Application of DNA fingerprints for cell-line individualization.

DNA fingerprints of 46 human cell lines were derived using minisatellite probes for hypervariable genetic loci. The incidence of 121 HaeIII DNA fragments among 33 cell lines derived from unrelated individuals was used to estimate allelic and genotypic frequencies for each fragment and for composite individual DNA fingerprints. We present a quantitative estimate of the extent of genetic difference between individuals, an estimate based on the percentage of restriction fragments at which they differ. The average percent difference (APD) among pairwise combinations from the population of 33 unrelated cell lines was 76.9%, compared with the APD in band sharing among cell lines derived from the same individual (less than or equal to 1.2%). Included in this survey were nine additional cell lines previously implicated as HeLa cell derivatives, and these lines were clearly confirmed as such by DNA fingerprints (APD less than or equal to 0.6%). On the basis of fragment frequencies in the tested cell line population, a simple genetic model was developed to estimate the frequencies of each DNA fingerprint in the population. The median incidence was 2.9 X 10(-17), and the range was 2.4 X 10(-21) to 6.6 X 10(-15). This value approximates the probability that a second cell line selected at random from unrelated individuals will match a given DNA fingerprint. Related calculations address the chance that any two DNA fingerprints would be identical among a large group of cell lines. This estimate is still very slight; for example, the chance of two or more common DNA fingerprints among 1 million distinct individuals is less than .001. The procedure provides a straightforward, easily interpreted, and statistically robust method for identification and individualization of human cells.     

Effect of rabbit line on a program of cryopreserved embryos by vitrification

The aim of this study was to assess the application of a cryopreservation program to preserve two selected rabbit lines. One of them was selected by litter size at weaning, line V (Synthetic breed). The second, line R (synthetic breed), was selected by growth rate. In this study, embryos were collected, from donor does belonging to the 7th and 15th generations of lines R and V, respectively, were vitrified and were stored from 1992-1993. Those embryos from donor does belonging to the 17th and 21st generations of lines R and V respectively, were vitrified and sotred from 1998-1999. Embryo transfers were carried out in 1999. Morphologically normal embryos at the morulae stage were cryopreserved by vitrification in a 2.8 M dimethyl-sulfoxide + 3.5 M ethylene-glycol + 0.3 g x L(-1) bovine serum albumine in Dulbecco phosphate buffered saline solution. The main problem in the cryopreservation program was the low embryo production efficiency: significant differences were obtained in recovery efficiency between lines and line R showed the lowest proportion of donor does with 55% (at least 4 normal embryos) vs. 72% in line V. However, after transfer in recipient does of line V, the fertility rate at birth (81%), the rate of alive born by pregnant recipients (43%) and the number of males and does with offspring (9 to 18 different males, 12 to 32 females) enabled the different generations from each line to be re-established and studies on the selection process genetic gain to be developed.     

Correlated effects of the response to conditioned medium in the flour beetle,Tribolium castaneum

Dispersal rates were measured in lines selected for high and low response of egg production to conditioned media, and responsivness of egg production was measured in lines selected for high and low dispersal. A positive correlation was found between these two traits, each of which had previously been found to have a simple genetic basis. It is suggested that in Tribolium castaneum the sensitivity to environmental conditions is mediated through a Sensor gene, which can activate either response, according to circumstances.     

Indirect consequences of artificial selection on plasticity to light quality in Arabidopsis thaliana

Covariation between light quality- and photoperiod-mediated phenotypic plasticity was investigated using Arabidopsis thaliana. Three episodes of artificial selection were imposed on an index that quantified the plastic response to reduced red to far-red ratios (R:FR), with higher index values indicating greater plasticity. Relative to control lines, two high plasticity (HP) lines showed 1.6- and 2.4-fold increases in the index; low plasticity (LP) lines showed 1.4- and 1.1-fold decreases. A factorial experiment combining high and low R:FR conditions with long and short photoperiods assessed indirect consequences of selection on plasticity. Despite divergent R:FR-mediated plasticities in HP vs. LP lines, all four lines showed increases in photoperiod-mediated responses and decreases in mean leaf number. Complex relationships among trait means, plasticities and underlying mechanisms caution against generalizing about the genetic architecture of plastic traits. Partially independent developmental and evolutionary responses to R:FR and photoperiod are somewhat unsurprising, given this species' cosmopolitan nature.     

Direct Response to Selection for Postweaning Gain in the Rat

The effectiveness of selection for 3–9-week gain was examined in a population of rats with a history of past selection for high 3–9-week gain. Lines were selected for high (U line) and low (D line) 3–9-week gain with two replicates of each line. Two randomly selected lines were also kept, one originating from the same base population as the two selected lines (R line) and the other originating from a population that had been randomly mated for the previous 27 generations (C line). Two replicates of each of these lines were kept. After seven generations of selection, a randomly selected line (relaxed line) was formed from each of the two upward- and each of the two downward-selected lines. Results have been presented for 13 generations of selection. The environmental trend for 3–9-week gain, as indicated by the randomly selected R and C lines, was consistently negative in all four lines. Realized heritabilities calculated by deviating the response to selection from the trend in the R or C lines resulted in non-significantly higher values in the D lines than the U lines. Six generations of relaxation of selection indicated no effect of natural selection in the U lines or the D lines. The relative magnitude of the drift, error and common environmental variances were estimated by the methods given by Hill (1971). The estimates of these parameters then led to calculation of the degree of bias in the sampling variances of the realized heritability estimates. As was predicted by Hill (1971), estimates of the variance of realized heritabilities obtained by using standard regression techniques were less than those obtained using Hill''s formulae. The results are discussed in relation to other similar studies with rats and mice.     

Characterization of radiation/fusion hybrids containing parts of human chromosome 10 and their use in mapping chromosome 10-specific probes.

We have characterized a panel of somatic cell hybrid cell lines which contain different portions of human chromosome 10. Genomic DNA from the somatic cell hybrids was tested for hybridization with each of an ordered set of probes used previously to construct a genetic map of chromosome 10, as well as several additional probes, previously localized by in situ hybridization. Hybridization of an unmapped probe to the cell line DNAs can be used to determine its most likely position on the chromosome relative to the mapped set of probes. Genomic DNA from two of the cell lines has been used to construct region-specific cosmid and bacteriophage libraries, and clones derived from these libraries were localized by hybridization to the panel of hybrid cell lines. Several of these probes reveal restriction fragment length polymorphisms which have been genetically mapped. Three of the probes map near the locus for multiple endocrine neoplasia type 2A, and one of these probes, BG-JC353 (D10S167), maps between RBP3 and TB14.34 (D10S34). Another probe, CRI-J282 (D10S104), is close to the FNRB locus. The panel of hybrid cell lines is thus useful for rapidly localizing unmapped probes and as a source of DNA for the construction of recombinant libraries derived from specific regions of the chromosome.     

Developmental and age-specific effects of selection on divergent virgin life span on fat content and starvation resistance in Drosophila melanogaster

Investigations into the genetic basis of longevity variation have shown life span to be positively correlated with starvation resistance and negatively with female fecundity, both of which rely on lipid content. To assess the firmness of this relation, we assayed correlated responses in age-specific relative fat content (RFC) and starvation resistance in lines successfully selected for divergent virgin life span. We have previously demonstrated that genetic differentiation in female fecundity between our selection lines had disappeared during relaxation of selection. Therefore, we also expected genetic differences in lipid content and starvation resistance to have disappeared. However, RFC and starvation resistance were still significantly lower in short-lived flies than in control flies. Surprisingly, also in long-lived flies RFC and starvation resistance were mostly, but not invariably, found to be significantly lower than in control flies. These results indicate that the genetic correlation of RFC and starvation resistance with reproduction has broken down. Furthermore, the relationship between life span and starvation resistance appears to be more complex than previously anticipated. Also, we could demonstrate that differences in RFC were not brought about by differences in lipid accumulation during adult life, but were already present at eclosion. These findings suggest that pre-adult developmental pathways already impact on the rate of ageing of the adult fly.     

Molecular modeling-based analysis of interactions in the RFC-dependent clamp-loading process

Replication and related processes in eukaryotic cells require replication factor C (RFC) to load a molecular clamp for DNA polymerase in an ATP-driven process, involving multiple molecular interactions. The detailed understanding of this mechanism is hindered by the lack of data regarding structure, mutual arrangement, and dynamics of the players involved. In this study, we analyzed interactions that take place during loading onto DNA of either the PCNA clamp or the Rad9-Rad1-Hus1 checkpoint complex, using computationally derived molecular models. Combining the modeled structures for each RFC subunit with known structural, biochemical, and genetic data, we propose detailed models of how two of the RFC subunits, RFC1 and RFC3, interact with the C-terminal regions of PCNA. RFC1 is predicted to bind PCNA similarly to the p21-PCNA interaction, while the RFC3-PCNA binding is proposed to be similar to the E. coli delta-beta interaction. Additional sequence and structure analysis, supported by experimental data, suggests that RFC5 might be the third clamp loader subunit to bind the equivalent PCNA region. We discuss functional implications stemming from the proposed model of the RFC1-PCNA interaction and compare putative clamp-interacting regions in RFC1 and its paralogs, Rad17 and Ctf18. Based on the individual intermolecular interactions, we propose RFC and PCNA arrangement that places three RFC subunits in association with each of the three C-terminal regions in PCNA. The two other RFC subunits are positioned at the two PCNA interfaces, with the third PCNA interface left unobstructed. In addition, we map interactions at the level of individual subunits between the alternative clamp loader/clamp system, Rad17-RFC(2-5)/Rad9-Rad1-Hus1. The proposed models of interaction between two clamp/clamp loader pairs provide both structural framework for interpretation of existing experimental data and a number of specific findings that can be subjected to direct experimental testing.     

Intra- and Interpopulation Genome Variation In Meloidogyne arenaria

The genetic heterogeneity of two M. arenaria race 2 populations (designated Pelion and Govan) was examined using RFLP analysis of 12 clonal lines established from single egg masses (six distinct clonal lines from each population). These populations are essentially identical by traditional biochemical and race identification schemes; however, the Govan population is more aggressive than the Pelion population, producing larger galls and exhibiting greater reproductive capabilities on many soybean cultivars and experimental accessions. Variation at the genomic DNA level was examined using probes representative of expressed DNA sequences present in the eukaryotic genome. Ribosomal DNA, interspersed repeated sequences, and cDNA probes were tested for detection of polymorphism within and between single egg mass lines of each population. Cloned cDNAs and ribosomal intergenic spacer sequences detect polymorphism both within and between populations, demonstrating the usefulness of these sequence classes for molecular genetic analysis of population structure and genome evolution.     

Genetic similarity and relationships of DNA fingerprints with performance and with heterosis in Japanese quail lines from two origins and under reciprocal recurrent or within-line selection for early egg production

DNA fingerprints of Japanese quail male and female pure line breeders were obtained with probes 33.6, 33.15, and R18.1 and they yielded a total of 59 scoreable bands. Bandsharing (0 < BS < 1) was calculated within and between six quail lines of two origins, and under reciprocal recurrent (AA and BB), within-line (DD and EE) or no (PP and FF) selection. Twenty one pair types were compared. BS was 0.30 higher within line than between lines. BS with the control line was smaller for reciprocal recurrent selection lines than for lines under individual selection. Bandsharing between the two reciprocal recurrent selection lines was 0.19 lower than between lines under individual selection. These results indicate that the two selection methods had different effects on the genetic constitution of the lines, in agreement with previous observations made from the analysis of biochemical polymorphisms with the same set of birds. Egg production and weight traits of pure and crossbred progeny from fingerprinted quail were obtained and compared, and a linear relationship with the measure of bandsharing was estimated. No significant regression coefficient of performance on BS was found over all progeny genetic types. Heterosis from individual matings could also be estimated under the two selection methods since the same birds were parents of both pure and crossbred performance-tested quail. The association of heterosis with the difference between BS of parents of the purebreds and BS of parents of their half-sib crossbreds was favourable and significant for early production traits in lines DD and EE, but no relationship was found in lines AA and BB. These results indicate that the high level of heterosis obtained through reciprocal recurrent selection, and the heterosis observed under within-line selection may have, partly at least, a different genetic determinism. Therefore, the relationship of heterosis with BS may also depend on the past history of selection in the lines.     

Use of a novel outbred by inbred F1 cross to detect genetic markers for growth

A unique outbred by inbred F1 resource population was established. The population structure facilitated the unique opportunity of examining gene by genetic background interaction through crossing two modern broiler sires with dams from two unrelated inbred lines, with no selection for growth rate, to produce about 600 F1 chicks. Pools of DNA were generated from the phenotypic extremes (20% high and low) for 8-week body weight for each of the four combinations of sire and dam line. For one sire family, pools were also separately generated for each sex. The pools were genoyped with 25 informative (segregating) microsatellites. This unique F1 cross between outbred and inbred populations allowed use of the inbred alleles as an 'internal control' for polymerase chain reaction amplification quality in DNA pools. Ten microsatellites showed marked differences (P < 0.05) in allele frequencies between high and low pools, suggesting an association between marker and quantitative trait loci (QTL). These differences were verified using selective genotyping. For many markers, differences in allele frequencies between the high and the low pools, or marker effect, varied between the two dam lines and the two sexes, suggesting an interaction between some genes and the genetic background as represented by different dam lines or sexes. The suggestive marker-QTL associations identified in this F1 population demonstrate the efficiency of this population design while different QTL effects in different genetic line crosses and sexes highlight the importance of gene by genetic background interaction in QTL detection.     

Rfc5, in cooperation with rad24, controls DNA damage checkpoints throughout the cell cycle in Saccharomyces cerevisiae

RAD24 and RFC5 are required for DNA damage checkpoint control in the budding yeast Saccharomyces cerevisiae. Rad24 is structurally related to replication factor C (RFC) subunits and associates with RFC subunits Rfc2, Rfc3, Rfc4, and Rfc5. rad24Delta mutants are defective in all the G(1)-, S-, and G(2)/M-phase DNA damage checkpoints, whereas the rfc5-1 mutant is impaired only in the S-phase DNA damage checkpoint. Both the RFC subunits and Rad24 contain a consensus sequence for nucleoside triphosphate (NTP) binding. To determine whether the NTP-binding motif is important for Rad24 function, we mutated the conserved lysine(115) residue in this motif. The rad24-K115E mutation, which changes lysine to glutamate, confers a complete loss-of-function phenotype, while the rad24-K115R mutation, which changes lysine to arginine, shows no apparent phenotype. Although neither rfc5-1 nor rad24-K115R single mutants are defective in the G(1)- and G(2)/M-phase DNA damage checkpoints, rfc5-1 rad24-K115R double mutants become defective in these checkpoints. Coimmunoprecipitation experiments revealed that Rad24(K115R) fails to interact with the RFC proteins in rfc5-1 mutants. Together, these results indicate that RFC5, like RAD24, functions in all the G(1)-, S- and G(2)/M-phase DNA damage checkpoints and suggest that the interaction of Rad24 with the RFC proteins is essential for DNA damage checkpoint control.     

Destabilizing Effect of Chicken Selection for the Functional Adrenal Reserves

Chicken lines produced by divergent selection for the functional adrenal reserves showed significant between-line differences in the content of corticosterone and other hormones (thyroxin, progesterone), as well as in body weight, early maturation, and egg yield. DNA fingerprinting with the pGB725 probe revealed molecular changes in genomic DNA of the chicken lines subjected to plus and minus selection. The genetic distances between the original population and the selected chicken lines, which were estimated from the molecular hybridization patterns, reflected the history of breeding. Analysis of mixed DNA from several individuals of each line revealed specific hybridization bands that could serve as DNA markers during selection for the high and low corticosterone levels in blood.     

Development and application of a 6.5 million feature affymetrix genechip® for massively parallel discovery of single position polymorphisms in lettuce (Lactuca spp.)

ABSTRACT: BACKGROUND: High-resolution genetic maps are needed in many crops to help characterize the genetic diversity that determines agriculturally important traits. Hybridization to microarrays to detect single feature polymorphisms is a powerful technique for marker discovery and genotyping because of its highly parallel nature. However, microarrays designed for gene expression analysis rarely provide sufficient gene coverage for optimal detection of nucleotide polymorphisms, which limits utility in species with low rates of polymorphism such as lettuce (Lactuca sativa). RESULTS: We developed a 6.5 million feature Affymetrix GeneChip? for efficient polymorphism discovery and genotyping, as well as for analysis of gene expression in lettuce. Probes on the microarray were designed from 26,809 unigenes from cultivated lettuce and an additional 8,819 unigenes from four related species (L. serriola, L. saligna, L. virosa and L. perennis). Where possible, probes were tiled with a 2 bp stagger, alternating on each DNA strand; providing an average of 187 probes covering approximately 600 bp for each of over 35,000 unigenes; resulting in up to 13 fold redundancy in coverage per nucleotide. We developed protocols for hybridization of genomic DNA to the GeneChip? and refined custom algorithms that utilized coverage from multiple, high quality probes to detect single position polymorphisms in 2 bp sliding windows across each unigene. This allowed us to detect greater than 18,000 polymorphisms between the parental lines of our core mapping population, as well as numerous polymorphisms between cultivated lettuce and wild species in the lettuce genepool. Using marker data from our diversity panel comprised of 52 accessions from the five species listed above, we were able to separate accessions by species using both phylogenetic and principal component analyses. Additionally, we estimated the diversity between different types of cultivated lettuce and distinguished morphological types. CONCLUSION: By hybridizing genomic DNA to a custom oligonucleotide array designed for maximum gene coverage, we were able to identify polymorphisms using two approaches for pair-wise.     

Rflps for Somatotropic Genes Identify Quantitative Trait Loci for Growth in Mice

Restriction fragment length polymorphisms for somatotropic genes were tested for associations with body weight and postweaning growth rate in mice. Polymorphisms for growth hormone (GH) and insulin-like growth factor 2 (IGF-2) genes were identified in stock population lines which had been subjected to long-term selection for high 42-day body weight (H lines) or randomly mated (FP and C lines). Two F2 populations of mice (5F2 and MF2) were generated from crosses between a single H line of mice and two unselected control lines and subsequently, two divergently weight selected sublines were generated from each F2 population. The GHh allele which had originally been fixed in three of four H lines and absent from all FP and C lines was found to have a significant (P less than 0.01) effect on 42-day weight and postweaning growth rate in the F2 populations. However, GHh was associated with lower 42-day weight in the F2 populations, suggesting that the positive association between GHh and weight in the stock population was unique to the high weight selected genetic background of those lines. In agreement with this, the frequency of GHh increased in sublines selected for high 42-day weight and decreased in sublines selected for low 42-day weight. The IGF-2H5 allele was associated with higher weights in a sex-dependent manner in 5F2. In the high selected subline derived from 5F2, a significant increase in the frequency of IGF-2H5 was observed. Therefore this allele, in contrast to GHh, appears to be a positive indicator of growth irrespective of genetic background.     

Destabilizing effect of chicken selection using the functional adrenal reserves criteria]

Chicken lines produced by divergent selection for the functional adrenal reserves showed significant between-line differences in the content of corticosterone and other hormones (thyroxin, progesterone), as well as in body weight, early maturation, and egg yield. DNA fingerprinting with the pGB725 probe revealed molecular changes in genomic DNA of the chicken lines subjected to plus and minus selection. The genetic distances between the original population and the selected chicken lines, which were estimated from the molecular hybridization patterns, reflected the history of breeding. Analysis of mixed DNA from several individuals of each line revealed specific hybridization bands that could serve as DNA markers during selection for the high and low corticosterone levels in blood.     

Molecular cytogenetic evaluation of chromosome instability inTriticum aestivum—Secale cereale disomic addition lines

The genetic stability of wheat/rye (‘Chinese Spring’/‘Imperial’) disomic addition lines was checked using the Feulgen method and fluorescent in situ hybridization (FISH). Feulgen staining detected varying proportions of disomic, monosomic, and telosomic plants among the progenies of the disomic addition lines. The greatest stability was observed for the 7R addition line, while the most unstable lines were those with 2R and 4R additions. Chromosome rearrangements were also detected using FISH. Based on the specific hybridization patterns of repetitive DNA probes pSc119.2 and (AAC)5, as well as ribosomal DNA probes (5S and 45S), isochromosomes were identified in the progenies of 1R and 4R addition lines. The results draw attention to the importance of continuous cytological checks on basic genetic materials by using FISH, because this method reveals chromosome rearrangements that could not be detected either with the conventional Feulgen staining technique or with molecular markers.     

Genetic distances estimated from DNA fingerprints in crosses of White Plymouth Rock chickens

Crosses were produced between two lines of White Plymouth Rock chickens, one of which had been selected for low 8-week body weight for 31 generations (L) and the other of which was a bantam population (B). The parental lines, reciprocal F1s, reciprocal F2s and all possible back-crosses to each parental line (total of 16 populations) were available for study. Blood was obtained from 10 females within each population. DNA was extracted from blood mixes (equal amounts of blood from each individual) for each population, and from blood samples of each individual in the two parental lines. Fourteen line-specific DNA fingerprint (DFP) bands (those bands present in one parental population, but not in the other parental population) were analysed (eight from line L and six from line B). Regression analyses were conducted to compare the known proportion of genomic contribution from each parental population with values based on relative band intensity obtained with a scanning densitometer. The resulting regression coefficient of 1.004 demonstrated that DFP analysis of relative band intensity is an effective method of estimating the relative proportion of genome contributed by parental populations.     

Construction and Characterization of the Microclone Library from Chromosome 1R in Rye

Two and five 1R chromosomes were microdissected from the metaphase spreads of rye ( Secale cereale L. ) root-rip cells with the aids of glass needles. The dissected chromosomes were amplified in vitro by the Sau3A linker adaptor mediated PCR technique, by which 0.3 to 2.5 kb smear DNA fragments were obtained. After hybridized with DIG labeled probes, it was confirmed that the PCR products of the microdissected chromosomes were homologous with the rye genomic DNA, and derived from the 1R chromosome as well. Then, the second round PCR products from five chromosomes of 1R were microcloned to construct the plasmid library, including 220 000 clones. 172 randomly selected clones were evaluated ranged in size from 300 to 1 800 bp. Furthermore, the genomic dot hybridization results indicated that the library contained nearly 42% medium/high repetitive sequences and 58% low/single copy sequences, and its redundancy was very low. In this research, many aspects of the 1R chromosome microclone library exceeded or approached those of the previous reports in the literatures. Those are potential for construction of a high density genetic map of chromosome IR, from which some important genes can be tagged and isolated.     

ATP utilization by yeast replication factor C. II. Multiple stepwise ATP binding events are required to load proliferating cell nuclear antigen onto primed DNA.

Binding of adenosine (3-thiotriphosphate) (ATPgammaS), a nonhydrolyzable analog of ATP, to replication factor C with a N-terminal truncation (Delta2-273) of the Rfc1 subunit (RFC) was studied by filter binding. RFC alone bound 1.8 ATPgammaS molecules. However, when either PCNA or primer-template DNA were also present 2.6 or 2.7 ATPgammaS molecules, respectively, were bound. When both PCNA and DNA were present 3.6 ATPgammaS molecules were bound per RFC. Order of addition experiments using surface plasmon resonance indicate that RFC forms an ATP-mediated binary complex with PCNA prior to formation of a ternary DNA.PCNA.RFC complex. An ATP-mediated complex between RFC and DNA was not competent for binding PCNA, and the RFC.DNA complex dissociated with hydrolysis of ATP. Based on these experiments a model is proposed in which: (i) RFC binds two ATPs (RFC.ATP(2)); (ii) this complex binds PCNA (PCNA.RFC.ATP(2)), which goes through a conformational change to reveal a binding site for one additional ATP (PCNA.RFC.ATP(3)); (iii) this complex can bind DNA to yield DNA.PCNA.RFC.ATP(3); (iv) a conformational change in the latter complex reveals a fourth binding site for ATP; and (v) the DNA.PCNA.RFC.ATP(4) complex is finally competent for completion of PCNA loading and release of RFC upon hydrolysis of ATP.