Whole-Genome Resequencing to Identify Selection Signatures Associated with High Fertility in Lüliang Black Goat
Lüliang black goat (LBG) is a unique livestock genetic resource of great significance for the local agriculture and economic development of Shanxi, China. However, the kidding rate of LBG is relatively low, which limits efforts to improve the reproductive performance and economic benefits of this br...
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2024-12-01
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| author | Xu Wang Zhenqi Zhou Xinrui Chai Jie Li Wannian Wang Zhixu Pang Lifen Cheng Caihong Cheng Liying Qiao Yangyang Pan Kaijie Yang Wenzhong Liu Jianhua Liu |
| author_facet | Xu Wang Zhenqi Zhou Xinrui Chai Jie Li Wannian Wang Zhixu Pang Lifen Cheng Caihong Cheng Liying Qiao Yangyang Pan Kaijie Yang Wenzhong Liu Jianhua Liu |
| author_sort | Xu Wang |
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| description | Lüliang black goat (LBG) is a unique livestock genetic resource of great significance for the local agriculture and economic development of Shanxi, China. However, the kidding rate of LBG is relatively low, which limits efforts to improve the reproductive performance and economic benefits of this breed. Therefore, improving the kidding characteristics of LBG is crucial for increasing its economic benefits. In this study, 20 LBG does were selected for whole-genome resequencing and divided into two groups: 10 in the T group (does with three consecutive kiddings of twin kids) and 10 in the S group (does with three consecutive kiddings of single kids). Based on whole-genome resequencing data, this study comprehensively assessed the population structure and genetic diversity of LBG and explored the related genes that affect reproductive performance. Three selection signal analysis methods—Fst (Fixation Index), π (nucleotide diversity), and XP-CLR (Cross Population Composite Likelihood Ratio)—were applied to screen a total of 838 genes, and enrichment analysis was performed to identify genes closely related to the reproductive performance of LBG, including <i>ENPP3</i>, <i>APC</i>, and <i>GLI2</i>. A generalized linear model was used to conduct a correlation analysis between non-synonymous mutations in the three genes and the number of kids produced. Two loci that were significantly correlated with kidding number were identified (<i>p</i> < 0.05): <i>GLI2</i> g.63400363 C>T and <i>GLI2</i> g.63417538 C>T. In general, the LBG population has high genetic diversity and good prospects for genetic improvement. The findings revealed that mining high-fecundity selection characteristics provides a basis for research on goat reproductive mechanisms. |
| format | Article |
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| institution | Kabale University |
| issn | 2076-2615 |
| language | English |
| publishDate | 2024-12-01 |
| publisher | MDPI AG |
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| series | Animals |
| spelling | doaj-art-a56f02c6a22c4a70bdbd4ebf6a4061702025-01-10T13:13:51ZengMDPI AGAnimals2076-26152024-12-011513610.3390/ani15010036Whole-Genome Resequencing to Identify Selection Signatures Associated with High Fertility in Lüliang Black GoatXu Wang0Zhenqi Zhou1Xinrui Chai2Jie Li3Wannian Wang4Zhixu Pang5Lifen Cheng6Caihong Cheng7Liying Qiao8Yangyang Pan9Kaijie Yang10Wenzhong Liu11Jianhua Liu12Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, Shanxi Agricultural University, Jinzhong 030801, ChinaDepartment of Animal Genetics, Breeding and Reproduction, College of Animal Science, Shanxi Agricultural University, Jinzhong 030801, ChinaDepartment of Animal Genetics, Breeding and Reproduction, College of Animal Science, Shanxi Agricultural University, Jinzhong 030801, ChinaDepartment of Animal Genetics, Breeding and Reproduction, College of Animal Science, Shanxi Agricultural University, Jinzhong 030801, ChinaDepartment of Animal Genetics, Breeding and Reproduction, College of Animal Science, Shanxi Agricultural University, Jinzhong 030801, ChinaDepartment of Animal Genetics, Breeding and Reproduction, College of Animal Science, Shanxi Agricultural University, Jinzhong 030801, ChinaShanxi Animal Husbandry Technology Extension Service Center, Taiyuan 030001, ChinaShanxi Animal Husbandry Technology Extension Service Center, Taiyuan 030001, ChinaDepartment of Animal Genetics, Breeding and Reproduction, College of Animal Science, Shanxi Agricultural University, Jinzhong 030801, ChinaDepartment of Animal Genetics, Breeding and Reproduction, College of Animal Science, Shanxi Agricultural University, Jinzhong 030801, ChinaDepartment of Animal Genetics, Breeding and Reproduction, College of Animal Science, Shanxi Agricultural University, Jinzhong 030801, ChinaDepartment of Animal Genetics, Breeding and Reproduction, College of Animal Science, Shanxi Agricultural University, Jinzhong 030801, ChinaDepartment of Animal Genetics, Breeding and Reproduction, College of Animal Science, Shanxi Agricultural University, Jinzhong 030801, ChinaLüliang black goat (LBG) is a unique livestock genetic resource of great significance for the local agriculture and economic development of Shanxi, China. However, the kidding rate of LBG is relatively low, which limits efforts to improve the reproductive performance and economic benefits of this breed. Therefore, improving the kidding characteristics of LBG is crucial for increasing its economic benefits. In this study, 20 LBG does were selected for whole-genome resequencing and divided into two groups: 10 in the T group (does with three consecutive kiddings of twin kids) and 10 in the S group (does with three consecutive kiddings of single kids). Based on whole-genome resequencing data, this study comprehensively assessed the population structure and genetic diversity of LBG and explored the related genes that affect reproductive performance. Three selection signal analysis methods—Fst (Fixation Index), π (nucleotide diversity), and XP-CLR (Cross Population Composite Likelihood Ratio)—were applied to screen a total of 838 genes, and enrichment analysis was performed to identify genes closely related to the reproductive performance of LBG, including <i>ENPP3</i>, <i>APC</i>, and <i>GLI2</i>. A generalized linear model was used to conduct a correlation analysis between non-synonymous mutations in the three genes and the number of kids produced. Two loci that were significantly correlated with kidding number were identified (<i>p</i> < 0.05): <i>GLI2</i> g.63400363 C>T and <i>GLI2</i> g.63417538 C>T. In general, the LBG population has high genetic diversity and good prospects for genetic improvement. The findings revealed that mining high-fecundity selection characteristics provides a basis for research on goat reproductive mechanisms.https://www.mdpi.com/2076-2615/15/1/36Lüliang black goatgenetic diversitysignal selectionreproductive traitskidding numbers |
| spellingShingle | Xu Wang Zhenqi Zhou Xinrui Chai Jie Li Wannian Wang Zhixu Pang Lifen Cheng Caihong Cheng Liying Qiao Yangyang Pan Kaijie Yang Wenzhong Liu Jianhua Liu Whole-Genome Resequencing to Identify Selection Signatures Associated with High Fertility in Lüliang Black Goat Animals Lüliang black goat genetic diversity signal selection reproductive traits kidding numbers |
| title | Whole-Genome Resequencing to Identify Selection Signatures Associated with High Fertility in Lüliang Black Goat |
| title_full | Whole-Genome Resequencing to Identify Selection Signatures Associated with High Fertility in Lüliang Black Goat |
| title_fullStr | Whole-Genome Resequencing to Identify Selection Signatures Associated with High Fertility in Lüliang Black Goat |
| title_full_unstemmed | Whole-Genome Resequencing to Identify Selection Signatures Associated with High Fertility in Lüliang Black Goat |
| title_short | Whole-Genome Resequencing to Identify Selection Signatures Associated with High Fertility in Lüliang Black Goat |
| title_sort | whole genome resequencing to identify selection signatures associated with high fertility in luliang black goat |
| topic | Lüliang black goat genetic diversity signal selection reproductive traits kidding numbers |
| url | https://www.mdpi.com/2076-2615/15/1/36 |
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