Genome-wide Comparative Analysis Reveals Selection Signatures for Reproduction Traits in Prolific Suffolk Sheep

Overview

Journal Front Genet

Date 2024 Jun 24

PMID 38911299

Authors

Hua Yang

Mengting Zhu

Mingyuan Wang

Huaqian Zhou

Jingjing Zheng

Lixia Qiu

Wenhua Fan

Jinghui Yang

Qian Yu

Yonglin Yang

Wenzhe Zhang

Affiliations

Soon will be listed here.

Abstract

The identification of genome-wide selection signatures can reveal the potential genetic mechanisms involved in the generation of new breeds through natural or artificial selection. In this study, we screened the genome-wide selection signatures of prolific Suffolk sheep, a new strain of multiparous mutton sheep, to identify candidate genes for reproduction traits and unravel the germplasm characteristics and population genetic evolution of this new strain of Suffolk sheep. Whole-genome resequencing was performed at an effective sequencing depth of 20× for genomic diversity and population structure analysis. Additionally, selection signatures were investigated in prolific Suffolk sheep, Suffolk sheep, and Hu sheep using fixation index ( ) and heterozygosity ) analysis. A total of 5,236.338 Gb of high-quality genomic data and 28,767,952 SNPs were obtained for prolific Suffolk sheep. Moreover, 99 selection signals spanning candidate genes were identified. Twenty-three genes were significantly associated with KEGG pathway and Gene Ontology terms related to reproduction, growth, immunity, and metabolism. Through selective signal analysis, genes such as , , and were found to be significantly correlated with reproductive traits in prolific Suffolk sheep and were highly associated with the mTOR signaling pathway, the melanogenic pathway, and the Hippo signaling pathways, among others. These results contribute to the understanding of the evolution of artificial selection in prolific Suffolk sheep and provide candidate reproduction-related genes that may be beneficial for the establishment of new sheep breeds.

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References

Sui X, Han X, Chen P, Wu Q, Feng J, Duan T . Baicalin Induces Apoptosis and Suppresses the Cell Cycle Progression of Lung Cancer Cells Through Downregulating Akt/mTOR Signaling Pathway. Front Mol Biosci. 2021; 7:602282. PMC: 7876332. DOI: 10.3389/fmolb.2020.602282. View

Varghese P, Abu-Asab M, Dimitriadis E, Dolinska M, Morcos G, Sergeev Y . Tyrosinase Nanoparticles: Understanding the Melanogenesis Pathway by Isolating the Products of Tyrosinase Enzymatic Reaction. Int J Mol Sci. 2021; 22(2). PMC: 7828394. DOI: 10.3390/ijms22020734. View

Liu Z, Tan X, Wang J, Jin Q, Meng X, Cai Z . Whole genome sequencing of Luxi Black Head sheep for screening selection signatures associated with important traits. Anim Biosci. 2022; 35(9):1340-1350. PMC: 9449392. DOI: 10.5713/ab.21.0533. View

Quan K, Li J, Han H, Wei H, Zhao J, Si H . Review of Huang-huai sheep, a new multiparous mutton sheep breed first identified in China. Trop Anim Health Prod. 2020; 53(1):35. PMC: 7683451. DOI: 10.1007/s11250-020-02453-w. View

Heallen T, Zhang M, Wang J, Bonilla-Claudio M, Klysik E, Johnson R . Hippo pathway inhibits Wnt signaling to restrain cardiomyocyte proliferation and heart size. Science. 2011; 332(6028):458-61. PMC: 3133743. DOI: 10.1126/science.1199010. View

Pillaiyar T, Manickam M, Jung S . Recent development of signaling pathways inhibitors of melanogenesis. Cell Signal. 2017; 40:99-115. DOI: 10.1016/j.cellsig.2017.09.004. View

Li W, Wong C, Zhang X, Kang W, Nakatsu G, Zhao Q . CAB39L elicited an anti-Warburg effect via a LKB1-AMPK-PGC1α axis to inhibit gastric tumorigenesis. Oncogene. 2018; 37(50):6383-6398. PMC: 6296350. DOI: 10.1038/s41388-018-0402-1. View

Cosso G, Nehme M, Luridiana S, Pulinas L, Curone G, Hosri C . Detection of Polymorphisms in the Gene and Their Association with Reproductive Performance in Awassi Ewes. Animals (Basel). 2021; 11(2). PMC: 7926687. DOI: 10.3390/ani11020583. View

Kriz V, Korinek V . Wnt, RSPO and Hippo Signalling in the Intestine and Intestinal Stem Cells. Genes (Basel). 2018; 9(1). PMC: 5793173. DOI: 10.3390/genes9010020. View

10.

He J, Zhang B, Chu M, Wang P, Feng T, Cao G . Polymorphism of insulin-like growth factor 1 gene and its association with litter size in Small Tail Han sheep. Mol Biol Rep. 2012; 39(10):9801-7. DOI: 10.1007/s11033-012-1846-y. View

11.

Price A, Patterson N, Plenge R, Weinblatt M, Shadick N, Reich D . Principal components analysis corrects for stratification in genome-wide association studies. Nat Genet. 2006; 38(8):904-9. DOI: 10.1038/ng1847. View

12.

Miao X, Luo Q, Zhao H, Qin X . Ovarian proteomic study reveals the possible molecular mechanism for hyperprolificacy of Small Tail Han sheep. Sci Rep. 2016; 6:27606. PMC: 4897777. DOI: 10.1038/srep27606. View

13.

Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N . The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009; 25(16):2078-9. PMC: 2723002. DOI: 10.1093/bioinformatics/btp352. View

14.

Li H, Durbin R . Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009; 25(14):1754-60. PMC: 2705234. DOI: 10.1093/bioinformatics/btp324. View

15.

Blouin J, Ged C, Bernardo-Seisdedos G, Cabantous T, Pinson B, Poli A . Identification of novel mutations in a patient with congenital erythropoietic porphyria and efficient treatment by phlebotomy. Mol Genet Metab Rep. 2021; 27:100722. PMC: 7890299. DOI: 10.1016/j.ymgmr.2021.100722. View

16.

Li X, Yang J, Shen M, Xie X, Liu G, Xu Y . Whole-genome resequencing of wild and domestic sheep identifies genes associated with morphological and agronomic traits. Nat Commun. 2020; 11(1):2815. PMC: 7272655. DOI: 10.1038/s41467-020-16485-1. View

17.

Harris M, Clark J, Ireland A, Lomax J, Ashburner M, Foulger R . The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res. 2003; 32(Database issue):D258-61. PMC: 308770. DOI: 10.1093/nar/gkh036. View

18.

Wang Z, Guo J, Guo Y, Yang Y, Teng T, Yu Q . Genome-Wide Detection of CNVs and Association With Body Weight in Sheep Based on 600K SNP Arrays. Front Genet. 2020; 11:558. PMC: 7297042. DOI: 10.3389/fgene.2020.00558. View

19.

Yao J, Wang Z, Cheng Y, Ma C, Zhong Y, Xiao Y . M2 macrophage-derived exosomal microRNAs inhibit cell migration and invasion in gliomas through PI3K/AKT/mTOR signaling pathway. J Transl Med. 2021; 19(1):99. PMC: 7937290. DOI: 10.1186/s12967-021-02766-w. View

20.

Zhang M, Wang S, Yi A, Qiao Y . microRNA-665 is down-regulated in gastric cancer and inhibits proliferation, invasion, and EMT by targeting PPP2R2A. Cell Biochem Funct. 2020; 38(4):409-418. DOI: 10.1002/cbf.3485. View