Association between <i>PPAR-δ</i> gene SNPs, haplotypes and resistances to SGIV and RGNNV in the orange-spotted grouper, <i>Epinephelus coioides</i>

HUANG Jianling; YANG Zimin; WANG Yuxin; LI Xinshuai; LIU Cuiyu; CHEN Jinpeng; QIN Qiwei; YANG Min

doi:10.7671/j.issn.1001-411X.202203022

Journal of South China Agricultural University > 2023 > 44(3): 391-401. > DOI: 10.7671/j.issn.1001-411X.202203022

HUANG Jianling, YANG Zimin, WANG Yuxin, et al. Association between PPAR-δ gene SNPs, haplotypes and resistances to SGIV and RGNNV in the orange-spotted grouper, Epinephelus coioides[J]. Journal of South China Agricultural University, 2023, 44(3): 391-401. DOI: 10.7671/j.issn.1001-411X.202203022

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Association between PPAR-δ gene SNPs, haplotypes and resistances to SGIV and RGNNV in the orange-spotted grouper, Epinephelus coioides

Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation/ College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China

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Received Date: March 10, 2022
Available Online: May 17, 2023

Graphical Abstract

Abstract

Abstract

Objective
To obtain the disease-resistant molecular markers in grouper (Epinephelus spp.), and serve for the selective breeding program of disease-resistant grouper strains, so as to solve the problem of frequent occurrence of grouper disease.

Method
Single nucleotide polymorphisms (SNPs) were screened based on PPAR-δ genomic DNA sequence, and association analysis of resistance to Singapore grouper iridovirus (SGIV) and red-spotted grouper nervous necrosis virus (RGNNV) was performed on these SNPs.

Result
A total of nine SNPs were detected in the susceptible and resistant groups against SGIV infection, all of which were located in the introns, with the polymorphism information contents (PICs) ranging from 0.177−0.375. Among the SNPs, SNP-S1(g.940T>A) showed low degree polymorphism (PIC<0.25), while the rest SNPs showed moderate degree polymorphism(0.25≤PIC<0.50). The association analysis showed that the genotype frequencies of SNP-S7 (g.4595T>A) were significantly different between SGIV susceptible and resistant groups (P<0.05), the TT and AA homozygous genotypes of SNP-S7 were correlated with SGIV resistance traits, while the AT heterozygous genotypes were correlated with SGIV susceptibility traits. In addition, a total of eight SNPs were detected in the susceptible and resistant groups agasinst RGNNV infection, among which SNP-N1 was located in the exon, with a synonymous mutation, and the rest SNPs were located in the introns, with the PICs ranging from 0.106−0.317. Among the SNPs, SNP-N1 (g.324G>A) and SNP-N2 (g.883A>G) showed low degree polymorphism (PIC<0.25), while the rest SNPs showed moderate degree polymorphism (0.25≤PIC<0.50). The association analysis showed that SNP-N5 (g.2510C>T) genotype frequencies were significantly different between RGNNV susceptible and resistant groups (P<0.05), the CT genotype of SNP-N5 was correlated with RGNNV resistance traits and the CC genotype was correlated with RGNNV susceptibility traits.

Conclusion
In this study, we successfully screened one SNP marker related to SGIV resistance and one SNP marker related to RGNNV resistance from PPAR-δ genomic DNA sequence. This finding can offer a technical support and a theoretical basis for resistance breeding of grouper.
- Epinephelus spp.,
- Singapore grouper iridovirus,
- Red-spotted grouper nervous necrosis virus,
- SNP,
- PPAR-δ gene

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References (31)

References

[1]	罗鸣, 陈傅晓, 刘龙龙, 等. 我国石斑鱼养殖疾病的研究进展[J]. 水产科学, 2013, 32(9): 549-554. doi: 10.3969/j.issn.1003-1111.2013.09.010
[2]	QIN Q W, CHANG S F, NGOH-LIM G H, et al. Characterization of a novel ranavirus isolated from grouper Epinephelus tauvina[J]. Diseases of Aquatic Organisms, 2003, 53(1): 1-9.
[3]	COSTA J Z, THOMPSON K D. Understanding the interaction between Betanodavirus and its host for the development of prophylactic measures for viral encephalopathy and retinopathy[J]. Fish and Shellfish Immunology, 2016, 53: 35-49. doi: 10.1016/j.fsi.2016.03.033
[4]	黄剑南, 郭志勋, 冯娟, 等. 鱼类诺达病毒及其所导致的疾病[J]. 水产学报, 2006, 30(6): 831-836.
[5]	VIGNAL A, MILAN D, SANCRISTOBAL M, et al. A review on SNP and other types of molecular markers and their use in animal genetics[J]. Genetics Selection Evolution, 2002, 34(3): 275-305. doi: 10.1186/1297-9686-34-3-275
[6]	高焕, 赖晓芳, 孟宪红, 等. 中国明对虾抗菌肽基因应答WSSV侵染的表达及其SNP分析[J]. 中国水产科学, 2011, 18(3): 646-653.
[7]	BAO Y, LI L, ZHANG G. Polymorphism of the superoxide dismutase gene family in the bay scallop (Argopecten irradians) and its association with resistance/susceptibility to Vibrio anguillarum[J]. Developmental and Comparative Immunology, 2010, 34(5): 553-561. doi: 10.1016/j.dci.2009.12.016
[8]	FU G H, BAI Z Y, XIA J H, et al. Characterization of the LECT2 gene and its associations with resistance to the big belly disease in Asian seabass[J]. Fish and Shellfish Immunology, 2014, 37(1): 131-138. doi: 10.1016/j.fsi.2014.01.019
[9]	DUNN S E, BHAT R, STRAUS D S, et al. Peroxisome proliferator-activated receptor delta limits the expansion of pathogenic Th cells during central nervous system autoimmunity[J]. Journal of Experimental Medicine, 2010, 207(8): 1599-1608. doi: 10.1084/jem.20091663
[10]	SUN L, SHI Y, WANG G, et al. PPAR-delta modulates membrane cholesterol and cytokine signaling in malignant B cells[J]. Leukemia, 2018, 32(1): 184-193. doi: 10.1038/leu.2017.162
[11]	NEEL J G, GRIMALDI P A. Physiological functions of peroxisome proliferator-activated receptor beta[J]. Physiological Reviews, 2014, 94(3): 795-858. doi: 10.1152/physrev.00027.2013
[12]	JI J D, KIM H J, RHO Y H, et al. Inhibition of IL-10-induced STAT3 activation by 15-deoxy-Delta12, 14-prostaglandin J2[J]. Rheumatology, 2005, 44(8): 983-988. doi: 10.1093/rheumatology/keh657
[13]	WANG Y, YU Y, WANG Q, et al. PPAR-δ of orange-spotted grouper exerts antiviral activity against fish virus and regulates interferon signaling and inflammatory factors[J]. Fish & Shellfish Immunology, 2019, 94: 38-49.
[14]	HUANG X, HAUNG Y, SUN J, et al. Characterization of two grouper Epinephelus akaara cell lines: Application to studies of Singapore grouper iridovirus (SGIV) propagation and virus-host interaction[J]. Aquaculture, 2009, 292(3/4): 172-179.
[15]	YANG M, WEI J, LI P, et al. MHC polymorphism and disease resistance to Singapore grouper iridovirus (SGIV) in the orange-spotted grouper, Epinephelus coioides[J]. Science Bulletin, 2016, 61(9): 693-699. doi: 10.1007/s11434-016-1055-5
[16]	YANG M, WANG Q, CHEN J, et al. Identification of candidate SNPs and genes associated with anti-RGNNV using GWAS in the red-spotted grouper, Epinephelus akaara[J]. Fish & Shellfish Immunology, 2021, 112: 31-37.
[17]	NORTON N, WILLIAMS N M, WILLIAMS H J, et al. Universal, robust, highly quantitative SNP allele frequency measurement in DNA pools[J]. Human Genetics, 2002, 110(5): 471-478. doi: 10.1007/s00439-002-0706-6
[18]	PARENTEAU J, ABOU ELELA S. Introns: Good day junk is bad day treasure[J]. Trends in Genetics, 2019, 35(12): 923-934. doi: 10.1016/j.tig.2019.09.010
[19]	SHAUL O. How introns enhance gene expression[J]. International Journal of Biochemistry & Cell Biology, 2017, 91: 145-155.
[20]	BOTSTEIN D, WHITE R L, SKOLNICK M, et al. Construction of a genetic linkage map in man using restriction fragment length polymorphisms[J]. American Journal of Human Genetics, 1980, 32(3): 314-331.
[21]	HUBERT S, BUSSEY J T, HIGGINS B, et al. Development of single nucleotide polymorphism markers for Atlantic cod (Gadus morhua) using expressed sequences[J]. Aquaculture, 2009, 296(1/2): 7-14.
[22]	周欣, 高风英, 卢迈新. 鱼类抗病育种研究进展[J]. 大连海洋大学学报, 2021, 36(3): 510-523. doi: 10.16535/j.cnki.dlhyxb.2020-156
[23]	WAN Q Y, SU J G, CHEN X H, et al. Genomic sequence comparison, promoter activity, SNP detection of RIG-I gene and association with resistance / susceptibility to grass carp reovirus in grass carp (Ctenopharyngodon idella)[J]. Developmental & Comparative Immunology, 2013, 39(4): 333-342.
[24]	HENG J F, SU J G, HUANG T, et al. The polymorphism and haplotype of TLR3 gene in grass carp (Ctenopharyngodon idella) and their associations with susceptibility / resistance to grass carp reovirus[J]. Fish & Shellfish Immunology, 2011, 30(1): 45-50.
[25]	SHEN Y B, ZHANG J B, XU X Y, et al. A new haplotype variability in complement C6 is marginally associated with resistance to Aeromonas hydrophila in grass carp[J]. Fish & Shellfish Immunology, 2013, 34(5): 1360-1365.
[26]	高风英, 卢迈新, 曹建萌, 等. 尼罗罗非鱼 NOD1 基因 SNP 位点和单倍型与抗无乳链球菌感染的关联分析[J]. 农业生物技术学报, 2018, 26(11): 1949-1961.
[27]	FU G H, LIU F, XIA J H, et al. The LBP gene and its association with resistance to Aeromonas hydrophila in tilapia[J]. International Journal of Molecular Sciences, 2014, 15(12): 22028-22041. doi: 10.3390/ijms151222028
[28]	FU G H, WAN Z Y, XIA J H, et al. The MCP-8 gene and its possible association with resistance to Streptococcus agalactiae in tilapia[J]. Fish & Shellfish Immunology, 2014, 40(1): 331-336.
[29]	LATRUFFE N, VAMECQ J. Peroxisome proliferators and peroxisome proliferator activated receptors (PPARs) as regulators of lipid metabolism[J]. Biochimie, 1997, 79(2/3): 81-94.
[30]	纪永吉. 牦牛PPARα、PPARγ、PPARδ基因的多态性与生长性状相关性研究[D]. 兰州: 甘肃农业大学, 2016.
[31]	丁克越. 不同单倍型块定义在单倍型块结构推断与htSNPs选择中的效应[D]. 北京: 中国协和医科大学, 2004.

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Association between PPAR-δ gene SNPs, haplotypes and resistances to SGIV and RGNNV in the orange-spotted grouper, Epinephelus coioides

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