Identification of Candidate Genes for Meat Color of Chicken by Combing Selection Signature Analyses and Differentially Expressed Genes
Meat color, an important index of chicken quality, is highly related to heme pigment, glycolysis, and intramuscular fat metabolisms. The objective of this study is to obtain candidate genes associated with meat color in chickens based on the comparison of fast-growing, white-feathered chickens (Line...
| Main Authors: | , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2022-02-01
|
| Series: | Genes |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2073-4425/13/2/307 |
| _version_ | 1797479867877425152 |
|---|---|
| author | Jiahong Sun Xiaodong Tan Xinting Yang Lu Bai Fuli Kong Guiping Zhao Jie Wen Ranran Liu |
| author_facet | Jiahong Sun Xiaodong Tan Xinting Yang Lu Bai Fuli Kong Guiping Zhao Jie Wen Ranran Liu |
| author_sort | Jiahong Sun |
| collection | DOAJ |
| description | Meat color, an important index of chicken quality, is highly related to heme pigment, glycolysis, and intramuscular fat metabolisms. The objective of this study is to obtain candidate genes associated with meat color in chickens based on the comparison of fast-growing, white-feathered chickens (Line B) and slow-growing, yellow-feathered chickens (Jingxing Yellow), which have significant differences in meat color. The differentially expressed genes (DEGs) between Line B and Jingxing Yellow were identified in beast muscle. The fixation index (<i>F<sub>ST</sub></i>) method was used to detect signatures of positive selection between the two breeds. Screening of 1109 genes by the <i>F<sub>ST</sub></i> and 1317 candidate DEGs identified by RNA-seq. After gene ontology analysis along with the Kyoto Encyclopedia of Genes and Genomes, 16 genes associated with glycolysis, fatty acid metabolism, protein metabolism, and heme content were identified as candidate genes that regulate the color of chicken breast meat, especially <i>TBXAS1</i> (redness), <i>GDPD5</i> (yellowness), <i>SLC2A6</i> (lightness), and <i>MMP27</i> (lightness). These findings should be helpful for further elucidating the molecular mechanisms and developing molecular markers to facilitate the selection of chicken meat color. |
| first_indexed | 2024-03-09T21:51:58Z |
| format | Article |
| id | doaj.art-82f5c582eee84d01b10ba0b2eb74bda9 |
| institution | Directory Open Access Journal |
| issn | 2073-4425 |
| language | English |
| last_indexed | 2024-03-09T21:51:58Z |
| publishDate | 2022-02-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Genes |
| spelling | doaj.art-82f5c582eee84d01b10ba0b2eb74bda92023-11-23T20:04:52ZengMDPI AGGenes2073-44252022-02-0113230710.3390/genes13020307Identification of Candidate Genes for Meat Color of Chicken by Combing Selection Signature Analyses and Differentially Expressed GenesJiahong Sun0Xiaodong Tan1Xinting Yang2Lu Bai3Fuli Kong4Guiping Zhao5Jie Wen6Ranran Liu7State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, ChinaState Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, ChinaState Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, ChinaState Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, ChinaState Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, ChinaState Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, ChinaState Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, ChinaState Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, ChinaMeat color, an important index of chicken quality, is highly related to heme pigment, glycolysis, and intramuscular fat metabolisms. The objective of this study is to obtain candidate genes associated with meat color in chickens based on the comparison of fast-growing, white-feathered chickens (Line B) and slow-growing, yellow-feathered chickens (Jingxing Yellow), which have significant differences in meat color. The differentially expressed genes (DEGs) between Line B and Jingxing Yellow were identified in beast muscle. The fixation index (<i>F<sub>ST</sub></i>) method was used to detect signatures of positive selection between the two breeds. Screening of 1109 genes by the <i>F<sub>ST</sub></i> and 1317 candidate DEGs identified by RNA-seq. After gene ontology analysis along with the Kyoto Encyclopedia of Genes and Genomes, 16 genes associated with glycolysis, fatty acid metabolism, protein metabolism, and heme content were identified as candidate genes that regulate the color of chicken breast meat, especially <i>TBXAS1</i> (redness), <i>GDPD5</i> (yellowness), <i>SLC2A6</i> (lightness), and <i>MMP27</i> (lightness). These findings should be helpful for further elucidating the molecular mechanisms and developing molecular markers to facilitate the selection of chicken meat color.https://www.mdpi.com/2073-4425/13/2/307breast muscleglycolysisheme pigmentslipid metabolism |
| spellingShingle | Jiahong Sun Xiaodong Tan Xinting Yang Lu Bai Fuli Kong Guiping Zhao Jie Wen Ranran Liu Identification of Candidate Genes for Meat Color of Chicken by Combing Selection Signature Analyses and Differentially Expressed Genes Genes breast muscle glycolysis heme pigments lipid metabolism |
| title | Identification of Candidate Genes for Meat Color of Chicken by Combing Selection Signature Analyses and Differentially Expressed Genes |
| title_full | Identification of Candidate Genes for Meat Color of Chicken by Combing Selection Signature Analyses and Differentially Expressed Genes |
| title_fullStr | Identification of Candidate Genes for Meat Color of Chicken by Combing Selection Signature Analyses and Differentially Expressed Genes |
| title_full_unstemmed | Identification of Candidate Genes for Meat Color of Chicken by Combing Selection Signature Analyses and Differentially Expressed Genes |
| title_short | Identification of Candidate Genes for Meat Color of Chicken by Combing Selection Signature Analyses and Differentially Expressed Genes |
| title_sort | identification of candidate genes for meat color of chicken by combing selection signature analyses and differentially expressed genes |
| topic | breast muscle glycolysis heme pigments lipid metabolism |
| url | https://www.mdpi.com/2073-4425/13/2/307 |
| work_keys_str_mv | AT jiahongsun identificationofcandidategenesformeatcolorofchickenbycombingselectionsignatureanalysesanddifferentiallyexpressedgenes AT xiaodongtan identificationofcandidategenesformeatcolorofchickenbycombingselectionsignatureanalysesanddifferentiallyexpressedgenes AT xintingyang identificationofcandidategenesformeatcolorofchickenbycombingselectionsignatureanalysesanddifferentiallyexpressedgenes AT lubai identificationofcandidategenesformeatcolorofchickenbycombingselectionsignatureanalysesanddifferentiallyexpressedgenes AT fulikong identificationofcandidategenesformeatcolorofchickenbycombingselectionsignatureanalysesanddifferentiallyexpressedgenes AT guipingzhao identificationofcandidategenesformeatcolorofchickenbycombingselectionsignatureanalysesanddifferentiallyexpressedgenes AT jiewen identificationofcandidategenesformeatcolorofchickenbycombingselectionsignatureanalysesanddifferentiallyexpressedgenes AT ranranliu identificationofcandidategenesformeatcolorofchickenbycombingselectionsignatureanalysesanddifferentiallyexpressedgenes |