Quantitative trait loci and candidate genes associated with starch pasting viscosity characteristics in cassava (Manihot esculenta Crantz)

Starch pasting viscosity is an important quality trait in cassava (Manihot esculenta Crantz) cultivars. The aim here was to identify loci and candidate genes associated with the starch pasting viscosity. Quantitative trait loci (QTL) mapping for seven pasting viscosity parameters was carried out using 100 lines of an F1 mapping population from a cross between two cassava cultivars Huay Bong 60 and Hanatee. Starch samples were obtained from roots of cassava grown in 2008 and 2009 at Rayong, and in 2009 at Lop Buri province, Thailand. The traits showed continuous distribution among the F1 progeny with transgressive variation. Fifteen QTL were identified from mean trait data, with Logarithm of Odds (LOD) values from 2.77-13.01 and phenotype variations explained (PVE) from10.0-48.4%. In addition, 48 QTL were identified in separate environments. The LOD values ranged from 2.55-8.68 and explained 6.6-43.7% of phenotype variation. The loci were located on 19 linkage groups. The most important QTL for pasting temperature (PT) (qPT.1LG1) from mean trait values showed largest effect with highest LOD value (13.01) and PVE (48.4%). The QTL co-localised with PT and pasting time (PTi) loci that were identified in separate environments. Candidate genes were identified within the QTL peak regions. However, the major genes of interest, encoding the family of glycosyl or glucosyl transferases and hydrolases, were located at the periphery of QTL peaks. The loci identified could be effectively applied in breeding programmes to improve cassava starch quality. Alleles of candidate genes should be further studied in order to better understand their effects on starch quality traits.

Usefulness of 10 genomic regions in soybean associated with sudden death syndrome resistance

Sudden death syndrome (SDS) is an important soybean [Glycine max (L) Merrill] disease caused by the soilborne fungus Fusarium virguliforme. Currently, 14 quantitative trait loci (QTL) had been confirmed associated with resistance or tolerance to SDS. The objective of the study was to evaluate usefulness of 10 of these QTL in controlling disease expression. Six populations were developed providing a total of 321 F2-derived lines for the study. Recombinant inbred lines (RIL) used as parents were obtained from populations of 'Essex' × 'Forrest' (EF), 'Flyer' × 'Hartwig' (FH), and 'Pyramid' × 'Douglas' (PD). Disease resistance was evaluated in the greenhouse at three different planting times, each with four replications, using sorghum infested with F. virguliforme homogeneously mixed in the soil (Luckew et al., Crop Sci 52:2215-2223, 2012). Four disease assessment criteria-foliar disease incidence (DI), foliar leaf scorch disease severity (DS), area under the disease progress curve (AUDPC), and root rot severity-were used. QTL were identified in more than one of the disease assessment criteria, mainly associated with lines in the most resistant categories. Five QTL (qRfs4, qRfs5, qRfs7, qRfs12, and Rfs16) were associated with at least one of the disease assessments across multiple populations. Of the five, qRfs4 was associated with DI, AUDPC, and root rot severity, and Rfs16 with AUDPC and root rot severity. The findings suggest it may be possible for plant breeders to focus on stacking a subset of the previously identified QTL to improve resistance to SDS in soybean.

Identification of QTL in soybean underlying resistance to herbivory by Japanese beetles (Popillia japonica, Newman)

Soybean [Glycine max (L.) Merr.] was one of the most important legume crops in the world in 2010. Japanese beetles (JB; Popillia japonica, Newman) in the US were an introduced and potentially damaging insect pest for soybean. JBs are likely to spread across the US if global warming occurs. Resistance to JB in soybean was previously reported only in plant introductions. The aims here were to identify loci underlying resistance to JB herbivory in recombinant inbred lines (RILs) derived from the cross of Essex x Forrest cultivars (EF94) and to correlate those with loci with factors that confer insect resistance in soybean cultivars. The RIL population was used to map 413 markers, 238 satellite markers and 177 other DNA markers. Field data were from two environments over 2 years. Pest severity (PS) measured defoliation on a 0-9 scale. Pest incidence (PI) was the percentage of plants within each RIL with beetles on them. Antibiosis and antixenosis data were from feeding assays with detached leaves in petri plates. Five QTL were detected for the mean PS field trait (16% < R (2) < 27%). The loci were within the intervals Satt632-A2D8 on linkage group (LG) A2 (chromosome 8); Satt583-Satt415 on LG B1 (11); Satt009-Satt530 on LG N (3); and close to two markers OB02_140 (LG E; 20 cM from Satt572) and OZ15_150 LG (19 cM from Satt291 C2). Two QTL were detected for the mean PI field trait (16% < R (2) < 18%) close to Satt385 on LG A1 and Satt440 on LG I. The no choice feeding studies detected three QTL that were significant; two for antixenosis (22% < R (2) < 24%) between Satt632-A2D8 on LG A2 (8) and Sat_039-Satt160 on LG F (13); and a major locus effect (R (2) = 54%) for antibiosis on LG D2 (17) between Satt464-Satt488. Therefore, loci underlying resistance to JB herbivory were a mixture of major and minor gene effects. Some loci were within regions underlying resistance to soybean cyst nematode (LGs A2 and I) and root knot nematode (LG F) but not other major loci underlying resistance to nematode or insect pests (LGs G, H and M).

Multigeneic QTL: the laccase encoded within the soybean Rfs2/rhg1 locus inferred to underlie part of the dual resistance to cyst nematode and sudden death syndrome

Multigeneic QTL present significant problems to analysis. Resistance to soybean (Glycine max (L) Merr.) sudden death syndrome (SDS) caused by Fusarium virguliforme was partly underlain by QRfs2 that was clustered with, or pleiotropic to, the multigeneic rhg1 locus providing resistance to soybean cyst nematode (SCN; Heterodera glycines). A group of five genes were found between the two markers that delimited the Rfs2/rhg1 locus. One of the five genes was predicted to encode an unusual diphenol oxidase (laccase; EC 1.10.3.2). The aim of this study was to characterize this member of the soybean laccase gene-family and explore its involvement in SDS resistance. A genomic clone and a full length cDNA was isolated from resistant cultivar 'Forrest' that were different among susceptible cultivars 'Asgrow 3244' and 'Williams 82' at four residues R/H168, I/M271, R/H330, E/K470. Additional differences were found in six of the seven introns and the promoter region. Transcript abundance (TA) among genotypes that varied for resistance to SDS or SCN did not differ significantly. Therefore the protein activity was inferred to underlie resistance. Protein expressed in yeast pYES2/NTB had weak enzyme activity with common substrates but good activity with root phenolics. The Forrest isoform may underlie both QRfs2 and rhg1.

Locus interactions underlie seed yield in soybeans resistant to Heterodera glycines

In soybean (Glycine max L. Merr.) combining resistance to cyst nematode (SCN; Heterodera glycines I.) with high seed yield remains problematic. Molecular markers linked to quantitative trait loci (QTL) have not provided a solution. Sets of markers describing a collection of favorable alleles (linkats) may assist plant breeders seeking to combine both traits. The objective of this analysis was to identify linkats in genomic regions underlying seed yield and root SCN resistance QTL. Used were groups of cultivars selected from a single recombinant inbred (RIL) population derived from 'Essex' by 'Forrest' (ExF). The yield was measured at four locations. SCN resistance was determined in greenhouse assays. The mean seed yield was used to define 3 groups (each n = 30), high, medium and low. SCN resistance formed 2 groups (SCN resistant (n = 21) and SCN susceptible (n = 69)). Microsatellite markers (213) alleles were compared with seed yield and root SCN (Hetrodera glycines) resistance using mean analysis. The number, size and position of potential linkats were determined. Loci, genomic regions and linkats associated with seed yield were identified on linkage group (LG) K and with root resistance to SCN e on LG E, G, and D1b+W. A method to identify co-localized genomic regions is presented.

Separate loci underlie resistance to root infection and leaf scorch during soybean sudden death syndrome

Soybean [Glycine max (L.) Merr.] cultivars show differences in their resistance to both the leaf scorch and root rot of sudden death syndrome (SDS). The syndrome is caused by root colonization by Fusarium virguliforme (ex. F. solani f. sp. glycines). Root susceptibility combined with reduced leaf scorch resistance has been associated with resistance to Heterodera glycines HG Type 1.3.6.7 (race 14) of the soybean cyst nematode (SCN). In contrast, the rhg1 locus underlying resistance to Hg Type 0 was found clustered with three loci for resistance to SDS leaf scorch and one for root infection. The aims of this study were to compare the inheritance of resistance to leaf scorch and root infection in a population that segregated for resistance to SCN and to identify the underlying quantitative trait loci (QTL). "Hartwig", a cultivar partially resistant to SDS leaf scorch, F. virguliforme root infection and SCN HG Type 1.3.6.7 was crossed with the partially susceptible cultivar "Flyer". Ninety-two F5-derived recombinant inbred lines and 144 markers were used for map development. Four QTL found in earlier studies were confirmed. One contributed resistance to leaf scorch on linkage group (LG) C2 (Satt277; P = 0.004, R2 = 15%). Two on LG G underlay root infection at R8 (Satt038; P = 0.0001 R2 = 28.1%; Satt115; P = 0.003, R2 = 12.9%). The marker Satt038 was linked to rhg1 underlying resistance to SCN Hg Type 0. The fourth QTL was on LG D2 underlying resistance to root infection at R6 (Satt574; P = 0.001, R2 = 10%). That QTL was in an interval previously associated with resistance to both SDS leaf scorch and SCN Hg Type 1.3.6.7. The QTL showed repulsion linkage with resistance to SCN that may explain the relative susceptibility to SDS of some SCN resistant cultivars. One additional QTL was discovered on LG G underlying resistance to SDS leaf scorch measured by disease index (Satt130; P = 0.003, R2 = 13%). The loci and markers will provide tagged alleles with which to improve the breeding of cultivars combining resistances to SDS leaf scorch, root infection and SCN HG Type 1.3.6.7.

The digestive fate of Escherichia coli glutamate dehydrogenase deoxyribonucleic acid from transgenic corn in diets fed to weanling pigs

Corn containing genetically engineered plasmid DNA encoding an Escherichia coli glutamate dehydrogenase (gdhA) was fed to 19-d-old weanling swine to trace the digestive fate of the transgenic DNA. Eight pens of 8 pigs were fed a commercial (nongdhA) starter for 2 wk. One pig was randomly selected from each pen for 0-h control samples. The remaining 56 pigs were transitioned onto a corn-soybean meal diet and fed a diet containing 58% gdhA corn for approximately 1 wk; immediately thereafter, liver, 10th rib muscle, white blood cells, and plasma from the hepatic portal vein and ingesta from the stomach, distal ileum, and large intestine were collected. The DNA was extracted and the concentration determined via spectrophotometry. Polymerase chain reaction and gel electrophoresis were performed with primers designed to amplify 490 bp that included the plasmid's ligation site between the maize ubiquitin and the gdhA genes. The gdhA corn-derived DNA and diet served as positive assay controls, and conventional corn DNA and distilled water acted as negative assay controls. Detection limits were 0.99 fg of target DNA confounded with 500 ng of conventional corn DNA per each 20 &L reaction. Transgenic DNA was detected in 71.43% of the stomach and 1.79% of the ileal ingesta samples from treatment animals but was not detected in the large intestine, white blood cells, plasma, liver, or muscle samples. Transgenic DNA was not detected in any sample from 0-h control animals. Stomach and ileal ingesta samples were further analyzed using real-time PCR. With an estimated limit of detection of 1.049 ag/microL, 89.29% of the stomach ingesta samples were positive (average 1.56 fg target DNA). The proportion of transgenic DNA to total DNA differed between diet and stomach ingesta samples (P < 0.001). Despite the greater sensitivity of real-time PCR, target DNA was detected in only 1.79% of ileal ingesta. These data suggest that the gdhA transgene began degradation in the stomach and was nondetectable in the large intestine.

Construction and characterization of two bacterial artificial chromosome libraries of pea (Pisum sativum L.) for the isolation of economically important genes

Pea (Pisum sativum L.) has a genome of about 4 Gb that appears to share conserved synteny with model legumes having genomes of 0.2-0.4 Gb despite extensive intergenic expansion. Pea plant inventory (PI) accession 269818 has been used to introgress genetic diversity into the cultivated germplasm pool. The aim here was to develop pea bacterial artificial chromosome (BAC) libraries that would enable the isolation of genes involved in plant disease resistance or control of economically important traits. The BAC libraries encompassed about 3.2 haploid genome equivalents consisting of partially HindIII-digested DNA fragments with a mean size of 105 kb that were inserted in 1 of 2 vectors. The low-copy oriT-based T-DNA vector (pCLD04541) library contained 55 680 clones. The single-copy oriS-based vector (pIndigoBAC-5) library contained 65 280 clones. Colony hybridization of a universal chloroplast probe indicated that about 1% of clones in the libraries were of chloroplast origin. The presence of about 0.1% empty vectors was inferred by white/blue colony plate counts. The usefulness of the libraries was tested by 2 replicated methods. First, high-density filters were probed with low copy number sequences. Second, BAC plate-pool DNA was used successfully to PCR amplify 7 of 9 published pea resistance gene analogs (RGAs) and several other low copy number pea sequences. Individual BAC clones encoding specific sequences were identified. Therefore, the HindIII BAC libraries of pea, based on germplasm accession PI 269818, will be useful for the isolation of genes underlying disease resistance and other economically important traits.

Genomic analysis of the rhg1 locus: candidate genes that underlie soybean resistance to the cyst nematode

The rhg1 gene or genes lie at a recessive or co-dominant locus, necessary for resistance to all Hg types of the soybean (Glycine max (L.) Merr.) cyst nematode (Heterodera glycines I.). The aim here was to identify nucleotide changes within a candidate gene found at the rhg1 locus that were capable of altering resistance to Hg types 0 (race 3). A 1.5 +/- 0.25 cM region of chromosome 18 (linkage group G) was shown to encompass rhg1 using recombination events from four near isogenic line populations and nine DNA markers. The DNA markers anchored two bacterial artificial chromosome (BAC) clones 21d9 and 73p6. A single receptor like kinase (RLK; leucine rich repeat-transmembrane-protein kinase) candidate resistance gene was amplified from both BACs using redundant primers. The DNA sequence showed nine alleles of the RLK at Rhg1 in the soybean germplasm. Markers designed to detect alleles showed perfect association between allele 1 and resistance to soybean cyst nematode Hg types 0 in three segregating populations, fifteen additional selected recombination events and twenty-two Plant Introductions. A quantitative trait nucleotide (QTN) [corrected] in the RLK at rhg1 was inferred that alters A87 to V87 in the context of H274 rather than N274. [corrected] Contiguous DNA sequence of 315 kbp of chromosome 18 (about 2 cM) contained additional gene candidates that may modulate resistance to other Hg-types including a variant laccase, a hydrogen-sodium ion antiport and two proteins of unknown function. A molecular basis for recessive and co-dominant resistance that involves interactions among paralagous disease-resistance genes was inferred that would improve methods for developing new nematode-resistant soybean cultivars.

An updated 'Essex' by 'Forrest' linkage map and first composite interval map of QTL underlying six soybean traits

DNA marker maps based on single populations are the basis for gene, loci and genomic analyses. Individual maps can be integrated to produce composite maps with higher marker densities if shared marker orders are consistent. However, estimates of marker order in composite maps must include sets of markers that were not polymorphic in multiple populations. Often some of the pooled markers were not codominant, or were not correctly scored. The soybean composite map was composed of data from five separate populations based on northern US germplasm but does not yet include 'Essex' by 'Forrest' recombinant inbred line (RIL) population (E x F) or any southern US soybean cultivars. The objectives were, to update the E x F map with codominant markers, to compare marker orders among this map, the Forrest physical map and the composite soybean map and to compare QTL identified by composite interval maps to the earlier interval maps. Two hundred and thirty seven markers were used to construct the core of the E x F map. The majority of marker orders were consistent between the maps. However, 19 putative marker inversions were detected on 12 of 20 linkage groups (LG). Eleven marker distance compressions were also found. The number of inverted markers ranged from 1 to 2 per LG. Thus, marker order inversions may be common in southern compared to northern US germplasm. A total of 61 QTL among 37 measures of six traits were detected by composite interval maps, interval maps and single point analysis. Seventeen of the QTL found in composite intervals had previously been detected among the 29 QTL found in simple interval maps. The genomic locations of the known QTL were more closely delimited. A genome sequencing project to compare Southern and Northern US soybean cultivars would catalog and delimit inverted regions and the associated QTL. Gene introgression in cultivar development programs would be accelerated.

Three minimum tile paths from bacterial artificial chromosome libraries of the soybean (Glycine max cv. 'Forrest'): tools for structural and functional genomics

BACKGROUND

The creation of minimally redundant tile paths (hereafter MTP) from contiguous sets of overlapping clones (hereafter contigs) in physical maps is a critical step for structural and functional genomics. Build 4 of the physical map of soybean (Glycine max L. Merr. cv. 'Forrest') showed the 1 Gbp haploid genome was composed of 0.7 Gbp diploid, 0.1 Gbp tetraploid and 0.2 Gbp octoploid regions. Therefore, the size of the unique genome was about 0.8 Gbp. The aim here was to create MTP sub-libraries from the soybean cv. Forrest physical map builds 2 to 4.

RESULTS

The first MTP, named MTP2, was 14,208 clones (of mean insert size 140 kbp) picked from the 5,597 contigs of build 2. MTP2 was constructed from three BAC libraries (BamHI (B), HindIII (H) and EcoRI (E) inserts). MTP2 encompassed the contigs of build 3 that derived from build 2 by a series of contig merges. MTP2 encompassed 2 Gbp compared to the soybean haploid genome of 1 Gbp and does not distinguish regions by ploidy. The second and third MTPs, called MTP4BH and MTP4E, were each based on build 4. Each was semi-automatically selected from 2,854 contigs. MTP4BH was 4,608 B and H insert clones of mean size 173 kbp in the large (27.6 kbp) T-DNA vector pCLD04541. MTP4BH was suitable for plant transformation and functional genomics. MTP4E was 4,608 BAC clones with large inserts (mean 175 kbp) in the small (7.5 kbp) pECBAC1 vector. MTP4E was suitable for DNA sequencing. MTP4BH and MTP4E clones each encompassed about 0.8 Gbp, the 0.7 Gbp diploid regions and 0.05 Gbp each from the tetraploid and octoploid regions. MTP2 and MTP4BH were used for BAC-end sequencing, EST integration, micro-satellite integration into the physical map and high information content fingerprinting. MTP4E will be used for genome sequence by pooled genomic clone index.

CONCLUSION

Each MTP and associated BES will be useful to deconvolute and ultimately finish the whole genome shotgun sequence of soybean.

Metabolite fingerprinting in transgenic Nicotiana tabacum altered by the Escherichia coli glutamate dehydrogenase gene

With about 200 000 phytochemicals in existence, identifying those of biomedical significance is a mammoth task. In the postgenomic era, relating metabolite fingerprints, abundances, and profiles to genotype is also a large task. Ion analysis using Fourier transformed ion cyclotron resonance mass spectrometry (FT-ICR-MS) may provide a high-throughput approach to measure genotype dependency of the inferred metabolome if reproducible techniques can be established. Ion profile inferred metabolite fingerprints are coproducts. We used FT-ICR-MS-derived ion analysis to examine gdhA (glutamate dehydrogenase (GDH; EC 1.4.1.1)) transgenic Nicotiana tabacum (tobacco) carrying out altered glutamate, amino acid, and carbon metabolisms, that fundamentally alter plant productivity. Cause and effect between gdhA expression, glutamate metabolism, and plant phenotypes was analyzed by 13NH4+ labeling of amino acid fractions, and by FT-ICR-MS analysis of metabolites. The gdhA transgenic plants increased ¹³N labeling of glutamate and glutamine significantly. FT-ICR-MS detected 2 012 ions reproducible in 2 to 4 ionization protocols. There were 283 ions in roots and 98 ions in leaves that appeared to significantly change abundance due to the measured GDH activity. About 58% percent of ions could not be used to infer a corresponding metabolite. From the 42% of ions that inferred known metabolites we found that certain amino acids, organic acids, and sugars increased and some fatty acids decreased. The transgene caused increased ammonium assimilation and detectable ion variation. Thirty-two compounds with biomedical significance were altered in abundance by GDH including 9 known carcinogens and 14 potential drugs. Therefore, the GDH transgene may lead to new uses for crops like tobacco.

Low level chromosome instability in embryonic cells of primary aneuploid mice

Karyotypic analyses of Down syndrome patients have identified a low level of chromosome mosaicism, suggesting that the primary aneuploid status of the cells promotes further chromosomal segregation errors. Sycp3-null female mice produce aneuploid oocytes, which after fusion with normal haploid sperm, result in offspring with systemic whole chromosome, aneuploid embryo cells. Using the Sycp3-null female as a model, we observe an increase in the number of embryonic cells at E7.0 that exhibit abnormal chromosomal bridges at the anaphas estage of mitosis. This result suggests that global changes in gene expression patterns resulting from primary aneuploidy can affect mitotic chromosome segregation, resulting in a low level of chromosomal instability. The increased level of chromosomal instability could in the absence of mitotic checkpoints, lead to chromosomal mosaicism within the adult organism, as seen in Down syndrome patients.

Genomic analysis of a region encompassing QRfs1 and QRfs2: genes that underlie soybean resistance to sudden death syndrome

Candidate genes were identified for two loci, QRfs2 providing resistance to the leaf scorch called soybean (Glycine max (L.) Merr.) sudden death syndrome (SDS) and QRfs1 providing resistance to root infection by the causal pathogen Fusarium solani f.sp. glycines. The 7.5 +/- 0.5 cM region of chromosome 18 (linkage group G) was shown to encompass a cluster of resistance loci using recombination events from 4 near-isogenic line populations and 9 DNA markers. The DNA markers anchored 9 physical map contigs (7 are shown on the soybean Gbrowse, 2 are unpublished), 45 BAC end sequences (41 in Gbrowse), and contiguous DNA sequences of 315, 127, and 110 kbp. Gene density was high at 1 gene per 7 kbp only around the already sequenced regions. Three to 4 gene-rich islands were inferred to be distributed across the entire 7.5 cM or 3.5 Mbp showing that genes are clustered in the soybean genome. Candidate resistance genes were identified and a molecular basis for interactions among the disease resistance genes in the cluster inferred.

Construction and characterization of a soybean bacterial artificial chromosome library and use of multiple complementary libraries for genome physical mapping

Two plant-transformation-competent large-insert binary clone bacterial artificial chromosome (hereafter BIBAC) libraries were previously constructed for soybean cv. Forrest, using BamHI or HindIII. However, they are not well suited for clone-based genomic sequencing due to their larger ratio of vector to insert size (27.6 kbp:125 kbp). Therefore, we developed a larger-insert bacterial artificial chromosome (BAC) library for the genotype in a smaller vector (pECBAC1), using EcoRI. The BAC library contains 38,400 clones; about 99.1% of the clones have inserts; the average insert size is 157 kbp; and the ratio of vector to insert size is much smaller (7.5 kbp:157 kbp). Colony hybridization with probes derived from several chloroplast and mitochondrial genes showed that 0.89% and 0.45% of the clones were derived from the chloroplast and mitochondrial genomes, respectively. Considering these data, the library represents 5.4 haploid genomes of soybean. The library was hybridized with six RFLP marker probes, 5S rDNA and 18S-5.8S-25S rDNA, respectively. Each RFLP marker hybridized to about six clones, and the 5S and 18S-5.8S-25S rDNA probes collectively hybridized to 402 BACs--about 1.05% of the clones in the library. The BAC library complements the existing soybean Forrest BIBAC libraries by using different restriction enzymes and vector systems. Together, the BAC and BIBAC libraries encompass 13.2 haploid genomes, providing the most comprehensive clone resource for a single soybean genotype for public genome research. We show that the BAC library has enhanced the development of the soybean whole-genome physical map and use of three complementary BAC libraries improves genome physical mapping by fingerprint analysis of most of the clones of the library. The rDNA-containing clones were also fingerprinted to evaluate the feasibility of constructing contig maps of the rDNA regions. It was found that physical maps for the rDNA regions could not be readily constructed by fingerprint analysis, using one or two restriction enzymes. Additional data to fingerprints and/or different fingerprinting methods are needed to build contig maps for such highly tandem repetitive regions and thus, the physical map of the entire soybean genome.

Definition of Soybean Genomic Regions That Control Seed Phytoestrogen Amounts

Soybean seeds contain large amounts of isoflavones or phytoestrogens such as genistein, daidzein, and glycitein that display biological effects when ingested by humans and animals. In seeds, the total amount, and amount of each type, of isoflavone varies by 5 fold between cultivars and locations. Isoflavone content and quality are one key to the biological effects of soy foods, dietary supplements, and nutraceuticals. Previously we had identified 6 loci (QTL) controlling isoflavone content using 150 DNA markers. This study aimed to identify and delimit loci underlying heritable variation in isoflavone content with additional DNA markers. We used a recombinant inbred line (RIL) population ( $n=100$ ) derived from the cross of “Essex” by “Forrest,” two cultivars that contrast for isoflavone content. Seed isoflavone content of each RIL was determined by HPLC and compared against 240 polymorphic microsatellite markers by one-way analysis of variance. Two QTL that underlie seed isoflavone content were newly discovered. The additional markers confirmed and refined the positions of the six QTL already reported. The first new region anchored by the marker BARC-Satt063 was significantly associated with genistein ( $P=0.009$, $Rcirc;2=29.5\%$ ) and daidzein ( $P=0.007$, $Rcirc;2=17.0\%$ ). The region is located on linkage group B2 and derived the beneficial allele from Essex. The second new region defined by the marker BARC-Satt129 was significantly associated with total glycitein ( $P=0.0005$, $Rcirc;2=32.0\%$ ). The region is located on linkage group D1a+Q and also derived the beneficial allele from Essex. Jointly the eight loci can explain the heritable variation in isoflavone content. The loci may be used to stabilize seed isoflavone content by selection and to isolate the underlying genes.

Differentially abundant mRNAs in rat liver in response to diets containing soy protein isolate

Soy diets influence cell growth, regulate lipid metabolism to lower blood cholesterol, and prevent bone losses. These biological effects are most likely due to effects of soy phytochemicals on the expression of genes. In this study, we fed 12 female obese Zucker rats (fa/fa) with a low- or a high-isoflavone soy protein diet and compared the gene expression with animals on a casein diet. Rat livers were compared by differential display of mRNA, and 62 unique sequences were identified. The change in mRNA abundance of these sequences was quantified by cDNA macroarray analysis. Thirty-three mRNAs showed more than twofold increase in abundance on soy diets compared with the control. The corresponding genes include carnitine palmitoyltransferase I, stromal cell-derived factor 1, a protein associated with MYC mRNA, basic transcription element binding protein, and expressed sequence tags (ESTs) of unknown function. Twenty-nine mRNAs showed a less than twofold change in abundance in the two diet treatments. For majority of the genes identified, there was not significant difference between the low- and high-isoflavone diet treatments. Therefore, the contrast between soy protein and casein caused the changes observed in mRNA abundance.

Resistance locus pyramids alter transcript abundance in soybean roots inoculated with Fusarium solani f.sp. glycines

Soybean Sudden Death Syndrome (SDS) is caused by Fusarium solani f.sp. glycines (Fsg). Six quantitative trait loci (QTLs), each conferring partial resistance to SDS, have been discovered in an Essex x Forrest recombinant inbred line (RIL) population, but their mode of action is not clear. This study aimed to identify genes (ESTs) whose mRNA transcripts were altered in abundance in soybean roots following inoculation of Fsg. Roots of the soybean variety Forrest (four resistance alleles) were inoculated with Fsg, and 14 days later RNA sequences that were differentially expressed relative to uninoculated roots were enriched using suppression subtraction and differential display. The abundance of these RNAs was quantified in inoculated and non-inoculated roots by macroarray hybridizations. A unigene set of 135 ESTs was identified and used in a further macroarray analysis. The abundance of 28 cDNA fragments was increased more than two-fold in inoculated compared to uninoculated roots of RIL 23 (six resistance alleles). In Forrest and Essex (two resistance alleles), the level of only one mRNA was increased two-fold in inoculated roots compared to the uninoculated roots. In Essex most of the mRNAs analyzed decreased in abundance (61/135 showed a two-fold decrease), while in Forrest most mRNA abundances did not change. Among the 28 cDNAs that revealed a two-fold or higher increase in mRNA abundance in RIL 23, 14% code for proteins known to be involved in plant defense, 21% in metabolism, 14% in cell structure and 4% in transport. Unannotated ESTs accounted for 43% of the genes, and 4% of the sequences were previously unknown. The plant defense-related genes that showed a differential response to Fsg inoculation suggested a role for the phenylproponoid pathway in soybean defense against Fsg. In Essex, genes involved in plant defense, cell wall synthesis, ethylene synthesis and metabolism were expressed at lower levels in inoculated roots. The difference in response between the 2-, 4- and 6-gene pyramids suggests that QTLs for SDS resistance serve to delay symptoms or confer resistance by maintaining or increasing the expression of specific genes after inoculation/infection.

Common loci underlie field resistance to soybean sudden death syndrome in Forrest, Pyramid, Essex, and Douglas

Soybean [ Glycine max (L.) Merr.] sudden death syndrome (SDS) caused by Fusarium solani f. sp. glycines results in severe yield losses. Resistant cultivars offer the most-effective protection against yield losses but resistant cultivars such as 'Forrest' and 'Pyramid' vary in the nature of their response to SDS. Loci underlying SDS resistance in 'Essex'&emsp14;x&emsp14;Forrest are well defined. Our objectives were to identify and characterize loci and alleles that underlie field resistance to SDS in Pyramidx'Douglas'. SDS disease incidence and disease severity were determined in replicated field trials in six environments over 4 years. One hundred and twelve polymorphic DNA markers were compared with SDS disease response among 90 recombinant inbred lines from the cross PyramidxDouglas. Two quantitative trait loci (QTLs) for resistance to SDS derived their beneficial alleles from Pyramid, identified on linkage group G by BARC-Satt163 (261-bp allele, P=0.0005, R(2)=16.0%) and linkage group N by BARC-Satt080 (230-bp allele, P=0.0009, R(2)=15.6%). Beneficial alleles of both QTLs were previously identified in Forrest. A QTL for re- sistance to SDS on linkage group C2 identified by BARC-Satt307 (292-bp allele, P=0.0008, R(2)=13.6%) derived the beneficial allele from Douglas. A beneficial allele of this QTL was previously identified in Essex. Recombinant inbred lines that carry the beneficial alleles for all three QTLs for resistance to SDS were significantly ( P</=0.05) more resistant than other recombinant inbred lines. Among these recombinant inbred lines resistance to SDS was environmentally stable. Therefore, gene pyramiding will be an effective method for developing cultivars with stable resistance to SDS.

Quantitative trait loci in Two Soybean Recombinant Inbred Line Populations Segregating for Yield and Disease Resistance

Molecular makers linked to quantitative trait loci (QTL) can assist soybean [Glycine max (L.) Merr.] breeders to combine traits of low heritability, such as yield, with disease resistance. The objective of this study was to identify markers linked to yield QTL in two recombinant inbred line (RIL) populations ['Essex' x 'Forrest' (ExF; n = 100) and 'Flyer' x 'Hartwig' (FxH; n = 94)] that also segregate for soybean cyst nematode (SCN) resistance genes (rhg1 and Rhg4). Each population was yield tested in four environments between 1996 and 1999. The resistant parents produced lower yields. Heritability of yield across four environments was 47% for ExF and 57% for FxH. Yield was normally distributed in both populations. High yielding, SCN resistant transgressive segregants were not observed. In the ExF RIL population, 134 microsatellite markers were compared against yield by ANOVA and MAPMAKER QTL. Regions associated with yield were identified by SATT294 on linkage group (LG.) C1 (P = 0.006, R(2) = 10%), SATT440 on LG. I (P = 0.007, R(2) = 10%), and SATT337 on LG. K (P = 0.004, R(2) = 10%). Essex provided the beneficial allele at SATT337. Mean yields among FxH RILs were compared against 33 microsatellite markers from LG. K. In addition 136 markers from randomly selected LGs were compared with extreme phenotypes by bulk segregant analysis. Two regions on LG. K (20 cM apart) associated with yield were identified by SATT326 (P = 0.0004, R(2) = 15%) and SATT539 (P = 0.0008, R(2) = 14%). Flyer provided both beneficial alleles. Both populations revealed a yield QTL in the interval (5 cM) between SATT337 and SATT326. These populations may share a common allele for yield in this region, given that about 40% of Flyer genome derived from Essex.

Conversion of AFLP bands into high-throughput DNA markers

The conversion of AFLP bands into polymorphic sequence-tagged-site (STS) markers is necessary for high-throughput genotype scoring. Technical hurdles that must be overcome arise from genome complexity (particularly sequence duplication), from the low-molecular-weight nature of the AFLP bands and from the location of the polymorphism within the AFLP band. We generated six STS markers from ten AFLP bands (four AFLPs were from co-dominant pairs of bands) in soybean (Glycine max). The markers were all linked to one of two loci, rhg1 on linkage group G and Rhg4 on linkage group A2, that confer resistance to the soybean cyst nematode (Heterodera glycines I.). When the polymorphic AFLP band sequence contained a duplicated sequence or could not be converted to a locus-specific STS marker, direct sequencing of BAC clones anchored to a physical map generated locus-specific flanking sequences at the polymorphic locus. When the polymorphism was adjacent to the restriction site used in the AFLP analysis, single primer extension was performed to reconstruct the polymorphism. The six converted AFLP markers represented 996 bp of sequence from alleles of each of two cultivars and identified eight insertions or deletions, two microsatellites and eight single-nucleotide polymorphisms (SNPs). The polymorphic sequences were used to design a non-electrophoretic, fluorometric assay (based on the TaqMan technology) and/or develop electrophoretic STS markers for high-throughput genotype determination during marker-assisted breeding for resistance to cyst nematode. We conclude that the converted AFLP markers contained polymorphism at a 10- to 20-fold higher frequency than expected for adapted soybean cultivars and that the efficiency of AFLP band conversion to STS can be improved using BAC libraries and physical maps. The method provides an efficient tool for SNP and STS discovery suitable for marker-assisted breeding and genomics.

Root Colonization of Soybean Cultivars in the Field by Fusarium solani f. sp. glycines

Soybean sudden death syndrome (SDS), caused by Fusarium solani f. sp. glycines, is a problem in some soybean-growing areas in the United States. Resistance is an important control strategy. In this study, root colonization of six soybean cultivars by F. solani f. sp. glycines was determined. Cultivars included susceptible P3981, CM497, and Spencer and field resistant LS90-1920, Pharaoh, and Ripley. All cultivars were tested in field experiments at different locations in southern Illinois in 1997 and 1998. Roots were collected at six sampling times and were dried and ground to isolate and enumerate the pathogen on a selective medium. SDS foliar disease index (FDX), the area under the F. solani f. sp. glycines population curve (AUPC), the incidence of colonized roots at 45 days after planting (RCI₄₅), and the root colonization rate (RCR) were used to compare cultivars. FDX on the three resistant cultivars was significantly lower than on the three susceptible cultivars. Means of AUPC on the three resistant cultivars were significantly lower than those on the susceptible CM497 and P3981. RCI₄₅ of Pharaoh was significantly lower than those of P3981 and Spencer. RCRs of all three resistant cultivars were significantly lower than that of P3981, and RCR of Ripley was also significantly lower than that of CM497. Based on combination of all cultivars, AUPC was significantly correlated with RCI₄₅ and RCR.

A nitrate reductase gene of the cyanobacterium Synechococcus PCC6301 inferred by heterologous hybridization, cloning and targeted mutagenesis

DNA probes from the narG gene of Escherichia coli, which encodes the large polypeptide of respiratory nitrate reductase, show cross-hybridization at low stringency to a single region of the genome of the cyanobacterium Synechococcus PCC6301. This segment of cyanobacterial DNA was cloned as the insert of plasmid pDN1 and characterized. RNA complementary to pDN1 was shown to be substantially more abundant in nitrate grown cells of Synechococcus PCC6301 than in ammonium grown cells, thus parallelling the nitrate induction and ammonium repression of nitrate reductase activity in cultures of this cyanobacterium. A mutant of Synechococcus PCC6301 deficient in nitrate reductase activity was obtained after a potentially mutagenic transformation treatment using pDN1 as a donor. This mutant was restored to the wild type phenotype following stable integrative transformation with pDN1 DNA. Taken together these data suggest that pDN1 might encode a polypeptide of nitrate reductase. pDN1 is distinct from three clones of genes involved in nitrate assimilation that were isolated previously from the related cyanobacterium Synechococcus PCC7942 (Kuhlemeier et al., 1984a, J. Bact. 159, 36-41, and 1984b, Gene 31, 109-116).

External beam irradiation versus 125 iodine implant in the definitive treatment of prostate carcinoma

We reviewed the record of all 983 patients seen at the Hahnemann University, Department of Radiation Oncology for evaluation of prostate cancer during the megavoltage era. We compared the results of 276 patients who were treated definitively with either external beam irradiation or Iodine 125 implantation. The groups were similar in most prognostic characteristics. Where appropriate, multivariate statistical techniques were used to compensate for the effects of differences in grade and stage between the two groups. There were striking differences between implant and external beam patients in both local failure rates and disease-free survival, mostly attributable to poor local control in the implant patients. Thirty-eight percent of the Stage A and B implant patients failed locally in the first 5 years whereas only 5% of a comparable group of external beam patients did so. A2 patients, however, exhibited similar disease-free survival in both cohorts. Complication rates were 11% in the implant group and 19% in the external beam group. We conclude that there are serious doubts about the efficacy of Iodine 125 implantation in maintaining local control, and that this translates into worse relapse-free survival. By contrast, local control and relapse-free survival may be satisfactory in the A2 patients, and complication rates may be lower with implant. The above suggests that Iodine 125 interstitial implantation is well suited to only a minority of early stage prostate cancer patients and that most patients with Stage B and C prostatic carcinoma should be treated with either external beam irradiation or with radical prostatectomy.

Analyses of Phaseolus vulgaris L. and P. coccineus Lam. hybrids by RFLP: preferential transmission of P. vulgaris alleles

Restriction fragment length polymorphism (RFLP) was determined among P. vulgaris genotypes and Phaseolus species using 19 probes. The incidence of polymorphism was high (70-86%) between species, but relatively low (22-26%) between genotypes of P. vulgaris. Suitable probes were identified for the analysis of P. vulgaris and P. coccineus hybrids. The segregation pattern in F2 populations was Mendelian for two probes (LHB and VEE20) and non-Mendelian for GS-g, CHS, and CHI. Statistical analyses indicated gametic selection with preferential transmission of the P. vulgaris alleles, which may account for the selective recovery of P. vulgaris progeny types observed earlier. The available hybrids of P. vulgaris and P. coccineus and the high degree of interspecific RFLP will facilitate the construction of a linkage map for Phaseolus.

cDNA sequence and differential expression of the gene encoding the glutamine synthetase γ polypeptide ofPhaseolus vulgaris L

We report the sequence of an essentially full-length glutamine synthetase (GS) cDNA clone (pcGS-γ1) isolated from a root nodule library ofPhaseolus vulgaris L. The polypeptide encoded by this cDNA has been producedin vitro by transcription/translation and shown to co-migrate on two-dimensional gels with the previously identified major cytosolic GS polypeptide (γ) of nodules. Two previously identified GS cDNA clones, pR-2 and pR-1 (see Gebhardtet al., EMBO J 5: 1429-1435, 1986) have similarly been shown to encode the α and β cytosolic GS polypeptides respectively. An RNase protection technique has been used to analyse specifically and quantitatively the abundance of mRNA related to these three GS cDNAs and to the cDNA (pcGS-δ1) encoding the chloroplast-located GS, during nodulation. Differences in the abundances of these mRNAs at different times suggest that they are not coordinately regulated. Moreover, using this technique mRNA specifically related to pcGS-γ1 was found at high levels in nodules but not in roots or leaves. Surprisingly the expression of this gene is not nodule-specific as previously suggested, as its mRNA was also detected, but at lower levels, in stems, petioles and in green cotyledons. By comparison, mRNA related to a leghaemoglobin gene was detected only in nodules. Comparisons of the relative abundances of the pcGS-γ1 mRNA and the γ polypeptide in different organs and at different stages during nodulation, suggest that the appearance of the γ polypeptide is largely under transcriptional control.

Detection of a homologue to an E. coli glutamate synthase gene in a cyanobacterium

The gltBY locus of E. coli, which codes for the two subunits of pyridine nucleotide dependent glutamate synthase, was used as a probe to detect homologues in genomic DNA of Synechococcus PCC6301, a unicellular cyanobacterium. Non-overlapping probes from gltB detected a single homologue with extensive homology, however gltY probes do not detect a strong homologue. The possibility that the gltB homologue encodes a ferredoxin-dependent glutamate synthase of the type found in cyanobacteria, algae and plants is discussed.

Magnesium-dependence of in vitro translation programmed by gene-specific mRNAs

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Expression of the Escherichia coli glutamate dehydrogenase gene in the cyanobacterium Synechococcus PCC6301 causes ammonium tolerance

The unicellular cyanobacterium Synechococcus PCC6301 lacks a hybridisable homologue of the strongly conserved gdhA gene of E. coli that encodes NADP-specific glutamate dehydrogenase. This is consistent with the failure to find this enzyme in extracts of the cyanobacterium. The E. coli gdhA gene was transferred to Synechococcus PCC6301 by transformation with an integrative vector. High levels of glutamate dehydrogenase activity, similar to those found in ammonium grown E. coli cells, were found in these transformants. These transformed cyanobacteria displayed an ammonium tolerant phenotype, consistent with the action of their acquired glutamate dehydrogenase activity as an ammonium detoxification mechanism. Minor differences in colony size and in growth at low light intensity were also observed.

The chloroplast-located glutamine synthetase of Phaseolus vulgaris L.: nucleotide sequence, expression in different organs and uptake into isolated chloroplasts

Work using a full-length cDNA clone has revealed that the plastid-located glutamine synthetase (GS) of Phaseolus vulgaris is encoded by a single nuclear gene. Nucleotide sequencing has shown that this cDNA is more closely related to a cDNA encoding the plastidic GS of Pisum sativum than to cDNAs encoding three different cytosolic GS subunits of P. vulgaris. The plastid GS subunits are initially synthesized as higher M r (47000) precursors containing an N-terminal presequence of about 50 amino acids which is structurally similar to the presequences of other nuclear-encoded chloroplast proteins. The precursor has been synthesized in vitro and is imported by isolated pea chloroplasts and processed to two polypeptides of the same size as native P. vulgaris chloroplast GS subunits (M r 42000). Experiments with fusion proteins show that the N-terminal 68 amino acids of this precursor allow the cytosolic GS subunit β also to be imported and processed by isolated chloroplasts. Polyadenylated mRNA specifically related to the plastidic GS gene is most highly abundant in chloroplast-containing organs (leaves and stems) but is also detectable in roots and nodules.

Screen-film mammographic technique for breast cancer screening

The values of dose and signal-to-noise ratio (SNR) for many techniques and breast thicknesses were computed and compared with a reference technique and breast thickness to provide a valid basis upon which to select a screening technique for screen-film mammography. The reference consisted of a Min-R/OM1 combination (or its equivalent) exposed through a 4.5-cm thick breast via 28 kV and a molybdenum target-beryllium window tube with a 0.03-mm Mo filter. Radiographs of an improved breast phantom were used to relate computed relative SNR values of techniques to diameters of the smallest calcific and soft-tissue objects demonstrated in mammograms. Without use of a grid, four Mo target/filtration combinations yielded similar computed dose and SNR levels, as did a tungsten target tube operated at 23 kV without a filter. Operation of the latter tube at 27.5 kV with a 0.051-mm rhodium filter should reduce dose by half but also SNR by 22%. However, such operation with a grid should greatly improve imaging moderate to large breasts without increasing dose over reference values.

Dosage evaluation in mammography

Estimates of breast dose per view are needed for selection of mammographic techniques and verification of their proper use. However, accurate dosimetry requires standardization of both the methodology and the assumed breast composition. Because several different methods have been reported, the authors developed a simple and reproducible method using a reference "average breast" composition of 50/50% water/fat by weight. Working curves were derived for average glandular and whole-breast dose per unit of exposure in air vs. HVL and thickness. When these curves are combined with on-site measurements of exposure per view, one obtains values of dose per view for each technique. Factors were also computed to correct dosage from the reference composition to other breast compositions.

Comparison of ion chamber and TLD dosimetry in mammography

An ionization chamber method has been developed to measure exposure vs depth in a uniform BR 12 "average breast" phantom. It employs a Memorial mammography chamber for exit exposure measurements; resulting data is then corrected for backscatter as well as for the exceptionally thin window of this chamber. A careful comparison has then been made with relative exposure vs depth curves obtained using TLD at several mammography beam qualities, for identical exposure factors and SSD values. Use of a correction for residual and background TL signals significantly improved agreement between TLD and ion chamber curves in the 28 to 35 kVp/0.03 mm Mo range of beam quality. Agreement was within +/- 5% for the Mo target tube, but TLD readings were 4%--8% higher than ion chamber values for the W/Mo target tube. At Xeromammography energies (45 kVp/1.6 mm Al), corrected TLD curve readings were 6% higher at depth than ion chamber curve values. TLD meaurements with 28 to 35 kVp/0.03 mm Mo beams tend to underestimate dosage to the midbreast parenchyma. For example, in a 5 cm "average breast", the underestimation ranges from 2%--10% for corrected, 10%--16% for uncorrected TLD readings.

A study of mammographic exposure and detail visibility using three systems: Xerox 125, Min-R, and Xonics XERG

A breast phantom of novel design has been used to measure visibility of simulated calcific and soft-tissue fibrillar details in mammography, as well as to determine the roentgen exposure vs. depth. Exposure data were combined with a model of the breast as compressed during mammography to compute the mean exposure to the ductal parenchyma (MDE). Three different imaging systems were compared over a wide range of x-ray beam energies and breast characteristics. "Dosage" criteria other than the MDE are discussed.

Rapid computation of diagnostic X-ray bremsstrahlung spectra

A method is described for rapid and accurate computation of diagnostic x-ray spectra. Accuracy limitations of Kramers' equation are overcome by providing intensity correction factors derived from published measured data. Use of a parameter based on the energy of the Kramers spectrum intensity peak permits deriving master factor curves which are remarkably independent of kVp, waveform and filtration. Computed and measured spectra generally agree to better than +/- 1 keV for beams generated at 100 kVp and below. Possible application of the method to higher energy diagnostic beams is discussed.

A breast phantom method for evaluating mammography technique

A new breast phantom has been designed for use in evaluating mammographic system performance. This phantom incorporates simulated calcifications and fibrillar objects in fat, of graded size, to permit measurements of detail visibility. A special methodology has been developed for measuring visible object size to achieve reproducible and clinically relevant results. Materials and construction of the phantom also permit carrying out dosimetry with an appropriate ionization chamber. Dosage and detail visibility measurements are reported for the Xerox 125, Min-R and Xonics systems. In addition to providing information regarding technique and image receptors, these results demonstrate the usefulness of the basic phantom design, and suggest possible improvements.

Edge sharpness and enhancement of electron radiographs (ERGs) produced with powder cloud development

Much renewed interest has developed in electrostatic imaging systems. This is partly because of their use of relatively inexpensive materials and their potential for improved diagnostic accuracy--a novel combination of image latitude with great detail contrast. All such systems can exhibit these image characteristics when developed by the generally used "powder cloud" technique or some similar partial development system. We have measured edge sharpness and enhancement of electron radiographs (ERGs) produced with the powder cloud technique. Edge sharpness can be excellent at low image-density levels, but deteriorates with increasing density. Edge enhancement is also appreciable; it appears to decrease somewhat with increasing image density, but no simple relationship has yet been shown.