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Abstract Background Next generation sequencing is transforming our understanding of transcriptomes. It can determine the expression level of transcripts with a dynamic range of over six orders of magnitude from multiple tissues, developmental stages or conditions. Patterns of gene expression provide insight into functions of genes with unknown annotation. Results The RNA Seq-Atlas presented here provides a record of high-resolution gene expression in a set of fourteen diverse tissues. Hierarchical clustering of transcriptional profiles for these tissues suggests three clades with similar profiles: aerial, underground and seed tissues. We also investigate the relationship between gene structure and gene expression and find a correlation between gene length and expression. Additionally, we find dramatic tissue-specific gene expression of both the most highly-expressed genes and the genes specific to legumes in seed development and nodule tissues. Analysis of the gene expression profiles of over 2,000 genes with preferential gene expression in seed suggests there are more than 177 genes with functional roles that are involved in the economically important seed filling process. Finally, the Seq-atlas also provides a means of evaluating existing gene model annotations for the Glycine max genome. Conclusions This RNA-Seq atlas extends the analyses of previous gene expression atlases performed using Affymetrix GeneChip technology and provides an example of new methods to accommodate the increase in transcriptome data obtained from next generation sequencing. Data contained within this RNA-Seq atlas of Glycine max can be explored at http://www.soybase.org/soyseq.

Abstract Background Soybean cyst nematode (Heterodera glycines, SCN) is the most economically damaging pathogen of soybean (Glycine max) in the U.S. The Rhg1 locus is repeatedly observed as the quantitative trait locus with the greatest impact on SCN resistance. The Glyma18g02680.1 gene at the Rhg1 locus that encodes an apparent leucine-rich repeat transmembrane receptor-kinase (LRR-kinase) has been proposed to be the SCN resistance gene, but its function has not been confirmed. Generation of fertile transgenic soybean lines is difficult but methods have been published that test SCN resistance in transgenic roots generated with Agrobacterium rhizogenes. Results We report use of artificial microRNA (amiRNA) for gene silencing in soybean, refinements to transgenic root SCN resistance assays, and functional tests of the Rhg1 locus LRR-kinase gene. A nematode demographics assay monitored infecting nematode populations for their progress through developmental stages two weeks after inoculation, as a metric for SCN resistance. Significant differences were observed between resistant and susceptible control genotypes. Introduction of the Rhg1 locus LRR-kinase gene (genomic promoter/coding region/terminator; Peking/PI 437654-derived SCN-resistant source), into rhg1- SCN-susceptible plant lines carrying the resistant-source Rhg4+ locus, provided no significant increases in SCN resistance. Use of amiRNA to reduce expression of the LRR-kinase gene from the Rhg1 locus of Fayette (PI 88788 source of Rhg1) also did not detectably alter resistance to SCN. However, silencing of the LRR-kinase gene did have impacts on root development. Conclusion The nematode demographics assay can expedite testing of transgenic roots for SCN resistance. amiRNAs and the pSM103 vector that drives interchangeable amiRNA constructs through a soybean polyubiqutin promoter (Gmubi), with an intron-GFP marker for detection of transgenic roots, may have widespread use in legume biology. Studies in which expression of the Rhg1 locus LRR-kinase gene from different resistance sources was either reduced or complemented did not reveal significant impacts on SCN resistance.

Abstract Background The nutritional and economic value of many crops is effectively a function of seed protein and oil content. Insight into the genetic and molecular control mechanisms involved in the deposition of these constituents in the developing seed is needed to guide crop improvement. A quantitative trait locus (QTL) on Linkage Group I (LG I) of soybean (Glycine max (L.) Merrill) has a striking effect on seed protein content. Results A soybean near-isogenic line (NIL) pair contrasting in seed protein and differing in an introgressed genomic segment containing the LG I protein QTL was used as a resource to demarcate the QTL region and to study variation in transcript abundance in developing seed. The LG I QTL region was delineated to less than 8.4 Mbp of genomic sequence on chromosome 20. Using Affymetrix® Soy GeneChip and high-throughput Illumina® whole transcriptome sequencing platforms, 13 genes displaying significant seed transcript accumulation differences between NILs were identified that mapped to the 8.4 Mbp LG I protein QTL region. Conclusions This study identifies gene candidates at the LG I protein QTL for potential involvement in the regulation of protein content in the soybean seed. The results demonstrate the power of complementary approaches to characterize contrasting NILs and provide genome-wide transcriptome insight towards understanding seed biology and the soybean genome.

Studies have indicated that exon and intron size and intergenic distance are correlated with gene expression levels and expression breadth. Previous reports on these correlations in plants and animals have been conflicting. In this study, next-generation sequence data, which has been shown to be more sensitive than previous expression profiling technologies, were generated and analyzed from 14 tissues. Our results revealed a novel dichotomy. At the low expression level, an increase in expression breadth correlated with an increase in transcript size because of an increase in the number of exons and introns. No significant changes in intron or exon sizes were noted. Conversely, genes expressed at the intermediate to high expression levels displayed a decrease in transcript size as their expression breadth increased. This was due to smaller exons, with no significant change in the number of exons. Taking advantage of the known gene space of soybean, we evaluated the positioning of genes and found significant clustering of similarly expressed genes. Identifying the correlations between the physical parameters of individual genes could lead to uncovering the role of regulation owing to nucleotide composition, which might have potential impacts in discerning the role of the noncoding regions. Key words: expression level, expression breadth, next-generation sequencing, physical clustering. Des etudes ont montre que la taille des introns et des exons ainsi que la distance intergeenique seraient corretees avec le niveau et l'etendue de l'expression geenique. Les etudes anteerieures sur ce sujet chez les plantes et les animaux se sont averees contradictoires. Dans cette etude, des domtoes de sequence de seconde generation, lesquelles fournissent des donnees transcriptomiques plus sensibles que celles obtenues a l'aide des techniques anteerieures, ont ete produites et analysees chez 14 tissus. Les resultats des auteurs revelent une nouvelle dichotomie. Chez les genes faiblement exprimes, un accroissement de l'etendue de l'expression etait correle avec un accroissement de la taille des transcrits attribuable a une augmentation du nombre d'exons et d'introns. Aucun changement quant a la taille des introns ou des exons n'a ete note;. Inversement, les genes exprimes de maniere intermeidiaire ou forte presentaient des transcrits dont la taille diminuait au fur et a mesure que s'accroissait l'etendue de leur expression. Cette reduction etait due a une reduction de la taille des exons, sans qu'il y ait eu reduction du nombre de ceux-ci. En tirant avantage de la connaissance de l'espace geenique chez le soya, les auteurs ont examine; le positionnement des genes et ont observe un groupement significatif des genes qui presentent un niveau d'expression semblable. L'identification de correlations entre les parameitres physiques de genes individuels pourrait permettre de mieux comprendre la re;gulation ge;nique de;coulant de la composition nucle;otidique, laquelle pourrait aider a discerner le role des regions non-codantes. Mots-cles: niveau d'expression, eetendue de l'expression, seequencage de seconde generation, groupement physique. [Traduit par la Redaction], Introduction The uniqueness of living organisms is dependent not only upon the suite of genic material available to them but also upon the subtleties of gene expression patterns. Some genes [...]

Brown stem rot (BSR) of soybean [Glycine max (L.) Merr.], caused by Phialophora gregata (Allington & D.W. Chamb.) W. Gams 1971, is an economically important disease prevalent in soybean producing regions of the north-central United States and Canada. To date, all BSR resistant genes identified are located on chromosome 16 (formerly molecular linkage group J). The objective of this study was to determine if four plant introductions from south-central China identified as BSR resistant have resistance genes mapping to the same location on chromosome 16 as previously mapped BSR resistance genes. The four plant introductions, PI 594637, PI 594638B, PI 594650A, and PI 594858B, were crossed to the BSR-susceptible cultivar 'Century 84' to develop four [F.sub.2] populations. Each segregating population and the parental lines were screened for BSR resistance in growth chamber conditions. The [F.sub.2:3] individual plants of each population were tested with the sire ale sequence repeat (SSR) markers Satt431 or Satt547, which map closely to BSR resistance quantitative trait loci (QTL) on chromosome 16. Associations between molecular data and phenotypic data used to validate QTL were analyzed using single factor ANOVA. Three of the four populations had markers on chromosome 16 significantly associated with BSR resistance with [R.sup.2] values from 24 to 48%. However, when marker Satt547 was regressed on BSR resistance in population PI 594637 x Century 84, no significant association was observed. This result suggests that PI 594637 could have a new BSR resistance gene. Transgressive segregation also was observed in this population, and highly BSR resistant progeny could be used in the development of BSR resistant cultivars. Additional research and testing in this population will be conducted to identify resistance QTL(s) from this source. doi: 10.2135/cropsci2010.03.0159

From 1970 to 2008 there were 2242 soybean [Glycine max (L) Merr.] cultivars registered in North America through U.S. Plant Variety Protection (PVP), U.S. utility patent, and journal registration. Of these, 80% were developed through proprietary and 20% through public programs. Our objective was to characterize the development and genetic diversity of North American soybean cultivars. The most frequently used germplasm for cultivar development were the cultivars Williams (parent used in last cross before inbreeding in 70 cultivars), A3127 (63), Essex (45), Amsoy (38), Corsoy (33), Wayne (30), Forrest (27), Hutcheson (25), MO13404 (23), and Bedford (23). Genetic diversity (1 - coefficient of parentage), estimated from pedigree lineage, was 0.89 overall. Genetic diversity was the same within public (0.89) and proprietary (0.89) cultivars. The cultivar A3127 is a major progenitor of recently developed proprietary cultivars registered from 1999 to 2008. Of these 494 cultivars, 23% have a genetic contribution of at least 25% from A3127. New cultivars were predominantly developed from the following crosses: two-parent (70% of cultivars developed), complex (12%), three-parent (5%), one backcross (5%), multiple (two, three, or four) backcrosses (3%), and five or greater backcrosses (2%). In comparisons where both parent and progeny were evaluated together, seed yield increased 3.2% per breeding cycle. In these comparisons, seed yield had a correlation of 0.29 with parental diversity. doi: 10.2135/cropsci2009.08.0456

The soybean aphid (Aphis glycines Matsumura) is a new invasive soybean [Glycine max (L.) Merr.] insect pest first identified in North America in 2000. A major aphid resistance gene Rag1 was identified and mapped from the maturity group VIII cultivar Dowling, and the gene has been introgressed into Midwest-adapted germplasm. The objective of this study was to test the associated effects of Rag1 on yield and several important agronomic traits in two elite Midwest-adapted soybean backgrounds. To do this, we tested two backcross populations that segregate for Rag1 with simple sequence repeat markers linked to the gene in field tests conducted in multiple environments with no detectable soybean aphid infestations. Across environments, Rag1 had no significant (P = 0.05) associated effects on yield, plant height, and lodging score in either population. However, Rag1 was significantly associated with a 2-d delay in maturity in one population. This delay in maturity is likely caused by linkage drag between Rag1 and gene(s) that delayed maturity. These results indicate that breeders can incorporate Rag1 into Midwest-adapted backgrounds without an associated yield reduction.

The soybean aphid (Aphis glycines Matsumura) is a major soybean [Glycine max (L.) Merr.] insect pest. Soybean plant introduction (PI) 200538 has strong resistance to the aphid. The objectives of our research were to determine the inheritance of resistance and to map gene(s) controlling resistance in PI 200538. [F.sub.2] populations developed from crosses between PI 200538 and three susceptible genotypes were tested for resistance and with DNA markers. [F.sub.2] plants from the cross 'lna' x PI 200538 segregated 114 resistant to 37 susceptible and [F.sub.2] plants from the cross 'Williams 82' x PI 200538 segregated 203 resistant to 65 susceptible when tested for resistance to soybean aphid biotype 1. [F.sub.2] plants from the cross LD02-4485 x PI 200538 segregated 167 resistant to 62 susceptible when tested for resistance to biotype 2. These populations fit a 3:1 genetic ratio (P = 0.89, 0.78, and 0.52, respectively) with resistance dominant over susceptibility. Segregation among [F.sub.2:3] families from the crosses supported the dominant resistance gene hypothesis. The gene mapped to soybean linkage group F, flanked by the simple sequence repeat marker loci Satt510, Soyhsp176, Satt114, and Sct_033, located in the same region as the aphid resistance gene Rag2. Since the resistance gene in PI 200538 also gave resistance to soybean aphid biotypes 1 and 2, it is possible that the gene is Rag2 and not a new aphid resistance gene. Therefore, PI 200538 may be an additional source of Rag2.

Soybean rust, caused by Phakopsora pachyrhizi (H. Sydow & Sydow), is a destructive soybean [Glycine max (L.) Merr.] disease and identification of new resistance genes is essential for effective rust management. Our research objectives were to map and confirm the location of resistance gene(s) in PI 594538A using a population of 98 [F.sub.3:4] lines from a cross between PI 594538A (reddish-brown [RB] lesions) and the susceptible cultivar Loda (tan [TAN] lesions). The lines were inoculated with the P. pachyrhizi isolate ZM01-1 from Zimbabwe. The RB resistance in PI 594538A mapped on linkage group G as a single dominant gene. This gene is likely an allele of Rpp1 or a new closely linked gene because it mapped within 1 cM of Rpp1 and ZM01-1 produced RB lesions on PI 594538A and TAN lesions on PI 200492, the original source of Rpp1. The mapping of the new Rpp1 allele, named Rpp1-b, was confirmed in a second population.

The soybean aphid [Aphis glycines Matsumura (Hemiptera: Aphididae)] is an invasive insect pest of soybean [Glycine max (L.) Merr.] that was first reported in North America in 2000. There are currently no reports of soybean aphid biotype diversity and this information is needed before aphid resistance genes are deployed. The objective of this research was to test for aphid biotype variation. The response of two A. glycines isolates, one collected in Ohio and the other in Illinois, were compared by infesting eight soybean genotypes in nonchoice tests. The same genotypes also were tested with the Ohio isolate using a choice test. In the nonchoice test, there was a significant (P < 0.0001) effect of aphid isolate, genotype, and a significant aphid isolate by soybean genotype interaction for the number of aphids per plant 10 and 15 d after infestation. The responses of the eight genotypes to the Ohio isolate in the choice test were similar to their responses in nonchoice tests. PI 200538 and PI 567597C were resistant to both the Ohio and Illinois isolates and will be useful sources of resistance to both isolates. These tests confirm that there are at least two distinct biotypes of A. glycines in North America.

The narrow genetic base of elite soybean, Glycine max (L.) Merr., germplasm may impede further attempts to improve grain yield and other important agronomic characters. Germplasm collections of wild soybean, Glycine soja Siebold & Zucc., are a source of genetic variability for soybean breeding programs. The objectives of this research were to use genetic markers to characterize diversity among 60 G. soja accessions collected in China and to compare this diversity with 18 U.S. ancestral soybean genotypes, 12 Chinese G. max plant introductions (PIs), and 47 elite soybean lines from the northern USA. These accessions were genotyped with a set of 72 simple sequence repeat markers. The G. soja accessions were found to contain more alleles per locus (17) than the U.S. ancestral genotypes (5.8), the Chinese PIs (5.5), or the elite lines (4.5). Multivariate analyses were able to separate the G. max lines from the G. soja accessions and identify the most diverse subset of G. soja accessions. Multidimensional scaling separated G. soja accessions from high and low latitudes, while Ward's clustering method separated the G. soja accessions into distinct clusters that tended to include accessions from similar geographical regions. These data will be useful to breeders selecting G. soja accessions as parents in a breeding program and for establishing a core collection of G. soja to be used in future research.

The occurrence of sudden death syndrome (SDS), caused by the fungus Fusarium solani (Mart.) Sacc. f. sp. glycines (FSG) (syn. Fusarium virguliforme Akoi, O'Donnell, Homma and Lattanzi), is unpredictable in soybean [Glycine max (L.) Merr.] field trials making it difficult to evaluate soybean for resistance to the pathogen. Our objective was to evaluate the effect of field inoculation, soil compaction, and irrigation on the occurrence and severity of SDS symptoms. Six inoculation treatments were tested which included applications of FSG-infested grain planted in the furrow with the soybean seed, broadcasted and incorporated into the soil before planting, or placed below the soybean seed just before planting. Soil was compacted by driving a tractor across the field once in early spring. Irrigation treatments were applied at combinations of growth stages V3, V7, R3, R4, and/or R5. Significant increases in foliar SDS severity were observed from inoculation and irrigation treatments (P < 0.05), but not from compaction treatments. The inoculation treatments that placed inoculum close to the seed resulted in the greatest foliar severity. Irrigation treatments during mid to late reproductive growth stages resulted in significant increases in SDS foliar symptom development. These results increase our understanding of what environmental conditions increase SDS field symptoms and will be useful to researchers establishing SDS field nurseries.

The soybean cyst nematode (SCN) (Heterodera glycines Ichinohe) continues to be the most damaging soybean pest [Glycine max (L.) Merr.] in the USA. A major gene that provides partial resistance to SCN is rhg1, which is located on linkage group (LG) G. The objectives of this study were to test the effect of rhg1 on SCN reproduction in both the field and greenhouse and on agronomic traits in the field. Two populations of near isogenic lines (NILs) that segregated for rhg1 were developed to test the effect of the gene. These NIL populations were tested for their ability to support SCN cyst development in a thermo-regulated water bath in a greenhouse and egg production estimated from soil samples taken from each plot in field tests. The NIL populations were evaluated for agronomic traits in field plots to determine the associated effects of rhg1 on these traits. In the greenhouse, NILs predicted to be carrying the resistance allele for rhg1 on the basis of a linked marker supported significantly (P < 0.01) fewer cysts than NILs carrying the susceptibility allele. In field tests, the final egg population density (Pf) was significantly lower and there was a smaller reproductive rate (Rf) in NILs carrying the resistance allele at rhg1 than susceptible NILs for both populations across and within environments in 2003. In only one population did the resistant NILs out-yield the susceptible NILs, and this occurred only when the initial SCN pressure was high [>500 SCN eggs [(100 [cm.sup.3] soil).sup.-1]]. These results show that resistance at rhg1 can have a large effect on SCN reproduction and may result in a significant yield increase., THE SCN RESISTANCE GENES in modern soybean cultivars in the USA can be traced to only a few plant introductions (PIs). This is especially true in the Midwest where PI [...]

Soybean cyst nematode (SCN) (Heterodera glycines Ichinohe), the most destructive pest of soybean [Glycine max (L.) Merrill], is estimated to be responsible for almost nine million megagrams in annual yield loss worldwide. Host plant resistance is the most cost-effective and environmentally friendly method of controlling SCN. Resistance is present among soybean plant introductions (PIs) and related wild species, such as Glycine soja Sieb. and Zucc. Molecular marker technology has ushered in a decade devoted to the identification and characterization of quantitative trait loci (QTL) underlying SCN. These genetic mapping efforts uncovered numerous locations of SCN resistance QTL in many PIs. In more than a decade of mapping SCN resistance QTL, there is some consistency in the results. In almost all studies involving various sources of resistance, the QTL conferring the greatest level of resistance mapped to the region containing rhg1 on linkage group (LG) G. In addition, a major resistance QTL was mapped in many sources to the region containing Rhg4 on LG A2. The mapping of QTL to these regions from many sources suggests that these sources may have resistance genes in common, which has caused concern over the possible dependence on a few resistance genes. Recently, two independent research groups reported cloning candidate genes for rhg1 and Rhg4. Despite these advances, there is some degree of trepidation, especially in the public sector, on the use of rhg1 and Rhg4 genetic mapping and cloning information in SCN resistance breeding because of intellectual property issues., SOYBEAN CYST NEMATODE is estimated to cause the greatest yield loss to soybean compared to any other pest worldwide. Most recent estimates include a loss of 7.6 million megagrams in [...]