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. 2020 Dec 29;11(1):49.
doi: 10.3390/ani11010049.

Functional Analysis of Haplotypes in Bovine PSAP Gene and Their Relationship with Beef Cattle Production Traits

Haidong Zhao  1 , Mingli Wu  1 , Xiaohua Yi  1 , Xiaoqin Tang  1 , Pingbo Chen  1 , Shuhui Wang  1 , Xiuzhu Sun  2
Affiliations

Functional Analysis of Haplotypes in Bovine PSAP Gene and Their Relationship with Beef Cattle Production Traits

Haidong Zhao et al. Animals (Basel). .

Abstract

The purpose of this study was to explore functional variants in the prosaposin (PSAP) three prime untranslated region (3' UTR) and clarify the relationship between the variants and morphological traits. Through Sanger sequencing, 13 variations were identified in bovine PSAP in four Chinese cattle breeds, with six of them being loci in 3' UTR. In particular, Nanyang (NY) cattle had a special genotype and haplotype distribution compared to the other three breeds. NY cattle with ACATG and GCGTG haplotypes had higher morphological traits than GTACA and GTACG haplotypes. The results of dual-luciferase reporter assay showed that ACATG and GCGTG haplotypes affected the morphological traits of NY cattle by altering the secondary structure of PSAP 3' UTR rather than the miR-184 target sites. The findings of this study could be an evidence of a complex and varying mechanism between variants and animal morphological traits and could be used to complement candidate genes for molecular breeding.

Keywords: PSAP; bovine; haplotypes; mRNA secondary structure; miR-184; morphological traits.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Sequencing of variants in bovine PSAP. (A) The genetic mapping of bovine PSAP by sequencing; (B) three single-nucleotide polymorphisms (SNPs) in the 14th intron of bovine PSAP; (C) two SNPs in the 15th exon of bovine PSAP; (D) five SNPs in bovine PSAP 3’ UTR; (E) two variants in the downstream region of bovine PSAP. P: the number variants in the fragment of PSAP; N: the number of bases in PSAP 3’ UTR.
Figure 2
Figure 2
χ2 test on genotypic and allele frequency distribution of variations in four Chinese cattle PSAP. QC: Qinchuan cattle; NY: Nanyang cattle; JX: Jiaxian red cattle; LX: Luxi cattle.
Figure 3
Figure 3
Linkage disequilibrium analysis (R2) of 13 variants in four cattle breeds. QC: Qinchuan cattle; NY: Nanyang cattle; JX: Jiaxian red cattle; LX: Luxi cattle.
Figure 4
Figure 4
Allele, genotype, and haplotype distribution in four cattle breeds. (A) The allele frequency of the N8 locus of bovine PSAP in four cattle breeds; (B) the genotype frequency of the N8 locus of bovine PSAP in four cattle breeds; (C) the haplotype frequency of five SNPs of bovine PSAP 3’ UTR in four cattle breeds. QC: Qinchuan cattle; NY: Nanyang cattle; JX: Jiaxian red cattle; LX: Luxi cattle.
Figure 5
Figure 5
Targeting of bta-miR-184 and four haplotypes of bovine PSAP 3’ UTR. (A) Four haplotypes and their targeting of bta-miR184 (red represents mismatch and green represents match); (B) relative luciferase activity of four haplotypes and bta-miR-184; (C) relative luciferase activity of two haplotype groups. ** p < 0.01.
Figure 6
Figure 6
mRNA secondary structure prediction of four haplotypes in PSAP 3’ UTR: (A) ACATG; (B) GCGTG; (C) GTACA; (D) GTACG.
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