REPRODUCTIVE SYSTEM AND POLLEN FLOW IN PROGENIES OF Qualea grandiflora Mart., A TYPICAL SPECIES OF THE BRAZILIAN CERRADO

This study analyzed the reproductive system and the pollen dispersion pattern of Qualea grandiflora progenies. This is a typical species from the Brazilian Cerrado about which there are not too many studies from the genetics point of view. The study was conducted in an area of 2.2 hectares located in the Conservation Unit managed by the Forest Institute of the state of São Paulo, Brazil (Assis State Forest). Total genomic DNA of 300 seeds from 25 plants (12 seeds from each plant) was extracted and amplified using specific primers to obtain microsatellite markers. Results showed that selfing is frequent among adults and progenies, and the species reproduces by outcrossing between related and unrelated individuals (0.913). The single-locus outcrossing rate was 0.632, which indicates that mating between unrelated individuals is more frequent than between related plants. The selfing rate was low (0.087), that is, the species is allogamous and self-fertilization is reduced. About 35% of the plants in the progenies were full-sibs, and about 57%, half-sibs. Besides, about 8% of the progenies were selfing siblings. The genetic differentiation coefficient within progenies was 0.139, whereas the fixation rate was about 27%. The estimate of the effective size revealed that the genetic representativeness of descent was lower than expected in random mating progenies: The analyzed samples corresponded to only 13.2 individuals of an ideal panmictic population. In environmental recovery programs, seeds, preferably from different fruits, should be collected from 95 trees to preserve the genetic diversity of the species.

Allozyme variation in a natural population of Stryphnodendron adstringens in the Rio Preto State Park, southeastern Brazil

Leaves and fruits from 63 Stryphnodendron adstringens trees were sampled in the Rio Preto State Park to analyze allozyme segregation, tissue specific expression of allozyme loci, and their genetic parameters. The enzyme systems ADH, EST, ACP, PGM, PGI, GDH, G6PDH, GOT, IDH, LAP, MDH, PER and SKDH were assessed by means of starch-gel electrophoresis. The polymorphic systems PGI, IDH, MDH and GOT demonstrated a dimeric quaternary structure, while EST and PER were monomeric. The total expected genetic diversity (H E) for leaves and seeds were 0.325 and 0.244 respectively. The effective number of alleles per locus (A E) was 1.58 in leaves and 1.42 in seeds. The values of H E and A E observed in S. adstringens were comparatively higher than the average values seen in allozyme studies of other woody plants. The values of the fixation indices for the population, considering leaves (f = 0.070) and seeds (f = 0.107), were not significant. The high values of genetic diversity and of effective number of alleles per locus, as well as the non-significant fixation index and the adjustments of the Hardy-Weinberg proportions between generations for the pgi-1, mdh-2 and idh-1 loci, indicated random mating in this population. The enzyme systems EST and PER demonstrated their best resolution in leaf tissues, while the MDH, IDH, PGI and GOT systems demonstrated their best resolution in seed tissues.

The automation and evaluation of nested clade phylogeographic analysis

Nested clade phylogeographic analysis (NCPA) is a popular method for reconstructing the demographic history of spatially distributed populations from genetic data. Although some parts of the analysis are automated, there is no unique and widely followed algorithm for doing this in its entirety, beginning with the data, and ending with the inferences drawn from the data. This article describes a method that automates NCPA, thereby providing a framework for replicating analyses in an objective way. To do so, a number of decisions need to be made so that the automated implementation is representative of previous analyses. We review how the NCPA procedure has evolved since its inception and conclude that there is scope for some variability in the manual application of NCPA. We apply the automated software to three published datasets previously analyzed manually and replicate many details of the manual analyses, suggesting that the current algorithm is representative of how a typical user will perform NCPA. We simulate a large number of replicate datasets for geographically distributed, but entirely random-mating, populations. These are then analyzed using the automated NCPA algorithm. Results indicate that NCPA tends to give a high frequency of false positives. In our simulations we observe that 14% of the clades give a conclusive inference that a demographic event has occurred, and that 75% of the datasets have at least one clade that gives such an inference. This is mainly due to the generation of multiple statistics per clade, of which only one is required to be significant to apply the inference key. We survey the inferences that have been made in recent publications and show that the most commonly inferred processes (restricted gene flow with isolation by distance and contiguous range expansion) are those that are commonly inferred in our simulations. However, published datasets typically yield a richer set of inferences with NCPA than obtained in our random-mating simulations, and further testing of NCPA with models of structured populations is necessary to examine its accuracy.

Comparison of selective genotyping strategies for prediction of breeding values in a population undergoing selection

Genomewide marker information can improve the reliability of breeding value predictions for young selection candidates in genomic selection. However, the cost of genotyping limits its use to elite animals, and how such selective genotyping affects predictive ability of genomic selection models is an open question. We performed a simulation study to evaluate the quality of breeding value predictions for selection candidates based on different selective genotyping strategies in a population undergoing selection. The genome consisted of 10 chromosomes of 100 cM each. After 5,000 generations of random mating with a population size of 100 (50 males and 50 females), generation G(0) (reference population) was produced via a full factorial mating between the 50 males and 50 females from generation 5,000. Different levels of selection intensities (animals with the largest yield deviation value) in G(0) or random sampling (no selection) were used to produce offspring of G(0) generation (G(1)). Five genotyping strategies were used to choose 500 animals in G(0) to be genotyped: 1) Random: randomly selected animals, 2) Top: animals with largest yield deviation values, 3) Bottom: animals with lowest yield deviations values, 4) Extreme: animals with the 250 largest and the 250 lowest yield deviations values, and 5) Less Related: less genetically related animals. The number of individuals in G(0) and G(1) was fixed at 2,500 each, and different levels of heritability were considered (0.10, 0.25, and 0.50). Additionally, all 5 selective genotyping strategies (Random, Top, Bottom, Extreme, and Less Related) were applied to an indicator trait in generation G(0), and the results were evaluated for the target trait in generation G(1), with the genetic correlation between the 2 traits set to 0.50. The 5 genotyping strategies applied to individuals in G(0) (reference population) were compared in terms of their ability to predict the genetic values of the animals in G(1) (selection candidates). Lower correlations between genomic-based estimates of breeding values (GEBV) and true breeding values (TBV) were obtained when using the Bottom strategy. For Random, Extreme, and Less Related strategies, the correlation between GEBV and TBV became slightly larger as selection intensity decreased and was largest when no selection occurred. These 3 strategies were better than the Top approach. In addition, the Extreme, Random, and Less Related strategies had smaller predictive mean squared errors (PMSE) followed by the Top and Bottom methods. Overall, the Extreme genotyping strategy led to the best predictive ability of breeding values, indicating that animals with extreme yield deviations values in a reference population are the most informative when training genomic selection models.

Acasalamento dirigido para aumentar a produção de animais geneticamente superiores e reduzir a variabilidade da progênie em bovinos

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Uso combinado de sêmen sexado e acasalamento dirigido sobre uma população de bovinos de corte submetida a seleção: estudo de simulação

Desenvolveu-se um estudo de simulação estocástica com o objetivo de verificar as consequências do uso combinado de acasalamento dirigido e sêmen sexado em uma população de bovinos de corte sob seleção. Simularam-se seis gerações de seleção para três cenários de acasalamento e uso de sêmen sexado. O primeiro cenário foi caracterizado por acasalamento aleatório e uso exclusivo de sêmen convencional. O segundo cenário caracterizou-se pelo uso de acasalamento associativo positivo nas 40% melhores vacas e acasalamento associativo negativo nas demais, sem uso de sêmen sexado. O terceiro cenário seguiu o mesmo procedimento de acasalamento do segundo, combinando-o com uso de sêmen sexado nas vacas submetidas a acasalamento associativo positivo. O acasalamento associativo positivo teve maior impacto no progresso genético que o uso de sêmen sexado, apesar de ter aumentado a incidência de endogamia na população. O uso de acasalamento associativo negativo foi ineficiente em reduzir a variabilidade dos animais destinados ao abate. O uso combinado de acasalmento associativo positivo e sêmen sexado aumentou a produção de animais geneticamente superiores.

Formando lotes uniformes de reprodutores múltiplos e usando-os em acasalamentos dirigidos, em populações Nelore

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Two-Way Selection for Daily Gain and Feed Conversion in a Composite Rabbit Population

We conducted a two-way selection experiment in a composite rabbit population to investigate the responses to selection for postweaning ADG and feed conversion (FC). Two generations of crossing, followed by four generations of random pair matings, preceded three generations of selection. Selection was practiced within four lines: high-feed conversion (HFC), low-feed conversion (LFC), high gain (HG), and low gain (LG). Data on 1,446 rabbits from the random mating and selection generations were fitted to an animal model to estimate heritabilities of and the genetic correlation between ADG and FC. The two-trait model included rabbit and common litter random effects and line, generation, and sex fixed effects. Estimates of heritability of ADG and FC were .48 and .29, respectively, and the genetic correlation between them was -.82. Common litter environmental effects accounted for a proportion of .11 and . 13 of the phenotypic variation of the two traits, respectively. For ADG (in g/d) the regressions of mean breeding values on generation number during the selection period were 1.23 ± .12 (P < .01) in the HG line and -.86 ± .12 (P < .01) in the LG line; the regressions for FC (in g feed/g gain) were -.07 ± .01 (P < .01) in the HFC line and .03 ± .01 (P < .05) in the LFC line. Selection for ADG was effective in improving ADG and FC.

Genetic structure of populations of Rhizoctonia solani AG-3 on potato in eastern North Carolina

A polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method was developed to identify and differentiate genotypes of Rhizoctonia solani anastomosis group 3 subgroup PT (AG-3 PT), a fungal pathogen of potato. Polymorphic co-dominant single-locus PCR-RFLP markers were identified after sequencing of clones from a genomic library and digestion with restriction enzymes. Multilocus genotypes were determined by a combination of PCR product and digestion with a specific restriction enzyme for each of seven loci. A sample of 104 isolates from one commercial field in each of five counties in eastern North Carolina was analyzed, and evidence for high levels of gene flow between populations was revealed. When data were clone-corrected and samples pooled into one single North Carolina population, random associations of alleles were found for all loci or pairs of loci, indicating random mating. However, when all genotypes were analyzed, the observed genotypic diversity deviated from panmixia and alleles within and between loci were not randomly associated. These findings support a model of population structure for R. solani AG-3 PT on potato that includes both recombination and clonality.

Population genetic evidence that basidiospores play an important role in the disease cycle of rice-infecting populations of Rhizoctonia solani AG-1 IA in Iran

The fungus Rhizoctonia solani AG-1 IA causes sheath blight, one of the most important rice diseases worldwide. The first objective of this study was to analyse the genetic structure of R. solani AG-1 IA populations from three locations in the Iranian Caspian Sea rice agroecosystem. Three population samples of R. solani AG-1 IA isolates were obtained in 2006 from infected rice fields separated by 126-263km. Each field was sampled twice during the season: at the early booting stage and 45days later at the early mature grain stage. The genetic structure of these three populations was analysed using nine microsatellite loci. While the population genetic structure from Tonekabon and Amol indicated high gene flow, they were both differentiated from Rasht. The high gene flow between Tonekabon and Amol was probably due mainly to human-mediated movement of infested seeds. The second objective was to determine the importance of recombination. All three populations exhibited a mixed reproductive mode, including both sexual and asexual reproduction. No inbreeding was detected, suggesting that the pathogen is random mating. The third objective was to determine if genetic structure within a field changes over the course of a growing season. A decrease in the proportion of admixed genotypes from the early to the late season was detected. There was also a significant (P=0·002) increase in the proportion of loci under Hardy-Weinberg equilibrium. These two lines of evidence support the hypothesis that basidiospores can be a source of secondary inoculum. © 2012 BSPP.

Passiflora na alimentação de codornas de postura

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Efeito da endogamia na seleção genômica em populções simuladas de aves poedeiras

Pós-graduação em Genética e Melhoramento Animal - FCAV

Sistema de reprodução em populações naturais de Peltophorum dubium

A Multi-locus mixed mating model and correlated mating model were used to analyze the mating system of four natural populations of Peltophorum dubium (Sprengel) Taubert from Western Sao Paulo State, Brazil. Open pollinated seeds were collected from 19 to 33 seed-trees per population and evaluated by allozyme electrophoresis analysis. Significant differences between pollen and ovule gene frequencies were detected in more than 50% of loci in each population, indicating deviations from random mating, probably due to correlated mating, self-fertilizations and mating among relatives. The comparison the fixation index estimated from seed trees ((F) over cap (m), ranged from 0.009 to 0.285) with their progenies ((F) over cap (p), ranged from 0.127 to 0.364) suggested selection against inbreeding between offspring of adult stages. The estimates of multi-locus outcrossing rate (t(m)) ranged from 0.557 to 0.924, indicating that the species has a mixed-mating system. Differences between multi-locus and single-locus outcrossing rate (t(m)-t(s))was positive and significantly different from zero for all populations, with values ranging from 0.092 to 0.111, suggesting mating among relatives within the populations, probably due to the presence of intra-population spatial genetic structure. The mean coefficient of co-ancestry (Theta) within progenies ranged from 0.147 to 0.251; confirming that the progenies are compounded by mixtures of different kinds of relatedness. The results are discussed from the view of genetic improvement and conservation of the species.

Eficiência reprodutiva e comportamento parental de camundongos isogênicos e heterogênicos produzidos em ambiente modificado

Pós-graduação em Zootecnia - FMVZ

Traditional linkage analysis in admixed families

Currently there is no general method to study the impact of population admixture within families on the assumptions of random mating and consequently, Hardy-Weinberg equilibrium (HWE) and linkage equilibrium (LE) and on the inference obtained from traditional linkage analysis. ^ First, through simulation, the effect of admixture of two populations on the log of the odds (LOD) score was assessed, using Prostate Cancer as the typical disease model. Comparisons between simulated mixed and homogeneous families were performed. LOD scores under both models of admixture (within families and within a data set of homogeneous families) were closest to the homogeneous family scores of the population having the highest mixing proportion. Random sampling of families or ascertainment of families with disease affection status did not affect this observation, nor did the mode of inheritance (dominant/recessive) or sample size. ^ Second, after establishing the effect of admixture on the LOD score and inference for linkage, the presence of induced disequilibria by population admixture within families was studied and an adjustment procedure was developed. The adjustment did not force all disequilibria to disappear but because the families were adjusted for the population admixture, those replicates where the disequilibria exist are no longer affected by the disequilibria in terms of maximization for linkage. Furthermore, the adjustment was able to exclude uninformative families or families that had such a high departure from HWE and/or LE that their LOD scores were not reliable. ^ Together these observations imply that the presence of families of mixed population ancestry impacts linkage analysis in terms of the LOD score and the estimate of the recombination fraction. ^