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Results for “Haplotype structures”

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PubMed1994

Hierarchical structure of mitochondrial DNA gene flow among humpback whales Megaptera novaeangliae, world-wide.

The genetic structure of humpback whale populations and subpopulation divisions is described by restriction fragment length analysis of the mitochondrial (mt) DNA from samples of 230 whales collected by biopsy darting in 11 seasonal habitats representing six subpopulations, or 'stocks', world-wide. The hierarchical structure of mtDNA haplotype diversity among population subdivisions is described using the analysis of molecular variance (AMOVA) procedure, the analysis of gene identity, and the genealogical relationship of haplotypes as constructed by parsimony analysis and distance clustering. These analyses revealed: (i) significant partitioning of world-wide genetic variation among oceanic populations, among subpopulations or 'stocks' within oceanic populations and among seasonal habitats within stocks; (ii) fixed categorical segregation of haplotypes on the south-eastern Alaska and central California feeding grounds of the North Pacific; (iii) support for the division of the North Pacific population into a central stock which feeds in Alaska and winters in Hawaii, and an eastern or 'American' stock which feeds along the coast of California and winters near Mexico; (iv) evidence of genetic heterogeneity within the Gulf of Maine feeding grounds and among the sampled feeding and breeding grounds of the western North Atlantic; and (v) support for the historical division between the Group IV (Western Australia) and Group V (eastern Australia, New Zealand and Tonga) stocks in the Southern Oceans. Overall, our results demonstrate a striking degree of genetic structure both within and between oceanic populations of humpback whales, despite the nearly unlimited migratory potential of this species. We suggest that the humpback whale is a suitable demographic and genetic model for the management of less tractable species of baleen whales and for the general study of gene flow among long-lived, mobile vertebrates in the marine ecosystem.

Animals↗

PubMed2003

Disparate patterns of population genetic structure and population history in two sympatric penaeid shrimp species (Farfantepenaeus aztecus and Litopenaeus setiferus) in the eastern United States.

Analysing the population genetic structures of sympatric species provides opportunities to compare patterns of population genetic structure and phylogeography in order to gain insight into the factors that influence the development of the observed patterns. In this study, we compared the population genetic structures and phylogeographies of brown shrimp (Farfantepenaeus aztecus) and white shrimp (Litopenaeus setiferus), two sympatric penaeid shrimp species that inhabit the waters of the eastern USA, using sequence analysis of the mitochondrial DNA control region. Brown shrimp showed no significant phylogenetic structure or population subdivision, and closely related haplotypes were geographically dispersed. Mismatch analysis indicated that brown shrimp experienced a late-Pleistocene era sudden population expansion. In contrast, white shrimp had a complex haplotype phylogeny consisting of two distinct lineages and two less well-defined sublineages, and the haplotypes and lineages were geographically structured. Mismatch analysis for white shrimp also showed evidence of sudden population expansion, albeit for each lineage separately and more recently than in the brown shrimp. These disparate patterns may have developed as a result of species-specific differences in physiological tolerances and habitat preferences that caused greater fluctuations in white shrimp population sizes and reductions in long-term effective population size relative to that of the brown shrimp, and thereby increased the susceptibility of the white shrimp populations to stochastic genetic change.

Animals↗

PubMed2005

Multiple sclerosis: MHC associations and therapeutic implications.

Multiple sclerosis (MS) is an autoimmune disease with an important genetic component. The strongest genetic association is with the major histocompatibility complex (MHC) region. Several MHC alleles predispose to the disease, the most prominent of which are certain alleles in the HLA-DR2 haplotype. Functional and structural studies have helped to explain the molecular basis of these associations. Although there is currently no curative treatment for MS, an increased understanding of the disease has aided the design of immunotherapies that act on the immune system more specifically than the longstanding drugs. Many of these therapies work at the antigen-specific level, disrupting the interaction between T-cell receptors and MHC molecules that leads to disease.

Animals↗

PubMed2026

Branching plasticity and candidate gene-hormone networks associated with shade responses in soybean under relay strip intercropping.

BACKGROUND: Branching is a key determinant of high-yield plant architecture in soybean, particularly in maize- soybean relay strip intercropping where plants experience an "initially shaded-then fully illuminated" light regime. However, the genetic regulation of branching responses to shading remains poorly understood. METHODS: We evaluated 11 branching-related traits across 202 soybean accessions grown under monoculture (SS) and relay strip intercropping (RI). Branch number (BN), branching incidence (BI), and total branch length (TBL) were assessed together with stress tolerance indices (STI) and relative distance plasticity index (RDPI). Genome-wide association studies (GWAS) using mixed linear model (MLM) and three-variance-component MLM (3VmrMLM) were combined with haplotype and protein structural analyses to refine candidate genes. RESULTS: Based on Pearson correlation analysis of all 11 traits, BN, BI, and TBL measured before maize harvest showed the strongest and most consistent associations with branch seed weight within the corresponding cropping system (BSW_SS under SS and BSW_RI under RI), whereas other traits showed weaker or environment-dependent associations. Higher STI values calculated from these traits during the co-growth phase were negatively associated with BSW_RI, suggesting weaker compensatory recovery after light restoration in genotypes with more stable early branching patterns between SS and RI. In contrast, mediation analysis indicated that RDPI was positively associated with BSW_RI mainly through improved mature branching architecture (MB_index), which accounted for approximately 70% of the total positive effect. GWAS identified 57 and 74 significant QTNs using MLM and 3VmrMLM, respectively, and LD-window genes were filtered for exonic nonsynonymous or premature stop-codon variants, yielding 883 genes with putative functional variants. Two high-confidence genes emerged: Glyma.02G058600 (PP2C55), exhibiting shading-specific haplotype effects likely linked to GA-mediated branch-stem balance, and Glyma.02G059900 (DA1-related protein), showing stable effects across environments and implicated in ABA-mediated suppression of axillary meristems. CONCLUSIONS: These results provide insight into the genetic and physiological basis of soybean branching responses under relay strip intercropping, clarify that branching plasticity and relative shade tolerance represent distinct response dimensions in this system, and identify putative loci that may be useful for breeding soybean cultivars with improved shade adaptation and yield stability.

Glycine max↗

PubMed2000

PEX7 gene structure, alternative transcripts, and evidence for a founder haplotype for the frequent RCDP allele, L292ter.

We recently reported cloning a cDNA encoding Pex7p, the peroxisomal PTS2 receptor. PEX7 mutations cause the peroxisome biogenesis disorder (PBD) rhizomelic chondrodysplasia punctata (RCDP). In a survey of 44 RCDP probands, we found that one PEX7 allele, L292ter, accounted for 50% of mutant PEX7 genes. Here we report the characterization of the PEX7 structural gene, which spans 102 kb on chromosome 6q21-q22.2 and contains at least 10 exons. In addition to the predominant full-length transcript, we identified eight smaller PEX7 transcripts generated by alternative exon splicing in several tissues. However, none of these splice forms was able to restore PTS2 protein import into peroxisomes when expressed in RCDP fibroblasts nor did they inhibit PTS2 protein import when expressed in normal fibroblasts. To determine whether the high frequency of the L292ter allele is due to a founder effect, we identified five polymorphic markers (four diallelic markers and one CA repeat) spanning the PEX7 gene. We show that all 12 L292ter homozygotes in our patient sample have an identical haplotype at these five sites, consistent with the hypothesis that the L292ter mutation arose once on an ancestral chromosome in the Caucasian population.

Alleles↗

PubMed1997

The self-incompatibility (S) haplotypes of Brassica contain highly divergent and rearranged sequences of ancient origin.

In Brassica, the recognition of self-related pollen by the stigma is controlled by the highly polymorphic S locus that encodes several linked and coadapted genes and can span several hundred kilobases. We used pulsed-field gel electrophoresis to analyze the structure of different S haplotypes. We show that the S2 and S13 haplotypes of Brassica oleracea contain extensive sequence divergence and rearrangement relative to each other. In contrast, haplotypic configuration is more conserved between B. oleracea S13 and B. campestris S8, two haplotypes that have been proposed to be derived from a common ancestral haplotype based on sequence comparisons. These results support the view that extensive restructuring of the S locus preceded speciation in Brassica. This structural heteromorphism, together with haplotype-specific sequences, may suppress recombination within the S locus complex, potentially providing a mechanism for maintaining the linkage of coadapted allelic combinations of genes over time.

Brassica↗

PubMed2005

Comparison of single-nucleotide polymorphisms and microsatellite markers for linkage analysis in the COGA and simulated data sets for Genetic Analysis Workshop 14: Presentation Groups 1, 2, and 3.

The papers in presentation groups 1-3 of Genetic Analysis Workshop 14 (GAW14) compared microsatellite (MS) markers and single-nucleotide polymorphism (SNP) markers for a variety of factors, using multiple methods in both data sets provided to GAW participants. Group 1 focused on data provided from the Collaborative Study on the Genetics of Alcoholism (COGA). Group 2 focused on data simulated for the workshop. Group 3 contained analyses of both data sets. Issues examined included: information content, signal strength, localization of the signal, use of haplotype blocks, population structure, power, type I error, control of type I error, the effect of linkage disequilibrium, and computational challenges. There were several broad resulting observations. 1) Information content was higher for dense SNP marker panels than for MS panels, and dense SNP markers sets appeared to provide slightly higher linkage scores and slightly higher power to detect linkage than MS markers. 2) Dense SNP panels also gave higher type I errors, suggesting that increased test thresholds may be needed to maintain the correct error rate. 3) Dense SNP panels provided better trait localization, but only in the COGA data, in which the MS markers were relatively loosely spaced. 4) The strength of linkage signals did not vary with the density of SNP panels, once the marker density was approximately 1 SNP/cM. 5) Analyses with SNPs were computationally challenging, and identified areas where improvements in analysis tools will be necessary to make analysis practical for widespread use.

Alcoholism↗

PubMed1993

Three Hsp70 genes are located in the C4-H-2D region: possible candidates for the Orch-1 locus.

The central region of the mouse MHC harbors a recombinational hot spot area. Most recombinations in this part of the complex take place between the Hsp70.1 gene and the G7 gene. This interval is of interest since structurally indistinguishable recombinant haplotypes do differ in functional behavior. Susceptibility to experimental allergic orchitis, which is controlled by the Orch-1 locus, is one example. We have analyzed the hot spot region at the molecular level in order to understand the molecular organization of this chromosomal segment. From a C57BL genomic library we constructed a cosmid contig bridging the interval between Hsp70.1 and G7. The Orch-1 gene maps to a 60-kb segment of DNA in which we found a new Hsp70 homologue, Hsp70.3. Thus, as in the human MHC, the central region of the mouse MHC harbors a cluster of three Hsp70 genes; Hsp70.1, Hsp70.3, and Hsc70t. Two other genes are located in this critical interval (G7b and G7a/Bat-6), and there might still be other undetected genes present in the region. Heat shock proteins play an important role in a large number of physiological processes and it is tempting to speculate that Hsc70t, which exhibits testis-specific expression, may be identical to Orch-1.

Animals↗

PubMed2006

Analysis of the DNA sequence and duplication history of human chromosome 15.

Here we present a finished sequence of human chromosome 15, together with a high-quality gene catalogue. As chromosome 15 is one of seven human chromosomes with a high rate of segmental duplication, we have carried out a detailed analysis of the duplication structure of the chromosome. Segmental duplications in chromosome 15 are largely clustered in two regions, on proximal and distal 15q; the proximal region is notable because recombination among the segmental duplications can result in deletions causing Prader-Willi and Angelman syndromes. Sequence analysis shows that the proximal and distal regions of 15q share extensive ancient similarity. Using a simple approach, we have been able to reconstruct many of the events by which the current duplication structure arose. We find that most of the intrachromosomal duplications seem to share a common ancestry. Finally, we demonstrate that some remaining gaps in the genome sequence are probably due to structural polymorphisms between haplotypes; this may explain a significant fraction of the gaps remaining in the human genome.

Animals↗

PubMed1999

Microsatellite polymorphism and genetic impact of restocking in mediterranean brown trout (Salmo trutta L.)

The genetic impact of restocking Mediterranean brown trout populations with hatchery stocks was investigated in the Orb River drainage (France), using genetic data from three microsatellite loci. We sampled two wild populations, the main river which is restocked each year and one of its tributaries which has not been restocked for 6 years. Each sample was divided into two age groups (juveniles/adults). Introgression of each native population by hatchery stocks was previously estimated using allele frequencies from two diagnostic protein-coding loci and one mtDNA haplotype. The genetic structure and allelic frequency at three microsatellite loci in native populations were compared with two hatchery samples belonging to stocks usually used for restocking this drainage. High levels of polymorphism (23-27 alleles per locus) were detected for two loci, whereas the third was less polymorphic. Polymorphism was significantly higher in the restocked population than in the now undisturbed population. Significant differences between age groups were observed in the main river, but not in its tributary. The introgression estimates using microsatellites were compared to those obtained from proteins and mtDNA. The different possible origins of alleles common to hatcheries and wild populations (homoplasy, ancestral polymorphism or introgression) are discussed.

Journal Article↗

PubMed1975

Mapping of the immune response genes in the major histocompatibility complex of the Rhesus monkey.

Interest in the Ir genes of rheus monkeys stems from their phylogenetic relationship to man and the extensive data already available on the major histocompatibility complex of the monkey. At least two independent dominant H-linked Ir genes have been identified in the rhesus. These genes control the ability of monkeys to respond to the random linear copolymer of glutamyl alanine (GA), or the dinitrophenyl conjugate of glutamyl lysine (DNP-GL). These synthetic polymers can elicit weak delayed-type skin reactions and strong humoral responses in some monkeys. In a series of unrelated monkeys phenotyped for the serologically defined RhL-A specificities of both segregant series, there were no correlations between any RhL-A specificity and responder status to the GA or DNP-GL polymers. However, segregation analysis of 21 rhesus families sired by 3 fathers indicated the capacity of the offspring to form antibodies was associated with genes coded for in the RhL-A complex. In three monkeys, verified recombination within the RhL-A complex between the genes coding for the serologically defined determinants (SD loci) and the gene(s) controlling the lymphocyte-activating determinants (Lad loci) responsible for mixed lymphocyte reactivity was established. In two of these monkeys the immune response genes controlling the DNP-GL response segregated with the Lad genes, while in the third case the Ir-GL gene segregated with the SD loci, tentatively localizing the Ir-GL gene between the SD and Lad loci. In addition, we have shown that genetically distinct genes control responsiveness to DNP-GL and GA. These genes were separated by recombination, thus one monkey inherited the Lad, Ir-GL, and SD loci from one paternal haplotype and by crossing over inherited the gene controlling GA responsiveness from the other paternal haplotype. The fine structure mapping of the RhL-A gene complex is compared with the H-2 and HL-A gene complexes. Several striking similarities were noted.

Alanine↗

PubMed1999

The effect of mating system differences on nucleotide diversity at the phosphoglucose isomerase locus in the plant genus Leavenworthia.

To test the theoretical prediction that highly inbreeding populations should have low neutral genetic diversity relative to closely related outcrossing populations, we sequenced portions of the cytosolic phosphoglucose isomerase (PgiC) gene in the plant genus Leavenworthia, which includes both self-incompatible and inbreeding taxa. On the basis of sequences of intron 12 of this gene, the expected low diversity was seen in both populations of the selfers Leavenworthia uniflora and L. torulosa and in three highly inbreeding populations of L. crassa, while high diversity was found in self-incompatible L. stylosa, and moderate diversity in L. crassa populations with partial or complete self-incompatibility. In L. stylosa, the nucleotide diversity was strongly structured into three haplotypic classes, differing by several insertion/deletion sequences, with linkage disequilibrium between sequences of the three types in intron 12, but not in the adjacent regions. Differences between the three kinds of haplotypes are larger than between sequences of this gene region from different species. The haplotype divergence suggests the presence of a balanced polymorphism at this locus, possibly predating the split between L. stylosa and its two inbreeding sister taxa, L. uniflora and L. torulosa. It is therefore difficult to distinguish between different potential causes of the much lower sequence diversity at this locus in inbreeding than outcrossing populations. Selective sweeps during the evolution of these populations are possible, or background selection, or merely loss of a balanced polymorphism maintained by overdominance in the populations that evolved high selfing rates.

Base Sequence↗

PubMed2026

Allelic variation and light-responsive regulation of FaMYB10-2 underlie tissue-specific anthocyanin accumulation in strawberry.

Anthocyanins critically determine fruit color, nutrition, and stress resilience in cultivated strawberry (Fragaria × ananassa), directly influencing consumer preference. Despite complex genetic and environmental regulation of their biosynthesis, the basis for tissue-specific pigmentation, notably the widespread occurrence of red skin and pale flesh, remains poorly understood. We integrated genomic, transcriptomic, and functional analyses across 200 cultivars to dissect receptacle pigmentation regulation. Approaches included FaMYB10-2 allele mining, promoter structural variant (SV) identification, expression profiling, regulatory interaction assays, and characterization of upstream light-responsive factors. FaMYB10-2 was identified as the key R2R3-MYB regulator of fruit anthocyanin biosynthesis. Alleles FaMYB10-2.2 and FaMYB10-2.3 encode truncated proteins retaining bHLH-binding capacity but lacking activation domains, functioning as dominant-negative repressors. A promoter SV 986 bp upstream of FaMYB10-2 was associated with reduced pale fruit due to cis-regulatory divergence. The SV (Alt) allele is prevalent in Asian cultivars, while the Ref allele is enriched in Western germplasm. Crucially, a light-responsive FaHYH-FaWRKY71 cascade activates FaMYB10-2 and structural genes haplotype-dependently, compensating for weak MYB activity in the skin. Our findings reveal a multilayered regulatory system integrating allelic variation, cis-regulatory divergence, and environmental signals, advancing anthocyanin understanding and providing engineering targets for polyploid crop color improvement.

Fragaria↗

PubMed2001

Mannose binding lectin and FcgammaRIIa (CD32) polymorphism in Spanish systemic lupus erythematosus patients.

OBJECTIVE: Mannose binding lectin (MBL) and FcgammaRII (CD32) polymorphisms have both been implicated as candidate susceptibility genes in systemic lupus erythematosus (SLE). The aim of this study was to evaluate the relationship of these polymorphisms with SLE. METHODS: We studied a cohort of 125 SLE patients from Barcelona, Spain and 138 geographically matched controls. Sequence-specific primer-polymerase chain reaction (SSP-PCR) amplification was used to determine CD32 and MBL structural polymorphisms. MBL haplotypes were established using sequence-specific oligonucleotide probing techniques. RESULTS: Patients carried the MBL codon 54 mutant allele more frequently than controls [odds ratio (OR) 2.2; 95% confidence interval (CI) 1.2-4.0; P=0.007] and the haplotype HY W52 W54 W57 was found to be significantly lower in cases compared with controls (OR 0.6; 95% CI 0.4-0.9; P=0.016). CONCLUSION: The MBL gene codon 54 mutant allele appears to be a risk factor for SLE, whilst haplotypes encoding for high levels of MBL are protective against the disease. Differences between controls and patients were not significant when considering the FcgammaRIIa polymorphisms; similar results were observed for renal affectation.

Acute-Phase Proteins↗

PubMed2001

Restricted effective queen dispersal at a microgeographic scale in polygynous populations of the ant Formica exsecta.

Ecological constraints on effective dispersal have been suggested to be a key factor influencing social evolution in animal societies as well as the shift from single queen colonies (monogyny) to multiple queen colonies (polygyny) in ants. However, little is known about the effective dispersal patterns of ant queens. Here we investigate the microgeographic genetic structure of mitochondrial haplotypes in polygynous populations of the ant Formica exsecta, both between pastures and among nests within pastures. An analysis of molecular variance revealed a very high genetic differentiation (phiST = 0.72) between pastures, indicating that queens rarely disperse successfully between pastures, despite the fact that pastures were sometimes as close as 1 km. Most of the pastures contained only a single haplotype, and haplotypes were frequently distinct between nearby pastures and even between groups of nests within the same pasture. In the three pastures that contained several haplotypes, haplotypes were not randomly distributed, the genetic differentiation between nests being phiST = 0.17, 0.52, and 0.69. This indicates that most queens are recruited within their parental colonies. However, a large proportion of nests contained more than one haplotype, demonstrating that colonies will sometimes accept foreign queens. The relatedness of mitochondrial genes among nestmates varied between 0.62 and 0.75 when relatedness was measured within each pasture and ranged between 0.72 and 1.0 when relatedness was assessed with all pastures as a reference population. Neighboring nests were more genetically similar than distant ones, and there was significant isolation by distance. This pattern may be due to new nests being formed by budding or by limited effective queen dispersal, probably on foot between neighboring nests. These results show that effective queen dispersal is extremely restricted even at a small geographical scale, a pattern consistent with the idea that ecological constraints are an important selective force leading to the evolution and maintenance of polygyny.

Animals↗

PubMed2004

Livestock trade history, geography, and parasite strains: the mitochondrial genetic structure of Echinococcus granulosus in Argentina.

A sample of 114 isolates of Echinococcus granulosus (Cestoda: Taeniidae) collected from different host species and sites in Argentina has been sequenced for 391 bp from the mitochondrial cytochrome c oxidase subunit I gene to analyze genetic variability and population structure. Nine different haplotypes were identified, 5 of which correspond to already characterized strains. Analysis of molecular variance and nested clade analysis of the distribution of haplotypes among localities within 3 main geographic regions indicate that geographic differentiation accounts for the overall pattern of genetic variability in E. granulosus populations. Significant geographic differentiation is also present when the sheep strain alone is considered. Our results suggest that geographic patterns are not due to actual restricted gene flow between regions but are rather a consequence of past history, probably related to the time and origin of livestock introduction in Argentina.

Analysis of Variance↗

PubMed1985

Chromosomal and genic sterility of hybrid type in mice and men.

Three mouse models of male-limited, hybrid-type sterility are available: the sterility controlled by the T-t genetic complex, the hybrid sterility system including the Hst-1 gene, and the sterility of carriers of various chromosomal anomalies. A large body of experimental evidence has been gathered on the nonrandom attraction between X chromosome and rearranged autosomes in meiosis of carriers of various male-sterile chromosomal rearrangements in mice and men. A hypothesis is evaluated relating the X-autosomal interaction to spermatogenic breakdown. New data on the structure of t haplotypes indicate the presence of chromosomal inversions, and this might point to a chromosomal type of sterility of tx/ty hybrids. Gene hybrid sterility-1 is responsible for different fertility of male hybrids between certain laboratory and wild mice. The availability of wild mice (Mus musculus) derived inbred strains PWB, PWD, and PWK may facilitate further study of the hybrid sterility phenomenon in the mouse.

Animals↗

PubMed2004

Analysis of the S-locus structure in Prunus armeniaca L. Identification of S-haplotype specific S-RNase and F-box genes.

The gametophytic self-incompatibility (GSI) system in Rosaceae has been proposed to be controlled by two genes located in the S -locusan S-RNase and a recently described pollen expressed S -haplotype specific F-box gene (SFB). However, in apricot (Prunus armeniaca L.) these genes had not been identified yet. We have sequenced 21 kb in total of the S -locus region in 3 different apricot S -haplotypes. These fragments contain genes homologous to the S-RNase and F-box genes found in other Prunus species, preserving their basic gene structure features and defined amino acid domains. The physical distance between the F-box and the S-RNase genes was determined exactly in the S2-haplotype (2.9 kb) and inferred approximately in the S 1-haplotype (< 49 kb) confirming that these genes are linked. Sequence analysis of the 5' flanking regions indicates the presence of a conserved region upstream of the putative TATA box in the S-RNase gene. The three identified S-RNase alleles (S1, S2 and S4) had a high allelic sequence diversity (75.3 amino acid identity), and the apricot F-box allelic variants (SFB1, SFB2 and SFB4) were also highly haplotype-specific (79.4 amino acid identity). Organ specific-expression was also studied, revealing that S1- and S2-RNases are expressed in style tissues, but not in pollen or leaves. In contrast, SFB1 and SFB2 are only expressed in pollen, but not in styles or leaves. Taken together, these results support these genes as candidates for the pistil and pollen S-determinants of GSI in apricot.

5' Flanking Region↗