Dataset Information

Polymorphisms in the Chicken Growth Differentiation Factor 9 Gene Associated with Reproductive Traits.

ABSTRACT: The aim of the study was to investigate GDF9 gene polymorphisms and their association with reproductive traits in chicken using DNA sequencing. A total of 279 Dongxiang blue-shelled (DX) chickens and 232 Luhua (LH) chickens were used for validation. We detected 15 single nucleotide polymorphisms (SNPs): nine SNPs were previously unreported in chicken, two were missense mutations, and only three exhibited significant associations with reproductive traits. G.17156387C>T was significantly associated with age at first egg (AFE) and weight of first egg (WFE) in both breeds. Birds carrying the CC genotype exhibited higher AFE and WFE values than those with the TT genotype. The SNP g.17156427A>G exhibited an association with egg weight at 300 days of age (EWTA) in DX but not in LH chickens. The SNP g.17156703A>C affected the AFE and EN (total number of eggs at 300 days of age) in DX chickens. In addition, certain diplotypes significantly affected AFE, BWTA (body weight at 300 days of age), and EN in both breeds. RT-PCR results showed that the GDF9 gene was highly expressed in stroma with cortical follicles (STR) and prehierarchal follicles. These results provided further evidence that the GDF9 gene is involved in determining reproductive traits in chicken.

SUBMITTER: Liu L

PROVIDER: S-EPMC6169235 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature

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Polymorphisms in the Chicken Growth Differentiation Factor 9 Gene Associated with Reproductive Traits.

Liu Lingbin L Cui Zhifu Z Xiao Qihai Q Zhang Haihan H Zhao Xiaoling X Wang Yan Y Yin Huadong H Li Diyan D Zhu Qing Q

BioMed research international 20180919

The aim of the study was to investigate <i>GDF9</i> gene polymorphisms and their association with reproductive traits in chicken using DNA sequencing. A total of 279 Dongxiang blue-shelled (DX) chickens and 232 Luhua (LH) chickens were used for validation. We detected 15 single nucleotide polymorphisms (SNPs): nine SNPs were previously unreported in chicken, two were missense mutations, and only three exhibited significant associations with reproductive traits. G.17156387C>T was significantly as ...[more]

PMID: 30327782

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Project description:BACKGROUND: Abundant evidence indicates that chicken reproduction is strictly regulated by the hypothalamic-pituitary-gonad (HPG) axis, and the genes included in the HPG axis have been studied extensively. However, the question remains as to whether any other genes outside of the HPG system are involved in regulating chicken reproduction. The present study was aimed to identify, on a genome-wide level, novel genes associated with chicken reproductive traits. METHODOLOGY/PRINCIPAL FINDING: Suppressive subtractive hybridization (SSH), genome-wide association study (GWAS), and gene-centric GWAS were used to identify novel genes underlying chicken reproduction. Single marker-trait association analysis with a large population and allelic frequency spectrum analysis were used to confirm the effects of candidate genes. Using two full-sib Ningdu Sanhuang (NDH) chickens, GARNL1 was identified as a candidate gene involved in chicken broodiness by SSH analysis. Its expression levels in the hypothalamus and pituitary were significantly higher in brooding chickens than in non-brooding chickens. GWAS analysis with a NDH two tail sample showed that 2802 SNPs were significantly associated with egg number at 300 d of age (EN300). Among the 2802 SNPs, 2 SNPs composed a block overlapping the GARNL1 gene. The gene-centric GWAS analysis with another two tail sample of NDH showed that GARNL1 was strongly associated with EN300 and age at first egg (AFE). Single marker-trait association analysis in 1301 female NDH chickens confirmed that variation in this gene was related to EN300 and AFE. The allelic frequency spectrum of the SNP rs15700989 among 5 different populations supported the above associations. Western blotting, RT-PCR, and qPCR were used to analyze alternative splicing of the GARNL1 gene. RT-PCR detected 5 transcripts and revealed that the transcript, which has a 141 bp insertion, was expressed in a tissue-specific manner. CONCLUSIONS/SIGNIFICANCE: Our findings demonstrate that the GARNL1 gene contributes to chicken reproductive traits.

Project description:Aim:The present study was performed to assess the association of single-nucleotide polymorphisms (SNPs) in the fatty acid-binding protein 4 (FABP4) gene with birth weight (BW), final weight (FW), and average daily gain (ADG) in three Egyptian sheep breeds. Materials and Methods:Genomic DNA was extracted from the blood samples of 50 male and female individuals representing Ossimi, Rahmani, and Barki sheep breeds. A 407 bp nucleotide (nt) segment from the first intron of FABP4 was amplified by polymerase chain reaction, sequenced, and analyzed in the different samples. Results:Sequence analysis of the determined segment (407 bp) revealed four SNPs (all transition types) at nt position 372 (CP011894.1:g.57605471) A>G, nt position 211 (CP011894.1:g.57605632) A>G, nt position 143 (CP011894.1:g.57605700) T>C, and nt position 111 (CP011894.1:g.57605732) T>C. The allelic and genotypic frequencies for the identified SNPs in the sheep breeds were calculated. At nt positions 372 and 211, two alleles were identified (A and G). Only two genotypes were present at nt position 372 (AA and AG), while three genotypes were present at nt position 211 (AA, AG, and GG). Two alleles (T and C) and three identified genotypes (TT, TC, and CC) were detected at nt positions 143 and 111. Analysis of the results revealed that AA genotype at nt position 372 is associated with higher estimates for BW, FW, and ADG when compared to all the other genotypes. Very high correlation coefficients were found between the genotypes 143-TT and 111-TT and also between 143-TC and 111-TC. The genotypes 372-AG, 211-GG, 211-AA, 143-TT, 143-CC, 111-TT, 111-TC, and 111-CC were associated with negative effects on BW, FW, and ADG. Conclusion:The detection of four SNPs in a partial sequence of the Egyptian ovine FABP4 gene intron 1 reflected that this gene harbors substantial diversity. In addition, a novel SNP at nt position 372 (CP011894.1:g.57605471) A>G was associated with higher estimates for BW, FW, and ADG.

Project description:Background and aimReproductive traits play an important role in population increases and the egg production (EP) abilities of Indonesian local ducks (ILD). The prolactin (PRL) gene is a single chain polypeptide hormone belonging to a family of growth hormone genes that are mainly synthesized in the anterior pituitary gland in all vertebrates. It has a significant effect on reproductive traits and EP. Single nucleotide polymorphisms (SNPs) present in PRL are a useful molecular marker for EP. This study aimed to identify the PRL polymorphisms based on these SNPs and to uncover the associations with reproductive traits in ILD.Materials and methodsA total of 280 ILDs consisting of Tegal and Magelang (F0) ducks and their reciprocal crosses, namely, Gallang (F1) and Maggal (F1), were maintained and specific variables were recorded, that is, age at first egg, body weight at first egg, first egg weight, and EP, for 90 days. Allele and genotype frequencies were used to determine the Hardy-Weinberg (H-W) equilibrium. The association between the SNP genotypes of PRL and reproductive traits was analyzed using one-way analysis of variance, following the GLM procedure of SAS. The genotypic effects on the reproductive traits were determined using regression analysis.ResultsThis study successfully amplified a polymerase chain reaction product of 190 bp, which was used to identify the SNP. Results indicated that PRL in ILDs is polymorphic. A SNP was found at position 164 nt (c.164G >A), consisting of three different genotypes, namely, GG, GA, and AA. The genotypes of Tegal and Magelang (F0), and Gallang (F1) populations were not in H-W equilibrium. The Maggal population (F1) was in H-W equilibrium. Significant associations were detected between the genotypes and EP in all ILDs (p<0.01), following a regression line of y=2.337x+64.605, with a determination coefficient of 0.0188 (r=0.14).ConclusionPRL can be recommended as a candidate gene for reproductive traits in ILD, especially EP.

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Polymorphisms in the Chicken Growth Differentiation Factor 9 Gene Associated with Reproductive Traits.

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Polymorphisms in the Chicken Growth Differentiation Factor 9 Gene Associated with Reproductive Traits.

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