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Genetic polymorphisms in SIRT5 gene and their association with carcass traits in Congjiang Xiang pigs

ABSTRACT

This study was conducted to investigate the polymorphism of the silence information regulator 5 (SIRT5) gene in 103 Congjiang Xiang pigs from Southwest China. We searched for SNP (single nucleotide polymorphism) loci of SIRT5 gene through sequence alignment and PCR. We obtained nine SNP loci: g.14135 A>C (intron 6), g.14247 C>A (intron 6), g.14305 C>T (exon 7), g.14335 C>T (exon 7), g.16603 T>C (intron 7), g.16613 T>C (intron 7), g.16800 G>A (intron 7), g.16812 C>G (intron 7), and g.16916 A>G (exon 8). Further analysis of SNP genotypes associated with the carcass traits of skin thickness, backfat thickness, and eye muscle area was carried out in pigs. We found that the genotypes g.14305 C>T (CC) and g.16812 C>G (CG) had certain advantages for improving the carcass traits of Congjiang Xiang pigs. The haplotype combination of the SIRT5 gene that improved skin thickness was H2H3:CCGGCTCA. These results may provide empirical support for molecular-based breeding of carcass traits in Congjiang Xiang pigs.

carcass traits; Congjiang Xiang pig; SIRT5; SNP

1. Introduction

The Congjiang Xiang pig, as a national Grade II protected livestock breed, is a valuable miniature pig breed primarily farmed in Guizhou Province, China. The breed is famous for its small size, early sexual maturity, adaptability to coarse feed, superior meat quality, low level of genetic diversity, and high level of homozygosity (Ran et al., 2016 Ran, M. L. ; Wang, M. F. ; Yang, A. Q. ; Li, Z. and Chen, B. 2016. The complete mitochondrial genome of Congjiang miniature pig ( Sus scrofa ). Mitochondrial DNA Part A 27:1787-1788. https://doi.org/10.3109/19401736.2014.963813
https://doi.org/10.3109/19401736.2014.96...
). Previous studies identified APOC3, APOA5, FUT1, PHKG1, and PRKAG3 as candidate genes for pork quality traits and flavor fatty acid composition and content (Jiang et al., 2005Jiang, X. P.; Liu, Y. G.; Xiong, Y. Z. and Deng, C. Y. 2005. Effects of FUT1 gene on meat quality and carcass traits in swine. Yi Chuan 27:566-570.; Ryan et al., 2012Ryan, M. T.; Hamill, R. M.; O'Halloran, A. M.; Davey, G. C.; McBryan, J.; Mullen, A. M.; McGee, C.; Gispert, M.; Southwood, O. I. and Sweeney, T. 2012. SNP variation in the promoter of the PRKAG3 gene and association with meat quality traits in pig. BMC Genetics 13:66. https://doi.org/10.1186/1471-2156-13-66
https://doi.org/10.1186/1471-2156-13-66...
; Hui et al., 2013Hui, Y. T.; Yang, Y. Q.; Liu, R. Y.; Zhang, Y. Y.; Xiang, C. J.; Liu, Z. Z.; Ding, Y. H.; Zhang, Y. L. and Wang, B. R. 2013. Significant association of APOA5 and APOC3 gene polymorphisms with meat quality traits in Kele pigs. Genetics and Molecular Research 12:3643-3650. https://doi.org/10.4238/2013.September.13.8
https://doi.org/10.4238/2013.September.1...
; Zappaterra et al., 2019). In addition, SIRT5 (silence information regulator 5), a member of the Sirtuin family, is involved in the metabolic processes of desuccinylation, demalonylation, and deglutarylation (Simó-Mirabet et al., 2018 Simó-Mirabet, P. ; Perera, E. ; Calduch-Giner, J. A. ; Afonso, J. M. and Pérez-Sánchez, J. 2018. Co-expression analysis of sirtuins and related metabolic biomarkers in juveniles of gilthead sea bream ( Sparus aurata ) with differences in growth performance. Frontiers in Physiology 9:608. https://doi.org/10.3389/fphys.2018.00608
https://doi.org/10.3389/fphys.2018.00608...
). It has been demonstrated that SIRT5 regulates the balance of fatty acid oxidation in mice (Rardin et al., 2013Rardin, M. J.; He, W.; Nishida, Y.; Newman, J. C.; Carrico, C.; Danielson, S. R.; Guo, A.; Gut, P.; Sahu, A. K.; Li, B.; Uppala, R.; Fitch, M.; Riiff, T.; Zhu, L.; Zhou, J.; Mulhern, D.; Stevens, R. D.; Ilkayeva, O. R.; Newgard, C. B.; Jacobson, M. P.; Hellerstein, M.; Goetzman, E. S.; Gibson, B. W. and Verdin, E. 2013. SIRT5 regulates the mitochondrial lysine succinylome and metabolic networks. Cell Metabolism 18:920-933. https://doi.org/10.1016/j.cmet.2013.11.013
https://doi.org/10.1016/j.cmet.2013.11.0...
). The browning of subcutaneous white fat in SIRT5 knockout mice was impaired, indicating that SIRT5 is also a key factor in the differentiation of brown fat (Shuai et al., 2019Shuai, L.; Zhang, L. N.; Li, B. H.; Tang, C. L.; Wu, L. Y.; Li, J. and Li, J. Y. 2019. SIRT5 Regulates brown adipocyte differentiation and browning of subcutaneous white adipose tissue. Diabetes 68:1449-1461. https://doi.org/10.2337/db18-1103
https://doi.org/10.2337/db18-1103...
). In livestock, SIRT5 has been demonstrated to regulate fat deposition in a Chinese indigenous cattle breed (Deng, 2014Deng, G. Q. 2014. SNPs detection of Sirt3 and Sirt5 genes in Qinchuan cattle and their correlation with body size and meat quality traits. Master's thesis. Northwest A&F University, Yangling, China.). However, little is known about SIRT5 polymorphism in pigs.

In recent years, studies with Congjiang Xiang pigs have focused on the processes of their testis development, fertility, and germplasm resources (Tang et al., 2018Tang, L. T.; Ran, X. Q.; Mao, N.; Zhang, F. P.; Niu, X.; Ruan, Y. Q.; Yi, F. L.; Li, S. and Wang, J. F. 2018. Analysis of alternative splicing events by RNA sequencing in the ovaries of Xiang pig at estrous and diestrous. Theriogenology 119:60-68. https://doi.org/10.1016/j.theriogenology.2018.06.022
https://doi.org/10.1016/j.theriogenology...
; Meng et al., 2020Meng, L. J.; Wang, W. Y.; Xu, Y. J.; Gong, T. and Yang, Y. 2020. Postnatal differentiation and regional histological variations in the ductus epididymidis of the Congjiang Xiang pig. Tissue and Cell 67:101411. https://doi.org/10.1016/j.tice.2020.101411
https://doi.org/10.1016/j.tice.2020.1014...
; Gong et al., 2021Gong, T.; Wang, W.; Xu, H.; Yang, Y.; Chen, X.; Meng, L.; Xu, Y.; Li, Z.; Wan, S. and Mu, Q. 2021. Longitudinal expression of testicular TAS1R3 from prepuberty to sexual maturity in Congjiang Xiang pigs. Animals 11:437. https://doi.org/10.3390/ani11020437
https://doi.org/10.3390/ani11020437...
). Carcass traits have always been an economic concern in pig breeding. The Congjiang Xiang pig is an economically important species in China, and thus it is worthwhile to improve its carcass traits.

In this study, we identified polymorphism of SIRT5 and examined its relationship with carcass traits. Therefore, this study aimed to provide a foundation for applying the SIRT5 gene in the breeding of Congjiang Xiang pigs.

2. Material and Methods

The study was carried out in Guiyang, Guizhou, China (26°63'65" N latitude, 106°75'75" E longitude, and elevation of 1125 m). Research on animals was approved by the institutional committee on animal use (case number: EAE-GZU-2021-T113). The experimental animals were maintained and processed in accordance with institutional guidelines for the care and use of animals.

2.1. Experimental animals and sample collection

One hundred and three blood samples were collected from healthy eight-month-old male Congjiang Xiang pigs, and the carcass traits of these pigs were measured. All pigs were obtained from a commercial farm in Southwest China (Guizhou Province).

2.2. Carcass trait measurement

The skin thickness (from the 6th to the 7th ribs of the right half of the carcass of each pig), backfat thickness (the average thickness of the thickest part of the shoulder, the joint of the thoracolumbar vertebrae, and the joint of the lumbar-sacral vertebrae on the right side of each pig), and eye muscle area (the area of a transverse section of the longissimus dorsi muscle at the last rib on the left side of the carcass) were measured using calipers (HOLEX, Germany) after slaughter.

2.3. Acquisition of DNA

Genomic DNA was extracted from each pig blood sample using an Ezup Column Genomic DNA Extraction Kit (Blood) (Sangon, China) and stored at –20 °C.

2.4. Primer design and synthesis

The porcine SIRT5 gene complete sequence (accession no.: NC_010449.5) was obtained from GenBank (https://www.ncbi.nlm.nih.gov/). Primers were designed using Primer Premier 5.0 (Singh et al., 1998Singh, V. K.; Mangalam, A. K.; Dwivedi, S. and Naik, S. 1998. Primer premier: program for design of degenerate primers from a protein sequence. BioTechniques 24:318-319. https://doi.org/10.2144/98242pf02
https://doi.org/10.2144/98242pf02...
) and synthesized by Sangon Co., Ltd., China. Table 1 lists the primer sequences and product lengths.

Table 1
Information of primers

2.5. Sequencing of the SIRT5 gene

The SIRT5 gene was characterized from 103 blood samples using the polymerase chain reaction (PCR), which was performed in a 20-μL reaction mixture containing 10 μL of 2 × Taq PCR Master Mix (CW Biotech, China), 1 μL of primers (10 μmol/L), 1 μL of complementary DNA (cDNA), and 7 μL of double distilled water (ddH2O). The reaction was pre-denatured for 2 min at 94 °C, followed by 35 cycles of denaturation for 30 s at 94 °C, annealing for 10 s at 60 °C, and extension for 30 s at 72 °C followed by a final extension for 30 s at 72 °C.

After electrophoresis, the rubber plate was removed, and the gel was placed in an irradiation instrument to observe the target bands. The optimal products were sent to Sangon Co., Ltd. (Shanghai, China), for sequencing, sequence alignment, single nucleotide polymorphism (SNP) analysis, and genotype determination.

2.6. Statistical analysis

The genotype frequency, allele frequency, polymorphism information content (PIC), effective number of alleles (Ne), heterozygosity (He), and homozygosity (Ho) were calculated. The statistical analysis of the associations between the carcass traits and the SNP of the SIRT5 gene was performed using SPSS Statistics 18. Duncan’s method was used for multiple comparisons. A P-value < 0.05 was considered significant. Values are reported as the mean ± standard deviation (SD). Haplotype analysis was performed using SHEsis software (http://analysis.bio-x.cn/myAnalysis.php). The equation for the animal model used was as follows:

Y i j = μ + h i + e i j

in which Yij is the trait being measured, μ is the population mean, hi is the effect of genotype or combined haplotype, and eij is the random error term.

3. Results

3.1. SNP locus mapping

We compared the results of SIRT5 gene with its gene sequences. DNAMAN software was used for the comparison process. In the comparative analysis, nine SNP were mined, and SNP were present in all of the exonic regions and several of the intronic regions of the SIRT5 gene in the Congjiang Xiang pig sequences.

Referring to the complete sequence of the porcine SIRT5 gene (taking the first transcription start site +1), the nine SNP (Figure 1) were named g.14135 A>C (intron 6), g.14247 C>A (intron 6), g.14305 C>T (exon 7), g.14335 C>T (exon 7), g.16603 T>C (intron 7), g.16613 T>C (intron 7), g.16800 G>A (intron 7), g.16812 C>G (intron 7), and g.16916 A>G (exon 8).

Figure 1
Sequencing map of SIRT5 gene SNP in Congjiang Xiang pigs.

3.2. Genetic diversity analysis

The Ne values of g.16603 T>C, g.16613 T>C, and g.16916 A>G loci were close to 2, indicating that the alleles of these three variants were evenly distributed in Congjiang Xiang pigs. The Ne and He values of the g.14135 A>C, g.14247 C>A, g.14305 C>T, and g.16800 G>A loci were low, indicating relatively low genetic variability and insufficient diversity excavation of species resources. The PIC values of these four loci were low polymorphic (PIC < 0.25), indicating that the genetic marker loci provided little genetic information (Table 2).

Table 2
Genetic indices of SIRT5 gene SNP site from Congjiang Xiang pigs

3.3. Correlations between SIRT5 gene variation and traits

The correlations between SIRT5 variation and traits in the Congjiang Xiang pigs were measured (Table 3). The skin thickness of individuals with the g.14305 C>T locus CC type was higher than that of individuals with the TT genotype by 14.04% (P<0.05). The skin thickness and eye muscle area of individuals with the g.16812 C>G locus CG type were greater than those of individuals with the GG type by 28.12 and 17.99%, respectively (P<0.05), but the difference in the level of individuals with the CC type was not significant (P>0.05).

Table 3
Correlations between SIRT5 variation loci and traits in the Congjiang Xiang pig

3.4. Haplotype combination analysis of different SNP loci

There were five haplotypes of four SNP loci (g.14335 C>T, g.16613 T>C, g.16812 C>G, and g.16916 A>G) in 43 Congjiang Xiang pigs, named H1:CCCG, H2:CCGG, H3:CTCA, H4:TCCG, and H5:TCGG, which were analyzed by the SHEsis software. Among these, H2, H3, and H4 were the main haplotypes, with frequencies of 27.8, 44.2, and 17.3%, respectively, while the H1 haplotype had the lowest frequency of 3.6% (Table 4).

Table 4
Haplotype construction and frequency of four SNP loci of SIRT5 gene

There were four haplotype combinations in 43 Congjiang Xiang pigs, H2H2:CCGGCCGG, H2H3:CCGGCTCA, H3H3:CTCACTCA, and H3H4:CTCATCCG. We found that skin thickness associated with H2H3 was superior to the H2H2 haplotype combination (Table 5).

Table 5
Haplotype combination analysis of four SNP loci of the SIRT5 gene

4. Discussion

Recent studies have reported that the SIRT5 gene regulates the activity of glyceraldehyde 3-phosphate dehydrogenase (GAPDH) through demethylation and further upregulates glycolytic flux (Nishida et al., 2015Nishida, Y.; Rardin, J. M.; Carrico, C.; He, W.; Sahu, A. K.; Gut, P.; Najjar, R.; Fitch, M.; Hellerstein, M.; Gibson, B. W. and Verdin, E. 2015. SIRT5 Regulates both cytosolic and mitochondrial protein malonylation with glycolysis as a major target. Molecular Cell 59:321-332. https://doi.org/10.1016/j.molcel.2015.05.022
https://doi.org/10.1016/j.molcel.2015.05...
). SIRT5 also increases the activity of very long-chain acyl-CoA dehydrogenase (VLCAD) by desuccinylation to promote fatty acid β-oxidation and ketone body production (Zhang et al., 2015Zhang, Y. X.; Bharathi, S. S.; Rardin, M. J.; Uppala, R.; Verdin, E.; Gibson, B. W. and Goetzman, E. S. 2015. SIRT3 and SIRT5 regulate the enzyme activity and cardiolipin binding of very long-chain acyl-CoA dehydrogenase. PLoS ONE 10:e0122297. https://doi.org/10.1371/journal.pone.0122297
https://doi.org/10.1371/journal.pone.012...
). Hong et al. (2020)Hong, J. Y.; Mei, C. G.; Raza, S. H. A.; Khana, R. W.; Cheng, G. and Zan, L. S. 2020. SIRT5 inhibits bovine preadipocyte differentiation and lipid deposition by activating AMPK and repressing MAPK signal pathways. Genomics 112:1065-1076. https://doi.org/10.1016/j.ygeno.2019.12.004
https://doi.org/10.1016/j.ygeno.2019.12....
reported that during the differentiation of preadipocytes, SIRT5 inhibited the expression of key genes that promote lipid formation and differentiation in fatty acid biosynthesis and PPAR pathways. SIRT5 plays an important role in biological processes such as maintaining the balance of lipid metabolism and promoting the mobilization of fatty acid oxidation. However, little is known concerning SNP of the SIRT5 gene in pigs. Our study detected nine SNP loci in the SIRT5 gene. As mentioned above, SIRT5 significantly inhibits the differentiation of bovine preadipocytes and simultaneously inhibits lipid synthesis and lipid deposition in adipocytes (Hong et al., 2020Hong, J. Y.; Mei, C. G.; Raza, S. H. A.; Khana, R. W.; Cheng, G. and Zan, L. S. 2020. SIRT5 inhibits bovine preadipocyte differentiation and lipid deposition by activating AMPK and repressing MAPK signal pathways. Genomics 112:1065-1076. https://doi.org/10.1016/j.ygeno.2019.12.004
https://doi.org/10.1016/j.ygeno.2019.12....
), and thus we speculated that the nine sites identified in this study may have potential roles in production and breeding of Congjiang Xiang pigs. The genetic diversity of these nine loci was quite different in Congjiang Xiang pigs. We used PIC values as indicators to evaluate the degree of genetic variation in the population. The PIC can be used to classify loci as highly polymorphic (PIC > 0.5), medium polymorphic (PIC between 0.25 and 0.5), and low polymorphic (PIC < 0.25). According to the PIC values, g.14135 A>C, g.14247 C>A, g.14305 C>T, and g.16800 G>A loci were low polymorphic in Congjiang Xiang pigs (PIC < 0.25). We speculate that the reasons for these results may be related to the intensity of artificial selection that may have affected allele frequencies and genotype frequencies (Zhang et al., 2023).

In this study, the g.14305 C>T locus genotype was significantly associated with skin thickness, and CC was the dominant genotype. The g.16812 C>G locus genotype was significantly associated with skin thickness and eye muscle area, and CG was the dominant genotype. Although the g.16812 C>G locus is in the intron and cannot be directly involved in protein coding, it has been demonstrated that mutations in the non-coding region affect processes such as mRNA stabilization, localization, and translation (Kosinska-Selbi et al., 2020)Kosinska-Selbi, B.; Mielczarek, M. and Szyda, J. 2020. Review: Long non-coding RNA in livestock. Animal 14:2003-2013. https://doi.org/10.1017/S1751731120000841
https://doi.org/10.1017/S175173112000084...
. Compared with SNP genotyping, haplotype combination analysis can provide a more comprehensive reference as to functional significance, because the various loci in the haplotype combination will affect each other rather than acting as a simple combination of various genotypes (Wang et al., 2011)Wang, Z. Y.; Wang, G. L.; Huang, J. M.; Li, Q. L.; Wang, C. F. and Zhong, J. F. 2011. Novel SNPs in the ATP1B2 gene and their associations with milk yield, milk composition and heat-resistance traits in Chinese Holstein cows. Molecular Biology Reports 38:1749-1755. https://doi.org/10.1007/s11033-010-0289-6
https://doi.org/10.1007/s11033-010-0289-...
. We combined the haplotypes of the four SNP loci of the SIRT5 gene and analyzed their correlations with carcass traits. The results showed that the dominant haplotype combination for skin thickness of the SIRT5 gene was H2H3:CCGGCTCA.

5. Conclusions

This study identified nine SNP loci through analysis of SIRT5 gene in Congjiang Xiang pigs. The CC genotype of the g.14305 C>T locus and the CG genotype of the g.16812 C>G locus were the dominant genotypes associated with carcass traits; and H2H3:CCGGCTCA was associated with skin thickness. These dominant genotype and haplotype combinations can be used as a primary reference in the breeding of Congjiang Xiang pigs.

Acknowledgments

We thank LetPub for its linguistic assistance during the preparation of this manuscript. The authors are grateful to the Science and Technology Program of Guizhou Province (QKHZC[2020]1Y031) for funding and facilitating this study.

References

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Edited by

Editors:
Luiz Fernando Brito
Carina Visser

Publication Dates

  • Publication in this collection
    24 May 2024
  • Date of issue
    2024

History

  • Received
    10 Oct 2022
  • Accepted
    28 Jan 2024
Sociedade Brasileira de Zootecnia Universidade Federal de Viçosa / Departamento de Zootecnia, 36570-900 Viçosa MG Brazil, Tel.: +55 31 3612-4602, +55 31 3612-4612 - Viçosa - MG - Brazil
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