Polymorphism and bioinformatics analysis of pig CAST gene

doi:10.3969/j.issn.1004-1524.2022.01.03

Acta Agriculturae Zhejiangensis ›› 2022, Vol. 34 ›› Issue (1): 17-23.DOI: 10.3969/j.issn.1004-1524.2022.01.03

• Animal Science • Previous Articles Next Articles

Polymorphism and bioinformatics analysis of pig CAST gene

XU Jingen¹(), JIN Erhui¹, WANG Chonglong², GU Youfang¹^,^*(), LI Qinggang²^,^*()

1. College of Animal Science, Anhui Science and Technology University, Anhui Province Key Laboratory of Animal Nutritional Regulation and Health, Fengyang 233100, Anhui, China
2. Institute of Animal Sciences and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230031, China

Received:2020-10-02 Online:2022-01-25 Published:2022-02-05
Contact: GU Youfang,LI Qinggang

Abstract

Abstract:

The aim of this study was to detect the CAST gene polymorphism of Berkshire pig, Huoshou black pig and their hybrid F₁ generation, and to analyze the effect of base variation on the mRNA secondary structure and CAST type Ⅲ protein by bioinformatics. The results showed that there were AA, AC and CC genotypes in Berkshire pig, Huoshou black pig and Berkshire × Huoshou black pig, and the frequency of allele A was higher than that of allele C. The mutation was in Hardy-Weinberg equilibrium in all three pig populations (P>0.05), and with moderate polymorphism (0.25<PIC<0.5). Bioinformatics prediction showed that c. 1980A>C slightly changed the secondary structure of porcine CAST gene mRNA sequence, and increased the minimum free energy. The p. Arg660Ser mutation resulted in a slight change in some physicochemical properties of the porcine CAST type Ⅲ protein, including molecular formula, molecular weight, isoelectric point, instability index, grand average of hydropathicity, positively charged residues (Arg and Lys) number. The secondary structure of porcine CAST type Ⅲ protein was not changed by the missense mutation, and the proportion of random coil and α-helix were higher before and after mutation. The p. Arg660Ser mutation was not located in the conserved domain of the porcine CAST type Ⅲ protein, but could lead to a decrease in the number of protein kinases that catalyzed the phosphorylation of adjacent p. 663Ser. In summary, the c.1980A>C mutation might have a certain impact on the transcription efficiency and function of the pig CAST gene.

Key words: pig, CAST gene, polymorphism, bioinformatics analysis

CLC Number:

S828

XU Jingen, JIN Erhui, WANG Chonglong, GU Youfang, LI Qinggang. Polymorphism and bioinformatics analysis of pig CAST gene[J]. Acta Agriculturae Zhejiangensis, 2022, 34(1): 17-23.

Figures/Tables 6

References 19

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种类(样本数) Type (sample number)	基因型频率(样本数) Genotype frequency (sample number)			基因频率 Gene frequency		P	多态信息含量 Polymorphism information content
种类(样本数) Type (sample number)	AA	AC	CC	A	C	P	多态信息含量 Polymorphism information content
巴克夏猪Berkshire pig (32)	0.562 5(18)	0.281 2(9)	0.156 3(5)	0.703 1	0.296 9	0.06	0.330 3
霍寿黑猪Huoshou black pig (48)	0.437 5(21)	0.500 0(24)	0.062 5(3)	0.687 5	0.312 5	0.26	0.337 4
巴克夏猪×霍寿黑猪	0.495 2(52)	0.428 6(45)	0.076 2(8)	0.709 5	0.290 5	0.68	0.327 2
Berkshire×Huoshou black pig (105)

种类(样本数) Type (sample number)	基因型频率(样本数) Genotype frequency (sample number)			基因频率 Gene frequency		P	多态信息含量 Polymorphism information content
种类(样本数) Type (sample number)	AA	AC	CC	A	C	P	多态信息含量 Polymorphism information content
巴克夏猪Berkshire pig (32)	0.562 5(18)	0.281 2(9)	0.156 3(5)	0.703 1	0.296 9	0.06	0.330 3
霍寿黑猪Huoshou black pig (48)	0.437 5(21)	0.500 0(24)	0.062 5(3)	0.687 5	0.312 5	0.26	0.337 4
巴克夏猪×霍寿黑猪	0.495 2(52)	0.428 6(45)	0.076 2(8)	0.709 5	0.290 5	0.68	0.327 2
Berkshire×Huoshou black pig (105)

序列 Sequence	分子式 Formula	分子量 Molecular weight/u	等电点 Theoretical pI	不稳定系数 Instability index	总平均亲水性 Grand average of hydropathicity	正电荷 (Arg和 Lys) 数 Number of positively charged residues (Arg+Lys)	负电荷 (Asp和 Glu) 数 Number of negatively charged residues (Asp+Glu)
突变前	C₃₃₀₉H₅₄₂₆N₉₂₀O₁₁₆₇S₁₁	77 123.61	5.21	45.69	-1.195	123	149
Before mutation
突变后	C₃₃₀₆H₅₄₁₉N₉₁₇O₁₁₆₈S₁₁	77 054.50	5.18	46.52	-1.189	122	149
After mutation

序列 Sequence	分子式 Formula	分子量 Molecular weight/u	等电点 Theoretical pI	不稳定系数 Instability index	总平均亲水性 Grand average of hydropathicity	正电荷 (Arg和 Lys) 数 Number of positively charged residues (Arg+Lys)	负电荷 (Asp和 Glu) 数 Number of negatively charged residues (Asp+Glu)
突变前	C₃₃₀₉H₅₄₂₆N₉₂₀O₁₁₆₇S₁₁	77 123.61	5.21	45.69	-1.195	123	149
Before mutation
突变后	C₃₃₀₆H₅₄₁₉N₉₁₇O₁₁₆₈S₁₁	77 054.50	5.18	46.52	-1.189	122	149
After mutation

Polymorphism and bioinformatics analysis of pig CAST gene

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