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. 2022 Feb 16;23(1):138.
doi: 10.1186/s12864-022-08362-6.

Genetic effect of an InDel in the promoter region of the NUDT15 and its effect on myoblast proliferation in chickens

Chengjie Wei #  1   2 , Yufang Niu #  1   2 , Bingjie Chen  1   2 , Panpan Qin  1   2 , Yanxing Wang  1   2 , Dan Hou  1   2 , Tong Li  1   2 , Ruiting Li  1   2 , Chunxiu Wang  1   2 , Huadong Yin  3 , Ruili Han  1   2 , Huifen Xu  1   2 , Yadong Tian  1   2 , Xiaojun Liu  1   2 , Xiangtao Kang  1   2 , Zhuanjian Li  4   5
Affiliations

Genetic effect of an InDel in the promoter region of the NUDT15 and its effect on myoblast proliferation in chickens

Chengjie Wei et al. BMC Genomics. .

Abstract

Background: Molecular breeding accelerates the speed of animal breeding. Screening molecular markers that can affect economic traits through genome-wide association studies (GWAS) can provide a theoretical basis for molecular breeding. At present, a large number of molecular markers have been screened in poultry research, but few reports on how molecular markers affect economic traits exist. It is particularly important to reveal the action mechanisms of molecular markers, which can provide more accurate information for molecular breeding.

Results: The aim of this study was to investigate the relationships between two indels (NUDT15-indel-2777 and NUDT15-indel-1673) in the promoter region of NUDT15 and growth and carcass traits in chickens and to explore the regulatory mechanism of NUDT15. Significant differences were found in genotype and allele frequencies among commercial broilers, commercial laying hens and dual-purpose chickens. The results of association analyses showed that these two indel loci could significantly affect growth traits, such as body weight, and carcass traits. Tissue expression profiling at E12 showed that the expression of NUDT15 was significantly higher in skeletal muscle, and time-expression profiling of leg muscle showed that the expression of NUDT15 in myoblasts was significantly higher in the E10 and E12 proliferation stages than in other stages. Promoter activity analysis showed that pro-1673-I and pro-1673-D significantly inhibited promoter activity, and the promoter activity of pro-1673-D was significantly lower than that of pro-1673-I. In addition, when NUDT15 was overexpressed or underwent interference in chicken primary myoblasts (CPMs), NUDT15 could inhibit the proliferation of CPMs.

Conclusion: The results suggest that the studied indels in the promoter region of NUDT15 may regulate the proliferation of CPMs by affecting NUDT15 expression, ultimately affecting the growth and carcass traits of chickens. These indel polymorphisms may be used together as molecular markers for improving economic traits in chickens.

Keywords: Cell proliferation; Indel; Muscle; NUDT15; Primary myoblast; Promoter.

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Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Fig. 1
Fig. 1
The relative position of two mutation sites. The two indel mutations of 23 bp in the promoter region of the NUDT15 gene, which were located 2777 bp and 1673 bp from the ATG and thus named NUDT15-indel-2777 and NUDT15-indel-1673
Fig. 2
Fig. 2
Sequencing comparison of two novel 23-bp indel mutations polymorphism of promoter region within the chicken NUDT15 gene and electrophoresis pattern. a NUDT15–2777-indel sequencing comparison. b NUDT15–1673-indel sequencing comparison. c Electrophoresis pattern of the NUDT15–2777-indel. d Electrophoresis pattern of the NUDT15–1673-indel
Fig. 3
Fig. 3
Expression analysis of the NUDT15 gene. a Tissue expression profiles of the NUDT15 gene in E10-old AA chickens. b Tissue expression profiles of the NUDT15 gene in 2-week-old AA chickens. c and d Spatiotemporal expression of the NUDT15 gene in leg muscle tissue of AA broiler and Lushi chickens. e and f Expression pattern of chicken NUDT15 mRNA for various genotypes of NUDT15–2777-indel and NUDT15–1673-indel (n = 6). Results are expressed as the mean ± SEM. Statistical significance of differences between means was assessed using independent sample t test. ∗p < 0.05, ∗∗p < 0.01
Fig. 4
Fig. 4
Genotype percentage statistics and growth curves. a Percentage of different genotypes in different populations. Commercial laying hens (Hy-Line), dual-purpose type (Xichuan, Guifei, Game fowl, Lushi, Changshun, Gushi),commercial broiler (Hubbard, Arbor Aceres). b Developmental changes in body weight of different genotypes of NUDT15 in F2 generation at different weeks. Results are expressed as the mean ± SEM. Statistical significance of differences between means was assessed using independent sample t test. ∗p < 0.05, ∗∗p < 0.01
Fig. 5
Fig. 5
The Promoter Activities of different genotypes of NUDT15(n = 3). Results are expressed as the mean ± SEM. Statistical significance of differences between means was assessed using independent sample t test. ∗p < 0.05
Fig. 6
Fig. 6
The Effect of lnc9141 on Myoblast Proliferation. a-k When overexpressing or inferring with NUDT15, respectively, (a and b) mRNA expression of NUDT15 were detected (n = 6); (c and d) mRNA expression of CCND1, CCNB2, and PCNA were detected (n = 6); (e-h) the number of proliferation cells was counted (n = 3); (i and j) Cell growth was measured after NUDT15 overexpression or inferring (n = 8); (k) Cell cycle analysis of CPMs with NUDT15 overexpression or inferring (n = 3)
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