Genome-wide association studies detects candidate genes for wool traits by re-sequencing in Chinese fine-wool sheep
Abstract Background The quality and yield of wool determine the economic value of the fine-wool sheep. Therefore, discovering markers or genes relevant to wool traits is the cornerstone for the breeding of fine-wool sheep. In this study, we used the Illumina HiSeq X Ten platform to re-sequence 460 s...
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| Format: | Article |
| Language: | English |
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BMC
2021-02-01
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| Series: | BMC Genomics |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12864-021-07399-3 |
| _version_ | 1819297694692147200 |
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| author | Hongchang Zhao Tingting Guo Zengkui Lu Jianbin Liu Shaohua Zhu Guoyan Qiao Mei Han Chao Yuan Tianxiang Wang Fanwen Li Yajun Zhang Fujun Hou Yaojing Yue Bohui Yang |
| author_facet | Hongchang Zhao Tingting Guo Zengkui Lu Jianbin Liu Shaohua Zhu Guoyan Qiao Mei Han Chao Yuan Tianxiang Wang Fanwen Li Yajun Zhang Fujun Hou Yaojing Yue Bohui Yang |
| author_sort | Hongchang Zhao |
| collection | DOAJ |
| description | Abstract Background The quality and yield of wool determine the economic value of the fine-wool sheep. Therefore, discovering markers or genes relevant to wool traits is the cornerstone for the breeding of fine-wool sheep. In this study, we used the Illumina HiSeq X Ten platform to re-sequence 460 sheep belonging to four different fine-wool sheep breeds, namely, Alpine Merino sheep (AMS), Chinese Merino sheep (CMS), Aohan fine-wool sheep (AHS) and Qinghai fine-wool sheep (QHS). Eight wool traits, including fiber diameter (FD), fiber diameter coefficient of variance (FDCV), fiber diameter standard deviation (FDSD), staple length (SL), greasy fleece weight (GFW), clean wool rate (CWR), staple strength (SS) and staple elongation (SE) were examined. A genome-wide association study (GWAS) was performed to detect the candidate genes for the eight wool traits. Results A total of 8.222 Tb of raw data was generated, with an average of approximately 8.59X sequencing depth. After quality control, 12,561,225 SNPs were available for analysis. And a total of 57 genome-wide significant SNPs and 30 candidate genes were detected for the desired wool traits. Among them, 7 SNPs and 6 genes are related to wool fineness indicators (FD, FDCV and FDSD), 10 SNPs and 7 genes are related to staple length, 13 SNPs and 7 genes are related to wool production indicators (GFW and CWR), 27 SNPs and 10 genes associated with staple elongation. Among these candidate genes, UBE2E3 and RHPN2 associated with fiber diameter, were found to play an important role in keratinocyte differentiation and cell proliferation. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment results, revealed that multitude significant pathways are related to keratin and cell proliferation and differentiation, such as positive regulation of canonical Wnt signaling pathway (GO:0090263). Conclusion This is the first GWAS on the wool traits by using re-sequencing data in Chinese fine-wool sheep. The newly detected significant SNPs in this study can be used in genome-selective breeding for the fine-wool sheep. And the new candidate genes would provide a good theoretical basis for the fine-wool sheep breeding. |
| first_indexed | 2024-12-24T05:18:05Z |
| format | Article |
| id | doaj.art-b9ba907091fc47028c0962c3e605af7d |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-24T05:18:05Z |
| publishDate | 2021-02-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-b9ba907091fc47028c0962c3e605af7d2022-12-21T17:13:32ZengBMCBMC Genomics1471-21642021-02-0122111310.1186/s12864-021-07399-3Genome-wide association studies detects candidate genes for wool traits by re-sequencing in Chinese fine-wool sheepHongchang Zhao0Tingting Guo1Zengkui Lu2Jianbin Liu3Shaohua Zhu4Guoyan Qiao5Mei Han6Chao Yuan7Tianxiang Wang8Fanwen Li9Yajun Zhang10Fujun Hou11Yaojing Yue12Bohui Yang13Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural SciencesLanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural SciencesLanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural SciencesLanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural SciencesLanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural SciencesLanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural SciencesLanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural SciencesLanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural SciencesGansu Provincial Sheep Breeding Technology Extension StationGansu Provincial Sheep Breeding Technology Extension StationXinjiang Gongnaisi Breeding Sheep FarmAohan Banner Breeding Sheep FarmLanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural SciencesLanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural SciencesAbstract Background The quality and yield of wool determine the economic value of the fine-wool sheep. Therefore, discovering markers or genes relevant to wool traits is the cornerstone for the breeding of fine-wool sheep. In this study, we used the Illumina HiSeq X Ten platform to re-sequence 460 sheep belonging to four different fine-wool sheep breeds, namely, Alpine Merino sheep (AMS), Chinese Merino sheep (CMS), Aohan fine-wool sheep (AHS) and Qinghai fine-wool sheep (QHS). Eight wool traits, including fiber diameter (FD), fiber diameter coefficient of variance (FDCV), fiber diameter standard deviation (FDSD), staple length (SL), greasy fleece weight (GFW), clean wool rate (CWR), staple strength (SS) and staple elongation (SE) were examined. A genome-wide association study (GWAS) was performed to detect the candidate genes for the eight wool traits. Results A total of 8.222 Tb of raw data was generated, with an average of approximately 8.59X sequencing depth. After quality control, 12,561,225 SNPs were available for analysis. And a total of 57 genome-wide significant SNPs and 30 candidate genes were detected for the desired wool traits. Among them, 7 SNPs and 6 genes are related to wool fineness indicators (FD, FDCV and FDSD), 10 SNPs and 7 genes are related to staple length, 13 SNPs and 7 genes are related to wool production indicators (GFW and CWR), 27 SNPs and 10 genes associated with staple elongation. Among these candidate genes, UBE2E3 and RHPN2 associated with fiber diameter, were found to play an important role in keratinocyte differentiation and cell proliferation. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment results, revealed that multitude significant pathways are related to keratin and cell proliferation and differentiation, such as positive regulation of canonical Wnt signaling pathway (GO:0090263). Conclusion This is the first GWAS on the wool traits by using re-sequencing data in Chinese fine-wool sheep. The newly detected significant SNPs in this study can be used in genome-selective breeding for the fine-wool sheep. And the new candidate genes would provide a good theoretical basis for the fine-wool sheep breeding.https://doi.org/10.1186/s12864-021-07399-3Fine-wool sheepRe-sequencingGWASEnrichment analysesWool traits |
| spellingShingle | Hongchang Zhao Tingting Guo Zengkui Lu Jianbin Liu Shaohua Zhu Guoyan Qiao Mei Han Chao Yuan Tianxiang Wang Fanwen Li Yajun Zhang Fujun Hou Yaojing Yue Bohui Yang Genome-wide association studies detects candidate genes for wool traits by re-sequencing in Chinese fine-wool sheep BMC Genomics Fine-wool sheep Re-sequencing GWAS Enrichment analyses Wool traits |
| title | Genome-wide association studies detects candidate genes for wool traits by re-sequencing in Chinese fine-wool sheep |
| title_full | Genome-wide association studies detects candidate genes for wool traits by re-sequencing in Chinese fine-wool sheep |
| title_fullStr | Genome-wide association studies detects candidate genes for wool traits by re-sequencing in Chinese fine-wool sheep |
| title_full_unstemmed | Genome-wide association studies detects candidate genes for wool traits by re-sequencing in Chinese fine-wool sheep |
| title_short | Genome-wide association studies detects candidate genes for wool traits by re-sequencing in Chinese fine-wool sheep |
| title_sort | genome wide association studies detects candidate genes for wool traits by re sequencing in chinese fine wool sheep |
| topic | Fine-wool sheep Re-sequencing GWAS Enrichment analyses Wool traits |
| url | https://doi.org/10.1186/s12864-021-07399-3 |
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