| Literature DB >> 30702781 |
Xiaopeng Li1, Yinglin Lu1, Xiaofan Liu1, Xiaolei Xie1, Kun Wang1, Debing Yu1.
Abstract
Egg production is an important economic trait in poultry, and it is of great significance to study the key genes and functional SNPs that affect egg laying performance. Follicle-stimulating hormone (FSH) plays an important physiological role in the reproductive performance of humans and animals by binding to its receptor (FSHR). Studies have shown that there are many transcriptional regulatory elements in the 5' flanking region of the FSHR gene that interact with transcription factors to regulate FSHR transcription. In this study, DNA sequencing was used to identify SNPs in the FSHR promoter sequence in both Dongxiang and Suken chickens. To detect the activity of the chicken FSHR gene promoter, we analysed the characteristics of the sequence and constructed three deletion vectors. We confirmed that the region (-18/-544) was the core promoter. Furthermore, five polymorphisms, including a 200-bp indel at -869, C-1684T, C-1608T, G-368A and T-238A, were detected in both the Dongxiang and Suken chickens. The age at first egg (AFE) for different genotype of -869 indel in Suken chicken was significantly different (p < 0.01). For SNP C-1684T in Dongxiang chickens, the CC genotype had higher egg number at 43 weeks of age (E43) than that of the TC genotype (p < 0.05). For SNP C-1684T in Suken chickens, the TC genotype had higher AFE than that of the CC genotype (p < 0.05). For SNP C-1608T in Suken chickens, the CC genotype had higher AFE than that of the TC genotype (p < 0.05). For SNP G-368A in Suken chickens, the AG genotype had higher AFE than that of the GG genotype (p < 0.05).Entities:
Keywords: zzm321990FSHRzzm321990; association analysis; core promoter; single nucleotide polymorphism
Mesh:
Substances:
Year: 2019 PMID: 30702781 PMCID: PMC6850157 DOI: 10.1111/rda.13412
Source DB: PubMed Journal: Reprod Domest Anim ISSN: 0936-6768 Impact factor: 2.005
Primers used for amplification of the follicle‐stimulating hormone receptor of Dongxiang and Suken chickens
| Primer | Primer sequence | Tm/°C | Product size/bp | Application |
|---|---|---|---|---|
| P1 | F:GGTATGGCTTACGCTTGTCTGT | 62 | 790 | Amplification |
| R:GATTGTTTGCTTGTTTCTTTCG | ||||
| P2 | F:AAAGGTGAGAATGGTGGAAT | 59 | 553 | Amplification |
| R:CCAGAGCTAAATAACGCACC | ||||
| P3 | F:AAAGGTGGTAGGGAGGAAGA | 62 | 740 | Amplification |
| R:CCTGGCAGATGAATATCCTG | ||||
| P4 | F:CGG | 61 | 1,461 | Plasmids construction |
| R:CCC | ||||
| P5 | F:CGG | 61 | 794 | Plasmids construction |
| R:CCC | ||||
| P6 | F:CGG | 61 | 526 | Plasmids construction |
| R:CCC | ||||
| P7 | F:GGTATGGCTTACGCTTGTCTGT | 62 | 790 | Genotyping |
| R:GATTGTTTGCTTGTTTCTTTCG | ||||
| P8 | F:TGTCTCTTAGTCTTATCAAACAACA | 60 | 492 | Genotyping |
| R:CCTGGCAGATGAATATCCTG | ||||
| P9 | F:AAAGGTGGTAGGGAGGAAGA | 62 | 740 | Genotyping |
| R:CCTGGCAGATGAATATCCTG | ||||
| P10 | F:ACAATCAAAACCCCAGCAAC | 62 | 741 | Genotyping |
| R:AATGAACCGGAATGCTTTTG |
The digestion sites of the enzymes are underlined.
Software online for promoter analysis
| Software name | URL | Purpose |
|---|---|---|
| UCSC |
| Promoter prediction |
| Promoter Scan |
| Core promoter prediction |
| Methprimer |
| CpG island prediction |
| Genomatix |
| TFBS prediction |
TFBS: Transcription factor binding site.
Figure 1Agarose gel photograph of 5′ regulatory region of Chicken FSHR gene. 1‐3: Amplified fragments of primers P1‐P3; M: DNA marker DL2000
Figure 2The 5′ regulation sequence of FSHR gene in chicken. The SNP sites are indicated by red background; the transcription factor binding sites are indicated by blue boxes
Figure 3The prediction result of CpG islands in promoter region of Chicken FSHR gene. Vertical lines indicate CpG sites
Figure 4A agarose gel photograph of deleted fragment in 5′ regulatory region of Chicken FSHR gene. B identification of recombinant vectors by restriction enzymes
Figure 5Promoter activity analysis of Chicken FSHR gene. ** indicates extremely significant difference (p < 0.01)
Figure 6Genotyping of the C−1684T, C−1608T, T−238A, G−368A and −869 indel mutations of the promoter region of chicken FSHR gene
Genotypes and allele frequency of the mutations of FSHR gene
| Polymorphism sites | Breed | Genotypic frequency | Allele and frequency |
| |||
|---|---|---|---|---|---|---|---|
| Genotype | Number | Frequency | Allele | Frequency | |||
| −869 indel | Dongxiang | AA | 4 | 0.04 | A | 0.082 | 15.830 |
| Aa | 11 | 0.09 | a | 0.918 | |||
| aa | 101 | 0.87 | |||||
| Suken | AA | 10 | 0.02 | A | 0.089 | 15.29 | |
| Aa | 57 | 0.13 | a | 0.911 | |||
| aa | 367 | 0.85 | |||||
| C−1684T | Dongxiang | CC | 42 | 0.36 | T | 0.379 | 1.125 |
| TC | 60 | 0.52 | C | 0.621 | |||
| TT | 14 | 0.12 | |||||
| Suken | CC | 85 | 0.30 | T | 0.518 | 9.051 | |
| TC | 248 | 0.53 | C | 0.482 | |||
| TT | 101 | 0.17 | |||||
| C−1608T | Dongxiang | CC | 39 | 0.34 | T | 0.457 | 3.204 |
| TC | 48 | 0.41 | C | 0.543 | |||
| TT | 29 | 0.25 | |||||
| Suken | CC | 312 | 0.72 | T | 0.217 | 166.7 | |
| TC | 56 | 0.13 | C | 0.783 | |||
| TT | 66 | 0.15 | |||||
| G−368A | Dongxiang | GG | 73 | 0.63 | A | 0.185 | 6.004 |
| AG | 43 | 0.37 | G | 0.815 | |||
| AA | 0 | 0 | |||||
| Suken | GG | 252 | 0.58 | A | 0.210 | 30.55 | |
| AG | 182 | 0.42 | G | 0.790 | |||
| AA | 0 | 0 | |||||
| T−238A | Dongxiang | AA | 63 | 0.54 | A | 0.720 | 1.775 |
| AT | 41 | 0.35 | T | 0.280 | |||
| TT | 12 | 0.11 | |||||
| Suken | AA | 138 | 0.32 | A | 0.530 | 9.64 | |
| AT | 184 | 0.42 | T | 0.470 | |||
| TT | 112 | 0.26 | |||||
χ 2 0.05 (2) = 5.99, χ 2 0.05(1) = 3.84, χ 2 0.01(1) = 6.63.
The chi‐square value with * means p < 0.05.
Association analysis of SNPs of FSHR gene with Dongxiang chicken egg performance
| Polymorphism sites | Genotype | Number | AFE |
| E43 |
|
|---|---|---|---|---|---|---|
| −869 indel | AA | 4 | 170.00 ± 7.53 | 0.704 | 56.25 ± 6.95 | 0.304 |
| Aa | 11 | 165.45 ± 10.21 | 60.82 ± 15.03 | |||
| aa | 101 | 165.28 ± 16.33 | 66.37 ± 16.93 | |||
| C−1684T | TT | 14 | 168.00 ± 14.82 | 0.222 | 65.71 ± 12.78 ab | 0.050 |
| TC | 60 | 167.28 ± 19.21 | 62.77 ± 19.11 b | |||
| CC | 42 | 162.19 ± 8.08 | 69.33 ± 13.08 a | |||
| C−1608T | TT | 29 | 165.14 ± 10.24 | 0.982 | 62.76 ± 19.20 | 0.287 |
| TC | 48 | 165.48 ± 19.85 | 68.35 ± 16.27 | |||
| CC | 39 | 165.87 ± 13.19 | 64.03 ± 14.76 | |||
| G−368A | GG | 73 | 165.89 ± 17.19 | 0.465 | 65.85 ± 16.07 | 0.569 |
| AG | 43 | 164.91 ± 12.70 | 64.91 ± 17.67 | |||
| AA | 0 | 0 | 0 | |||
| T−238A | TT | 12 | 164.08 ± 11.57 | 0.800 | 72.42 ± 13.70 | 0.292 |
| AT | 41 | 164.59 ± 16.44 | 65.51 ± 14.01 | |||
| AA | 63 | 166.41 ± 15.90 | 64.17 ± 18.46 |
In the same group, different superscripts mean significant difference (p < 0.05).
Association analysis of SNPs of FSHR gene with Suken chicken egg performance
| Polymorphism sites | Genotype | Number | AFE |
| E43 |
|
|---|---|---|---|---|---|---|
| −869 indel | AA | 10 | 160.40 ± 5.54A | 0.005 | 96.70 ± 19.33 | 0.390 |
| Aa | 57 | 157.25 ± 2.90B | 104.19 ± 14.27 | |||
| aa | 367 | 157.12 ± 3.06B | 103.40 ± 16.18 | |||
| C−1684T | TT | 101 | 157.24 ± 3.14ab | 0.030 | 101.70 ± 16.35 | 0.452 |
| TC | 248 | 157.48 ± 3.70a | 104.08 ± 15.85 | |||
| CC | 85 | 156.58 ± 2.09b | 103.18 ± 16.12 | |||
| C−1608T | TT | 66 | 156.74 ± 3.60ab | 0.023 | 102.67 ± 17.30 | 0.234 |
| TC | 56 | 156.35 ± 1.92b | 106.75 ± 16.45 | |||
| CC | 312 | 157.51 ± 3.42a | 102.88 ± 15.63 | |||
| G−368A | GG | 252 | 156.83 ± 2.88b | 0.003 | 104.27 ± 15.27 | 0.161 |
| AG | 182 | 157.83 ± 3.78a | 102.08 ± 16.95 | |||
| AA | 0 | 0 | 0 | |||
| T−238A | TT | 112 | 157.08 ± 3.29 | 0.674 | 104.19 ± 16.99 | 0.758 |
| AT | 184 | 157.20 ± 3.20 | 103.35 ± 15.45 | |||
| AA | 138 | 157.44 ± 3.52 | 102.67 ± 16.02 |
In the same group, different superscripts mean significant difference (p < 0.05).