Detection of structural variants linked to mutton flavor and odor in two closely related black goat breeds
Abstract Background Mutton quality is closely related to genetic variants and gene expression alterations during growth and development, resulting in differences in nutritional values, flavor, and odor. Results We first evaluated and compared the composition of crude protein, crude fat, cholesterol,...
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2024-10-01
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| Online Access: | https://doi.org/10.1186/s12864-024-10874-2 |
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| author | Lingle Chang Xi Niu Shihui Huang Derong Song Xueqin Ran Jiafu Wang |
| author_facet | Lingle Chang Xi Niu Shihui Huang Derong Song Xueqin Ran Jiafu Wang |
| author_sort | Lingle Chang |
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| description | Abstract Background Mutton quality is closely related to genetic variants and gene expression alterations during growth and development, resulting in differences in nutritional values, flavor, and odor. Results We first evaluated and compared the composition of crude protein, crude fat, cholesterol, amino acid (AA), and fatty acid (FA) in the longissimus dorsi muscle of Guizhou black goats (GZB, n = 5) and Yunshang black goats (YBG, n = 6). The contents of cholesterol and FA related to odor in GZB were significantly lower than that in YBG, while the concentrations of umami amino acids and intramuscular fat were significantly higher in GZB. Furthermore, structural variants (SVs) in the genomes of GZB (n = 30) and YBG (n = 11) were explored. It was found that some regions in Chr 10/12/18 were densely involved with a large number of SVs in the genomes of GZB and YBG. By setting F ST ≥ 0.25, we got 837 stratified SVs, of which 25 SVs (involved in 12 genes, e.g., CORO1A, CLIC6, PCSK2, and TMEM9) were limited in GZB. Functional enrichment analysis of 14 protein-coding genes (e.g., ENPEP, LIPC, ABCA5, and SLC6A15) revealed multiple terms and pathways related with metabolisms of AA, FA, and cholesterol. The SVs (n = 10) obtained by the whole genome resequencing were confirmed in percentages of 36.67 to 86.67% (n = 96) by PCR method. The SVa and SVd polymorphisms indicated a moderate negative correlation with HMGCS1 activity (n = 17). Conclusion This study is the first to comprehensively reveal potential SVs related to mutton nutritional values, flavor, and odor based on genomic compare between two black goat breeds with closely genetic relationship. The SVs generated in this study provide a data resource for deeper studies to understand the genomic characteristics and possible evolutionary outcomes with better nutritional values, flavor and extremely light odor. |
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| spelling | doaj-art-dbfaa6391fb24ea9beb94451ad3221752025-08-20T02:17:39ZengBMCBMC Genomics1471-21642024-10-0125111110.1186/s12864-024-10874-2Detection of structural variants linked to mutton flavor and odor in two closely related black goat breedsLingle Chang0Xi Niu1Shihui Huang2Derong Song3Xueqin Ran4Jiafu Wang5College of Animal Science, Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region (Ministry of Education), Guizhou UniversityInstitute of Agro-Bioengineering/Key Laboratory of Plant Resource Conservative and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences, Guizhou UniversityCollege of Animal Science, Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region (Ministry of Education), Guizhou UniversityBijie Academy of Agricultural SciencesCollege of Animal Science, Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region (Ministry of Education), Guizhou UniversityInstitute of Agro-Bioengineering/Key Laboratory of Plant Resource Conservative and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences, Guizhou UniversityAbstract Background Mutton quality is closely related to genetic variants and gene expression alterations during growth and development, resulting in differences in nutritional values, flavor, and odor. Results We first evaluated and compared the composition of crude protein, crude fat, cholesterol, amino acid (AA), and fatty acid (FA) in the longissimus dorsi muscle of Guizhou black goats (GZB, n = 5) and Yunshang black goats (YBG, n = 6). The contents of cholesterol and FA related to odor in GZB were significantly lower than that in YBG, while the concentrations of umami amino acids and intramuscular fat were significantly higher in GZB. Furthermore, structural variants (SVs) in the genomes of GZB (n = 30) and YBG (n = 11) were explored. It was found that some regions in Chr 10/12/18 were densely involved with a large number of SVs in the genomes of GZB and YBG. By setting F ST ≥ 0.25, we got 837 stratified SVs, of which 25 SVs (involved in 12 genes, e.g., CORO1A, CLIC6, PCSK2, and TMEM9) were limited in GZB. Functional enrichment analysis of 14 protein-coding genes (e.g., ENPEP, LIPC, ABCA5, and SLC6A15) revealed multiple terms and pathways related with metabolisms of AA, FA, and cholesterol. The SVs (n = 10) obtained by the whole genome resequencing were confirmed in percentages of 36.67 to 86.67% (n = 96) by PCR method. The SVa and SVd polymorphisms indicated a moderate negative correlation with HMGCS1 activity (n = 17). Conclusion This study is the first to comprehensively reveal potential SVs related to mutton nutritional values, flavor, and odor based on genomic compare between two black goat breeds with closely genetic relationship. The SVs generated in this study provide a data resource for deeper studies to understand the genomic characteristics and possible evolutionary outcomes with better nutritional values, flavor and extremely light odor.https://doi.org/10.1186/s12864-024-10874-2Structural variantFixation indexMuttonGuizhou black goatYunshang black goat |
| spellingShingle | Lingle Chang Xi Niu Shihui Huang Derong Song Xueqin Ran Jiafu Wang Detection of structural variants linked to mutton flavor and odor in two closely related black goat breeds BMC Genomics Structural variant Fixation index Mutton Guizhou black goat Yunshang black goat |
| title | Detection of structural variants linked to mutton flavor and odor in two closely related black goat breeds |
| title_full | Detection of structural variants linked to mutton flavor and odor in two closely related black goat breeds |
| title_fullStr | Detection of structural variants linked to mutton flavor and odor in two closely related black goat breeds |
| title_full_unstemmed | Detection of structural variants linked to mutton flavor and odor in two closely related black goat breeds |
| title_short | Detection of structural variants linked to mutton flavor and odor in two closely related black goat breeds |
| title_sort | detection of structural variants linked to mutton flavor and odor in two closely related black goat breeds |
| topic | Structural variant Fixation index Mutton Guizhou black goat Yunshang black goat |
| url | https://doi.org/10.1186/s12864-024-10874-2 |
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