• Our findings highlight the value of uniparental haplogroups and STR haplotype data for elucidating biosocial events among these populations. (nature.com)
  • Seven thousand five hundred fifty-six (7556) haplotypes of 46 subclades in 17 major haplogroups were considered in terms of their base (ancestral) haplotypes and timespans to their common ancestors, for the purposes of designing of time-balanced haplogroup tree. (scirp.org)
  • DNA genealogy of major haplogroups of Y chromosome (Part 1). (scirp.org)
  • We predicted Y-chromosome haplogroups and found that J2 and R1a were the most prevalent. (bioone.org)
  • Y haplogroups were identified through typing of biallelic polymorphisms in the nonrecombining part of the chromosome. (blogspot.com)
  • Haplotypes within haplogroups were analyzed with seven microsatellite loci. (blogspot.com)
  • The total part of the lineages of western Eurasian origin ("Caucasoid") was about 6% (4 haplotypes, haplogroups H, J, and U). Most of Y chromosomes in the Yakut population (87%) belonged to haplogroup N3 (HG16), delineated by the T-C substitution at the Tat locus. (blogspot.com)
  • Y-specific Dmrt1 haplotypes cluster into two main haplogroups, Y A and Y B , with a phylogeographic signal that parallels mtDNA haplotypes: Y A populations, with mostly well-differentiated sex chromosomes, occur primarily south of the main alpine ridge that bisects Switzerland, while Y B populations, with mostly undifferentiated (proto-)sex chromosomes, occur north of this ridge. (datadryad.org)
  • A genomic region of particular interest for sweet cherry (Prunus avium L.) breeding is a quantitative trait locus (QTL) "hotspot" on chromosome 2. (wur.nl)
  • In the present study, we report on the mapping of a second MKS locus (MKS2) to chromosome 11q13, by homozygosity mapping in seven families that do not show linkage to chromosome 17q21-q24 (maximum LOD score 4.41 at recombination fraction .01). (nih.gov)
  • The dominant theoretical model for the early stages of sex chromosome evolution 3 , 4 , 5 predicts that recombination will be selected against in the region between a sex determining gene and a nearby locus with alleles of sex-specific effect. (nature.com)
  • Therefore, in this system, current models of sex chromosome evolution predict that recombination would be selected against between the sex determining locus and linked loci involved in colouration. (nature.com)
  • On the whole, a susceptibility locus for disc herniation and autosomal recessive spastic paraplegia was found on chromosome 6q23.3-q24.1. (bmj.com)
  • The Y-haplotype effect might result from differences in the penetrance of alleles at the sex-determining locus (such that sex reversal and ensuing X-Y recombination are more frequent in Y B populations), and/or fixation of an inversion on Y A (as supported by the empirical observation that Y A haplotypes might not recombine in XY A females). (datadryad.org)
  • The search led to a haplotype falling in a chromosome 4 locus that's undergone balancing selection early in the human lineage. (genomeweb.com)
  • A genome-wide linkage search in family F1 identified a 6.5 Mb locus for this disorder on chromosome 16q23.2-24.1. (molvis.org)
  • The single nucleotide polymorphism microarray analysis excluded a shared founder haplotype between the families and refined the locus to 3.1 Mb. (molvis.org)
  • Thousands of loci were found in each genome where reads spanning 2 or 3 SNPs displayed more than two haplotypes, indicating that the locus is heterogeneous. (biomedcentral.com)
  • Haplotype analysis, linkage disequilibrium, and homozygosity mapping indicated that HLA-DQ/DR is the major IGAD1 locus, and suggest the autoimmune pathogenesis of IgAD/CVID. (lu.se)
  • By May 2023 about 350.000 Y chromosomes typed for 9-29 STR loci have been directly submitted by worldwide forensic institutions and universities. (wikipedia.org)
  • Most interestingly, the affected fetuses of southern Tunisian ancestry shared a particular haplotype at loci D11S911 and D11S906, suggesting that a founder effect is involved. (nih.gov)
  • This process would shrink the pseudoautosomal region in favour of expanding X- and Y-specific regions, creating a male supergene on the Y chromosome containing multiple colouration loci and thereby resolving sexually antagonistic selection. (nature.com)
  • So far, 16 loci have been identified, both on autosomal and X chromosomes. (bmj.com)
  • For example, consider a diploid organism and two bi-allelic loci (such as SNPs ) on the same chromosome. (wikipedia.org)
  • For a given individual, there are nine possible configurations (haplotypes) at these two loci (shown in the Punnett square below). (wikipedia.org)
  • For individuals heterozygous at both loci, the gametic phase is ambiguous - in these cases, you do not know which haplotype you have, e.g. (wikipedia.org)
  • After accounting for known malaria risky loci and other potential confounders such as parasite diversity, they narrowed in on a suspicious new chromosome 4 site falling between the FREM3 gene and the GYPE, GYPB, and GYPA genes, which code for glycophorin proteins expressed in the red blood cell membrane. (genomeweb.com)
  • [8] A haplogroup is a group of similar haplotypes that share a common ancestor with a single-nucleotide polymorphism mutation . (wikipedia.org)
  • In order to identify single nucleotide polymorphism (SNP) markers that would be suitable for assays, we aligned sequence data from 125 Holstein bulls to the alternative haplotypes. (usda.gov)
  • Differential cultural adaption by populations from the North Lebanese Mountains are clearly aligned with the L1b haplotype STR haplogroup clusters, indicating pre-existing and persistent cultural barriers marked by the transmission of L1b lineages. (nature.com)
  • 2010). Human Y chromosome haplogroup R-V88: A paternal genetic record of early mid Holocene trans-Saharan con- nections and the spread of Chadic languages. (scirp.org)
  • Y-chromosome haplogroup]. (dadamo.com)
  • The term ' haplogroup ' refers to the SNP/ unique-event polymorphism (UEP) mutations that represent the clade to which a collection of particular human haplotypes belong. (wikipedia.org)
  • Chromosomes of haplogroup N3 displayed the presence of 19 microsatellite haplotypes, the most frequent of which encompassed 54% chromosomes of this haplogroup. (blogspot.com)
  • Hifiasm with Hi-C integrated assembly resulted in a 331 Mb genome of C. australis with two haplotypes of nine pseudochromosomes with an N50 of 36.3 Mb and 98.8% genome assembly completeness (BUSCO). (qld.gov.au)
  • A total of 97 different haplotypes were identified, of which 96 haplotypes were unique and 1 occurred twice. (nih.gov)
  • Therefore, given a set of possible haplotype resolutions, these methods choose those that use fewer different haplotypes overall. (wikipedia.org)
  • Retrospective analyses were then performed to evaluate the accuracy of MAS for BCWD resistance using these three favorable haplotypes. (usda.gov)
  • The accuracy of MAS was estimated with the Pearson correlation coefficient between the total number of favorable haplotypes in the two parents and the family BCWD survival rates. (usda.gov)
  • These methods work by applying the observation that certain haplotypes are common in certain genomic regions. (wikipedia.org)
  • This reflects that certain SNP allelic combinations never appear within the population, implying that only certain haplotypes are biologically viable and generationally maintained. (scirp.org)
  • However, it is possible to estimate the probability of a particular haplotype when phase is ambiguous using a sample of individuals. (wikipedia.org)
  • When the haploblocks and their haplotypes were used to explore genetic diversity, ancestry, and recombination patterns, and then integrated with previous QTL results for fruit size, the results indicated that favorable alleles at this QTL hotspot are under positive selection in breeding. (wur.nl)
  • The genetic framework provided by a haploblock approach and knowledge of haplotype-level diversity sets the stage for assigning breeding utility to these haplotypes. (wur.nl)
  • The Malanis are characterized by a generally low Y-chromosome haplotype diversity. (bioone.org)
  • In order to trace the origins and migratory patterns that may have led to the genetic isolation and autosomal clustering in some of these communities we analyzed Y-chromosome STR and SNP sample data from 6327 individuals, in addition to whole genome autosomal sample data from 609 individuals, from Mount Lebanon and other surrounding communities. (nature.com)
  • FDY originated 2 million years ago from a duplication of a contiguous autosomal segment of 11 kb containing five genes that inserted into the Y chromosome. (speakerdeck.com)
  • We provide comprehensive guidance on the required sequencing depths and reliably assign more than 95% of alleles (NA12878) to their parental haplotypes using as few as 10 Strand-seq libraries in combination with 10-fold coverage PacBio data or, alternatively, 10X Genomics linked-read sequencing data. (pacb.com)
  • A haplotype ( haploid genotype ) is a group of alleles in an organism that are inherited together from a single parent. (wikipedia.org)
  • First, it is used to mean a collection of specific alleles (that is, specific DNA sequences) in a cluster of tightly linked genes on a chromosome that are likely to be inherited together-that is, they are likely to be conserved as a sequence that survives the descent of many generations of reproduction. (wikipedia.org)
  • It is thought that identifying these statistical associations and a few alleles of a specific haplotype sequence can facilitate identifying all other such polymorphic sites that are nearby on the chromosome. (wikipedia.org)
  • Therefore, the dynamically independent statistical genomic units we use are SNP haplotypes together with alleles within SNP sites that are not in contiguous LD with any other SNPs. (scirp.org)
  • By investigating 92 common-frog populations from a wide range of elevations throughout Switzerland, we show that sex-chromosome differentiation strongly correlates with alleles at the candidate sex-determining gene Dmrt1 . (datadryad.org)
  • Alleles were called in GeneMapper 4.0 (Fisher Scientific), and Y haplotypes ( Dmrt ) were defined by comparing sexed adult samples. (datadryad.org)
  • Differentiated vs. undifferentiated chromosomes were called via a threshold of Y-like alleles across Chr01 (outside Dmrt ), in individuals with a Dmrt- Y genotype. (datadryad.org)
  • We sought to assemble alternative haplotypes of regions of the cattle genome that may harbor alleles that confer increased disease resistance or susceptibility. (usda.gov)
  • The PTC nontaster haplotype is a genetic marker that may be used to identify subsets of schizophrenia patients who potentially harbor vulnerability genes in this region of chromosome 7q. (johnshopkins.edu)
  • Here we show that in the presence of the risk haplotype, the expression of the KIAA0319 gene is reduced but the expression of the other two genes remains unaffected. (ox.ac.uk)
  • This chromosome scale, and haplotype resolved C. australis genome will facilitate the study of important genes for citrus breeding and will also allow the enhanced definition of the evolutionary relationships between wild and domesticated citrus species. (qld.gov.au)
  • It is noteworthy that type II collagen and vitamin D receptor genes map in the same region on chromosome 12q13.11, according to the UCSC Genome Browser database. (bmj.com)
  • The haplotype map, or "HapMap," is a tool that allows researchers to find genes and genetic variations that affect health and disease. (genome.gov)
  • By scouring other regions in the genome that have reportedly undergone balancing selection events, meanwhile, the researchers identified half a dozen other variants with less pronounced ties to malaria that fell near genes belonging to ancient balanced polymorphism haplotypes. (genomeweb.com)
  • The gene mutated in this disorder lies within a 3.1 Mb interval containing 33 genes on chromosome 16q23.3-24.1 (chr16:83639061 - 86716445, hg19). (molvis.org)
  • Methods We selected bacterial artificial chromosome (BAC) clones harboring key IGC genes from public and private libraries and sequenced the inserts with long-read sequencing technologies. (usda.gov)
  • The reason for this is simple but has proven difficult to tackle - instead of inheriting one copy of every chromosome from both the father and from the mother (as in humans) potatoes inherit two copies of each chromosome from each parent, making them a species with four copies of each chromosome (tetraploid). (mpg.de)
  • The reasoning in doing so is twofold: first, language is an inherited cultural trait and thus the language phylae often correlate with genetic traits not the least to Y chromosome polymorphisms. (wikipedia.org)
  • The genotypes of two nonsynonymous coding single-nucleotide polymorphisms in TAS2R38 were assayed for 176 schizophrenia patients and 229 healthy control individuals, and the two-allele haplotypes were estimated. (johnshopkins.edu)
  • Starting with the assumption that a single NGS read (or read pair) must come from one haplotype, we built a procedure for directly observing haplotypes at a local level by examining 2 or 3 adjacent single nucleotide polymorphisms (SNPs) which are close enough on the genome to be spanned by individual reads. (biomedcentral.com)
  • A significant, protective effect was found when three single-nucleotide polymorphisms (ERCC2 rs13181, ERCC1 rs3212986, and GLTSCR1 rs1035938) located near each other on chromosome 19 were modeled as a haplotype. (cdc.gov)
  • The Y Chromosome Haplotype Reference Database (YHRD) is an open-access, annotated collection of population samples typed for Y chromosomal sequence variants. (wikipedia.org)
  • Because strong correlations exist between geographic areas and Y chromosomal variants, the YHRD population database was structured to display the geographic, linguistic and phylogenetic relationship of searched haplotype profiles. (wikipedia.org)
  • The ability of nanopore technology to sequence any length of nucleic acid molecule allows for unprecedented resolution of complex structural variants, as well as identification and haplotype phasing of single nucleotide alterations. (nanoporetech.com)
  • This stretch on chromosome 3 contains multiple genetic variants that are almost always inherited together, forming a block known as a haplotype. (sciencenews.org)
  • Of 13 genetic variants that make up the risky haplotype, 11 were found in the DNA of a 50,000 year-old Neandertal from Vindija Cave in Croatia ( SN: 10/10/17 ), and three were shared with two Neandertals from the Altai mountains in Russia. (sciencenews.org)
  • Thirty-six of the validated SNPs were clustered on chromosomes Omy3, Omy8 and Omy25. (usda.gov)
  • Three SNPs from each QTL region were used for haplotype association analysis. (usda.gov)
  • Sets of nearby SNPs on the same chromosome are inherited in blocks. (genome.gov)
  • This pattern of SNPs on a block is a haplotype. (genome.gov)
  • Blocks may contain a large number of SNPs, but a few SNPs are enough to uniquely identify the haplotypes in a block. (genome.gov)
  • The HapMap is a map of these haplotype blocks and the specific SNPs that identify the haplotypes are called tag SNPs. (genome.gov)
  • Using just the tag SNPs, researchers are able to find chromosome regions that have different haplotype distributions in the two groups of people, those with a disease or response and those without. (genome.gov)
  • A second generation human haplotype map of over 3.1 million SNPs. (genome.gov)
  • As dynamic sites in the human genome, SNPs are often highly correlated into combinations referred to as haploblocks whose haplotypes are maintained throughout generations with fixed frequencies within a given population. (scirp.org)
  • If individual reads span both SNPs, then these combinations are directly observable and it is possible to list haplotypes. (biomedcentral.com)
  • Sex chromosomes evolve once recombination is halted between a homologous pair of chromosomes. (nature.com)
  • Sex chromosomes are typically thought to evolve as recombination is halted between a homologous pair of chromosomes in one sex. (nature.com)
  • The offspring gets one chromosome in each pair from each parent. (wikipedia.org)
  • A set of pairs of chromosomes is called diploid and a set of only one half of each pair is called haploid. (wikipedia.org)
  • The Y-chromosome contains 59 million bits of information, each of which is encoded by a "base pair. (smgf.org)
  • Microfluidic whole genome haplotyping is a technique for the physical separation of individual chromosomes from a metaphase cell followed by direct resolution of the haplotype for each allele. (wikipedia.org)
  • The analysis of a sequence such as a region of a chromosome, a haplotype, a gene, or an allele for its involvement in controlling the phenotype of a specific trait, metabolic pathway, or disease. (bvsalud.org)
  • We study a preprocessing routine relevant in pan-genomic analyses: consider a set of aligned haplotype sequences of complete human chromosomes. (biomedcentral.com)
  • The structure of female (mtDNA) and male (Y-chromosome haplotypes) lineages in the Yakut population was examined. (blogspot.com)
  • To determine mtDNA haplotypes, sequencing of hypervariable segment I and typing of haplotype-specific point substitutions in the other parts of the mtDNA molecule were performed. (blogspot.com)
  • Two important objectives are pursued: (1) the generation of reliable frequency estimates for Y-STR haplotypes and Y-SNP haplotypes to be used in the quantitative assessment of matches in forensic and kinship cases and (2) the characterization of male lineages to draw conclusions about the origins and history of human populations. (wikipedia.org)
  • Members of the apolipoprotein gene cluster (APOA1/C3/A4/A5) on human chromosome 11q23 play an important role in lipid metabolism. (doe.gov)
  • what's more, multiple copies of each chromosome also make the reconstruction of the potato genome a far greater technical challenge than was the case for the human genome. (mpg.de)
  • The elucidation of the entire human genome has made possible our current effort to develop a haplotype map of the human genome. (genome.gov)
  • A haplotype map of the human genome. (genome.gov)
  • A stretch of DNA on human chromosome 3 was previously found to be associated with an increased risk of developing severe disease from coronavirus infection and of being hospitalized. (sciencenews.org)
  • Moreover, the site in question has been shown as a site of balancing selection in the past, with an overlapping human and chimpanzee haplotype in this region. (genomeweb.com)
  • We describe an extended GWAS meta-analysis of 3,260 COVID-19 patients with respiratory failure and 12,483 population controls from Italy, Spain, Norway and Germany, as well as hypothesis-driven targeted analysis of the human leukocyte antigen (HLA) region and chromosome Y haplotypes. (cdc.gov)
  • It can be all the chromosomes from one of the parents or a minor part of a chromosome, for example a sequence of 9000 base pairs . (wikipedia.org)
  • Our results highlight the need for new methods to analyze genomic variation because existing ones do not systematically consider local haplotypes. (biomedcentral.com)
  • Other research themes are molecular and genomic ecology, e.g. immune gene evolution, telomere ecology and sex chromosome evolution in birds. (lu.se)
  • The dominant model of sex chromosome evolution posits that recombination is suppressed between emerging X and Y chromosomes in order to resolve sexual conflict. (nature.com)
  • Although we have a detailed understanding of the evolutionary consequences of the loss of recombination for sex chromosome evolution 1 , 2 , we still do not understand the evolutionary forces acting to halt recombination in the first place. (nature.com)
  • In most organisms, meiotic recombination is crucial for the accurate partitioning of chromosomes. (mskcc.org)
  • Furthermore, the distribution of recombination sites across the genome has implications for the creation of new haplotype blocks and for genome integrity. (mskcc.org)
  • Although most non-Africans carry some Neandertal DNA as a relic of ancient interbreeding, inheritance of the COVID-19 susceptibility haplotype was patchy. (sciencenews.org)
  • Reasons for these contrasted evolutionary trajectories remain unclear, but species such as common frogs with polymorphism in the extent of sex-chromosome differentiation may potentially deliver important clues. (datadryad.org)
  • Elevation has only a marginal effect, opposing previous suggestions of a major role for climate on sex-chromosome differentiation. (datadryad.org)
  • In 2001, mutations were discovered in the IKB kinase-complex-associated protein ( IKBKAP ) gene, with a major haplotype mutation located in the donor splice site of intron 20. (medscape.com)
  • Dense and accurate whole-chromosome haplotyping of individual genomes. (pacb.com)
  • Recent advances in genome sequencing and assembly techniques have made it possible to achieve chromosome level reference genomes for citrus. (qld.gov.au)
  • Relatively few genomes have been anchored at the chromosome level and/or are haplotype phased, with the available genomes of varying accuracy and completeness. (qld.gov.au)
  • We show that although the nascent Y chromosome encompasses nearly half of the linkage group, there has been no perceptible degradation of Y chromosome gene content or activity. (nature.com)
  • By performing a whole genome linkage search, we mapped a recessive gene for this disorder to a 6.5 Mb interval on chromosome 16q23.2-24.2. (molvis.org)
  • In 1993, using genetic linkage, the gene for familial dysautonomia was localized to the distal long arm of chromosome 9(q31) with sufficient DNA markers to permit prenatal diagnosis and carrier identification for families in which an individual had been affected. (medscape.com)
  • We also analyzed 17 Y-chromosome STRs in 30 individuals to assess the paternal gene pool. (bioone.org)
  • These recombinations defined five haploblocks containing 5-15 markers and exhibiting 7-11 haplotypes each. (wur.nl)
  • Two- and three-marker haplotypes from the 1q41 region similarly showed strong transmission distortion in the collection of 332 SLE families. (elsevierpure.com)
  • The slowest 22 marker haplotype panel (out of the 67 marker panel) and their mutation rate constants employed for calculations timespans to the most ancient common ancestors. (scirp.org)
  • 12 15 13 12 29 22 10 11 12 16 11 15 would be called a 12-marker haplotype. (smgf.org)
  • This lack of haplotype-level analyses can be explained by a lack of methods that can produce dense and accurate chromosome-length haplotypes at reasonable costs. (pacb.com)
  • It has been associated with other chromosomal abnormalities involving chromosome 18. (lu.se)
  • Construct reference-quality, chromosome-spanning assemblies and phase haplotypes to explore genome function and species evolution. (arimagenomics.com)
  • We then used a hierarchical assembly approach to combine the assemblies into alternative haplotype regions. (usda.gov)
  • Studying a subset of Middle Eastern and northern African MKS families, we have recently excluded the chromosome 17 region and have suggested a genetic heterogeneity. (nih.gov)
  • Using replicate wild populations with differing levels of sexually antagonistic selection for colour, we also show that sexual selection leads to greater expansion of the non-recombining region and increased Y chromosome divergence. (nature.com)
  • A recent genetic study of Tibetan Y-chromosomes suggests that about 5,000-6,000 years ago, a subgroup of the Proto-Sino-Tibetan people, who had settled in the Yellow River valley, diverged from the ancestors of the Han Chinese and migrated, probably following the "Zang (Tibet)-Mien corridor," from the upper Yellow River region westward to Qinghai province and then southward to the Himalayas . (newworldencyclopedia.org)
  • The OCA2 gene is located in a region of chromosome 15 that is often deleted in individuals with Angelman syndrome. (medlineplus.gov)
  • We introduce the technique of Local Haplotyping Analysis (LHA) which shows that evidence for heterogeneity is strong and directly observable in Next Generation Sequencing (NGS) data. (biomedcentral.com)
  • Instead, we examine all possible haplotypes with the explicit aim of evaluating evidence for heterogeneity in the tissue. (biomedcentral.com)
  • abstract = "Phenylthiocarbamide (PTC) taste sensitivity is an inherited trait determined primarily by allelic variation of the tastereceptor gene TAS2R38 on chromosome 7q. (johnshopkins.edu)
  • These results provide empirical support for longstanding models of sex chromosome catalysis, and suggest an important role for sexual selection and sexual conflict in genome evolution. (nature.com)
  • Genetic testing encompasses a broad range of laboratory tests performed to analyze DNA, RNA, chromosomes, proteins, and certain metabolites using biochemical, cytogenetic, or molecular methods or a combination of these methods. (cdc.gov)
  • The synteny analysis showed conserved regions between the two haplotypes with some structural variations in Chromosomes 2, 4, 7 and 8. (qld.gov.au)
  • Looking at all of these base pairs is impractical, so geneticists have identified a number of specific chromosome locations that can be used for analysis and comparison. (smgf.org)
  • Results Using a hierarchical assembly approach with long-read sequencing technologies, we assembled nine IGC haplotypes from 48 pre-selected BACs. (usda.gov)
  • These haplotypes were compared to the recently released ARS-UCDv1.2 cattle reference assembly and showed good contiguity with that reference. (usda.gov)
  • Our chromosome conformation capture technology simplifies your chromatin folding studies and allows you to determine DNA contact frequencies and chromosome conformation. (qiagen.com)
  • Over the entire QTL hotspot, 30 extended haplotypes were identified for which parental gametes could be determined. (wur.nl)
  • Positive lod score values were obtained for chromosome 6q22.31-q24.1, with evidence of three homozygous intervals. (bmj.com)
  • There was an overrepresentation of the major PTC nontaster haplotype among patients of European descent, relative to control individuals of similar ancestry. (johnshopkins.edu)
  • C) on chromosome 4q25 with atrial fibrillation (AF), but phenotype alterations conferred by this SNP have not been described. (nature.com)
  • Three haplotypes, Omy3TGG, Omy8GCG and Omy25CGG, were found to be associated with BCWD resistance in the 2015TLUM generation. (usda.gov)
  • In addition to verifying this association in another 14,000 African individuals, the team estimated that individuals with a protective version of the haplotype are roughly 33 percent less likely to suffer from severe malaria than their counterparts without it. (genomeweb.com)