Genetic studies of the Syrian hamster. VIII. The sex-linked gene Tortoiseshell

The occurrence of sex-linked yellow is described and designated as tortoiseshell (symbol To). The phenotype produced by the heterozygous female (To+) is a mosaic of that of ToTo and ++. Genetic inactivation of one X chromosome per cell is thus indicated. The To gene interacts phenotypically with genes Ba, Ds and Wh.     

Conflicting phylogenetic signals in the SlX1/Y1 gene in Silene

Background  

Increasing evidence from DNA sequence data has revealed that phylogenies based on different genes may drastically differ from each other. This may be due to either inter- or intralineage processes, or to methodological or stochastic errors. Here we investigate a spectacular case where two parts of the same gene (SlX1/Y1) show conflicting phylogenies within Silene (Caryophyllaceae). SlX1 and SlY1 are sex-linked genes on the sex chromosomes of dioecious members of Silene sect. Elisanthe.     

Dosage compensation of sex-linked genes in Drosophila melanogaster. The activities of glucose-6-phosphate dehydrogenase and 6-phosphogluconate dehydrogenase in flies with normal and disturbed genetic balance

Summary The phenomenon of dosage compensation in Drosophila melanogaster which consists in doubling of the activity of the X-chromosome genes in males as compared to those in females was studied.The specific activities of 6-phosphogluconate dehydrogenase (6PGD) and glucose-6-phosphate dehydrogenase (G6PD) determined by the sex-linked structural genes Pgd and Zw respectively were studied in flies carrying duplications for different regions of the X-chromosome. The increase in dose of Pgd and Zw in females resulting from the addition of an extra X-chromosome or X-fragments leads to a proportional rise in the specific activities of 6PGD and G6PD. On the other had the addition to females of the X-chromosome carrying no Pgd gene or X-fragments lacking Pgd and Zw has no effect on the enzyme activities. Thus we failed to reveal in the X-chromosome any compensatory genes envisaged by Muller, which would repress sex-linked structural genes proportional to their dose.The 6PGD and G6PD levels in phenotypically male-like intersexes carrying two X-chromosomes and three autosome sets (2X3A) is 30% higher than in diploid (2X2A) or triploid (3X3A) females. However the specific activities of the enzymes in female-like intersexes are the same as in regular females. The levels of 6PGD and G6PD per one X-chromosome are 1.5–2.0 times higher in the intersexes than in the normal females and metafemales (3X2A). The results indicate that the level of expression of the X-chromosome is determined by the X:A ratio. It is suggested that the decreased X:A ratio in males is responsible for the hyperactivation of their X-chromosomes.     

Identifying new sex-linked genes through BAC sequencing in the dioecious plant Silene latifolia

Background

Silene latifolia represents one of the best-studied plant sex chromosome systems. A new approach using RNA-seq data has recently identified hundreds of new sex-linked genes in this species. However, this approach is expected to miss genes that are either not expressed or are expressed at low levels in the tissue(s) used for RNA-seq. Therefore other independent approaches are needed to discover such sex-linked genes.

Results

Here we used 10 well-characterized S. latifolia sex-linked genes and their homologs in Silene vulgaris, a species without sex chromosomes, to screen BAC libraries of both species. We isolated and sequenced 4 Mb of BAC clones of S. latifolia X and Y and S. vulgaris genomic regions, which yielded 59 new sex-linked genes (with S. vulgaris homologs for some of them). We assembled sequences that we believe represent the tip of the Xq arm. These sequences are clearly not pseudoautosomal, so we infer that the S. latifolia X has a single pseudoautosomal region (PAR) on the Xp arm. The estimated mean gene density in X BACs is 2.2 times lower than that in S. vulgaris BACs, agreeing with the genome size difference between these species. Gene density was estimated to be extremely low in the Y BAC clones. We compared our BAC-located genes with the sex-linked genes identified in previous RNA-seq studies, and found that about half of them (those with low expression in flower buds) were not identified as sex-linked in previous RNA-seq studies. We compiled a set of ~70 validated X/Y genes and X-hemizygous genes (without Y copies) from the literature, and used these genes to show that X-hemizygous genes have a higher probability of being undetected by the RNA-seq approach, compared with X/Y genes; we used this to estimate that about 30 % of our BAC-located genes must be X-hemizygous. The estimate is similar when we use BAC-located genes that have S. vulgaris homologs, which excludes genes that were gained by the X chromosome.

Conclusions

Our BAC sequencing identified 59 new sex-linked genes, and our analysis of these BAC-located genes, in combination with RNA-seq data suggests that gene losses from the S. latifolia Y chromosome could be as high as 30 %, higher than previous estimates of 10-20 %.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1698-7) contains supplementary material, which is available to authorized users.     

Genetic studies in dioecious melandrium. I

Sex-linked and sex-influenced inheritance are of interest because of their relation to the still intriguing problem of sex detrmination. Genes involved in the formation of the sex organs are regarded to be sex-determining genes. These genes may be present in all chromosomes including the sex-chromosomes. Other genes present in the sex-chromosomes, but not involved in sex determination, are the sex-linked genes. A mutation for narrow leaves we came across in ourM. ablum material is regarded as a case of sex linkage. Also the certation effect observed inM. album andM. dioicum must have been caused by genes on the sex-chromosomes. In both cases, however, it is not altogether unikekely, that the genes, regarded as sex-linked ones, actually take in the process of sex-determination.Sex-determining genes might influence the effect of other genes, that are therefore called sex-influenced genes. We observed a number of such sex-influenced characters inMelandrium.InM. album, female plants are, on the whole, larger than male plants, having larger stems and leaves. The petals, however, are larger in male plants, except in families with very broad petals. The leaves and petals are narrower in female plants than in male ones, except in families with very broad leaves and families with broad petals, where the difference in shape was no longer present. Usually, slightly more anthocyanin is formed in male plants than in females both in petals and the green parts. More glandular hairs were observed on male plants than on female ones.Insofar the observations were made inM. dioicum the same results were obtained.We regard these phenomena to be an expression of the different physiological conditions in female and in male plants, these conditions being provoked by the sex-determinging genes and more favourable for vegetative growth in female than in male plants.     

Sex determination in Actinidia. 1. Sex-linked markers and progeny sex ratio in diploid A. chinensis

 First results from two strategies aimed at elucidating the genetics of sex in the dioecious genus Actinidia Lindl. (Actinidiaceae) support the hypothesis that sex-determining genes are localized in a pair of chromosomes which, although cytologically indistinguishable, function like an XX/XY system with male heterogamety. A. chinensis Planch., a close relative of the kiwifruit [A. deliciosa (A. Chev.) CF Liang et AR Ferguson], has diploid and tetraploid races. Bulk segregant analysis to find sex-linked markers revealed two markers whose inheritance patterns in three diploid families showed X and Y linkage and indicated that the male is the heterogametic sex. Some recombination between the markers and the sex-determining loci was also demonstrated. Sex ratios in 12 progenies from controlled crosses varied around 1:1, as expected for an XX/XY system. Received: 20 December 1995 / Revision accepted: 24 April 1997     

Gene modulation in Drosophila: Dosage compensation of Pgd + and Zw + genes

The sex-linked Pgd ⁺ and Zw ⁺ genes of Drosophila melanogaster and their associated enzyme activities 6-phosphogluconate dehydrogenase and glucose 6-phosphate dehydrogenase were employed in an analysis of the relationship between dosage compensation and the location of genes in the genome. In the genotypes examined, the enzyme activity specified by each copy of the gene is twice in males what it is in females. This is true of normal, structurally rearranged, and duplication genotypes. Dosage compensation, therefore, is a regulatory function associated with single structural genes or small chromosomal segments and does not depend on the gene's physical location on the X chromosome.This research was supported by NIH Grant No. 5-R01-HD04859.     

AFLP-derived STS markers for the identification of sex in Asparagus officinalis L.

For a simple, rapid and PCR-based screening of sex in the cultivated asparagus (Asparagus officinalis L.), we developed five STS markers from previously mapped, low-copy, sex-linked AFLP markers. A male/female PCR assay was feasible with these STS markers either by direct amplification or by digestion with restriction enzymes. Similar to the AFLP markers from which they were derived, STS4150.1, STS4150.2, STS4150.3 and STS3156 did not give recombinants in five different populations. STS3660 could be scored codominantly, enabling the differentiation of XY from YY males in the screened F₂ mapping population. The use of the sex-linked STS markers should allow early identification of sex, thus accelerating the breeding process for new asparagus varieties. Further, 10 additional AFLP markers obtained with PstI/MseI primer combinations have been mapped on the L5 chromosome, bringing the total number of known AFLP and STS markers flanking the sex locus to 24. These markers can be utilized for fine mapping of the sex gene in asparagus, which will pave the way for a map-based cloning approach. Received: 31 May 1999 / Accepted: 22 June 1999     

The role of chromosomal rearrangements in the evolution of <Emphasis Type="Italic">Silene latifolia</Emphasis> sex chromosomes

Silene latifolia is a model plant for studies of the early steps of sex chromosome evolution. In comparison to mammalian sex chromosomes that evolved 300 mya, sex chromosomes of S. latifolia appeared approximately 20 mya. Here, we combine results from physical mapping of sex-linked genes using polymerase chain reaction on microdissected arms of the S. latifolia X chromosome, and fluorescence in situ hybridization analysis of a new cytogenetic marker, Silene tandem repeat accumulated on the Y chromosome. The data are interpreted in the light of current genetic linkage maps of the X chromosome and a physical map of the Y chromosome. Our results identify the position of the centromere relative to the mapped genes on the X chromosome. We suggest that the evolution of the S. latifolia Y chromosome has been accompanied by at least one paracentric and one pericentric inversion. These results indicate that large chromosomal rearrangements have played an important role in Y chromosome evolution in S. latifolia and that chromosomal rearrangements are an integral part of sex chromosome evolution.     

A rearrangement of the Z chromosome topology influences the sex-linked gene display in the European corn borer, <Emphasis Type="Italic">Ostrinia nubilalis</Emphasis>

Males are homogametic (ZZ) and females are heterogametic (WZ) with respect to the sex chromosomes in many species of butterflies and moths (insect order Lepidoptera). Genes on the Z chromosome influence traits involved in larval development, environmental adaptation, and reproductive isolation. To facilitate the investigation of these traits across Lepidoptera, we developed 43 degenerate primer pairs to PCR amplify orthologs of 43 Bombyx mori Z chromosome-linked genes. Of the 34 orthologs that amplified by PCR in Ostrinia nubilalis, 6 co-segregated with the Z chromosome anchor markers kettin (ket) and lactate dehydrogenase (ldh), and produced a consensus genetic linkage map of ~89 cM in combination with 5 AFLP markers. The O. nubilalis and B. mori Z chromosomes are comparatively co-linear, although potential gene inversions alter terminal gene orders and a translocation event disrupted synteny at one chromosome end. Compared to B. mori orthologs, O. nubilalis Z chromosome-linked genes showed conservation of tissue-specific and growth-stage-specific expression, although some genes exhibited species-specific expression across developmental stages or tissues. The O. nubilalis Z chromosome linkage map provides new tools for isolating quantitative trait loci (QTL) involved in sex-linked traits that drive speciation and it exposes genome rearrangements as a possible mechanism for differential gene regulation in Lepidoptera.     

The Nature of Quantitative Genetic Variation in Drosophila. III. Mechanism of Dosage Compensation for Sex-Linked Abdominal Bristle Polygenes

Seventeen lines, each homozygous for a different X chromosome but all with a common autosomal genetic background, were constructed and assayed for abdominal bristle number to determine whether dosage compensation operates for sex-linked genes affecting this character.—The regression coefficient of male mean on female mean using a logarithmic scale was 0.90 ± 0.13 and the genetic regression coefficient 0.92, neither differing significantly from unity. The genetic components of variance in males and females were also very similar (0.000234 or 0.000228, respectively). These results indicate that dosage compensation is complete (or nearly so) for sex-linked genes affecting this character. The bristle scores of females did not differ in reciprocal crosses between these lines, thus dosage compensation does not operate by paternal X inactivation.—The question of an adequate scale for abdominal bristle number had to be examined during the study. A logarithmic scale appeared to be adequate for both genotypic and environmental differences.     

A new plant sex-linked gene with high sequence diversity and possible introgression of the X copy

We describe patterns of DNA sequence diversity in a newly identified sex-linked gene, SlX9/SlY9, in Silene latifolia (Caryophyllaceae). The copies on both sex chromosomes seem to be functional, and each maps close to the respective X- and Y-linked copy of another sex-linked gene pair, SlCypX/SlCypY. The Y-linked copy has low diversity, similar to what has been found for several other Y-linked genes in S. latifolia, and consistent with the theoretical expectations of hitch-hiking processes occurring on a non-recombining chromosome. However, SlX9 has higher diversity than other genes on the S. latifolia X chromosome. We evaluate the hypothesis of introgression from the closely related species S. dioica as an explanation for the high sequence diversity observed.     

Overlapping deficiencies refine the map position of the sex-linked actin gene of Drosophila melanogaster

A ³H-labelled actin-specific probe was hybridized to Drosophila melanogaster X chromosomes heterozygous for deficiencies in the 5C region. The results suggest that the sex-linked actin gene resides in the overlap region of Df(1)C149 and Df(1)N73 at 5C3-4.     

Die Zuordnung der Koppelungsgruppen zu den Chromosomen bei der Stechmücke Culex pipiens L.

Zusammenfassung Die Numerierung der drei Koppelungsgruppen von Culex pipiens L. (Laven, 1967b) stimmt mit der bisherigen auf der Größe der Chromosomen beruhenden cytologischen Numerierung (Rai, 1963; Dennhöfer, 1968) überein.Das kurze Chromosomenpaar (I) trägt die geschlechtsbestimmenden Faktoren M bzw. m und die geschlechtsgekoppelten Gene der 1. Koppelungsgruppe.Das mittellange Paar (II) entspricht der 2. Koppelungsgruppe, der die Augenfarbmutation ruby (Iltis, Barr, McCelland und Myers, 1965) angehört. Die ungefähre Lokalisierung dieses Allels wird diskutiert.Das längste der Homologenpaare (III) ist der 3. Koppelungsgruppe gleichzusetzen, der z. B. die männchenbegrenzte Palpenmutation kps (Laven, 1955, 1957) angehört.

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The correlation of linkage-groups with chromosomes in the mosquito, Culex pipiens L.

In Culex pipiens L. eight lines with X-ray induced reciprocal translocations and one line with an inversion have been analysed. In such aberrations which are inherited like sex-linked factors, the smallest chromosome is always involved. The sex determining factors M and m respectively are situated on this small chromosome. — The pericentric inversion described here behaves like an autosomal factor and causes semisterility both in females and males due to crossing-over within the inverted region. It is shown that the chromosome of intermediate size carries this inversion and that it belongs to the same linkage group 2 as the eye color mutation ruby. The correlation of linkage groups with chromosomes of the mosquito Culex pipiens is the following: Linkage group 1 bears the sex-factors M and m resp. and the sex-linked genes and is the smallest chromosome (I). Linkage group 2 with the eye color mutation ruby is identical with the chromosome of medium size (II). Linkage group 3 with the male-limited mutation kps is correlated with the longest chromosome (III) (Zusammenfassung see p. 50)

     

谭清苏铁性别连锁的RAPD和SCAR分子标记

利用RAPD(Random amplified polymorphic DNA)分子标记技术,寻找谭清苏铁（Cycas tanqingii）中与性别相关的分子标记,筛选了160个10bp的随机引物,产生了2500多个RAPD条带。只有引物S0465 (CCCCGGTAAC)产生了一条大约500bp的雌性特异RAPD标记,该分子标记出现在所有的供试雌性植株中,而所有的供试雄性植株都不具有该标记。对该特异片段进行了克隆和序列测定,并根据序列分析结果将RAPD标记转化为重复性和特异性更好的特异特征序列扩增区域（SCAR）分子标记,并命名为STQC-S465-483。分子标记的建立可用于谭清苏铁幼苗性别的早期鉴定,为谭清苏铁就地保护和迁地保护提供技术支持。     

Additional taxonomic coverage of the doubly uniparental inheritance in bivalves: Evidence of sex-linked heteroplasmy in the razor clam Solen marginatus Pulteney, 1799, but not in the lagoon cockle Cerastoderma glaucum (Bruguière, 1789)

In animals, doubly uniparental inheritance (DUI) is a major exception to the common strict maternal inheritance of mitochondria. To date, DUI has only been found in many bivalve species, but its distribution is still unclear. Given the great species richness of the class, much effort is needed to further investigate the occurrence of DUI in unsampled species. A compelling evidence of DUI is generally the presence of a sex-linked heteroplasmy, where two divergent mitochondrial lineages are found: One is isolated from the male germline, and the other one is isolated from the female germline and, normally, from the soma of both sexes. In the present study, we investigated the sex-linked heteroplasmy in the razor clam Solen marginatus Pulteney, 1799 and in the lagoon cockle Cerastoderma glaucum (Bruguière, 1789) using two mitochondrial markers (cox1 and rrnL). We found evidence of DUI in the species S. marginatus, with a divergence up to 21% for the rrnL gene, but not in C. glaucum. Moreover, our phylogenetic reconstruction includes all the available data for heterodont species with sex-linked heteroplasmy and suggests multiple origins of DUI in this subclass, as well as the presence of DUI in other species of the genus Solen.     

Evolution of ZZ/ZW and XX/XY sex-determination systems in the closely related medaka species, <Emphasis Type="Italic">Oryzias hubbsi</Emphasis> and <Emphasis Type="Italic">O. dancena</Emphasis>

A DM-domain gene on the Y chromosome was identified as the sex-determining gene in the medaka, Oryzias latipes, and named DMY (also known as dmrt1bY). However, this gene is absent in most Oryzias fishes, suggesting that closely related species have another sex-determining gene. In fact, it has been demonstrated that the Y chromosome in O. dancena is not homologous to that in O. latipes, whereas both species have an XX/XY sex-determination system. Through a progeny test of sex-reversed fish and a linkage analysis of isolated sex-linked DNA markers, we show that O. hubbsi, which is one of the most closely related species to O. dancena, has a ZZ/ZW system. In addition, genetic and fluorescence in situ hybridization mapping of the sex-linked markers revealed that sex chromosomes in O. hubbsi and O. dancena are not homologous, indicating different origins of these ZW and XY sex chromosomes. Furthermore, we found that O. hubbsi has morphologically heteromorphic sex chromosomes, in which the W chromosome has 4,6-diamidino-2-phenylindole (DAPI)-positive heterochromatin blocks and is larger than the Z chromosome, although such differentiated sex chromosomes have not been observed in other Oryzias species. These findings suggest that a variety of sex-determining mechanisms and sex chromosomes have evolved in Oryzias.     

Development of sex-linked PCR markers for gender identification in Actinidia

 Two sex-linked random amplified polymorphic DNA (RAPD) markers identified from Actinidia chinensis were converted into sequence-characterised amplified regions (SCARs) for the large-scale screening of Actinidia breeding populations. Initial SCAR primers converted one RAPD (SmX) into a dominant marker, but the other (SmY), which was potentially more useful because of its linkage to the male determining ‘Y’ locus, failed to retain polymorphism. This difficulty was overcome by cloning and sequencing the alternate ‘allele’ from female plants, and then designing ‘allele’-specific primers that utilised nucleotide differences between the sexes. Using a quick squash-blot method of DNA extraction, the SCAR primers were tested in 120 A. chinensis plants to determine their gender. The system is now in use for large-scale screening of seedling populations in the Actinidia breeding programme. The sex-linked SCAR primers also functioned with plants from some other geographically separate accessions of A. chinensis and with plants in the closely related polyploid species A. deliciosa, but did not amplify a sex-linked band in more distantly related species of Actinidia. Received: 27 December 1997 / Accepted: 5 March 1998