Identification of Runs of Homozygosity Islands and Functional Variants in Wenchang Chicken
Wenchang chickens, a native breed in the Hainan province of China, are famous for their meat quality and adaptability to tropical conditions. For effective management and conservation, in the present study, we systematically investigated the characteristics of genetic variations and runs of homozygo...
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MDPI AG
2023-05-01
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| Series: | Animals |
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| Online Access: | https://www.mdpi.com/2076-2615/13/10/1645 |
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| author | Shuaishuai Tian Wendan Tang Ziqi Zhong Ziyi Wang Xinfeng Xie Hong Liu Fuwen Chen Jiaxin Liu Yuxin Han Yao Qin Zhen Tan Qian Xiao |
| author_facet | Shuaishuai Tian Wendan Tang Ziqi Zhong Ziyi Wang Xinfeng Xie Hong Liu Fuwen Chen Jiaxin Liu Yuxin Han Yao Qin Zhen Tan Qian Xiao |
| author_sort | Shuaishuai Tian |
| collection | DOAJ |
| description | Wenchang chickens, a native breed in the Hainan province of China, are famous for their meat quality and adaptability to tropical conditions. For effective management and conservation, in the present study, we systematically investigated the characteristics of genetic variations and runs of homozygosity (ROH) along the genome using re-sequenced whole-genome sequencing data from 235 Wenchang chickens. A total of 16,511,769 single nucleotide polymorphisms (SNPs) and 53,506 ROH segments were identified in all individuals, and the ROH of Wenchang chicken were mainly composed of short segments (0–1 megabases (Mb)). On average, 5.664% of the genome was located in ROH segments across the Wenchang chicken samples. According to several parameters, the genetic diversity of the Wenchang chicken was relatively high. The average inbreeding coefficient of Wenchang chickens based on <i>F<sub>HOM</sub></i>, <i>F<sub>GRM</sub></i>, and <i>F<sub>ROH</sub></i> was 0.060 ± 0.014, 0.561 ± 0.020, and 0.0566 ± 0.01, respectively. A total of 19 ROH islands containing 393 genes were detected on 9 different autosomes. Some of these genes were putatively associated with growth performance (<i>AMY1a</i>), stress resistance (<i>THEMIS2</i>, <i>PIK3C2B</i>), meat traits (<i>MBTPS1</i>, <i>DLK1</i>, and <i>EPS8L2</i>), and fat deposition (<i>LANCL2</i>, <i>PPARγ</i>). These findings provide a better understanding of the degree of inbreeding in Wenchang chickens and the hereditary basis of the characteristics shaped under selection. These results are valuable for the future breeding, conservation, and utilization of Wenchang and other chicken breeds. |
| first_indexed | 2024-03-11T04:00:37Z |
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| id | doaj.art-6728cb1e640542989c9e9b46fb0b1c32 |
| institution | Directory Open Access Journal |
| issn | 2076-2615 |
| language | English |
| last_indexed | 2024-03-11T04:00:37Z |
| publishDate | 2023-05-01 |
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| spelling | doaj.art-6728cb1e640542989c9e9b46fb0b1c322023-11-18T00:10:08ZengMDPI AGAnimals2076-26152023-05-011310164510.3390/ani13101645Identification of Runs of Homozygosity Islands and Functional Variants in Wenchang ChickenShuaishuai Tian0Wendan Tang1Ziqi Zhong2Ziyi Wang3Xinfeng Xie4Hong Liu5Fuwen Chen6Jiaxin Liu7Yuxin Han8Yao Qin9Zhen Tan10Qian Xiao11Hainan Key Laboratory of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, College of Animal Science and Technology, Hainan University, Haikou 570228, ChinaHainan Key Laboratory of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, College of Animal Science and Technology, Hainan University, Haikou 570228, ChinaHainan Key Laboratory of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, College of Animal Science and Technology, Hainan University, Haikou 570228, ChinaHainan Key Laboratory of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, College of Animal Science and Technology, Hainan University, Haikou 570228, ChinaHainan Key Laboratory of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, College of Animal Science and Technology, Hainan University, Haikou 570228, ChinaHainan Key Laboratory of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, College of Animal Science and Technology, Hainan University, Haikou 570228, ChinaHainan Key Laboratory of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, College of Animal Science and Technology, Hainan University, Haikou 570228, ChinaHainan Key Laboratory of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, College of Animal Science and Technology, Hainan University, Haikou 570228, ChinaHainan Key Laboratory of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, College of Animal Science and Technology, Hainan University, Haikou 570228, ChinaHainan Key Laboratory of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, College of Animal Science and Technology, Hainan University, Haikou 570228, ChinaHainan Key Laboratory of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, College of Animal Science and Technology, Hainan University, Haikou 570228, ChinaHainan Key Laboratory of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, College of Animal Science and Technology, Hainan University, Haikou 570228, ChinaWenchang chickens, a native breed in the Hainan province of China, are famous for their meat quality and adaptability to tropical conditions. For effective management and conservation, in the present study, we systematically investigated the characteristics of genetic variations and runs of homozygosity (ROH) along the genome using re-sequenced whole-genome sequencing data from 235 Wenchang chickens. A total of 16,511,769 single nucleotide polymorphisms (SNPs) and 53,506 ROH segments were identified in all individuals, and the ROH of Wenchang chicken were mainly composed of short segments (0–1 megabases (Mb)). On average, 5.664% of the genome was located in ROH segments across the Wenchang chicken samples. According to several parameters, the genetic diversity of the Wenchang chicken was relatively high. The average inbreeding coefficient of Wenchang chickens based on <i>F<sub>HOM</sub></i>, <i>F<sub>GRM</sub></i>, and <i>F<sub>ROH</sub></i> was 0.060 ± 0.014, 0.561 ± 0.020, and 0.0566 ± 0.01, respectively. A total of 19 ROH islands containing 393 genes were detected on 9 different autosomes. Some of these genes were putatively associated with growth performance (<i>AMY1a</i>), stress resistance (<i>THEMIS2</i>, <i>PIK3C2B</i>), meat traits (<i>MBTPS1</i>, <i>DLK1</i>, and <i>EPS8L2</i>), and fat deposition (<i>LANCL2</i>, <i>PPARγ</i>). These findings provide a better understanding of the degree of inbreeding in Wenchang chickens and the hereditary basis of the characteristics shaped under selection. These results are valuable for the future breeding, conservation, and utilization of Wenchang and other chicken breeds.https://www.mdpi.com/2076-2615/13/10/1645Wenchang chickeninbreedinggenetic diversityruns of homozygosityselection signatures |
| spellingShingle | Shuaishuai Tian Wendan Tang Ziqi Zhong Ziyi Wang Xinfeng Xie Hong Liu Fuwen Chen Jiaxin Liu Yuxin Han Yao Qin Zhen Tan Qian Xiao Identification of Runs of Homozygosity Islands and Functional Variants in Wenchang Chicken Animals Wenchang chicken inbreeding genetic diversity runs of homozygosity selection signatures |
| title | Identification of Runs of Homozygosity Islands and Functional Variants in Wenchang Chicken |
| title_full | Identification of Runs of Homozygosity Islands and Functional Variants in Wenchang Chicken |
| title_fullStr | Identification of Runs of Homozygosity Islands and Functional Variants in Wenchang Chicken |
| title_full_unstemmed | Identification of Runs of Homozygosity Islands and Functional Variants in Wenchang Chicken |
| title_short | Identification of Runs of Homozygosity Islands and Functional Variants in Wenchang Chicken |
| title_sort | identification of runs of homozygosity islands and functional variants in wenchang chicken |
| topic | Wenchang chicken inbreeding genetic diversity runs of homozygosity selection signatures |
| url | https://www.mdpi.com/2076-2615/13/10/1645 |
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