SummaryLinear increases in light interception, energy conversion, and partitioning efficiencies have driven past yield gains in soybean. In modern cultivars, canopy light interception and harvest index are reaching theoretical maximum values.

Soybean (Glycine max Merr.) is the world's most widely grown legume and provides an important source of protein and oil. Global soybean production and yield per hectare increased steadily over the past century with improved agronomy and development of cultivars suited to a wide range of latitudes. In order to meet the needs of a growing world population without unsustainable expansion of the land area devoted to this crop, yield must increase at a faster rate than at present. Here, the historical basis for the yield gains realized in the past 90 years are examined together with potential metabolic targets for achieving further improvements in yield potential. These targets include improving photosynthetic efficiency, optimizing delivery and utilization of carbon, more efficient nitrogen fixation and altering flower initiation and abortion. Optimization of investment in photosynthetic enzymes, bypassing photorespiratory metabolism, engineering the electron transport chain and engineering a faster recovery from the photoprotected state are different strategies to improve photosynthesis in soybean. These potential improvements in photosynthetic carbon gain will need to be matched by increased carbon and nitrogen transport to developing soybean pods and seeds in order to maximize the benefit. Better understanding of control of carbon and nitrogen transport along with improved knowledge of the regulation of flower initiation and abortion will be needed to optimize sink capacity in soybean. Although few single targets are likely to deliver a quantum leap in yields, biotechnological advances in molecular breeding techniques that allow for alteration of the soybean genome and transcriptome promise significant yield gains.

Efficient methods for accurate and meaningful high-throughput plant phenotyping are limiting the development and breeding of stress-tolerant crops. A number of emerging techniques, specifically remote sensing methods, have been identified as promising tools for plant phenotyping. These remote sensing methods can be used to accurately and rapidly relate variations in leaf optical properties with important plant characteristics, such as chemistry, morphology, and photosynthetic properties at the leaf and canopy scales. In this study, we explored the potential to utilize optical (λ = 500-2,400 nm) near-surface remote sensing reflectance spectroscopy to evaluate the effects of ozone pollution on photosynthetic capacity of soybean (Glycine max Merr.). The research was conducted at the Soybean Free Air Concentration Enrichment (SoyFACE) facility where we subjected plants to ambient (44 nL L(-1)) and elevated ozone (79-82 nL L(-1) target) concentrations throughout the growing season. Exposure to elevated ozone resulted in a significant loss of productivity, with the ozone-treated plants displaying a ~30 % average decrease in seed yield. From leaf reflectance data, it was also clear that elevated ozone decreased leaf nitrogen and chlorophyll content as well as the photochemical reflectance index (PRI), an optical indicator of the epoxidation state of xanthophyll cycle pigments and thus physiological status. We assessed the potential to use leaf reflectance properties and partial least-squares regression (PLSR) modeling as an alternative, rapid approach to standard gas exchange for the estimation of the maximum rates of RuBP carboxylation (V c,max), an important parameter describing plant photosynthetic capacity. While we did not find a significant impact of ozone fumigation on V c,max, standardized to a reference temperature of 25 °C, the PLSR approach provided accurate and precise estimates of V c,max across ambient plots and ozone treatments (r (2) = 0.88 and RMSE = 13.4 μmol m(-2) s(-1)) based only on the variation in leaf optical properties and despite significant variability in leaf nutritional status. The results of this study illustrate the potential for combining the phenotyping methods used here with high-throughput genotyping methods as a promising approach for elucidating the basis for ozone tolerance in sensitive crops.

To investigate the genetic factors underlying a major quantitative trait locus (QTL) contributing to low seed stachyose content in two separate populations derived from soybean [Glycine max (L.) Merr.] line PI200508, the recently released ‘Williams 82’ whole genome shotgun (WGS) sequence was exploited for candidate gene discovery. The physical interval containing a low stachyose QTL from PI200508 was identified in the WGS, and screened for areas that could be exploited for linkage mapping purposes. Microsatellite sequences designed in these areas were used to develop new markers, creating tighter linkage with the QTL. Examination of the Williams 82 sequence in this interval and the corresponding glyma0.1b gene model, available through the Phytozome website (http://www.phytozome.org), revealed one candidate gene with significant homology to previously characterized galactosyltransferase genes from Arabidopsis, pea, and cucumber. Sequencing of the annotated coding region for this gene revealed a single unique sequence polymorphism between PI200508, and lines exhibiting wild‐type expression of stachyose content. The mutant phenotype appears to have arisen from a 3 bp deletion, and is easily distinguished from the wild‐type allele via a marker presented in this study. This mutation‐specific marker explained 88 to 94% of the phenotypic variation for seed stachyose content, and 76% for seed sucrose content, traits that exhibited a strong negative correlation in this study (p < 0.01).

Helicobacter pylori is the dominant member of the gastric microbiota and has been associated with an increased risk of gastric cancer and peptic ulcers in adults. H. pylori populations have migrated and diverged with human populations, and health effects vary. Here, we describe the whole genome of the cag-positive strain V225d, cultured from a Venezuelan Piaroa Amerindian subject. To gain insight into the evolution and host adaptation of this bacterium, we undertook comparative H. pylori genomic analyses. A robust multiprotein phylogenetic tree reflects the major human migration out of Africa, across Europe, through Asia, and into the New World, placing Amerindian H. pylori as a particularly close sister group to East Asian H. pylori. In contrast, phylogenetic analysis of the host-interactive genes vacA and cagA shows substantial divergence of Amerindian from Old World forms and indicates new genotypes (e.g., VacA m3) involving these loci. Despite deletions in CagA EPIYA and CRPIA domains, V225d stimulates interleukin-8 secretion and the hummingbird phenotype in AGS cells. However, following a 33-week passage in the mouse stomach, these phenotypes were lost in isolate V225-RE, which had a 15-kb deletion in the cag pathogenicity island that truncated CagA and eliminated some of the type IV secretion system genes. Thus, the unusual V225d cag architecture was fully functional via conserved elements, but the natural deletion of 13 cag pathogenicity island genes and the truncation of CagA impaired the ability to induce inflammation.Helicobacter pylori is a microaerophilic bacterium of the Epsilonproteobacteria that has colonized the stomach since early in human evolution (45) and diverged with ancient human migrations (24, 45, 92). Thus, several major H. pylori populations, such as hpAfrica1, hpEurope, hspEAsia, and hspAmerind, whose names indicate their original geographic associations (45, 51), have been defined. In particular, similarities between the hspAmerind and hspEAsia populations suggest that the first colonizers of the New World brought H. pylori with them (24, 28). With recent mixing of human groups, H. pylori populations are also mixing and competing, with an apparent dominance by the hpEurope population at least in Latin America (19).H. pylori usually does not cause illness, but colonization with strains bearing the cag (cytotoxin-associated gene) pathogenicity island (cag PAI) (3,7,25,52,57,61,63) is associated with an increased risk of noncardia gastric adenocarcinoma and peptic ulcer disease (56,64). Nonetheless, a high prevalence of cag-positive H. pylori strains occurs concurrently with low gastric cancer rates in Africa (40) and some regions in Latin America, such as the Venezuelan savannas and Amazonas (29,53). Moreover, clinical and epidemiological data provide evidence for an inverse relationship between H. pylori colonization and the prevalence of certain metabolic disorders, esophageal diseases, asthma and allergic disorders, and acute infectious diseases, as well as a direct relationship wit...

Phytophthora root and stem rot of soybean, caused by Phytophthora sojae Kaufmann & Gerdemann, is a serious limitation to soybean [Glycine max (L.) Merr.] production in the USA. Partial resistance or field resistance to P. sojae in soybean is effective against multiple races of the pathogen and is a form of incomplete resistance. An interspecific recombinant inbred line (RIL) population consisting of 298 individuals derived from the cross of V71–370 by PI407162 was inoculated with the P. sojae isolate C2S1 using the slant board technique in three separate experiments (designated as 2005, 2006a, and 2006b). In each replication, seven day old seedlings from each RIL were inoculated and lesion lengths were recorded 7 d later to assess partial resistance with three replications for the 2005 and 2006a experiments and one replication for the 2006b screening. Interval mapping located a lesion length QTL on each of the molecular linkage groups (MLGs)–J (chrom. 16),‐I (chrom. 20) and–G (chrom. 18) in all three experiments. The lesion length QTL on MLG‐J accounted for 32, 42, and 22% of the phenotypic variation in the 2005, 2006a and 2006b experiments, respectively. Mapped QTL locations in the current study provide breeders with new sources of P. sojae resistance and suggest that new sources may be identified in soybean germplasm.

Since its discovery in the early 1960's, abscisic acid (ABA) has received considerable attention as an important phytohormone, and more recently, as a candidate medicinal in humans. In plants it has been shown to regulate important physiological processes such as response to drought stress, and dormancy. The discovery of ABA synthesis in animal cells has generated interest in the possible parallels between its role in plant and animal systems. The importance of this molecule has prompted the development of several methods for the chemical synthesis of ABA, which differ significantly from the biosynthesis of ABA in plants through the mevalonic acid pathway. ABA recognition in plants has been shown to occur at both the intra- and extracellularly but little is known about the perception of ABA by animal cells. A few ABA molecular targets have been identified in vitro (e.g., calcium signaling, G protein-coupled receptors) in both plant and animal systems. A unique finding in mammalian systems, however, is that the peroxisome proliferator-activated receptor, PPAR gamma, is upregulated by ABA in both in vitro and in vivo studies. Comparison of the human PPAR gamma gene network with Arabidopsis ABA-related genes reveal important orthologs between these groups. Also, ABA can ameliorate the symptoms of type II diabetes, targeting PPAR gamma in a similar manner as the thiazolidinediones class of anti-diabetic drugs. The use of ABA in the treatment of type II diabetes, offers encouragement for further studies concerning the biomedical applications of ABA.

Soybean mosaic virus (SMV) is a prevalent virus infecting soybean (Glycine max L. Merr) worldwide. The incorporation of Rsv4, conferring resistance to all currently known strains in the United States, can assist in creating durable virus resistance in soybean. Additionally, lines heterozygous at the Rsv4 locus often express a late susceptible phenotype, showing symptoms only in mid to late vegetative growth. In this study the wholegenome shotgun sequence (WGS) of soybean was utilized for fi ne mapping and examining potential Rsv4 gene candidates in two populations. Six markers, designed from the WGS, were used to localize Rsv4 in the same, 1.3-cM region in both mapping populations, a physical interval of less than 100 kb on chromosome 2. This region contained no sequences previously related to virus resistance, namely nucleotide binding site-leucine rich repeat gene sequences or eukaryotic translation initiation factors. Instead, sequence analysis revealed several predicted transcription factors and unknown protein products. We conclude that Rsv4 likely belongs to a new class of resistance genes that interfere with viral infection and cell-to-cell movement, and delay vascular movement.