Dataset Information

Genome-wide genetic structure and selection signatures for color in 10 traditional Chinese yellow-feathered chicken breeds.

ABSTRACT: BACKGROUND:Yellow-feathered chickens (YFCs) have a long history in China. They are well-known for the nutritional and commercial importance attributable to their yellow color phenotype. Currently, there is a huge paucity in knowledge of the genetic determinants responsible for phenotypic and biochemical properties of these iconic chickens. This study aimed to uncover the genetic structure and the molecular underpinnings of the YFCs trademark coloration. RESULTS:The whole-genomes of 100 YFCs from 10 major traditional breeds and 10 Huaibei partridge chickens from China were re-sequenced. Comparative population genomics based on autosomal single nucleotide polymorphisms (SNPs) revealed three geographically based clusters among the YFCs. Compared to other Chinese indigenous chicken genomes incorporated from previous studies, a closer genetic proximity within YFC breeds than between YFC breeds and other chicken populations is evident. Through genome-wide scans for selective sweeps, we identified RALY heterogeneous nuclear ribonucleoprotein (RALY), leucine rich repeat containing G protein-coupled receptor 4 (LGR4), solute carrier family 23 member 2 (SLC23A2), and solute carrier family 2 member 14 (SLC2A14), besides the classical beta-carotene dioxygenase 2 (BCDO2), as major candidates pigment determining genes in the YFCs. CONCLUSION:We provide the first comprehensive genomic data of the YFCs. Our analyses show phylogeographical patterns among the YFCs and potential candidate genes giving rise to the yellow color trait of the YFCs. This study lays the foundation for further research on the genome-phenotype cross-talks that define important poultry traits and for formulating genetic breeding and conservation strategies for the YFCs.

SUBMITTER: Huang X

PROVIDER: S-EPMC7171827 | biostudies-literature | 2020 Apr

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Genome-wide genetic structure and selection signatures for color in 10 traditional Chinese yellow-feathered chicken breeds.

Huang Xunhe X Otecko Newton O NO Peng Minsheng M Weng Zhuoxian Z Li Weina W Chen Jiebo J Zhong Ming M Zhong Fusheng F Jin Sihua S Geng Zhaoyu Z Luo Wei W He Danlin D Ma Cheng C Han Jianlin J Ommeh Sheila C SC Zhang Yaping Y Zhang Xiquan X Du Bingwang B

BMC genomics 20200420 1

<h4>Background</h4>Yellow-feathered chickens (YFCs) have a long history in China. They are well-known for the nutritional and commercial importance attributable to their yellow color phenotype. Currently, there is a huge paucity in knowledge of the genetic determinants responsible for phenotypic and biochemical properties of these iconic chickens. This study aimed to uncover the genetic structure and the molecular underpinnings of the YFCs trademark coloration.<h4>Results</h4>The whole-genomes o ...[more]

PMID: 32312230

Similar Datasets

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:Indigenous breeds develop their own genomic characteristics by adapting to local environments or cultures over long periods of time. Most of them are not particularly productive in commercial terms, but they have abilities to survive in harsh environments or tolerate to specific diseases. Their adaptive characteristics play an important role as genetic materials for improving commercial breeds. As a step toward this goal, we analyzed the genome of Korean indigenous goats within 10 goat breeds. We collected 136 goat individuals by sequencing 46 new goats and employing 90 publicly available goats. Our whole-genome data was comprised of three indigenous breeds (Korean indigenous goat, Iranian indigenous goat, and Moroccan indigenous goat; n = 29, 18, 20), six commercial breeds (Saanen, Boer, Anglo-Nubian, British Alpine, Alpine, and Korean crossbred; n = 16, 11, 5, 5, 2, 13), and their ancestral species (Capra aegagrus; n = 17). We identified that the Iranian indigenous goat and the Moroccan indigenous goat have relatively similar genomic characteristics within a large category of genomic diversity but found that the Korean indigenous goat has unique genomic characteristics distinguished from the other nine breeds. Through population analysis, we confirmed that these characteristics have resulted from a near-isolated environment with strong genetic drift. The Korean indigenous goat experienced a severe genetic bottleneck upon entering the Korean Peninsula about 2,000 years ago, and has subsequently rarely experienced genetic interactions with other goat breeds. From selection analysis and gene-set enrichment analysis, we revealed selection signals for Salmonella infection and cardiomyopathy in the genome of the Korean indigenous goat. These adaptive characteristics were further identified with genomic-based evidence. We uncovered genomic regions of selective sweeps in the LBP and BPI genes (Salmonella infection) and the TTN and ITGB6 genes (cardiomyopathy), among several candidate genes. Our research presents unique genomic characteristics and distinctive selection signals of the Korean indigenous goat based on the extensive comparison. Although the adaptive traits require further validation through biological experiments, our findings are expected to provide a direction for future biodiversity conservation strategies and to contribute another option to genomic-based breeding programmes for improving the viability of Capra hircus.

Dataset Information

Genome-wide genetic structure and selection signatures for color in 10 traditional Chinese yellow-feathered chicken breeds.

Publications

Genome-wide genetic structure and selection signatures for color in 10 traditional Chinese yellow-feathered chicken breeds.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets