Dataset Information

Haplotype analysis of genomic prediction by incorporating genomic pathway information based on high-density SNP marker in Chinese yellow-feathered chicken.

ABSTRACT: Genomic selection using single nucleotide polymorphism (SNP) markers is now intensively investigated in breeding and has been widely utilized for genetic improvement. Currently, several studies have used haplotype (consisting of multiallelic SNPs) for genomic prediction and revealed its performance advantage. In this study, we comprehensively evaluated the performance of haplotype models for genomic prediction in 15 traits, including 6 growth, 5 carcass, and 4 feeding traits in a Chinese yellow-feathered chicken population. We adopted 3 methods to define haplotypes from high-density SNP panels, and our strategy included combining Kyoto Encyclopedia of Genes and Genomes pathway information and considering linkage disequilibrium (LD) information. Our results showed an increase in prediction accuracy due to haplotypes ranging from -0.04∼27.16% in all traits, where the significant improvements were found in 12 traits. The estimates of haplotype epistasis heritability were strongly correlated with the accuracy increase by haplotype models. In addition, incorporating genomic annotation information could further increase the accuracy of the haplotype model, where the further increase in accuracy is significantly relative to the increase of relative haplotype epistasis heritability. The genomic prediction using LD information for constructing haplotypes has the best prediction performance among the 4 traits. These results uncovered that haplotype methods were beneficial for genomic prediction, and the accuracy could be further increased by incorporating genomic annotation information. Moreover, using LD information would potentially improve the performance of genomic prediction.

SUBMITTER: Ye H

PROVIDER: S-EPMC10024239 | biostudies-literature | 2023 Feb

REPOSITORIES: biostudies-literature

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Haplotype analysis of genomic prediction by incorporating genomic pathway information based on high-density SNP marker in Chinese yellow-feathered chicken.

Ye Haoqiang H Xu Zhenqiang Z Bello Semiu Folaniyi SF Zhu Qianghui Q Kong Shaofen S Zheng Ming M Fang Xiang X Jia Xinzheng X Xu Haiping H Zhang Xiquan X Nie Qinghua Q

Poultry science 20230207 5

Genomic selection using single nucleotide polymorphism (SNP) markers is now intensively investigated in breeding and has been widely utilized for genetic improvement. Currently, several studies have used haplotype (consisting of multiallelic SNPs) for genomic prediction and revealed its performance advantage. In this study, we comprehensively evaluated the performance of haplotype models for genomic prediction in 15 traits, including 6 growth, 5 carcass, and 4 feeding traits in a Chinese yellow- ...[more]

PMID: 36907129

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Project description:Carcass traits in broiler chickens are complex traits that are influenced by multiple genes. To gain deeper insights into the genetic mechanisms underlying carcass traits, here we conducted a weighted single-step genome-wide association study (wssGWAS) in a population of Chinese yellow-feathered chicken. The objective was to identify genomic regions and candidate genes associated with carcass weight (CW), eviscerated weight with giblets (EWG), eviscerated weight (EW), breast muscle weight (BMW), drumstick weight (DW), abdominal fat weight (AFW), abdominal fat percentage (AFP), gizzard weight (GW), and intestine length (IL). A total of 1,338 broiler chickens with phenotypic and pedigree information were included in this study. Of these, 435 chickens were genotyped using a 600K single nucleotide polymorphism chip for association analysis. The results indicate that the most significant regions for 9 traits explained 2.38% to 5.09% of the phenotypic variation, from which the region of 194.53 to 194.63Mb on chromosome 1 with the gene RELT and FAM168A identified on it was significantly associated with CW, EWG, EW, BMW, and DW. Meanwhile, the 5 traits have a strong genetic correlation, indicating that the region and the genes can be used for further research. In addition, some candidate genes associated with skeletal muscle development, fat deposition regulation, intestinal repair, and protection were identified. Gene ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses suggested that the genes are involved in processes such as vascular development (CD34, FGF7, FGFR3, ITGB1BP1, SEMA5A, LOXL2), bone formation (FGFR3, MATN1, MEF2D, DHRS3, SKI, STC1, HOXB1, HOXB3, TIPARP), and anatomical size regulation (ADD2, AKT1, CFTR, EDN3, FLII, HCLS1, ITGB1BP1, SEMA5A, SHC1, ULK1, DSTN, GSK3B, BORCS8, GRIP2). In conclusion, the integration of phenotype, genotype, and pedigree information without creating pseudo-phenotype will facilitate the genetic improvement of carcass traits in chickens, providing valuable insights into the genetic architecture and potential candidate genes underlying carcass traits, enriching our understanding and contributing to the breeding of high-quality broiler chickens.

Project description:The objective of this research was to investigate the effects of Mahuang and Tuer chickens, 2 representatives of the native chicken breed, and the slaughter age on meat quality and flavor compounds of soft-boiled chickens (SCs) in comparison to a commercial cross boiler. A total of 432 chicks were randomly allocated into the following groups: 817 groups raised for 55 d, and Mahuang and Tuer chickens raised for 60, 65, 70, and 75 days (d). After the completion of rearing period, the chickens were slaughtered, and 5 carcasses per group were randomly selected for SC manufacturing. Meat quality was determined based on product yield, pH, color, meat tenderness, and textural and sensorial attributes. The volatile compounds of chicken breast were identified by gas chromatography-ion mobility spectrometry (GC-IMS). The results showed that the yellow-feathered chicken breed, especially Mahuang chicken, had a higher product yield, and lower shear force and sensorial scores than the cross broiler. The pH, L* and b* values in SC breast meat were not significantly influenced by breed (P > 0.05), while greater a* was observed in SC of yellow-feathered chickens compared to cross broilers. The slaughter age had a significant effect on the pH, color, shear force, and textural properties of SC (P < 0.05). The meat tenderness of SC was significantly decreased as the age of chicken increased from 65 d to 75 d (P < 0.05). The relatively young age of yellow-feathered chickens (60 d and 65 d) was rated to have a higher overall sensory score of SC (P < 0.05). A total of 65 organic volatile compounds were identified in SC, including 18 aldehydes, 16 alcohols, 10 ketones, 9 esters, 2 acids, 3 furans, 5 pyrazines, and 2 sulfur-containing compounds. Three chicken breeds were separately clustered in the plot of principal component analysis, indicating breed-specific flavor characteristics. Collectively, the present study provides valuable information for SC processing in terms of carcass selection of yellow-feathered chicken breeds and slaughter age.

Project description:BackgroundHigh density (HD) SNP genotyping arrays are an important tool for genetic analyses of animals and plants. Although the chicken is one of the most important farm animals, no HD array is yet available for high resolution genetic analysis of this species.ResultsWe report here the development of a 600 K Affymetrix® Axiom® HD genotyping array designed using SNPs segregating in a wide variety of chicken populations. In order to generate a large catalogue of segregating SNPs, we re-sequenced 243 chickens from 24 chicken lines derived from diverse sources (experimental, commercial broiler and layer lines) by pooling 10-15 samples within each line. About 139 million (M) putative SNPs were detected by mapping sequence reads to the new reference genome (Gallus_gallus_4.0) of which ~78 M appeared to be segregating in different lines. Using criteria such as high SNP-quality score, acceptable design scores predicting high conversion performance in the final array and uniformity of distribution across the genome, we selected ~1.8 M SNPs for validation through genotyping on an independent set of samples (n = 282). About 64% of the SNPs were polymorphic with high call rates (>98%), good cluster separation and stable Mendelian inheritance. Polymorphic SNPs were further analysed for their population characteristics and genomic effects. SNPs with extreme breach of Hardy-Weinberg equilibrium (P < 0.00001) were excluded from the panel. The final array, designed on the basis of these analyses, consists of 580,954 SNPs and includes 21,534 coding variants. SNPs were selected to achieve an essentially uniform distribution based on genetic map distance for both broiler and layer lines. Due to a lower extent of LD in broilers compared to layers, as reported in previous studies, the ratio of broiler and layer SNPs in the array was kept as 3:2. The final panel was shown to genotype a wide range of samples including broilers and layers with over 100 K to 450 K informative SNPs per line. A principal component analysis was used to demonstrate the ability of the array to detect the expected population structure which is an important pre-investigation step for many genome-wide analyses.ConclusionsThis Affymetrix® Axiom® array is the first SNP genotyping array for chicken that has been made commercially available to the public as a product. This array is expected to find widespread usage both in research and commercial application such as in genomic selection, genome-wide association studies, selection signature analyses, fine mapping of QTLs and detection of copy number variants.

Dataset Information

Haplotype analysis of genomic prediction by incorporating genomic pathway information based on high-density SNP marker in Chinese yellow-feathered chicken.

Publications

Haplotype analysis of genomic prediction by incorporating genomic pathway information based on high-density SNP marker in Chinese yellow-feathered chicken.

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