Two novel SNPs in the coding region of the bovine PRDM16 gene and its associations with growth traits

Abstract

As a zinc-finger protein, PR domain containing 16 (PRDM16) controls brown fat determination by stimulating brown fat-selective genes expression while suppressing the expression of genes selective for white fat cells, whose mutations were associated with myelodysplastic syndrome (MDS) and leukemogenesis in human and murine model of leukemia. To date, no polymorphisms of PRDM16 gene in bovine had been reported. Herein, PCR-SSCP and DNA sequencing methods were employed to screen the genetic variation within PRDM16 gene in 1031 Chinese indigenous bovine. The results revealed two novel silent mutations: XM_001788152: m.1641T>C (547aa), 1881G>A (627aa). Hence, we described the PvuII and HaeIII forced PCR-RFLP methods for detecting these mutations, respectively. In the forced PCR-RFLP analysis with PvuII, the frequencies of bovine PRDM16-C allele varied from 0.044 to 0.506 in four Chinese native breeds. In the forced PCR-RFLP analysis with HaeIII, the frequencies of bovine PRDM16-G allele were 0.474, 0.494, 0.576 and 0.906 for Jiaxian (JX), Nanyang (NY), Qinchuan (QC) and Chinese Holstein (CH) population. Significant statistical differences between genotypic frequencies implied that both of the polymorphic loci were significantly associated with cattle breeds by the chi square test (chi2 = 190.058, P < 0.001 and chi2 = 118.239, P < 0.001 for PvuII; chi2 = 209.842, P < 0.001 and chi2 = 108.711, P < 0.001 for HaeIII). The associations of the PvuII and HaeIII forced PCR-RFLPs of bovine PRDM16 loci with growth traits were analyzed in Nanyang breed. The two SNPs were associated with body weight and average daily gain in Nanyang aged 12 months, individuals with genotype TT and AA showed significantly better body weight (P < 0.05) and average daily gain (P < 0.01) at 12 months, respectively.

Bivariate Genome-Wide Association Analysis of the Growth and Intake Components of Feed Efficiency

“…Previous studies reported genomic regions associated with ADG on BTA 2, 4–7, 9, 11, 14–20, 22, 23, 26, and 28 [38]–[52]. The SNPs associated with ADG in the present study (Table 4) were mapped to chromosomes previously linked to ADG, with the exception of rs41629972 located on BTA13.…”

Impacts of single nucleotide polymorphisms and haplotypes in the bovine Dapper1 gene on body weight

“…These results are consistent with those of our previous studies (Wang et al, 2010;Xu et al, 2011). For example, Xu et al (2011) found that at the P7 locus of the paired box 7 gene, only two genotypes occur in CY cattle.…”

Whole Genome Sequencing Reveals Signatures for Artificial Selection for Different Sizes in Japanese Primitive Dog Breeds

“…With the F ST , H p and XP-CLR with sliding window approaches, nine genes (PRDM16, ZNF382, ZNF461, ERGIC2, ENSCAFG00000033351, CCDC61, ALDH3A2, ENSCAFG00000011141, and ENSCAFG00000018533) were found to show selection signatures. Among these genes, PRDM16 was reported to be associated with growth traits in some species, such as bovine and chicken (Wang et al, 2010;Wu et al, 2021). It is known that PRDM16 controls a brown fat/skeletal muscle switch (Seale et al, 2008), and it might take a role in the growth of Mame Shiba Inu.…”