PMC:4502369 / 29715-32371 JSONTXT

{"target":"http://pubannotation.org/docs/sourcedb/PMC/sourceid/4502369","sourcedb":"PMC","sourceid":"4502369","source_url":"https://www.ncbi.nlm.nih.gov/pmc/4502369","text":"When compared to the DE gene lists, 57 nonsynonymous SNPs were present in upregulated genes in the testis and 67 were present in the oviduct (Table S7). In the oviduct, the 67 genes were involved in 16 different biological processes, including, e.g., reproduction, cellular component morphogenesis, and cell cycle. The polymorphisms in reproduction-related genes were confirmed by visualization with the Integrative genomics viewer (IGV) (Robinson et al. 2011; Thorvaldsdottir, Robinson and Mesirov 2013). Three oviduct genes (FRAS1, TCF4, and PGR) were associated with reproduction, and QTL regions for sow reproductive traits have been previously identified within these regions (Table S8). FRAS1 has been localized in embryonic epithelial basement membranes in the mouse (Chiotaki et al. 2007), and mutations within the gene have been shown to cause Fraser syndrome in humans (Hoefele et al. 2013; Ogur et al. 2011; Vogel et al. 2012). PGR, a progesterone receptor, is highly expressed in the ovary and in the oviduct, which makes it a good candidate gene for sow reproduction. Progesterone is critical for successful ovulation and for the multi-faceted functioning of the oviduct in mammalian reproduction (Akison and Robker 2012). Several nonsynonymous SNPs were identified within PGR (Table S8). TCF4 is a transcription factor and is widely expressed. In the testis, five upregulated genes (ADAT1, SPAG6, PIWIL2, PKDREJ, and DNAH8) with nonsynonymous variations had a classified role in reproduction. A QTL for male reproduction has only been identified for the genomic region around DNAH8 (chromosome 7: 39,286,129-39,569,290). This region was associated with epididymis weight. In addition, a high number of additional QTL have been associated with this region (n = 232; http://www.animalgenome.org/). DNAH8 has a role in sperm motility and has been shown to be crucial for male fertility (Fossella et al. 2000; Olds-Clarke and Johnson 1993; Samant et al. 2002). The identified QTL for epididymis weight within the DNAH8 region may be influenced by a lower epididymal sperm count due to malformed sperm. Furthermore, PKDREJ appeared to contain several nonsynonymous SNPs, including two deleterious based on SIFT analysis (Table S8). PKDREJ is a male germ cell–specific polycystin, which is required for acrosome reaction during sperm–egg fusion (Butscheid et al. 2006; Sutton et al. 2006). PKDREJ has also been identified on the surface of ejaculated boar spermatozoa (Zigo et al. 2013). Thus, these variants may be considered strong candidate polymorphisms for boar fertility, although identification of a phenotypic effect requires further study.","tracks":[{"project":"2_test","denotations":[{"id":"25917919-21221095-43377657","span":{"begin":455,"end":459},"obj":"21221095"},{"id":"25917919-22517427-43377658","span":{"begin":499,"end":503},"obj":"22517427"},{"id":"25917919-17251066-43377659","span":{"begin":791,"end":795},"obj":"17251066"},{"id":"25917919-23473829-43377660","span":{"begin":895,"end":899},"obj":"23473829"},{"id":"25917919-22029163-43377661","span":{"begin":913,"end":917},"obj":"22029163"},{"id":"25917919-22510445-43377662","span":{"begin":932,"end":936},"obj":"22510445"},{"id":"25917919-22827383-43377663","span":{"begin":1229,"end":1233},"obj":"22827383"},{"id":"25917919-10602986-43377664","span":{"begin":1914,"end":1918},"obj":"10602986"},{"id":"25917919-8416830-43377665","span":{"begin":1944,"end":1948},"obj":"8416830"},{"id":"25917919-12297094-43377666","span":{"begin":1964,"end":1968},"obj":"12297094"},{"id":"25917919-16261614-43377667","span":{"begin":2371,"end":2375},"obj":"16261614"},{"id":"25917919-16883570-43377668","span":{"begin":2391,"end":2395},"obj":"16883570"},{"id":"25917919-23916641-43377669","span":{"begin":2489,"end":2493},"obj":"23916641"}],"attributes":[{"subj":"25917919-21221095-43377657","pred":"source","obj":"2_test"},{"subj":"25917919-22517427-43377658","pred":"source","obj":"2_test"},{"subj":"25917919-17251066-43377659","pred":"source","obj":"2_test"},{"subj":"25917919-23473829-43377660","pred":"source","obj":"2_test"},{"subj":"25917919-22029163-43377661","pred":"source","obj":"2_test"},{"subj":"25917919-22510445-43377662","pred":"source","obj":"2_test"},{"subj":"25917919-22827383-43377663","pred":"source","obj":"2_test"},{"subj":"25917919-10602986-43377664","pred":"source","obj":"2_test"},{"subj":"25917919-8416830-43377665","pred":"source","obj":"2_test"},{"subj":"25917919-12297094-43377666","pred":"source","obj":"2_test"},{"subj":"25917919-16261614-43377667","pred":"source","obj":"2_test"},{"subj":"25917919-16883570-43377668","pred":"source","obj":"2_test"},{"subj":"25917919-23916641-43377669","pred":"source","obj":"2_test"}]}],"config":{"attribute types":[{"pred":"source","value type":"selection","values":[{"id":"2_test","color":"#93ecaf","default":true}]}]}}