Project description:Japanese quail (Coturnix coturnix japonica) reach sexual maturity early, breed rapidly and successfully, and cost less and require less space than other birds raised for their meat and eggs. Given the value of this species for commercial production and experimental use as well as recent increasing demand, more studies are necessary to determine chromosomal regions and genes associated with gender and breed-differentiation in the species. Identification of sex-related genes can help target chromosomal regions for molecular sexing purposes. This study employed Trinity and edgeR for transcriptome analysis of next-generation RNA-seq data, which included 4 tissues obtained from 3 different breeds of Japanese quail (wild, miniature, and jumbo). The initial goal was to identify genes related to sexual dimorphism, as well as potential novel candidate genes for molecular sexing. Analysis and interpretation of differentially expressed genes shared between female and male tissue contrast groups provided insight into sex-related differences. Several of the genes identified in the present study as significant sex-related genes have been previously found in avian gene expression analyses (e.g. NIPBL, UBAP2), and other genes found differentially expressed in this study and not previously associated with sex-related differences may be considered potential candidates for molecular sexing (e.g. TERA, MYP0, PPR17, CASQ2). Additionally, other genes likely associated with neuronal and brain development (e.g. CHKA, NYAP), as well as body development and size differentiation (e.g. ANKRD26, GRP87) in quail were identified. Expression of homeobox protein regulating genes in the sex-related contrast group revealed two genes (HXC4, ISL1) that may regulate sex-specific anatomical development. Results of these analyses expand the currently limited pool of knowledge on the genetic features of the quail breed and could allow for more effective molecular sexing as well as selective breeding for traits important in commercial production.

Project description:Japanese quail (Coturnix coturnix japonica) reach sexual maturity early, breed rapidly and successfully, and cost less and require less space than other birds raised for their meat and eggs. Given the value of this species for commercial production and experimental use as well as recent increasing demand, more studies are necessary to determine chromosomal regions and genes associated with gender and breed-differentiation in the species. Identification of sex-related genes can help target chromosomal regions for molecular sexing purposes. This study employed Trinity and edgeR for transcriptome analysis of next-generation RNA-seq data, which included 4 tissues obtained from 3 different breeds of Japanese quail (wild, miniature, and jumbo). The initial goal was to identify genes related to sexual dimorphism, as well as potential novel candidate genes for molecular sexing. Analysis and interpretation of differentially expressed genes shared between female and male tissue contrast groups provided insight into sex-related differences. Several of the genes identified in the present study as significant sex-related genes have been previously found in avian gene expression analyses (e.g. NIPBL, UBAP2), and other genes found differentially expressed in this study and not previously associated with sex-related differences may be considered potential candidates for molecular sexing (e.g. TERA, MYP0, PPR17, CASQ2). Additionally, other genes likely associated with neuronal and brain development (e.g. CHKA, NYAP), as well as body development and size differentiation (e.g. ANKRD26, GRP87) in quail were identified. Expression of homeobox protein regulating genes in the sex-related contrast group revealed two genes (HXC4, ISL1) that may regulate sex-specific anatomical development. Results of these analyses expand the currently limited pool of knowledge on the genetic features of the quail breed and could allow for more effective molecular sexing as well as selective breeding for traits important in commercial production. This study employed Trinity and edgeR for transcriptome analysis of next-generation RNA-seq data, which included 4 tissues obtained from 3 different breeds of Japanese quail (wild, miniature, and jumbo).

Project description:Despite sharing much of their genomes, males and females are often highly dimorphic, reflecting at least in part the resolution of sexual conflict in response to sexually antagonistic selection. Sexual dimorphism arises owing to sex differences in gene expression, and steroid hormones are often invoked as a proximate cause of sexual dimorphism. Experimental elevation of androgens can lead to masculinization of behavior, physiology, and gene expression, but knowledge of the role of hormones remains incomplete, including how the sexes differ in their gene expression in response to exposure to hormones. We addressed these questions in a bird species with a long history of behavioral endocrinological and ecological study, the dark-eyed junco (Junco hyemalis), using a species-specific microarray. Focusing on two brain regions involved in sexually dimorphic behavior and regulation of hormone secretion, we identified 1,639 genes that differed in expression by sex in the ventromedial telencephalon and 768 in hypothalamus. In response to experimentally elevated testosterone, females exhibited a more “male-like” expression pattern than control females; unexpectedly, male expression patterns became more “female-like” rather than hyper-masculinized when compared to control males. This sex difference in pattern arose both because testosterone altered regulation of different genes in each sex and because testosterone altered regulation of the same genes differentially, i.e., up in one sex, down in the other. Hormonally regulated gene expression is a key genetic and physiological mechanism underlying sexual dimorphism, and further study should help to explain how it relates to the resolution of sexual conflict. Males and females can be highly dimorphic in metabolism and physiology despite sharing nearly identical genomes, and males and females both respond phenotypically to elevated testosterone, a steroid hormone that alters gene expression. Only recently has it become possible to learn how a hormone like testosterone affects global gene expression in non-model systems, and whether it affects the same genes in males and females. To investigate the transcriptional mechanisms by which testosterone exerts its metabolic and physiological effects on the periphery, we compared gene expression by sex and in response to experimentally elevated testosterone in a well-studied bird species, the dark-eyed junco (Junco hyemalis). We identified 324 genes in the liver, and 733 in the pectoralis muscle that were differentially expressed between males and females. In addition, we identified 1,872 genes that were differentially expressed between testosterone-treated and control individuals in at least one tissue and sex. Testosterone-treatment altered the expression of only130 genes in both males and females in the same tissue. These substantial differences in transcriptional response to testosterone suggest that males and females may employ different pathways when responding to elevated testosterone, despite the fact that many phenotypic effects of experimentally elevated testosterone are similar in the sexes. In contrast, of the 130 genes that were affected by testosterone-treatment in both sexes, 78% were regulated in the same direction (e.g. either higher or lower in testosterone-treated than control males and females). Thus, it appears that testosterone acts through both unique and shared transcriptional pathways in males and females, suggesting multiple mechanisms by which sexual conflict can be mediated.

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Sex differences and effect of testosterone on the transcriptome in brain regions underlying quail sexual behavior

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