Genetic Diversity and Structure of Two Prominent Zebu Cattle Breeds Adapted to the Arid Region of India Inferred from Microsatellite Polymorphism

This study aims to assess the genetic diversity and population structure of two major zebu dairy breeds (Tharparkar and Rathi) adapted to the arid region of Rajasthan state of India. Various variability estimates indicate the existence of sufficient within-breed genetic diversity. Mean estimates of F-statistics are significantly different from zero: F _IS = 0.112 ± 0.029, F _IT = 0.169 ± 0.033, F _ST = 0.065 ± 0.017. The overall positive value of F _IS (0.112) and an F _IT value (0.169) that is more than the F _ST (0.065) indicate departure from random mating. The drift-based estimates reflect a moderate yet significant level of breed differentiation between the Tharparkar and Rathi breeds. The evaluation of an exact test, showing that allele frequencies across all the loci differed significantly, supports the population differentiation. This is paralleled by the outcome of neighbor-joining clustering based on allele-sharing distance measures. The allocation of a high percentage of individuals (95.7%) to their population of origin and correspondence analysis further substantiates the existence of a cohesive genetic structure in both the breeds.     

Genetics of complement C4. Two homoduplication haplotypes C4S C4S and C4F C4F in a family

Summary A family in which two homoduplicated C4 haplotypes (or supergenes) segregate is described. One haplotype C4F ^* 3 C4F ^*2.2 is composed of two C4F alleles and the other C4S ^* 5.1 C4S ^*1 of two C4S alleles. The C4F duplication haplotype is a partial inhibitor of the Rodgers antigen, and judged from our family and population material, it seems to be rather frequent and associated with HLAB ^*35, Bf ^* F, and HLAD/DR ^*1. The C4S duplication haplotype is Rg(a-) and is not identified in individuals without another S, Ch(a+) variant.This work was supported by grant No 12-1727 from the Danish Medical Research Council     

Limitation to Carbon Assimilation of Two Perennial Species in Semi-Arid South-East Spain

Diurnal and seasonal changes of net photosynthetic rate (P_n) and the efficiency of photosystem 2 (F_v/F_m) were measured on two perennial species growing on a soil catena in semi-arid south-east Spain. Stipa tenacissima, a tussock grass, grows on shallow soil at the top of the catena and Retama sphaerocarpa, a leguminous shrub, grows in the valley bottom. A linear relationship was found between light saturated photosynthetic rates (P_max) and diffusive leaf conductance (g_l) in both Retama and Stipa indicating that the intercellular CO₂ concentration (c_i) was maintained constant in both species diurnally. Relatively high values of calculated c_i in Retama cladodes suggested that was not the primary limitation to carbon assimilation. F_v/F_m for the two species when well watered was around 0.8. Although Retama cladodes maintained this value throughout the year, F_v/F_m decreased to a minimum of 0.43 in Stipa leaves, at the end of the dry season. Our data suggest that plants in the Rambla Honda can substantially reduce transpiration without reducing photosynthetic rates to the same extent by closing their stomata, because P_n is reduced primarily by high respiration, decreased mesophyll conductance and by photoinhibition or permanent damage of photosystem 2.     

Two forms of sustained xanthophyll cycle-dependent energy dissipation in overwintering Euonymus kiautschovicus

Seasonal differences in PSII efficiency (F_v/F_m), the conversion state of the xanthophyll cycle (Z + A)/ (V + A + Z), and leaf adenylate status were investigated in Euonymus kiautschovicus. On very cold days in winter, F_v/F_m assessed directly in the field remained low and Z + A high throughout day and night in both sun and shade leaves. Pre-dawn transfer of leaves from subfreezing temperatures in the field to room temperature revealed that recovery (increases in F_v/F_m and conversion of Z + A to violaxanthin) consisted of one, rapid phase in shade leaves, whereas in sun leaves a rapid phase was followed by a slow phase requiring days. The pre-dawn ATP/ADP ratio, as well as that determined at midday, was similar when comparing overwintering leaves with those sampled in the summer, although pre-dawn levels of ATP + ADP were elevated in all leaves during winter relative to summer. After a natural transition to warmer days during the winter, pre-dawn F_v/F_m and Z + A in shade leaves had returned to values typical for summer, whereas in sun leaves F_v/F_m and Z + A levels remained intermediate between the cold day in winter and the summer day. Thus two distinct forms of sustained (Z + A)-dependent energy dissipation were identified based upon their differing characteristics. The form that was sustained on cold days but relaxed rapidly upon warming occurred in all leaves and may result from maintenance of a low lumenal pH responsible for the nocturnal engagement of (Z + A)-dependent thermal dissipation exclusively on very cold days in the winter. The form that was sustained even upon warming and correlated with slow Z + A to violaxanthin conversion occurred only in sun leaves and may represent a sustained engagement of (Z + A)-dependent energy dissipation associated with an altered PSII protein composition. In the latter, warm-sustained form, uncoupler or cycloheximide infiltration had no effect on the slow phase of recovery, but lincomycin infiltration inhibited the slow increase in F_v/F_m and the conversion of Z + A to violaxanthin.     

Two classes of Flac mutants insensitive to transfer inhibition by an F-like R factor

Summary Mutants of Flac episomes whose transfer is no longer inhibited by the fi ⁺ R factor R100 are shown to be of at least two types. One is recessive in transient heterozygotes containing Fhis and R100 in addition to the Flac mutant. The other is dominant. The occurrence of recessive mutants suggests that inhibition of F transfer by R100 requires an F-specified gene product in addition to that produced by the R factor. Synthesis of the F product or its interaction with the R100 product to give the true inhibitor seems to be a slow process. Since the inhibitor and mutations of the transfer gene traJ both affect a plasmid-specific transfer product, F-pilus formation, and surface exclusion, we propose that the inhibitor prevents the synthesis or function of the traJ product.Supported by a George Murray Scholarship from the University of Adelaide, Australia.     

Two quantitative trait loci affecting progressive hearing loss in 101/H mice

Although recent progress in identifying genes involved in deafness has been remarkable, the genetic basis of progressive hearing loss (or age-related hearing loss) is poorly understood because of the extreme difficulty in studying such a late-onset, complex disease in human populations. Several inbred strains of mice such as 129P1/ReJ, C57BL/6J, DBA/2J, and BALB/cByJ have been reported to exhibit age-related hearing loss and provide valuable models for human nonsyndromic progressive deafness. In this article we show that 101/H mice also exhibit progressive deafness with early onset. Linkage analysis of F₂ populations derived from crosses between the 101/H and the MAI/Pas and MBT/Pas wild-derived mice suggested at least two major quantitative trait loci (QTLs) that influence progressive hearing loss. A first QTL, designated Phl1, was mapped with a maximum LOD score of 6.7 to the centromeric region of Chromosome 17, where no deafness-related QTL has been mapped so far. A second QTL, designated Phl2, mapped to Chromosome 10 and exhibited a maximum LOD score of 5.3. The map position of Phl2 near the well-known QTL of age-related hearing loss (Ahl) suggested the possibility of allelism, although the Ahl mutation itself did not segregate in these crosses. Finally, we found some evidence of epistatic interaction between Phl1 and Phl2. Electronic Supplementary Material Electronic Supplementary material is available for this article at and accessible for authorised users. Tomoji Mashimo, Alexandra E. Erven, and Sarah L. Spiden contributed equally to this work.     

Two recessive genes controlling thermophotoperiod-sensitive male sterility in wheat

Male sterility of wheat-breeding line 337S (Triticum aestivum L.) is sensitive to both short day-length/low temperature and long day-length/high temperature. 337S was crossed with the common wheat variety, Huamai No. 8 and the F₁ was highly fertile. The F₂ population segregated in a 15:1 ratio for fertility/sterility in 243 individuals under long day-length/high-temperature. The two thermophotoperiod-responsive male sterile genes were mapped to chromosomes 5B and 2B using Simple Sequence Repeat (SSR) markers and bulked segregant analysis. Partial linkage maps around the sterility loci of chromosomes 2B and 5B were constructed using the 243 individuals in the F₂ population. One gene (wptms1) for male sterility was flanked by the SSR markers Xgwm335 and Xgwm371 at a genetic distance in chromosome 5B of 4.1 and 24.4 cM, respectively. The second gene (wptms2) was mapped between markers Xgwm374 and Xgwm120 at a genetic distance of 6.6 and 20.9 cM, respectively. The closest linked markers Xgwm335 (wptms1) and Xgwm374 (wptms2) explained 53 and 38% of phenotypic variation for the fertility. The SSR markers provide a useful tool to transfer the male sterile genes into elite wheat germplasm.     

Photosynthetic Characteristics of Two New Chlorophyll b-Less Rice Mutants

Two yellow rice mutants VG28-1 and VG30-5 were obtained during the tissue culture process from a rice plant (cv. Zhonghua No.11 japonica) with inserted maize Ds transposon element. Absorption spectra and pigment composition showed that two mutants had no chlorophyll (Chl) b and lower Chl a content in comparison to the wild type (WT). Net photosynthetic rate (P _N), total electron transport rate (J_F), photochemical quenching (q_p), quantum yield of PS2 dependent non-cyclic electron transport (_PS2), fraction of P_rate, and leaf area were lower but F_v/F_m and apparent quantum yield (AQY) remained at similar levels as in the WT plant. Xanthophyll cycle pool size (V+A+Z) on a Chl basis, and de-epoxidation state were enhanced in the mutants. The mutants had larger amounts of soluble protein and ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBPCO), especially the small subunit of RuBPCO, than WT. The characteristics of two rice mutants differed somewhat from the other common Chl b-less mutants originating from mutagenic agent treatments.     

Injectability Evaluation: An Open Issue

The current work aimed to propose a system of scoring to rationalize and support the selection of the optimal diameter and length of needles. Four formulations at different viscosity and needles ranging from 21 to 26 G and length ranging from 16 to 40 mm were used. Plunger-stopper breakloose force, maximum force (F _max), and dynamic glide force were measured by a texture analyzer at the crosshead speed of 1 mm/s. Testing was carried out into air or human subcutaneous tissue. The manual injectability of the highest viscosity product was assessed by ten evaluators. The comparison of the panel test score and the quantitative measurements of the forces permitted to score a given needle-syringe-formulation system keeping also in consideration the pressure created in the subcutaneous space and muscles at the injection site. In particular, the following relationship was drawn: at the F _max up to 250 mPa, the injection was practically impossible; at F _max ranging from 160 to 250 mPa, the injection was very difficult; at F _max in the 125–160 mPa range, the injection was feasible, though with some difficulty; when the values of F _max were lower 125 mPa, the injection went smoothly. On the basis of these preliminary data, a system of scoring the needle-syringe-formulation system is proposed to rationalize and support the selection of the optimal diameter and length of needles, keeping also in consideration the pressure created in the subcutaneous space and muscles at the injection site.     

Molecular mapping of leaf rust resistance gene <Emphasis Type="Italic">LrBi16</Emphasis> in Chinese wheat cultivar Bimai 16

Leaf rust, caused by Puccinia triticina, is one of the most widespread diseases in common wheat (Triticum aestivum L.) globally. With the objective of identifying and mapping new genes for resistance to leaf rust, F₁, F₂ plants and F₃ lines from a cross between resistant cultivar Bimai 16 and susceptible cultivar Thatcher were inoculated with Chinese Puccinia triticina pathotypes FHTT and PHTS in the greenhouse. In the first seedling test, Bimai 16, Thatcher, 20 F₁ plants, 359 F₂ plants and 298 F₃ lines were inoculated with pathotype FHTT. A set of 1,255 simple sequence repeat (SSR) primer pairs were used to test the parents, and resistant and susceptible bulks. Seven polymorphic markers on chromosome 7BL were used for genotyping the F₂ and F₃ populations. The results indicated that Bimai 16 carried a single dominant resistance gene, temporarily designated LrBi16, closely linked to SSR markers Xcfa2257 and Xgwm344, with genetic distances of 2.8 and 2.9 cM, respectively. In the second seedling test, two dominant resistance genes were identified in Bimai 16 based on seedling reactions of 254 F₂ plants inoculated with pathotype PHTS. One of the genes was LrBi16, and the other was likely to be LrZH84, which is located in chromosome 1BL. The seedling reaction pattern of plants with LrBi16 was different from that of the Thatcher lines, with Lr14a and Lr14b located on chromosome 7BL. It was concluded that LrBi16 is likely to be a new leaf rust resistance gene.     

Identification of disulfide bond isomerase substrates reveals bacterial virulence factors

Bacterial pathogens are exposed to toxic molecules inside the host and require efficient systems to form and maintain correct disulfide bonds for protein stability and function. The intracellular pathogen Francisella tularensis encodes a disulfide bond formation protein ortholog, DsbA, which previously was reported to be required for infection of macrophages and mice. However, the molecular mechanisms by which F. tularensis DsbA contributes to virulence are unknown. Here, we demonstrate that F. tularensis DsbA is a bifunctional protein that oxidizes and, more importantly, isomerizes complex disulfide connectivity in substrates. A single amino acid in the conserved cis‐proline loop of the DsbA thioredoxin domain was shown to modulate both isomerase activity and F. tularensis virulence. Trapping experiments in F. tularensis identified over 50 F. tularensis DsbA substrates, including outer membrane proteins, virulence factors, and many hypothetical proteins. Six of these hypothetical proteins were randomly selected and deleted, revealing two novel proteins, FTL_1548 and FTL_1709, which are required for F. tularensis virulence. We propose that the extreme virulence of F. tularensis is partially due to the bifunctional nature of DsbA, that many of the newly identified substrates are required for virulence, and that the development of future DsbA inhibitors could have broad anti‐bacterial implications.     

Phenotypic plasticity to drought in seedlings of the warm season grass Panicum coloratum is related to collection site

Phenotypic plasticity is the ability of organisms to modify their phenotype in response to environmental changes. We estimated and compared the amount of phenotypic plasticity in response to drought in seedlings of different accessions of two varieties (var. makarikariense and var. coloratum) of Panicum coloratum, an allogamous warm season perennial grass, introduced and collected in sites in Argentina with different precipitation regimes. Amount of phenotypic plasticity was quantified in shoot/root biomass, blade/sheath biomass, specific leaf area and leaf area ratio (leaf area/total biomass) and mean phenotypic plasticity was estimated. The two genetically distinct varieties differed in the phenotypic plasticity of leaf area ratio (p = 0.008, F‐test), with var. makarikariense showing higher phenotypic plasticity. Accessions within varieties differed in phenotypic plasticity of leaf area ratio, specific leaf area, blade/sheath biomass and mean phenotypic plasticity (p < 0.05, F‐test). A strong relationship (r = 0.82, p < 0.01, F‐test) between mean phenotypic plasticity of each accession and precipitation variability was found. Relationships between phenotypic plasticity of blade/sheath biomass and leaf area ratio with annual mean precipitation were r = 0.86 and r = 0.75, respectively (p < 0.05; p < 0.01, F‐test, respectively). Evidence of a decoupling between phenotypic plasticity of above‐ versus belowground characters was apparent; outcomes on the interpretation of the variability in phenotypic plasticity and the potential applications of this variability are presented.     

The hybrid protein interactome contributes to rice heterosis as epistatic effects

Heterosis is the phenomenon in which hybrid progeny exhibits superior traits in comparison with those of their parents. Genomic variations between the two parental genomes may generate epistasis interactions, which is one of the genetic hypotheses explaining heterosis. We postulate that protein?protein interactions specific to F₁ hybrids (F₁‐specific PPIs) may occur when two parental genomes combine, as the proteome of each parent may supply novel interacting partners. To test our assumption, an inter‐subspecies hybrid interactome was simulated by in silico PPI prediction between rice japonica (cultivar Nipponbare) and indica (cultivar 9311). Four‐thousand, six‐hundred and twelve F₁‐specific PPIs accounting for 20.5% of total PPIs in the hybrid interactome were found. Genes participating in F₁‐specific PPIs tend to encode metabolic enzymes and are generally localized in genomic regions harboring metabolic gene clusters. To test the genetic effect of F₁‐specific PPIs in heterosis, genomic selection analysis was performed for trait prediction with additive, dominant and epistatic effects separately considered in the model. We found that the removal of single nucleotide polymorphisms associated with F₁‐specific PPIs reduced prediction accuracy when epistatic effects were considered in the model, but no significant changes were observed when additive or dominant effects were considered. In summary, genomic divergence widely dispersed between japonica and indica rice may generate F₁‐specific PPIs, part of which may accumulatively contribute to heterosis according to our computational analysis. These candidate F₁‐specific PPIs, especially for those involved in metabolic biosynthesis pathways, are worthy of experimental validation when large‐scale protein interactome datasets are generated in hybrid rice in the future.     

Spatial distribution and effects of Lantana camara invasion on soil properties and native vegetation community composition in Tugwi-Mukosi Recreational Park,Masvingo, Zimbabwe

This study investigated spatial distribution and effects of Lantana camara invasion on soil properties and vegetation composition in Tugwi-Mukosi Recreational Park. Supervised classification with the Random Forest classifier was used to map L. camara in the park. The study area was stratified into two categories based on soil type and the extent of L. camara invasion. Stratified random sampling was used in data collection to assess differences in species diversity and soil properties in the park. Results revealed that L. camara covered an area of 1772 ha. Using Random Forest classification, the study obtained an accuracy score of 92.1% and an F1 score of 86.25%. Two-way ANOVA showed significant effect of L. camara invasion on soil moisture (F = 28.143, p = 0.000), organic matter (F = 13.377, p = 0.003), pH (F = 1272.369, p = 0.000), total nitrogen (F = 51.762, p = 0.000), total phosphorus (F = 5.000, p = 0.045), woody species density (F = 4.987, p = 0.027), basal area (F = 10.393, p = 0.001), grass species richness (F = 196.258, p = 0.000) and grass cover (F = 3.637, p = 0.042). These results suggest that L. camara was modifying the soil and vegetation properties of the ecosystem which has implications on biodiversity.     

Comparison of Photosynthetic Traits Between Two Typical Shrubs: Legume and Non-Legume in Hunshandak Sandland

In Huanshandak Sandland, China, net photosynthetic rate (P _N), transpiration rate (E), stomatal conductance (g _s), intercellular CO₂ concentration (C _i), water use efficiency (WUE), photochemical efficiency of photosystem 2 (F_v/F_m), and leaf nitrogen content were compared for Hedysarum fruticosum var. mongolicum (H.f.m.), a nitrogen fixing shrub, and Salix gordejevii (S.g.), a nitrogen non-fixing shrub. P _N, E, and g _s of the two shrubs were similar in trends, i.e. two peaks were observed in diurnal courses. However, except C _i, other parameters of H.f.m. were higher during the measured days than those of S.g. The midday depression of P _N was mainly due to decrease in stomata conductance and to reduction of F_v/F_m at midday. The higher P _N of H.f.m. was consistent with the higher leaf N content and there was a positive relation between them. In addition, several C₄ traits were found in H.f.m., i.e. high saturation irradiance and WUE, low dark respiration rate, and C _i, which partly resulted in higher P _N. This seems to indicate that the C₃ plant H.f.m. may have C₄ photosynthesis pathway or C₄ enzymes.     

Two components of onset and recovery during photoinhibition of Ulva rotundata

Short-term (up to 5 h) transfers of shade-adapted (100 mol · m^–2 · s^–1) clonal tissue of the marine macroalga Ulva rotundata Blid. (Chlorophyta) to higher irradiances (1700, 850, and 350 mol · m^–2 · s^–1) led to photoinhibition of room-temperature chlorophyll fluorescence and O₂ evolution. The ratio of variable to maximum (F_v/F_m) and variable (F_v) fluorescence, and quantum yield () declined with increasing irradiance and duration of exposure. This decline could be resolved into two components, consistent with the separation of photoinhibition into energy-dissipative processes (photoprotection) and damage to photosystem II (PSII) by excess excitation. The first component, a rapid decrease in F_v/F_m and in F_v, corresponds to an increase in initial (F_o) fluorescence and is highly sensitive to 1 mM chloramphenicol. This component is rapidly reversible under dim (40 mol · m^–2 · s^–1) light, but is less reversible with increasing duration of exposure, and may reflect damage to PSII. The second (after 1 h exposure) component, a slower decline in F_v/F_m and F_v with declining F_o, appears to be associated with the photoprotective interconversion of violaxanthin to zeaxanthin and is sensitive to dithiothreitol. The accumulation of zeaxanthin in U. rotundata is very slow, and may account for the predominance of increases in F_o at high irradiances.Abbreviations and Symbols CAP chloramphenicol - DTT dithiothreitol - F_o, F_m, F_v initial, maximum, and variable fluorescence - quantum yield - PFD photon flux density - PSII photosystem II To whom correspondence should be addressedWe are grateful to O. Björkman and S. Thayer, Carnegie Institution of Washington, Stanford, Cal., USA, for analysis of xanthophyll pigments reported here. This research was supported by National Science Foundation grant OCE-8812157 to C.B.O. and J.R. Support for G.L. was provided by a NSF-CNRS (Centre National de la Recherche Scientifique) exchange fellowship.     

Population Genetic Structure of Two Columnar Cacti with a Patchy Distribution in Eastern Brazil

The genetic variability and population genetic structure of six populations of Praecereus euchlorus and Pilosocereus machrisii were investigated. The genetic variability in single populations of Pilosocereus vilaboensis, Pilosocereus aureispinus, and Facheiroa squamosa was also examined. All of these cacti species have a patchy geographic distribution in which they are restricted to small areas of xeric habitats in eastern Brazil. An analysis of genetic structure was used to gain insights into the historical mechanisms responsible for the patchy distribution of P. euchlorus and P. machrisii. High genetic variability was found at the populational level in all species (P=58.9–92.8%, A_p=2.34–3.33, H_e=0.266–0.401), and did not support our expectations of low variability based on the small population size. Substantial inbreeding was detected within populations (F_IS=0.370–0.623). In agreement with their insular distribution patterns, P. euchlorus and P. machrisii had a high genetic differentiation (F_ST=0.484 and F_ST=0.281, respectively), with no evidence of isolation by distance. Accordingly, estimates of gene flow (N_m) calculated from F_ST and private alleles were below the level of N_m=1 in P. machrisii and P. euchlorus. These results favored historical fragmentation as the mechanism responsible for the patchy distribution of these two species. The genetic distance between P. machrisii and P. vilaboensis was not compatible with their taxonomic distinction, indicating a possible local speciation event in this genus, or the occurrence of introgression events.     

Randomization Analysis of Incomplete Data in Some Basic Designs

The first two randomization moments of W = Tt.S.S./(Tt.S.S. + Error S.S.) are derived in case of (a) a completely randomized design with one observation missing using (I) Yates method of fitting constants and (II) the available observations only and in case of (b) a randomized block design in which one treatment is tested twice by mistake in a block and another treatment is not tested at all in that block using (I) all the available observations and (II) the data after deleting the observation due to the treatment tested by mistake in place of another treatment in a block. It is concluded that in each of the two cases for a completely randomized design, the F-test is unbiased whereas in each of the two cases for a randomized block design the F-test is in general not unbiased. However, if one treatment is tested twice by mistake in randomly chosen plots of some block, the F-test is unbiased in both cases for a randomized block design. For a completely randomized design the F-test is found to be a good approximation to the corresponding randomized test if N ≧ 80 in case (I) whereas in case (II) this approximation is of the same accuracy as that of case (I) if N ≧ 90. For a randomized block design it is seen that in case (I), the F-test provides a good approximation to the corresponding randomization test if v≧r≧7 and in case (II) this approximation is of the same accuracy if r≧6 and r(v-1)≧45. The analysis of several uniformity trial data shows that for values of “N” in the neighbourhood of 50 the agreement of the first two moments of “W” under the randomization theory and normal theory are reasonably close in all the four cases considered.