Haplotype block and superblock structures of the alpha1-adrenergic receptor genes reveal echoes from the chromosomal past

A significant proportion of the human genome is contained within haplotype blocks across which pairwise linkage disequilibrium (LD) is very high. However, LD is also often high between markers at more remote distances, and within different haplotype blocks. Here, we evaluate the origins of haplotype block structure in the three genes for alpha1 adrenergic receptors (alpha1-AR) in the human genome ( ADRA1A, ADRA1B and ADRA1D) by genotyping dense single-nucleotide polymorphism (SNP) marker maps, and show that LD signals between distant markers are due to the presence of extended haplotype superblocks in individuals with ancient chromosomes which have escaped historic recombination. ARs mediate the physiological effects of epinephrine and norepinephrine, and are targets of many therapeutic drugs. This work has identified haplotype backgrounds of alpha1-AR missense variants, haplotype block structures in US Caucasians and African Americans, and haplotype tag SNPs for each block, and we present strong evidence for ancient haplotype block superstructure at these genes which has been partially disrupted by recombination, and evidence for reinstatement of linkage disequilibrium by subsequent recombination events. ADRA1A is comprised of four haplotype blocks in US Caucasians, while in African Americans Block 1 is split. ADRA1B has four blocks in US Caucasians, but in African Americans only the first two blocks are present. ADRA1D has two blocks in US Caucasians, and the first block is replaced by two smaller blocks in African Americans. For both ADRA1A and ADRA1B, haplotype superstructures may represent a novel, higher-level hierarchy in the human genome, which may reduce redundancy of testing by further aggregation of genotype data.Electronic Supplementary Material Supplementary material is available in the online version of this article at Communicated by W. R. McCombie     

Development of sequence-specific PCR markers linked to the Tardus gene that reduces pod shattering in narrow-leafed lupin (Lupinus angustifolius L.)

Seed pods of wild-type narrow-leafed lupins (Lupinus angustifolius L.) shatter upon maturity, dispersing their seeds. Recessive alleles of the genes Tardus and Lentus that confer reduced pod shattering have been incorporated into domesticated cultivars to facilitate harvesting. Tardus was mapped in an F₈ recombinant inbred population of a cross between domesticated and wild lupins. A microsatellite–anchored fragment length polymorphism marker (TaM1), which mapped 2.1 cM from Tardus, was converted to a locus-specific PCR assay. Marker TaM2, a restriction fragment length polymorphism marker was converted to a PCR assay and mapped to 3.9 cM on the other side of Tardus. Marker TaM3, a cleaved amplified polymorphic sequence marker, was positioned along-side marker TaM1 at 3.9 cM from Tardus. One or more markers was polymorphic in 70% of possible pairwise crosses between Australian domesticated lines and wild accessions tested, indicating wide applicability of the markers in crosses between wild and domesticated germplasm.     

Allele frequencies of 6 autosomal STR loci in the Xibo nationality with phylogenetic structure among Chinese populations

In the present study, we investigated the genetic polymorphisms of 6 autosomal STR loci Hum-CSF1PO, D13S317, D5S818, D16S539, TH01, and TPOX in the Xibo population of Liaoning, northeastern China as well as its genetic relationships with other populations in China. No significant deviations from Hardy-Weinberg equilibrium could be found for all loci. Allele frequencies in the Xibo population ranged from 0.001 to 0.507. Among all the 6 loci, D16S539 had the highest polymorphism (PIC = 0.8632), whereas TPOX had the lowest (PIC = 0.5179). A phylogenic tree was constructed using Poptree 2 software. In the phylogenic tree, Xibo population has a distant relationship with the other populations.     

The effects of linkage and gene flow on local adaptation: a two-locus continent-island model

Population subdivision and migration are generally considered to be important causes of linkage disequilibrium (LD). We explore the combined effects of recombination and gene flow on the amount of LD, the maintenance of polymorphism, and the degree of local adaptation in a subdivided population by analyzing a diploid, deterministic continent–island model with genic selection on two linked loci (i.e., no dominance or epistasis). For this simple model, we characterize explicitly all possible equilibrium configurations. Simple and intuitive approximations for many quantities of interest are obtained in limiting cases, such as weak migration, weak selection, weak or strong recombination. For instance, we derive explicit expressions for the measures and r² (the squared correlation in allelic state) of LD. They depend in qualitatively different ways on the migration rate. Remarkably high values of r² are maintained between weakly linked loci, especially if gene flow is low. We determine how the maximum amount of gene flow that admits preservation of the locally adapted haplotype, hence of polymorphism at both loci, depends on recombination rate and selection coefficients. We also investigate the evolution of differentiation by examining the invasion of beneficial mutants of small effect that are linked to an already present, locally adapted allele. Mutants of much smaller effect can invade successfully than predicted by naive single-locus theory provided they are at least weakly linked. Finally, the influence of linkage on the degree of local adaptation, the migration load, and the effective migration rate at a neutral locus is explored. We discuss possible consequences for the evolution of genetic architecture, in particular, for the emergence of clusters of tightly linked, slightly beneficial mutations and the evolution of recombination and chromosome inversions.     

Nucleotide variation at the dopa decarboxylase (<Emphasis Type="Italic">Ddc</Emphasis>) gene in natural populations of <Emphasis Type="Italic">Drosophila melanogaster</Emphasis>

We studied nucleotide sequence variation at the gene coding for dopa decarboxylase (Ddc) in seven populations of Drosophila melanogaster. Strength and pattern of linkage disequilibrium are somewhat distinct in the extensively sampled Spanish and Raleigh populations. In the Spanish population, a few sites are in strong positive association, whereas a large number of sites in the Raleigh population are associated nonrandomly but the association is not strong. Linkage disequilibrium analysis shows presence of two groups of haplotypes in the populations, each of which is fairly diverged, suggesting epistasis or inversion polymorphism. There is evidence of two forms of natural selection acting on Ddc. The McDonald-Kreitman test indicates a deficit of fixed amino acid differences between D. melanogaster and D. simulans, which may be due to negative selection. An excess of derived alleles at high frequency, significant according to the H-test, is consistent with the effect of hitchhiking. The hitchhiking may have been caused by directional selection downstream of the locus studied, as suggested by a gradual decrease of the polymorphism-to-divergence ratio. Altogether, the Ddc locus exhibits a complicated pattern of variation apparently due to several evolutionary forces. Such a complex pattern may be a result of an unusually high density of functionally important genes.     

Asian population frequencies and haplotype distribution of killer cell immunoglobulin-like receptor (KIR) genes among Chinese, Malay, and Indian in Singapore

Killer cell immunoglobulin-like receptors (KIR) gene frequencies have been shown to be distinctly different between populations and contribute to functional variation in the immune response. We have investigated KIR gene frequencies in 370 individuals representing three Asian populations in Singapore and report here the distribution of 14 KIR genes (2DL1, 2DL2, 2DL3, 2DL4, 2DL5, 2DS1, 2DS2, 2DS3, 2DS4, 2DS5, 3DL1, 3DL2, 3DL3, 3DS1) with two pseudogenes (2DP1, 3DP1) among Singapore Chinese (n = 210); Singapore Malay (n = 80), and Singapore Indian (n = 80). Four framework genes (KIR3DL3, 3DP1, 2DL4, 3DL2) and a nonframework pseudogene 2DP1 were detected in all samples while KIR2DS2, 2DL2, 2DL5, and 2DS5 had the greatest significant variation across the three populations. Fifteen significant linkage patterns, consistent with associations between genes of A and B haplotypes, were observed. Eighty-four distinct KIR profiles were determined in our populations, 38 of which had not been described in other populations. KIR haplotype studies were performed using nine Singapore Chinese families comprising 34 individuals. All genotypes could be resolved into corresponding pairs of existing haplotypes with eight distinct KIR genotypes and eight different haplotypes. The haplotype A2 with frequency of 63.9% was dominant in Singapore Chinese, comparable to that reported in Korean and Chinese Han. The A haplotypes predominate in Singapore Chinese, with ratio of A to B haplotypes of approximately 3:1. Comparison with KIR frequencies in other populations showed that Singapore Chinese shared similar distributions with Chinese Han, Japanese, and Korean; Singapore Indian was found to be comparable with North Indian Hindus while Singapore Malay resembled the Thai. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

RETRACTED ARTICLE: An analysis of population structure and linkage disequilibrium using multilocus data in 187 maize inbred lines

This study analyzes population structure and linkage disequilibrium (LD) among 187 commonly used Chinese maize inbred lines, representing the genetic diversity among public, commercial and historically important lines for corn breeding. Seventy SSR loci, evenly distributed over 10 chromosomes, were assayed for polymorphism. The identified 290 alleles served to estimate population structure and analyze the genome-wide LD. The population of lines was highly structured, showing 6 subpopulations: BSSS (American BSSS including Reid), PA (group A germplasm derived from modern U.S. hybrids in China), PB (group B germplasm derived from modern U.S. hybrid in China), Lan (Lancaster Surecrop), LRC (derivative lines from Lvda Reb Cob, a Chinese landrace) and SPT (derivative lines from Si-ping-tou, a Chinese landrace). Forty lines, which formerly had an unknown and/or miscellaneous origin and pedigree record, were assigned to the appropriate group. Relationship estimates based on SSR marker data were quantified in a Q matrix, and this information will inform breeder’s decisions regarding crosses. Extensive inter- and intra-chromosomal LD was detected between 70 microsatellite loci for the investigated maize lines (2109 loci pairs in LD with D′ > 0.1 and 93 out of them at P < 0.01).This suggests that rapidly evolving microsatellites may track recent population structure. Interlocus LD decay among the diverse maize germplasm indicated that association studies in QTLs and/or candidate genes might avoid nonfunctional and spurious associations since most of the LD blocks were broken between diverse germplasm. The defined population structure and the LD analysis present the basis for future association mapping. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Association of the polymorphisms in the 5'-untranslated region of PTEN gene with type 2 diabetes in a Japanese population

Phosphatase and tensin homolog deleted on chromosome 10 (PTEN) is known to act as a lipid phosphatase hydrolyzing phosphatidylinositol (PI)(3,4,5)P(3) to PI(4,5)P(2). Since the PI3-kinase product, PI(3,4,5)P(3), is an important second messenger leading to the metabolic action of insulin, PTEN functions as a potent negative regulator of insulin signaling and its gene is one of the possible candidates involved in susceptibility to the development of type 2 (non-insulin-dependent) diabetes. In the present study, we investigated the polymorphisms of the PTEN gene in Japanese patients with type 2 diabetes and non-diabetic control subjects. We identified three mutations of the gene in the type 2 diabetes patients. Among these mutations, the frequency of the substitution of C with G at position -9 (-9C-->G) (SNP1), located in the untranslated region of exon 1, was significantly higher in type 2 diabetic patients than in control subjects. In addition, transfection of the PTEN gene with SNP1 resulted in a significantly higher expression level of PTEN protein compared with that of the wild-type PTEN gene in Cos1 and Rat1 cells. Furthermore, insulin-induced phosphorylation of Akt in HIRc cells was decreased more greatly by transfection of SNP1 PTEN gene than that of wild-type PTEN gene. These findings suggest that the change of C to G at position -9 of the PTEN gene is associated with the insulin resistance of type 2 diabetes due possibly to a potentiated hydrolysis of the PI3-kinase product.     

Design and synthesis of novel and potent GPR119 agonists with a spirocyclic structure

Exploration of alternative structures of the substituted piperidine or piperazine ring which are characteristic in most of the reported GPR119 agonists provided novel spirocyclic cyclohexane derivatives. The representative 17 with a high three-dimensionality exhibited potent agonistic activity (EC₅₀?=?4?nM) with no CYP inhibitory activity (IC₅₀ >10?μM). Compound 17 also displayed hypoglycemic activity with insulin secretion dependent on glucose concentration in an intraperitoneal glucose tolerance test in rats.     

Evidence of a complex phylogeographic structure in the Indomalayan pencil-tailed tree mouse Chiropodomys gliroides (Rodentia: Muridae) in eastern Indochina

The paper presents the first phylogeography of the Indomalayan pencil-tailed tree mouse, Chiropodomys gliroides, an arboreal rodent widely distributed in SE Asia. Fifty four specimens of C. gliroides, sampled throughout eastern Indochina (Vietnam and Laos), have been sequenced for the mitochondrial (cytb and control region) and nuclear (IRBP) genes. The results have revealed the existence of two highly divergent allopatric lineages showing a genetic divergence of 12% cytb and occurring in different regions of Vietnam. The northern lineage occurs in northern and central Vietnam, central Laos and the highlands of southern Vietnam, and the southern lineage occurs in lowlands of southern Vietnam. In the south, representatives of both lineages were collected at the distance of less than 130 km from each other. The occurrence of both genetic lineages in southern Vietnam seems to testify for an important role of Dalat Plateau as a possible refuge for small mammals. Yet, our results do not support the assignment of Chiropodomys neither to the Micromys division of Murinae, nor to a close phylogenetic link between Chiropodomys and Hapalomys.     

Carnitine palmitoyltransferase 2: analysis of membrane association and complex structure with a substrate analog

The mitochondrial membrane-associated carnitine palmitoyltransferase system is a validated target for the treatment of type 2 diabetes mellitus. To further facilitate structure-based drug discovery, we determined the crystal structure of rat CPT-2 (rCPT-2) in complex with the substrate analogue palmitoyl-aminocarnitine at 1.8A resolution. Biochemical analyses revealed a strong effect of this compound on rCPT-2 activity and stability. Using a computational approach we examined the membrane association of rCPT-2. The protein interacts with the membrane as a functional monomer and the calculations confirm the presence of a membrane association domain that consists of layers of hydrophobic and positively charged residues.     

Genetic structure of expanding wolf (Canis lupus) populations in Italy and Croatia,and the early steps of the recolonization of the Eastern Alps

After centuries of range contraction and demographic declines wolves are now expanding in Europe, colonizing regions from where they have been absent for centuries. Wolf colonizing the western Alps originate by the expansion of the Italian population. Vagrant wolves of Italian and Dinaric-Balkan origins have been recently observed in the Eastern Alps. In this study we compared the genetic structure of wolf populations in Italy and Croatia, aiming to identify the sources of the ongoing recolonization of the Eastern Alps. DNA samples, extracted from 282 Italian and 152 Croatian wolves, were genotyped at 12 autosomal microsatellites (STR), four Y-linked STR and at the hypervariable part of the mitochondrial DNA control-region (mtDNA CR1). Wolves in Croatia and Italy underwent recent demographic bottlenecks, but they differ in genetic diversity and population structure. Wolves in Croatia were more variable at STR loci (N_A = 7.4, H_O = 0.66, H_E = 0.72; n = 152) than wolves in Italy (N_A = 5.3, H_O = 0.57, H_E = 0.58; n = 282). We found four mitochondrial DNA (mtDNA CR1) and 11 Y-STR haplotypes in Croatian wolves, but only one mtDNA CR1 and three Y-STR haplotypes in Italy. Wolves in Croatia were subdivided into three genetically distinct subpopulations (in Dalmatia, Gorski kotar and Lika regions), while Italian wolves were not sub-structured. Assignment testing shows that the eastern and central Alps are recolonized by wolves dispersing from both the Italian and Dinaric populations. The recolonization of the Alps will predictably continue in the future and the new population will be genetically admixed and very variable with greater opportunities for local adaptations and survival.     

Genetic variability in a genomic region with long-range linkage disequilibrium reveals traces of a bottleneck in the history of the European population

The inference of the demographic history of populations from genetic variability data is not only of academic interest. It also provides background information for the identification of genes which may have played a role in human evolution or in the aetiology of human disease. To obtain a clear picture of this background, it is necessary to compare data obtained from a number of genomic loci. Due to its very low recombination rate, the NF1 gene region can be regarded as a further suitable locus. A combined resequencing and SNP typing project in a European population disclosed the presence of only two well separated subgroups of NF1 sequences. Statistical analysis revealed a bimodal distribution of the pairwise differences, a positive value of Tajima’s D and a TMRCA of 700,000 years for the whole sample, and pairwise differences indicative for a growing population and TMRCAs of 130,000 to 150,000 years for the subgroups. Together, the data lead to a model that the recent European population went through a bottleneck during the last 150,000 years of its history. Regarding the given timeframe, this bottleneck could either reflect a speciation event which led to the anatomically modern human (AMH), or a severe reduction of the population size during the emigration of AMHs out of Africa or the immigration into Europe.     

Recombination and lineage‐specific gene loss in the aflatoxin gene cluster of Aspergillus flavus

Aflatoxins produced by Aspergillus flavus are potent carcinogens that contaminate agricultural crops. Recent efforts to reduce aflatoxin concentrations in crops have focused on biological control using nonaflatoxigenic A. flavus strains AF36 (=NRRL 18543) and NRRL 21882 (the active component of afla‐guard^®). However, the evolutionary potential of these strains to remain nonaflatoxigenic in nature is unknown. To elucidate the underlying population processes that influence aflatoxigenicity, we examined patterns of linkage disequilibrium (LD) spanning 21 regions in the aflatoxin gene cluster of A. flavus. We show that recombination events are unevenly distributed across the cluster in A. flavus. Six distinct LD blocks separate late pathway genes aflE, aflM, aflN, aflG, aflL, aflI and aflO, and there is no discernable evidence of recombination among early pathway genes aflA, aflB, aflC, aflD, aflR and aflS. The discordance in phylogenies inferred for the aflW/aflX intergenic region and two noncluster regions, tryptophan synthase and acetamidase, is indicative of trans‐species evolution in the cluster. Additionally, polymorphisms in aflW/aflX divide A. flavus strains into two distinct clades, each harbouring only one of the two approved biocontrol strains. The clade with AF36 includes both aflatoxigenic and nonaflatoxigenic strains, whereas the clade with NRRL 21882 comprises only nonaflatoxigenic strains and includes all strains of A. flavus missing the entire gene cluster or with partial gene clusters. Our detection of LD blocks in partial clusters indicates that recombination may have played an important role in cluster disassembly, and multilocus coalescent analyses of cluster and noncluster regions indicate lineage‐specific gene loss in A. flavus. These results have important implications in assessing the stability of biocontrol strains in nature.     

Expression genetics and haplotype analysis reveal cis regulation of serine carboxypeptidase I (Cxp1), a candidate gene for malting quality in barley (Hordeum vulgare L.)

Using a cDNA array-based functional genomics approach in barley, several candidate genes for malting quality including serine carboxypeptidase I (Cxp1) were previously identified (Potokina et al. in Mol Breed 14:153, 2004). The gene was mapped as a single nucleotide polymorphism (SNP) marker on chromosome 3H using the Steptoe (feeding grade) × Morex (malting grade) mapping population. Subsequently, the relative level of Cxp1 expression was determined by real-time RT-PCR for each of the 134 progeny lines and mapped as a quantitative trait. Only one quantitative trait locus (QTL) could be identified that significantly influenced the level of the Cxp1 expression. The expressed QTL maps to the same region on chromosome 3H as does the structural gene and corresponds to a QTL for “diastatic power,” one among several traits measured to assess malting quality. An analysis of 90 barley cultivars sampled from a worldwide collection revealed six SNPs at the Cxp1 locus, three of which display complete linkage disequilibrium and define two haplotypes. The Cxp1 expression level in a set of barley accessions showing haplotype I was significantly higher than that of accessions displaying haplotype II. The data provide evidence that (1) the expression of Cxp1 is regulated in cis and that (2) the level of diastatic power in the barley seed is influenced by the level of Cxp1 expression. Supplementary material is available in the online version of this article at     

Linkage disequilibrium and founder effect analysis of the NF1 gene in French Canadians from the Quebec population

We genotyped 19 neurofibromatosis type 1 (NF1) families from French Canadians of the Quebec population with four intragenic microsatellites (IVS26-2.3, IVS27AC28.4, IVS27AC33.1, and IVS38GT53.0). Linkage analysis of the four microsatellite markers among the 19 NF1 families indicates that the four microsatellites are strongly linked with NF1 disease (LOD = 2.76-3.64). The four markers are associated (P = 0-0.077) except marker pair IVS26-2.3/IVS27AC33.1 (P = 0.18 or 0.17). However, perhaps due to the high mutation rate of the NF1 gene, no founder effect for NF1 was detected in the Quebec French Canadians.     

Fasciola hepatica demonstrates high levels of genetic diversity,a lack of population structure and high gene flow: possible implications for drug resistance

Fasciola hepatica, the liver fluke, is a trematode parasite of considerable economic importance to the livestock industry and is a re-emerging zoonosis that poses a risk to human health in F. hepatica-endemic areas worldwide. Drug resistance is a substantial threat to the current and future control of F. hepatica, yet little is known about how the biology of the parasite influences the development and spread of resistance. Given that F. hepatica can self-fertilise and therefore inbreed, there is the potential for greater population differentiation and an increased likelihood of recessive alleles, such as drug resistance genes, coming together. This could be compounded by clonal expansion within the snail intermediate host and aggregation of parasites of the same genotype on pasture. Alternatively, widespread movement of animals that typically occurs in the UK could promote high levels of gene flow and prevent population differentiation. We identified clonal parasites with identical multilocus genotypes in 61% of hosts. Despite this, 84% of 1579 adult parasites had unique multilocus genotypes, which supports high levels of genotypic diversity within F. hepatica populations. Our analyses indicate a selfing rate no greater than 2%, suggesting that this diversity is in part due to the propensity for F. hepatica to cross-fertilise. Finally, although we identified high genetic diversity within a given host, there was little evidence for differentiation between populations from different hosts, indicating a single panmictic population. This implies that, once those emerge, anthelmintic resistance genes have the potential to spread rapidly through liver fluke populations.