Genetic Diversity and Selection Signal Analysis of Hu Sheep Based on SNP50K BeadChip

Overview

Journal Animals (Basel)

Date 2024 Oct 16

PMID 39409733

Authors

Keyan Ma

Juanjuan Song

Dengpan Li

Taotao Li

Youji Ma

Affiliations

Soon will be listed here.

Abstract

This research is designed to examine the genetic diversity and kinship among Hu sheep, as well as to discover genes associated with crucial economic traits. A selection of 50 unrelated adult male Hu sheep underwent genotyping with the SNP50K BeadChip. Seven indicators of genetic diversity were assessed based on high-quality SNP data: effective population size (), polymorphic information content (), polymorphic marker ratio (), expected heterozygosity (), observed heterozygosity (), effective number of alleles, and minor allele frequency (). Plink software was employed to compute the IBS genetic distance matrix and detect runs of homozygosity (ROHs), while the G matrix and principal component analysis were performed using GCTA software. Selective sweep analysis was carried out using ROH, Pi, and Tajima's D methodologies. This study identified a total of 64,734 SNPs, of which 56,522 SNPs remained for downstream analysis after quality control. The population displayed relatively high genetic diversity. The 50 Hu sheep were ultimately grouped into 12 distinct families, with families 6, 8, and 10 having the highest numbers of individuals, each consisting of 6 sheep. Furthermore, a total of 294 ROHs were detected, with the majority having lengths between 1 and 5 Mb, and the inbreeding coefficient was 0.01. In addition, 41, 440, and 994 candidate genes were identified by ROH, Pi, and Tajima's D methods, respectively, with 3 genes overlapping (, and ). These results offer valuable insights for future Hu sheep breeding, genetic assessment, and population management.

References

Botstein D, White R, Skolnick M, Davis R . Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet. 1980; 32(3):314-31. PMC: 1686077. View

An Z, Shi L, Hou G, Zhou H, Xun W . Genetic diversity and selection signatures in Hainan black goats revealed by whole-genome sequencing data. Animal. 2024; 18(6):101147. DOI: 10.1016/j.animal.2024.101147. View

Cai K, Liu R, Wei L, Wang X, Cui H, Luo N . Genome-wide association analysis identify candidate genes for feed efficiency and growth traits in Wenchang chickens. BMC Genomics. 2024; 25(1):645. PMC: 11212279. DOI: 10.1186/s12864-024-10559-w. View

Xu S, Ren X, Yang G, Xie X, Zhao Y, Zhang M . Genome-wide association analysis identifies the genetic basis of fat deposition in the tails of sheep (Ovis aries). Anim Genet. 2017; 48(5):560-569. DOI: 10.1111/age.12572. View

Ma K, Chen N, Wang H, Li Q, Shi H, Su M . The regulatory role of BMP4 in testicular Sertoli cells of Tibetan sheep. J Anim Sci. 2022; 101. PMC: 9838805. DOI: 10.1093/jas/skac393. View

Huang D, Sherman B, Tan Q, Kir J, Liu D, Bryant D . DAVID Bioinformatics Resources: expanded annotation database and novel algorithms to better extract biology from large gene lists. Nucleic Acids Res. 2007; 35(Web Server issue):W169-75. PMC: 1933169. DOI: 10.1093/nar/gkm415. View

Zhong T, Wang X, Huang C, Yang L, Zhao Q, Chen X . A genome-wide perspective on the diversity and selection signatures in indigenous goats using 53 K single nucleotide polymorphism array. Animal. 2023; 17(3):100706. DOI: 10.1016/j.animal.2023.100706. View

Kijas J, Lenstra J, Hayes B, Boitard S, Porto Neto L, San Cristobal M . Genome-wide analysis of the world's sheep breeds reveals high levels of historic mixture and strong recent selection. PLoS Biol. 2012; 10(2):e1001258. PMC: 3274507. DOI: 10.1371/journal.pbio.1001258. View

Chen S, Batool A, Wang Y, Hao X, Chang C, Cheng C . The control of male fertility by spermatid-specific factors: searching for contraceptive targets from spermatozoon's head to tail. Cell Death Dis. 2016; 7(11):e2472. PMC: 5260884. DOI: 10.1038/cddis.2016.344. View

10.

Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira M, Bender D . PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet. 2007; 81(3):559-75. PMC: 1950838. DOI: 10.1086/519795. View

11.

Ghoreishifar S, Eriksson S, Johansson A, Khansefid M, Moghaddaszadeh-Ahrabi S, Parna N . Signatures of selection reveal candidate genes involved in economic traits and cold acclimation in five Swedish cattle breeds. Genet Sel Evol. 2020; 52(1):52. PMC: 7487911. DOI: 10.1186/s12711-020-00571-5. View

12.

VanRaden P . Efficient methods to compute genomic predictions. J Dairy Sci. 2008; 91(11):4414-23. DOI: 10.3168/jds.2007-0980. View

13.

Huang C, Ge F, Ren W, Zhang Y, Wu X, Zhang Q . Copy number variation of the HPGDS gene in the Ashidan yak and its associations with growth traits. Gene. 2020; 772:145382. DOI: 10.1016/j.gene.2020.145382. View

14.

Ma K, Song J, Li D, Wu Y, Wang C, Liu Z . Genomic structure analysis and construction of DNA fingerprint for four sheep populations. Animal. 2024; 18(4):101116. DOI: 10.1016/j.animal.2024.101116. View

15.

Kumar S, Stecher G, Li M, Knyaz C, Tamura K . MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms. Mol Biol Evol. 2018; 35(6):1547-1549. PMC: 5967553. DOI: 10.1093/molbev/msy096. View

16.

Gomez Proto G, Mancin E, Sartori C, Mantovani R . Unraveling inbreeding patterns and selection signals in Alpine Grey cattle. Animal. 2024; 18(5):101159. DOI: 10.1016/j.animal.2024.101159. View

17.

Nei M, Li W . Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc Natl Acad Sci U S A. 1979; 76(10):5269-73. PMC: 413122. DOI: 10.1073/pnas.76.10.5269. View

18.

Cheng J, Cao X, Peng S, Wang X, Li Z, Elnour I . Transcriptional regulation of the bovine FGFR1 gene facilitates myoblast proliferation under hypomethylation of the promoter. J Cell Physiol. 2020; 235(11):8667-8678. DOI: 10.1002/jcp.29711. View

19.

Abdurahman A, Du X, Yao Y, Sulaiman Y, Aniwashi J, Li Q . Smad4 Feedback Enhances BMPR1B Transcription in Ovine Granulosa Cells. Int J Mol Sci. 2019; 20(11). PMC: 6600593. DOI: 10.3390/ijms20112732. View

20.

Signer-Hasler H, Burren A, Ammann P, Drogemuller C, Flury C . Runs of homozygosity and signatures of selection: a comparison among eight local Swiss sheep breeds. Anim Genet. 2019; 50(5):512-525. DOI: 10.1111/age.12828. View