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Results for “programmed genetic variation”

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At least 127 records · Page 7Linked to original sources
PubMed2004

Genetic diversity analysis in valencia peanut (Arachis hypogaea L.) using microsatellite markers.

Cultivated peanut or groundnut (Arachis hypogaea L) is an important source of oil and protein. Considerable variation has been recorded for morphological, physiological and agronomic traits, whereas few molecular variations have been recorded for this crop. The identification and understanding of molecular genetic diversity in cultivated peanut types will help in effective genetic conservation along with efficient breeding programs in this crop. The New Mexico breeding program has embarked upon a program of improvement of Valencia peanut (belonging to the sub species fastigiata), because efforts to improve the yield potential are lacking due to lack of identified divergent exotic types. For the first time, this study has shown molecular diversity using microsatellite markers in the cultivated Valencia peanut (sub spp. fastigiata) from around the globe. In this investigation, 48 cultivated Valencia peanut genotypes have been selected and analyzed using 18 fluorescently labeled SSR (f-SSR) primer pairs. These primer pairs amplified 120 polymorphic loci among the genotypes screened and amplified from 3 to 19 alleles with an average of 6.9 allele per primer pair. The f-SSR marker data was further analyzed using cluster algorithms and principal component analysis. The results indicated that (1) considerable genetic variations were discovered among the analyzed genotypes; (2) The f-SSR based clustering could identify the putative pedigree types of the present Valencia types of diverse origins, and (3) The f-SSR in general is sufficient to obtain estimates of genetic divergence for the material in study. The results are being utilized in our breeding program for parental selection and linkage map construction.

Arachis↗
PubMed2005

QTL mapping and the genetic basis of adaptation: recent developments.

Quantitative trait loci (QTL) mapping has been used in a number of evolutionary studies to study the genetic basis of adaptation by mapping individual QTL that explain the differences between differentiated populations and also estimating their effects and interaction in the mapping population. This analysis can provide clues about the evolutionary history of populations and causes of the population differentiation. QTL mapping analysis methods and associated computer programs provide us tools for such an inference on the genetic basis and architecture of quantitative trait variation in a mapping population. Current methods have the capability to separate and localize multiple QTL and estimate their effects and interaction on a quantitative trait. More recent methods have been targeted to provide a comprehensive inference on the overall genetic architecture of multiple traits in a number of environments. This development is important for evolutionary studies on the genetic basis of multiple trait variation, genotype by environment interaction, host-parasite interaction, and also microarray gene expression QTL analysis.

Adaptation, Biological↗
PubMed2005

Mitochondrial haplotype diversity in the tortoise species Testudo graeca from North Africa and the Middle East.

BACKGROUND: To help conservation programs of the endangered spur-thighed tortoise and to gain better insight into its systematics, genetic variation and evolution in the tortoise species Testudo graeca (Testudines: Testudinidae) was investigated by sequence analysis of a 394-nucleotide fragment of the mitochondrial 12S rRNA gene for 158 tortoise specimens belonging to the subspecies Testudo graeca graeca, Testudo graeca ibera, Testudo graeca terrestris, and a newly recognized subspecies Testudo graeca whitei. A 411-nucleotide fragment of the mitochondrial D-loop was additionally sequenced for a subset of 22 T. graeca, chosen because of their 12S gene haplotype and/or geographical origin. RESULTS: Haplotype networks generated by maximum-likelihood and neighbor-joining analyses of both the separate and the combined sequence data sets suggested the existence of two main clades of Testudo graeca, comprising Testudo graeca from northern Africa and Testudo graeca from the Turkey and the Middle East, respectively. CONCLUSION: Mitochondrial DNA haplotyping suggests that the tortoise subspecies of T. g. graeca and T. g. ibera are genetically distinct, with a calculated divergence time in the early or middle Pleistocene. Other proposed subspecies could not clearly be recognized based upon their mt haplotypes and phylogenetic position, and were either part of the T. g. graeca or of the T. g. ibera clade, suggesting that genetic evidence for the existence of most of the 15 proposed subspecies of T. graeca is weak.

Africa, Northern↗
PubMed1989

[Genetic regulatory mechanisms of bacterial virulence].

Bacterial virulence is due to the action of different virulence factors (e.g. adhesins, toxins, capsules). Virulence factors are encoded by special genes termed as virulence genes or virulence determinants. The degree of virulence of one particular bacterial strain depends on the activity of the corresponding virulence genes. Several mechanisms are involved in the regulation of activity of virulence determinants: plasmids and bacteriophages may be received or lost and chromosomal sequences may be deleted. Such processes are directly responsible for the presence or absence of virulence genes in the bacterial genome. Programmed genetic rearrangements may lead to a switch of promoter sequences and are therefore responsible for a variation of virulence expression. "Jumping" of DNA sequences (transposition) and subsequent recombinational events may also cause antigenic variation of virulence factors. In addition frame shift mutations may influence the expression of virulence genes. Transregulatory factors may also influence the expression of virulence factors of pathogenic bacteria. These systems positively influence the expression of different virulence factors in a coordinative manner. They can be triggered by environmental signals.

Animals↗
PubMed1988

Parental age dependent changes as a source of genetic variation in Drosophila melanogaster.

It has been shown repeatedly that numerous cumulative changes occur in chromosomes of D. melanogaster, as an effect of ageing which, especially in the homozygous state, significantly affect different fitness components of their carriers. It appears that the observed age-affected events are produced by systematic and ontogenetically programmed changes in genetic loads at specific chromosomes, which are transferable to following generations. It has been suggested that such changes could be of mutational origin, and that they could be more frequent at gene loci which are epigenetically active during ontogenesis. It was demonstrated that a large sample of identical chromosomes behave quite differently in the homozygous state when obtained from aged compared to non-aged parents, producing a significant decrease in relative viability, length of preadult development, and longevity of their carriers, as well as in the frequency of recombinations of corresponding chromosomes. A specific treatment by streptomycin resulted in remarkably milder effects of ageing, which is in accordance with the statement of some authors that such a treatment may diminish the frequency of spontaneous recessive mutations in their carriers. Thus the observed age-affected changes could be an important source of developmental and evolutionary variation of living organisms.

Aging↗
PubMed2003

Mapping quantitative trait loci affecting female reproductive traits on porcine chromosome 8.

An understanding of the genetic control of porcine female reproductive performance would offer the opportunity to utilize natural variation and improve selective breeding programs through marker-assisted selection. The Chinese Meishan is one of the most prolific pig breeds known, farrowing three to five more viable piglets per litter than the European Large White breed. This difference in prolificacy is attributed to the Meishan's superior prenatal survival levels. The present study utilized a three-generation cross in which the founder grandparental animals were purebred Meishan and Large White pigs in a scan for quantitative trait loci (QTL) on porcine chromosome 8 (SSC8) associated with reproductive performance. Reproductive traits, including number of corpora lutea (ovulation rate), teat number, litter size, and prenatal survival, were recorded for as many as 220 F2 females. Putative QTL for the related traits of litter size and prenatal survival were identified at the distal end of the long arm of SSC8. A physiological candidate gene, SPP1, was found to lie within the 95% confidence interval of these QTL. A suggestive QTL for teat number was revealed on the short arm of SSC8. The present study demonstrates, to our knowledge, the first independent confirmation of QTL for fecundity on SSC8, and these QTL regions provide a crucial starting point in the search for the causal genetic variants.

Algorithms↗
PubMedDate not supplied

Microsatellite diversity in captive bottlenose dolphins (Tursiops truncatus).

The utility of microsatellites for managing captive Tursiops truncatus was investigated. Specifically the level of genetic diversity among the loci examined and their usefulness for resolving paternity was assessed. Overall a relatively low level of genetic variation was found among captive dolphins. In addition, a high percentage of common alleles was found among dolphins belonging to different morphotypes (inshore versus offshore). The implications of these findings are discussed and suggestions are given for the use of genetic markers in captive propagation programs for T. truncatus.

Animals↗
PubMed2006

Molecular scanning of the gene for programmed cell death-1 (PDCD-1) as a candidate for type 1 diabetes susceptibility.

Multiple genes are involved in the susceptibility to autoimmune type 1 diabetes. The immunoreceptor programmed cell death-1 (PDCD-1), an inhibitory costimulatory molecule regulating peripheral tolerance, was reported to play a role in the development of type 1 diabetes, making the human PDCD-1 gene, PDCD1, as a candidate for disease susceptibility. In this article, we sequenced all 5 exons and exon-intron junctions of PDCD1 in Japanese subjects, and found 10 sequence variants. Preliminary data suggested no association of these polymorphisms with type 1 diabetes. These sequence variants are valuable for further studies to clarify contribution of PDCD1 to susceptibility to type 1 diabetes.

Amino Acid Substitution↗
PubMed2000

Control of insect pests with entomopathogenic nematodes: the impact of molecular biology and phylogenetic reconstruction.

Entomopathogenic nematodes are excellent biological control agents. Utilization of these nematodes is developing rapidly with almost a doubling of newly described species in the past five years. Advances in molecular biology and phylogenetic reconstruction have revolutionized understanding of population structure, identification, genetic improvement, systematics, and the symbiosis between entomopathogenic nematodes and their bacteria. Population structure provides the most fundamental information for reliable identification of species and unique genetic variants. Such information could be further assessed for nematode potential as biological control agents. Phylogenetic reconstruction is an important approach for understanding multitrophic interactions among entomopathogenic nematodes, symbiotic bacteria, and their insect hosts. Phylogenetic reconstruction is also important for the development of a natural and stable type of systematics, which can provide guidelines for selecting appropriate entomopathogenic nematode species for particular biological control programs.

Animals↗
PubMed2003

Congenital adrenal hyperplasia: should nationwide screening be implemented in Thailand?

A project to establish the Thailand National Neonatal Screening Program was started in 1996 with the objective of screening every newborn for congenital hypothyroidism and phenylketonuria. Over a million newborns were screened and over 430 abnormal cases were detected. A study was also conducted to determine the feasibility of including CAH screening in the program. The incidence of this disease has not yet been clearly determined. Since 1999, 58,563 newborns have been screened for CAH and 144 newborns with serum 17-OHP higher than 40 ng/mL were recalled for confirmatory tests. Of those, 68 were retested and 6 were found to have elevated 17-OHP levels. Two were confirmed with salt wasting CAH one month after birth, two others were diagnosed with another disease that caused electrolyte imbalance, one patient died, and the sixth required further clinical diagnosis. Five other babies were reported dead before the second specimens could be collected for confirmation. It appears that CAH may be one of the underlying causes of death among Thai newborns and the incidence may be higher than thus far shown due to incomplete confirmation of positive screens and deaths to some infants.

Adrenal Hyperplasia, Congenital↗
PubMed2007

Appraisal of the consequences of the DDT-induced bottleneck on the level and geographic distribution of neutral genetic variation in Canadian peregrine falcons, Falco peregrinus.

Peregrine falcon populations underwent devastating declines in the mid-20th century due to the bioaccumulation of organochlorine contaminants, becoming essentially extirpated east of the Great Plains and significantly reduced elsewhere in North America. Extensive re-introduction programs and restrictions on pesticide use in Canada and the United States have returned many populations to predecline sizes. A proper population genetic appraisal of the consequences of this decline requires an appropriate context defined by (i) meaningful demographic entities; and (ii) suitable reference populations. Here we explore the validity of currently recognized subspecies designations using data from the mitochondrial control region and 11 polymorphic microsatellite loci taken from 184 contemporary individuals from across the breeding range, and compare patterns of population genetic structure with historical patterns inferred from 95 museum specimens. Of the three North American subspecies, the west coast marine subspecies Falco peregrinus pealei is well differentiated genetically in both time periods using nuclear loci. In contrast, the partitioning of continental Falco peregrinus anatum and arctic Falco peregrinus tundrius subspecies is not substantiated, as individuals from these subspecies are historically indistinguishable genetically. Bayesian clustering analyses demonstrate that contemporary genetic differentiation between these two subspecies is mainly due to changes within F. p. anatum (specifically the southern F. p. anatum populations). Despite expectations and a variety of tests, no genetic bottleneck signature is found in the identified populations; in fact, many contemporary indices of diversity are higher than historical values. These results are rationalized by the promptness of the recovery and the possible introduction of new genetic material.

Animals↗
PubMedDate not supplied

Genetics of human body size and shape: complex segregation analysis.

The genetic component in a mixed heritability model, including major gene, multifactorial and sibling environment transmissible components, was studied for some 20 anthropometric traits in two ethnically different samples. The first sample comprised 305 Mexican nuclear families, and the second comprised 83 Ashkenazi Jewish nuclear families living in Israel. All variables, after adjustment for age and sex, were subjected to principal-components analysis (PCA) in each sample separately. The mixed model of inheritance as implemented in the computer program POINTER was used in the present study. An attempt was made to evaluate genetic effects in the variation of the first principal components (PCs). PCA showed a clear separation of variables and was easily interpretable. The PC1 was a credibly general size factor. This factor alone accounted for about 30% of the total variance. Other components are rather shape factors for various combinations of traits. The testing of several genetic hypothesis showed the following: (1) For all factor scores the genetic component was high and statistically significant. (2) In a Mexican sample, for PC1 and PC2, both major gene and polygenes contributed significantly to the total variation of these variables; in the major locus the alleles were most probably codominant. (3) For all other PCs the major gene effect hypothesis was rejected, with more than 50% of the variation attributable to the polygenes contribution. (4) No evidence was found for sibling environmental resemblance in either sample.

Adolescent↗
PubMed2004

Implications of the age range in a population-based BRCA1 testing program with eligibility based on family history of breast and ovarian cancer.

The current options available to BRCA1 mutation carriers can be classified as either cancer risk reduction or increased disease surveillance. Risk reduction might be preferable to young women. Increased surveillance might be more attractive to women when their cancer risk is highest. The aim of this report is to estimate the sensitivity, specificity and ability to detect carriers for a population-based BRCA1 testing program with eligibility based on family history of cancer, and examine the effect of age on the program's performance. A computer model was used to simulate the incidence of breast and ovarian cancer in a woman's family, based on her BRCA1 mutation carrier status. Age-specific estimates of the sensitivity and specificity for family history as an indicator of mutation status were applied to local population figures. Sensitivity of the program increased with the age of the proband and the size of her family. Sensitivity ranged from 0.33 for 20-year-olds with small families, to 0.98 for 60-year-olds with large families. Specificity was greater than 0.95, regardless of a woman's age or family size. If 0.12% of people carry a BRCA1 mutation, a province-wide testing program for people aged 20-69 with referrals based only on family history would have a sensitivity of 0.55. Only 2% of the genetic test results would be positive. The acceptability of a genetic testing program depends on its sensitivity and specificity, and on the options available to women who are found to carry a mutation. Compared with variation due to family size, the program sensitivity and specificity does not differ substantially amongst the various age groups.

Adult↗
PubMed1995

DnaSP, DNA sequence polymorphism: an interactive program for estimating population genetics parameters from DNA sequence data.

DnaSP, DNA sequence polymorphism, is an interactive computer program for the analysis of DNA polymorphism from nucleotide sequence data. The program, addressed to molecular population geneticists, calculates several measures of DNA sequence variation within and between populations, linkage disequilibrium parameters and Tajima's D statistic. The program, which is written in Visual Basic v. 3.0 and runs on an IBM-compatible PC under Windows, can handle a large number of sequences of up to thousands of nucleotides each.

Animals↗
PubMed2025

Exploration of the genetic diversity of Avena Fatua L. (wild oat) through genotyping-by-sequencing and SDS-PAGE.

BACKGROUND: The consumption of oats has rapidly increased due to their exceptional nutritional value. However, concerns over genetic erosion have emerged as oat breeding programs rely on a highly limited genetic pool. This study aimed to expand the genetic diversity pool of oats by collecting wild oat (Avena fatua L.) populations in South Korea and assessing their genetic diversity and seed storage protein patterns. RESULTS: A total of 237 A. fatua individuals were collected in 2022 from eight regions in the southwestern coastal areas of South Korea. Genetic diversity and seed storage protein patterns were analyzed using genotyping-by-sequencing (GBS) and sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE). The GBS analysis identified 20,836 single-nucleotide polymorphisms (SNPs). An analysis of molecular variance (AMOVA) based on regional populations revealed that 40.9% of the genetic variation was attributed to differences among populations, while 59.1% was within populations, indicating high genetic differentiation within regional populations. Subsequent population structure analysis and discriminant analysis of principal components (DAPC) both stated the formation of two distinct genetic groups, with an AMOVA value of 70.9% between the groups, suggesting a high level of genetic variation. Pairwise FST analysis was conducted to compare the genetic differentiation between two populations, revealing that Jindo and Jangheung exhibited the highest level of genetic differentiation (FST = 0.795) among the geographic groups. Seed storage proteins were analyzed using SDS-PAGE, and the patterns were grouped using k-means clustering. A comparison between the groups based on protein patterns and those based on genetic variation revealed no significant correlation. CONCLUSION: This study provides data on the genetic diversity of A. fatua, a wild relative of cultivated oats, aimed at expanding the genetic pool of oats for future breeding programs. These findings are expected to be a foundational resource for oat breeding and genetic improvement efforts.

Genetic Variation↗
PubMed2006

High ponderal index at birth predicts high estradiol levels in adult women.

Inter-individual variation in levels of sex hormones results from differences in genetic, developmental, and environmental factors. We tested a hypothesis that programming of the fetal neuroendocrine axis may predispose some women to produce higher levels of steroid hormones during their menstrual cycles as adults. One hundred forty-five regularly menstruating 24- to 36- year-old women collected daily saliva samples for one menstrual cycle. Data on women's birth weights and birth lengths were obtained from medical records. A positive relationship was observed between ponderal index at birth (an indicator of nutritional status, calculated as birth weight/(birth length)(3)) and levels of estradiol (E2) in menstrual cycles, after controlling for potential confounding factors. Mean E2 was 16.4 pmol/l in the low ponderal index tertile, 17.3 pmol/l in the moderate ponderal index tertile, and 19.6 pmol/l in the high ponderal index tertile (the high ponderal index group had significantly higher E2 than both low and moderate ponderal index groups, P=0.0001). This study shows a positive association between ponderal index recorded for women at birth and levels of E2 measured during their menstrual cycles as adults. This suggests that conditions during fetal life influence adult production of reproductive hormones and may contribute to inter-individual variation in reproductive function. In addition, because large size at birth is one of the factors linked with an increased risk of breast cancer, our findings provide a physiological link for the observed positive relationship between indicators of energetic conditions during fetal growth and breast cancer in women.

Adult↗