bHLH genes polymorphisms and their association with growth traits in the Pacific oyster <i>Crassostrea gigas</i> -- Journal of Oceanology and Limnology,2020,38(3):862-868

	Cite this paper:
	CHEN Na, LI Li, LI Chenghua, LIN Zhihua, MENG Jie, LIU Sheng, SONG Kai, BAO Yongbo. bHLH genes polymorphisms and their association with growth traits in the Pacific oyster Crassostrea gigas[J]. Journal of Oceanology and Limnology, 2020, 38(3): 862-868

bHLH genes polymorphisms and their association with growth traits in the Pacific oyster Crassostrea gigas

CHEN Na^1,2, LI Li³, LI Chenghua², LIN Zhihua¹, MENG Jie³, LIU Sheng³, SONG Kai³, BAO Yongbo¹

1 Zhejiang Key Laboratory of Aquatic Germplasm Resources, College of Biological & Environmental Sciences, Zhejiang Wanli University, Ningbo 315121, China;
2 School of Marine Sciences, Ningbo University, Ningbo 315211, China;
3 Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China

Abstract:

The basic helix-loop-helix (bHLH) genes encode a large superfamily of transcription factors in the Pacific oyster (Crassostrea gigas), and play a very important role in regulation of growth and development. To investigate the oyster growth traits and the associations with bHLH genes variations, we analyzed the gene polymorphisms-traits association in a wild population, and confirmed the results in another independent wild population by targeted gene re-sequencing and SNPshot analysis. After screening the single nucleotide polymorphisms (SNPs) in three candidate genes of the bHLH family (88 bHLH genes in two wild oyster populations in total), we identified the allele CgLoblHLH4-T/G located in the exon of the CgLoblHLH4 gene. This allele is a non-synonymous mutation (Phe/Leu) with an extremely significant association with shell width (P<0.01) and allele G is beneficial to shell width. This SNP on the CgLoblHLH4 gene might have a potential value as a genetic marker of growth traits that could be used in breeding in C. gigas in the future.

Key words: Crassostrea gigas|basic helix-loop-helix (bHLH)|re-sequencing|single nucleotide polymorphism (SNP) shot|growth traits

Received: 2019-03-16 Revised: 2019-07-02

Tools

PDF (424 KB) Free

Print this page

Add to favorites

Email this article to others

Authors

Articles by CHEN Na

Articles by LI Li

Articles by LI Chenghua

Articles by LIN Zhihua

Articles by MENG Jie

Articles by LIU Sheng

Articles by SONG Kai

Articles by BAO Yongbo

References:
Atchley W R, Fitch W M. 1997. A natural classification of the basic helix-loop-helix class of transcription factors.Proceedings of the National Academy of Sciences of the United States of America, 94(10):5 172-5 176, https://doi.org/10.1073/pnas.94.10.5172.
Bao Y B, Xu F, Shimeld S M. 2017. Phylogenetics of lophotrochozoan bHLH genes and the evolution of lineage-specific gene duplicates. Genome Biology and Evolution, 9(4):869-886, https://doi.org/10.1093/gbe/evx047.
Cong R H, Kong L F, Yu H, Li Q. 2014. Association between polymorphism in the insulin receptor -related receptor gene and growth traits in the Pacific oyster Crassostrea gigas. Biochemical Systematics and Ecology, 54:144-149, https://doi.org/10.1016/j.bse.2014.02.003.
Fournier-Level A, Korte A, Cooper M D, Nordborg M, Schmitt J, Wilczek A M. 2011. A map of local adaptation in Arabidopsis thaliana. Science, 334(6052):86-89, https://doi.org/10.1126/science.1209271.
Gaut B. 2012. Arabidopsis thaliana as a model for the genetics of local adaptation. Nature Genetics, 44(2):115-116, https://doi.org/10.1038/ng.1079.
Guo H H, Bao Z M, Li J Q, Lian S S, Wnag S, He Y, Fu X T, Zhang L L, Hu X L. 2012. Molecular characterization of TGF-β type I receptor gene (Tgfbr1) in Chlamys farreri, and the association of allelic variants with growth traits.PLoS One, 7(11):e51005, https://doi.org/10.1371/journal.pone.0051005.
Guo S X, Hu Y H, Ding Y S, Liu J M, Zhang M, Ma R L, Guo H, Wang K, He J, Yan Y Z, Rui D S, Sun F, Mu L T, Niu Q, Zhang J Y, Li S G. 2015. Association between eight functional polymorphisms and haplotypes in the cholesterol ester transfer protein (CETP) gene and dyslipidemia in national minority adults in the far west region of China. International Journal of Environmental Research and Public Health, 12(12):15 979-15 992, https://doi.org/10.3390/ijerph121215036.
Guo X M. 2009. Use and exchange of genetic resources in molluscan aquaculture. Reviews in Aquaculture, 1(3-4):251-259, https://doi.org/10.1111/j.1753-5131.2009.01014.x.
Huvet A, Jeffroy F, Fabioux C, Daniel J Y, Quillien V, Van Wormhoudt A, Moal J, Samain J F, Boudry P, Pouvreau S. 2008. Association among growth, food consumptionrelated traits and amylase gene polymorphism in the Pacific oyster Crassostrea gigas. Animal Genetics, 39(6):662-665, https://doi.org/10.1111/j.1365-2052.2008.01776.x.
Lai X S, Zhang C G, Wang J, Wang C, Lan X Y, Lei C Z, Chen H. 2013. Developmental expression patterns and association study with growth traits of bovine Bhlhe40 gene. Molecular Biology, 47(5):674-680, https://doi.org/10.1134/s0026893313050105.
Ledent V, Vervoort M. 2001. The basic helix-loop-helix protein family:comparative genomics and phylogenetic analysis. Genome Research, 11(5):754-770, https://doi.org/10.1101/gr.177001.
Li H, Durbin R. 2009. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25(14):1 754-1 760, https://doi.org/10.1093/bioinformatics/btp324.
Li L, Li A, Song K, Meng J, Guo X M, Li S M, Li C Y, De Wit P, Que H Y, Wu F C, Wang W, Qi H G, Xu F, Cong R H, Huang B Y, Li Y X, Wang T, Tanh X Y, Liu S, Li B S, Shi R H, Liu Y L, Bu C, Zhang C, He W M, Zhao S C, Li H J, Zhang S D, Zhang L L, Zhang G F. 2018. Divergence and plasticity shape adaptive potential of the Pacific oyster.Nature Ecology & Evolution, 2(11):1 751-1 760, https://doi.org/10.1038/s41559-018-0668-2.
Liu M, Peng J, Xu D Q, Zheng R, Li F E, Li J L, Zuo B, Lei M G, Xiong Y Z, Deng C Y, Jiang S W. 2008. Association of MYF5 and MYOD1 gene polymorphisms and meat quality traits in large white×meishan F2 pig populations.Biochemical Genetics, 46(11-12):720-732, https://doi.org/10.1007/s10528-008-9187-1.
Lo Presti R, Lisa C, Di Stasio L. 2010. Molecular genetics in aquaculture. Italian Journal of Animal Science, 8(3):299-313, https://doi.org/10.4081/ijas.2009.299.
McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo M A. 2010. The genome analysis toolkit:a mapreduce framework for analyzing next-generation DNA sequencing data. Genome Research, 20(9):1 297-1 303, https://doi.org/10.1101/gr.107524.110.
Morin P A, Luikart G, Wayne R K, the SNP Workshop Group. 2004. SNPs in ecology, evolution and conservation.Trends in Ecology & Evolution, 19(4):208-216, https://doi.org/10.1016/j.tree.2004.01.009.
Park Y J, Lee J K, Kim N S. 2009. Simple sequence repeat polymorphisms (SSRPs) for evaluation of molecular diversity and germplasm classification of minor crops.Molecules, 14(11):4 546-4 569, https://doi.org/10.3390/molecules14114546.
Prudence M, Moal J, Boudry P, Daniel J Y, Quéré C, Jeffroy F, Mingant C, Ropert M, Bédier E, Van Wormhoudt A, Samain J F, Huvet A. 2006. An amylase gene polymorphism is associated with growth differences in the Pacific cupped oyster Crassostrea gigas. Animal Genetics, 37(4):348-351, https://doi.org/10.1111/j.1365-2052.2006.01481.x.
Qi H G, Song K, Li C Y, Wang W, Li B S, Li L, Zhang G F. 2017. Construction and evaluation of a high-density SNP array for the Pacific oyster (Crassostrea gigas). PLoS One, 12(3):e0174007, https://doi.org/10.1371/journal.pone.0174007.
She Z C, Li L, Qi H G, Song K, Que H Y, Zhang G F. 2015.Candidate gene polymorphisms and their association with glycogen content in the pacific oyster Crassostrea gigas.PLoS One, 10(5):e0124401, https://doi.org/10.1371/journal.pone.0124401.
Wang J F, Qi H G, Li L, Que H Y, Wang D, Zhang G F. 2014.Discovery and validation of genic single nucleotide polymorphisms in the Pacific oyster Crassostrea gigas.Molecular Ecology Resources, 15(1):123-135, https://doi.org/10.1111/1755-0998.12278.
Wu Y, Pi J S, Pan A L, Pu Y J, Du J P, Shen J, Liang Z H, Zhang J R. 2012. An SNP in the MyoD1 gene intron 2 associated with growth and carcass traits in three duck populations.Biochemical Genetics, 50(11-12):898-907, https://doi.org/10.1007/s10528-012-9530-4.
Xue M, Zan L S, Gao L, Wang H B. 2011. A novel polymorphism of the myogenin gene is associated with body measurement traits in native Chinese breeds. Genetics & Molecular Research, 10(4):2 721-2 728, https://doi.org/10.4238/2011.November.4.6.
Zhang G F, Fang X D, Guo X M, Li L, Luo R B, Xu F, Yang P C, Zhang L L, Wang X T, Qi H G, Xiong Z Q, Que H Y, Xie Y L, Holland P W H, Paps J, Zhu Y P, Wu F C, Chen Y X, Wang J F, Peng C F, Meng J, Yang L, Liu J, Wen B, Zhang N, Huang Z Y, Zhu Q H, Feng Y, Mount A, Hedgecock D, Xu Z, Liu Y J, Domazet-Lošo T, Du Y S, Sun X Q, Zhang S D, Liu B H, Cheng P Z, Jiang X T, Li J, Fan D D, Wang W, Fu W J, Wang T, Wang B, Zhang J B, Peng Z Y, Li Y, Li N, Wang J P, Chen M S, He Y, Tan F J, Song X R, Zheng Q M, Huang R L, Yang H L, Du X D, Chen L, Yang M, Gaffney P M, Wang S, Luo L H, She Z C, Ming Y, Huang W, Zhang S, Huang B Y, Zhang Y, Qu T, Ni P X, Miao G Y, Wang J Y, Wang Q, Steinberg C E W, Wang H Y, Li N, Qian L M, Zhang G J, Li Y R, Yang H M, Liu X, Wang J, Yin Y, Wang J. 2012. The oyster genome reveals stress adaptation and complexity of shell formation. Nature, 490(7418):49-54, https://doi.org/10.1038/nature11413.
Zhong X X, Li Q, Yu H, Kong L F. 2013. Development and Validation of single-nucleotide polymorphism markers in the pacific oyster, Crassostrea gigas, using high-resolution melting analysis. Journal of the World Aquaculture Society, 44(3):455-465, https://doi.org/10.1111/jwas.12044.