Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Gene Pool”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 541 records · Page 30Linked to original sources
PubMed2004

Cassava breeding: opportunities and challenges.

Although cassava is a major food crop, its scientific breeding began only recently compared with other crops. Significant progress has been achieved, particularly in Asia where cassava is used mainly for industrial processes and no major biotic constraints affect its productivity. Cassava breeding faces several limitations that need to be addressed. The heterozygous nature of the crop and parental lines used to generate new segregating progenies makes it difficult to identify parents with good breeding values. Breeding so far has been mainly based on a mass phenotypic recurrent selection. There is very little knowledge on the inheritance of traits of agronomic relevance. Several approaches have been taken to overcome the constraints in the current methodologies for the genetic improvement of cassava. Evaluations at early stages of selection allow for estimates of general combining ability effect or breeding values of parental lines. Inbreeding by sequential self-pollination facilitates the identification of useful recessive traits, either already present in the Manihot gene pool or induced by mutagenesis.

Breeding↗
PubMed1972

Patterns of Genetic Differentiation in the Slender Wild Oat Species Avena barbata.

Allozyme frequencies at five enzyme loci were determined for 14 California populations of Avena barbata, a species introduced to California from the Mediterranean Basin during the colonization of North America. Allelic frequencies at these loci were also determined in Mediterranean collections of this species. The pattern of divergence of the California populations from the ancestral gene pool was not random and was strongly correlated with environment; thus, the pattern is not in accord with the hypothesis that most electrophoretically detectable variants are adaptively neutral. Rates of gene substitution in California were also not in accord with the neutrality hypothesis. The observations are, however, compatible with predictions of Neo-Darwinian evolutionary theory. We interpret these observations to indicate that natural selection plays a major role in determining the unique patterns of distribution of genetic variability in the slender wild oat in California.

Journal Article↗
PubMed1992

Sexually antagonistic genes: experimental evidence.

When selection differs between the sexes, a mutation beneficial to one sex may be harmful to the other (sexually antagonistic). Because the sexes share a common gene pool, selection in one sex can interfere with the other's adaptive evolution. Theory predicts that sexually antagonistic mutations should accumulate in tight linkage with a new sex-determining gene, even when the harm to benefit ratio is high. Genetic markers and artificial selection were used to make a pair of autosomal genes segregate like a new pair of sex-determining genes in a Drosophila melanogaster model system. A 29-generation study provides experimental evidence that sexually antagonistic genes may be common in nature and will accumulate in response to a new sex-determining gene.

Animals↗
PubMed2005

Exploring Lactobacillus plantarum genome diversity by using microarrays.

Lactobacillus plantarum is a versatile and flexible species that is encountered in a variety of niches and can utilize a broad range of fermentable carbon sources. To assess if this versatility is linked to a variable gene pool, microarrays containing a subset of small genomic fragments of L. plantarum strain WCFS1 were used to perform stringent genotyping of 20 strains of L. plantarum from various sources. The gene categories with the most genes conserved in all strains were those involved in biosynthesis or degradation of structural compounds like proteins, lipids, and DNA. Conversely, genes involved in sugar transport and catabolism were highly variable between strains. Moreover, besides the obvious regions of variance, like prophages, other regions varied between the strains, including regions encoding plantaricin biosynthesis, nonribosomal peptide biosynthesis, and exopolysaccharide biosynthesis. In many cases, these variable regions colocalized with regions of unusual base composition. Two large regions of flexibility were identified between 2.70 and 2.85 and 3.10 and 3.29 Mb of the WCFS1 chromosome, the latter being close to the origin of replication. The majority of genes encoded in these variable regions are involved in sugar metabolism. This functional overrepresentation and the unusual base composition of these regions led to the hypothesis that they represented lifestyle adaptation regions in L. plantarum. The present study consolidates this hypothesis by showing that there is a high degree of gene content variation among L. plantarum strains in genes located in these regions of the WCFS1 genome. Interestingly, based on our genotyping data L. plantarum strains clustered into two clearly distinguishable groups, which coincided with an earlier proposed subdivision of this species based on conventional methods.

Bacterial Proteins↗
PubMed1987

Research note: differences in major histocompatibility complex gene frequencies associated with feed efficiency and laying performance.

Associations between egg production and feed efficiency and the genes of the major histocompatibility complex (MHC) of the chicken were investigated. Breeders were selected on the basis of indexes incorporating information on body weight and egg mass, with or without feed consumption information. Over 1,000 progeny were serotyped for the erythrocyte antigen B (Ea-B) after the 6th generation of selection. The B2 and B13 haplotypes accounted for over 75% of the Ea-B gene pool in all lines. Comparing each index-selected line with the control B2 significantly increased in frequency at the expense of B13. This study further implicates MHC-linked genes as important in the physiology of growth and reproduction in the chicken.

Animal Nutritional Physiological Phenomena↗
PubMed1977

Genetic studies of the Macushi and Wapishana Indians. II. Data on 12 genetic polymorphisms of the red cell and serum proteins: gene flor between the tribes.

Blood samples from 509 Macushi (3 villages) and 623 Wapishana (11 villages) of Northern Brasil and Southern Guyana have been analyzed with respect to the phenotype and gene frequencies at the following 12 polymorphic loci: ABO, Kell-Cellano, MNSs, Rh, P, Duffy, Kidd, Diego, Lewis, Group-specific component, and the immunoglobulin allotypes of the Gm and Inv systems. The data suggest that 5-6% of the Wapishana gene pool is derived from non-Indians but only 1-2% of the Macushi. Inter- and intratribal genetic distances between villages are calculated for these data in an effort to understand gene flow between the tribes and to account for the unusual distribution of a newly-discovered genetic polymorphism of erythrocyte esterase A thus far limited to these 2 tribes (Neel et al., 1977). The data are puzzling and consistent with the possibility that both the Carib-speaking Macushi and the Arawak-speaking Wapishana have derived the esterase A allele in question from some third group now extinct or thus far undiscovered. Intertribal genetic distances based on gene frequencies at 6 loci are derived for 20 Amerindian tribes (including these 2); the "central" position of these 2 tribes can in part be explained by the active migration matrix connecting them.

ABO Blood-Group System↗
PubMed1999

Phylogeny of rice genomes with emphasis on origins of allotetraploid species.

The rice genus, Oryza, which comprises 23 species and 9 recognized genome types, represents an enormous gene pool for genetic improvement of rice cultivars. Clarification of phylogenetic relationships of rice genomes is critical for effective utilization of the wild rice germ plasm. By generating and comparing two nuclear gene (Adh1 and Adh2) trees and a chloroplast gene (matK) tree of all rice species, phylogenetic relationships among the rice genomes were inferred. Origins of the allotetraploid species, which constitute more than one-third of rice species diversity, were reconstructed based on the Adh gene phylogenies. Genome types of the maternal parents of allotetraploid species were determined based on the matK gene tree. The phylogenetic reconstruction largely supports the previous recognition of rice genomes. It further revealed that the EE genome species is most closely related to the DD genome progenitor that gave rise to the CCDD genome. Three species of the CCDD genome may have originated through a single hybridization event, and their maternal parent had the CC genome. The BBCC genome species had different origins, and their maternal parents had either a BB or CC genome. An additional genome type, HHKK, was recognized for Oryza schlechteri and Porteresia coarctata, suggesting that P. coarctata is an Oryza species. The AA genome lineage, which contains cultivated rice, is a recently diverged and rapidly radiated lineage within the rice genus.

Alcohol Dehydrogenase↗
PubMed1997

The two common mutations causing factor XI deficiency in Jews stem from distinct founders: one of ancient Middle Eastern origin and another of more recent European origin.

Previous studies showed that factor XI (FXI) deficiency commonly observed in Ashkenazi Jews is caused by two similarly frequent mutations, type II (Glu117stop) and type III (Phe283Leu) with allele frequencies of 0.0217 and 0.0254, respectively. In Iraqi Jews, who represent the ancient gene pool of Jews, only the type II mutation was observed with an allele frequency of 0.0167. In this study we sought founder effects for each mutation by examination of four FXI gene polymorphisms enabling haplotype analysis in affected Jewish patients of Ashkenazi, Iraqi, and other origins and in Arab patients. Initial population surveys of 387 Middle Eastern Jews (excluding Iraqi Jews), 560 North African/Sephardic Jews, and 382 Arabs revealed allele frequencies for the type II mutation of 0.0026, 0.0027, and 0.0065, respectively. In contrast, the type III mutation was not detected in any of these populations. All 60 independent chromosomes bearing the type III mutation were solely observed in Ashkenazi Jewish patients and were characterized by a relatively rare haplotype. All 103 independent chromosomes bearing the type II mutation in patients of Ashkenazi, Iraqi, Yemenite, Syrian, and Moroccan Jewish origin and of Arab origin were characterized by another distinct haplotype that was rare among normal Ashkenazi Jewish, Iraqi Jewish, and Arab chromosomes. These findings constitute the first example of a mutation common to Ashkenazi Jews, non-Ashkenazi Jews, and Arabs and are consistent with the origin of type II mutation in a founder before the divergence of the major segments of Jews. Our findings also indicate that the type III mutation arose more recently in an Ashkenazi Jewish individual.

Africa, Northern↗
PubMed1984

Primary structural evidence that the H-2Dq region encodes at least three distinct gene products: Dq, Lq, and Rq.

Class I gene products D, L, and R encoded by the D region of the H-2q haplotype were isolated by sequential immunoprecipitation from Nonidet P-40 extracts of B10.AKM murine spleen cells. Primary structural comparisons of these molecules were made by tryptic peptide map analyses and radiochemical amino acid sequence determinations. Partial NH2-terminal radiosequence analyses of the peptides generated by CNBr cleavage of these three molecules defined the Rq molecule as a gene product that is distinct from the Dq and Lq molecules. Comparative tryptic peptide map analyses of [3H]arginine-, [3H]lysine-, or [3H]mannose-labeled molecules were performed to determine if the Dq and Lq molecules could be distinguished. The two molecules were identical in their [3H]lysine-labeled peptides (17 in common) and [3H]mannose-labeled glycopeptides but could be differentiated by their [3H]arginine-labeled peptides (18 of 21 in common). These results suggest an amino acid sequence homology of 99% or greater between the Dq and Lq molecules. These data therefore provide structural evidence for three D region gene products and suggest that their antigenic differences are not due to post-translational glycosylation differences. Thus, the D region of the H-2q haplotype may provide an example of a relatively recent class I gene duplication, indicating that these genes are in a dynamic state of evolution through expansion or contraction of the gene pool.

Amino Acid Sequence↗
PubMed1996

African-American HLA class II allele and haplotype diversity.

Molecular genetic techniques were used to type nine loci in the HLA class II region in 241 unrelated African-Americans from New York City (NYC). Several effects attributable to recent genetic admixture were evident: the number of distinct class II alleles and haplotypes was larger in the African-Americans than in people of African or European origin, the allele frequencies were more consistently even, and linkage disequilibrium was present across the entire class II region. The African-American DRB1 allele frequencies almost always fell between frequencies among samples from northern Europe and the Gambia, two possible founding populations. The exceptions are attributed to the contribution of other genetically dissimilar African groups to the African-American gene pool. DRB1 allele frequencies (specifically DRB1*1501) and some haplotypes of DRB1-DPB1 were different in our NYC and the 11th International Histocompatibility Workshop (IHW) samples of African-Americans. The high level of allele and haplotype diversity found in African-Americans has important implications for the construction of pools of unrelated potential donors for tissue transplantation.

Alleles↗
PubMed1997

African-American HLA class II allele and haplotype diversity.

Molecular genetic techniques were used to type nine loci in the HLA class II region in 241 unrelated African-Americans from New York City (NYC). Several effects attributable to recent genetic admixture were evident: the number of distinct class II alleles and haplotypes was larger in the African-Americans than in people of African or European origin, the allele frequencies were more consistently even, and linkage disequilibrium was present across the entire class II region. The African-American DRB1 allele frequencies almost always fell between frequencies among samples from northern Europe and the Gambia, two possible founding populations. The exceptions are attributed to the contribution of other genetically dissimilar African groups to the African-American gene pool. DRB1 allele frequencies (specifically DRB1*1501) and some haplotypes of DRB1-DPB1 were different in our NYC and the 11th International Histocompatibility Workshop (IHW) samples of African-Americans. The high level of allele and haplotype diversity found in African-Americans has important implications for the construction of pools of unrelated potential donors for tissue transplantation.

Alleles↗
PubMed1987

Gene 1.2 protein of bacteriophage T7. Effect on deoxyribonucleotide pools.

The gene 1.2 protein of bacteriophage T7, a protein required for phage T7 growth on Escherichia coli optA1 strains, has been purified to apparent homogeneity and shown to restore DNA packaging activity of extracts prepared from E. coli optA1 cells infected with T7 gene 1.2 mutants (Myers, J. A., Beauchamp, B. B., White, J. H., and Richardson, C. C. (1987) J. Biol. Chem. 262, 5280-5287). After infection of E. coli optA1 by T7 gene 1.2 mutant phage, under conditions where phage DNA synthesis is blocked, the intracellular pools of dATP, dTTP, and dCTP increase 10-40-fold, similar to the increase observed in an infection with wild-type T7. However, the pool of dGTP remains unchanged in the mutant-infected cells as opposed to a 200-fold increase in the wild-type phage-infected cells. Uninfected E. coli optA+ strains contain severalfold higher levels of dGTP compared to E. coli optA1 cells. In agreement with this observation, dGTP can fully substitute for purified gene 1.2 protein in restoring DNA packaging activity to extracts prepared from E. coli optA1 cells infected with T7 gene 1.2 mutants. dGMP or polymers containing deoxyguanosine can also restore packaging activity while dGDP is considerably less effective. dATP, dTTP, dCTP, and ribonucleotides have no significant effect. The addition of dGTP or dGMP to packaging extracts restores DNA synthesis. Gene 1.2 protein elevates the level of dGTP in these packaging extracts and restores DNA synthesis, thus suggesting that depletion of a guanine deoxynucleotide pool in E. coli optA1 cells infected with T7 gene 1.2 mutants may account for the observed defects.

DNA Replication↗
PubMedDate not supplied

Genetic position of Valencia (Spain) in the Mediterranean basin according to Alu insertions.

In this work, eight human-specific Alu insertion polymorphisms (ACE, TPA25, PV92, APO, FXIIIB, D1, A25, and B65) were typed in 106 unrelated healthy individuals born in the province of Valencia (Spain), with the aim of analyzing the genetic relationships between this region of the Iberian Peninsula and other Mediterranean populations. To that end, Alu data on Eastern European, Western European, and North African populations were compiled from previous studies. The genetic information was stressed by means of genetic distances (R matrix method), nonmetric multidimensional scaling (MDS) and analyses of molecular variance (AMOVA). In Valencia, the most common Alu insertion was APO (0.940), and the least frequent was A25 (0.104). The average gene diversity (GD) computed for the sample examined was comparatively high (0.382). The insertion frequencies estimated for the eight Alu markers were very similar to the mean frequencies calculated for the whole set of populations included in the study, suggesting the hybrid nature of the Valencia's gene pool. MDS and AMOVA results generated from Alu data reveal that the Mediterranean has acted as a strong genetic boundary between the north (Europe) and the south (Northern Africa), resulting in significant gene diversity between the populations of the two regions. Restricted exclusively to the European scope, we suggest the possibility that the Mediterranean could have also acted as a migratory passageway, propitiating the dissemination of cultures and genes between the east and west of Europe and giving rise to some homogenization of gene frequencies among coastal dwelling populations.

Alu Elements↗
PubMed1985

In vivo transfer of genetic information between gram-positive and gram-negative bacteria.

A 1427-bp DNA fragment containing the kanamycin resistance gene, aphA-3, of plasmid pIP1433 from Campylobacter coli was inserted into a shuttle vector. Full expression of aphA-3 was obtained in Bacillus subtilis and in Escherichia coli. This DNA fragment was sequenced in its entirety and the starting point for aphA-3 transcription in B. subtilis, C. coli and E. coli was determined by S1 nuclease mapping. The sequence of the promoter consists of the hexanucleotides TTGACA and TATAAT, with a spacing of 17 bp. The nucleotide sequence of the aphA-3 gene from C. coli and from the streptococcal plasmid pJH1 are identical whereas they differ by two substitutions and deletion of a codon from that cloned from the staphylococcal plasmid pSH2. These results indicate a recent extension of the resistant gene pool of Gram-positive cocci to Gram-negative bacilli. From an analysis of the DNA sequences surrounding the promoter region, we concluded that the DNA fragment containing the aphA-3 gene in plasmid pJH1 has evolved by deletions from a sequence similar to that found in plasmid pIP1433.

Bacillus subtilis↗
PubMed1985

V beta gene polymorphism and a major polyclonal T cell receptor idiotype.

Genetic polymorphism in the beta variable gene pool (V beta) is responsible for the strain-specific distribution of the KJ16 T cell receptor (TcR) marker on 20% of peripheral T cells. KJ16+ strains carry two homologous V beta genes that are absent in KJ16- strains. All functional KJ16+ T cell hybrids tested express a member of this V beta subset. mRNA hybridizing to this variable-region probe can be easily detected in total splenic T cells of a prototype KJ16+ strain. Thus, 20% of the TcR from the cytotoxic and helper T cell population, with various MHC restrictions and antigen reactivities, can be generated from two V beta genes. However, their deletion appears to have no effect on the functionality of the T cell repertoire.

Animals↗
PubMed2001

Global analysis of differential gene expression after transformation with the v-H-ras oncogene in a murine tumor model.

Mouse PB-3c mast cells stably transfected with the v-H-ras oncogene induce tumor formation in vivo when implanted into mice. Such tumor cells are characterized by an autocrine IL-3 loop. DNA microarrays allow simultaneous transcript imaging of several thousand genes and the technique was applied in this tumor model to analyse gene expression following malignant transformation. Using three independent tumor lines derived from the same precursor the expression of about 400 out of 11 000 genes was modulated in each tumor. A subset of only 75 genes (0.68%) is shared and up- or downregulated in all three lines. A significant portion of this gene pool possesses functions related to tumorigenesis such as cell adhesion, signaling or transcriptional regulation. Apart from a number of expressed sequence tags (EST's) we find downregulation of four interferon-inducible genes in the tumor lines. Finally, when we extrapolate our data to the complete mouse genome, we estimate that about 500 genes are differentially expressed in tumor cells compared to the precursor cell PB-3c.

Animals↗
PubMed2000

On the origin and domestication history of Barley (Hordeum vulgare).

Remains of barley (Hordeum vulgare) grains found at archaeological sites in the Fertile Crescent indicate that about 10,000 years ago the crop was domesticated there from its wild relative Hordeum spontaneum. The domestication history of barley is revisited based on the assumptions that DNA markers effectively measure genetic distances and that wild populations are genetically different and they have not undergone significant change since domestication. The monophyletic nature of barley domestication is demonstrated based on allelic frequencies at 400 AFLP polymorphic loci studied in 317 wild and 57 cultivated lines. The wild populations from Israel-Jordan are molecularly more similar than are any others to the cultivated gene pool. The results provided support for the hypothesis that the Israel-Jordan area is the region in which barley was brought into culture. Moreover, the diagnostic allele I of the homeobox gene BKn-3, rarely but almost exclusively found in Israel H. spontaneum, is pervasive in western landraces and modern cultivated varieties. In landraces from the Himalayas and India, the BKn-3 allele IIIa prevails, indicating that an allelic substitution has taken place during the migration of barley from the Near East to South Asia. Thus, the Himalayas can be considered a region of domesticated barley diversification.

Base Sequence↗
PubMed2004

Ethiopian mitochondrial DNA heritage: tracking gene flow across and around the gate of tears.

Approximately 10 miles separate the Horn of Africa from the Arabian Peninsula at Bab-el-Mandeb (the Gate of Tears). Both historic and archaeological evidence indicate tight cultural connections, over millennia, between these two regions. High-resolution phylogenetic analysis of 270 Ethiopian and 115 Yemeni mitochondrial DNAs was performed in a worldwide context, to explore gene flow across the Red and Arabian Seas. Nine distinct subclades, including three newly defined ones, were found to characterize entirely the variation of Ethiopian and Yemeni L3 lineages. Both Ethiopians and Yemenis contain an almost-equal proportion of Eurasian-specific M and N and African-specific lineages and therefore cluster together in a multidimensional scaling plot between Near Eastern and sub-Saharan African populations. Phylogeographic identification of potential founder haplotypes revealed that approximately one-half of haplogroup L0-L5 lineages in Yemenis have close or matching counterparts in southeastern Africans, compared with a minor share in Ethiopians. Newly defined clade L6, the most frequent haplogroup in Yemenis, showed no close matches among 3,000 African samples. These results highlight the complexity of Ethiopian and Yemeni genetic heritage and are consistent with the introduction of maternal lineages into the South Arabian gene pool from different source populations of East Africa. A high proportion of Ethiopian lineages, significantly more abundant in the northeast of that country, trace their western Eurasian origin in haplogroup N through assorted gene flow at different times and involving different source populations.

Base Sequence↗