Transcriptome Profiling Unveils Key Genes Regulating the Growth and Development of Yangzhou Goose Knob

Overview

Journal Int J Mol Sci

Publisher MDPI

Specialties Biochemistry
Chemistry
Molecular Biology

Date 2024 Apr 27

PMID 38673752

Authors

Xinlei Xu

Suyu Fan

Wangyang Ji

Shangzong Qi

Linyu Liu

Zhi Cao

Qiang Bao

Yang Zhang

Qi Xu

Guohong Chen

Affiliations

Soon will be listed here.

Abstract

Goose is one of the most economically valuable poultry species and has a distinct appearance due to its possession of a knob. A knob is a hallmark of sexual maturity in goose () and plays crucial roles in artificial selection, health status, social signaling, and body temperature regulation. However, the genetic mechanisms influencing the growth and development of goose knobs remain completely unclear. In this study, histomorphological and transcriptomic analyses of goose knobs in D70, D120, and D300 Yangzhou geese revealed differential changes in tissue morphology during the growth and development of goose knobs and the key core genes that regulate goose knob traits. Observation of tissue sections revealed that as age increased, the thickness of the knob epidermis, cuticle, and spinous cells gradually decreased. Additionally, fat cells in the dermis and subcutaneous connective tissue transitioned from loose to dense. Transcriptome sequencing results, analyzed through differential expression, Weighted Gene Co-expression Network Analysis (WGCNA), and pattern expression analysis methods, showed D70-vs.-D120 (up-regulated: 192; down-regulated: 423), D70-vs.-D300 (up-regulated: 1394; down-regulated: 1893), and D120-vs.-D300 (up-regulated: 1017; down-regulated: 1324). A total of 6243 differentially expressed genes (DEGs) were identified, indicating varied expression levels across the three groups in the knob tissues of D70, D120, and D300 Yangzhou geese. These DEGs are significantly enriched in biological processes (BP) such as skin morphogenesis, the regulation of keratinocyte proliferation, and epidermal cell differentiation. Furthermore, they demonstrate enrichment in pathways related to goose knob development, including ECM-receptor interaction, NF-kappa B, and PPAR signaling. Through pattern expression analysis, three gene expression clusters related to goose knob traits were identified. The joint analysis of candidate genes associated with goose knob development and WGCNA led to the identification of key core genes influencing goose knob development. These core genes comprise , , , , , , , , , , and . In summary, this study provides a reference for understanding the molecular mechanisms of goose knob growth and development and provides effective ideas and methods for the genetic improvement of goose knob traits.

References

Goluch Z, Haraf G . Goose Meat as a Source of Dietary Manganese-A Systematic Review. Animals (Basel). 2023; 13(5). PMC: 10000036. DOI: 10.3390/ani13050840. View

Hochmann J, Sobrinho J, Villa L, Sichero L . The Asian-American variant of human papillomavirus type 16 exhibits higher activation of MAPK and PI3K/AKT signaling pathways, transformation, migration and invasion of primary human keratinocytes. Virology. 2016; 492:145-54. DOI: 10.1016/j.virol.2016.02.015. View

Zhang Y, Xu X, Ji W, Qi S, Bao Q, Cao Z . Relationship of knob morphometric analysis with production performance and meat quality in Yangzhou goose (). Front Physiol. 2023; 14:1291202. PMC: 10663212. DOI: 10.3389/fphys.2023.1291202. View

Reddy S, Andl T, Lu M, Morrisey E, Millar S . Expression of Frizzled genes in developing and postnatal hair follicles. J Invest Dermatol. 2004; 123(2):275-82. DOI: 10.1111/j.0022-202X.2004.23215.x. View

Liu Y, Brunner L, Rebling J, Ben-Yehuda Greenwald M, Werner S, Detmar M . Non-invasive longitudinal imaging of VEGF-induced microvascular alterations in skin wounds. Theranostics. 2022; 12(2):558-573. PMC: 8692907. DOI: 10.7150/thno.65287. View

Androulakis I, Yang E, Almon R . Analysis of time-series gene expression data: methods, challenges, and opportunities. Annu Rev Biomed Eng. 2007; 9:205-28. PMC: 4181347. DOI: 10.1146/annurev.bioeng.9.060906.151904. View

Klopfenstein D, Zhang L, Pedersen B, Ramirez F, Warwick Vesztrocy A, Naldi A . GOATOOLS: A Python library for Gene Ontology analyses. Sci Rep. 2018; 8(1):10872. PMC: 6052049. DOI: 10.1038/s41598-018-28948-z. View

Wan Y, Wang Z, Guo X, Ma C, Fang Q, Geng Z . Phenotypic characteristics of upright and pendulous comb among chicken breeds and association with growth rate and egg production. Anim Sci J. 2017; 89(1):250-256. DOI: 10.1111/asj.12922. View

Deng Y, Hu S, Luo C, Ouyang Q, Li L, Ma J . Integrative analysis of histomorphology, transcriptome and whole genome resequencing identified DIO2 gene as a crucial gene for the protuberant knob located on forehead in geese. BMC Genomics. 2021; 22(1):487. PMC: 8244220. DOI: 10.1186/s12864-021-07822-9. View

10.

Gao Y, Wang X, Yan H, Zeng J, Ma S, Niu Y . Comparative Transcriptome Analysis of Fetal Skin Reveals Key Genes Related to Hair Follicle Morphogenesis in Cashmere Goats. PLoS One. 2016; 11(3):e0151118. PMC: 4784850. DOI: 10.1371/journal.pone.0151118. View

11.

Zhang Y, Xu X, Ji W, Qi S, Bao Q, Zhang Y . Morphological, anatomical and histological studies on knob and beak characters of six goose breeds from China. Front Physiol. 2023; 14:1241216. PMC: 10493296. DOI: 10.3389/fphys.2023.1241216. View

12.

Seeger M, Paller A . The Roles of Growth Factors in Keratinocyte Migration. Adv Wound Care (New Rochelle). 2015; 4(4):213-224. PMC: 4397993. DOI: 10.1089/wound.2014.0540. View

13.

Bartels T, Brinkmeier J, Portmann S, Krautwald-Junghanns M, Kummerfeld N, Boos A . Osteological investigations of the incidence of cranial alterations in domestic ducks (Anas platyrhynchos f. dom.) with feather crests. Ann Anat. 2001; 183(1):73-80. DOI: 10.1016/S0940-9602(01)80017-0. View

14.

Love M, Huber W, Anders S . Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014; 15(12):550. PMC: 4302049. DOI: 10.1186/s13059-014-0550-8. View

15.

Li C, Feng C, Ma G, Fu S, Chen M, Zhang W . Time-course RNA-seq analysis reveals stage-specific and melatonin-triggered gene expression patterns during the hair follicle growth cycle in Capra hircus. BMC Genomics. 2022; 23(1):140. PMC: 8848980. DOI: 10.1186/s12864-022-08331-z. View

16.

Wright D, Rubin C, Schutz K, Kerje S, Kindmark A, Brandstrom H . Onset of sexual maturity in female chickens is genetically linked to loci associated with fecundity and a sexual ornament. Reprod Domest Anim. 2012; 47 Suppl 1:31-6. DOI: 10.1111/j.1439-0531.2011.01963.x. View

17.

Lee H, Jang M, Kim H, Kwak W, Park W, Hwang J . Comparative Transcriptome Analysis of Adipose Tissues Reveals that ECM-Receptor Interaction Is Involved in the Depot-Specific Adipogenesis in Cattle. PLoS One. 2013; 8(6):e66267. PMC: 3689780. DOI: 10.1371/journal.pone.0066267. View

18.

Ji W, Hou L, Yuan X, Gu T, Chen Z, Zhang Y . Identifying molecular pathways and candidate genes associated with knob traits by transcriptome analysis in the goose (Anser cygnoides). Sci Rep. 2021; 11(1):11978. PMC: 8184827. DOI: 10.1038/s41598-021-91269-1. View

19.

Dorshorst B, Harun-Or-Rashid M, Bagherpoor A, Rubin C, Ashwell C, Gourichon D . A genomic duplication is associated with ectopic eomesodermin expression in the embryonic chicken comb and two duplex-comb phenotypes. PLoS Genet. 2015; 11(3):e1004947. PMC: 4366209. DOI: 10.1371/journal.pgen.1004947. View

20.

Li Y, Shi R, Yuan R, Jiang Y . Comprehensive transcriptional analysis of pig facial skin development. PeerJ. 2023; 11:e15955. PMC: 10470455. DOI: 10.7717/peerj.15955. View