Single nucleotide polymorphism screening and bioinformatics analysis of ATF4 gene in Cherry Valley ducks

doi:10.3969/j.issn.1004-1524.2020.02.05

›› 2020, Vol. 32 ›› Issue (2): 218-225.DOI: 10.3969/j.issn.1004-1524.2020.02.05

• Animal Science • Previous Articles Next Articles

Single nucleotide polymorphism screening and bioinformatics analysis of ATF4 gene in Cherry Valley ducks

TAN Guanghui, QIN Yuanyu, LI Jiezhang, WU Lei, YUE Yong, ZHANG Yiyu^*

Key Laboratory of Plateau and Mountain Animal Genetics and Breeding, Ministry of Education, College of Animal Science, Guizhou University, Guiyang 550025, China

Received:2019-08-30 Online:2020-02-25 Published:2020-03-13

Abstract

Abstract: To screen out the mutant individuals of activating transcription factor 4 (ATF4) gene in Cherry Valley duck population and breed excellent poultry breeds with good egg shell quality, a DNA mixing pool was constructed with Cherry Valley duck as the test object. The ATF4 gene coding sequence was obtained by common PCR fragmentation amplification and screening. single nucleotide polymorphism sites (SNPs) and bioinformatics analysis were examined. The results showed that the coding region of ATF4 gene of Cherry Valley duck was 1 065 bp in length, encoding 354 amino acids. The protein was unstable and soluble. There were no signal peptide but two N-glycosylation sites. Four SNPs were screened in the CDS region of ATF4 gene, namely A⁹⁰⁹G, G⁶³⁶A, G⁸¹³A and T⁸⁶⁷A, except that T⁸⁶⁷A was a missense mutation. All of them were synonymous mutations. Four SNPs caused changes in the secondary structure and free energy of RNA and gene frequency. The primary components of the secondary and tertiary structures of proteins were α-helix, random curl and extended chain. After T⁸⁶⁷A mutation, the secondary and tertiary structures of proteins had all changed, and the contents of α-helix, extended chain and β-fold had all increased, while the contents of random curl had decreased. In conclusion, ATF4 gene of Cherry Valley duck had abundant polymorphism, which provided a theoretical basis for molecular marker-assisted selection to improve the egg shell quality of Cherry Valley duck.

Key words: Cherry Valley ducks, ATF4 gene, SNPs, bioinformatics

CLC Number:

S834

TAN Guanghui, QIN Yuanyu, LI Jiezhang, WU Lei, YUE Yong, ZHANG Yiyu. Single nucleotide polymorphism screening and bioinformatics analysis of ATF4 gene in Cherry Valley ducks[J]. , 2020, 32(2): 218-225.

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Single nucleotide polymorphism screening and bioinformatics analysis of ATF4 gene in Cherry Valley ducks

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