Screening of polymorphic loci and bioinformatics analysis of the SAA3 gene in Hainan Black goats

Chen Xiangying; Chen Taoyu; Gao Hongyan; Chen Si; Man Churiga; Du Li; Wang Fengyang; Chen Qiaoling

doi:10.20154/j.cnki.issn1672-9692.2025.03.001

Abstract：This study aimed to investigate the structural characteristics and genetic distribution of the SAA3 gene in Hainan Black goats,providing a reference for further exploration of its expression regulation mechanisms and immune functions.Blood samples from 200 Hainan Black goats were collected.Sanger sequencing was used to detect single nucleotide polymorphisms(SNPs)in the sequences of SAA3 gene.Linkage disequilibrium analysis was performed on the identified SNPs,and bioinformatics software was employed to analyze the SAA3-encoded protein and its promoter region.Results revealed four SNPs in the promoter region:SNP1(g.25808412C>A),SNP2(g.25808226C>G),SNP3(g.25808088A>G),and SNP4(g.25807925C>G).Among these,only SNP3 exhibited low polymorphism and deviated from the Hardy-Weinberg equilibrium(P<0.05).Haplotype analysis showed that the frequencies of H1,H2,and H3 haplotypes were 0.712,0.258,and 0.030,respectively,with H1(CCAC)being the dominant haplotype.Bioinformatics analysis indicated that the coding sequence(CDS)region of the SAA3 gene spans 131 bp,encoding a protein with a molecular weight of 14.59 kDa and a theoretical isoelectric point(pI)of 9.44.The secondary structure of the protein comprised 71.76%α-helices and 28.24%random coils.Phylogenetic tree analysis demonstrated that the encoded amino acid sequence shares the closest relationship with ruminants sheep and cattle.The study suggests that the SAA3 gene in Hainan Black goats is relatively conserved,with no mutation sites detected in the CDS region.Four SNPs were identified in the promoter region,among which SNP4 may reduce the binding of transcription factor AP-2α to the promoter,thereby influencing the regulatory expression of the SAA3 gene.