شناسایی سازوکارهای تنظیمی درگیر در بلوغ جنسی و باروری بزهای ماده براساس رویکرد تجزیه و تحلیل شبکه‌های تنظیمی و مسیرهای عملکردی

REFERENCES

Andrews, S. (2010). FastQC: A quality control tool for high throughput sequence data. Retrieved December 5, 2023, from http://www.bioinformatics.babraham.ac.uk/projects/fastqc

Bedenbaugh, M. N., Bowdridge, E. C., & Hileman, S. M. (2020). Role of neurokinin B in ovine puberty. Domestic Animal Endocrinology, 73, 106442. https://doi.org/10.1016/j.domaniend.2020.106442

Ben Braiek, M., Moreno-Romieux, C., Allain, C., Bardou, P., Bordes, A., Debat, F., Drögemüller, C., Plisson-Petit, F., Portes, D., Sarry, J., Tadi, N., Woloszyn, F., & Fabre, S. (2022). A nonsense variant in CCDC65 gene causes respiratory failure associated with increased lamb mortality in French Lacaune dairy sheep. Genes, 13(1), 45. https://doi.org/10.3390/genes13010045

Bolger, A. M., Lohse, M., & Usadel, B. (2014). Trimmomatic: A flexible trimmer for Illumina sequence data. Bioinformatics, 30(15), 2114–2120. https://doi.org/10.1093/bioinformatics/btu170

Fatima, A., & Morris, D. G. (2013). MicroRNAs in domestic livestock. Physiological Genomics, 45(16), 685–696. https://doi.org/10.1152/physiolgenomics.00008.2013

Gil, M., Rudy, M., Duma-Kocan, P., Stanisławczyk, R., Krajewska, A., Dziki, D., & Hassoon, W. H. (2024). Sustainability of alternatives to animal protein sources: A comprehensive review. Sustainability, 16(17), 7701. https://doi.org/10.3390/su16177701

Gipson, I. K., Ho, S. B., Spurr-Michaud, S. J., Tisdale, A. S., Zhan, Q., Torlakovic, E., ... Hill, J. A., III. (1997). Mucin genes expressed by human female reproductive tract epithelia. Biology of Reproduction, 56(4), 999–1011. https://doi.org/10.1095/biolreprod56.4.999

Hodge, R. G., & Ridley, A. J. (2020). Regulation and functions of RhoU and RhoV. Small GTPases, 11(1), 8–15. https://doi.org/10.1080/21541248.2019.1636104

Horani, A., Ferkol, T. W., Shoseyov, D., Wasserman, M. G., Oren, Y. S., Kerem, B., Amirav, I., Cohen-Cymberknoh, M., Dutcher, S. K., Brody, S. L., Elpeleg, O., & Kerem, E. (2013). LRRC6 mutation causes primary ciliary dyskinesia with dynein arm defects. PLoS ONE, 8(3), e59436. https://doi.org/10.1371/journal.pone.0059436

Jarrell, Z. R., Ahammad, M. U., Sweeney, K., Wilson, J. L., & Benson, A. P. (2020). Characterization of sperm-associated antigen 6 expression in the reproductive tract of the domestic rooster (Gallus domesticus) and its impact on sperm mobility. Poultry Science, 99(11), 6188–6195. https://doi.org/10.1016/j.psj.2020.08.029

Jin, M. L., Gong, Y., Ji, P., Hu, X., & Shao, Z. M. (2023). In vivo CRISPR screens identify RhoV as a pro‐metastasis factor of triple‐negative breast cancer. Cancer Science, 114(6), 2375–2385. https://doi.org/10.1111/cas.15769

Kim, D., Langmead, B., & Salzberg, S. L. (2015). HISAT: A fast spliced aligner with low memory requirements. Nature Methods, 12(4), 357–360. https://doi.org/10.1038/nmeth.3317

Kott, E., Duquesnoy, P., Copin, B., Legendre, M., Dastot-Le Moal, F., Montantin, G., ... & Amselem, S. (2012). Loss-of-function mutations in LRRC6, a gene essential for proper axonemal assembly of inner and outer dynein arms, cause primary ciliary dyskinesia. The American Journal of Human Genetics, 91(5), 958–964. https://doi.org/10.1016/j.ajhg.2012.09.014

Laird, M. K., & Hore, T. A. (2021). Primordial germ cell expression of SSEA1 and DDX4 (VASA) in female Trichosurus vulpecula (Marsupialia) reveals conserved and unique molecular patterns during marsupial germ cell development. Reproduction, Fertility and Development. https://doi.org/10.1071/RD21100

Li, J., Xue, Y., Zhong, T., Wang, L., Li, L., Zhang, H., & Zhan, S. (2025). Differential expression of lncRNAs in ovarian tissue of Meigu goats during the sexually immature and mature periods. Current Issues in Molecular Biology, 47(6), 395. https://doi.org/10.3390/cimb47060395

Li, R., Yu, Y., Jaafar, S. O., Baghchi, B., Farsimadan, M., Arabipour, I., & Vaziri, H. (2022). Genetic variants miR-126, miR-146a, miR-196a2, and miR-499 in polycystic ovary syndrome. British Journal of Biomedical Science, 79, 10209. https://doi.org/10.3389/bjbs.2021.10209

Liao, Y., Smyth, G. K., & Shi, W. (2014). featureCounts: An efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics, 30(7), 923–930. https://doi.org/10.1093/bioinformatics/btt656

Lin, Y., Sun, L., Dai, J., Lv, Y., Liao, R., Shen, X., & Gao, J. (2024). Characterization and comparative analysis of whole-transcriptome sequencing in high- and low-fecundity Chongming White goat ovaries during the estrus phase. Animals, 14(7), 988. https://doi.org/10.3390/ani14070988

Ling, Y., Zheng, Q., Jing, J., Sui, M., Zhu, L., Li, Y., ... & Zhang, X. (2020). RNA-Seq reveals miRNA role shifts in seven stages of skeletal muscles in goat fetuses and kids. Frontiers in Genetics, 11, 684. https://doi.org/10.3389/fgene.2020.00684

Liu, Y., Cao, G., Xie, Y., & Chu, M. (2023). Screening of puberty related differentially expressed genes from ovary tissues of Jining Grey goat based on suppression subtractive hybridization. Pakistan Journal of Zoology, 55(4), 1637. https://doi.org/10.17582/journal.pjz/20210720100705

Lorès, P., Coutton, C., El Khouri, E., Stouvenel, L., Givelet, M., Thomas, L., Rode, B., Schmitt, A., Louis, B., Sakheli, Z., Chaudhry, M., Fernandez-Gonzales, A., Mitsialis, A., Dacheux, D., Wolf, J. P., Papon, J. F., Gacon, G., Escudier, E., Arnoult, C., ... Touré, A. (2018). Homozygous missense mutation L673P in adenylate kinase 7 (AK7) leads to primary male infertility and multiple morphological anomalies of the flagella but not to primary ciliary dyskinesia. Human Molecular Genetics, 27(7), 1196–1211. https://doi.org/10.1093/hmg/ddy034

Love, M. I., Huber, W., & Anders, S. (2014). Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biology, 15(12), 550. https://doi.org/10.1186/s13059-014-0550-8

Lu, Y., Ma, R., Li, D., Gao, Y., Sheng, Z., Shi, J., ... & He, X. (2025). Genomic and Molecular Mechanisms of Goat Environmental Adaptation. Biology, 14(6), 654  https://doi.org/10.3390/biology14060654

Lv, Y., Liu, Y., Wang, Y., Kong, F., Pang, Q., & Hu, G. (2021). CCDC114, DNAI2, and TOP2A involvement in the effects of tibolone treatment on postmenopausal endometrium. BMC Women's Health, 21(1), 240. https://doi.org/10.1186/s12905-021-01353-0

Muhetapa, M., Zhu, M., Qi, A., & Yiming, S. (2025). Identification of genomic variants and candidate genes for reproductive traits and growth traits in Pishan Red sheep using whole-genome resequencing. Biology, 14(6), 636. https://doi.org/10.3390/biology14060636

Nepusz, T., Yu, H., & Paccanaro, A. (2012). Detecting overlapping protein complexes in protein–protein interaction networks. Nature Methods, 9(5), 471–472. https://doi.org/10.1038/nmeth.1938

Olmo, L., Nguyen, H. V., Nguyen, X. B., Bui, T. N., Ngo, C. T. K., Nguyen, V. D., Hoang, N., Morales, L. E., & Walkden-Brown, S. (2024). Goat meat supply and demand in Vietnam: Global context and opportunities and risks for smallholder producers. Animal Production Science, 64, AN23416. https://doi.org/10.1071/AN23416

Pereira, R., Piva, I., Campos, M., Fernandes, R., Baldini, A., & Barbosa, M. (2023). Characterization of a DRC1 null variant associated with primary ciliary dyskinesia and female infertility. Journal of Assisted Reproduction and Genetics, 40, 1234–1242. https://doi.org/10.1007/s10815-023-02755-6

Popescu, A., Marcuta, A., Marcuta, L., & Tindeche, C. (2021). Trends in goats' livestock and goat milk, meat, and cheese production in the world in the period 1990–2019: A statistical approach. Scientific Papers Series Management, Economic Engineering in Agriculture & Rural Development, 21(1), 531–536.

Qin, P., Pan, Z., Zhang, W., Wang, R., Li, X., Lu, J., ... & Fang, F. (2024). Integrative proteomic and transcriptomic analysis in the female goat ovary to explore the onset of puberty. Journal of Proteomics, 301, 105183. https://doi.org/10.1016/j.jprot.2024.105183

Ren, Y., He, J., Liu, G., Wei, C., Li, X., Mao, J., & Huang, X. (2025). Construction of coexpression networks affecting litter size in goats based on transcriptome analysis. Animals, 15(11), 1505.

Sánchez-Torres, J. D., Hernández-Sánchez, J. P., & González-Domínguez, A. (2019). RNA-seq transcriptome analysis in ovarian tissue of Pelibuey breed to explore the regulation of prolificacy. Genes, 10(5), 358. https://doi.org/10.3390/genes10050358

Sapiro, R., Kostetskii, I., Olds-Clarke, P., Gerton, G. L., Radice, G. L., & Strauss, J. F., III. (2002). Male infertility, impaired sperm motility, and hydrocephalus in mice deficient in sperm-associated antigen 6. Molecular and Cellular Biology, 22(17), 6298–6305. https://doi.org/10.1128/mcb.22.17.6298-6305.2002

Schreck, L., et al. (2024). Infertility and pregnancy outcomes among adults with primary ciliary dyskinesia. Human Reproduction Open, 2024(3), hoae039. https://doi.org/10.1093/hropen/hoae039

Shivakumar, P. (2024). Role of livestock in a changing world: Implications for human health, nutrition, and global wellness. The Scientific Frontiers, 1(1), 32–35.

Shorter, S. L., Albaghdadi, A. J., & Kan, F. W. (2016). Alterations in oviductal cilia morphology and reduced expression of axonemal dynein in diabetic NOD mice. Tissue and Cell, 48(6), 588–595. https://doi.org/10.1016/j.tice.2016.08.001

Su, F., Guo, X., Wang, Y., Wang, Y., Cao, G., & Jiang, Y. (2018). Genome-wide analysis on the landscape of transcriptomes and their relationship with DNA methylomes in the hypothalamus reveals genes related to sexual precocity in Jining Gray goats. Frontiers in Endocrinology, 9, 501. https://doi.org/10.3389/fendo.2018.00501

Sun, Z., Hong, Q., Liu, Y., Ren, C., He, X., Jiang, Y., Ouyang, Y., Chu, M., & Zhang, Z. (2022). Oviduct transcriptomic reveals the regulation of mRNAs and lncRNAs related to goat prolificacy in the luteal phase. Animals, 12(20), 2823. https://doi.org/10.3390/ani12202823

Szklarczyk, D., Gable, A. L., Lyon, D., Junge, A., Wyder, S., Huerta-Cepas, J., Simonovic, M., Doncheva, N. T., Morris, J. H., Bork, P., Jensen, L. J., & von Mering, C. (2019). STRING v11: Protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic Acids Research, 47(D1), D607–D613. https://doi.org/10.1093/nar/gky1131

Tada, O., & Mashamaite, P. K. (2025). Phenotypic plasticity in trait performance of common dairy goat breeds under diverse environments: a systematic review. Frontiers in Animal Science, 6, 1640241. https://doi.org/10.3389/fanim.2025.1640241

Upreti, D., & Ansari, S. (2025). Fertility management in sheep and goats: Best practices for breeding success. Agri Roots, 3(1), 22–27.

Wang, J. X., Jiao, J. Q., Li, Q., Long, B., Wang, K., Liu, J. P., ... & Li, P. F. (2011). miR-499 regulates mitochondrial dynamics by targeting calcineurin and dynamin-related protein-1. Nature Medicine, 17(1), 71–78. https://doi.org/10.1038/nm.2298

Wang, T., Zhang, Y., Zhao, Y., & Li, J. (2020). Identification of key genes and potential new biomarkers for ovarian aging: A study based on RNA-sequencing data. Frontiers in Genetics, 11, 590660. https://doi.org/10.3389/fgene.2020.590660

Wang, X., Zhu, B., Xiong, S., Sheng, X., Qi, X., Huang, Q., ... & Ni, H. (2018). Expression and function of MUC1 in uterine tissues during early pregnancy in sheep after natural oestrous or artificially-induced oestrous. Theriogenology, 108, 339–347. https://doi.org/10.1016/j.theriogenology.2017.12.030

Wang, Y., Chao, T., Li, Q., He, P., Zhang, L., & Wang, J. (2024a). Metabolomic and transcriptomic analyses reveal the potential mechanisms of dynamic ovarian development in goats during sexual maturation. International Journal of Molecular Sciences, 25(18), 9898. https://doi.org/10.3390/ijms25189898

Wang, Y., Wang, J., Li, Q., Xuan, R., Guo, Y., He, P., & Chao, T. (2023). Characterization of microRNA expression profiles in the ovarian tissue of goats during the sexual maturity period. Journal of Ovarian Research, 16, 234. https://doi.org/10.1186/s13048-023-01318-8

Wang, Y., Wang, J., Li, Q., Xuan, R., Guo, Y., He, P., Duan, Q., Du, S., & Chao, T. (2024b). Transcriptomic and metabolomic data of goat ovarian and uterine tissues during sexual maturation. Scientific Data, 11, 777. https://doi.org/10.1038/s41597-024-03565-w

Wang, Z., Wang, R., Pan, C., Chen, H., Qu, L., Wu, L., Guo, Z., Zhu, H., & Lan, X. (2022). Genetic variations and mRNA expression of goat DNAH1 and their associations with litter size. Cells, 11(8), 1371. https://doi.org/10.3390/cells11081371

Xu, H., Sun, W., Pei, S., Li, W., Li, F., & Yue, X. (2022). Identification of key genes related to postnatal testicular development based on transcriptomic data of testis in Hu sheep. Frontiers in Genetics, 12, 773695. https://doi.org/10.3389/fgene.2022.773695

Zhang, B., Zhu, G., Wu, J., Xie, H., Cui, J., Qian, W., ... & Liu, Y. (2025). Transcriptome and DNA methylation analysis of the goat pineal gland during puberty. Scientific Reports, 15(1), 2269. https://doi.org/10.1038/s41598-024-84559-x

Zhang, H., Bao, S., Zhao, X., Bai, Y., Lv, Y., Gao, P., Li, F., & Zhang, W. (2024). Genome-wide association study and phenotype prediction of reproductive traits in large white pigs. Animals, 14(23), 3348. https://doi.org/10.3390/ani14233348

Zhang, L., Liu, X., & Xu, H. (2023). Application of single-cell RNA sequencing in ovarian development. Biomolecules, 13(1), 47. https://doi.org/10.3390/biom13010047

Zhu, M., Guo, H., Li, X., Zhao, Y., Jin, Y., Wang, Y., ... & He, X. (2023a). Changes in serum hormones and ovarian transcriptome profiles in pubertal goats. Journal of Ovarian Research, 16, 92. https://doi.org/10.1186/s13048-023-01150-0

Zhu, Y., Ye, J., Qin, P., Yan, X., Gong, X., Li, X., ... & Fang, F. (2023b). Analysis of serum reproductive hormones and ovarian genes in pubertal female goats. Journal of Ovarian Research, 16(1), 69. https://doi.org/10.1186/s13048-023-01150-0