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PubMedDate not supplied

An autosomal genetic linkage map of the chicken.

We have developed an autosomal genetic linkage map of the chicken genome using a subpanel of 52 DNAs from a previously described reference backcross mapping population. The population derived from a cross of an inbred Red Jungle Fowl male and a highly inbred White Leghorn female. The backcross subpanel used was made up of offspring of a single F1 male with four White Leghorn females. Ninety-eight markers consisting of classical and erythrocyte antigen genes, restriction fragment length polymorphisms, random amplified polymorphic DNA, and chicken CR1 repeat-element polymorphisms were typed. Seventy-two of these markers were resolved into 19 linkage groups. Four of the linkage groups were assigned to chromosomes 1, 4, and 17. Four linkage groups were associated with linkage groups published earlier. Linkages within approximately 27 cM can be detected with a lod score of 3 with the panel used. The preliminary map contains approximately 590 cM within the linkage groups, and approximately 70% of the randomly selected markers fell in one of the groups; however, a considerable portion of the genome may remain outside of the existing linkage groups. These markers greatly expand the existing linkage map of the chicken genome.

Animals↗
PubMed2006

Mining and characterizing microsatellites from citrus ESTs.

Freely available computer programs were arranged in a pipeline to extract microsatellites from public citrus EST sequences, retrieved from the NCBI. In total, 3,278 bi- to hexa-type SSR-containing sequences were identified from 56,199 citrus ESTs. On an average, one SSR was found per 5.2 kb of EST sequence, with the tri-nucleotide motifs as the most abundant. Primer sequences flanking SSR motifs were successfully identified from 2,295 citrus ESTs. Among those, a subset (100 pairs) were synthesized and tested to determine polymorphism and heterozygosity between/within two genera, sweet orange (C. sinensis) and Poncirus (P. trifoliata), which are the parents of the citrus core mapping population selected for an international citrus genomics effort. Eighty-seven pairs of primers gave PCR amplification to the anticipated SSRs, of which 52 and 35 appear to be homozygous and heterozygous, respectively, in sweet orange, and 67 and 20, respectively, in Poncirus. By pairing the loci between the two intergeneric species, it was found that 40 are heterozygous in at least one species with two alleles (9), three alleles (28), or four alleles (3), and the remaining 47 are homozygous in both species with either one allele (31) or two alleles (16). These EST-derived SSRs can be a resource used for understanding of the citrus SSR distribution and frequency, and development of citrus EST-SSR genetic and physical maps. These SSR primer sequences are available upon request.

Alleles↗
PubMed2001

Integration of microstructural and functional aspects of human somatosensory areas 3a, 3b, and 1 on the basis of a computerized brain atlas.

In this study we analyzed structural and functional aspects of the human primary somatosensory areas 3a, 3b, and 1 on the basis of a computerized brain atlas. The approach overcomes many of the problems associated with subjective architectonic parcellations of the cortex and with 'classical" brain maps published in a "rigid" print format. Magnetic resonance (MR) scans were obtained from ten postmortem brains. The brains were serially sectioned at 20 microm, and sections were stained for cell bodies. Areas 3a, 3b, and 1 were delineated statistically on the basis of differences in the laminar densities of neuronal cell bodies. The borders of the areas were topographically variable across different brains and did not match macroanatomical landmarks of the postcentral gyrus. After correction of the sections for deformations due to histological processing, each brain's 3-D reconstructed histological volume and the volume representations of areas 3a, 3b, and 1 were adapted to the reference brain of a computerized atlas and superimposed in 3-D space. For each area, a population map was generated that described, for each voxel, how many brains had a representation of that area. Despite considerable interindividual variability, representations of areas 3a, 3b, and 1 in > or = 50% of the brains were found in the fundus of the central sulcus, in the rostral bank, and on the crown of the postcentral gyrus, respectively. For each area, a volume of interest (VOI) was defined that encompassed that area's representation in > or = 50% of the brains. Despite close spatial relationship in the postcentral gyrus, the three VOIs overlapped by < 1% of their volumes. Changes in regional cerebral blood flow (rCBF) were measured with positron emission tomography when six right-handed subjects discriminated differences in the speed of a rotating brush stimulating the palmar surface of the right hand. With co-registered MR images, the rCBF data were adapted to the same reference brain and superimposed with the microstructural VOIs. Discrimination of moving stimuli, contrasted to rest, increased the rCBF in the VOIs of areas 3b and 1, but not in area 3a. This approach opens up the possibility of (1) defining VOIs of cortical areas which are not based on macroanatomical landmarks but instead on observer-independent cytoarchitectonic mapping of postmortem brains and of (2) determining in these VOIs changes in rCBF data obtained from functional imaging experiments.

Adult↗
PubMed2002

Isolate-specific QTLs of resistance to leaf stripe (Pyrenophora graminea) in the 'Steptoe' x 'Morex' spring barley cross.

Leaf stripe caused by the fungus Pyrenophora graminea represents a serious threat to grain yield in organically grown barley and in conventional Nordic and Mediterranean districts, for which resistant cultivars are necessary. A medium-density, molecular marker map derived from a 'Steptoe' (partially resistant) x 'Morex' (susceptible) spring barley cross and its derived doubled-haploid mapping population inoculated with the fungus made it possible to identify QTLs of resistance to leaf stripe. In order to investigate isolate-specificity of partial resistance, the 'Steptoe' x 'Morex' segregating population was inoculated with two highly virulent P. graminea isolates, Dg2 and Dg5. The present study demonstrates that partial resistance to leaf stripe of cv 'Steptoe' is governed in part by shared loci and in part by isolate-specific ones. One QTL is common to the resistance for the two isolates, on the long arm of chromosome 2 (2H), two QTLs are linked on chromosome 3 (3H), and the remaining two are isolate-specific, respectively for isolate Dg2 on chromosome 2 (2H) and for isolate Dg5 on chromosome 7 (5H). The QTL in common is that with the major effect on the resistance for each isolate, explaining 18.3% and 30.9% R(2) respectively for Dg2 and Dg5. The isolate-specific QTLs mapped in the 'Steptoe' x 'Morex' barley reference map support the assumption of Parlevliet and Zadoks (1977) that partial resistance may be due to minor gene-for-minor-gene interactions. Map comparisons of the QTLs with the known qualitative resistance genes to leaf stripe, Rdg1 (2H) and Rdg2 (7H), as well as with other QTLs of partial resistance in barley, show that the QTL for resistance to both isolates mapped on the long arm of chromosome 2 (2H) does not coincide with the qualitative Rdg1 gene but is linked to it at about 30 cM. One isolate-specific QTL of resistance to P. graminea, mapped on the short arm of chromosome 2 (2H), is coincident with a QTL for resistance to Pyrenophora teres previously mapped in the 'Steptoe' x 'Morex' cross.

Chromosome Mapping↗
PubMed1998

Mapping quantitative trait loci using multiple families of line crosses.

To avoid a loss in statistical power as a result of homozygous individuals being selected as parents of a mapping population, one can use multiple families of line crosses for quantitative trait genetic linkage analysis. Two strategies of combining data are investigated: the fixed-model and the random-model strategies. The fixed-model approach estimates and tests the average effect of gene substitution for each parent, while the random-model approach treats each effect of gene substitution as a random variable and directly estimates and tests the variance of gene substitution. Extensive Monte Carlo simulations verify that the two strategies perform equally well, although the random model is preferable in combining data from a large number of families. Simulations also show that there may be an optimal sampling strategy (number of families vs. number of individuals per family) in which QTL mapping reaches its maximum power and minimum estimation error. Deviation from the optimal strategy reduces the efficiency of the method.

Chromosome Mapping↗
PubMed2003

Identification of AFLP markers linked to fertility restorer genes for tournefortii cytoplasmic male-sterility system in Brassica napus.

The tournefortii cytoplasmic male-sterility system is being used as a method of pollination control to develop hybrids in Brassica napus. Genetic analyses have indicated that two dominant genes, one major ( Rft1) and another minor ( Rft2), were required to achieve complete fertility restoration. Though the major gene ( Rft1) can cause complete fertility restoration on its own, its expression was significantly enhanced in the presence of the minor gene ( Rft2). In the absence of Rft1, Rft2 caused only partial fertility restoration. We used a pair of near-isogenic lines (NILs), differing for the presence/absence of Rf genes, to identify AFLP markers linked to fertility restorer genes. A total of 64 EcoRI/ MseI primer combinations were surveyed which produced 3,225 bands, of which 19 (0.006%) were polymorphic between parental NILs. Primer combinations which led to the identification of polymorphic bands present in fertile parental NILs were used for assaying a mapping population of 70 F(2) plants for determining the segregation pattern of markers. Initial screening resulted in the identification of five AFLP markers. The recombination analyses of these AFLP markers revealed that at least two (EACC/MCTT(105), EAAG/MCTC(80)) were present in the same linkage group along with the Rf loci. Marker EACC/MCTT(105) was separated from the major gene ( Rft1) by a distance of 18.1 cM, while it was 33.2 cM away from the minor fertility restorer gene ( Rft2). Another marker EAAG/MCTC(80) was also located adjacent to Rft1 at a distance of 18.1 cM, but on other side. Identification of flanking markers (EACC/MCTT(105), EAAG/MCTC(80)) for the major fertility restorer gene ( Rft1) provides a crucial component for marker-assisted selection and map-based cloning of the restorer genes, and can hence be used to construct elite restorer genotypes.

Brassica↗
PubMed2004

QTL mapping of chromosomal regions conferring reproductive frost tolerance in barley ( Hordeum vulgare L.).

Spring radiation frost is a major abiotic stress in southern Australia, reducing yield potential and grain quality of barley by damaging sensitive reproductive organs in the latter stages of development. Field-based screening methods were developed, and genetic variation for reproductive frost tolerance was identified. Mapping populations that were segregating for reproductive frost tolerance were screened and significant QTL identified. QTL on chromosome 2HL were identified for frost-induced floret sterility in two different populations at the same genomic location. This QTL was not associated with previously reported developmental or stress-response loci. QTL on chromosome 5HL were identified for frost-induced floret sterility and frost-induced grain damage in all three of the populations studied. The locations of QTL were coincident with previously reported vegetative frost tolerance loci close to the vrn- H1 locus. This locus on chromosome 5HL has now been associated with response to cold stress at both vegetative and reproductive developmental stages in barley. This study will allow reproductive frost tolerance to be seriously pursued as a breeding objective by facilitating a change from difficult phenotypic selection to high-throughput genotypic selection.

Acclimatization↗
PubMed2004

Duplicate chlorophyll-deficient loci in soybean.

Three lethal-yellow mutants have been identified in soybean (Glycine max (L.) Merr.), and assigned genetic type collection numbers T218H, T225H, and T362H. Previous genetic evaluation of T362H indicated allelism with T218H and T225H and duplicate-factor inheritance. Our objectives were to confirm the inheritance and allelism of T218H and T225H and to molecularly map the locus and (or) loci conditioning the lethal-yellow phenotype. The inheritance of T218H and T225H was 3 green : 1 lethal yellow in their original parental source germplasm of Glycine max 'Illini' and Glycine max 'Lincoln', respectively. In crosses to unrelated germplasm, a 15 green : 1 lethal yellow was observed. Allelism tests indicated that T218H and T225H were allelic. The molecular mapping population was Glycine max 'Minsoy' x T225H and simple sequence repeat (SSR) markers were used. The first locus, designated y18-1, was located on soybean molecular linkage group B2, between SSR markers Satt474 and Satt534, and linked to each by 4.4 and 13.4 cM, respectively. The second locus, designated y18-2, was located on soybean molecular linkage group D2, between SSR markers Satt543 and Sat-001, and linked to each by 2.2 and 4.4 cM, respectively.

Chlorophyll↗
PubMed2006

Distribution of microsatellites in the genome of Medicago truncatula: a resource of genetic markers that integrate genetic and physical maps.

Microsatellites are tandemly repeated short DNA sequences that are favored as molecular-genetic markers due to their high polymorphism index. Plant genomes characterized to date exhibit taxon-specific differences in frequency, genomic location, and motif structure of microsatellites, indicating that extant microsatellites originated recently and turn over quickly. With the goal of using microsatellite markers to integrate the physical and genetic maps of Medicago truncatula, we surveyed the frequency and distribution of perfect microsatellites in 77 Mbp of gene-rich BAC sequences, 27 Mbp of nonredundant transcript sequences, 20 Mbp of random whole genome shotgun sequences, and 49 Mbp of BAC-end sequences. Microsatellites are predominantly located in gene-rich regions of the genome, with a density of one long (i.e., > or = 20 nt) microsatellite every 12 kbp, while the frequency of individual motifs varied according to the genome fraction under analysis. A total of 1,236 microsatellites were analyzed for polymorphism between parents of our reference intraspecific mapping population, revealing that motifs (AT)n, (AG)n, (AC)n, and (AAT)n exhibit the highest allelic diversity. A total of 378 genetic markers could be integrated with sequenced BAC clones, anchoring 274 physical contigs that represent 174 Mbp of the genome and composing an estimated 70% of the euchromatic gene space.

Alleles↗
PubMed1984

Allosuppression: evidence for the involvement of both "noncytotoxic" and cytotoxic T cells.

Allogeneic suppressor cells were generated by priming to a minor histocompatibility antigen. C57BL/10 female mice were primed to the male-specific minor transplantation antigen, H-Y. After boosting, anti-male-primed cells could potently suppress the secondary antibody response of male spleen cells in vitro. Anti-male suppressor cells were H-2-restricted, radiation-resistant T cells which could act on either T or B cells in the responding population. Mapping the restriction elements for anti-male suppressor cells revealed two distinct subpopulations of effector cells. The majority subpopulation was restricted to H-Y in the context of the H-2Db molecule. These cells were probably cytotoxic T cells as they were inhibited by culture of the suppressor cells in pyrilamide (a histamine receptor antagonist, which prevents the maturation of cytotoxic T cells from their precursors). The second subpopulation of suppressor cells was restricted to H-Y in the context of H-2K or I region-coded molecules. as neither H-2Kb nor H-2Ib molecules can act as restriction elements for anti-male-specific cytotoxic T cells, this subpopulations was almost certainly not composed of conventional cytotoxic cells. Furthermore, these cells were not affected by culture in pyrilamide. Together these two populations act to completely inhibit the anti-trinitrophenyl (TNP) plaque-forming cell response of male spleen cells in vitro.

Animals↗
PubMed2006

Panzea: a database and resource for molecular and functional diversity in the maize genome.

Serving as a community resource, Panzea (http://www.panzea.org) is the bioinformatics arm of the Molecular and Functional Diversity in the Maize Genome project. Maize, a classical model for genetic studies, is an important crop species and also the most diverse crop species known. On average, two randomly chosen maize lines have one single-nucleotide polymorphism every approximately 100 bp; this divergence is roughly equivalent to the differences between humans and chimpanzees. This exceptional genotypic diversity underlies the phenotypic diversity maize needs to be cultivated in a wide range of environments. The Molecular and Functional Diversity in the Maize Genome project aims to understand how selection has shaped molecular diversity in maize and then relate molecular diversity to functional phenotypic variation. The project will screen 4000 loci for the signature of selection and create a wide range of maize and maize-teosinte mapping populations. These populations will be genotyped and phenotyped, permitting high-power and high-resolution dissection of the traits and relating the molecular diversity to functional variation. Panzea provides access to the genotype, phenotype and polymorphism data produced by the project through user-friendly web-based database searches and data retrieval/visualization tools, as well as a wide variety of information and services related to maize diversity.

Chromosome Mapping↗
PubMed2005

Quantitative trait loci controlling vernalisation requirement, heading time and number of panicles in meadow fescue (Festuca pratensis Huds.).

The "BF14/16xHF2/7" mapping population of meadow fescue (Festuca pratensis Huds.) was characterised for number of panicles produced by non-vernalised plants in the field, vernalisation requirement (number of weeks at 6 degrees C and 8 h photoperiod), as well as days to heading, number of panicles and proportion of shoots heading after a 12 weeks vernalisation treatment. Quantitative trait loci (QTLs) were identified and compared to QTLs and genes related to the induction of flowering in cereals and grasses. A region on chromosome 1F affected days to heading and the proportion of shoots heading. Chromosome 4F appeared to have several genes with a strong effect on vernalisation requirement. The strongest effects were located in the proximal end of 4F and may correspond to the earliness per se (eps) QTL eps6L.2 in barley and a heading time QTL in perennial ryegrass. A part of the meadow fescue orthologue of VRN1 was sequenced and mapped to another region of 4F that also had a strong effect on vernalisation requirement. The proximal end of chromosome 5F had QTLs for days to heading and proportion of heading shoots. Syntenic regions in wheat and barley contain eps-loci. A QTL for number of panicles in the field and a QTL for proportion of heading shoots were present on chromosome 6. A region on 7F affected the variation in number of panicles among plants without a vernalisation requirement, and is syntenic to regions in perennial ryegrass, barley and rice containing orthologues of Arabidopsis thaliana CO.

Arabidopsis Proteins↗
PubMed1999

Isolation of microsatellite and RAPD markers flanking the Yr15 gene of wheat using NILs and bulked segregant analysis.

Microsatellite and random amplified polymorphic DNA (RAPD) primers were used to identify molecular markers linked to the Yr15 gene which confer resistance to stripe rust (Puccina striiformis Westend) in wheat. By using near isogenic lines (NILs) for the Yr15 gene and a F2 mapping population derived from crosses of these lines and phenotyped for resistance, we identified one microsatellite marker (GWM33) and one RAPD marker (OPA19(800)) linked to Yr15. Then, bulked segregant analysis was used in addition to the NILs to identify RAPD markers linked to the target gene. Using this approach, two RAPD markers linked to Yr15 were identified, one in coupling (UBC199(700)) and one in repulsion phase (UBC212(1200)). After MAPMAKER linkage analysis on the F2 population, the two closest markers were shown to be linked to Yr15 within a distance of about 12 cM. The recombination rates were recalculated using the maximum likelihood technique to take into account putative escaped individuals from the stripe rust resistance test and obtain unbiased distance estimates. As a result of this study, the stripe rust resistance gene Yr15 is surrounded by two flanking PCR markers, UBC199(700) and GWM33, at about 5 cM from each side.

Chromosome Mapping↗
PubMed2004

Identification of markers tightly linked to sbm recessive genes for resistance to Pea seed-borne mosaic virus.

Two virus resistance loci on linkage groups II and VI have provided the only sources of natural resistance against Pea seed-borne mosaic virus (PSbMV, Potyviridae) in the important crop plant Pisum sativum L. A combination of parallel approaches was used to collate linked markers, particularly for sbm-1 resistance on linkage group VI. We have identified sequences derived from the genes for the eukaryotic translation initiation factors eIF4E and eIF(iso)4E as being very tightly linked to the resistance gene clusters on linkage groups VI and II, respectively. In particular, no recombinants between sbm-1 and eIF4E were found amongst 500 individuals of an F2 cross between the BC4 resistant line (JI1405) and its recurrent susceptible parent 'Scout'. In a different mapping population, the gene eIF(iso)4E was also shown to be linked to sbm-2 on linkage group II. A parallel cDNA-AFLP comparison of pairs of resistant and susceptible lines also identified an expressed tag marker just 0.7 cM from sbm-1. eIF4E and eIF(iso)4E have been associated with resistance to related viruses in other hosts. This correlation strengthens the use of our markers as valuable tools to assist in breeding multiple virus resistances into peas, and identifies potential targets for resistance gene identification in pea.

Agriculture↗
PubMed1995

[Dipole analysis of data base for body surface potential maps of normal population].

The dipolarity of the body surface potential distribution and locus of the main dipole were estimated by means of the least square method in data base for body surface potential maps of normal population. The main dipole moved smoothly within the actual cardiac region and was inscribed in a clockwise direction during the QRS. The nondipolar content (residue) showed time-dependent fluctuation the QRS. The main dipole during the T wave moved near the center of the heart. The nondipolar content during the ST-T period was less fluctuation than that during the QRS. These results indicated that a large percentage of the body surface potential maps of normal population could be represented by a single moving dipole.

Aging↗
PubMed1998

Quantitative trait loci affecting differences in floral morphology between two species of monkeyflower (Mimulus).

Conspicuous differences in floral morphology are partly responsible for reproductive isolation between two sympatric species of monkeyflower because of their effect on visitation of the flowers by different pollinators. Mimulus lewisii flowers are visited primarily by bumblebees, whereas M. cardinalis flowers are visited mostly by hummingbirds. The genetic control of 12 morphological differences between the flowers of M. lewisii and M. cardinalis was explored in a large linkage mapping population of F2 plants n = 465 to provide an accurate estimate of the number and magnitude of effect of quantitative trait loci (QTLs) governing each character. Between one and six QTLs were identified for each trait. Most (9/12) traits appear to be controlled in part by at least one major QTL explaining >/=25% of the total phenotypic variance. This implies that either single genes of individually large effect or linked clusters of genes with a large cumulative effect can play a role in the evolution of reproductive isolation and speciation.

Chromosome Mapping↗
PubMed2003

Mapping QTL for traits associated with resistance to ferrous iron toxicity in rice (Oryza sativa L.), using japonica chromosome segment substitution lines.

A mapping population of 66 japonica chromosome segment substitution lines (CSSLs) in indica genetic background, derived from a cross between a japonica variety Asominori and an indica variety IR24 by the single-seed descent, backcrossing and marker-assisted selection, was used to detect quantitative trait loci (QTLs) for leaf bronzing index (LBI), stem dry weight (SDW), plant height (PH), root length (RL) and root dry weight (RDW) under Fe2+ stress condition in rice. Two parents and 66 japonica CSSLs were phenotyped for the traits by growing them in Fe2+ toxicity nutrient solution. A total of fourteen QTLs were detected on chromosome 3, 6, 7, 9, 11 and 12, respectively, with LOD of QTLs ranging from 2.72 to 6.63. Three QTLs controlling LBI were located at the region of C515-XNpb279, R2638-C1263 and G1465-C950 on chromosome 3, 9 and 11, their contributions to whole variation were 16.45%, 11.16% and 28.02%, respectively. Comparing with the other mapping results, the QTL for LBI located at the region of C515-XNpb279 on chromosome 3 was identical with the QTL for chlorophyll content on a rice function map. The results indicated that ferrous iron toxicity of rice is characterized by bronzing spots on the lower leaves, which spread over the whole leaves, causing the lower leaves to turn dark gray and to product chlorophyll catabolites or derivatives which reduce cytotoxicity of some heavy metals, such as ferrous iron. Furthermore, the QTL for LBI, SDW and RDW located at the region of G1465-C950 on chromosome 11 is a major QTL. Whether the QTL for SDW, PH, RL and RDW at the region of XNpb386-XNpb342 on chromosome 6 is associated with resistance to ferrous iron toxicity need further studies. Our goal is to identify breeding materials for resistance to Fe2+ toxicity through marker-assisted selection based on the detected markers.

Chromosome Mapping↗
PubMed2004

Mapping of transposable element Dissociation inserts in Brassica oleracea following plant regeneration from streptomycin selection of callus.

To investigate the potential of heterologous transposons as a gene-tagging system in broccoli (Brassica oleracea var. italica), we have introduced a Dissociation ( Ds)-based two-element transposon system. Ds has been cloned into a 35S-SPT excision-marker system, with transposition being driven by an independent 35S-transposase gene construct. In three successive selfed generations of plants, there was no evidence of germinal-excision events. In a previous study, we overcame this apparent inability to produce B. oleracea plants with germinal excisions by performing a novel tissue-culture technique to select for fully green shoots from seed with somatic excision events. The results showed a very high efficiency of regeneration of fully green plants (up to 65%), and molecular analysis showed that the plants contained the equivalent of a germinal-excision event. In this study, we followed the previous work by using inverse and nested PCR to generate probes of flanking genomic DNA adjacent to independently reinserted Ds elements, and these were hybridised to DNA from a double-haploid mapping population of B. oleracea. Seventeen Ds insertions and the original Ds T-DNA site have been localised, and these are spread over six (out of nine) linkage groups. Distribution of inserts show that 15 were found on a different linkage group to the original 'launch' site, and of these 11 were found to be clustered on two separate groups. Previous studies in other plant species have found that germinal excision of Ds predominantly moves to sites linked close to the donor site. However, this study shows a potential to produce plants with Ds insertion scattered over many unlinked sites.

Blotting, Southern↗