Tetralocular ovary and high silique width in yellow sarson lines of Brassica rapa (subspecies trilocularis) are due to a mutation in Bra034340 gene,a homologue of CLAVATA3 in Arabidopsis

Key message

Genetic locus for tetralocular ovary ( tet - o ) in Brassica rapa was identified and it was shown that the number of locules and width of silique are associated.

Abstract

Brassica rapa is a highly polymorphic species containing many vegetables and oleiferous types. An interesting group of oleiferous types is the yellow sarson group (subspecies trilocularis) grown mostly in eastern India. This group contains lines that have bilocular ovaries, a defining trait of Brassicaceae, but also lines that have tetralocular ovaries. Yellow sarson lines commonly have high silique width which is further enhanced in the tetralocular types. We mapped the locus influencing tetralocular ovary in B. rapa using three mapping populations (F₂, F₆ and F₇) derived from a cross between Chiifu (subspecies pekinensis, having bilocular ovary) and Tetralocular (having tetralocular ovary). QTL mapping of silique width was undertaken using the three mapping populations and a F₂ population derived from a cross between Chiifu and YSPB-24 (a bilocular line belonging to yellow sarson group). Qualitative mapping of the trait governing locule number (tet-o) in B. rapa mapped the locus to linkage group A4. QTL mapping for silique width detected a major QTL on LG A4, co-mapping with the tet-o locus in bilocular/tetralocular cross. This QTL was not detected in the bilocular/bilocular cross. Saturation mapping of the tet-o region with SNP markers identified Bra034340, a homologue of CLAVATA3 of Arabidopsis thaliana, as the candidate gene for locule number. A C → T transition at position 176 of the coding sequence of Bra034340 revealed co-segregation with the tetralocular phenotype. The study of silique related traits is of interest both for understanding evolution under artificial selection and for breeding of cultivated Brassica species.     

Combined use of bulked segregant analysis and microarrays reveals SNP markers pinpointing a major QTL for resistance to Phytophthora capsici in pepper

Key message

Bulked segregant analysis (BSA) using Affymetrix GeneChips revealed candidate genes underlying the major QTL for Phytophthora capsici resistance in Capsicum . Using the candidate genes, reliable markers for Phytophthora resistance were developed and validated.

Abstract

Phytophthora capsici L. is one of the most destructive pathogens of pepper (Capsicum spp.). Resistance of pepper against P. capsici is controlled by quantitative trait loci (QTL), including a major QTL on chromosome 5 that is the predominant contributor to resistance. Here, to maximize the effect of this QTL and study its underlying genes, an F₂ population and recombinant inbred lines were inoculated with P. capsici strain JHAI1-7 zoospores at a low concentration (3 × 10³/mL). Resistance phenotype segregation ratios for the populations fit a 3:1 and 1:1 (resistant:susceptible) segregation model, respectively, consistent with a single dominant gene model. Bulked segregant analysis (BSA) using Affymetrix GeneChips revealed a single position polymorphism (SPP) marker mapping to the major QTL. When this SPP marker (Phyto5SAR) together with other SNP markers located on chromosome 5 was used to confirm the position of the major QTL, Phyto5SAR showed the highest LOD value at the QTL. A scaffold sequence (scaffold194) containing Phyto5SAR was identified from the C. annuum genome database. The scaffold contained two putative NBS-LRR genes and one SAR 8.2A gene as candidates for contributing to P. capsici resistance. Markers linked to these genes were developed and validated by testing 100 F₁ commercial cultivars. Among the markers, Phyto5NBS1 showed about 90 % accuracy in predicting resistance phenotypes to a low-virulence P. capsici isolate. These results suggest that Phyto5NBS1 is a reliable marker for P. capsici resistance and can be used for identification of a gene(s) underlying the major QTL on chromosome 5.     

Deriving fluorometer-specific values of relative PSI fluorescence intensity from quenching of F 0 fluorescence in leaves of Arabidopsis thaliana and Zea mays

The effect of stepwise increments of red light intensities on pulse-amplitude modulated (PAM) chlorophyll (Chl) fluorescence from leaves of A. thaliana and Z. mays was investigated. Minimum and maximum fluorescence were measured before illumination (F ₀ and F _M, respectively) and at the end of each light step ( $ F^{\prime}_{0} $ and $ F^{\prime}_{\text{M}} $ , respectively). Calculated $ F^{\prime}_{0} $ values derived from F ₀, F _M and $ F^{\prime}_{\text{M}} $ fluorescence according to Oxborough and Baker (1997) were lower than the corresponding measured $ F^{\prime}_{0} $ values. Based on the concept that calculated $ F^{\prime}_{0} $ values are under-estimated because the underlying theory ignores PSI fluorescence, a method was devised to gain relative PSI fluorescence intensities from differences between calculated and measured $ F^{\prime}_{0} $ . This method yields fluorometer-specific PSI data as its input data (F ₀, F _M, $ F^{\prime}_{0} $ and $ F^{\prime}_{\text{M}} $ ) depend solely on the spectral properties of the fluorometer used. Under the present conditions, the PSI contribution to F ₀ fluorescence was 0.24 in A. thaliana and it was independent on the light acclimation status; the corresponding value was 0.50 in Z. mays. Correction for PSI fluorescence affected Z. mays most: the linear relationship between PSI and PSII photochemical yields was clearly shifted toward the one-to-one proportionality line and maximum electron transport was increased by 50 %. Further, correction for PSI fluorescence increased the PSII reaction center-specific parameter, 1/F ₀ ? 1/F _M, up to 50 % in A. thaliana and up to 400 % in Z. mays.     

Changes in stem water content influence sap flux density measurements with thermal dissipation probes

Key message

Stem WC may decline during the day. Zero-flow dT _m increases when WC decreases. Use of nighttime dT _m in the calculation of sap flux density during the day might introduce errors.

Abstract

There is increasing evidence of diel variation in water content of stems of living trees as a result of changes in internal water reserves. The interplay between dynamic water storage and sap flow is of current interest, but the accuracy of measurement of both variables has come into question. Fluctuations in stem water content may induce inaccuracy in thermal-based measurements of sap flux density because wood thermal properties are dependent on water content. The most widely used thermal method for measuring sap flux density is the thermal dissipation probe (TDP) with continuous heating, which measures the influence of moving sap on the temperature difference between a heated needle and a reference needle vertically separated in the flow stream. The objective of our study was to investigate how diel fluctuations in water content could influence TDP measurements of sap flux density. We analysed the influence of water content on the zero-flow maximum temperature difference, dT _m, which is used as the reference for calculating sap flux density, and present results of a dehydration experiment on cut branch segments of American sycamore (Platanus occidentalis L.). We demonstrate both theoretically and experimentally that dT _m increases when stem water content declines. Because dT _m is measured at night when water content is high, this phenomenon could result in underestimations of sap flux density during the day when water content is lower. We conclude that diel dynamics in water content should be considered when TDP is used to measure sap flow.     

Oxaloacetate decarboxylase from Acetobacter aceti

An oxaloacetate (OAA) decarboxylase (EC 4.1.1.3) has been purified 72-fold from Acetobacter aceti cells grown on ethanol, and its molecular weight was estimated to be about 80,000 by gel filtration. Several properties distinguished this enzyme from the OAA decarboxylase from A. xylinum:

1. It was not a constitutive enzyme; the activity was 6- to 20-fold higher in cells grown on a C₂ substrate (acetate or ethanol) than in cells grown on a C₃ compound (pyruvate or propionate).
2. The optimum pH was 7.5; a value of 5.6 was reported for the enzyme from A. xylinum.
3. The enzyme did not need a divalent cation and was not inhibited by EDTA.
4. The K _mvalue for OAA was found to be 0.22 mM. It was not affected by the addition of nicotinamide adenine dinucleotide.
5. The enzyme activity was neither inhibited by acetate nor by L-malate.

In addition, the OAA decarboxylase from A. aceti was insensitive to monovalent cations, avidin or acetyl coenzyme A.     

Sur l'espace topologique lié à une nouvelle théorie de l'apprentissage

There have been two contrasting doctrines concerning learning, more generally about acquisition of knowledge: empiricism and rationalism. The theory of learning in such a field as artificial intelligence seems to fall within the empiricist framework. On the hand, N. Chomsky and his followers have discussed, during the last decade, concerning learning, especially about language learning, from the rationalist point of view (Chomsky, 1965). The main feature in the rationalist approach toward a theory of learning lies in the speculation that in order to acquire knowledge it is indispensable for a learner to be endowed with “innate ideas”, and that “experience” in the external world are merely subsidiary types of information for the learner. If this is acceptable, we can inquire: Under what kind of innate ideas can the learner understand the structure of the external world? In our previous paper (Uesaka, Aizawa, Ebara, and Ozeki, 1973), we formalized this by introducing the mathematical notion of “learnability”, and gave a partial answer to the above inquiry. In this formalization we assumed that the set F of objects to be learned consists of mappings of N to itself, where N is the set of positive integers. Then, constructing a topological space (F, \(\mathcal{O}\) ) by an appropriate family \(\mathcal{O}\) of open sets, we observed that the notion of learnability can be well described in terms of topological properties of the learning space (F, \(\mathcal{O}\) ). Many problems must be solved, however, before we raise the theory to a complete model of the rationalist theory of learning. The topological study of the space (F, \(\mathcal{O}\) ) is, we believe, the first step toward this approach. In this context, we discuss the topological aspects of this space. Now we define \(\mathcal{O}\) as follows: By N ² we mean the direct product of two N's. Let s be a subset of N ². If, for any (x, y), (x′, y′) in s, x=x′ implies y=y′, then we say that s is single-valued. Let f ∈ F, If, for any (x, y) in s, y=f(x), then f is said to be on s, denoted as \(f\underline \supseteq s\) . Let \(\pi \left( s \right) = \left\{ {g;g \in F,g\underline \supseteq s} \right\}\) . A single-valued finite subset of N ² is called datum. Let D denote the family of all data. Let \(\mathcal{O}* = \left\{ \phi \right\} \cup \left\{ {\pi \left( d \right);d \in D} \right\}\) , and \(\mathcal{O}\) denote the family of all subsets of F, each of which is written as \(\mathop \cup \limits_\alpha W_{\alpha }\) , where W _α is in \(\mathcal{O}*\) . Then, it is easily seen that \(\mathcal{O}\) satisfies the axiom of the open system of a topological space. It is shown that the learning space (F, \(\mathcal{O}\) ) has the following properties:

1. It satisfies the first and the second countability axioms.
2. It is separable and is totally disconnected.
3. It is a Hausdorff space and, further, is regular and normal.
4. It is neither compact nor locally compact.
5. It is metrizable, or more precisely there exists a complete but not totally bounded metric space which is homeomorphic to learning space.
6. Any of its subspace can be embedded into its special subspace.

     

QTL mapping in autotetraploids using SNP dosage information

Key message

Dense linkage maps derived by analysing SNP dosage in autotetraploids provide detailed information about the location of, and genetic model at, quantitative trait loci.

Abstract

Recent developments in sequencing and genotyping technologies enable researchers to generate high-density single nucleotide polymorphism (SNP) genotype data for mapping studies. For polyploid species, the SNP genotypes are informative about allele dosage, and Hackett et al. (PLoS ONE 8:e63939, 2013) presented theory about how dosage information can be used in linkage map construction and quantitative trait locus (QTL) mapping for an F₁ population in an autotetraploid species. Here, QTL mapping using dosage information is explored for simulated phenotypic traits of moderate heritability and possibly non-additive effects. Different mapping strategies are compared, looking at additive and more complicated models, and model fitting as a single step or by iteratively re-weighted modelling. We recommend fitting an additive model without iterative re-weighting, and then exploring non-additive models for the genotype means estimated at the most likely position. We apply this strategy to re-analyse traits of high heritability from a potato population of 190 F₁ individuals: flower colour, maturity, height and resistance to late blight (Phytophthora infestans (Mont.) de Bary) and potato cyst nematode (Globodera pallida), using a map of 3839 SNPs. The approximate confidence intervals for QTL locations have been improved by the detailed linkage map, and more information about the genetic model at each QTL has been revealed. For several of the reported QTLs, candidate SNPs can be identified, and used to propose candidate trait genes. We conclude that the high marker density is informative about the genetic model at loci of large effects, but that larger populations are needed to detect smaller QTLs.     

Effect of hydration level in primary bean leaves on the activity of photosystems 1 and 2 in isolated chloroplasts

Water stress in the leaves was induced by gradual decreasing of substrate moisture in five-day cycles.The hydration level of the leaves was characterized by their water potential (ψ_w), osmotic potential (ψ_s), pressure potential ψ_p and water saturation deficit(ΔW _sat ).The activities of Photosystems 1 and 2 were determined polarographically with Pt/Ag(AgOH) electrode as changes in oxygen concentration in chloroplast suspensions. The shape of light curves of Hill reaction was not influenced by leaf (ψ_w), hence both quantum efficiency and dark phase of this process were affected in a similar manner by water deficit. The activities of both photosystems measured at saturating photon flux density declined with the lowering of leaf (ψ_w) (in the range from -5 to -14 x 10⁵ Pa) and the decrease in activity of Photosystem 2 was more rapid than that of Photosystem 1. The ratio of activities of Photosystems 1 and 2 was mildly enhanced by a lowering of (ψ_w), but it decreased with increasing age. The lowering of ψ_winduced lowering in the chlorophyll a/b ratio thus concealing the usual ontogenetic course of this ratio.     

Use of synteny to identify candidate genes underlying QTL controlling stomatal traits in faba bean (Vicia faba L.)

Key message

We have identified QTLs for stomatal characteristics on chromosome II of faba bean by applying SNPs derived from M. truncatula , and have identified candidate genes within these QTLs using synteny between the two species.

Abstract

Faba bean (Vicia faba L.) is a valuable food and feed crop worldwide, but drought often limits its production, and its genome is large and poorly mapped. No information is available on the effects of genomic regions and genes on drought adaptation characters such as stomatal characteristics in this species, but the synteny between the sequenced model legume, Medicago truncatula, and faba bean can be used to identify candidate genes. A mapping population of 211 F₅ recombinant inbred lines (Mélodie/2 × ILB 938/2) were phenotyped to identify quantitative trait loci (QTL) affecting stomatal morphology and function, along with seed weight, under well-watered conditions in a climate-controlled glasshouse in 2013 and 2014. Canopy temperature (CT) was evaluated in 2013 under water-deficit (CTd). In total, 188 polymorphic single nucleotide polymorphisms (SNPs), developed from M. truncatula genome data, were assigned to nine linkage groups that covered ~928 cM of the faba bean genome with an average inter-marker distance of 5.8 cM. 15 putative QTLs were detected, of which eight (affecting stomatal density, length and conductance and CT) co-located on chromosome II, in the vicinity of a possible candidate gene—a receptor-like protein kinase found in the syntenic interval of M. truncatula chromosome IV. A ribose-phosphate pyrophosphokinase from M. truncatula chromosome V, postulated as a possible candidate gene for the QTL for CTd, was found some distance away in the same chromosome. These results demonstrate that genomic information from M. truncatula can successfully be translated to the faba bean genome.     

Biosystematic study of Berlandiera (Compositae)

Berlandiera is revised to includeB. subacaulis, B. pumila, B. texana, andB. lyrata with its varietieslyrata andmacrophylla. All species may be induced to interbreed readily, producing F₁ progeny which are vigorous but with reduced fertility. Sympatric species produce natural hybrids which are proposed here asB. Xhumilis (=B. pumila XB. subacaulis) andB. Xbetonicifolia (=B. pumila XB. texana). All taxa investigated hadn = 15 chromosomes, including new counts forB. subacaulis and all six F₁ hybrids.     

ATP-driven succinate oxidation in the catabolism of Desulfuromonas acetoxidans

The oxidation of succinate with elemental sulphur in Desulfuromonas acetoxidans was investigated using a membrane preparation of this bacterium. The following results were obtained:

1. The preparation catalyzed the oxidation of succinate with sulphur and NAD. These reactions were dependent on ATP and were abolished by the presence of protonophores or dicyclohexylcarbodiimide (DCCD).
2. The membrane preparation also catalyzed the reduction of fumarate with H₂S or with NADH. These activities were not dependent on ATP and were not affected by protonophores or DCCD.
3. By extraction-reincorporation experiments it could be shown that menaquinone is involved in electron transport between H₂S and fumarate and between NADH and fumarate.
4. The membrane fraction catalyzed the reduction of the water-soluble menaquinone-analogue dimethylnaphthoquinone (DMN) by succinate, H₂S, or NADH, and the oxidation of DMNH₂ by fumarate. These activities were not dependent on the presence of menaquinone and were not influenced by ATP.
5. The activities involving succinate oxidation or fumarate reduction were similarly sensitive to 2(n-nonyl)-4-hydroxyquinoline-N-oxide, while H₂S and NADH oxidation by DMN were not affected by the inhibitor.

It is concluded that the catabolism of D. acetoxidans involves the energy-driven oxidation of succinate with elemental sulphur or NAD as electron acceptors and that menaquinone is a component of the electron transport chain catalyzing these reactions.     

Combined Effects of Lead and Acid Rain on Photosynthesis in Soybean Seedlings

To explore how lead (Pb) and acid rain simultaneously affect plants, the combined effects of Pb and acid rain on the chlorophyll content, chlorophyll fluorescence reaction, Hill reaction rate, and Mg²⁺-ATPase activity in soybean seedlings were investigated. The results indicated that, when soybean seedlings were treated with Pb or acid rain alone, the chlorophyll content, Hill reaction rate, Mg²⁺-ATPase activity, and maximal photochemical efficiency (F _v/F _m) were decreased, while the initial fluorescence (F ₀) and maximum quantum yield (Y) were increased, compared with those of the control. The combined treatment with Pb and acid rain decreased the chlorophyll content, Hill reaction rate, Mg²⁺-ATPase activity, F _v/F _m, and Y and increased F ₀ in soybean seedlings. Under the combined treatment with Pb and acid rain, the two factors showed additive effects on the chlorophyll content in soybean seedlings and exhibited antagonistic effects on the Hill reaction rate. Under the combined treatment with high-concentration Pb and acid rain, the two factors exhibited synergistic effects on the Mg²⁺-ATPase activity, F ₀, F _v/F _m, as well as Y. In summary, the inhibition of the photosynthetic process is an important physiological basis for the simultaneous actions of Pb and acid rain in soybean seedlings.     

A study on the mechanism of energy coupling in the redox chain

The present study demonstrates that the mitochondrial respiratory chain includes not three but four energy coupling sites, the fourth site being localized at the NADPH→NAD⁺ step.

1. The NADPH→NAD⁺-directed transhydrogenase reaction in sonicated beef heart submitochondrial particles energizes the particle membrane as judged by two membrane potential probes, i.e. uptake of a penetrating anion, phenyldicarbaundecaborane (PCB^?), and enhancement of anilinonaphthalene sulfonate (ANS^?) fluorescence.
2. The reverse reaction (NADH→NADP⁺) is accompanied by the oppositely directed anion movement, i.e. PCB^? efflux.
3. Being insensitive to rotenone, antimycin, cyanide, and oligomycin, both the influx and efflux of PCB^? coupled with transhydrogenase reaction can be prevented or reversed by uncouplers.
4. Equalization of concentrations of the transhydrogenase substrates and products also prevents (or reverses) the PCB^? influx coupled with oxidation of NADPH by NAD⁺, as well as the PCB^? efflux coupled with reduction of NADP⁺ by NADH.
5. The transhydrogenase-linked PCB^? uptake depends linearly on the energy yield of the oxidation reaction calculated according to formula $$\Delta G = RTln\frac{{[NADPH] x [NAD^ + ]}}{{[NADP^ + ] x [NADH]^ \cdot }}$$ No threshold value of Δ was found. Measurable PCB^? transport was still observed at Δ≤0.5 kcal/mole NADPH oxidized.
6. Partial uncoupling of transhydrogenase reaction and PCB^? transport, induced by low concentrations ofp-trifluoromethoxycarbonylcyanide phenylhydrazone (FCCP), dinitrophenol, or by removing coupling factor F₁, results in the decrease of the slope of the straight line showing the PCB^? uptake as a function of Δ. Oligomycin improves the coupling in F₁-deprived particles, the slope being increased. Rutamycin, dicyclohexylcarbodiimide (DCCD) and reconstitution of particles with F₁, also increase the coupling.
7. In phosphorylating particles oxidizing succinate by O₂, both the energy-dependent NADH→NADP⁺ hydrogen transfer and PCB^? influx possess equal sensitivity to FCCP, which is lower than the sensitivity of oxidative phosphorylation. Similarly, the decrease in the succinate oxidation rate induced by malonate arrests first phosphorylation and then under higher malonate concentration, PCB^? influx. The rate of NADPH→NAD⁺ transhydrogenase reaction was found to be lower than the threshold value of rate of succinate oxidation, still coupled with phosphorylation. Respectively, the values of PCB^? uptake under transhydrogenase reaction are lower than those inherent in phosphorylating oxidation of succinate.

The conclusion is made that the NADPH→NAD⁺-directed transhydrogenase reaction generates the membrane potential of the same polarity as respiration and ATP hydrolysis but of a lower magnitude (“plus” inside particles; the forward hydrogen transfer). The NADH→NADP⁺-directed transhydrogenase reaction forms the membrane potential of the opposite polarity (“minus” inside particles; the reverse hydrogen transfer). Under conditions used, the transhydrogenase-produced membrane potential proves to be too low to support ATP synthesis (and, most probably, the synthesis of any other high-energy compound) maintaining, nevertheless, some electrophoretic ion fluxes. A conclusion is made that transhydrogenase forms a membrane potential with no high-energy intermediates involved.     

Formyl-met-tRNA inff supMet,a questionable initiator tRNA in eukaryotic systems

Met-tRNA _inff ^supMet is a much more efficient initiator in cell-free eukaryotic protein synthesis than the formylated species. Chemically and enzymatically formylated Met-tRNA _inff ^supMet exhibit the same activity. In contrast acetyl Met-tRNA _inff ^supMet is unable to initiate polypeptides in vitro.     

Genetic polymorphisms of blood proteins in the troops of Japanese macaques,Macaca fuscata: IV. Erythrocyte esterase polymorphism inMacaca fuscata

Genetic variation at the locus controlling A₁ band of erythrocyte esterase was found in the Japanese macaque,Macaca fuscata. Existence of four alleles,Es-A ₁ ¹ ,Es-A ₁ ² ,Es-A ₁ ³ , andEs-A ₁ ⁴ , controlling the mobility of the band and codominance relation between them were postulated. A majority of the troops examined were monomorphic inEs-A ₁ 1-1 phenotype, and the variant phenotypes were observed to occur only in Yugawara-Ihama, Arashiyama, and Koshima areas.