Transcriptome analysis reveals key genes and pathways associated with egg production in Nandan-Yao domestic chicken

Adetula, 2018, Transcriptome sequencing reveals key potential long non-coding RNAs related to duration of fertility trait in the uterovaginal junction of egg-laying hens, Sci. Rep., 8, 13185, 10.1038/s41598-018-31301-z Ariyadi, 2013, Expression of tight junction molecule "claudins" in the lower oviductal segments and their changes with egg-laying phase and gonadal steroid stimulation in hens, Theriogenology, 79, 211, 10.1016/j.theriogenology.2012.10.018 Bader, 2003, An automated method for finding molecular complexes in large protein interaction networks, BMC Bioinformatics, 4, 2, 10.1186/1471-2105-4-2 Bhattacharya, 2019, Polymorphisms in GnRHI and GnRHII genes and their association with egg production and egg quality traits in chicken, Br. Poult. Sci., 3, 187, 10.1080/00071668.2019.1575505 Biscarini, 2010, Estimation of heritability and breeding values for early egg production in laying hens from pooled data, Poult. Sci., 89, 1842, 10.3382/ps.2010-00730 Bolger, 2014, Trimmomatic: a flexible trimmer for illumina sequence data, Bioinformatics, 30, 2114, 10.1093/bioinformatics/btu170 Budna, 2017, Morphogenesis-related gene-expression profile in porcine oocytes before and after in vitro maturation, Zygote, 25, 331, 10.1017/S096719941700020X Cho, 2008, Fibroblast growth factor 7 stimulates in vitro growth of oocytes originating from bovine early antral follicles, Mol. Reprod. Dev., 75, 1736, 10.1002/mrd.20912 Cui, 2006, Gene expression of Cox5a, 5b, or 6b1 and their roles in preimplantation mouse embryos, Biol. Reprod., 74, 601, 10.1095/biolreprod.105.045633 Dong, 2019, Genomic analysis reveals pleiotropic alleles at EDN3 and BMP7 involved in chicken comb color and egg production, Front. Genet., 10, 612, 10.3389/fgene.2019.00612 Fairfull, 1990, Genetics of egg production in chickens Finotello, 2015, Measuring differential gene expression with RNA-seq: challenges and strategies for data analysis, Brief. Funct. Genomics, 14, 130, 10.1093/bfgp/elu035 Franceschini, 2013, STRINGv9.1: protein-protein interaction networks, with increased coverage andintegration, Nucleic Acids Res., 41, D808, 10.1093/nar/gks1094 Furr, 1973, Luteinizing hormone and progesterone in peripheral blood during the ovulatory cycle of the hen Gallus domesticus, J. Endocrinol., 57, 159, 10.1677/joe.0.0570159 Han, 2015, Association between BMP15 gene polymorphism and reproduction traits and its tissues expression characteristics in chicken, PLoS One, 11 Jackowska, 2013, Differential expression of Gdf9, Tgfb1, Tgfb2 and Tgfb3 in porcine oocytes isolated from follicles of different size before and after culture in vitro, Acta Vet. Hung., 61, 99, 10.1556/avet.2012.061 Jeong, 2012, Cell-specific and temporal aspects of gene expression in the chicken oviduct at different stages of the laying cycle, Biol. Reprod., 6, 172 Kang, 2013, Identification of miRNAs associated with sexual maturity in chicken ovary by illumina small RNA deep sequencing, BMC Genomics, 14, 352, 10.1186/1471-2164-14-352 Kim, 2015, HISAT: a fast spliced aligner with low memory requirements, Nat. Methods, 12, 357, 10.1038/nmeth.3317 Li, 2011, Genetic effect of the follicle-stimulating hormone receptor gene on reproductive traits in Beijing You chickens, Poult. Sci., 90, 2487, 10.3382/ps.2010-01327 Liu, 2001, Frequency of preovulatory luteinizing hormone surges and egg production rate in Turkey hens, Biol. Reprod., 64, 1769, 10.1095/biolreprod64.6.1769 Liu, 2018, Identification of hub genes and key pathways associated with two subtypes of diffuse large B-cell lymphoma based on gene expression profiling via integrated bioinformatics, Biomed. Res. Int., 2018, 3574534 Love, 2014, Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2, Genome Biol., 15, 550, 10.1186/s13059-014-0550-8 Luan, 2014, Transcriptome profiling identifies differentially expressed genes in huoyan goose ovaries between the laying period and ceased period, PLoS One, 9, 10.1371/journal.pone.0113211 Onagbesan, 2006, Effects of genotype and feed allowance on plasma luteinizing hormones, follicle-stimulating hormones, progesterone, estradiol levels, follicle differentiation, and egg production rates of broiler breeder hens, Poult. Sci., 85, 1245, 10.1093/ps/85.7.1245 Pan, 2011, Sox2 modulates reprogramming of gene expression in two-cell mouse embryos, Biol. Reprod., 85, 409, 10.1095/biolreprod.111.090886 Pertea, 2015, StringTie enables improved reconstruction of a transcriptome from RNA-seq reads, Nat. Biotechnol., 33, 290, 10.1038/nbt.3122 Pertea, 2016, Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown, Nat. Protoc., 11, 1650, 10.1038/nprot.2016.095 Poggenpoel, 1996, Response to long-term selection for egg production in laying hens, Br. Poult. Sci., 37, 743, 10.1080/00071669608417904 Sahraeian, 2017, Gaining comprehensive biological insight into the transcriptome by performing a broad-spectrum RNA-seq analysis, Nat. Commun., 8, 59, 10.1038/s41467-017-00050-4 Schmieder, 2011, Quality control and preprocessing of metagenomic datasets, Bioinformatics, 27, 863, 10.1093/bioinformatics/btr026 Shannon, 2003, Cytoscape: a software environment for integrated models of biomolecular interaction networks, Genome Res., 13, 2498, 10.1101/gr.1239303 Silva, 1984, Análise genética de características de importância econômica em poedeiras leves, Rev. Bras. Zootec., 13, 82 Stapane, 2019, The glycoproteins EDIL3 and MFGE8 regulate vesicle-mediated eggshell calcification in a new model for avian biomineralization, J. Biol. Chem., 294, 14526, 10.1074/jbc.RA119.009799 Vanmontfort, 1995, Developmental changes in immunoreactive inhibin and FSH in plasma of chickens from hatch to sexual maturity, Br. Poult. Sci., 36, 779, 10.1080/00071669508417822 Wang, 2019, Hypothalamic and pituitary transcriptome profiling using RNA-sequencing in high-yielding and low-yielding laying hens, Sci. Rep., 1, 10285, 10.1038/s41598-019-46807-3 Wilding, 2005, The maternal age effect: a hypothesis based on oxidative phosphorylation, Zygote, 13, 317, 10.1017/S0967199405003382 Williams, 1978, Control of the preovulatory surge of luteinizing hormone in the hen (Gallus domesticus): the role of progesterone and androgens, J. Endocrinol., 77, 57, 10.1677/joe.0.0770057 Wu, 2017, Expressed microRNA associated with high rate of egg production in chicken ovarian follicles, Anim. Genet., 48, 205, 10.1111/age.12516 Wu, 2020, Transcriptomic analyses of the hypothalamic-pituitary-gonadal axis identify candidate genes related to egg production in Xinjiang Yili geese, Animals (Basel), 10, 90, 10.3390/ani10010090 Yang, 2019, Comparative mRNA and miRNA expression in european mouflon (Ovis musimon) and sheep (Ovis aries) provides novel insights into the genetic mechanisms for female reproductive success, Heredity, 122, 172, 10.1038/s41437-018-0090-1 Yin, 2020, The transcriptome landscapes of ovary and three oviduct segments during chicken (Gallus gallus) egg formation, Genomics, 112, 243, 10.1016/j.ygeno.2019.02.003 Yu, 2012, clusterProfiler: an R package for comparing biological themes among gene clusters, Omics, 16, 284, 10.1089/omi.2011.0118 Yuan, 2015, Identification of promising mutants associated with egg production traits revealed by genome-wide association study, PLoS One, 10, 10.1371/journal.pone.0140615 Zhang, 2019, Transcriptome analysis of ovary in relatively greater and lesser egg producing Jinghai yellow chicken, Anim. Reprod. Sci., 208, 10.1016/j.anireprosci.2019.106114