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

[1]	李婧, 郭月英, 任霆, 等. 钙蛋白酶抑制蛋白及CAST基因对肉品质及嫩度的影响[J]. 食品工业, 2013, 34(6): 141-144.
	LI J, GUO Y Y, REN T, et al. The affection of calpastatin and CAST gene to meat quality and tenderness[J]. The Food Industry, 2013, 34(6): 141-144.(in Chinese with English abstract)
[2]	ERNST C W, ROBIC A, YERLE M, et al. Mapping of calpastatin and three microsatellites to porcine chromosome 2q2·1-Q2·4[J]. Animal Genetics, 1998, 29(3): 212-215. DOI URL
[3]	MEYERS S N, RODRIGUEZ-ZAS S L, BEEVER J E. Fine-mapping of a QTL influencing pork tenderness on porcine chromosome 2[J]. BMC Genetics, 2007, 8: 69. DOI URL
[4]	PARR T, SENSKY P L, BARDSLEY R G, et al. Calpastatin expression in porcine cardiac and skeletal muscle and partial gene structure[J]. Archives of Biochemistry and Biophysics, 2001, 395(1): 1-13. DOI URL
[5]	PARR T, JEWELL K K, SENSKY P L, et al. Expression of calpastatin isoforms in muscle and functionality of multiple calpastatin promoters[J]. Archives of Biochemistry and Biophysics, 2004, 427(1): 8-15. DOI URL
[6]	CIOBANU D C, BASTIAANSEN J W M, LONERGAN S M, et al. New alleles in calpastatin gene are associated with meat quality traits in pigs1[J]. Journal of Animal Science, 2004, 82(10): 2829-2839. DOI URL
[7]	STALDER K J, ROTHSCHILD M F, LONERGAN S M. Associations between two gene markers and indicator traits affecting fresh and dry-cured ham processing quality[J]. Meat Science, 2005, 69(3): 451-457. DOI URL
[8]	RYBARCZYK A, KMIEC M, TERMAN A, et al. The effect of CAST and RYR1 polymorphisms on carcass and meat quality traits in Pietrain crossbred pigs[J]. Animal Science Papers and Reports, 2012, 30(3): 241-248.
[9]	URBAŃSKI P, PIERZCHAŁA M, TERMAN A, et al. The relationship between the polymorphism of the porcine CAST gene and productive traits in pigs[J]. Canadian Journal of Animal Science, 2015, 95(3): 361-367. DOI URL
[10]	张璐, 曹洪战, 芦春莲, 等. 4个猪种CAST基因与背膘厚关系的研究[J]. 黑龙江畜牧兽医, 2009(1): 8-9.
	ZHANG L, CAO H Z, LU C L, et al. Study on the correlation of the CAST gene and thickness of backfat in four types of pigs[J]. Heilongjiang Animal Science and Veterinary Medicine, 2009(1): 8-9.(in Chinese with English abstract)
[11]	孙立彬, 孟和, 王起山, 等. 猪2型钙蛋白酶抑制蛋白基因cDNA的克隆序列分析[J]. 上海交通大学学报(农业科学版), 2005, 23(3): 266-270.
	SUN L B, MENG H, WANG Q S, et al. Cloning and sequence analysis of cDNA encoding porcine calpastatin[J]. Journal of Shanghai Jiao Tong University (Agricultural Science), 2005, 23(3): 266-270.(in Chinese with English abstract)
[12]	ŠKRLEP M, ČANDEK-POTOKAR M, KAVAR T, et al. Association of PRKAG3 and CAST genetic polymorphisms with traits of interest in dry-cured ham production: comparative study in France, Slovenia and Spain[J]. Livestock Science, 2010, 128(1/2/3): 60-66. DOI URL
[13]	MEYERS S N, BEEVER J E. Investigating the genetic basis of pork tenderness: genomic analysis of porcine CAST[J]. Animal Genetics, 2008, 39(5): 531-543. DOI URL
[14]	杨晓慧, 刘源, 武英, 等. 猪钙蛋白酶抑制蛋白基因的多态性分析[J]. 中国畜牧杂志, 2006, 42(19): 8-9.
	YANG X H, LIU Y, WU Y, et al. Polymorphism analysis of pig calpastatin gene[J]. Chinese Journal of Animal Science, 2006, 42(19): 8-9. (in Chinese)
[15]	李朋, 尹雪, 张冬杰, 等. 新民猪和皮民猪CAST基因的多态性检测分析[J]. 黑龙江畜牧兽医, 2012(11): 56-58.
	LI P, YIN X, ZHANG D J, et al. Polymorphism detection and analysis of the CAST genes from new Min pigs and the F₁ generations of Pietrain×new Min pig[J]. Heilongjiang Animal Science and Veterinary Medicine, 2012(11): 56-58.(in Chinese with English abstract)
[16]	BUCHANAN F C, FITZSIMMONS C J, VAN KESSEL A G, et al. Association of a missense mutation in the bovine leptin gene with carcass fat content and leptin mRNA levels[J]. Genetics Selection Evolution, 2002, 34: 105. DOI URL
[17]	谭光辉, 覃媛钰, 李杰章, 等. 樱桃谷鸭ATF4基因SNPs筛查及生物信息学分析[J]. 浙江农业学报, 2020, 32(2): 218-225.
	TAN G H, QIN Y Y, LI J Z, et al. Single nucleotide polymorphism screening and bioinformatics analysis of ATF4 gene in Cherry Valley ducks[J]. Acta Agriculturae Zhejiangensis, 2020, 32(2): 218-225.(in Chinese with English abstract)
[18]	TAKANO E, MAKI M, MORI H, et al. Pig heart calpastatin: identification of repetitive domain structures and anomalous behavior in polyacrylamide gel electrophoresis[J]. Biochemistry, 1988, 27(6): 1964-1972. DOI URL
[19]	PONTREMOLI S, VIOTTI P L, MICHETTI M, et al. Modulation of inhibitory efficiency of rat skeletal muscle calpastatin by phosphorylation[J]. Biochemical and Biophysical Research Communications, 1992, 187(2): 751-759. DOI URL

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

RichHTML

PDF (PC)

Knowledge

Abstract

Cite this article

share this article

Figures/Tables 6

References 19

Related Articles 15

Recommended Articles

Metrics

Comments

[1]	YANG Chun, LIANG Sihui, WANG Anran, CHEN Juan, LI Yan, LIN Kaiqin, MI Xiaozeng, QIAO Dahe, CHEN Zhengwu, GUO Yan. Characteristic metabolite content and cold resistance of 54 tea germplasms [J]. Acta Agriculturae Zhejiangensis, 2025, 37(9): 1860-1871.
[2]	HUANG Weihong, LIU Yi, ZHENG Fuming. Inhibition mechanism of epigallocatechin gallate on glucoamylase [J]. Acta Agriculturae Zhejiangensis, 2025, 37(9): 1951-1957.
[3]	CONG Jianmin, HUANG Weijian, YIN Xinxing, LIU Jinping, ZHAO Yong. Effect of 5-azacytosine on somatic embryo-induced DNA methylation in Fraxinus mandschurica [J]. Acta Agriculturae Zhejiangensis, 2025, 37(8): 1648-1657.
[4]	ZHANG Ruonan, MEN Xiaoming, QIN Kaipeng, WANG Binbin, WU Jie, DING Xiangbin, XU Ziwei, QI Keke. Comparative study on growth performance, carcass quality, meat performance and profitability of different crossbreed combinations of Lvjiahei pigs [J]. Acta Agriculturae Zhejiangensis, 2025, 37(6): 1203-1211.
[5]	DI Yancui, JI Zelin, WANG Yuanyuan, LOU Shihao, ZHANG Tao, GUO Zhixin, SHEN Shunshan, PIAO Fengzhi, DU Nanshan, DONG Xiaoxing, DONG Han. Identification, subcellular localization and expression analysis of tomato SlMYB52 gene [J]. Acta Agriculturae Zhejiangensis, 2025, 37(4): 808-819.
[6]	LU Nanyang, ZHAO Tinglei, ZHOU Ying, YAO Yanlai, LI Penghao, HONG Chunlai, ZHU Weijing, HONG Leidong, ZHANG Tao, ZHU Fengxiang. Study on bioconversion process of gibberellin fermentation residue with fly maggots (Lucilia sericata) [J]. Acta Agriculturae Zhejiangensis, 2025, 37(4): 901-908.
[7]	FEI Junnan, WANG Binbin, MEN Xiaoming, XU Ziwei. Effect of different slaughter weights on carcass traits and meat flavor of ‘Lvjiahei’ pig [J]. Acta Agriculturae Zhejiangensis, 2025, 37(3): 559-567.
[8]	ZHAO Jiahao, XU Xing, ZHOU Weidong, YANG Hua, ZHAO Xihong, WANG Wen. Characteristics of bacteria community and antibiotic resistance genes in piggery wastewater and surrounding water environment [J]. Acta Agriculturae Zhejiangensis, 2025, 37(3): 621-632.
[9]	WANG Binbin, QI Keke, MEN Xiaoming, XU Ziwei. Application and perspect of genomic selection in pork quality breeding [J]. Acta Agriculturae Zhejiangensis, 2025, 37(3): 726-735.
[10]	ZHANG Meiying, MO Qian, QI Xiushuang, TONG Ningning, KONG Fan, LIU Zheng’an, LYU Changping, PENG Liping. Cloning and expression analysis of peony PoLPAT2 gene [J]. Acta Agriculturae Zhejiangensis, 2025, 37(2): 321-328.
[11]	JIANG Wenjun, SHU Hongsuo, CHEN Zhengman, REN Dianting, YANG Dang, TIAN Rongjiang, DU Zhaokui. Cloning, expression, and bioinformatics analysis of KoWRKY43 gene in Kandelia obovata [J]. Acta Agriculturae Zhejiangensis, 2024, 36(8): 1832-1843.
[12]	ZHU Yanyu, YU Wentao, GAO Shuilian, LYU Shuiyuan, WANG Pan, JIN Wanmin, GUI Wenjing, LIN Yi, YE Naixing. The diversity of tea germplasm resources and genetic relationship of ‘Tieguanyin’-derived varieties in Anxi, Fujian, China [J]. Acta Agriculturae Zhejiangensis, 2024, 36(7): 1591-1601.
[13]	XIANG Jin, WANG Chunyuan, WU Yan, TAN Yuancheng, YANG Suan, ZHANG Yiyu. CRISP3 gene SNP identification and its impact on reproductive traits in Kela pigs [J]. Acta Agriculturae Zhejiangensis, 2024, 36(6): 1270-1278.
[14]	MA Li’na, TIAN Jinyang, WANG Jin, ZHAO Zhengwei, MA Qing. Association of FGF5 and COQ9 gene polymorphism and growth traits in Tan sheep [J]. Acta Agriculturae Zhejiangensis, 2024, 36(5): 1015-1023.
[15]	LI Yaping, JIN Fulai, HUANG Zonggui, ZHANG Tao, DUAN Xiaojing, JIANG Wu, TAO Zhengming, CHEN Jiadong. Identification and expression pattern analysis of glycoside hydrolase GH3 gene family in Dendrobium officinale [J]. Acta Agriculturae Zhejiangensis, 2024, 36(4): 790-799.