SNPs Identification of ITPR1 Gene and Its Correlation with Eggshell Quality Traits in Sansui Ducks (Anas platyrhyncha domestica)
LI Jie-Zhang, TAN Guang-Hui, WU Lei, QIN Yuan-Yu, ZHANG Yi-Yu*
Key Laboratory of Genetics, Breeding and Reproduction of Plateau Mountain Animals, Ministry of Education/College of Animal Science, Guizhou University, Guiyang 550025, China
Abstract：Inositol 1,4,5-trisphosphate receptor 1 (ITPR1) is intracellular Ca2+ release channel protein, and could influence the mineralization and quality of eggshell in poultry by regulating the transport and release of calcium ions in the eggshell gland. In this study, the PCR product direct sequencing method and sequence alignment technology were used to identify the ITPR1 genetic variation sites of 186 Sansui duck (Anas platyrhyncha domestica), and the correlation between SNP mutation sites and eggshell quality was analyzed. The results showed that a total of 14 mutation sites were detected in the main functional domain and some introns of Sansui duck ITPR1 gene. There were 5 mutant sites, g.46455T>C, g.46459C>A, g.46564A>G, g.46581A>T, g.46649T>G, detected in the 8th intron. There were 6 mutant sites, g.55537A>G, g.55610T>C, g.55620G>T, g.55664A>G, g.55680C>T, g.55709T>G, detected in the 15th intron. There were 2 mutant sites, g.72601T>G and g.72843A>G, detected in the 30th intron. There was a synonymous mutation site g.124036C>T detected in the 42nd exon. All of the 14 mutation sites produced 3 genotypes, all of which were moderately polymorphic. The chi-square fitness test results showed that the genotype distribution of 14 mutation sites were consistent with the Hardy-Weinberg equilibrium (P>0.05). Based on linkage unbalance analysis,there were strong linkage imbalance between each two sites of g.46455T>C, g.46459C>A, g.46564A>G, g.46581A>T and g.46649T>G. There were strong linkage imbalance between each two sites of g.46581A>T, g.55537A>G, g.55620G>T, g.55664A>G, g.55680C>T and g.55709T>G. There was also strong linkage imbalance between g.72601T>G and g.72843A>G. A total of 13 kinds of haplotypes were found in 14 SNPs, of which H2 (CAGTGACTGTGGGC) was dominant haplotype with a frequency of 0.131, and H11 (TCAATGCGAC) was an inferior haplotype with a frequency of 0.060. The correlation analysis showed that 13 SNPs had significant correlation with eggshell thickness of Sansui duck except g.72843A>G site; Only g.46581A>T site had significant correlation with egg shape index (P<0.05); Except g.55610TC, g.55664AG, g.72601TG and g.72843AG, the other 10 sites had significant correlation on egg weight (P<0.05); g.46459C>A, g.55664A>G and g.124036C>T sites were significantly associated with eggshell weight (P<0.05); Except g.124036C>T site, the other 13 sites were significantly correlated with eggshell strength (P<0.05). In conclusion, the DNA sequence of the main functional domain of ITPR1 gene in the Sansui duck was relatively conservative, while intron genetic variation was abundant. Moreover, the 14 SNPs found in this study were significantly correlated with at least 2 eggshell quality indexes, indicating that the genetic variation of ITPR1 gene might affect eggshell quality and could be used as a genetic marker for the selection of eggshell quality of ducks.
1 覃媛钰, 张依裕, 罗华伦, 等. 2019. SFRP5基因遗传变异对长顺绿壳蛋鸡胸肌肌肉品质的影响[J]. 农业生物技术学报, 27(04): 703-711. (Qin Y Y, Zhang Y Y, Luo H L, et al.2019. Effect of genetic variation of SFRP5 gene on breast muscle quality of changshun blue-eggshell chicken (Gallus gallus domesticus)[J]. Journal of Agricultural Biotechnology, 27(04): 703-711.) 2 文禹粱, 王翔宇, 郭晓飞, 等. 2019. 不同产羔数小尾寒羊BMP4基因表达及其错义突变与产羔数关联分析[J]. 农业生物技术学报, 27(01): 80-88. (Wen Y L, Wang X Y, Guo X X, et al.2019. BMP4 gene expression in Small Tail Han sheep (Ovis aries) with different litter size and association analysis between its missense mutation and litter size[J]. Journal of Agricultural Biotechnology, 27(01): 80-88.) 3 赵宪林, 曹少杰, 王俊全, 等. 2018. MC4R基因多态性及基因型组合与藏羊生长性状的关联分析[J]. 农业生物技术学报, 26(3): 429-436. (Zhao X L, Cao S J, Wang J Q, et al.2018. Correlation analysis of polymorphism and genotype combination of MC4R gene and growth traits of Tibetan sheep (Ovis aries)[J]. Journal of Agricultural Biotechnology, 26(3): 429-436.) 4 Arias J, Mann K, Nys Y, et al.2008. Eggshell growth and matrix macromolecules[M]. Handbook of Biomineralization: Biological Aspects and Structure Formation,Wiley‐VCH Verlag GmbH, pp. 309-327. 5 Berridge M J, Taylor C W.1993. Inositol trisphosphate and calcium signaling[J]. Nature, 361(6410): 315-325. 6 Beauchamp N J, Daly M E, Makris M, et al.1998. A novel mutation in intron K of the PROS1 gene causes aberrant RNA splicing and is a common cause of protein S deficiency in a UK thrombophilia cohort[J]. Thromb Haemost, 79(6): 1086-1091. 7 Carrasco M A, Jaimovich E, Kemmerling U, et al.2004. Signal transduction and gene expression regulated by calcium release from internal stores in excitable cells[J]. Biological Research, 37(4): 701-712. 8 Choi J Y, Hwang C Y, Lee B, et al.2016. Age-associated repression of type 1 inositol 1, 4, 5-triphosphate receptor impairs muscle regeneration[J]. Aging, 8(9): 2062-2076. 9 Chang K C.2000. Critical regulatory domains in intron 2 of a porcine sarcomeric myosin heavy chain gene[J]. Journal of Muscle Research & Cell Motility, 21(5): 451-461. 10 Carneiro M, Hu D, Archer J, et al.2017. Dwarfism and altered craniofacial development in rabbits is caused by a 12.1 kb deletion at the HMGA2 locus[J]. Genetics, 205(2): 955-965. 11 Choi J Y, Jang H J, Park J W, et al.2018.Characterization of gene expression and genetic variation of horse ERBB receptor feedback inhibitor 1 in Thoroughbreds[J]. Asian-Australasian Journal of Animal Sciences, 31(3): 309-315. 12 Duan Z, Chen S, Sun C, et al.2015. Polymorphisms in ion transport genes are associated with eggshell mechanical property[J]. PLOS ONE, 10(6): e0130160. 13 Hamilton R, Hollands K, Voisey P, et al.1979. Relationship between egg shell quality and shell breakage and factors that affect shell breakage in the field-A review[J]. Worlds Poultry Science Journal, 35(3): 177-190. 14 Hir H L, Nott A, Moore M J.2003. How introns influence and enhance eukaryotic gene expression[J]. Trends in Biochemical Sciences, 28(4): 215-220. 15 Hirschey M D, Shimazu T, Goetzman E, et al.2010. SIRT3regulates mitochondrial fatty-acid oxidation by reversible enzyme deacetylation[J]. Nature, 464(7285): 121-125. 16 Huang L, Chardon J W, Carter M T, et al.2012. Missense mutations in ITPR1 cause autosomal dominant congenital nonprogressive spinocerebellar ataxia[J]. Orphanet Journal of Rare Diseases, 7(1): 1150-1172. 17 Jonchère V, Brionne A, Gautron J, et al.2012. Identification of uterine ion transporters for mineralisation precursors of the avian eggshell[J]. BMC Physiology, 12(1): 1472-6793. 18 Komar A A.2007. Silent SNPs: Impact on gene function and phenotype[J]. Pharmacogenomics, 8(8): 1075-1080. 19 Mikoshiba K.2007. IP3 receptor/Ca2+ channel: From discovery to new signaling concepts[J]. Journal of neurochemistry, 102(5): 1426-1446. 20 Moura G R, Pinheiro M, Freitas A, et al.2011. Species-specific codon context rules unveil non-neu-trality effects of synonymous mutations[J]. PLOS ONE, 6(10): e26817. 21 Maxwell T.2012. The eggshell: Structure, composition and mineralization[J]. Frontiers in Bioscience, 17(1): 1266-1280. 22 Narayanan D, Adebiyi A, Jaggar J H.2012. Inositol trisphosphate receptors in smooth muscle cells[J]. American Journal of Physiology-Heart and Circulatory Physiology, 302(11): H2190-H2210. 23 Nys Y, Guyot N.2011. Improving the safety and quality of eggs and egg products, Volume: Egg Chemistry, Production and Consumption[M]. Cambridge: Woodhead Publishing, pp. 83-132. 24 Nys Y, Gautron J, Garcia-Ruiz J M, et al.2004. Avian eggshell mineralization: Biochemical and functional characterization of matrix proteins[J]. Comptes Rendus-Palevol, 3(6-7): 560-562. 25 Rodriguez-Navarro A, Yebra A, Nys Y, et al.2007. Analysis of avian eggshell microstructure using X-ray area detectors[J]. European Journal of Mineralogy, 19(3): 391-398. 26 Parolin Schnekenberg R, Perkins E M, Miller J W, et al.2015. De novo point mutations in patients diagnosed with ataxic cerebral palsy[J]. Brain, 138(7): 1817-1832. 27 Soulsby M D, Wojcikiewicz R J.2005. The type Ⅲ inositol 1,4,5-trisphosphate receptor is phosphorylated by cAMP-dependent protein kinase at three sites[J]. Biochemical Journal, 392(3): 493-497. 28 Sauna Z E, Kinchi-Sarfaty C.2011. Understanding the contribution of synonymous mutations to human disease[J]. Nature Reviews Genetics, 12(10): 683-691. 29 Supek F, Minana B, Valcaler J, et al.2014. Synonymous mutations frequently act as driver mutations in human cancers[J]. Cell, 156(6): 1324-1335. 30 Sasaki M, Ohba C, Iai M, et al.2015. Sporadic infantile-onset spinocerebellar ataxia caused by missense mutations of the inositol 1,4,5-triphosphate receptor type 1 gene[J]. Journal of Neurology, 262(5): 1278-1284. 31 Santos C P, Aguiar A F, Giometti I C, et al.2018. High final energy of gallium arsenide laser increases MyoD gene expression during the intermediate phase of muscle regeneration after cryoinjury in rats[J]. Lasers in Medical Science, 33(4): 1-8. 32 Verkhratsky A.2004. Endoplasmic reticulum calcium signaling in nerve cells[J]. Biological Research, 37(4): 693-699. 33 Wu L J, Zhuo M.2009. Targeting the NMDA receptor subunit NR2B for the treatment of neuropathic pain[J]. Neurotherapeutics, 6(4): 693-702. 34 Weqierski T, Kuznicki J.2018. Neuronal calcium signaling via store-operated channels in health and disease[J]. Cell Calcium, 74(9): 102-111. 35 Wang J, Cui K, Yang Z, et al.2019. Transcriptome analysis of improved wool production in skin-specific transgenic sheep overexpressing ovine β-catenin[J]. International Journal of Molecular Sciences, 20(3): 620-622. 36 Xiang G H, Ren J L, Hal T, et al.2018. Editing porcine IGF2 regulatory element improved meat production in Chinese Bama pigs[J]. Cellular and Molecular Life Sciences, 75(24): 4619-4628. 37 Zhuo M.2009. Plasticity of NMDA receptor NR2B subunit in memory and chronic pain[J]. Molecular Brain, 2(4): 410-414.
