中国美利奴羊毛密度相关基因的筛选

doi:10.6048/j.issn.1001-4330.2025.06.025

新疆农业科学 ›› 2025, Vol. 62 ›› Issue (6): 1530-1542.DOI: 10.6048/j.issn.1001-4330.2025.06.025

中国美利奴羊毛密度相关基因的筛选

马海叶¹^,²(), 李忠慧², 王嘉俊¹^,², 唐丽苹¹^,², 狄江³(), 李文蓉²()

1.新疆农业大学动物科学学院,乌鲁木齐 830052
2.新疆畜牧科学院生物技术研究所,乌鲁木齐 830026
3.新疆畜牧科学院畜牧研究所,乌鲁木齐 830026

收稿日期:2024-11-28 出版日期:2025-06-20 发布日期:2025-07-29
通信作者: 李文蓉(1969-),女,江苏海安人,研究员,博士,研究方向为家畜遗传育种,(E-mail)xjlwr@126.com;
狄江(1969-),男,研究员,博士,研究方向为动物遗传育种与繁殖,(E-mail)dijiang69@163.com
作者简介:马海叶(1999-),女,甘肃平凉人,硕士研究生,研究方向为动物遗传育种与繁殖,(E-mail)2627047120@qq.com
基金资助:
“十四五”国家重点研发计划课题“绵羊高繁殖力及优异毛用种质资源精准鉴定”(2021YFD1200901)

Identification of genes associated with wool density traits in Chinese Merino sheep

MA Haiye¹^,²(), LI Zhonghui², WANG Jiajun¹^,², TANG Liping¹^,², DI Jiang³(), LI Wenrong²()

1. College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China
2. Biotechnology Institute, Xinjiang Academy of Animal Sciences, Urumqi 830026, China
3. Animal Science Institute of Xinjiang Academy of Animal Sciences, Urumqi 830026, China

Received:2024-11-28 Published:2025-06-20 Online:2025-07-29
Supported by:
14th Five-Year National Key R & D Program Project“Accurate Identification of High Fertility and Excellent Wool Germplasm Resources of Sheep”(2021YFD1200901)

摘要/Abstract

摘要：

【目的】分析中国美利奴羊毛密度表型差异,筛选影响中国美利奴羊毛密度性状相关的候选基因,为阐明中国美利奴羊毛密度的分子调控机制提供参考。【方法】采用毛丛法对中国美利奴羊的羊毛密度和毛囊密度进行测定、统计分析,选择不同羊毛密度中国美利奴羊皮肤进行转录组测序,鉴定与羊毛密度性状相关的候选基因。【结果】中国美利奴高羊毛密度组(HWD组)的平均羊毛密度(9 852.02±1 673.98)根/cm²,极显著高于低羊毛密度组(LWD组)(5 390.61±1 365.67)根/cm²(P<0.01)。HWD组与LWD组平均初级毛囊密度差异不显著,HWD组的平均次级毛囊密度、初级毛囊密度与次级毛囊密度比值、平均总毛囊密度均极显著高于LWD组(P<0.01)。利用羊毛密度显著差异的中国美利奴羊皮肤转录组数据,HWD组相对于LWD组,共筛选出521个差异表达基因,其中280个基因表达上调、241个基因表达下调。通过高、低密度组间差异基因富集、差异基因互作和差异基因表达验证等分析,筛选出KRT18、KRT16、LOC101116157、CCN3、SPARC、C7、ATP12A、ANGPT4、WNT16、S100A1及S100A4等,影响了中国美利奴羊毛生长及密度的差异表达基因。【结论】不同羊毛密度的细毛羊皮肤组织的基因表达谱存在差异,这些基因表达可通过改变皮肤毛囊及羊毛生长等过程影响羊毛密度。

关键词: 中国美利奴羊; 羊毛密度; RNA-seq; 候选基因

Abstract:

【Objective】 This study aims to analyze the phenotypic differences of wool density in Chinese Merino and screen candidate genes related to wool density traits in Chinese Merino in the hope of providing reference for elucidating the molecular regulation mechanism of wool density in the sheep. 【Methods】 The wool density and hair follicle density of Chinese Merino sheep were measured and statistically analyzed by biostatistical methods. Meanwhile, the skin of Chinese Merino sheep with different wool densities was selected for transcriptome sequencing to identify candidate genes related to wool density traits. 【Results】 The average wool density of Chinese Merino high wool density group ( HWD group ) was (9,852.02±1,673.98) roots / cm², which was significantly higher than that of low wool density group ( LWD group ) (5,390.61±1,365.67) roots / cm² ( P < 0.01 ). There was no significant difference in the average primary hair follicle density between the HWD group and the LWD group. The average secondary hair follicle density, the ratio of primary hair follicle density to secondary hair follicle density, and the average total hair follicle density in the HWD group were significantly higher than those in the LWD group (P < 0.01 ). Using the skin transcriptome data of Chinese Merino sheep with different wool densities, a total of 521 differential genes were screened out in the HWD group compared with the LWD group, of which 280 were up-regulated and 241 were down-regulated. Through the analysis of differential gene enrichment, differential gene interaction and differential gene expression verification between high and low density groups, KRT18, KRT16, KRT86, KRT38, LOC101116157, CCN3, SPARC, C7, ATP12A, ANGPT4, WNT16, S100A1 and S100A4 differentially expressed genes were screened, which affected the growth and density of Chinese Merino wool. 【Conclusion】 There are differences in gene expression profiles of skin tissues of fine wool sheep with different wool densities. The different expression of these genes may affect wool density by changing the process of skin hair follicles and wool growth.

Key words: Chinese merino sheep; density; RNA-seq; candidate gene

中图分类号:

S826.8

马海叶, 李忠慧, 王嘉俊, 唐丽苹, 狄江, 李文蓉. 中国美利奴羊毛密度相关基因的筛选[J]. 新疆农业科学, 2025, 62(6): 1530-1542.

MA Haiye, LI Zhonghui, WANG Jiajun, TANG Liping, DI Jiang, LI Wenrong. Identification of genes associated with wool density traits in Chinese Merino sheep[J]. Xinjiang Agricultural Sciences, 2025, 62(6): 1530-1542.

图/表 11

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基因 Gene	引物序列 Primer	产物长度 Product length(bp)	GenBank登录号 GenBank accession numer
β-actin	F:AAGGACCTCTACGCCAACAC R:GTAACGCAGCTAACAGTCCG	279	NM_001009784.3
ADIPOQ	F:TCTTCTACTGCTGCTAGCCC R:TAGGACCAACGAGACCTGGAT	197	NM_001308565.1
KRT16	F:CTGGAGATGCAGATCGAAGGC R:TCACTGTTAAAGGCCGCTTC	263	XM_060394896.1
SPARC	F:CCTTGCCTGATGAGACAGAAGT R:GTGTTGCTCTCGTCCAGTTC	202	NM_001166202.1
IL37	F:GACACAACAAGCCATCCCTG R:CAGGATAGCGGAAGGTGCAG	171	XM_027965788.2
CNN3	F:GATCTGTGACACCAAAGAGACG R:CTGTTCGATGCAGTTGACACT	118	XM_004011765.5
ANGPT4	F:AATGCTGAAGAACAACACGC R:AGCTGGATCTCCATTCGGGA	225	XM_027977034.3
KRT18	F:AGACTGGGGACACTACCTGA R:CACTCTCCACAGACTGGCG	170	XM_027967273.2
C7	F:TCAGTCTGGGTCCTTAGGAGG R:AGGCCTCTTCCATCGTTGTG	167	XM_004017017.6
ATP12A	F:CGGTACCTGATGCTGTCACC R:ATACCGACGCTCTTGGCAAT	106	XM_004012313.6

基因 Gene	引物序列 Primer	产物长度 Product length(bp)	GenBank登录号 GenBank accession numer
β-actin	F:AAGGACCTCTACGCCAACAC R:GTAACGCAGCTAACAGTCCG	279	NM_001009784.3
ADIPOQ	F:TCTTCTACTGCTGCTAGCCC R:TAGGACCAACGAGACCTGGAT	197	NM_001308565.1
KRT16	F:CTGGAGATGCAGATCGAAGGC R:TCACTGTTAAAGGCCGCTTC	263	XM_060394896.1
SPARC	F:CCTTGCCTGATGAGACAGAAGT R:GTGTTGCTCTCGTCCAGTTC	202	NM_001166202.1
IL37	F:GACACAACAAGCCATCCCTG R:CAGGATAGCGGAAGGTGCAG	171	XM_027965788.2
CNN3	F:GATCTGTGACACCAAAGAGACG R:CTGTTCGATGCAGTTGACACT	118	XM_004011765.5
ANGPT4	F:AATGCTGAAGAACAACACGC R:AGCTGGATCTCCATTCGGGA	225	XM_027977034.3
KRT18	F:AGACTGGGGACACTACCTGA R:CACTCTCCACAGACTGGCG	170	XM_027967273.2
C7	F:TCAGTCTGGGTCCTTAGGAGG R:AGGCCTCTTCCATCGTTGTG	167	XM_004017017.6
ATP12A	F:CGGTACCTGATGCTGTCACC R:ATACCGACGCTCTTGGCAAT	106	XM_004012313.6

样本序号 Sample	HWD组个体羊毛密度 (根/cm²) Individual wool density of HWD group (roots /cm²)	样本号 Sample	LWD组个体羊毛密度 (根/cm²) Individual wool density in LWD group (roots /cm²)
M₁	9 599.86±740.78	X₁	4 784.16±528.16
M₂	7 580.63±564.01	X₂	4 465.07±161.07
M₃	9 224.80±148.86	X₃	6 020.73±447.87
M₄	12 183.55±249.22	X₄	4 530.65±215.19
M₅	7 447.33±193.86	X₅	7 423.50±48.50
M₆	10 037.68±520.97	X₆	7 086.63±218.13
M₇	12 119.28±312.94	X₇	6 046.34±607.34
M₈	9 676.79±642.13	X₈	3 112.43±698.43
M₉	11 493.81±779.05	X₉	4 286.698±88.89
M₁₀	9 156.43±433.57	X₁₀	6 149.94±75.94
平均羊毛密度 (根/cm²) Average wool density (roots /cm²)	9 852.02±1 673.98^A	平均羊毛密度 (根/cm²) Average wool density (roots /cm²)	5 390.61±1365.67^B

样本序号 Sample	HWD组个体羊毛密度 (根/cm²) Individual wool density of HWD group (roots /cm²)	样本号 Sample	LWD组个体羊毛密度 (根/cm²) Individual wool density in LWD group (roots /cm²)
M₁	9 599.86±740.78	X₁	4 784.16±528.16
M₂	7 580.63±564.01	X₂	4 465.07±161.07
M₃	9 224.80±148.86	X₃	6 020.73±447.87
M₄	12 183.55±249.22	X₄	4 530.65±215.19
M₅	7 447.33±193.86	X₅	7 423.50±48.50
M₆	10 037.68±520.97	X₆	7 086.63±218.13
M₇	12 119.28±312.94	X₇	6 046.34±607.34
M₈	9 676.79±642.13	X₈	3 112.43±698.43
M₉	11 493.81±779.05	X₉	4 286.698±88.89
M₁₀	9 156.43±433.57	X₁₀	6 149.94±75.94
平均羊毛密度 (根/cm²) Average wool density (roots /cm²)	9 852.02±1 673.98^A	平均羊毛密度 (根/cm²) Average wool density (roots /cm²)	5 390.61±1365.67^B

毛囊密度 Hair follicle density	HWD组 HWD group (n=3)	LWD组 LWD group (n=3)
初级毛囊密度 Primary hair follicle density(个/mm²)	11.73±0.88	11.47±1.17
次级毛囊密度 Secondary hair follicle density(个/mm²)	123.77±6.56^A	75.60±6.82^B
总毛囊密度 Total hair follicle density(个/mm²)	135.5±7.21^A	87.08±7.04^B
次级毛囊/ 初级毛囊 Secondary follicle primary follicle (S/P)	10.57±0.54^A	6.64±0.83^B

中国美利奴羊毛密度相关基因的筛选

Identification of genes associated with wool density traits in Chinese Merino sheep

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Metrics

样本名称 Sample name	原始数据 Raw reads	有效数据 Clean reads	总碱基数(G) Raw bases(G)	Q20 (%)	Q30 (%)	GC (%)	有效比对位置 Total mapped reads	唯一比对位置 Uniq mapped reads
HWD1	99 631 888	98 403 852	14.94	96.95	91.71	43.5	76760706 (78.01%)	74966784 (76.18%)
HWD4	84 552 020	83 407 436	12.68	96.58	90.88	43.53	74051906 (88.78%)	72554208 (86.99%)
HWD5	91 710 628	90 393 514	13.76	97.26	92.37	44.43	80665002 (89.24%)	78763920 (87.13%)
LWD1	86 716 742	85 687 388	13.01	97.14	92.11	43.73	75754520 (88.41%)	74119478 (86.50%)
LWD2	76 853 470	75 812 706	11.53	96.84	91.47	44.07	68094896 (89.82%)	66541090 (87.77%)
LWD3	84 070 894	82 835 182	12.61	96.91	91.63	43.9	73686020 (88.95%)	71999760 (86.92%)

基因 Gene	差异倍数 Log2(FC)	pvale	GO term名称/通路名称 GO term name/Channel name	GO ID/通路ID GO ID/Path ID
KRT16 (LOC101108147)	3.908 358 258	0.001 5	雌激素信号通路、中间丝细胞骨架、细胞迁移的负调控、中间丝	ko04915、GO:0045111、GO:0030336、GO:0005882
K38	-0.990 508 546	0.049	雌激素信号通路、中间丝细胞骨架、中间丝	ko04915、GO:0045111、GO:0005882
KRT18	8.52E-10	1.07E-06	角蛋白、中间丝、中间丝细胞骨架	GO:0045095、GO:0005882、GO:0045111
KRT2	-1.107 283 021	0.0337	中间丝细胞骨架、中间丝	GO:0045111、GO:0005882、
KRT86 (LOC101112469)	-0.929 762 743	0.025 9	角蛋白、中间丝、中间丝细胞骨架	GO:0045095、GO:0005882、GO:0045111
LOC114113396	-0.873 803 919	0.000 0	中间丝、中间丝细胞骨架	GO:0005882、GO:0045111
LOC101102526	-0.793 473 605	0.002 1	角蛋白、中间丝、中间丝细胞骨架	GO:0045095、GO:0005882、GO:0045111
LOC114110489	-0.704 724 41	0.024 2	角蛋白、中间丝、中间丝细胞骨架	GO:0045095、GO:0005882、GO:0045111
LOC105604740	-1.055 040 848	0.006 0	角蛋白、中间丝、中间丝细胞骨架	GO:0045095、GO:0005882、GO:0045111
LOC105604748	-0.678 692 255	0.034 9	角蛋白、中间丝、中间丝细胞骨架	GO:0045095、GO:0005882、GO:0045111
LOC114116854	-1.014 303 349	0.000 0	角蛋白、中间丝、中间丝细胞骨架	GO:0045095、GO:0005882、GO:0045111
LOC106991399	-0.645 218 659	0.001 5	角蛋白、中间丝、中间丝细胞骨架	GO:0045095、GO:0005882、GO:0045111
LOC101108798	-0.747 533 195	0.032 4	角蛋白、中间丝、中间丝细胞骨架	GO:0045095、GO:0005882、GO:0045111
PPARGC1A	-0.653 304 401	0.013 0	AMPK信号通路、脂肪细胞因子信号通路、Apelin信号通路、胰岛素信号通路、长寿调节通路	ko04152、ko04920、ko04371、ko04211
ADIPOQ	4.171 096 047	0.000 0	PPAR信号通路、AMPK信号通路、脂肪细胞因子信号通路	ko03320、ko04152、ko04920
LPL	1.566 831 306	0.0000	PPAR信号通路、胆固醇代谢	ko03320、ko04979、
PCK1	3.028 853 484	0.0000	PPAR信号通路、AMPK信号通路、脂肪细胞因子信号通路、胰岛素信号通路	ko03320、ko04152、ko04920、ko04910
PLIN1	2.050 184 714	0.0003	PPAR信号通路、脂肪细胞中脂肪分解的调节、Apelin信号通路	ko03320、ko04923、ko04371
AQP7	3.191 035 154	0.000 0	脂肪细胞中脂肪分解的调节、PPAR信号通路	ko04923、ko03320
LOC114110557	1.354 378 402	0.017 1	PPAR信号通路	ko03320
LOC101116157	2.169 032 359	0.004 4	甲状腺激素合成、	ko04918
LOC101105860	2.051 008 032	0.000 0	卡波西肉瘤相关疱疹病毒感染	ko05167
IL37	-1.009 125 479	0.021 4	病毒蛋白与细胞因子和细胞因子受体的相互作用、细胞因子-细胞因子受体相互作用	ko04061、ko04060
ACVR1C	1.941 346 561	0.0001	细胞因子-细胞因子受体相互作用、调节干细胞多能性的信号通路、TGF-β信号通路	ko04060、ko04550、ko04350
CCN3	0.830 009 455	0.0000	细胞外基质、外封装结构、细胞间连接、糖胺聚糖结合蛋白质、感觉知觉调节、细胞成分运动的负性调节	GO:0031012、GO:0030312、GO:0005911、GO:0005539
SPARC	-0.740 383 421	0.036 5	含胶原的细胞外基质、外封装结构、基底膜、细胞外基质结合、胶原蛋白结合、含胶原的细胞外基质	GO:0031012、GO:0030312、GO:0005604、GO:0050840、GO:0005518、GO:0062023
C7	1.533 434 994	0.0070	补体和凝血级联反应、系统性红斑狼疮、朊病毒疾病	ko04610、ko05322、ko05020
ATP12A	0.769 716 368	0.0190	氧化磷酸化	ko00190
ANGPT4	0.857 573 739	0.000 1	MAPK信号通路、PI3K-Akt信号通路	ko04010、ko04151
WNT16	-0.695 275 741	0.007 9	调节干细胞多能性的信号通路、癌症中的转录失调、乳腺癌、Wnt信号通路	ko04550、ko05202、ko05224、ko04310
ESR1	-0.709 884 33	0.000 4	雌激素信号通路、乳腺癌	ko04915、ko05224
S100A4	0.701 756 699	0.003 9	血液循环、血液循环的调节、心脏收缩、钙依赖性蛋白结合、循环系统过程	GO:0008015、GO:1903522、GO:0003015、GO:0048306、GO:0003013
S100A1	0.685 870 126	0.037 3	NF-kB信号通路、NF-kB信号通路正调节、钙依赖性蛋白结合	GO:0007249、GO:0043123、GO:0022832、GO:0048306

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