean still need to be identified owing to the difficulty of root sampling. In this study, we used 150 wild and 50 cultivated soybean varieties to collect root image samples. We analyzed root morphological traits using acquired-image. Except for the main total length (MTL), the root morphological traits for most cultivated and wild plants were significantly different. According to correlation analysis, the wild and cultivated plants showed a significant correlation among total root length (TRL), projected area (PA), forks, total lateral length (TLL), link average diameter, and MTL. In particular, TRL was highly correlated with PA in both cultivated (0.92) and wild (0.82) plants compared with between MTL (0.43 for cultivated and 0.27 for wild) and TLL (0.82 for cultivated and 0.52 for wild). According to principal component analysis results, both plants could be separated; however, there was some overlap of the traits among the wild and cultivated individuals from some regions. Nevertheless, variation among the cultivated plants was higher than that found in the wild plants. Furthermore, three groups, including MTL, TLL, and the remaining traits, could explain all the variances.

Molecular characterization of the Saccharomycopsis fibuligera ATF genes, encoding alcohol acetyltransferase for volatile acetate ester formation.

Aroma ester components produced by fermenting yeast cells via alcohol acetyltransferase (AATase)-catalyzed intracellular reactions are responsible for the fruity character of fermented alcoholic beverages, such as beer and wine. Acetate esters are reportedly produced at relatively high concentrations by non-Saccharomyces species. Here, we identified 12 ATF orthologues (SfATFs) encoding putative AATases, in the diploid genome of Saccharomycopsis fibuligera KJJ81, an isolate from wheat-based Nuruk in Korea. The identified SfATF proteins (SfAtfp) display low sequence identities with S. cerevisiae Atf1p (between 13.3 and 27.0%). All SfAtfp identified, except SfAtf(A)4p and SfAtf(B)4p, contained the activation domain (HXXXD) conserved in other Atf proteins. Culture supernatant analysis using headspace gas chromatography mass spectrometry confirmed that the recombinant S. cerevisiae strains expressing SfAtf(A)2p, SfAtf(B)2p, and SfAtf(B)6p produced high levels of isoamyl and phenethyl acetates. The volatile aroma profiles generated by the SfAtf proteins were distinctive from that of S. cerevisiae Atf1p, implying difference in the substrate preference. Cellular localization analysis using GFP fusion revealed the localization of SfAtf proteins proximal to the lipid particles, consistent with the presence of amphipathic helices at their N- and C-termini. This is the first report that systematically characterizes the S. fibuligera ATF genes encoding functional AATases responsible for acetate ester formation using higher alcohols as substrate, demonstrating their biotechnological potential for volatile ester production.

Fine-mapping and candidate gene analysis for the foxglove aphid resistance gene Raso2 from wild soybean PI 366121.

KEY MESSAGE: The foxglove aphid resistance gene Raso2 from PI 366121 was fine-mapped to 77 Kb region, and one candidate gene was identified. The foxglove aphid (FA: Aulacorthum solani Kaltenbach) is an important insect pest that causes serious yield losses in soybean. The FA resistance gene Raso2 from wild soybean PI 366121 was previously mapped to a 13 cM interval on soybean chromosome 7. However, fine-mapping of Raso2 was needed to improve the effectiveness of marker-assisted selection (MAS) and to eventually clone it. The objectives of this study were to fine-map Raso2 from PI 366121 using Axiom® 180 K SoyaSNP array, to confirm the resistance and inheritance of Raso2 in a different background, and to identify candidate gene(s). The 105 F4:8 recombinant inbred lines were used to fine-map the gene and to test antibiosis and antixenosis of Raso2 to FA. These efforts resulted in the mapping of Raso2 on 1 cM interval which corresponds to 77 Kb containing eight annotated genes based on the Williams 82 reference genome assembly (Wm82.a2.v1). Interestingly, all nonsynonymous substitutions were in Glyma.07g077700 which encodes the disease resistance protein containing LRR domain and expression of the gene in PI 366121 was significantly higher than that in Williams 82. In addition, distinct SNPs within Glyma.07g077700 that can distinguish PI 366121 and diverse FA-susceptible soybeans were identified. We also confirmed that Raso2 presented the resistance to FA and the Mendelian inheritance for single dominant gene in a different background. The results of this study would provide fundamental information on MAS for development of FA-resistant cultivars as well as functional study and cloning of the candidate gene in soybean.

Genetic Diversity and Genome-Wide Association Study of Seed Aspect Ratio Using a High-Density SNP Array in Peanut (Arachis hypogaea L.).

Peanut (Arachis hypogaea L.) is one of the important oil crops of the world. In this study, we aimed to evaluate the genetic diversity of 384 peanut germplasms including 100 Korean germplasms and 284 core collections from the United States Department of Agriculture (USDA) using an Axiom_Arachis array with 58K single-nucleotide polymorphisms (SNPs). We evaluated the evolutionary relationships among 384 peanut germplasms using a genome-wide association study (GWAS) of seed aspect ratio data processed by ImageJ software. In total, 14,030 filtered polymorphic SNPs were identified from the peanut 58K SNP array. We identified five SNPs with significant associations to seed aspect ratio on chromosomes Aradu.A09, Aradu.A10, Araip.B08, and Araip.B09. AX-177640219 on chromosome Araip.B08 was the most significantly associated marker in GAPIT and Regularization method. Phosphoenolpyruvate carboxylase (PEPC) was found among the eleven genes within a linkage disequilibrium (LD) of the significant SNPs on Araip.B08 and could have a strong causal effect in determining seed aspect ratio. The results of the present study provide information and methods that are useful for further genetic and genomic studies as well as molecular breeding programs in peanuts.

QTL Mapping and Candidate Gene Analysis for Pod Shattering Tolerance in Soybean (Glycine max).

Pod shattering is an important reproductive process in many wild species. However, pod shattering at the maturing stage can result in severe yield loss. The objectives of this study were to discover quantitative trait loci (QTLs) for pod shattering using two recombinant inbred line (RIL) populations derived from an elite cultivar having pod shattering tolerance, namely "Daewonkong", and to predict novel candidate QTL/genes involved in pod shattering based on their allele patterns. We found several QTLs with more than 10% phenotypic variance explained (PVE) on seven different chromosomes and found a novel candidate QTL on chromosome 16 (qPS-DS16-1) from the allele patterns in the QTL region. Out of the 41 annotated genes in the QTL region, six were found to contain SNP (single-nucleotide polymorphism)/indel variations in the coding sequence of the parents compared to the soybean reference genome. Among the six potential candidate genes, Glyma.16g076600, one of the genes with known function, showed a highly differential expression levels between the tolerant and susceptible parents in the growth stages R3 to R6. Further, Glyma.16g076600 is a homolog of AT4G19230 in Arabidopsis, whose function is related to abscisic acid catabolism. The results provide useful information to understand the genetic mechanism of pod shattering and could be used for improving the efficiency of marker-assisted selection for developing varieties of soybeans tolerant to pod shattering.

Noninvasive Assessment of Exosome Pharmacokinetics In Vivo: A Review.

Exosomes, intraluminal vesicles that contain informative DNA, RNA, proteins, and lipid membranes derived from the original donor cells, have recently been introduced to therapy and diagnosis. With their emergence as an alternative to cell therapy and having undergone clinical trials, proper analytical standards for evaluating their pharmacokinetics must now be established. Molecular imaging techniques such as fluorescence imaging, magnetic resonance imaging, and positron emission tomography (PET) are helpful to visualizing the absorption, distribution, metabolism, and excretion of exosomes. After exosomes labelled with a fluorescer or radioisotope are administered in vivo, they are differentially distributed according to the characteristics of each tissue or lesion, and real-time biodistribution of exosomes can be noninvasively monitored. Quantitative analysis of exosome concentration in biological fluid or tissue samples is also needed for the clinical application and industrialization of exosomes. In this review, we will discuss recent pharmacokinetic applications to exosomes, including labelling methods for in vivo imaging and analytical methods for quantifying exosomes, which will be helpful for evaluating pharmacokinetics of exosomes and improving exosome development and therapy.

Korean soybean core collection: Genotypic and phenotypic diversity population structure and genome-wide association study.

A core collection is a subset that represents genetic diversity of the total collection. Soybean (Glycine max (L.) Merr.) is one of major food and feed crops. It is the world's most cultivated annual herbaceous legume. Constructing a core collection for soybean could play a pivotal role in conserving and utilizing its genetic variability for research and breeding programs. To construct and evaluate a Korean soybean core collection, genotypic and phenotypic data as well as population structure, were analyzed. The Korean soybean core collection consisted of 430 accessions selected from 2,872 collections based on Affymetrix Axiom® 180k SoyaSNP array data. The core collection represented 99% of genotypic diversity of the total collection. Analysis of population structure clustered the core collection into five subpopulations. Accessions from South Korea and North Korea were distributed across five subpopulations. Analysis of molecular variance indicated that only 2.01% of genetic variation could be explained by geographic origins while 16.18% of genetic variation was accounted for by subpopulations. Genome-wide association study (GWAS) for days to flowering, flower color, pubescent color, and growth habit confirmed that the core collection had the same genetic diversity for tested traits as the total collection. The Korean soybean core collection was constructed based on genotypic information of the 180k SNP data. Size and phenotypic diversity of the core collection accounted for approximately 14.9% and 18.1% of the total collection, respectively. GWAS of core and total collections successfully confirmed loci associated with tested traits. Consequently, the present study showed that the Korean soybean core collection could provide fundamental and practical material and information for both soybean genetic research and breeding programs.

Preparation and Characterization of Transparent Polyimide⁻Silica Composite Films Using Polyimide with Carboxylic Acid Groups.

Polyimide (PI) composite films with thicknesses of approximately 100 µm were prepared via a sol⁻gel reaction of 3-aminopropyltrimethoxysilane (APTMS) with poly(amic acid) (PAA) composite solutions using a thermal imidization process. PAA was synthesized by a conventional condensation reaction of two diamines, 3,5-diaminobenzoic acid (DABA), which has a carboxylic acid side group, and 2,2'-bis(trifluoromethyl)benzidine (TFMB), with 4,4'-(hexafluoroisopropylidene)diphthalic anhydride (6FDA) in N,N-dimethylacetamide (DMAc). The PAA⁻silica composite solutions were prepared by mixing PAA with carboxylic acid side groups and various amounts of APTMS in a sol⁻gel process in DMAc using hydrochloric acid as a catalyst. The obtained PI⁻silica composite films showed relatively good thermal stability, and the thermal stability increased with increasing APTMS content. The optical properties and in-plane coefficient of thermal expansion (CTE) values of the PI⁻silica composite films were investigated. The CTE of the PI⁻silica composite films changed from 52.0 to 42.1 ppm/°C as the initial content of APTMS varied. The haze values and yellowness indices of the composite films increased as a function of the APTMS content.

Silicon Confers Soybean Resistance to Salinity Stress Through Regulation of Reactive Oxygen and Reactive Nitrogen Species.

Salt stress is one of the major abiotic stressors that causes huge losses to the agricultural industry worldwide. Different strategies have been adopted over time to mitigate the negative impact of salt stress on plants and reclaim salt-affected lands. In the current study, we used silicon (Si) as a tool for salinity alleviation in soybean and investigated the influence of exogenous Si application on the regulation of reactive oxygen and reactive nitrogen species and other salt stress-related parameters of the treated plants. Our results revealed that the canopy temperature was much higher in sole NaCl-treated plants but declined in Si + NaCl-treated plants. Furthermore, the chlorophyll contents decreased with sole NaCl treatment, whereas Si + NaCl-treated plants showed improved chlorophyll contents. In addition, Si application normalized the photosynthetic responses, such as transpiration rate (E) and net photosynthesis rate (PN ) in salt-treated plants, and reduced the activity of ascorbate peroxidase and glutathione under salt stress. The expression levels of antioxidant-related genes GmCAT1, GmCAT2, and GmAPX1 started to decline at 12 h after addition of Si to NaCl-treated plants. Similarly, the S-nitrosothiol and nitric oxide (NO)-related genes were upregulated in the salt stress condition but reduced after Si supplementation. Si application downregulated genes associated with reactive oxygen species and reactive nitrogen species and reduced enzymatic and non-enzymatic antioxidants of the treated plants. Results of the current study conclude that Si mitigated the adverse effects of NaCl-induced stress by modulating the crosstalk between antioxidants and NO scavengers. It is suggested that Si may be used in agricultural systems for alleviating salt stress.

Advancements in breeding, genetics, and genomics for resistance to three nematode species in soybean.

KEY MESSAGE: Integration of genetic analysis, molecular biology, and genomic approaches drastically enhanced our understanding of genetic control of nematode resistance and provided effective breeding strategies in soybeans. Three nematode species, including soybean cyst (SCN, Heterodera glycine), root-knot (RKN, Meloidogyne incognita), and reniform (RN, Rotylenchulus reniformis), are the most destructive pests and have spread to soybean growing areas worldwide. Host plant resistance has played an important role in their control. This review focuses on genetic, genomic studies, and breeding efforts over the past two decades to identify and improve host resistance to these three nematode species. Advancements in genetics, genomics, and bioinformatics have improved our understanding of the molecular and genetic mechanisms of nematode resistance and enabled researchers to generate large-scale genomic resources and marker-trait associations. Whole-genome resequencing, genotyping-by-sequencing, genome-wide association studies, and haplotype analyses have been employed to map and dissect genomic locations for nematode resistance. Recently, two major SCN-resistant loci, Rhg1 and Rhg4, were cloned and other novel resistance quantitative trait loci (QTL) have been discovered. Based on these discoveries, gene-specific DNA markers have been developed for both Rhg1 and Rhg4 loci, which were useful for marker-assisted selection. With RKN resistance QTL being mapped, candidate genes responsible for RKN resistance were identified, leading to the development of functional single nucleotide polymorphism markers. So far, three resistances QTL have been genetically mapped for RN resistance. With nematode species overcoming the host plant resistance, continuous efforts in the identification and deployment of new resistance genes are required to support the development of soybean cultivars with multiple and durable resistance to these pests.

[Prognostic value of preoperative positron emission tomography-computed tomography in surgically resected gastric cancer].

BACKGROUND/AIMS: The diagnostic value of PET-CT, in gastric cancer is well known, but the prognostic value of pretreatment PET-CT has not been adequately evaluated. This study aimed to investigate the preoperative prognostic value of PET-CT in gastric cancer patients. METHODS: A total of 107 patients underwent surgical treatment for gastric cancer from April 2007 to December 2010 at Dong-A University Medical Center after confirming the presence of F-18 fluorodeoxyglucose (FDG) uptake on preoperative PET-CT. Among these patients, the following subjects were excluded: follow-up loss (13), palliative resection (5), neoadjuvant chemotherapy (1), and unrelated death (1). The remaining 87 patients were included in this study and data were collected by retrospectively reviewing the medical records. The median follow-up duration, defined as the period from operation to last imaging study date, was 34.2±14.8 months. FDG uptake values were represented by maximal standardized uptake value (SUVmax). In order to assess the correlation between SUVmax and recurrence, Kaplan-Meier's survival analysis with log-rank test and cox proportional hazard model were performed. Receiver operating characteristic (ROC) curve was employed to determine the optimal cutoff value of SUVmax. RESULTS: The result of Kaplan-Meier's survival analysis with log-rank test were significantly different between high SUVmax group and low SUVmax group (p=0.035), the cutoff value of which was 5.6. However, in multivariate analysis with cox proportional hazard model, T-staging, N-staging and SUVmax did not show statistical significance (p=0.190, p=0.307, and p=0.436, respectively). CONCLUSIONS: High SUVmax on PET-CT in gastric cancer can be a useful prognostic factor.

Identification and molecular mapping of two soybean aphid resistance genes in soybean PI 587732.

Soybean [Glycine max (L.) Merr.] continues to be plagued by the soybean aphid (Aphis glycines Matsumura: SA) in North America. New soybean resistance sources are needed to combat the four identified SA biotypes. The objectives of this study were to determine the inheritance of SA resistance in PI 587732 and to map resistance gene(s). For this study, 323 F2 and 214 F3 plants developed from crossing PI 587732 to two susceptible genotypes were challenged with three SA biotypes and evaluated with genetic markers. Choice tests showed that resistance to SA Biotype 1 in the first F2 population was controlled by a gene in the Rag1 region on chromosome 7, while resistance to SA Biotype 2 in the second population was controlled by a gene in the Rag2 region on chromosome 13. When 134 F3 plants segregating in both the Rag1 and Rag2 regions were tested with a 1:1 mixture of SA Biotypes 1 and 2, the Rag2 region and an interaction between the Rag1 and Rag2 regions were significantly associated with the resistance. Based on the results of the non-choice tests, the resistance gene in the Rag1 region in PI 587732 may be a different allele or gene from Rag1 from Dowling because the PI 587732 gene showed antibiosis type resistance to SA Biotype 2 while Rag1 from Dowling did not. The two SA resistance loci and genetic marker information from this study will be useful in increasing diversity of SA resistance sources and marker-assisted selection for soybean breeding programs.

Inheritance of soybean aphid resistance in 21 soybean plant introductions.

KEY MESSAGE: The Rag2 region was frequently identified among 21 F 2 populations evaluated for soybean aphid resistance, and dominant gene action and single-gene resistance were also commonly identified. The soybean aphid [Aphis glycines Matsumura (Hemiptera: Aphididae)] is one of the most important insect pests of soybean [Glycine max (L.) Merr] in the northern USA and southern Canada, and four resistance loci (Rag1-rag4) have been discovered since the pest was identified in the USA in 2000. The objective of this research was to determine whether resistance expression in recently identified soybean aphid-resistant plant introductions (PIs) was associated with the four Rag loci using a collection of 21 F2 populations. The F2 populations were phenotyped with soybean aphid biotype 1, which is avirulent on plants having any of the currently identified Rag genes, using choice tests in the greenhouse and were tested with genetic markers linked to the four Rag loci. The phenotyping results indicate that soybean aphid resistance is controlled by a single dominant gene in 14 PIs, by two genes in three PIs, and four PIs had no clear Mendelian inheritance patterns. Genetic markers flanking Rag2 were significantly associated with aphid resistance in 20 PIs, the Rag1 region was significantly identified in five PIs, and the Rag3 region was identified in one PI. These results show that single dominant gene action at the Rag2 region may be a major source for aphid resistance in the USDA soybean germplasm collection.

Molecular mapping of soybean rust resistance in soybean accession PI 561356 and SNP haplotype analysis of the Rpp1 region in diverse germplasm.

Soybean rust (SBR), caused by Phakopsora pachyrhizi Sydow, is one of the most economically important and destructive diseases of soybean [Glycine max (L.) Merr.] and the discovery of novel SBR resistance genes is needed because of virulence diversity in the pathogen. The objectives of this research were to map SBR resistance in plant introduction (PI) 561356 and to identify single nucleotide polymorphism (SNP) haplotypes within the region on soybean chromosome 18 where the SBR resistance gene Rpp1 maps. One-hundred F(2:3) lines derived from a cross between PI 561356 and the susceptible experimental line LD02-4485 were genotyped with genetic markers and phenotyped for resistance to P. pachyrhizi isolate ZM01-1. The segregation ratio of reddish brown versus tan lesion type in the population supported that resistance was controlled by a single dominant gene. The gene was mapped to a 1-cM region on soybean chromosome 18 corresponding to the same interval as Rpp1. A haplotype analysis of diverse germplasm across a 213-kb interval that included Rpp1 revealed 21 distinct haplotypes of which 4 were present among 5 SBR resistance sources that have a resistance gene in the Rpp1 region. Four major North American soybean ancestors belong to the same SNP haplotype as PI 561356 and seven belong to the same haplotype as PI 594538A, the Rpp1-b source. There were no North American soybean ancestors belonging to the SNP haplotypes found in PI 200492, the source of Rpp1, or PI 587886 and PI 587880A, additional sources with SBR resistance mapping to the Rpp1 region.

Epidemiological characteristics of pulmonary pneumocystosis and concurrent infections in pigs in Jeju Island, Korea.

Epidemiological characteristics of swine pulmonary Pneumocystis (P.) carinii and concurrent infections were surveyed on Jeju Island, Korea, within a designated period in 172 pigs submitted from 54 farms to the Department of Veterinary Medicine, Jeju National University. The submitted cases were evaluated by histopathology, immunohistochemistry, PCR/RT-PCR, and bacteriology. P. carinii infection was confirmed in 39 (22.7%) of the 172 pigs. Histopathologically, the lungs had moderate to severe lymphohistioctyic interstitial pneumonia with variable numbers of fungal organisms within lesions. Furthermore, porcine reproductive and respiratory syndrome virus (PRRSV) and porcine circovirus type 2 (PCV-2) co-infection was a common phenomenon (12.8%, 20.5%, and 48.7% were positive for PRRS, PCV-2, or both, respectively, as determined by PCR/RT-PCR). Infection was much more concentrated during winter (December to March) and 53.8% of the infected pigs were 7- to 8-weeks old. In addition, three pigs showed co-infection with bacteria such as Pasteurella multocida and Streptococcus suis. The results of the present study suggest that the secondary P. carinii infection is common following primary viral infection in swine in Korea. They further suggest that co-infection of P. carinii might be enhanced by the virulence of primary pathogens or might have synergistic effects in the pigs with chronic wasting diseases.

Fine mapping of the soybean aphid-resistance gene Rag2 in soybean PI 200538.

The discovery of biotype diversity of soybean aphid (SA: Aphis glycines Matsumura) in North America emphasizes the necessity to identify new aphid-resistance genes. The soybean [Glycine max (L.) Merr.] plant introduction (PI) 200538 is a promising source of SA resistance because it shows a high level of resistance to a SA biotype that can overcome the SA-resistance gene Rag1 from 'Dowling'. The SA-resistance gene Rag2 was previously mapped from PI 200538 to a 10-cM marker interval on soybean chromosome 13 [formerly linkage group (LG) F]. The objective of this study was to fine map Rag2. This fine mapping was carried out using lines derived from 5,783 F(2) plants at different levels of backcrossing that were screened with flanking genetic markers for the presence of recombination in the Rag2 interval. Fifteen single nucleotide polymorphism (SNP) markers and two dominant polymerase chain reaction-based markers near Rag2 were developed by re-sequencing target intervals and sequence-tagged sites. These efforts resulted in the mapping of Rag2 to a 54-kb interval on the Williams 82 8x assembly (Glyma1). This Williams 82 interval contains seven predicted genes, which includes one nucleotide-binding site-leucine-rich repeat gene. SNP marker and candidate gene information identified in this study will be an important resource in marker-assisted selection for aphid resistance and for cloning the gene.

Fine mapping the soybean aphid resistance gene Rag1 in soybean.

The soybean aphid (Aphis glycines Matsumura) is an important soybean [Glycine max (L.) Merr.] pest in North America. The dominant aphid resistance gene Rag1 was previously mapped from the cultivar 'Dowling' to a 12 cM marker interval on soybean chromosome 7 (formerly linkage group M). The development of additional genetic markers mapping closer to Rag1 was needed to accurately position the gene to improve the effectiveness of marker-assisted selection (MAS) and to eventually clone it. The objectives of this study were to identify single nucleotide polymorphisms (SNPs) near Rag1 and to position these SNPs relative to Rag1. To generate a fine map of the Rag1 interval, 824 BC(4)F(2) and 1,000 BC(4)F(3) plants segregating for the gene were screened with markers flanking Rag1. Plants with recombination events close to the gene were tested with SNPs identified in previous studies along with new SNPs identified from the preliminary Williams 82 draft soybean genome shotgun sequence using direct re-sequencing and gene-scanning melt-curve analysis. Progeny of these recombinant plants were evaluated for aphid resistance. These efforts resulted in the mapping of Rag1 between the two SNP markers 46169.7 and 21A, which corresponds to a physical distance on the Williams 82 8x draft assembly (Glyma1.01) of 115 kilobase pair (kb). Several candidate genes for Rag1 are present within the 115-kb interval. The markers identified in this study that are closely linked to Rag1 will be a useful resource in MAS for this important aphid resistance gene.

Claudin-7 is highly expressed in chromophobe renal cell carcinoma and renal oncocytoma.

Claudin-7 has recently been suggested to be a distal nephron marker. We tested the possibility that expression of claudin-7 could be used as a marker of renal tumors originating from the distal nephron. We examined the immunohistochemical expression of claudin-7 and parvalbumin in 239 renal tumors, including 179 clear cell renal cell carcinoma (RCC)s, 29 papillary RCCs, 20 chromophobe RCCs, and 11 renal oncocytomas. In addition, the methylation specific-PCR (MSP) of claudin-7 was performed. Claudin-7 and parvalbumin immunostains were positive in 3.4%, 7.8% of clear cell RCCs, 34.5%, 31.0% of papillary RCCs, 95.0%, 80.0% of chromophobe RCCs, and 72.7%, 81.8% of renal oncocytomas, respectively. The sensitivity and specificity of claudin-7 in diagnosing chromophobe RCC among subtypes of RCC were 95.0% and 92.3%. Those of parvalbumin were 80.0% and 88.9%. The expression pattern of claudin-7 was mostly diffuse in chromophobe RCC and was either focal or diffuse in oncocytoma. All of the cases examined in the MSP revealed the presence of unmethylated promoter of claudin-7 without regard to claudin-7 immunoreactivity. Hypermethylation of the promoter might not be the underlying mechanism for loss of its expression in RCC. Claudin-7 can be used as a useful diagnostic marker in diagnosing chromophobe RCC and oncocytoma.