title: Comprehensive Identification of Sexual Dimorphism-Associated Differentially Expressed Genes in Two-Way Factorial Designed RNA-Seq Data on Japanese Quail (Coturnix coturnix japonica).
abstract: Japanese quail (Coturnix coturnix japonica) reach sexual maturity earlier, breed rapidly and successfully, and cost less and require less space than other birds raised commercially. Given the value of this species for food production and experimental use, more studies are necessary to determine chromosomal regions and genes associated with gender and breed-differentiation. This study employed Trinity and edgeR for transcriptome analysis of next-generation RNA-seq data, which included 4 tissues obtained from 3 different breeding lines of Japanese quail (random bred control, heavy weight, low weight). Differentially expressed genes shared between female and male tissue contrast groups were analyzed to identify genes related to sexual dimorphism as well as potential novel candidate genes for molecular sexing. Several of the genes identified in the present study as significant sex-related genes have been previously found in avian gene expression analyses (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 (TERA, MYP0, PPR17, CASQ2). Additionally, other genes likely associated with neuronal and brain development (CHKA, NYAP), as well as body development and size differentiation (ANKRD26, GRP87) in quail were identified. Expression of homeobox protein regulating genes (HXC4, ISL1) shared between our two sex-related contrast groups (Female Brain vs. Male Brain and Ovary vs. Testis) indicates that these genes may regulate sex-specific anatomical development. Results reveal 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.
authors.affiliation: Department of Animal Sciences, University of Illinois, Urbana, IL 61801, United States of America.
authors.forename: Kelsey
authors.initials: K
authors.lastname: Caetano-Anolles
authors.affiliation: Interdisciplinary Program in Bioinformatics, Seoul National University, Kwan-ak St. 599, Kwan-ak Gu, Seoul, South Korea 151-741, Republic of Korea.
authors.forename: Minseok
authors.initials: M
authors.lastname: Seo
authors.affiliation: Department of Animal Sciences, University of Illinois, Urbana, IL 61801, United States of America.
authors.forename: Sandra
authors.initials: S
authors.lastname: Rodriguez-Zas
authors.affiliation: Department of Animal Biotechnology, Chonbuk National University, Jeonju 561-756, Republic of Korea.
authors.forename: Jae-Don
authors.initials: JD
authors.lastname: Oh
authors.affiliation: Department of Agricultural Biotechnology, Animal Biotechnology Major, and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Republic of Korea.
authors.forename: Jae Yong
authors.initials: JY
authors.lastname: Han
authors.affiliation: Department of Animal Sciences, The Ohio State University, Columbus, OH 43210, United States of America.
authors.forename: Kichoon
authors.initials: K
authors.lastname: Lee
authors.affiliation: Department of Agricultural Biotechnology, Animal Biotechnology Major, and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Republic of Korea.
authors.forename: Tae Sub
authors.initials: TS
authors.lastname: Park
authors.affiliation: Faculty of Animal Science and Biotechnology, Kyungpook National University, Sangju 37224, Korea.
authors.forename: Sangsu
authors.initials: S
authors.lastname: Shin
authors.affiliation: Department of Animal Biotechnology, Faculty of Biotechnology, Jeju National University, Jeju 690-756, Republic of Korea.
authors.forename: Zhang
authors.initials: Z
authors.lastname: Jiao Jiao
authors.affiliation: Department of Animal Biotechnology, Faculty of Biotechnology, Jeju National University, Jeju 690-756, Republic of Korea.
authors.forename: Mrinmoy
authors.initials: M
authors.lastname: Ghosh
authors.affiliation: Department of Animal Biotechnology, Faculty of Biotechnology, Jeju National University, Jeju 690-756, Republic of Korea.
authors.forename: Dong Kee
authors.initials: DK
authors.lastname: Jeong
authors.affiliation: CHO&KIM genomics, Main Bldg. #514, SNU Research Park, Seoul National University Mt.4-2, NakSeoungDae, Gwanakgu, Seoul 151-919, Republic of Korea.
authors.forename: Seoae
authors.initials: S
authors.lastname: Cho
authors.affiliation: Interdisciplinary Program in Bioinformatics, Seoul National University, Kwan-ak St. 599, Kwan-ak Gu, Seoul, South Korea 151-741, Republic of Korea; Department of Agricultural Biotechnology, Animal Biotechnology Major, and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Republic of Korea; CHO&KIM genomics, Main Bldg. #514, SNU Research Park, Seoul National University Mt.4-2, NakSeoungDae, Gwanakgu, Seoul 151-919, Republic of Korea.
authors.forename: Heebal
authors.initials: H
authors.lastname: Kim
authors.affiliation: Department of Animal Biotechnology, Chonbuk National University, Jeonju 561-756, Republic of Korea.
authors.forename: Ki-Duk
authors.initials: KD
authors.lastname: Song
authors.affiliation: Department of Animal Biotechnology, Chonbuk National University, Jeonju 561-756, Republic of Korea.
authors.forename: Hak-Kyo
authors.initials: HK
authors.lastname: Lee
mesh_terms: D000818:Animals; D030161:Avian Proteins / Q000235:genetics; D001835:Body Weight / Q000235:genetics; D001921:Brain / Q000378:metabolism; D001947:Breeding; D016000:Cluster Analysis; D003370:Coturnix / Q000145:classification / Q000235:genetics*; D005260:Female; D020869:Gene Expression Profiling / Q000379:methods* / Q000706:statistics & numerical data; D008297:Male; D020411:Oligonucleotide Array Sequence Analysis; D010053:Ovary / Q000378:metabolism; D020133:Reverse Transcriptase Polymerase Chain Reaction; D017423:Sequence Analysis, RNA / Q000379:methods* / Q000706:statistics & numerical data; D012737:Sex Factors; D013045:Species Specificity; D013737:Testis / Q000378:metabolism; D059467:Transcriptome / Q000235:genetics*
chemical_list: D030161:Avian Proteins