1
|
Han ZP, Yang RZ, Zhou W, Zhang LL, Wang JR, Liu CJ, Liu SD. Population structure and selection signal analysis of indigenous sheep from the southern edge of the Taklamakan Desert. BMC Genomics 2024; 25:681. [PMID: 38982349 PMCID: PMC11232224 DOI: 10.1186/s12864-024-10581-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 06/28/2024] [Indexed: 07/11/2024] Open
Abstract
Analyzing the genetic diversity and selection characteristics of sheep (Ovis aries) holds significant value in understanding their environmental adaptability, enhancing breeding efficiency, and achieving effective conservation and rational utilization of genetic resources. In this study, we utilized Illumina Ovine SNP 50 K BeadChip data from four indigenous sheep breeds from the southern margin of the Taklamakan Desert (Duolang sheep: n = 36, Hetian sheep: n = 74, Kunlun sheep: n = 27, Qira black sheep: n = 178) and three foreign meat sheep breeds (Poll Dorset sheep: n = 105, Suffolk sheep: n = 153, Texel sheep: n = 150) to investigate the population structure, genetic diversity, and genomic signals of positive selection within the indigenous sheep. According to the Principal component analysis (PCA), the Neighbor-Joining tree (NJ tree), and Admixture, we revealed distinct clustering patterns of these seven sheep breeds based on their geographical distribution. Then used Cross Population Extended Haplotype Homozygosity (XP-EHH), Fixation Index (FST), and Integrated Haplotype Score (iHS), we identified a collective set of 32 overlapping genes under positive selection across four indigenous sheep breeds. These genes are associated with wool follicle development and wool traits, desert environmental adaptability, disease resistance, reproduction, and high-altitude adaptability. This study reveals the population structure and genomic selection characteristics in the extreme desert environments of native sheep breeds from the southern edge of the Taklimakan Desert, providing new insights into the conservation and sustainable use of indigenous sheep genetic resources in extreme environments. Additionally, these findings offer valuable genetic resources for sheep and other mammals to adapt to global climate change.
Collapse
Affiliation(s)
- Zhi-Peng Han
- College of Animal Science and Technology, Tarim University, Alar, 843300, China
- Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Alar, 843300, China
| | - Rui-Zhi Yang
- College of Animal Science and Technology, Tarim University, Alar, 843300, China
- Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Alar, 843300, China
| | - Wen Zhou
- College of Animal Science and Technology, Tarim University, Alar, 843300, China
- Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Alar, 843300, China
| | - Lu-Lu Zhang
- College of Animal Science and Technology, Tarim University, Alar, 843300, China
- Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Alar, 843300, China
| | - Jie-Ru Wang
- College of Animal Science and Technology, Tarim University, Alar, 843300, China
- Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Alar, 843300, China
| | - Chun-Jie Liu
- College of Animal Science and Technology, Tarim University, Alar, 843300, China
- Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Alar, 843300, China
| | - Shu-Dong Liu
- College of Animal Science and Technology, Tarim University, Alar, 843300, China.
- Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Alar, 843300, China.
| |
Collapse
|
2
|
Cui Z, Amevor FK, Lan X, Tang B, Qin S, Fu P, Liu A, Liu L. Integrative metabolomics and transcriptomics analysis revealed specific genes and metabolites affecting meat quality of chickens under different rearing systems. Poult Sci 2024; 103:103994. [PMID: 38991385 DOI: 10.1016/j.psj.2024.103994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2024] [Revised: 06/07/2024] [Accepted: 06/19/2024] [Indexed: 07/13/2024] Open
Abstract
Different rearing systems have varying effect on animal welfare and meat quality of poultry. Currently, there are no established standards for the rearing systems of Chinese indigenous chickens. Our study aimed to investigate the effects of different rearing systems on the meat quality, gene profiles, and metabolites of Chinese indigenous chickens (Nanchuan chicken). 10-wk-old Nanchuan chickens (n=360) were randomly divided into 3 groups (cage, net, and free-range groups), with 6 replicates per group (20 chickens per replicate). The experiment lasted for 12 wk. At 154-days-old, 36 healthy chickens (6 males and 6 females per group) were randomly selected, euthanized, and their breast muscles were collected to assess the meat quality parameters and histomorphological characteristics. Additionally, breast muscles from 18 random hens (3 males and 3 females per group) were used for metabolomics and RNA-seq analysis. The results showed that rearing systems significantly affected the meat quality and myofiber characteristics. The meat quality of breast muscles from free-range chickens was superior to that of caged chickens, characterized by more tender meat and smaller myofiber cross-sectional areas. Integrative metabolomics and transcriptomics analysis revealed that the differentially expressed genes of chicken breast muscles were primarily involved in the myofiber differentiation. Mechanically, the improved meat quality of breast muscle in free-range chickens were mainly associated with enhanced skeletal muscle differentiation facilitated by fibromodulin, increased levels of up-regulated Acetyl-L-carnitine and Propionylcarnitine level, and decreased levels of Nonanoic acid and Elaidic acid abundance (Graphical abstract). This provides a comprehensive understanding of the most effective and sustainable breeding, production, and rearing systems for Chinese indigenous chickens. It also contributes to the current knowledge of the molecular mechanisms underlying the effects of rearing systems on growth performance and meat quality of chickens.
Collapse
Affiliation(s)
- Zhifu Cui
- College of Animal Science and Technology, Southwest University, Beibei, 400715 Chongqing, P. R. China
| | - Felix Kwame Amevor
- State Key Laboratory of Swine and Poultry Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan Province, P. R. China
| | - Xi Lan
- College of Animal Science and Technology, Southwest University, Beibei, 400715 Chongqing, P. R. China
| | - Bincheng Tang
- College of Animal Science and Technology, Southwest University, Beibei, 400715 Chongqing, P. R. China
| | - Simeng Qin
- College of Animal Science and Technology, Southwest University, Beibei, 400715 Chongqing, P. R. China
| | - Penghui Fu
- College of Animal Science and Technology, Southwest University, Beibei, 400715 Chongqing, P. R. China
| | - Anfang Liu
- College of Animal Science and Technology, Southwest University, Beibei, 400715 Chongqing, P. R. China
| | - Lingbin Liu
- College of Animal Science and Technology, Southwest University, Beibei, 400715 Chongqing, P. R. China.
| |
Collapse
|
3
|
Xiao L, Qi L, Fu R, Nie Q, Zhang X, Luo W. A large-scale comparison of the meat quality characteristics of different chicken breeds in South China. Poult Sci 2024; 103:103740. [PMID: 38701629 PMCID: PMC11087722 DOI: 10.1016/j.psj.2024.103740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 03/26/2024] [Accepted: 04/03/2024] [Indexed: 05/05/2024] Open
Abstract
Meat quality traits are essential for producing high-quality broilers, but the genetic improvement has been limited by the complexity of measurement methods and the numerous traits involved. To systematically understand the meat quality characteristics of different broiler breeds, this study collected data on slaughter performance, skin color, fat deposition, and meat quality traits of 434 broilers from 12 different breeds in South China. The results showed that there was no significant difference in the live weight and slaughter weight of various broiler breeds at their respective market ages. Commercial broiler breeds such as Xiaobai and Huangma chickens had higher breast muscle and leg muscle rates. The skin and abdominal fat of Huangma chickens cultivated in the consumer market in South China exhibited significantly higher levels of yellowness compared to other varieties. Concerning fat traits, we observed that Wenchang chickens exhibited a strong ability to fat deposition, while the younger breeds showed lower fat deposition. Additionally, there were significant positive correlations found among different traits, including traits related to weight, traits related to fat, and skin color of different parts. Hierarchical clustering analysis revealed that fast-growing and large broiler Xiaobai chickens formed a distinct cluster based on carcass characteristics, skin color, and meat quality traits. Principal component analysis (PCA) was used to extract multiple principal components as substitutes for complex meat quality indicators, establishing a chicken meat quality evaluation model to differentiate between different breeds of chickens. At the same time, we identified 46, 22, and 20 SNP loci and their adjacent genes that were significantly associated with muscle mass traits, fat deposition, and skin color through genome-wide association studies (GWAS). The above results are helpful for systematically understanding the differences and characteristics of meat quality traits among different breeds.
Collapse
Affiliation(s)
- Liangchao Xiao
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangzhou 510642, China
| | - Lin Qi
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangzhou 510642, China
| | - Rong Fu
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangzhou 510642, China
| | - Qinghua Nie
- State Key Laboratory of Livestock and Poultry Breeding, and Lingnan Guangdong Laboratory of Agriculture, South China Agricultural University, Guangzhou 510642, China; Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangzhou 510642, China
| | - Xiquan Zhang
- State Key Laboratory of Livestock and Poultry Breeding, and Lingnan Guangdong Laboratory of Agriculture, South China Agricultural University, Guangzhou 510642, China; Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangzhou 510642, China
| | - Wen Luo
- State Key Laboratory of Livestock and Poultry Breeding, and Lingnan Guangdong Laboratory of Agriculture, South China Agricultural University, Guangzhou 510642, China; Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangzhou 510642, China.
| |
Collapse
|
4
|
Yuan C, Jiang Y, Wang Z, Chen G, Chang G, Bai H. Effects of Sex on Growth Performance, Carcass Traits, Blood Biochemical Parameters, and Meat Quality of XueShan Chickens. Animals (Basel) 2024; 14:1556. [PMID: 38891603 PMCID: PMC11171365 DOI: 10.3390/ani14111556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 05/21/2024] [Accepted: 05/22/2024] [Indexed: 06/21/2024] Open
Abstract
The demand for high-quality chilled chicken has continued to increase in China. Chickens are sexually dimorphic, and to better understand the specific differences in chicken production based on sex, we examined how sex affects growth performance, carcass traits, and meat quality of yellow-feathered chickens. Male and female Xueshan chickens were used as the experimental model. Although males exhibited better growth performance, including body weight (BW), body slope, keel, shank length, and shank girth (p < 0.05), as well as carcass traits, such as dressed weight, leg muscle, and lean meat, females had higher carcass and breast muscle yields (p < 0.05). Males had higher follicle density and yellowness (b*) of the skin and better skin than females (p < 0.05). Among blood biochemical parameters, the serum content of corticosterone (CORT) was higher in males, while those of superoxide dismutase (SOD), glutathione peroxidase (GSH-PX), total antioxidant capacity (T-AOC), and catalase (CAT) were lower in males than in females (p < 0.05). The pH levels, shear force, and moisture content quality were better in male breast meat, while the intramuscular fat content (IMF) was lower in males than in females (p < 0.05). The redness (a*) and moisture content were higher in male leg meat, while the pH, water-loss rate (WLR), lightness (L*), and IMF were lower (p < 0.05). The muscle fiber diameter and cross-sectional area were also higher in males (p < 0.05). Consumers felt that soup of male chicken was better than female (p < 0.05), while mouthfeel and tenderness acceptance of breast meat were different between the sexes. These results indicate that female chickens can be marketed as a whole carcass, while males are more suitable for processed carcass products. This study provides significant insights into the production and processing methodologies of yellow-feathered chickens.
Collapse
Affiliation(s)
- Chunyou Yuan
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Ministry of Education of China, Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou 225009, China; (C.Y.); (G.C.); (G.C.)
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Y.J.); (Z.W.)
| | - Yong Jiang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Y.J.); (Z.W.)
| | - Zhixiu Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Y.J.); (Z.W.)
| | - Guohong Chen
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Ministry of Education of China, Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou 225009, China; (C.Y.); (G.C.); (G.C.)
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Y.J.); (Z.W.)
| | - Guobin Chang
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Ministry of Education of China, Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou 225009, China; (C.Y.); (G.C.); (G.C.)
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Y.J.); (Z.W.)
| | - Hao Bai
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Ministry of Education of China, Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou 225009, China; (C.Y.); (G.C.); (G.C.)
| |
Collapse
|
5
|
Cha J, Jin D, Kim JH, Kim SC, Lim JA, Chai HH, Jung SA, Lee JH, Lee SH. Genome-wide association study revealed the genomic regions associated with skin pigmentation in an Ogye x White Leghorn F2 chicken population. Poult Sci 2023; 102:102720. [PMID: 37327746 PMCID: PMC10404675 DOI: 10.1016/j.psj.2023.102720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 04/03/2023] [Accepted: 04/10/2023] [Indexed: 06/18/2023] Open
Abstract
Skin color in chickens is an economically important trait that determines the first impression of a consumer toward a broiler and can ultimately affect consumer choice in the market. Therefore, identification of genomic regions associated with skin color is crucial for increasing the sales value of chickens. Although previous studies have attempted to reveal the genetic markers associated with the skin coloration in chickens, most were limited to investigations of candidate genes, such as melanin-related genes, and focused on case/control studies based on a single or small population. In this study, we performed a genome-wide association study (GWAS) on 770 F2 intercrosses produced by an experimental population of 2 chicken breeds, namely Ogye and White Leghorns, with different skin colors. The GWAS demonstrated that the L* value among the 3 skin color traits is highly heritable, and the genomic regions located on 2 chromosomes (20 and Z) were detected to harbor SNPs significantly associated with the skin color trait, accounting for most of the total genetic variance. Particular genomic regions spanning a ∼2.94 Mb region on GGA Z and a ∼3.58 Mb region on GGA 20 were significantly associated with skin color traits, and in these regions, certain candidate genes, including MTAP, FEM1C, GNAS, and EDN3, were found. Our findings could help elucidate the genetic mechanisms underlying chicken skin pigmentation. Furthermore, the candidate genes can be used to provide a valuable breeding strategy for the selection of specific chicken breeds with ideal skin coloration.
Collapse
Affiliation(s)
- Jihye Cha
- Animal Genome & Bioinformatics, National Institute of Animal Science, Rural Development Administration, Wanju 55365, South Korea
| | - Daehyeok Jin
- Animal Genetic Resources Research Center, National Institute of Animal Science, Rural Development Administration, Hamyang 50000, South Korea
| | - Jae-Hwan Kim
- Animal Genome & Bioinformatics, National Institute of Animal Science, Rural Development Administration, Wanju 55365, South Korea
| | - Seung-Chang Kim
- Animal Genetic Resources Research Center, National Institute of Animal Science, Rural Development Administration, Hamyang 50000, South Korea
| | - Jin A Lim
- Animal Genome & Bioinformatics, National Institute of Animal Science, Rural Development Administration, Wanju 55365, South Korea
| | - Han-Ha Chai
- Animal Genome & Bioinformatics, National Institute of Animal Science, Rural Development Administration, Wanju 55365, South Korea
| | - Seul A Jung
- Animal Genome & Bioinformatics, National Institute of Animal Science, Rural Development Administration, Wanju 55365, South Korea
| | - Jun-Heon Lee
- Department of Animal Science and Biotechnology, Chungnam National University, Daejeon 34134, South Korea
| | - Seung-Hwan Lee
- Department of Animal Science and Biotechnology, Chungnam National University, Daejeon 34134, South Korea.
| |
Collapse
|
6
|
Arora R, Sharma R, Ahlawat S, Chhabra P, Kumar A, Kaur M, Vijh RK, Lal SB, Mishra DC, Farooqi MS, Srivastava S. Transcriptomics reveals key genes responsible for functional diversity in pectoralis major muscles of native black Kadaknath and broiler chicken. 3 Biotech 2023; 13:253. [PMID: 37396468 PMCID: PMC10310660 DOI: 10.1007/s13205-023-03682-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 06/21/2023] [Indexed: 07/04/2023] Open
Abstract
RNA sequencing-based expression profiles from pectoralis major muscles of black meat (Kadaknath) and white meat (broiler) chicken were compared to identify differentially expressed genes. A total of 156 genes with log2 fold change ≥ ± 2.0 showed higher expression in Kadaknath and 68 genes were expressed at a lower level in comparison to broiler. Significantly enriched biological functions of up-regulated genes in Kadaknath were skeletal muscle cell differentiation, regulation of response to reactive oxygen, positive regulation of fat cell differentiation and melanosome. Significant ontology terms up-regulated in broiler included DNA replication origin binding, G-protein coupled receptor signaling pathway and chemokine activity. Highly inter-connected differentially expressed genes in Kadaknath (ATFs, C/EPDs) were observed to be important regulators of cellular adaptive functions, while in broiler, the hub genes were involved in cell cycle progression and DNA replication. The study is an attempt to get an insight into the transcript diversity of pectoralis major muscles of Kadaknath and broiler chicken. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03682-0.
Collapse
Affiliation(s)
- Reena Arora
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
- Animal Biotechnology Division, G T Road By-Pass, P O Box 129, Karnal, Haryana 132001 India
| | - Rekha Sharma
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - Sonika Ahlawat
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - Pooja Chhabra
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - Ashish Kumar
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - Mandeep Kaur
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | | | - Shashi Bhushan Lal
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | | | - Md. Samir Farooqi
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Sudhir Srivastava
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| |
Collapse
|
7
|
Zi X, Ge X, Zhu Y, Liu Y, Sun D, Li Z, Liu M, You Z, Wang B, Kang J, Dou T, Ge C, Wang K. Transcriptome Profile Analysis Identifies Candidate Genes for the Melanin Pigmentation of Skin in Tengchong Snow Chickens. Vet Sci 2023; 10:vetsci10050341. [PMID: 37235424 DOI: 10.3390/vetsci10050341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 05/05/2023] [Accepted: 05/08/2023] [Indexed: 05/28/2023] Open
Abstract
Tengchong Snow chickens are one of the most precious, black-boned chickens in Yunnan province and usually produce black meat. However, we found a small number of white meat traits in the chicken population during feeding. In order to determine the pattern of melanin deposition and the molecular mechanism of formation in the Tengchong Snow chicken, we measured the luminance value (L value) and melanin content in the skin of black meat chickens (Bc) and white meat chickens (Wc) using a color colorimeter, ELISA kit, and enzyme marker. The results showed that the L value of skin tissues in black meat chickens was significantly lower than that of white meat chickens, and the L value of skin tissues gradually increased with an increase in age. The melanin content of skin tissues in black meat chickens was higher than that of white meat chickens, and melanin content in the skin tissues gradually decreased with an increase in age, but this difference was not significant (p > 0.05); the L value of skin tissues in black meat chickens was negatively correlated with melanin content, and the correlation coefficient was mostly above -0.6. In addition, based on the phenotypic results, we chose to perform the comparative transcriptome profiling of skin tissues at 90 days of age. We screened a total of 44 differential genes, of which 32 were upregulated and 12 were downregulated. These DEGs were mainly involved in melanogenesis, tyrosine metabolism and RNA transport. We identified TYR, DCT, and EDNRB2 as possible master effector genes for skin pigmentation in Tengchong Snow black meat chickens through DEGs analysis. Finally, we measured the mRNA of TYR, DCT, MC1R, EDNRB2, GPR143, MITF, and TYRP1 genes through a quantitative real-time polymerase chain reaction (qPCR) and found that the mRNA of all the above seven genes decreased with increasing age. In conclusion, our study initially constructed an evaluation system for the black-boned traits of Tengchong Snow chickens and found key candidate genes regulating melanin deposition, which could provide an important theoretical basis for the selection and breeding of black-boned chickens.
Collapse
Affiliation(s)
- Xiannian Zi
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Xuehai Ge
- Shenzhen Hualong Sunda Information Technology Co., Ltd., Shenzhen 518000, China
| | - Yixuan Zhu
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Yong Liu
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Dawei Sun
- Yunnan Animal Science and Veterinary Institute, Kunming 650224, China
| | - Zijian Li
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Mengqian Liu
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Zhengrong You
- Zhaotong Animal Husbandry and Veterinary Technology Extension Station, Zhaotong 657000, China
| | - Bo Wang
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Jiajia Kang
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Tengfei Dou
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Changrong Ge
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Kun Wang
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| |
Collapse
|
8
|
Variations in BCO2 Coding Sequence Causing a Difference in Carotenoid Concentration in the Skin of Chinese Indigenous Chicken. Genes (Basel) 2023; 14:genes14030671. [PMID: 36980942 PMCID: PMC10048632 DOI: 10.3390/genes14030671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/03/2023] [Accepted: 03/07/2023] [Indexed: 03/11/2023] Open
Abstract
Carotenoid consumption decreases the risk of cancer, osteoporosis, or neurodegenerative diseases through interrupting the formation of free radicals. The deposition of carotenoids in chicken skin makes the skin color turn from white into yellow. The enzyme β-carotene oxygenase 2 (BCO2) plays a key role during the degradation process of carotenoids in skin. How the BCO2 affects the skin color of the chicken and whether it is the key factor that results in the phenotypic difference between yellow- and white-skin chickens are still unclear. In this research, the measurement of the concentration of carotenoids in chicken skin by HPLC showed that the carotenoid concentration in chickens with a yellow skin was significantly higher than that in white-skin chickens. Moreover, there were significant differences in BCO2 gene expression in the back skin between yellow- and white-skin chickens. Scanning the SNPs in BCO2 gene revealed a G/A mutation in exon 6 of the BCO2 gene in white and yellow skin chicken. Generally, one SNP c.890A>G was found to be associated with the chicken skin color and may be used as a genetic marker in breeding for yellow skin in Chinese indigenous chickens.
Collapse
|
9
|
He S, Ren T, Lin W, Yang X, Hao T, Zhao G, Luo W, Nie Q, Zhang X. Identification of candidate genes associated with skin yellowness in yellow chickens. Poult Sci 2023; 102:102469. [PMID: 36709583 PMCID: PMC9922980 DOI: 10.1016/j.psj.2022.102469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 12/04/2022] [Accepted: 12/29/2022] [Indexed: 01/11/2023] Open
Abstract
The yellow color of the skin is an important economic trait for yellow chickens. Low and non-uniform skin yellowness would reduce economic efficiency. However, the regulatory mechanism of chicken skin yellowness has not been fully elucidated. In this study, we evaluated the skin yellowness of 819 chickens by colorimeter and digital camera, which are from the same batch and the same age of 2 pure lines with significant differences in skin yellowness. A total of 982 candidate differential expressed genes (DEGs) were detected in duodenal tissue by RNA-seq analysis for high and low yellowness chickens. Among the DEGs, we chose fatty acid translocase (CD36) gene and identified a single nucleotide polymorphism (SNP) upstream of the CD36 gene that was significantly associated with skin yellowness at multiple parts of the chicken, and its different genotypes had significant effects on the promoter activity of the CD36 gene. These findings will help to further elucidate the molecular mechanism of chicken skin yellowness and is helpful for improving chicken skin yellowness.
Collapse
Affiliation(s)
- Shizi He
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong, China,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Guangzhou, 510642, Guangdong, China
| | - Tuanhui Ren
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong, China,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Guangzhou, 510642, Guangdong, China
| | - Wujian Lin
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong, China,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Guangzhou, 510642, Guangdong, China
| | - Xiuxian Yang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong, China,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Guangzhou, 510642, Guangdong, China
| | - Tianqi Hao
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong, China,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Guangzhou, 510642, Guangdong, China
| | - Guoxi Zhao
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong, China,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Guangzhou, 510642, Guangdong, China
| | - Wen Luo
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong, China,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Guangzhou, 510642, Guangdong, China
| | - Qinghua Nie
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong, China,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Guangzhou, 510642, Guangdong, China
| | - Xiquan Zhang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Guangzhou, 510642, Guangdong, China.
| |
Collapse
|
10
|
Indigenous, Yellow-Feathered Chickens Body Measurements, Carcass Traits, and Meat Quality Depending on Marketable Age. Animals (Basel) 2022; 12:ani12182422. [PMID: 36139280 PMCID: PMC9495107 DOI: 10.3390/ani12182422] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 09/08/2022] [Accepted: 09/09/2022] [Indexed: 11/21/2022] Open
Abstract
Given an increasing trend in slaughter and chilling for the sale of chickens in China, it is important to determine the marketable age of chickens for chilled sales. This study determined the effects of two marketable ages on the body measurements, carcass traits, and meat quality of yellow-feathered chickens. A total of 360 healthy one-day-old male Xueshan chickens were raised in six pens (straw-covered floor, numbered 1 to 6) and treated in the same manner (free access to food and water) until day 100. Sixty chickens from pens numbered 1 to 3 and 4 to 6 were selected to determine the body measurements, carcass traits, and meat quality at two slaughter ages (90 and 100 days), respectively. One hundred-day-old chickens had a higher body slope, cockscomb, keel, shank lengths, and higher live and dressed weights (p < 0.05). The abdomen skin follicle density, a*(redness) and b*(yellowness) values were higher in 100-day-old chickens (p < 0.05), whereas the 90-day-old chickens were characterized by better spotted skin. For the breast muscle, pH, shear force, a*, moisture, and protein and intramuscular fat contents were lower; moreover, L*(lightness) and b* were higher in 90-day-old chickens. In leg muscles, the pH, shear force, L*, b* and collagen content were lower; furthermore, the a* and moisture contents were higher in 90-day-old chickens (p < 0.05). These findings indicate that two marketable ages both have pros and cons, but 90 days chickens perform better on carcass appearance, and producers can adjust the marketable age to meet needs of different consumers. This study provides a unique idea and theoretical reference for breeding and marketing yellow-feathered chickens.
Collapse
|
11
|
Deng S, Liu R, Li C, Xu X, Zhou G. Meat quality and flavor compounds of soft-boiled chickens: Effect of Chinese yellow-feathered chicken breed and slaughter age. Poult Sci 2022; 101:102168. [PMID: 36228527 PMCID: PMC9573924 DOI: 10.1016/j.psj.2022.102168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 08/11/2022] [Accepted: 08/30/2022] [Indexed: 11/29/2022] Open
Abstract
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.
Collapse
Affiliation(s)
- Shaolin Deng
- Key Laboratory of Meat Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Rui Liu
- College of Food Science and Engineering, Yangzhou University, Industrial Engineering Center for Huaiyang Cuisine of Jiangsu Province, Yangzhou, 225127, China
| | - Chunbao Li
- Key Laboratory of Meat Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xinglian Xu
- Key Laboratory of Meat Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Guanghong Zhou
- Key Laboratory of Meat Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China.
| |
Collapse
|
12
|
The Effect of Breed and Age on the Growth Performance, Carcass Traits and Metabolic Profile in Breast Muscle of Chinese Indigenous Chickens. Foods 2022; 11:foods11030483. [PMID: 35159633 PMCID: PMC8834177 DOI: 10.3390/foods11030483] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 01/24/2022] [Accepted: 01/26/2022] [Indexed: 02/05/2023] Open
Abstract
Indigenous chickens possess desirable characteristics and account for considerable proportions of the total chicken production in China. The current study examined the growth performance, carcass characteristics and muscle metabolites among a crossbred broiler and two indigenous, yellow-feathered chickens (Mahuang and Tuer) with different ages (60 and 75 days). Results indicated that the crossbred broiler had better feed efficiency, higher breast and thigh muscle yield, as well as a lower abdominal fat percentage than Mahuang and Tuer chickens (p < 0.05). Gas chromatography–mass spectrometry-based metabolomics and multivariate analysis revealed sugars, amino acids and organic acids were the predominant metabolites that differed among the three chicken breeds. Growth performance and carcass traits of yellow-feathered chickens exhibited significant differences with the extension of the feeding period (p < 0.05). Moreover, differential metabolites reflected altered aminoacyl-tRNA biosynthesis, ATP-binding cassette transporters, pantothenate and CoA biosynthesis, as well as glutathione metabolism in yellow-feathered chickens affected by age. Collectively, this study contributes to a deeper understanding of the production efficiency and chemical composition of precursor flavor in Chinese indigenous, yellow-feathered chicken.
Collapse
|