Genome-Wide Selective Signatures Reveal Candidate Genes Associated with Hair Follicle Development and Wool Shedding in Sheep
Hair follicle development and wool shedding in sheep are poorly understood. This study investigated the population structures and genetic differences between sheep with different wool types to identify candidate genes related to these traits. We used Illumina ovine SNP 50K chip genotyping data of 79...
| Main Authors: | , , , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2021-11-01
|
| Series: | Genes |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2073-4425/12/12/1924 |
| _version_ | 1797504297863217152 |
|---|---|
| author | Zhihui Lei Weibo Sun Tingting Guo Jianye Li Shaohua Zhu Zengkui Lu Guoyan Qiao Mei Han Hongchang Zhao Bohui Yang Liping Zhang Jianbin Liu Chao Yuan Yaojing Yue |
| author_facet | Zhihui Lei Weibo Sun Tingting Guo Jianye Li Shaohua Zhu Zengkui Lu Guoyan Qiao Mei Han Hongchang Zhao Bohui Yang Liping Zhang Jianbin Liu Chao Yuan Yaojing Yue |
| author_sort | Zhihui Lei |
| collection | DOAJ |
| description | Hair follicle development and wool shedding in sheep are poorly understood. This study investigated the population structures and genetic differences between sheep with different wool types to identify candidate genes related to these traits. We used Illumina ovine SNP 50K chip genotyping data of 795 sheep populations comprising 27 breeds with two wool types, measuring the population differentiation index (Fst), nucleotide diversity (θπ ratio), and extended haplotype homozygosity among populations (XP-EHH) to detect the selective signatures of hair sheep and fine-wool sheep. The top 5% of the Fst and θπ ratio values, and values of XP-EHH < −2 were considered strongly selected SNP sites. Annotation showed that the <i>PRX</i>, <i>SOX18</i>, <i>TGM3</i>, and <i>TCF3</i> genes related to hair follicle development and wool shedding were strongly selected. Our results indicated that these methods identified important genes related to hair follicle formation, epidermal differentiation, and hair follicle stem cell development, and provide a meaningful reference for further study on the molecular mechanisms of economically important traits in sheep. |
| first_indexed | 2024-03-10T04:02:39Z |
| format | Article |
| id | doaj.art-a47629bc53ba42babf324444e6d5a815 |
| institution | Directory Open Access Journal |
| issn | 2073-4425 |
| language | English |
| last_indexed | 2024-03-10T04:02:39Z |
| publishDate | 2021-11-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Genes |
| spelling | doaj.art-a47629bc53ba42babf324444e6d5a8152023-11-23T08:30:28ZengMDPI AGGenes2073-44252021-11-011212192410.3390/genes12121924Genome-Wide Selective Signatures Reveal Candidate Genes Associated with Hair Follicle Development and Wool Shedding in SheepZhihui Lei0Weibo Sun1Tingting Guo2Jianye Li3Shaohua Zhu4Zengkui Lu5Guoyan Qiao6Mei Han7Hongchang Zhao8Bohui Yang9Liping Zhang10Jianbin Liu11Chao Yuan12Yaojing Yue13Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, ChinaLanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, ChinaLanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, ChinaLanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, ChinaCollege of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, ChinaLanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, ChinaLanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, ChinaLanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, ChinaLanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, ChinaLanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, ChinaCollege of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, ChinaLanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, ChinaLanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, ChinaLanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, ChinaHair follicle development and wool shedding in sheep are poorly understood. This study investigated the population structures and genetic differences between sheep with different wool types to identify candidate genes related to these traits. We used Illumina ovine SNP 50K chip genotyping data of 795 sheep populations comprising 27 breeds with two wool types, measuring the population differentiation index (Fst), nucleotide diversity (θπ ratio), and extended haplotype homozygosity among populations (XP-EHH) to detect the selective signatures of hair sheep and fine-wool sheep. The top 5% of the Fst and θπ ratio values, and values of XP-EHH < −2 were considered strongly selected SNP sites. Annotation showed that the <i>PRX</i>, <i>SOX18</i>, <i>TGM3</i>, and <i>TCF3</i> genes related to hair follicle development and wool shedding were strongly selected. Our results indicated that these methods identified important genes related to hair follicle formation, epidermal differentiation, and hair follicle stem cell development, and provide a meaningful reference for further study on the molecular mechanisms of economically important traits in sheep.https://www.mdpi.com/2073-4425/12/12/1924sheepSNP chipselective signaturesFstθπ ratioXP-EHH |
| spellingShingle | Zhihui Lei Weibo Sun Tingting Guo Jianye Li Shaohua Zhu Zengkui Lu Guoyan Qiao Mei Han Hongchang Zhao Bohui Yang Liping Zhang Jianbin Liu Chao Yuan Yaojing Yue Genome-Wide Selective Signatures Reveal Candidate Genes Associated with Hair Follicle Development and Wool Shedding in Sheep Genes sheep SNP chip selective signatures Fst θπ ratio XP-EHH |
| title | Genome-Wide Selective Signatures Reveal Candidate Genes Associated with Hair Follicle Development and Wool Shedding in Sheep |
| title_full | Genome-Wide Selective Signatures Reveal Candidate Genes Associated with Hair Follicle Development and Wool Shedding in Sheep |
| title_fullStr | Genome-Wide Selective Signatures Reveal Candidate Genes Associated with Hair Follicle Development and Wool Shedding in Sheep |
| title_full_unstemmed | Genome-Wide Selective Signatures Reveal Candidate Genes Associated with Hair Follicle Development and Wool Shedding in Sheep |
| title_short | Genome-Wide Selective Signatures Reveal Candidate Genes Associated with Hair Follicle Development and Wool Shedding in Sheep |
| title_sort | genome wide selective signatures reveal candidate genes associated with hair follicle development and wool shedding in sheep |
| topic | sheep SNP chip selective signatures Fst θπ ratio XP-EHH |
| url | https://www.mdpi.com/2073-4425/12/12/1924 |
| work_keys_str_mv | AT zhihuilei genomewideselectivesignaturesrevealcandidategenesassociatedwithhairfollicledevelopmentandwoolsheddinginsheep AT weibosun genomewideselectivesignaturesrevealcandidategenesassociatedwithhairfollicledevelopmentandwoolsheddinginsheep AT tingtingguo genomewideselectivesignaturesrevealcandidategenesassociatedwithhairfollicledevelopmentandwoolsheddinginsheep AT jianyeli genomewideselectivesignaturesrevealcandidategenesassociatedwithhairfollicledevelopmentandwoolsheddinginsheep AT shaohuazhu genomewideselectivesignaturesrevealcandidategenesassociatedwithhairfollicledevelopmentandwoolsheddinginsheep AT zengkuilu genomewideselectivesignaturesrevealcandidategenesassociatedwithhairfollicledevelopmentandwoolsheddinginsheep AT guoyanqiao genomewideselectivesignaturesrevealcandidategenesassociatedwithhairfollicledevelopmentandwoolsheddinginsheep AT meihan genomewideselectivesignaturesrevealcandidategenesassociatedwithhairfollicledevelopmentandwoolsheddinginsheep AT hongchangzhao genomewideselectivesignaturesrevealcandidategenesassociatedwithhairfollicledevelopmentandwoolsheddinginsheep AT bohuiyang genomewideselectivesignaturesrevealcandidategenesassociatedwithhairfollicledevelopmentandwoolsheddinginsheep AT lipingzhang genomewideselectivesignaturesrevealcandidategenesassociatedwithhairfollicledevelopmentandwoolsheddinginsheep AT jianbinliu genomewideselectivesignaturesrevealcandidategenesassociatedwithhairfollicledevelopmentandwoolsheddinginsheep AT chaoyuan genomewideselectivesignaturesrevealcandidategenesassociatedwithhairfollicledevelopmentandwoolsheddinginsheep AT yaojingyue genomewideselectivesignaturesrevealcandidategenesassociatedwithhairfollicledevelopmentandwoolsheddinginsheep |