Genetic interaction between homoeotic Sex combs reduced and Regulator of bithorax (or trithorax) genes of Drosophila melanogaster

Summary Regulator of bithorax (Rg-bx)^–, or trithorax (trx)^– lethal larvae occasionally show a homoeotic transformation of the dorsal prothorax to mesothoracic structures. This transformation suggests a reduced activity of the Sex combs reduced (Scr) gene on the basis of gene dosage studies, as well as enhanced expression of the phenotypes of the weak Scr ^– alleles in Rg-bx ^– larvae. Morphological observations of adult flies doubly heterozygous for Rg-bx and Scr mutations also suggest the enhancement of an aspect of Scr adult phenotypes. I conclude that the Rg-bx ⁺ gene function is required for the optimal expression of the Scr gene in larval and imaginai cells.     

Male- and female-specific variants of doublesex gene products have different roles to play towards regulation of Sex combs reduced expression and sex comb morphogenesis in Drosophila

Sexually dimorphic characters have two-fold complexities in pattern formation as they have to get input from both somatic sex determination as well as the positional determining regulators. Sex comb development in Drosophila requires functions of the somatic sex-determining gene doublesex and the homeotic gene Sex combs reduced. Attempts have not been made to decipher the role of dsx in imparting sexually dimorphic expression of SCR and the differential function of sex-specific variants of dsx products in sex comb development. Our results in this study indicate that male-like pattern of SCR expression is independent of dsx function, and dsx ^F must be responsible for bringing about dimorphism in SCR expression, whereas dsx ^M function is required with Scr for the morphogenesis of sex comb.     

Beetle horns are regulated by the Hox gene,Sex combs reduced,in a species‐ and sex‐specific manner

Discovering the mechanisms that underlie the origin of novel features represents a major frontier in developmental and evolutionary biology. Here we begin to characterize the role of the Hox gene Sex combs reduced (Scr) during the development and evolution of a morphologically novel trait: beetle horns. Beetle horns develop as epidermal outgrowths from the prothorax and/or head, and size and location vary dramatically across species and between sexes. Using both comparative gene expression and larval RNA interference in two species of the horned beetle genus Onthophagus, we show that Scr functions in patterning adult labial mouthpart identity and suppressing wing development in the prothorax. At the same time, however, our results illustrate that Scr has acquired, within its ancestral domain of expression, additional new functions including the regulation of prepupal growth and pupal remodeling of pronotal horn primordia. Furthermore, comparative analyses of our results across both Onthophagus species, which differ in location of horn development (thoracic horns vs. thoracic and head horns) as well as patterns of sexual dimorphism (traditional vs. reversed sexual dimorphism), reveal surprising differences in exactly when, where, and to what degree Scr regulates horn formation in different sexes. These observations suggest that the interactions between Scr and its targets in the regulation of horn development can diversify quickly over remarkably short phylogenetic distances. More generally, our results suggest that the Hox complex can play an integral role in the development and evolution of novel complex traits while maintaining traditional patterning responsibilities.     

Allele Distributions and Frequencies of the Six Prion Protein Gene (PRNP) Polymorphisms in Asian Native Cattle, Japanese Breeds, and Mythun (Bos frontalis)

Six polymorphic sites of the bovine prion protein gene (PRNP) were genotyped in 569 animals of Asian native cattle, Japanese breeds, purebred mythun (Bos frontalis), and mythun × cattle composite animals. At the 23-bp indel site, a deletion (23?) allele was a major allele in all populations except mythun. At the 12-bp indel site, an insertion (12+) allele was a major allele in all populations. The 14-bp indel site was polymorphic in all Asian native cattle. In the octapeptide repeat region, a six-repeat allele was a major allele in all populations, and 5/5 and 4/6 genotypes were detected in Japanese Black and Mongolian cattle and in mythun, respectively. Two nonsynonymous single nucleotide polymorphisms (SNPs) (K3T and S154N) were detected in Asian native cattle and mythun. Haplotype analysis using the genotypes of the six sites estimated 33 different haplotypes. The haplotype 23? 12? K 6 S 14+ was found in all populations.     

BIM1 Encodes a Microtubule-binding Protein in Yeast

A previously uncharacterized yeast gene (YER016w) that we have named BIM1 (binding to microtubules) was obtained from a two-hybrid screen of a yeast cDNA library using as bait the entire coding sequence of TUB1 (encoding α-tubulin). Deletion of BIM1 results in a strong bilateral karyogamy defect, hypersensitivity to benomyl, and aberrant spindle behavior, all phenotypes associated with mutations affecting microtubules in yeast, and inviability at extreme temperatures (i.e., ≥37°C or ≤14°C). Overexpression of BIM1 in wild-type cells is lethal. A fusion of Bim1p with green fluorescent protein that complements the bim1Δ phenotypes allows visualization in vivo of both intranuclear spindles and extranuclear microtubules in otherwise wild-type cells. A bim1 deletion displays synthetic lethality with deletion alleles of bik1, num1, and bub3 as well as a limited subset of tub1 conditional-lethal alleles. A systematic study of 51 tub1 alleles suggests a correlation between specific failure to interact with Bim1p in the two-hybrid assay and synthetic lethality with the bim1Δ allele. The sequence of BIM1 shows substantial similarity to sequences from organisms across the evolutionary spectrum. One of the human homologues, EB1, has been reported previously as binding APC, itself a microtubule-binding protein and the product of a gene implicated in the etiology of human colon cancer.     

Extensive polymorphism of the FUT2 gene in an African (Xhosa) population of South Africa

The human secretor type α(1,2)fucosyltrans-ferase gene (FUT2) polymorphism was investigated in Xhosa and Caucasian populations of South Africa by polymerase chain reaction–restriction fragment length polymorphism and DNA sequencing. Six new base substitutions were found in the coding region of FUT2. A single base (C) deletion at nucleotide 778, which led to a frame shift and produced a stop codon at codon 275, was responsible for the enzyme inactivation. Three nonsynonymous base substitutions, A40G (Ile¹⁴Val), C379T (Arg¹²⁷Cys), and G481A (Asp¹⁶¹Asn), and two synonymous base substitutions, A375G (Glu¹²⁵) and C480T (His¹⁶⁰), were also identified in functional alleles. As a result, seven new alleles, Se ⁴⁰ , Se ⁴⁸¹ , Se ^40,481 , Se ^357,480 , Se ^357,379,480 , Se ³⁷⁵ , and se ^357,480,778 were identified. Population studies revealed that an allele containing a nonsense mutation G428A (Trp¹⁴³stop) (se ⁴²⁸ ) was the common null allele in both Xhosa and Caucasian populations, whereas an allele containing a missense A385T (Ile¹²⁹Phe) mutation (se ^357,385 ), which is the common null allele in Orientals, was found to be absent from both populations. The heterozygosity rates of FUT2 genotypes were as high as 0.75 in the Xhosa population and 0.65 in the Caucasian population. Therefore, the extensive polymorphism and race specificity of the FUT2 gene make it suitable for application as a new tool in genetic studies of modern human evolutionary history. Received: 23 March 1998 / Accepted: 9 May 1998     

An autosome-wide search using longitudinal data for loci linked to type 2 diabetes progression

Background

Aberrant and non-functional RHD alleles are much more frequent in Africans than in Europeans. The DAU cluster of RHD alleles exemplifies that the alleles frequent in Africans have evaded recognition until recently. A comprehensive survey of RHD alleles in any African population was lacking.

Results

We surveyed the molecular structure and frequency of RHD alleles in Mali (West Africa) by evaluating 116 haplotypes. Only 69% could be attributed to standard RHD (55%) or the RHD deletion (14%). The aberrant RHD allele DAU-0 was predicted for 19%, RHDΨ for 7% and Ccde ^s for 4% of all haplotypes. DAU-3 and the new RHD allele RHD(L207F), dubbed DMA, were found in one haplotype each. A PCR-RFLP for the detection of the hybrid Rhesus box diagnostic for the RHD deletion in Europeans was false positive in 9 individuals, including all carriers of RHDΨ . Including two silent mutations and the RHD deletion, a total of 9 alleles could be differentiated.

Conclusion

Besides standard RHD and the RHD deletion, DAU-0, RHDΨ and Ccde ^s are major alleles in Mali. Our survey proved that the most frequent alleles of West Africans have been recognized allowing to devise reliable genotyping and phenotyping strategies.     

Intracellular Population Genetics: Evidence for Random Drift of Mitochondrial Allele Frequencies in SACCHAROMYCES CEREVISIAE and SCHIZOSACCHAROMYCES POMBE

We report evidence for random drift of mitochondrial allele frequencies in zygote clones of Saccharomyces cerevisiae and Schizosaccharomyces pombe. Monofactorial and bifactorial crosses were done, using strains resistant or sensitive to erythromycin (alleles E^R, E^S), oligomycin (O^R, O^S), or diuron (D^R, D^S). The frequencies of resistant and sensitive cells (and thus the frequencies of the resistant and sensitive alleles) were determined for each of a number of clones of diploid cells arising from individual zygotes. Allele frequencies were extremely variable among these zygote clones; some clones were "uniparental," with mitochondrial alleles from only one parent present. These observations suggest random drift of the allele frequencies in the population of mitochondrial genes within an individual zygote and its diploid progeny. Drift would cease when all the cells in a clone become homoplasmic, due to segregation of the mitochondrial genomes during vegetative cell divisions. To test this, we delayed cell division (and hence segregation) for varying times by starving zygotes in order to give drift more time to operate. As predicted, delaying cell division resulted in an increase in the variance of allele frequencies among the zygote clones and an increase in the proportion of uniparental zygote clones. The changes in form of the allele frequency distributions resembled those seen during random drift in finite Mendelian populations. In bifactorial crosses, genotypes as well as individual alleles were fixed or lost in some zygote clones. However, the mean recombination frequency for a large number of clones did not increase when cell division was delayed. Several possible molecular mechanisms for intracellular random drift are discussed.     

Sex and the Single Cell. I. on the Action of Major Loci Affecting Sex Determination in DROSOPHILA MELANOGASTER

Sex determination in Drosophila melanogaster is under the control of the X chromosome:autosome ratio and at least four major regulatory genes: transformer (tra), transformer-2 (tra-2), doublesex (dsx) and intersex (ix). Attention is focused here on the roles of these four loci in sex determination. By examining the sexual phenotype of clones of homozygous mutant cells produced by mitotic recombination in flies heterozygous for a given recessive sex-determination mutant, we have shown that the tra, tra-2 and dsx loci determine sex in a cell-autonomous manner. The effect of removing the wild-type allele of each locus (by mitotic recombination) at a number of times during development has been used to determine when the wild-type alleles of the tra, tra-2 and dsx loci have been transcribed sufficiently to support normal sexual development. The wild-type alleles of all three loci are needed into the early pupal period for normal sex determination in the cells that produce the sexually dimorphic (in pigmentation) cuticle of the fifth and sixth dorsal abdominal segments. tra⁺ and tra-2⁺ cease being needed shortly before the termination of cell division in the abdomen, whereas dsx⁺ is required at least until the end of division. By contrast, in the foreleg, the wild-type alleles of tra⁺ and tra-2⁺ have functioned sufficiently for normal sexual differentiation to occur by about 24 to 48 hours before pupariation, but dsx⁺ is required in the foreleg at least until pupariation.——A comparison of the phenotypes produced in mutant/deficiency and homozygous mutant-bearing flies shows that dsx, tra-2 and tra mutants result in a loss of wild-type function and probably represent null alleles at these genes.—All possible homozygous doublemutant combinations of ix, tra-2 and dsx have been constructed and reveal a clear pattern of epistasis: dsx > tra, tra-2 > ix. We conclude that these genes function in a single pathway that determines sex. The data suggest that these mutants are major regulatory loci that control the batteries of genes necessary for the development of many, and perhaps all, secondary sexual characteristics.—The striking similarities between the properties of these loci and those of the homeotic loci that determine segmental and subsegmental specialization during development suggest that the basic mechanisms of regulation are the same in the two situations. The phenotypes and interactions of these sex-determination mutants provide the basis for the model of how the wild-type alleles of these loci act together to effect normal sex determination. Implications of these observations for the function of other homeotic loci are discussed.     

Study of the ref(2)P locus of Drosophila melanogaster

The ref(2)P gene of Drosophila melanogaster is implicated in sigma rhabdovirus multiplication. Two common alleles of ref(2)P are known, ref(2)P ⁰ which permits sigma virus multiplication and ref(2)P ^pwhich is restrictive for most sigma virus strains. This gene maps to the cytogenetic region 37E3-F3. Using Df(2L)E55 (=Df(2L)37D2-El;37F5-38A1), we have screened for lethal, semi-lethal and visible mutations following diepoxybutane (DEB) or ethyl methanesulfonate (EMS) mutagenesis. Our data confirm than DEB is mor efficient than EMS at inducing deletions. The mutations obtained in this region define 14 complementation groups. One of them, l(2)37Dh, appears to be a general enhancer of Minute and Minute-like mutations. None of the mutations were allelic to the ref(2)P locus. Loss-of-function alleles of ref(2)P (called null) were selected following DEB mutagenesis. Homozygous or hemizygous ref(2)P ^nullflies are male sterile. These flies, like homozygous or hemizygous ref(2)P ⁰flies, are fully permissive for sigma virus replication. We suggest that the ref(2)P products interact with viral products, but that this interaction is not necessary for an efficient viral cycle.     

Protein markers and seed size variation in common bean segregating populations

Selection and random genetic drift are the two main forces affecting allele frequencies in common bean breeding programs. Therefore, knowledge on allele frequency changes attributable to these forces is of fundamental importance for breeders. The changes in frequencies of alleles of biochemical markers were examined in F₂ to F₇ populations derived from crosses between cultivated Mesoamerican and Andean common bean accessions (Phaseolus vulgaris L.). Biochemical markers included the seed proteins phaseolin, lectin and other seed polypeptides, and six isozymes. The Schaffer’s test detected a high significant linear trend of the 63% of the polymorphic loci studied, meaning that directional selection was acting on those loci. Associations between seed size traits, phaseolin seed-storage protein and isozyme markers were detected based on the comparisons of the progeny genotypic means. In the interracial populations the intermediate form PhaH/T, b6, and Rbcs ⁹⁸ alleles had a positive effect on seed size. In the inter-gene pool populations, a higher transmission of Mesoamerican alleles in all loci was showed, although the Andean alleles Pha^T, Skdh ¹⁰⁰ , Rbcs ⁹⁸ , and Diap ¹⁰⁰ showed positive effects on seed weight. Our results suggest that phaseolin and other seed proteins markers are linked to loci affecting seed size. These markers have good potential for improving the results of the selection and should be considered as a strategy for germplasm enhancement and to avoid the reduced performance of the inter-gene pool populations.     

Sheep major histocompatibility (OLA) complex: linkage between a scrapie susceptibility/resistance locus and the OLA complex in Ile-de-France sheep progenies

As seen on their family trees, Ile-de-France sheep with scrapie show genetic susceptibility to this disease, which is transmitted via scr ^s, an autosomal recessive gene. Scrapie occurred in homozygous recessive sheep, whereas the presence of the dominant resistance allele Scr ^r sufficed to prevent this disease in heterozygous animals. This hypothesis, previously proposed by Parry (1962), was tested in a study involving 133 crossings of sheep of different genotypes, and verified in the observed progenies. In a contaminated environment, susceptibility to the disease seemed to be transmitted by the scr ^s gene, whose frequency was increasing and varied in different progenies: the gene was propagated by inbreeding combined with selection; scrapie did not appear in the progeny of a homozygous resistant ram with the Scr ^r/Scr^r genotype. On the family trees, linkage between the Scr locus and the OLA-A and -B loci is clearly visible; it often allowed the transmission of resistance or susceptibility haplotypes to be detected by OLA typing and followed from one generation to the next. The Scr ^r, OLA-A4, B6 haplotype was not found in any diseased sheep born before 1979, but was propagated by healthy sheep. During and after 1979, several recombinations of this haplotype were observed, giving a recombined haplotype with reciprocal linkage (scr ^s, OLA-A4, B6), disseminated by one sire in particular. The rate of recombination of Scr and OLA loci is estimated to be between 11 and 16 %. The possibility of early selection against the disease without loss of qualities desired by the breeder is discussed.     

An Indel Polymorphism in the Hybrid Incompatibility Gene Lethal Hybrid Rescue of Drosophila Is Functionally Relevant

Hybrid incompatibility (HI) genes are frequently observed to be rapidly evolving under selection. This observation has led to the attractive conjecture that selection-derived protein-sequence divergence is culpable for incompatibilities in hybrids. The Drosophila simulans HI gene Lethal hybrid rescue (Lhr) is an intriguing case, because despite having experienced rapid sequence evolution, its HI properties are a shared function inherited from the ancestral state. Using an unusual D. simulans Lhr hybrid rescue allele, Lhr², we here identify a conserved stretch of 10 amino acids in the C terminus of LHR that is critical for causing hybrid incompatibility. Altering these 10 amino acids weakens or abolishes the ability of Lhr to suppress the hybrid rescue alleles Lhr¹ or Hmr¹, respectively. Besides single-amino-acid substitutions, Lhr orthologs differ by a 16-aa indel polymorphism, with the ancestral deletion state fixed in D. melanogaster and the derived insertion state at very high frequency in D. simulans. Lhr² is a rare D. simulans allele that has the ancestral deletion state of the 16-aa polymorphism. Through a series of transgenic constructs we demonstrate that the ancestral deletion state contributes to the rescue activity of Lhr². This indel is thus a polymorphism that can affect the HI function of Lhr.     

A first genotyping assay of French cattle breeds based on a new allele of the extension gene encoding the melanocortin-1 receptor (Mc1r)

The seven transmembrane domain melanocortin-1 receptor (Mc1r) encoded by the coat color extension gene (E) plays a key role in the signaling pathway of melanin synthesis. Upon the binding of agonist (melanocortin hormone, α-MSH) or antagonist (Agouti protein) ligands, the melanosomal synthesis of eumelanin and/or phaeomelanin pigments is stimulated or inhibited, respectively. Different alleles of the extension gene were cloned from unrelated animals belonging to French cattle breeds and sequenced. The wild type E allele was mainly present in Normande cattle, the dominant E^D allele in animals with black color (i.e. Holstein), whereas the recessive e allele was identified in homozygous animals exhibiting a more or less strong red coat color (Blonde d''Aquitaine, Charolaise, Limousine and Salers). A new allele, named E¹, was found in either homozygous (E¹/E¹) or heterozygous (E¹/E) individuals in Aubrac and Gasconne breeds. This allele displayed a 4 amino acid duplication (12 nucleotides) located within the third cytoplasmic loop of the receptor, a region known to interact with G proteins. A first genotyping assay of the main French cattle breeds is described based on these four extension alleles.     

<Emphasis Type="Italic">Sex combs reduced</Emphasis> (<Emphasis Type="Italic">Scr</Emphasis>) regulatory region of <Emphasis Type="Italic">Drosophila</Emphasis> revisited

The Hox gene Sex combs reduced (Scr) is responsible for the differentiation of the labial and prothoracic segments in Drosophila. Scr is expressed in several specific tissues throughout embryonic development, following a complex path that must be coordinated by an equally complex regulatory region. Although some cis-regulatory modules (CRMs) have been identified in the Scr regulatory region (~75 kb), there has been no detailed and systematic study of the distinct regulatory elements present within this region. In this study, the Scr regulatory region was revisited with the aim of filling this gap. We focused on the identification of Initiator elements (IEs) that bind segmentation factors, Polycomb response elements (PREs) that are recognized by the Polycomb and Trithorax complexes, as well as insulators and tethering elements. To this end, we summarized all currently available information, mainly obtained from high throughput ChIP data projects. In addition, a bioinformatic analysis based on the evolutionary conservation of regulatory sequences using the software MOTEVO was performed to identify IE and PRE candidates in the Scr region. The results obtained by this combined strategy are largely consistent with the CRMs previously identified in the Scr region and help to: (i) delimit them more accurately, (ii) subdivide two of them into different independent elements, (iii) identify a new CRM, (iv) identify the composition of their binding sites and (v) better define some of their characteristics. These positive results indicate that an approach that integrates functional and bioinformatic data might be useful to characterize other regulatory regions.