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A genome-wide single nucleotide polymorphism scan reveals genetic markers associated with fertility rate in Chinese Jing Hong chicken.

ABSTRACT: The function of the sperm storage tubules is directly correlated with the fertility of laying hens. However, little is known about the molecular mechanisms regulating the fertility traits in chicken. To identify genetic markers associated with reproductive traits, we calculated fertility rate at 61 to 69 wk (51 D) of Jing Hong chickens parent generation as the phenotype and the genotype were detected by the chicken 600K Affymetrix Axiom High Density single nucleotide polymorphisms (SNP)-array. The genome-wide association study using 190 Jing Hong hens showed that the 20 SNP in chromosomes 3 and 13 were significantly associated with fertility rate. To verify these results, a total of 1900 Jing Hong laying hens from 2 populations (P1 and P2) were further genotyped by polymerase chain reaction-restriction fragments length polymorphisms method. The association analysis results revealed that 12 polymorphisms (AX-75769978, AX-76582632, AX-75730546, AX-75730496, AX-75730588, AX-76530282, AX-76530329, AX-76529310, AX-75769906, AX-75755394, AX-80813697 and AX-76582809) out of 20 showed highly significant effects (P < 0.0001) on fertility rate in P1, P2 and P1+P2. Six haplotypes (TTAA, TTGG, TTAG, CTAA, CTGG, and CTAG) were inferred based on significant loci (AX-75730546 and AX-76530282) also showed significant association with fertility rate, where haplotype CTAG was shown to be markedly associated with the significantly highest (P < 0.0001) fertility rate (in P1, 86.42 ± 0.59; P2, 85.98 ± 0.59 and P1+P2, 86.16 ± 0.42) followed by other haplotypes for the irrespective of population studied. Collectively, we report for the first time that 12 SNP in the chromosomes 3 and 13 were significantly associated with fertility rate during the later stage of egg production, which could be used as the potential genetic markers that would be able to facilitate in the selection and improvement of fertility rate through chicken breeding.

SUBMITTER: Azmal SA

PROVIDER: S-EPMC7597651 | biostudies-literature | 2020 Jun

REPOSITORIES: biostudies-literature

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A genome-wide single nucleotide polymorphism scan reveals genetic markers associated with fertility rate in Chinese Jing Hong chicken.

Azmal Syed Ali SA Nan Jiuhong J Bhuiyan Ali Akbar AA Elokil Abdelmotaleb Ahmed AA Ali Mohammad Ishaque MI Adetula Adeyinka Abiola AA Ma Shuai S Sun Chenghao C Han Zhongdong Z Yuan Jingwei J Li Shijun S

Poultry science 20200410 6

The function of the sperm storage tubules is directly correlated with the fertility of laying hens. However, little is known about the molecular mechanisms regulating the fertility traits in chicken. To identify genetic markers associated with reproductive traits, we calculated fertility rate at 61 to 69 wk (51 D) of Jing Hong chickens parent generation as the phenotype and the genotype were detected by the chicken 600K Affymetrix Axiom High Density single nucleotide polymorphisms (SNP)-array. T ...[more]

PMID: 32475420

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Project description:The improvement of egg production is of vital importance in the chicken industry to maintain optimum output throughout the laying period. Because of the elongation of the egg-laying cycle, a drop in egg-laying rates in the late laying period has provoked great concern in the poultry industry. In this study, we calculated the egg-laying rate at weeks 61-69 (60 days) of Jing Hong chickens parent generation as the phenotype, and the genotype were detected by the chicken 600K Affymetrix Axiom High Density (HD) Single Nucleotide Polymorphisms (SNP)-array. The Genome-Wide Association Study (GWAS) result showed that the egg production trait is significantly associated with five SNPs (AX-75745366, AX-75745380, AX-75745340, AX-75745388, and AX-75745341), which are in the rap guanine nucleotide exchange factor 6 (RAPGEF6) gene on chicken chromosome 13. A total of 1676 Chinese commercial Jing Hong laying hens-including two populations, P1 population (858 hens) and P2 population (818 hens)-were genotyped using the Polymerase Chain Reaction-Restriction Fragments Length Polymorphisms (PCR-RFLP) method for the association analysis of egg-laying rates for the verification of the GWAS results. Genotypic and allelic frequencies of five SNPs were inconsistent with Hardy-Weinberg equilibrium, and the average population genetics parameters considering all the SNP values; i.e., gene homozygosity (Ho), gene heterozygosity (He), the effective number of alleles (Ne), and the polymorphism information content (PIC) were 0.75, 0.25, 1.40, and 0.20 in P1; 0.71, 0.29, 1.46, and 0.24 in P2; and 0.73, 0.27, 1.43, and 0.22 in P1 + P2 populations, respectively. The association analysis results revealed that out of the five polymorphisms, three of them (AX-75745366, AX-75745340, and AX-75745341; Patent applying No: 201810428916.5) had highly significant effects on egg-laying rates according to the GWAS results. Population-specific association analyses also showed similar significant association effects with this trait. Four haplotypes (AAGG, AAAG, AGGG, and AGAG) were inferred based on significant loci (AX-75745340 and AX-75745341) and also showed significant associations with the egg-laying rate, where haplotype AAGG had the highest egg-laying rate, with the exception of the egg-laying rate in P1 population, followed by other haplotypes. Furthermore, genotypes TT, AA, and GG showed the highest egg-laying rate compared to the corresponding genotypes at AX-75745366, AX-75745340, and AX-75745341 SNP loci in P1+P2, respectively. A similar result was found in the population-specific analysis except for the P1 population, in which TC genotype showed the highest egg-laying rate. No significant association was found in the egg-laying rate during the 60 days laying period for the SNPs (AX-75745380 and AX-75745388) in any group of population (p ? 0.05). Collectively, we report for the first time that 3 SNPs in the RAPGEF6 gene were significantly associated with the egg-laying rate during the later stage of egg production, which could be used as the potential candidate molecular genetic markers that would be able to facilitate in the selection and improvement of egg production traits through chicken breeding.

Project description:BACKGROUND:Fertility preservation for both medical and non-medical reasons are gaining increasing attention world-wide. This study aimed to evaluate the awareness, knowledge and acceptance on fertility preservation in Hong Kong Chinese. METHODS:This was a cross-sectional study carried out between June 2016 to March 2017. A self-administered questionnaire was distributed by convenience sampling. RESULTS:Forty two percent of subjects returned the questionnaire (n?=?296/697). Among them, only 54.3% were aware of any means of fertility preservation. Tertiary educated individuals are more aware than less educated individuals (73.6% versus 46.6%, p?<?0.001). The most commonly known method is oocyte cryopreservation (94.3%). Most of the respondents (80%) were interested to know about fertility preservation, 84.1% considered fertility preservation counselling necessary and 83.3% would consider undergoing fertility preservation if a treatment has a high chance of causing infertility despite the possibility of delay in cancer treatment. Up to 93.9% agreed to set up a dedicated referral centre with government funding and 73.4% agreed that fertility preservation for medical indication should be provided as a government funded service. In terms of fertility preservation for non-medical reason, 65.5 and 70.4% agreed that fertility preservation should be offered to single men and women without partner respectively, while only 53.3 and 50% agreed that fertility preservation is acceptable for delay in childbearing for career development in female and male respectively. CONCLUSION:There was a low awareness but positive attitude towards fertility preservation among Hong Kong Chinese. Acceptance towards medically indicated fertility preservation is high while a considerable number also accepts it for non-medical reasons. Educational campaigns are required to arouse awareness of fertility preservation to prevent individuals being deprived of the option due to lack of knowledge. Dedicated referral centre with established efficient patient referral pathways and financial support should be provided to improve the provision and uptake of fertility preservation service to enhance the reproductive potential and life options of women.

Dataset Information

A genome-wide single nucleotide polymorphism scan reveals genetic markers associated with fertility rate in Chinese Jing Hong chicken.

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A genome-wide single nucleotide polymorphism scan reveals genetic markers associated with fertility rate in Chinese Jing Hong chicken.

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