Progressive erosion of genetic and epigenetic variation in callus-derived cocoa (Theobroma cacao) plants

Relatively little is known about the timing of genetic and epigenetic forms of somaclonal variation arising from callus growth. We surveyed for both types of change in cocoa (Theobroma cacao) plants regenerated from calli of various ages, and also between tissues from the source trees. For genetic change, we used 15 single sequence repeat (SSR) markers from four source trees and from 233 regenerated plants. For epigenetic change, we used 386 methylation-sensitive amplified polymorphism (MSAP) markers on leaf and explant (staminode) DNA from two source trees and on leaf DNA from 114 regenerants. Genetic variation within source trees was limited to one slippage mutation in one leaf. Regenerants were far more variable, with 35% exhibiting at least one mutation. Genetic variation initially accumulated with culture age but subsequently declined. MSAP (epigenetic) profiles diverged between leaf and staminode samples from source trees. Multivariate analysis revealed that leaves from regenerants occupied intermediate eigenspace between leaves and staminodes of source plants but became progressively more similar to source tree leaves with culture age. Statistical analysis confirmed this rather counterintuitive finding that leaves of ‘late regenerants’ exhibited significantly less genetic and epigenetic divergence from source leaves than those exposed to short periods of callus growth.

Genetic changes, intra- and inter-specific introgression in farmed Nile tilapia (Oreochromis niloticus) in Thailand

Fourteen microsatellite loci were used to examine genetic changes of four strains in Nile tilapia (Oreochromis niloticus) derived from genetically improved farmed tilapia (GIFT) and two strains derived from a local Chitralada strain of Nile tilapia in Thailand. Reference populations, including the ninth generation of GIFT strain, the original Chitralada strain, two conspecific reference populations from Ivory Coast and Uganda, and one population each of Oreochromis mossambicus and Oreochromis aureus, were also examined. Despite minor genetic changes, three of the four GIFT-derived populations retained their purity as GIFT while genetic variation did not decline. One of the GIFT-derived populations showed high levels of introgression from the Chitralada strain. Likewise, introgression from GIFT to the Chitralada-derived populations was seen. Inter-specific introgression from O. mossambicus was observed in the GIFT reference population and one of the Chitralada-derived strains. Introgression from O. aureus was detected in one of the GIFT-derived populations with a history of intensive inter-strain crossing. However, the introgression resulted in elevated genetic variation relative to the Chitralada original strains.

Genetic and phenotypic trends for growth traits of buffaloes in Brazil

The objectives this paper were to estimate genetic parameters and genetic and phenotypic trends of birth weight (BWT) and weights adjusted to 205 (WT205), 365 (WT365) and 550 (P550) days of age of beef buffaloes born from 1985 to 2003 in Brazil. For BWT and WT205 the model included direct and maternal genetic and maternal environment as random effects and contemporary and genetic groups as fixed effects. For WT365 and WT550 the same model was used except without direct maternal and maternal environmental effects. The genetic and phenotypic trends were estimated by regression of means of dependent variables on birth year of animals Regressions were obtained by using two methodologies: 1) linear regression; and 2) non-parametric splined regression. The direct heritability estimates were 0.09, 0.45, 0.46 and 0.58 for BWT, WT205, WT365 and WT550, respectively. The direct genetic trends from linear regression were 0.01, 0.23, 0.58 and 1.40 kg per year for PN, WT205, VVT365 and WT550, respectively (P<0.001 for all). Phenotypic trends were strongly positive while genetic trends were consistently positive but small. Genetic parameters indicate potential for increased rate of genetic change with full implementation of genetic improvement programs.

Life history, ecology and the biogeography of strong genetic breaks among 15 species of PaciWc rockWsh, Sebastes

Strong genetic change over short spatial scales is surprising among marine species with high dispersal potential. Concordant breaks among several species signals a role for geographic barriers to dispersal. Along the coast of California, such breaks have not been seen across the biogeographic barrier of Point Conception, but other potential geographic boundaries have been surveyed less often.;We tested for strong-population structure in 11 species of Sebastes sampled across two regions containing potential dispersal barriers, and conducted a meta-analysis including four additional species. We show two strong breaks north of Monterey Bay, spanning an oceanographic gradient and an upwelling jet. Moderate genetic structure is just as common in the north as it is in the south, across the biogeographic break at Point Conception. Gene Xow is generally higher among deep-water species, but these conclusions are confounded by phylogeny. Species in the subgenus Sebastosomus have higher structure than those in the subgenus;Pteropodus, despite having larvae with longer pelagic phases. DiVerences in settlement behavior in the face of ocean currents might help explain these diVerences. Across similar species across the same coastal environment, we document a wide variety of patterns in gene Xow, suggesting that interaction of individual species traits such as settlement behavior with environmental factors such as;oceanography can strongly impact population structure

Gene targeting approaches to complex genetic diseases: atherosclerosis and essential hypertension.

Gene targeting allows precise, predetermined changes to be made in a chosen gene in the mouse genome. To date, targeting has been used most often for generation of animals completely lacking the product of a gene of interest. The resulting "knockout" mice have confirmed some hypotheses, have upset others, but have rarely been uninformative. Models of several human genetic diseases have been produced by targeting--including Gaucher disease, cystic fibrosis, and the fragile X syndrome. These diseases are primarily determined by defects in single genes, and their modes of inheritance are well understood. When the disease under study has a complex etiology with multiple genetic and environmental components, the generation of animal models becomes more difficult but no less valuable. The problems associated with dissecting out the individual genetic factors also increases substantially and the distinction between causation and correlation is often difficult. To prove causation in a complex system requires rigorous adherence to the principle that the experiments must allow detection of the effects of changing only a single variable at one time. Gene targeting experiments, when properly designed, can test the effects of a precise genetic change completely free from the effects of differences in any other genes (linked or unlinked to the test gene). They therefore allow proofs of causation.

Genetic resource impacts of habitat loss and degradation; reconciling empirical evidence and predicted theory for neotropical trees

The theoretical impacts of anthropogenic habitat degradation on genetic resources have been well articulated. Here we use a simulation approach to assess the magnitude of expected genetic change, and review 31 studies of 23 neotropical tree species to assess whether empirical case studies conform to theory. Major differences in the sensitivity of measures to detect the genetic health of degraded populations were obvious. Most studies employing genetic diversity (nine out of 13) found no significant consequences, yet most that assessed progeny inbreeding (six out of eight), reproductive output (seven out of 10) and fitness (all six) highlighted significant impacts. These observations are in line with theory, where inbreeding is observed immediately following impact, but genetic diversity is lost slowly over subsequent generations, which for trees may take decades. Studies also highlight the ecological, not just genetic, consequences of habitat degradation that can cause reduced seed set and progeny fitness. Unexpectedly, two studies examining pollen flow using paternity analysis highlight an extensive network of gene flow at smaller spatial scales (less than 10 km). Gene flow can thus mitigate against loss of genetic diversity and assist in long-term population viability, even in degraded landscapes. Unfortunately, the surveyed studies were too few and heterogeneous to examine concepts of population size thresholds and genetic resilience in relation to life history. Future suggested research priorities include undertaking integrated studies on a range of species in the same landscapes; better documentation of the extent and duration of impact; and most importantly, combining neutral marker, pollination dynamics, ecological consequences, and progeny fitness assessment within single studies.

Defective interfering viral particles in acute dengue infections

While much of the genetic variation in RNA viruses arises because of the error-prone nature of their RNA-dependent RNA polymerases, much larger changes may occur as a result of recombination. An extreme example of genetic change is found in defective interfering (DI) viral particles, where large sections of the genome of a parental virus have been deleted and the residual sub-genome fragment is replicated by complementation by co-infecting functional viruses. While most reports of DI particles have referred to studies in vitro, there is some evidence for the presence of DI particles in chronic viral infections in vivo. In this study, short fragments of dengue virus (DENV) RNA containing only key regulatory elements at the 3' and 5' ends of the genome were recovered from the sera of patients infected with any of the four DENV serotypes. Identical RNA fragments were detected in the supernatant from cultures of Aedes mosquito cells that were infected by the addition of sera from dengue patients, suggesting that the sub-genomic RNA might be transmitted between human and mosquito hosts in defective interfering (DI) viral particles. In vitro transcribed sub-genomic RNA corresponding to that detected in vivo could be packaged in virus like particles in the presence of wild type virus and transmitted for at least three passages in cell culture. DENV preparations enriched for these putative DI particles reduced the yield of wild type dengue virus following co-infections of C6-36 cells. This is the first report of DI particles in an acute arboviral infection in nature. The internal genomic deletions described here are the most extensive defects observed in DENV and may be part of a much broader disease attenuating process that is mediated by defective viruses.

Review ["Telling the Evolutionary Time : Molecular Clocks and the Fossil Record" edited by Philip C. J. Donoghue and M. Paul Smith]

Determining the temporal scale of biological evolution has traditionally been the preserve of paleontology, with the timing of species originations and major diversifications all being read from the fossil record. However, the ages of the earliest (correctly identified) records will underestimate actual origins due to the incomplete nature of the fossil record and the necessity for lineages to have evolved sufficiently divergent morphologies in order to be distinguished. The possibility of inferring divergence times more accurately has been promoted by the idea that the accumulation of genetic change between modern lineages can be used as a molecular clock (Zuckerkandl and Pauling, 1965). In practice, though, molecular dates have often been so old as to be incongruent even with liberal readings of the fossil record. Prominent examples include inferred diversifications of metazoan phyla hundreds of millions of years before their Cambrian fossil record appearances (e.g., Nei et al., 2001) and a basal split between modern birds (Neoaves) that is almost double the age of their earliest recognizable fossils (e.g., Cooper and Penny, 1997).

Characterization of ENU-induced mutations in red blood cell structural proteins

Murine models with modified gene function as a result of N-ethyl-N-nitrosourea (ENU) mutagenesis have been used to study phenotypes resulting from genetic change. This study investigated genetic factors associated with red blood cell (RBC) physiology and structural integrity that may impact on blood component storage and transfusion outcome. Forward and reverse genetic approaches were employed with pedigrees of ENU-treated mice using a homozygous recessive breeding strategy. In a “forward genetic” approach, pedigree selection was based upon identification of an altered phenotype followed by exome sequencing to identify a causative mutation. In a second strategy, a “reverse genetic” approach based on selection of pedigrees with mutations in genes of interest was utilised and, following breeding to homozygosity, phenotype assessed. Thirty-three pedigrees were screened by the forward genetic approach. One pedigree demonstrated reticulocytosis, microcytic anaemia and thrombocytosis. Exome sequencing revealed a novel single nucleotide variation (SNV) in Ank1 encoding the RBC structural protein ankyrin-1 and the pedigree was designated Ank1EX34. The reticulocytosis and microcytic anaemia observed in the Ank1EX34 pedigree were similar to clinical features of hereditary spherocytosis in humans. For the reverse genetic approach three pedigrees with different point mutations in Spnb1 encoding RBC protein spectrin-1β, and one pedigree with a mutation in Epb4.1, encoding band 4.1 were selected for study. When bred to homozygosity two of the spectrin-1β pedigrees (a, b) demonstrated increased RBC count, haemoglobin (Hb) and haematocrit (HCT). The third Spnb1 mutation (spectrin-1β c) and mutation in Epb4.1 (band 4.1) did not significantly affect the haematological phenotype, despite these two mutations having a PolyPhen score predicting the mutation may be damaging. Exome sequencing allows rapid identification of causative mutations and development of databases of mutations predicted to be disruptive. These tools require further refinement but provide new approaches to the study of genetically defined changes that may impact on blood component storage and transfusion outcome.

Stock assessment of the Queensland-New South Wales tailor fishery (Pomatomus saltatrix)

Data on catch sizes, catch rates, length-frequency and age composition from the Australian east coast tailor fishery are analysed by three different population dynamic models: a surplus production model, an age-structured model, and a model in which the population is structured by both age and length. The population is found to be very heavily exploited, with its ability to reproduce dependent on the fishery’s incomplete selectivity of one-year-old fish. Estimates of recent harvest rates (proportion of fish available to the fishery that are actually caught in a single year) are over 80%. It is estimated that only 30–50% of one-year-old fish are available to the fishery. Results from the age-length-structured model indicate that both exploitable biomass (total mass of fish selected by the fishery) and egg production have fallen to about half the levels that prevailed in the 1970s, and about 40% of virgin levels. Two-year-old fish appear to have become smaller over the history of the fishery. This is assumed to be due to increased fishing pressure combined with non-selectivity of small one-year-old fish, whereby the one-year-old fish that survive fishing are small and grow into small two-year-old fish the following year. An alternative hypothesis is that the stock has undergone a genetic change towards smaller fish; the true explanation is unknown. The instantaneous natural mortality rate of tailor is hypothesised to be higher than previously thought, with values between 0.8 and 1.3 yr–1 consistent with the models. These values apply only to tailor up to about three years of age, and it is possible that a lower value applies to fish older than three. The analysis finds no evidence that fishing pressure has yet affected recruitment. If a recruitment downturn were to occur, however, under current management and fishing pressure there is a strong chance that the fishery would need a complete closure for several years to recover, and even then recovery would be uncertain. Therefore it is highly desirable to better protect the spawning stock. The major recommendations are • An increase in the minimum size limit from 30cm to 40cm in order to allow most one-year-old fish to spawn, and • An experiment on discard mortality to gauge the proportion of fish between 30cm and 40cm that are likely to survive being caught and released by recreational line fishers (the dominant component of the fishery, currently harvesting roughly 1000t p.a. versus about 200t p.a. from the commercial fishery).

Cancer gene signatures in risk stratification: use in personalized medicine

Cancer is a complex disease which arises due to a series of genetic changes related to cell division and growth control. Cancer remains the second leading cause of death in humans next to heart diseases. As a testimony to our progress in understanding the biology of cancer and developments in cancer diagnosis and treatment methods, the overall median survival time of all cancers has increased six fold one year to six years during the last four decades. However, while the median survival time has increased dramatically for some cancers like breast and colon, there has been only little change for other cancers like pancreas and brain. Further, not all patients having a single type of tumour respond to the standard treatment. The differential response is due to genetic heterogeneity which exists not only between tumours, which is called intertumour heterogeneity, but also within individual tumours, which is called intratumoural heterogeneity. Thus it becomes essential to personalize the cancer treatment based on a specific genetic change in a given tumour. It is also possible to stratify cancer patients into low- and high-risk groups based on expression changes or alterations in a group of genes gene signatures and choose a more suitable mode of therapy. It is now possible that each tumour can be analysed using various high-throughput methods like gene expression profiling and next-generation sequencing to identify its unique fingerprint based on which a personalized or tailor-made therapy can be developed. Here, we review the important progress made in the recent years towards personalizing cancer treatment with the use of gene signatures.

The review of recent advances in fish genetics and biotechnology

Great advances have been, and are being made in our knowledge of the genetics and molecular biology (including genomics, proteomics and structural biology). Global molecular profiling technologies such as microassays using DNA or oligonucleotide chip, and protein and lipid chips are being developed. The application of such biotechnological advances are inevitable in aquaculture in the areas of improvement of aquaculture stocks where many molecular markers such as RFLPs, AFLDs and RAPD are now available for genome analysis, finger printing and genetic linkage mapping. Transgenic technology has been developed in a number of fish species and research is being pursed to produce transgenic fish carrying genes that encode antimicrobial peptides such as lysozyme thereby achieving disease resistance in fish. Also it is a short cut to achieving genetic change for fast growth and other desirable traits like early sexual maturity, temperature tolerance and feed conversion efficiency. KEYWORDS: Fish genetics, transgenesis, monoploidy, diploidy, polyploidy,gynogenesis, androgenesis, cryopreservation.

水稻同源四倍体高代自交系农艺性状分析及遗传差异研究

课题组在不断地创制新的同源四倍体材料的同时，连续多年以提高结实率为目的培育、筛选自交系材料，已获得自交繁殖十二年的高代自交系材料。相对于诱导创制初期，材料表现出的结实率低，同种系单株间的差异较大；高代材料已表现出较显著的结实率提升和较一致的农艺性状表型。 本实验选取课题组多年培育的同源四倍体水稻高代自交系材料，通过形态学、农艺性状和细胞遗传学比较，研究水稻同源四倍体与二倍体之间的异同。结果显示，所有同源四倍体材料的染色体组成均为2N=4X=48，花粉母细胞(PMC)减数分裂行为较正常，99%以上的染色体都能在减数分裂中期I（MI）发生联会、配对，形成四价体和二价体，这与理论染色体组构成相符。在减数分裂过程中，结实率较高的材料染色体异常现象较少而结实率较低的材料染色体异常现象较严重。统计分析表明，二价体和四价体的比例对结实率没有显著影响，但是三价体的数目对结实率有一定影响。这一结果表明了结实率和细胞减数分裂行为可能存在相关性，同源四倍体的减数分裂行为为筛选高结实率的同源四倍体种系提供了依据。 然后，对同源四倍体水稻高代自交系材料进行农艺性状和品质性状的统计与分析。主要针对结实率、每穗实粒数、有效分蘖和穗长等主要农艺性状，以及直链淀粉含量这一重要的品质性状进行统计。将统计结果与1996年诱导加倍的初代材料的数据相对比分析，结果显示所有材料经过多代选育培养，其农艺性状已经有了较显著的提高，同时同源四倍体材料的农艺性状稳定性也有了较显著的提升。如结实率的提高幅度较大，所有材料的平均结实率均显著高于加倍初代，而同种材料不同单株间的结实率差异也显著地减少，变异系数（CV）的平均值由1996年的41.15%减少到了2008年的28.81%。其他重要农艺性状也有不同程度的改良，种内变异系数也相应地降低。此外，实验测量了同源四倍体材料和来源二倍体材料的直链淀粉含量。分析结果显示，部分材料的直链淀粉含量与二倍体亲本产生了较显著的差异，这可能是诱导加倍过程中的遗传变异造成的；同源四倍体材料的种内变异系数（CV）平均值由1996年的6%下降到了2008年的3.88%，显示出在品质性状方面，同源四倍体材料的遗传稳定性也有较显著的增加。同源四倍体材料农艺性状经过多年的选育，表现出一定的提升，同时，经过多年自交纯化，所有材料种系内的性状差异逐渐缩小，说明同源四倍体水稻的遗传稳定性随着自交纯化而增强，这为同源四倍体水稻的进一步选育打下了良好的基础。 最后，通过测量连续两年的自交系材料的遗传多态性，分析材料间遗传差异和种群遗传结构，深入研究连续两代材料间的遗传差异，研究同源四倍体水稻与二倍体材料遗传稳定性之间的差异。实验采用18对SSR微卫星标记对连续两代15个材料，共94份样本进行差异分析。通过扩增条带长度多态性分析，计算不同材料以及同种材料不同世代间的遗传距离，构建同源四倍体和二倍体水稻的分子指纹库，并绘制聚类图。结果显示，同源四倍体和二倍体不同材料间的遗传差异比较大，遗传距离处于0.4757至0.2816之间；而相同品种不同世代材料间的遗传差异较小，但也表现出一定的遗传差异。同种同源四倍体材料不同世代间的遗传差异比二倍体材料更大，两代四倍体材料间遗传距离处于0.1359至0.0485之间；而两代二倍体材料间的遗传距离处于均小于0.0388。结果表明，同源四倍体水稻高代材料具有一定的遗传稳定性，但与来源二倍体材料相比，其世代间的遗传变异性仍然较强。这种结果说明，经过多代的自交纯化培育，同源四倍体水稻材料能够建立起相对稳定的遗传结构，同时，其强于二倍体亲本的变异性有能够为新品种的选育，农艺性状、品质性状的改良提供一定的遗传基础。此外，分析结果表明通过分子标记辅助检验，水稻材料间的遗传多态性能够有效地区分不同的品种，这为水稻品种的分子鉴定提供了一定的依据。 本研究从细胞学鉴定，农艺性状统计分析以及分子标记辅助聚类分析多方面地对同源四倍体水稻高代系进行了研究，对探究同源四倍体水稻的遗传规律，进一步揭示其遗传特性、农艺性状的遗传构成，为进一步选育优质的多倍体水稻提供了一定的理论依据。 This group insists on creating new Autotetraploid Rice (Oryza sativa L.) materials, while improving the seed-setting of them for many years, cultivated and selected the inbred line materials, has obtained the high generation inbred lines after twelve years cultivation. Compared to the early induced materials, which shown the low seed setting, and the large difference between the different plants in the same germ-line; the high generation materials have shown significant improvement in seed setting and more uniform phenotype agronomic traits. The autotetraploid rice high generation inbred lines material, which has been cultivated for more than 12 years, was chose in this experiment. The similarities and differences between autotetraploid and diploid rice was studied through morphological, agronomic and cytogenetic ways. The results showed that all the chromosome of autotetraploid materials are composed of 2N=4X=48, the pollen mother cells (PMC) meiosis behavior is normal, more than 99% chromosomes in metaphase I(MI) were federated and paired to form tetravalents or bivalents, which constitutes a consistent theory of genome. In the meiosis process, the material with a higher seed setting showed less chromosome abnormal than the material whose seed setting is lower. However, statistical analysis showed that the bivalent and tetravalent rate had no significant impact on seed setting, but the number of trivalent had a certain impact on seed setting. The result shows that the seed setting may be related to the meiosis behavior, which provides a basis to cultivate new autotetraploid germ line with high seed setting through the meiotic behavior. Furthermore, the agronomic and quality traits of autotetraploid rice high generation inbred material were statistically analyzed. The statistically analysis was focused on major agronomic traits such as: seed setting, grains per panicle, effective tillers and panicle length, as well as the important quality trait amylose content. The statistic data was compared with the data in 1996, when the first induced generation of autotetraploid material, and the result shows that after a multi-generation breeding, the agronomic traits has been significantly improved in all the materials, while the stability of agronomic traits also significant upgraded. For instant, the seed setting increased significantly, the average seed setting of all materials was significantly higher than the first induced generation, and the differences between different plants in the same species also significantly reduced, the average of the coefficient of variation (CV) was reduced from 41.15% in 1996 to 28.81% in 2008. Other important agronomic traits had improved in different degrees; the coefficient of variation within species is also reduced accordingly. In addition, the amylose content of autotetraploid and diploid materials was measured in this experiment. The results shows that the amylose content of some of the material differed from diploid parents significantly, it may caused by the genetic change during the inducing, autotetraploid materials intra-specific coefficient of variation (CV) average reduced from 6% in 1996 to 3.88% in 2008, shows that this is a significant increase of quality traits stability in autotetraploid rice. Agronomic traits of autotetraploid material shows some improvement after years of breeding, at the same time, after years of purification, all material within the germ-line gradually narrow the differences in traits indicates that autotetraploid rice genetic stability was enhanced, which laid a good foundation for the further autotetraploid rice breeding. Finally, this experiment studied the genetic differences between materials of two generations and researched the difference of genetic stability between diploid and autotetraploid rice materials through investigating the genetic polymorphism, genetic differences between materials and population genetic structure of inbred line materials of two consecutive years.18 pairs of SSR microsatellite markers for 15 materials of two generations were used in this experiment, and the total of 94 samples were analyzed. Through the amplification length polymorphism analysis of different materials and materials in different generations, the genetic distance between materials and generations was analyzed, a diploid and autotetraploid rice molecular fingerprint database and map rendering cluster were constructed. The result shows that the genetic distance is between 0.4757 to 0.2816 among different autotetraploid and diploid materials; the genetic distance between different generations of same species was less, but also shows a certain degree of genetic differences. The inter-generational genetic differences of autotetraploid materials were greater than of the diploid materials, which are 0.1359 to 0.0485 as the genetic distance; comparing with the 0.0388 of diploid materials. The result shows that high generation inbred autotetraploid rice material has a certain genetic stability, but the genetic variation between generations is still strong comparing with the source diploid materials. It indicates that, after many generations of purification cultivation, autotetraploid rice materials established a relatively stable genetic structure, at the same time, stronger variability than its diploid parents are useful in the breeding of new varieties, provides a genetic foundation to the agronomic and quality traits improvement. In addition, the analysis result shows that the through the molecular marker-assisted testing, rice genetic polymorphism between materials can effectively distinguish different species, provides a certain basis for molecular identification of varieties of rice. A series of investigation such as cytological identification, statistical analysis of agronomic traits, molecular marker-assisted cluster analysis was applied in this experiment to research genetic pattern of autotetraploid rice high generation inbred lines, revealed the genetic characteristics and the genetic composition of agronomic traits, provides a theoretical basis for the further selection of high quality autotetraploid rice.

A Síndrome progeróide de Hutchinson-Gilford e suas complicações na cavidade oral

Projeto de Pós-Graduação/Dissertação apresentado à Universidade Fernando Pessoa como parte dos requisitos para obtenção do grau de Mestre em Medicina Dentária