Whole-genome resequencing of major populations revealed domestication-related genes in yaks
© 2024. The Author(s)..
BACKGROUND: The yak is a symbol of the Qinghai-Tibet Plateau and provides important basic resources for human life on the plateau. Domestic yaks have been subjected to strong artificial selection and environmental pressures over the long-term. Understanding the molecular mechanisms of phenotypic differences in yak populations can reveal key functional genes involved in the domestication process and improve genetic breeding.
MATERIAL AND METHOD: Here, we re-sequenced 80 yaks (Maiwa, Yushu, and Huanhu populations) to identify single-nucleotide polymorphisms (SNPs) as genetic variants. After filtering and quality control, remaining SNPs were kept to identify the genome-wide regions of selective sweeps associated with domestic traits. The four methods (π, XPEHH, iHS, and XP-nSL) were used to detect the population genetic separation.
RESULTS: By comparing the differences in the population stratification, linkage disequilibrium decay rate, and characteristic selective sweep signals, we identified 203 putative selective regions of domestic traits, 45 of which were mapped to 27 known genes. They were clustered into 4 major GO biological process terms. All known genes were associated with seven major domestication traits, such as dwarfism (ANKRD28), milk (HECW1, HECW2, and OSBPL2), meat (SPATA5 and GRHL2), fertility (BTBD11 and ARFIP1), adaptation (NCKAP5, ANTXR1, LAMA5, OSBPL2, AOC2, and RYR2), growth (GRHL2, GRID2, SMARCAL1, and EPHB2), and the immune system (INPP5D and ADCYAP1R1).
CONCLUSIONS: We provided there is an obvious genetic different among domestic progress in these three yak populations. Our findings improve the understanding of the major genetic switches and domestic processes among yak populations.
| Medienart: |
E-Artikel |
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| Erscheinungsjahr: |
2024 |
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| Erschienen: |
2024 |
| Enthalten in: |
Zur Gesamtaufnahme - volume:25 |
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| Enthalten in: |
BMC genomics - 25(2024), 1 vom: 17. Jan., Seite 69 |
| Sprache: |
Englisch |
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| Beteiligte Personen: |
Peng, Wei [VerfasserIn] |
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| Links: |
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| Anmerkungen: |
Date Completed 19.01.2024 Date Revised 21.01.2024 published: Electronic Citation Status MEDLINE |
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| doi: |
10.1186/s12864-024-09993-7 |
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| funding: |
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| Förderinstitution / Projekttitel: |
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| 245 | 1 | 0 | |a Whole-genome resequencing of major populations revealed domestication-related genes in yaks |
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| 500 | |a Date Revised 21.01.2024 | ||
| 500 | |a published: Electronic | ||
| 500 | |a Citation Status MEDLINE | ||
| 520 | |a © 2024. The Author(s). | ||
| 520 | |a BACKGROUND: The yak is a symbol of the Qinghai-Tibet Plateau and provides important basic resources for human life on the plateau. Domestic yaks have been subjected to strong artificial selection and environmental pressures over the long-term. Understanding the molecular mechanisms of phenotypic differences in yak populations can reveal key functional genes involved in the domestication process and improve genetic breeding | ||
| 520 | |a MATERIAL AND METHOD: Here, we re-sequenced 80 yaks (Maiwa, Yushu, and Huanhu populations) to identify single-nucleotide polymorphisms (SNPs) as genetic variants. After filtering and quality control, remaining SNPs were kept to identify the genome-wide regions of selective sweeps associated with domestic traits. The four methods (π, XPEHH, iHS, and XP-nSL) were used to detect the population genetic separation | ||
| 520 | |a RESULTS: By comparing the differences in the population stratification, linkage disequilibrium decay rate, and characteristic selective sweep signals, we identified 203 putative selective regions of domestic traits, 45 of which were mapped to 27 known genes. They were clustered into 4 major GO biological process terms. All known genes were associated with seven major domestication traits, such as dwarfism (ANKRD28), milk (HECW1, HECW2, and OSBPL2), meat (SPATA5 and GRHL2), fertility (BTBD11 and ARFIP1), adaptation (NCKAP5, ANTXR1, LAMA5, OSBPL2, AOC2, and RYR2), growth (GRHL2, GRID2, SMARCAL1, and EPHB2), and the immune system (INPP5D and ADCYAP1R1) | ||
| 520 | |a CONCLUSIONS: We provided there is an obvious genetic different among domestic progress in these three yak populations. Our findings improve the understanding of the major genetic switches and domestic processes among yak populations | ||
| 650 | 4 | |a Journal Article | |
| 650 | 4 | |a Domestication | |
| 650 | 4 | |a Population stratification | |
| 650 | 4 | |a Selective sweep | |
| 650 | 4 | |a Yaks | |
| 650 | 7 | |a OSBPL2 protein, human |2 NLM | |
| 650 | 7 | |a Receptors, Steroid |2 NLM | |
| 650 | 7 | |a ANTXR1 protein, human |2 NLM | |
| 650 | 7 | |a Microfilament Proteins |2 NLM | |
| 650 | 7 | |a Receptors, Cell Surface |2 NLM | |
| 650 | 7 | |a SMARCAL1 protein, human |2 NLM | |
| 650 | 7 | |a EC 2.7.7.- |2 NLM | |
| 650 | 7 | |a DNA Helicases |2 NLM | |
| 650 | 7 | |a EC 3.6.4.- |2 NLM | |
| 650 | 7 | |a HECW1 protein, human |2 NLM | |
| 650 | 7 | |a EC 2.3.2.26 |2 NLM | |
| 650 | 7 | |a Nerve Tissue Proteins |2 NLM | |
| 650 | 7 | |a Ubiquitin-Protein Ligases |2 NLM | |
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| 650 | 7 | |a HECW2 protein, human |2 NLM | |
| 650 | 7 | |a EC 2.3.2.26 |2 NLM | |
| 650 | 7 | |a SPATA5 protein, human |2 NLM | |
| 650 | 7 | |a ATPases Associated with Diverse Cellular Activities |2 NLM | |
| 650 | 7 | |a EC 3.6.4.- |2 NLM | |
| 700 | 1 | |a Fu, Changqi |e verfasserin |4 aut | |
| 700 | 1 | |a Shu, Shi |e verfasserin |4 aut | |
| 700 | 1 | |a Wang, Guowen |e verfasserin |4 aut | |
| 700 | 1 | |a Wang, Hui |e verfasserin |4 aut | |
| 700 | 1 | |a Yue, Binglin |e verfasserin |4 aut | |
| 700 | 1 | |a Zhang, Ming |e verfasserin |4 aut | |
| 700 | 1 | |a Liu, Xinrui |e verfasserin |4 aut | |
| 700 | 1 | |a Liu, Yaxin |e verfasserin |4 aut | |
| 700 | 1 | |a Zhang, Jun |e verfasserin |4 aut | |
| 700 | 1 | |a Zhong, Jincheng |e verfasserin |4 aut | |
| 700 | 1 | |a Wang, Jiabo |e verfasserin |4 aut | |
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