Population genetic study of the Alatyr region of the Republic of Chuvashiia

Population genetic characteristics were estimated in the Alatyr' raion (administrative district) of the Republic of Chuvashia, which has long been populated by three ethnic groups. The ethnic assortativeness values in the town of Alatyr' and the rural area of the district were 1.17 and 1.21, respectively, for Russians; 1.14 and 4.82, respectively, for Chuvashes; and 1.33 and 2.45, respectively, for Mordovians. Wright's statistics were as follows: Fst = 0.00358, Fit = 0.00178, and Fis = 0.00134. The migration indices were 0.0264 for Alatyr' and 0.0178 for the district. The endogamy indices for the total and the Russian populations of Alatyr' were 0.47 and 0.53, respectively. The parameters of isolation by distance were a = 0.000189 and b = 0.00959 for the urban and a = 0.000318 and b = 0.00919 for the rural area. Schemes of the genetic landscape were constructed. The influence of the polyethnic composition on the genetic structure of the population is discussed.     

Analysis of Marital Migrations in Two Ouluses of the Republic of Sakha (Yakutia)

The marital migration structure of two ouluses (administrative districts) of the Republic of Sakha (Yakutia) that have long been populated by three ethnic groups were studied on the basis of marriage records. Population genetic characteristics were calculated for each ethnic group. The ethnic assortativeness values were 30.9 in Evens, 1.36 and 4.46 in Russians, and 1.03 and 4.51 in Yakuts. The endogamy indices for the oulus and republican ethnic populations, respectively, were 0.83 and 1.0 in Evens, 0.41 and 0.99 in Yakuts, and 0.08 and 0.14 in Russians. The parameters of isolation by distance were the following: a = 0.0013 and b = 0.0020 in the Gornyi oulus; a= 0.0048 and b = 0.0014 in the Krest-Khaldzhai rural municipality;a = 0.0086 and b = 0.0095 in the Topolinoe rural municipality; anda= 0.0106 and b= 0.0013 in the Megino-Aldan rural municipality.     

Inbreeding and endogamy in Tatarstan

The random inbreeding (F _st) and local inbreeding (a) values have been calculated for populations of the district and rural municipality ranks of 16 and 13 raions (administrative districts) of Tatarstan, Russia, respectively. The correlations between all inbreeding values are positive and vary from 0.38 to 0.80. The endogamy index has been calculated for populations of the district rank; it varies from 0.45 in Pestrechinskii raion to 0.74 in Aktanyshskii raion. Cartographic extrapolation of the endogamy indices has been performed.     

Marriage-migration characteristics of the urban and rural populations of Udmurtia

Marriage records of six raions (districts) of Udmurtia and the city of Glazov (a total of 10518 records) have been used to calculate marriage-migration parameters. The endogamy indices of the rural and urban Udmurt populations are 0.59 (from 0.48 to 0.76 in individual districts) and 0.29, respectively, and those of the rural and urban Russian populations are 0.33 and 0.47, respectively. The mean ethnic assortativeness values are 1.05 and 0.89 for the rural and urban Udmurt populations, respectively, and 2.13 and 1.44 for the rural and urban Russian populations, respectively. The parameters of isolation by distance for the rural Udmurt population are the following: σ = 52.4, a = 0.00035, and b = 0.012; those for the urban Udmurt population are 54.1, 0.00020, and 0.010, respectively.     

Inheritance pattern of downy mildew resistance in advanced generations of sorghum*

In a project aimed to incorporate downy mildew resistance into sorghum hybrid seed parents, we screened F₄ and F₅ families for resistance to the ICRISAT Centre isolate of the pathogen using a greenhouse seedling screening technique. The families originated from a cross of 296B (susceptible) and IS 18757 [(QL-3) resistant]. The F₄s were obtained from agronomic selection in F₂s and F₃s, and the F₅ families from advancing plants identified as resistant in segregating F₄ families. The resistant plants were more than double the number of susceptible plants in the F₄ and almost so in the F₅ suggesting that resistance to downy mildew was dominant. Of the four genetic models examined (a single-locus model and three two-locus models with complementary, inhibitory, and a combination of complementary and inhibitory interactions), the two-locus model with independent segregation and a combination of complementary and inhibitory inter-allelic interaction appeared to be most appropriate in explaining the segregation patterns within and among F₄ and F₅ families. Accordingly, for resistance to P. sorghi, the suggested genotypes for IS 18757 is Pl_aPl_aPl_bPl_b and for 296B is Pl_aPl_aPl_bPl_b.     

Mutagenic Analysis of the F 0 Stator Subunits

The a and b subunits constitute the stator elements in the F₀ sector of F₁F₀-ATP synthase.Both subunits have been difficult to study by physical means, so most of the information onstructure and function relationships in the a and b subunits has been obtained using mutagenesisin combination with biochemical methods. These approaches were used to demonstrate thatthe a subunit in association with the ring of c subunits houses the proton channel throughF₁F₀-ATP synthase. The map of the amino acids contributing to the proton channel is probablycomplete. The two b subunits dimerize, forming an extended flexible unit in the peripheralstalk linking the F₁ and F₀ sectors. The unique characteristics of specific amino acid substitutionsaffecting the a and b subunits suggested differential effects on rotation during F₁F₀-ATPaseactivity.     

Mapping of quantitative trait loci and development of allele-specific markers for seed weight in Brassica napus

Seed weight is an important component of grain yield in oilseed rape (Brassica napus L.), but the genetic basis for the important quantitative trait is still not clear. In order to identify the genes for seed weight in oilseed rape, QTL mapping for thousand seed weight (TSW) was conducted with a doubled haploid (DH) population and an F₂ population. A complete linkage map of the DH population was constructed using 297 simple sequence repeat (SSR) markers. Among nine TSW QTLs detected, two major QTLs, TSWA7a and TSWA7b, were stably identified across years and collectively explained 27.6–37.9% of the trait variation in the DH population. No significant epistatic interactions for TSW detected in the DH population indicate that the seed weight variation may be primarily attributed to additive effects. The stability and significance of TSWA7a and TSWA7b were further validated in the F₂ population with different genetic backgrounds. By cloning BnMINI3a and BnTTG2a, two B. napus homologous genes to Arabidopsis thaliana, allele-specific markers were developed for TSWA5b and TSWA5c, two TSW QTLs on A5, respectively. The importance of the major and minor QTLs identified was further demonstrated by analysis of the allelic effects on TSW in the DH population.     

Intensity of nitrification in soil as a function of time and soil moisture

Proceeding from three previously derived expressions for the intensity of nitrification in soil as a function of time (logΣN=K.logt+q), as a function of incubation moisture (logΣN=A.pF _i+B), as a function of initial moisture (logΣN=C.pF _v+D), it was shown that the nitrification intensity as a function of time and of moisture can be expressed by the bilinear function log ΣN=a.pF _i.logT+b.pF _i+c.logt+d; as a function of time and of initial moisture by the bilinear function logΣ=N=a.pF _v.logt+b.pF _v+c.logt+d; as a function of initial and incubation moisture by the bilinear function log ΣN=a.pF _ipF _v+b.pF _i+c.pF _v+d. The intensity of nitrification as a function of time, incubation moisture and initial moisture may be expressed by the multilinear function log ΣN=a.pF _i.pF _v.logt+b.pF _i.pF _v+c.pF _i.logt+d.pF _v.logt+e .pF _i+f.pF _v=g.logt+h. This function is valid for all the incubation moistures lying between pF _i 3.0 and 4.0 and for all initial moistures between 3.5 and 5.9 provided that the incubation temperature remains constant.     

Genetic Demographic Description of the Ust-Aldan Rural Population of Sakha Republic (Yakutia): Migrations and Marriage Structure

Migrations, dynamics of the gametic structure of rural populations, and marriage structure with respect to birthplaces and inbreeding estimated from isonymy have been studied in the Ust-Aldan ulus (administrative district) of Sakha Republic (Yakutia). The villages studied (Byadi, Dyupsya, and Cheriktey) are characterized by intense migration; however, the migration radius is small (most migrations occur within the district). The rural populations studied differ in the intensities and directions of gamete flows and their dynamics. There is no substantial gamete flow into the Ust-Aldan population from outside Sakha Republic. About 50% of marriages contracted in this population are homolocal (between residents of the same district); the endogamy is low (15%). In most cases of heterolocal marriages (contracted between residents of different districts), one of the spouses is a local resident. The inbreeding estimated from isonymy is F _IT = 0.002930 in Yakuts; it is mainly accounted for by the nonrandom component (F _IS = 0.002232 and F _ST = 0.000700).     

Subunit Organization of the Stator Part of the F 0 Complex from Escherichia coli ATP Synthase

Membrane-bound ATP synthases (F₁F₀) catalyze the synthesis of ATP via a rotary catalyticmechanism utilizing the energy of an electrochemical ion gradient. The transmembrane potentialis supposed to propel rotation of a subunit c ring of F₀ together with subunits and of F₁,hereby forming the rotor part of the enzyme, whereas the remainder of the F₁F₀ complexfunctions as a stator for compensation of the torque generated during rotation. This reviewfocuses on our recent work on the stator part of the F₀ complex, e.g., subunits a and b. Usingepitope insertion and antibody binding, subunit a was shown to comprise six transmembranehelixes with both the N- and C-terminus oriented toward the cytoplasm. By use of circulardichroism (CD) spectroscopy, the secondary structure of subunit b incorporated intoproteoliposomes was determined to be 80% -helical together with 14% turn conformation, providingflexibility to the second stalk. Reconstituted subunit b together with isolated ac subcomplexwas shown to be active in proton translocation and functional F₁ binding revealing the nativeconformation of the polypeptide chain. Chemical crosslinking in everted membrane vesiclesled to the formation of subunit b homodimers around residues bQ37 to bL65, whereas bA32Ccould be crosslinked to subunit a, indicating a close proximity of subunits a and b near themembrane. Further evidence for the proposed direct interaction between subunits a and b wasobtained by purification of a stable ab ₂ subcomplex via affinity chromatography using Histags fused to subunit a or b. This ab ₂ subcomplex was shown to be active in proton translocationand F₁ binding, when coreconstituted with subunit c. Consequences of crosslink formationand subunit interaction within the F₁F₀ complex are discussed.     

Evaluation of the Effect of Light Intensity on the Measurement of the Photosynthetic Rate in Plankton Microalgae by the Chlorophyll Fluorescence Method

The use of relative variable fluorescence (RVF) of chlorophyll, as measured in the presence of Diuron, an inhibitor of electron transfer, for the estimation of the photosynthetic activity of plankton microalgae was analyzed under a wide range of light intensities in the PAR region. Oxygen evolution rates (estimated by the method of light and dark bottles and the amperometric method), RVF, and chlorophyll a concentration were measured in parallel in natural algal cenoses and microecosystems. When the previously used regression equation, in the form A = b(F/F _d)C _chl I, where A is O₂ evolution rate (g/(m³ h), F/F _d is RVF (relative units), C _chl is chlorophyll a concentration (mg/m³), and I is light intensity (W/m²), was verified in the PAR region, we observed a nonlinear dependence of the correction coefficient b on I, which can be described by the formula b = 6.227 × 10³I. This result agrees with the hypothesis that chlorophyll a fluorescence quenching comprises photochemical (qQ) and energy (qE) components. On the basis of the energy model, we determined the upper limit b _max = 0.003 for light intensity range I< 4.4 W/m² and the lower limit b _min = 0.0003 for I = 400 W/m².     

Mapping and validation of quantitative trait loci for spikelets per panicle and 1,000-grain weight in rice (Oryza sativa L.)

This study identified four and five quantitative trait loci (QTLs) for 1,000-grain weight (TGW) and spikelets per panicle (SPP), respectively, using rice recombinant inbred lines. QTLs for the two traits (SPP3a and TGW3a, TGW3b and SPP3b) were simultaneously identified in the two intervals between RM3400 and RM3646 and RM3436 and RM5995 on chromosome 3. To validate QTLs in the interval between RM3436 and RM5995, a BC₃F₂ population was obtained, in which TGW3b and SPP3b were simultaneously mapped to a 2.6-cM interval between RM15885 and W3D16. TGW3b explained 50.4% of the phenotypic variance with an additive effect of 1.81 g. SPP3b explained 29.1% of the phenotypic variance with an additive effect of 11.89 spikelets. The interval had no effect on grain yield because it increased SPP but decreased TGW and vice versa. Grain shape was strongly associated with TGW and was used for QTL analysis in the BC₃F₂ population. Grain length, grain width, and grain thickness were also largely controlled by TGW3b. At present, it is not clear whether one pleiotropic QTL or two linked QTLs were located in the interval. However, the conclusion could be made ultimately by isolation of TGW3b. The strategy for TGW3b isolation is discussed.     

Genetic Structure of the Volga–Ural and Central Asian Populations Inferred from the Data on Alu Polymorphism

NineAlu loci (Ya5NBC5, Ya5NBC27, Ya5NBC148, Ya5NBC182, YA5NBC361, ACE, ApoA1, PV92, TPA25) were analyzed in six ethnic populations (Trans-Ural Bashkirs, Tatars-Mishars, Mordovians-Moksha, Mountain Maris, Udmurts, and Komi-Permyaks) of the Volga–Ural region and in three Central Asian populations (Uzbeks, Kazakhs, and Uigurs). All Alu insertions analyzed appeared to be polymorphic in all populations examined. The frequency of insertion varied from 0.110 in Mountain Maris at the Ya5NBC5 locus to 0.914 in Tatars at the ApoA1 locus. The data on the allele frequency distribution at nine loci point to the existence of substantial genetic diversity in the populations examined. The value of the observed heterozygosity averaged over nine Alu insertions varied from 0.326 in Mountain Maris to 0.445 in Kazakhs and Uigurs. The level of the interpopulation genetic differences for the Volga–Ural population (F _st = 0.061) was higher than for the populations of Central Asia (F _st = 0.024), Europe (F _st = 0.02), and Southeastern Asia (F _st = 0.018). The populations examined were highly differentiated both in respect of linguistic characteristics and the geographical position. The data obtained confirmed the effectiveness of the marker system used for the assessment of genetic differentiation and the relationships between the ethnic groups.     

Molecular mapping of a gene ‘ld(t)’ controlling cleistogamy in rice

Cleistogamy is the self-pollination within closed spikelets and is expected to be a useful genetic tool for prevention of possible gene transfer in transgenic crops, for maintenance of genetic purity in autogamous crops, and for increased tolerance to biotic and abiotic stresses. Mapping of the gene ld(t), which is responsible for lack of lodicules inside spikelets and causes cleistogamy, was carried out using F₂ and F₃ populations derived from a cleistogamous (CL) mutant CL-SNU × Milyang 23 cross. A number of STS markers along chromosomes were developed and bulked segregant analysis was adopted for preliminary mapping. The results showed that the ld(t) was located at the end region of chromosome 1L, flanked by S01178b (an STS marker developed for the locus at 178 cM based on the rice genetic map reported by Japanese Rice Genome Project) at 0.8 cM and co-segregated with S01181a and S01181b (an STS marker developed for the locus at 181 cM).     

Cytogenetic analysis of hybrids derived from wheat and <Emphasis Type="Italic">Tritipyrum</Emphasis> using conventional staining and genomic <Emphasis Type="Italic">in situ</Emphasis> hybridization

The new salt tolerant cereal, Tritipyrum (2n=6x=42, AABBE^bE^b) offers potential to introduce desirable characters for wheat improvements. This study was aimed to generate a segregating population from Iranian local wheat cultivars (2n=6x=42, AABBDD) and Tritipyrum crosses, study of the meiotic behaviour in F₂ hybrids and identification of E^b chromosomes in F₃ individuals. Results showed meiotic abnormalities in F₂ plants and different pairing frequency in the meiosis among F₂ plants. Genomic in situ hybridization revealed that total and E^b chromosome number of F₃ seeds ranged from 39 to 45 and 0 to 10, respectively. A significant prevalence of hyper-aneuploidy was observed among F₃ genotypes. C-banding patterns identified E^b chromosomes in Tritipyrum, indicating that it also can be useful to study wheat-Tritipyrum derivatives.     

Genetic variation, genetic structure and effective population size in the tropical holoparasitic endophyteBdallophyton bambusarum (Rafflesiaceae)

The genetic population structure inBdallophyton bambusarum, an endoparasite, was studied in ten subpopulations from a subdeciduous tropical forest in Veracruz Mexico. The sample was analyzed using seven polymorphic loci in cellulose acetate electrophoresis. Isozyme data indicated that the subpopulations ofB. bambusarum contained high genetic variability (H_ep = 0.452 ± 0.045, S.E.). Our analysis suggests that almost each inflorescence ofB. bambusarum is an individual. The subpopulations studied were genetically similar (average Nei's genetic identity 0.941 ± 0.051 and F _st values 0.097 ± 0.026), suggesting that genetic differentiation among subpopulations was small. Direct estimates of effective population size was derived from observations of three fluorescent dyes, and from the genetic neighborhood area derived from these data. The neighborhood area, multiplied by the total density of individuals, gave an N_e = 124.84 plants, and when corrected to consider the proportion of males and females gave an N_e = 118.59 individuals. An indirect estimate of Nm was obtained from the F _st values (mean Nm=2.037), giving an indirect estimate of the effective population size N_b = 12.8 individuals. Both values are relatively high when compared to other plant studies. The gene flow and/or effective populations size of the studied subpopulations ofB. bambusarum are believed to be large enough to prevent differentiation among subpopulations due to genetic drift.     

Genetics of gel consistency in rice (Oryza sativa L.)

Inheritance of gel consistency in rice was studied in crossés involving highamylose, low-gelatinizalion temperature parents with hard, medium, and soft gel consistency. The results of single-grain analysis of parents, F₁, F₂, B₁F₁, B₂F₂, and their reciprocal crosses from a single-season harvest showed that the differences between hard and soft, hard and medium, and medium and soft gel consistency are under monogenic control and that modifiers affect the expression of the trait. Multiple alleles at the same locus, hereby designated asgec ^a for medium gel consistency andgec ^b for soft gel consistency, were recessive to the wild type allele for hard gel consistency andgec ^a was dominant overgec ^b. The results indicate that selection for desired gel consistency can effectively be done in early segregating generations.     

ESTIMATION OF GENETIC NEIGHBORHOOD PARAMETERS FROM POLLEN AND SEED DISPERSAL IN THE MARINE ANGIOSPERM ZOSTERA MARINA L.

The relative importance of random genetic drift and local adaptation in causing population substructuring in plant species remains an important empirical question. Here I estimate the effective size of the genetic neighborhood, N_b, as a means of evaluating the likely role of genetic drift in creating genetic differentiation within a population of a marine plant, Zostera marina L. (eelgrass). Calculations of effective neighborhood size are based on field estimates of pollen and seed-dispersal distributions, an electrophoretic estimate of the mating system using open-pollinated progeny arrays, and determination of the effective density of reproductive individuals in the population. Neighborhood area calculated from the parent-offspring dispersal variances was equal to N_a = 524 m²; variance in the seed-dispersal distribution contributes more than twice as much as variance in pollen dispersal to N_a. Including an outcrossing rate slightly different from random, estimated neighborhood size for Z. marina is N_b = 6255. This estimate is one of the largest reported for plants or animals and indicates that genetic drift in small neighborhoods is highly unlikely to cause genetic substructuring in the study population. High gene-flow levels provided by the marine environment appear to prevent genetic isolation by distance among eelgrass patches, but the importance of drift through founder events in this population characterized by high patch turnover cannot be discounted and is the subject of ongoing study.     

Diversity and genetic structure of three species of Dioon Lindl. (Zamiaceae, Cycadales) from the Pacific seaboard of Mexico

We have estimated levels of genetic diversity and partitioning in the Mexican endemic cycad species Dioon sonorense, Dioon tomasellii, and Dioon holmgrenii, whose populations are exclusively distributed along the Pacific seaboard. For the three species, the patterns of variation at 19 allozyme loci in a total of 11 populations were evaluated. The average number of alleles per locus was in the range 2.05–1.68, corresponding to the northernmost population of D. sonorense (Mazatán), and the southernmost population of Dioon holmgrenii (Loxicha), respectively. In turn, the percentage of polymorphic loci peaked (94.73) in the El Higueral and Altamirano populations of Dioon tomasellii, and was estimated to be lowest (57.89) in the Loxicha population of D. holmgrenii. The mean expected heterozygosis varied markedly between taxa, with relatively high indices for D. sonorense and D. tomasellii (H_E = 0.314 and 0.295, respectively) and substantially lower values for D. holmgrenii (H_E = 0.170). Comparison of the inferred genetic structure based on F‐statistics for the three species also indicated differences along the north‐south Pacific seaboard axis. For D. sonorense and D. tomasellii, local inbreeding (F_IS) was zero but global inbreeding (F_IT) values were positive and significantly different from zero (0.130 and 0.116, respectively). By contrast, values of both F_IT and F_IS were negative and significantly different from zero (?0.116 and ?0.201, respectively) for D. holmgrenii. The genetic differentiation between populations (F_ST) had positive values in all taxa and corresponded with their geographic location along the north‐south axis: according to this statistic, D. sonorense was the most differentiated species (F_ST = 0.151), D. tomasellii had intermediate values (F_ST = 0.145), and D. holmgrenii was the less differentiated taxon (F_ST = 0.069). Finally, a phenogram representing Nei's genetic distances among populations displayed three major groups, each one corresponding to each of the studied species. Within D. tomasellii (of intermediate geographic distribution), a further division into two clusters corresponded precisely to the pair of populations that are geographically divided by the Trans Mexican Neovolcanic Mountains. © 2008 The Linnean Society of London, Biological Journal of the Linnean Society, 2008, 94 , 765–776.     

Effect of gamma radiation on mutant induction of <Emphasis Type="Italic">Fagopyrum dibotrys</Emphasis> Hara

Agronomic traits, photosynthetic pigments, gas exchange, and chlorophyll (Chl) fluorescence parameters of red stem buckwheat (Fagopyrum dibotrys Hara) mutants induced by γ-radiation were compared with green control at seedling stage. Plant height, number of first-class branches, and rhizome biomass were inhibited significantly (p<0.01). Chl a, Chl b, and Chl a+b contents decreased with elevated dose of γ-rays, while increasing carotenoid content indicated that buckwheat was capable of adjusting to the radiation damage. Decrease in net photosynthetic rate was the result of both stomatal and non-stomatal limitations. Fluorescence parameters, such as F₀, F_m, F_v/F_m, F_v/F₀, Φ_PS2, electron transport rate, and photochemical quenching declined significantly (p<0.01) as compared with control due to photoinhibition, while non-photochemical quenching increased to enhance thermal dissipation. Lower parameters implied that leaf tissue was damaged significantly by high dose of γ-radiation and therefore leaf senescence was accelerated.