Genome-wide selection signaling reveals candidate genes associated with double-coated fleece in Hotan sheep

doi:10.6048/j.issn.1001-4330.2025.03.027

Xinjiang Agricultural Sciences ›› 2025, Vol. 62 ›› Issue (3): 766-774.DOI: 10.6048/j.issn.1001-4330.2025.03.027

• Animal Husbandry Veterinarian • Previous Articles Next Articles

Genome-wide selection signaling reveals candidate genes associated with double-coated fleece in Hotan sheep

ZHANG Yanwei¹^,²(), XU Xinming³, YU Lijuan², TIAN Yuezhen², XIE Mengwan¹^,², TANG Liping¹^,², ZHENG Peiyu¹^,², SONG Nannan¹^,², DI Jiang²()

1. College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China
2. Key Laboratory of Genetics Breeding and Reproduction of Xinjiang Cashmere and Wool Sheep / Key Laboratory of Evaluation and Utilization of Livestock and Poultry Resources (Sheep) of the Ministry of Agriculture and Rural Areas/Institute of Animal Sciences, Xinjiang Academy of Animal Sciences, Urumqi 830011, China
3. Key Laboratory of Animal Biotechnology of Xinjiang, Institute of Biotechnology/Xinjiang Academy of Animal Sciences, Urumqi 830011, China

Received:2024-08-22 Online:2025-03-20 Published:2025-05-14
Correspondence author: DI Jiang
Supported by:
Key Laboratory Open Project of Xinjiang Uygur Autonomous Region(2020D04035);National Key R&D Program Project(2021YFD1200901);Tianshan Innovation Team Program Project(2022D14018);Earmarked Fund of China Agriculture Research System(CARS-39)

全基因组选择信号筛选和田羊异质被毛相关候选基因

张彦威¹^,²(), 徐新明³, 于丽娟², 田月珍², 谢梦婉¹^,², 唐丽苹¹^,², 郑培宇¹^,², 宋楠楠¹^,², 狄江²()

1.新疆农业大学动物科学学院,乌鲁木齐 830052
2.新疆畜牧科学院畜牧研究所/新疆绒毛用羊遗传育种与繁殖实验室/农业农村部畜禽资源(羊)评价利用重点实验室,乌鲁木齐 830011
3.新疆畜牧科学院生物技术研究所/新疆动物生物技术重点实验室,乌鲁木齐 830011

通讯作者: 狄江
作者简介:张彦威(1997-),男,新疆石河子人,硕士研究生,研究方向为动物遗传育种,(E-mail) original10012@163.com
基金资助:
新疆维吾尔自治区重点实验室开放课题(2020D04035);国家重点研发计划项目(2021YFD1200901);天山创新团队计划(2022D14018);国家绒毛用羊产业技术体系建设专项(CARS-39)

Abstract

Abstract:

【Objective】This project aims to screen out genes and pathways related to the double-coated fleece of Hotan sheep in the hope of providing a theoretical basis for further analysis of the molecular regulation mechanism ofdouble-coated fleece of the sheep.【Methods】The genome-wide SNPs derived from Hotan sheep with double-coated fleece and Chinese Merino sheep with single-coated fleece were used to determine candidate genes associated with double-coated fleece in Hotan sheep. Healthy adult female Hotan sheep and Chinese Merino sheep were selected with 15 individuals each, blood samples were collected from jugular vein, and genomic DNA was extracted for re-sequencing. Selection signal detection was performed based on whole genome SNPs, and top 1% of Fst and θπRatio value were set as thresholds. SNPs harbored in the strongly selected genomic regions were annotated, then GO function and KEGG pathway enrichment analysis were carried out to further screen out the candidate genes and biologicalpathways related to the double-coated fleece traits of Hotan sheep. 【Results】Our results showed that totally 732 selected genes were identified by Fst and θπRatio approaches, and these genes were significantly enriched into several KEGG pathways related to wool traits, even 1 biological process pathway related to hair follicle development.【Conclusion】Multiple pathways related to wool traits and five key candidate genes (BMPR2, LPAR6, RARA,CDC6 and BNC1) that may be related to Hotan sheep double-coated fleece were screened.

Key words: Hotan Sheep; coat type; candidate gene; selection signals

摘要：

【目的】被毛类型是绵羊重要的品种特征之一,但是其形成的分子基础目前仍不清楚。筛选出与和田羊异质被毛有关的基因和通路,为进一步解析和田羊异质被毛的分子调控机制提供理论依据。【方法】对异质被毛和田羊和同质被毛中国美利奴羊的基因组信息进行选择信号分析,研究筛选出与和田羊被毛类型相关的候选基因。选取健康和田羊和中国美利奴羊成年母羊各15只,颈静脉采血,提取基因组DNA进行基因组重测序,基于全基因SNPs进行选择信号检测分析。将Fst和θπRatio的top1%作为阈值,筛选出SNPs位点进行注释,并对注释基因进行GO功能和KEGG通路富集分析,确定与和田羊异质被毛性状相关的候选基因和生物学通路。【结果】Fst和θπRatio两种方法共鉴别出732个受选择基因,这些基因被显著富集到多个与羊毛性状有关的KEGG通路和1条与毛囊发育有关的生物学过程通路。【结论】筛选出多个羊毛性状有关的通路和5个(BMPR2、LPAR6、RARA、CDC6和BNC1)可能与和田羊异质被毛相关的关键候选基因。

关键词: 和田羊, 被毛类型, 候选基因, 选择信号

CLC Number:

S826

ZHANG Yanwei, XU Xinming, YU Lijuan, TIAN Yuezhen, XIE Mengwan, TANG Liping, ZHENG Peiyu, SONG Nannan, DI Jiang. Genome-wide selection signaling reveals candidate genes associated with double-coated fleece in Hotan sheep[J]. Xinjiang Agricultural Sciences, 2025, 62(3): 766-774.

张彦威, 徐新明, 于丽娟, 田月珍, 谢梦婉, 唐丽苹, 郑培宇, 宋楠楠, 狄江. 全基因组选择信号筛选和田羊异质被毛相关候选基因[J]. 新疆农业科学, 2025, 62(3): 766-774.

Figures/Tables 8

References 31

[1]	Wang H Y, Li S W, Wu T H, et al. The effect of androgen on wool follicles and keratin production in Hetian sheep[J]. Brazilian Journal of Biology, 2021, 81(3): 526-536. DOI PMID
[2]	何元园. 和田地毯用毛结构性能及其评价体系研究[D]. 乌鲁木齐: 新疆大学, 2016.
	HE Yuanyuan. Study on structural properties and evaluation system of wool for Hotan carpet[D]. Urumqi: Xinjiang University, 2016.
[3]	郭欣芸. 羊毛纤维品质对地毯性能的影响[D]. 乌鲁木齐: 新疆大学, 2017.
	GUO Xinyun. Influence of wool fiber quality on carpet performance[D]. Urumqi: Xinjiang University, 2017.
[4]	Tian D H, Han B Y, Li X, et al. Genetic diversity and selection of Tibetan sheep breeds revealed by whole-genome resequencing[J]. Animal Bioscience, 2023, 36(7): 991-1002.
[5]	Li X K, Su R, Wan W T, et al. Identification of selection signals by large-scale whole-genome resequencing of Cashmere goats[J]. Scientific Reports, 2017, 7(1): 15142. DOI PMID
[6]	Lv F H, Cao Y H, Liu G J, et al. Whole-genome resequencing of worldwide wild and domestic sheep elucidates genetic diversity, introgression, and agronomically important loci[J]. Molecular Biology and Evolution, 2022, 39(2): msab353.
[7]	国家畜禽遗传资源委员会组. 中国畜禽遗传资源志-羊志[M]. 北京: 中国农业出版社, 2011.
	National Livestock andPoultry Resources Commission. Animal genetic resources in China[M]. Beijing: China Agriculture Press, 2011.
[8]	Manangwa O, De Meeûs T, Grébaut P, et al. Detecting Wahlund effects together with amplification problems: Cryptic species, null alleles and short allele dominance in Glossina pallidipes populations from Tanzania[J]. Molecular Ecology Resources, 2019, 19(3): 757-772. DOI PMID
[9]	He X M, Qin Z L, Teng R, et al. Characterization of growth secondary hair in Min pig activated by follicle stem cell stimulated by Wnt and BMP signaling pathway[J]. Animals, 2023, 13(7): 1239.
[10]	Li A G, Koster M I, Wang X J. Roles of TGFβ signaling in epidermal/appendage development[J]. Cytokine & Growth Factor Reviews, 2003, 14(2): 99-111.
[11]	Liu Z H, Liu Z C, Mu Q, et al. Identification of key pathways and genes that regulate Cashmere development in Cashmere goats mediated by exogenous melatonin[J]. Frontiers in Veterinary Science, 2022, 9: 993773.
[12]	Akiyama M. Isolated autosomal recessive woolly hair/hypotrichosis: genetics, pathogenesis and therapies[J]. Journal of the European Academy of Dermatology and Venereology, 2021, 35(9): 1788-1796. DOI PMID
[13]	Zhao B R, Luo H P, He J M, et al. Comprehensive transcriptome and methylome analysis delineates the biological basis of hair follicle development and wool-related traits in Merino sheep[J]. BMC Biology, 2021, 19(1): 197. DOI PMID
[14]	Zhao B R, Luo H P, Huang X X, et al. Integration of a single-step genome-wide association study with a multi-tissue transcriptome analysis provides novel insights into the genetic basis of wool and weight traits in sheep[J]. Genetics, Selection, Evolution, 2021, 53(1): 56.
[15]	Gong G, Fan Y X, Yan X C, et al. Identification of genes related to hair follicle cycle development in Inner Mongolia Cashmere goat by WGCNA[J]. Frontiers in Veterinary Science, 2022, 9: 894380.
[16]	Wang X X, Liu Y H, He J, et al. Regulation of signaling pathways in hair follicle stem cells[J]. Burns & Trauma, 2022, 10: tkac022.
[17]	Bae S, Yoon Y G, Kim J Y, et al. Melatonin increases growth properties in human dermal papilla spheroids by activating AKT/GSK3β/β-Catenin signaling pathway[J]. PeerJ, 2022, 10: e13461.
[18]	Wu T H, Zhang Y M, Krishnan S, et al. Bioactive small molecule enhances skin burn wound healing and hair follicle regeneration by activating PI3K/AKT signaling pathway: a preclinical evaluation in animal model[J]. Journal of Biomedical Nanotechnology, 2022, 18(2): 463-473. DOI PMID
[19]	Bao Q, Ma X M, Jia C J, et al. Resequencing and signatures of selective scans point to candidate genetic variants for hair length traits in long-haired and normal-haired Tianzhu white yak[J]. Frontiers in Genetics, 2022, 13: 798076.
[20]	Jaapar M S, Chung E L T, Nayan N, et al. Digestibility, growth performance, body measurement and hormone of sheep fed with different levels of Brachiaria decumbens diets[J]. Tropical Life Sciences Research, 2023, 34(1): 67-83.
[21]	Liu K X, Zhang L Y, Qi Q, et al. Growth hormone treatment improves the development of follicles and oocytes in prepubertal lambs[J]. Journal of Ovarian Research, 2023, 16(1): 132. DOI PMID
[22]	Brooks A J, Waters M J. The growth hormone receptor: mechanism of activation and clinical implications[J]. Nature Reviews Endocrinology, 2010, 6(9): 515-525. DOI PMID
[23]	Waters M. The growth hormone receptor[J]. Growth Hormone & IGF Research: Official Journal of the Growth Hormone Research Society and the International IGF Research Society, 2006
[24]	Wynn P C, Wallace A L, Kirby A C, et al. Effects of growth hormone administration on wool growth in merino sheep[J]. Australian Journal of Biological Sciences, 1988, 41(2): 177-187. PMID
[25]	Liang B M, Bai T Y, Zhao Y, et al. Two mutations at KRT74 and EDAR synergistically drive the fine-wool production in Chinese sheep[J]. Journal of Advanced Research, 2024, 57: 1-13.
[26]	陈磊, 贺三刚, 刘书东, 等. 绵羊EDAR基因的克隆、序列分析及其在毛囊发育过程中的表达[J]. 西北农业学报, 2017, 26(10): 1415-1421.
	CHEN Lei, HE Sangang, LIU Shudong, et al. Cloning, sequencing and quantitative expression of EDAR gene in sheep during hair follicle development period[J]. Acta Agriculturae Boreali-occidentalis Sinica, 2017, 26(10): 1415-1421.
[27]	Kinzel B, Pikiolek M, Orsini V, et al. Functional roles of Lgr4 and Lgr5 in embryonic gut, kidney and skin development in mice[J]. Developmental Biology, 2014, 390(2): 181-190. DOI PMID
[28]	Vorstenbosch J, Nguyen C M, Zhou S F, et al. Overexpression of CD109 in the epidermis differentially regulates ALK1 versus ALK5 signaling and modulates extracellular matrix synthesis in the skin[J]. Journal of Investigative Dermatology, 2017, 137(3): 641-649. DOI PMID
[29]	Wegner J, Loser K, Apsite G, et al. Laminin α5 in the keratinocyte basement membrane is required for epidermal-dermal intercommunication[J]. Matrix Biology, 2016, 56: 24-41. DOI PMID
[30]	Devenport D, Fuchs E. Planar polarization in embryonic epidermis orchestrates global asymmetric morphogenesis of hair follicles[J]. Nature Cell Biology, 2008, 10(11): 1257-1268. DOI PMID
[31]	Jin M L, Lu J, Fei X J, et al. Selection signatures analysis reveals genes associated with high-altitude adaptation in Tibetan goats from Nagqu, Tibet[J]. Animals, 2020, 10(9): 1599.

品种 Breeds	数量 Numbers	原始数据 Raw Base(bp)	有效数据 Clean Base(bp)	有效数据率 Effective Rate(%)	Q20(%)	Q30(%)	GC含量 GC Content (%)
和田羊 Hetian sheep	15	31 326 299 320	31 260 865 560	99.79	97.59	93.28	44.08
中国美利奴 Chinese Merino	15	30 628 533 060	30 565 940 940	99.80	97.35	92.75	44.34

品种 Breeds	数量 Numbers	原始数据 Raw Base(bp)	有效数据 Clean Base(bp)	有效数据率 Effective Rate(%)	Q20(%)	Q30(%)	GC含量 GC Content (%)
和田羊 Hetian sheep	15	31 326 299 320	31 260 865 560	99.79	97.59	93.28	44.08
中国美利奴 Chinese Merino	15	30 628 533 060	30 565 940 940	99.80	97.35	92.75	44.34

品种 Breeds	有效条数 Clean reads	比对后条数 Mapped reads	比对率 Mapping rate(%)	平均测序深度 Average depth(X)	1X覆盖度 Coverage 1X(%)	4X覆盖度 Coverage 4X(%)
和田羊 Hetian sheep	203 772 939	202 894 709	99.57	9.93	95.26	88.33
中国美利奴 Chinese Merino	208 405 770	207 622 159	99.62	10.03	95.37	89.05

品种 Breeds	有效条数 Clean reads	比对后条数 Mapped reads	比对率 Mapping rate(%)	平均测序深度 Average depth(X)	1X覆盖度 Coverage 1X(%)	4X覆盖度 Coverage 4X(%)
和田羊 Hetian sheep	203 772 939	202 894 709	99.57	9.93	95.26	88.33
中国美利奴 Chinese Merino	208 405 770	207 622 159	99.62	10.03	95.37	89.05

项目Items		SNPs
基因上游1 kb区域		73,578
外显子区域Exonic	使基因获得终止密码的变异	269
	使基因失去终止密码的变异	53
	同义变异	64 719
	非同义变异	33 948
内含子区Intronic		4 456 025
剪接位点Splicing site		191
基因下游1 kb区域1 kb region downstream of gene		75 763
基因上游1 kb区域,同时也在另一基因下游1 kb区域upstream/downstream		1 982
基因间区Intergenic		7 212 892
转换Ts		8 722 670
颠换Tv		3 313 523
Ts/Tv		2.632
位点总数Total		12 036 193

Genome-wide selection signaling reveals candidate genes associated with double-coated fleece in Hotan sheep

全基因组选择信号筛选和田羊异质被毛相关候选基因

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References 31

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Metrics

染色体 CHROM	开始位置/bp BIN_START	结束位置/bp BIN_END	Fst	Log2θπRatio CM-HT	基因 GENE
Chr.2	218 802 583	218 802 754	0.290 624	1.687 196 657	BMPR2
Chr.10	20 495 317	20 495 320	0.448 557	2.558 174 077	LPAR6
Chr.11	22 587 426	22 587 429	0.615 329	2.647 344 435	RARA
Chr.11	22 635 131	22 635 134	0.606 593	2.564 477 692	CDC6
Chr.18	21 203 099	21 203 102	0.279 822	1.710 228 359	BNC1

主要富集通路的名称 Names of major enrichment pathways	主要通路所富集的基因 Genes enriched by major pathways
毛囊发育 hair follicle development	EDAR、PIAS4、LAMA5、VANGL2、LDB1、CD109、LGR5、LGR4
PI3K-Akt信号通路 PI3K-Akt signaling pathway	LAMA5、CSF3、PRKAA1、FLT1、LAMA2、LAMA3、PRKCA、GHR、RELN、LPAR5、LPAR6、CDK4、CCNE1、CREB3L2、KIT、EIF4E、JAK1
生长激素的合成、分泌和作用 Growth hormone synthesis、 secretion and action	GHR、MAP2K4、PLCB4、SOCS1、SST、CREB3L2、PLCG2、PRKCA
Rap1信号通路 Rap1 signaling pathway	PLCB4、FLT1、LPAR5、CNR1、CALML6、KIT、PRKCA、PRKD1、TLN2、ITGAL
磷脂酶D信号通路 Phospholipase D signaling pathway	PLCB4、LPAR5、LPAR6、DGKB、DGKA、KIT、PLCG2、PRKCA、CYTH1

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[3]	YANG Hui-guo;YU Jian-guo;HAO Geng;CHEN Tong. Study on Mitochondrial DNA D-loop Sequence of Hotan Sheep [J]. , 2013, 50(5): 959-962.