A major and stable QTL associated with seed weight in soybean across multiple environments and genetic backgrounds

Key message

We detected a QTL for single seed weight in soybean that was stable across multiple environments and genetic backgrounds with the use of two recombinant inbred line populations.

Abstract

Single seed weight (SSW) in soybean is a key determinant of both seed yield and the quality of soy food products, and it exhibits wide variation. SSW is under genetic control, but the molecular mechanisms of such control remain unclear. We have now investigated quantitative trait loci (QTLs) for SSW in soybean and have identified such a QTL that is stable across multiple environments and genetic backgrounds. Two populations of 225 and 250 recombinant inbred lines were developed from crosses between Japanese and US cultivars of soybean that differ in SSW by a factor of ~2, and these populations were grown in at least three different environments. A whole-genome panel comprising 304 simple sequence repeat (SSR) loci was applied to mapping in each population. We identified 15 significant QTLs for SSW dispersed among 11 chromosomes in the two populations. One QTL located between Sat_284 and Sat_292 on chromosome 17 was detected (3.6 < LOD < 14.1) in both populations grown in all environments. This QTL, tentatively designated qSw17-1, accounted for 9.4–20.9 % of phenotypic variation in SSW, with a dominant allele being associated with increased SSW. Given its substantial effect on SSW, qSw17-1 is an attractive target for positional cloning, and SSR markers closely associated with this locus may prove useful for marker-assisted selection for SSW control in soybean.     

Using the Guttman scale to define and estimate measurement error in items over time: the case of cognitive decline and the meaning of "points lost"

We used a Guttman model to represent responses to test items over time as an approximation of what is often referred to as "points lost" in studies of cognitive decline or interventions. To capture this meaning of "point loss", over four successive assessments, we assumed that once an item is incorrect, it cannot be correct at a later visit. If the loss of a point represents actual decline, then failure of an item to fit the Guttman model over time can be considered measurement error. This representation and definition of measurement error also permits testing the hypotheses that measurement error is constant for items in a test, and that error is independent of "true score", which are two key consequences of the definition of "measurement error"--and thereby, reliability--under Classical Test Theory. We tested the hypotheses by fitting our model to, and comparing our results from, four consecutive annual evaluations in three groups of elderly persons: a) cognitively normal (NC, N?=?149); b) diagnosed with possible or probable AD (N?=?78); and c) cognitively normal initially and a later diagnosis of AD (converters, N?=?133). Of 16 items that converged, error-free measurement of "cognitive loss" was observed for 10 items in NC, eight in converters, and two in AD. We found that measurement error, as we defined it, was inconsistent over time and across cognitive functioning levels, violating the theory underlying reliability and other psychometric characteristics, and key regression assumptions.     

The three-dimensional structure of septum site-determining protein MinD from Pyrococcus horikoshii OT3 in complex with Mg-ADP

BACKGROUND: In Escherichia coli, the cell division site is determined by the cooperative activity of min operon products MinC, MinD, and MinE. MinC is a nonspecific inhibitor of the septum protein FtsZ, and MinE is the supressor of MinC. MinD plays a multifunctional role. It is a membrane-associated ATPase and is a septum site-determining factor through the activation and regulation of MinC and MinE. MinD is also known to undergo a rapid pole-to-pole oscillation movement in vivo as observed by fluorescent microscopy. RESULTS: The three-dimensional structure of the MinD-2 from Pyrococcus horikoshii OT3 (PH0612) has been determined at 2.3 A resolution by X-ray crystallography using the Se-Met MAD method. The molecule consists of a beta sheet with 7 parallel and 1 antiparallel strands and 11 peripheral alpha helices. It contains the classical mononucleotide binding loop with bound ADP and magnesium ion, which is consistent with the suggested ATPase activity. CONCLUSIONS: Structure analysis shows that MinD is most similar to nitrogenase iron protein, which is a member of the P loop-containing nucleotide triphosphate hydrolase superfamily of proteins. Unlike nitrogenase or other member proteins that normally work as a dimer, MinD was present as a monomer in the crystal. Both the 31P NMR and Malachite Green method exhibited relatively low levels of ATPase activity. These facts suggest that MinD may work as a molecular switch in the multiprotein complex in bacterial cell division.     

Synergistic activation of the Arabidopsis NADPH oxidase AtrbohD by Ca2+ and phosphorylation

Plant respiratory burst oxidase homolog (rboh) proteins, which are homologous to the mammalian 91-kDa glycoprotein subunit of the phagocyte oxidase (gp91(phox)) or NADPH oxidase 2 (NOX2), have been implicated in the production of reactive oxygen species (ROS) both in stress responses and during development. Unlike mammalian gp91(phox)/NOX2 protein, plant rboh proteins have hydrophilic N-terminal regions containing two EF-hand motifs, suggesting that their activation is dependent on Ca(2+). However, the significance of Ca(2+) binding to the EF-hand motifs on ROS production has been unclear. By employing a heterologous expression system, we showed that ROS production by Arabidopsis thaliana rbohD (AtrbohD) was induced by ionomycin, which is a Ca(2+) ionophore that induces Ca(2+) influx into the cell. This activation required a conformational change in the EF-hand region, as a result of Ca(2+) binding to the EF-hand motifs. We also showed that AtrbohD was directly phosphorylated in vivo, and that this was enhanced by the protein phosphatase inhibitor calyculin A (CA). Moreover, CA itself induced ROS production and dramatically enhanced the ionomycin-induced ROS production of AtrbohD. Our results suggest that Ca(2+) binding and phosphorylation synergistically activate the ROS-producing enzyme activity of AtrbohD.     

Heme content of recombinant catalase from Psychrobacter sp. T-3 altered by host Escherichia coli cell growth conditions

The catalase gene of Psychrobacter sp. T-3 was cloned, and the gene product (PktA) was overexpressed in Escherichia coli. The specific activity of the purified PktA was slightly lower than that of the native purified enzyme obtained from Psychrobacter sp. T-3. Spectrophotometric measurements of the purified enzymes suggested that the recombinant PktA contains a mixture of heme b and d, although the native enzyme contains the sole heme b. An addition of the heme precursor 5-aminolevulinic acid (ALA) to the medium increased the heme b content of the recombinant PktA, and the resulting enzyme showed higher specific activity than the native enzyme. This is the first report that shows the heme content of overproduced catalase altered by the host cell growth conditions.     

Aggregated seed dispersal by wreathed hornbills at a roost site in a moist evergreen forest of Thailand

Hornbills (Bucerotidae) are widely regarded as important seed dispersers in tropical forests in Africa and Asia. We investigated how the roosting behavior of wreathed hornbills (Aceros undulatus) influences seed deposition and seedling survival at a roost site in a moist evergreen forest of Khao Yai National Park, Thailand. Fallen fruits and seeds were collected in traps that were placed around a roosting site for 14 months, and seedlings were monitored in adjacent quadrats for 3 years. Seedfall and seedlings of species represented in the hornbill diet occurred at significantly higher densities in the traps and quadrats located beneath the crown of the roosting tree than in those located beyond the crown. With the exception of Cinnamomum subavenium, the seeds and seedlings of most diet species rarely survived beyond the first year. The quality of hornbill dispersal to this roosting site may be poor due to the highly concentrated seedfall, which results in high seed and seedling mortality. However, the number of seeds deposited by each hornbill each day at roosting sites is relatively low. Wreathed hornbills are primarily scatter dispersers during the day and probably serve as agents of seed dispersal in the moist evergreen forest of Khao Yai.     

Stress-induced environmental changes in a single cell as revealed by fluorescence lifetime imaging.

The fluorescence lifetime image of HeLa cells expressing an enhanced green fluorescent protein (EGFP)-fusion protein changes under stress, which allows noninvasive determination of the status of individual cells.