Long-read sequencing-based transcriptomic landscape in longissimus dorsi and transcriptome-wide association studies for growth traits of meat rabbits
Rabbits are an attractive meat livestock species that can efficiently convert human-indigestible plant biomass, and have been commonly used in biological and medical researches. Yet, transcriptomic landscape in muscle tissue and association between gene expression level and growth traits have not be...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2024-01-01
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| Series: | Frontiers in Veterinary Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fvets.2024.1320484/full |
| _version_ | 1797349432432263168 |
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| author | Xianbo Jia Zhe Kang Guozhi Wang Kai Zhang Xiangchao Fu Congyan Li Songjia Lai Shi-Yi Chen |
| author_facet | Xianbo Jia Zhe Kang Guozhi Wang Kai Zhang Xiangchao Fu Congyan Li Songjia Lai Shi-Yi Chen |
| author_sort | Xianbo Jia |
| collection | DOAJ |
| description | Rabbits are an attractive meat livestock species that can efficiently convert human-indigestible plant biomass, and have been commonly used in biological and medical researches. Yet, transcriptomic landscape in muscle tissue and association between gene expression level and growth traits have not been specially studied in meat rabbits. In this study Oxford Nanopore Technologies (ONT) long-read sequencing technology was used for comprehensively exploring transcriptomic landscape in Longissimus dorsi for 115 rabbits at 84 days of age, and transcriptome-wide association studies (TWAS) were performed for growth traits, including body weight at 84 days of age and average daily gain during three growth periods. The statistical analysis of TWAS was performed using a mixed linear model, in which polygenic effect was fitted as a random effect according to gene expression level-based relationships. A total of 18,842 genes and 42,010 transcripts were detected, among which 35% of genes and 47% of transcripts were novel in comparison with the reference genome annotation. Furthermore, 45% of genes were widely expressed among more than 90% of individuals. The proportions (±SE) of phenotype variance explained by genome-wide gene expression level ranged from 0.501 ± 0.216 to 0.956 ± 0.209, and the similar results were obtained when explained by transcript expression level. In contrast, neither gene nor transcript was detected by TWAS to be statistically significantly associated with these growth traits. In conclusion, these novel genes and transcripts that have been extensively profiled in a single muscle tissue using long-read sequencing technology will greatly improve our understanding on transcriptional diversity in rabbits. Our results with a relatively small sample size further revealed the important contribution of global gene expression to phenotypic variation on growth performance, but it seemed that no single gene has an outstanding effect; this knowledge is helpful to include intermediate omics data for implementing genetic evaluation of growth traits in meat rabbits. |
| first_indexed | 2024-03-08T12:30:09Z |
| format | Article |
| id | doaj.art-5f457ef8abb643a9806bd0c7548917be |
| institution | Directory Open Access Journal |
| issn | 2297-1769 |
| language | English |
| last_indexed | 2024-03-08T12:30:09Z |
| publishDate | 2024-01-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Veterinary Science |
| spelling | doaj.art-5f457ef8abb643a9806bd0c7548917be2024-01-22T04:28:36ZengFrontiers Media S.A.Frontiers in Veterinary Science2297-17692024-01-011110.3389/fvets.2024.13204841320484Long-read sequencing-based transcriptomic landscape in longissimus dorsi and transcriptome-wide association studies for growth traits of meat rabbitsXianbo Jia0Zhe Kang1Guozhi Wang2Kai Zhang3Xiangchao Fu4Congyan Li5Songjia Lai6Shi-Yi Chen7Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, ChinaFarm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, ChinaFarm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, ChinaSichuan Academy of Grassland Sciences, Chengdu, ChinaSichuan Academy of Grassland Sciences, Chengdu, ChinaAnimal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, ChinaFarm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, ChinaFarm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, ChinaRabbits are an attractive meat livestock species that can efficiently convert human-indigestible plant biomass, and have been commonly used in biological and medical researches. Yet, transcriptomic landscape in muscle tissue and association between gene expression level and growth traits have not been specially studied in meat rabbits. In this study Oxford Nanopore Technologies (ONT) long-read sequencing technology was used for comprehensively exploring transcriptomic landscape in Longissimus dorsi for 115 rabbits at 84 days of age, and transcriptome-wide association studies (TWAS) were performed for growth traits, including body weight at 84 days of age and average daily gain during three growth periods. The statistical analysis of TWAS was performed using a mixed linear model, in which polygenic effect was fitted as a random effect according to gene expression level-based relationships. A total of 18,842 genes and 42,010 transcripts were detected, among which 35% of genes and 47% of transcripts were novel in comparison with the reference genome annotation. Furthermore, 45% of genes were widely expressed among more than 90% of individuals. The proportions (±SE) of phenotype variance explained by genome-wide gene expression level ranged from 0.501 ± 0.216 to 0.956 ± 0.209, and the similar results were obtained when explained by transcript expression level. In contrast, neither gene nor transcript was detected by TWAS to be statistically significantly associated with these growth traits. In conclusion, these novel genes and transcripts that have been extensively profiled in a single muscle tissue using long-read sequencing technology will greatly improve our understanding on transcriptional diversity in rabbits. Our results with a relatively small sample size further revealed the important contribution of global gene expression to phenotypic variation on growth performance, but it seemed that no single gene has an outstanding effect; this knowledge is helpful to include intermediate omics data for implementing genetic evaluation of growth traits in meat rabbits.https://www.frontiersin.org/articles/10.3389/fvets.2024.1320484/fullTWASvariance componentsbody weightaverage daily gaingrowth performance |
| spellingShingle | Xianbo Jia Zhe Kang Guozhi Wang Kai Zhang Xiangchao Fu Congyan Li Songjia Lai Shi-Yi Chen Long-read sequencing-based transcriptomic landscape in longissimus dorsi and transcriptome-wide association studies for growth traits of meat rabbits Frontiers in Veterinary Science TWAS variance components body weight average daily gain growth performance |
| title | Long-read sequencing-based transcriptomic landscape in longissimus dorsi and transcriptome-wide association studies for growth traits of meat rabbits |
| title_full | Long-read sequencing-based transcriptomic landscape in longissimus dorsi and transcriptome-wide association studies for growth traits of meat rabbits |
| title_fullStr | Long-read sequencing-based transcriptomic landscape in longissimus dorsi and transcriptome-wide association studies for growth traits of meat rabbits |
| title_full_unstemmed | Long-read sequencing-based transcriptomic landscape in longissimus dorsi and transcriptome-wide association studies for growth traits of meat rabbits |
| title_short | Long-read sequencing-based transcriptomic landscape in longissimus dorsi and transcriptome-wide association studies for growth traits of meat rabbits |
| title_sort | long read sequencing based transcriptomic landscape in longissimus dorsi and transcriptome wide association studies for growth traits of meat rabbits |
| topic | TWAS variance components body weight average daily gain growth performance |
| url | https://www.frontiersin.org/articles/10.3389/fvets.2024.1320484/full |
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