全基因组重测序挖掘史宾格母犬的产仔数性状候选基因

doi:10.12300/j.issn.1674-5817.2025.149

摘要/Abstract

摘要：

目的通过挖掘调控史宾格种母犬产仔数的候选基因，解析其繁殖力遗传机制，为该品种高繁殖力基因组的选择育种提供参考。方法采用全基因组重测序技术，根据窝均产仔数，将经产3窝以上的史宾格种母犬分为高产组和低产组，通过选择信号分析，筛选固定指数（fixation index，F_st）与核苷酸多态性（nucleotide diversity，Pi）高选择区域的交集，结合基因注释与功能富集分析筛选候选基因。结果史宾格种母犬高产组平均窝产仔数为（7.41±1.27）只，显著高于低产组的（3.82±1.20）只（P＜0.05）；高产组的总活仔数为（7.06±1.10）只，极显著高于低产组的（3.67±1.11）只（P＜0.01）。全基因组重测序共检测到3 155 706个单核苷酸多态性（single nucleotide polymorphism，SNP），其中63.09%位于基因间区，33.96%位于内含子区，外显子区、3'非翻译区（untranslated region，UTR）、5'UTR分别占0.38%、0.57%、0.09%；外显子区SNP中，非同义变异共有5 256个（占43.55%）。经注释筛选得到1 752个差异基因，通过基因本体（gene ontology，GO）功能富集分析与京都基因和基因组数据库（Kyoto Encyclopedia of Genes and Genomes，KEGG）通路富集分析，最终确定13个与繁殖性能相关的候选基因（WDR35、SMAD7、RPGR、RERGL、PGRMC2、LOC482182、GIMD1、COX7B2、COX16、BMPR2、BMP6、BICD1、SLC9C1），其功能涉及生殖激素调控、胚胎发育、GTP酶激活及卵细胞凋亡等。结论史宾格种母犬产仔数性状经历了显著的人工选择，筛选出的13个候选基因在卵细胞成熟、妊娠初期调控中发挥关键作用，为解析犬繁殖性状的遗传机制提供了新的分子依据。

关键词: 史宾格种母犬, 产仔数性状, 全基因组重测序, 候选基因

Abstract:

Objective Candidate genes related to the regulation of litter size traits in English Springer Spaniel breeding bitches are explored, and the genetic mechanism underlying fertility in this breed is investigated, in order to provide reference molecular markers for genomic selection of high fecundity. Methods Whole genome resequencing was performed on English Springer Spaniel breeding bitches that had given birth to at least 3 litters, and the bitches were divided into a high-litter-size group and a low-litter-size group according to the average litter size. Selection signal analysis was used to obtain the intersection of fixation index (F_st) and nucleotide diversity (Pi) signals as highly selected regions, and candidate genes were screened based on gene annotation and functional enrichment analysis. Results The average litter size in the high-litter-size group (7.41±1.27) was significantly higher than that in the low-litter-size group (3.82±1.20) (P＜0.05), and the total number of live offspring in the high-litter-size group (7.06±1.10) was extremely significantly higher than that in the low-litter-size group (3.67±1.11) (P＜0.01). A total of 3 155 706 SNPs were detected in the two groups, 63.09% of which were located in intergenic regions, 33.96% in intronic regions, and 0.38％, 0.57％, and 0.09％ in exonic regions, 3' untranslated regions (UTRs), and 5'UTRs, respectively. Among the SNPs in exonic regions, 5 256 were nonsynonymous variants, accounting for 43.55%. A total of 1 752 differential genes were identified after annotation screening. Gene ontology （GO） and Kyoto Encyclopedia of Genes and Genomes （KEGG) enrichment analyses identified 13 candidate genes that may affect reproductive performance and litter size traits, including WDR35, SMAD7, RPGR, RERGL, PGRMC2, LOC482182, GIMD1, COX7B2, COX16, BMPR2, BMP6, BICD1, and SLC9C1. Their functions mainly involve reproductive hormone regulation, embryonic development, GTPase activation, and oocyte apoptosis. Conclusion English Springer Spaniel breeding bitches have undergone significant artificial selection for litter size traits. These 13 candidate genes play key roles in oocyte maturation and regulation during early pregnancy, providing a new molecular basis for elucidating the genetic mechanism of canine reproductive traits.

Key words: English Springer Spaniel breeding bitches, Litter size trait, Whole genome resequencing, Candidate genes

中图分类号:

Q95-33

高一龙,贺星亮,周肖鹏,等. 全基因组重测序挖掘史宾格母犬的产仔数性状候选基因[J]. 实验动物与比较医学, 2026, 46(3): 378-387. DOI: 10.12300/j.issn.1674-5817.2025.149.

GAO Yilong,HE Xingliang,ZHOU Xiaopeng,et al. Mining Candidate Genes for Litter Size Traits in English Springer Spaniel Bitches Based on Whole Genome Resequencing[J]. Laboratory Animal and Comparative Medicine, 2026, 46(3): 378-387. DOI: 10.12300/j.issn.1674-5817.2025.149.

图/表 7

表 1 高产组和低产组史宾格种母犬产仔数性状的比较 (只，

x ˉ

±s)

Table 1 Comparison of litter size trait between high-litter-size and low-litter-size groups of English Springer Spaniel breeding bitches

xˉ±s)
">

组别

Group

总产仔数

Total number of litter size

总活仔数

Total number of live offspring

高产组High-litter-size group

7.41±1.27^a

7.06±1.10^b

低产组Low-litter-size group

3.82±1.20

3.67±1.11

表 1 高产组和低产组史宾格种母犬产仔数性状的比较 (只， $x ˉ$ ±s)

Table 1 Comparison of litter size trait between high-litter-size and low-litter-size groups of English Springer Spaniel breeding bitches

组别

Group

总产仔数

Total number of litter size

总活仔数

Total number of live offspring

高产组High-litter-size group

7.41±1.27^a

7.06±1.10^b

低产组Low-litter-size group

3.82±1.20

3.67±1.11

表 2 史宾格种母犬高产仔数组与低产仔数组的全基因组重测序数据

Table 2 Whole genome resequencing data of English Springer Spaniel breeding bitches in the high-litter-size and low-litter-size groups

样本编号 Sample number	质控后有效测序段数/条 Number of effective sequencing segments after quality control/reads	比对数/条 Comparison quantity/reads	比对率/% Comparison rate/%	平均测序深度/倍 Mean sequencing depth/fold	Q20/%	Q30/%	GC碱基比例/% GC content/%
JCS-01-DC	49 701 009	49 495 473	99.59	3.015 7	96.84	91.44	40.31
JCS-02-GC	57 569 978	57 424 899	99.75	3.500 8	96.94	91.66	40.50
JCS-06-DC	50 170 943	50 035 322	99.73	3.048 7	96.91	91.60	40.44
JCS-11-GC	56 648 593	56 504 709	99.75	3.446 4	97.01	91.80	40.39
JCS-13-DC	63 501 199	63 282 693	99.66	3.858 8	97.04	91.79	41.18
JCS-15-DC	67 124 038	66 904 179	99.67	4.075 1	96.98	91.76	40.54
JCS-17-DC	60 312 575	60 159 920	99.75	3.674 5	97.05	91.92	40.44
JCS-18-DC	56 651 718	56 505 792	99.74	3.449 1	97.10	92.02	40.49
JCS-20-DC	52 034 437	51 854 996	99.66	3.158 3	96.90	91.61	41.38
JCS-25-DC	46 446 939	46 318 986	99.72	2.825 3	96.89	91.54	40.39
JCS-27-DC	51 579 104	51 417 318	99.69	3.131 1	96.98	91.77	40.37
JCS-30-GC	57 620 774	57 306 085	99.45	3.472 1	98.04	94.40	40.97
JCS-32-DC	56 929 134	56 841 636	99.85	3.451 3	98.01	94.35	40.98
JCS-36-GC	61 621 912	61 516 493	99.83	3.733 4	98.06	94.47	40.86
JCS-38-GC	59 543 985	59 452 953	99.85	3.616 1	97.97	94.22	40.01
JCS-41-GC	55 343 670	55 265 057	99.86	3.354 7	98.03	94.42	40.32
JCS-47-GC	53 077 925	52 998 639	99.85	3.219 2	98.03	94.39	40.13
JCS-49-GC	47 499 774	47 414 328	99.82	2.878 9	98.03	94.39	40.06
JCS-50-GC	50 683 884	50 608 669	99.85	3.078 6	98.02	94.37	40.11
JCS-52-GC	56 492 470	56 374 197	99.79	3.424 0	98.03	94.37	40.03

表 3 SNP 检测统计信息及注释结果

Table 3 Statistics and annotation results of SNP detection

序号 No.	分类 Category	SNP数量 Number of SNP
1	基因间区	1 991 050
2	基因上游1 kb区域	27 445
3	基因下游1 kb区域	32 011
4	5'UTR	2 885
5	3'UTR	17 833
6	剪切位点	72
7	内含子区域	1 071 830
8	外显子区域	12 068
	非同义变异	5 256
	同义变异	6 208
	获得终止密码子变异	73
	失去终止密码子变异	19
9	未知	512
10	总数	3 155 706

注：A，高产组和低产组史宾格种母犬之间群体分化的F_st分布情况；B～C，高产组（B）和低产组（C）史宾格种母犬群体的Pi分析结果。2条虚线分别代表2种选择阈值（A~C中上面虚线表示F_st值或Pi值前1%，下面虚线表示F_st值或Pi值前5%）。DC，低产组；GC，高产组。
">

图1 高产组和低产组史宾格种母犬群体的F_st分布与Pi分析结果
注：A，高产组和低产组史宾格种母犬之间群体分化的F_st分布情况；B～C，高产组（B）和低产组（C）史宾格种母犬群体的Pi分析结果。2条虚线分别代表2种选择阈值（A~C中上面虚线表示F_st值或Pi值前1%，下面虚线表示F_st值或Pi值前5%）。DC，低产组；GC，高产组。

Figure 1 F_st distribution and Pi analysis results of high-litter-size and low-litter-size groups of English Springer Spaniel breeding bitches
Note： A， Distribution of F_st for population differentiation between the high-litter-size group and low-litter-size group of English Springer Spaniel breeding bitches； B-C， Pi analysis results of the high-litter-size group （B） and low-litter-size group （C） of English Springer Spaniel breeding bitches. The two dotted lines represent two selection thresholds （The top dotted line in A to C represents the top 1% of F_st or Pi values， and the bottom dotted line represents the top 5% of F_st or Pi values）. DC， low-litter-size group； GC， high-litter-size group.

注：a，高产仔数组史宾格种母犬群体的信号选择区域；b，低产仔数组史宾格种母犬群体的信号选择区域。绿色和红色区域为Pi值前5%区域；橘色区域为F_st值前5%区域。点图代表不同窗口内相应的F_st和Pi值；紫色和粉色圆点为F_st值和Pi值的交集，即候选基因位点。
">

图2 F_st、Pi选择消除分析结果
注：a，高产仔数组史宾格种母犬群体的信号选择区域；b，低产仔数组史宾格种母犬群体的信号选择区域。绿色和红色区域为Pi值前5%区域；橘色区域为F_st值前5%区域。点图代表不同窗口内相应的F_st和Pi值；紫色和粉色圆点为F_st值和Pi值的交集，即候选基因位点。

Figure 2 Selection sweep analysis results of F_st and Pi
Note： a， Signal selection regions of the high-litter-size group of English Springer Spaniel breeding bitches； b， Signal selection regions of the low-litter-size group of English Springer Spaniel breeding bitches. The green and red areas are the top 5% region of Pi values； the orange area is the top 5% region of F_st values. Dot plots represent the corresponding F_st and Pi values within different windows； the purple and pink dots represent the intersection of F_st and Pi values， i.e.， candidate gene loci.

注：BP，生物过程；CC，细胞组分；MF，分子功能；CellP.，细胞过程；EnvlP.，环境信息处理；GenlP.，遗传信息处理；HumaD.，人类疾病；Metab.，代谢；OrgaS.，生物体系统。
">

图3 差异基因的GO条目（A）和KEGG通路（B）富集分析结果
注：BP，生物过程；CC，细胞组分；MF，分子功能；CellP.，细胞过程；EnvlP.，环境信息处理；GenlP.，遗传信息处理；HumaD.，人类疾病；Metab.，代谢；OrgaS.，生物体系统。

Figure 3 GO terms （A） and KEGG pathways （B） enriched for differential genes
Note： BP， Biological process； CC， Cellular component； MF， Molecular function； CellP.， Cellular processes； EnvlP.， Environmental Information processing； GenlP.， Genetic information processing； HumaD.， Human diseases； Metab.， Metabolism； OrgaS.， Organismal systems.

表 4 候选基因的染色体座位、SNP变异注释及GO、KEGG富集分析

Table 4 Chromosomal loci, SNP variation annotation, and GO and KEGG enrichment analysis of candidate genes

基因 Gene	基因所在染色体及起始位点 The chromosome and start site of the gene	基因功能及注释 Gene function and annotation	通路名称 Pathway name
WDR35	Chr 17:15 000 306	与细胞内的纤毛发生、纤毛维持及相关信号通路调控相关	纤毛内运输通路、Hedgehog信号通路
SMAD 7	Chr 15:31 542 000	调控卵巢颗粒细胞增殖与凋亡	丝裂原激活的蛋白激酶信号通路
RPGR	Chr X:33 060 949	调控视网膜感光细胞的纤毛功能和蛋白质运输	纤毛组装与维持通路、GTP酶信号通路
RERGL	Chr 27:28 947 686	小GTP酶编码基因，涉及细胞增殖、分化和信号传导	大鼠肉瘤基因（Ras）信号通路
PGRMC 2	Chr 19:12 726 628	参与激素代谢、细胞应激响应的多功能基因	类固醇激素生物合成通路
LOC482182	Chr 13:59 333 984	未表征基因，可能与神经系统发育及细胞增殖调控有关	细胞表面信号传递
GIMD1	Chr 32:27 203 619	参与GTP酶活性调控，介导细胞信号转导过程，与雌性动物胚胎发育、繁殖周期调控相关	免疫细胞活化与存活调控
COX7B 2	Chr 13:42 746 234	线粒体呼吸链复合体Ⅳ（细胞色素c氧化酶）的一个亚基，参与细胞能量代谢关键过程	氧化磷酸化通路
COX16	Chr 8:44 007 617	线粒体COX复合体组装的关键辅助因子，通过调控细胞色素c氧化酶正确形成以维持线粒体呼吸功能	细胞色素c氧化酶、复合物组装通路
BMPR 2	Chr 37:11 386 691	骨形态发生蛋白受体家族的重要成员，属于丝氨酸/苏氨酸激酶受体，在细胞信号转导、胚胎发育、组织稳态及疾病发生中发挥关键作用	骨形态生成蛋白信号通路
BMP 6	Chr 35:7 810 492	可抑制颗粒细胞凋亡，促进雌激素合成，维持卵泡正常生长	生殖系统调控通路
BICD1	Chr 27:16 534 098	作为细胞内物质运输辅助因子，参与调控卵细胞成熟、受精和早期胚胎形成	参与囊泡介导的运输和高尔基体到内质网的逆向运输等通路
SLC 9C 1	Chr 33:16 824 626	溶质载体基因，与精子的运动和生育能力相关	离子跨膜运输通路

表 4 候选基因的染色体座位、SNP变异注释及GO、KEGG富集分析

Table 4 Chromosomal loci, SNP variation annotation, and GO and KEGG enrichment analysis of candidate genes

基因 Gene	基因所在染色体及起始位点 The chromosome and start site of the gene	基因功能及注释 Gene function and annotation	通路名称 Pathway name
WDR35	Chr 17:15 000 306	与细胞内的纤毛发生、纤毛维持及相关信号通路调控相关	纤毛内运输通路、Hedgehog信号通路
SMAD 7	Chr 15:31 542 000	调控卵巢颗粒细胞增殖与凋亡	丝裂原激活的蛋白激酶信号通路
RPGR	Chr X:33 060 949	调控视网膜感光细胞的纤毛功能和蛋白质运输	纤毛组装与维持通路、GTP酶信号通路
RERGL	Chr 27:28 947 686	小GTP酶编码基因，涉及细胞增殖、分化和信号传导	大鼠肉瘤基因（Ras）信号通路
PGRMC 2	Chr 19:12 726 628	参与激素代谢、细胞应激响应的多功能基因	类固醇激素生物合成通路
LOC482182	Chr 13:59 333 984	未表征基因，可能与神经系统发育及细胞增殖调控有关	细胞表面信号传递
GIMD1	Chr 32:27 203 619	参与GTP酶活性调控，介导细胞信号转导过程，与雌性动物胚胎发育、繁殖周期调控相关	免疫细胞活化与存活调控
COX7B 2	Chr 13:42 746 234	线粒体呼吸链复合体Ⅳ（细胞色素c氧化酶）的一个亚基，参与细胞能量代谢关键过程	氧化磷酸化通路
COX16	Chr 8:44 007 617	线粒体COX复合体组装的关键辅助因子，通过调控细胞色素c氧化酶正确形成以维持线粒体呼吸功能	细胞色素c氧化酶、复合物组装通路
BMPR 2	Chr 37:11 386 691	骨形态发生蛋白受体家族的重要成员，属于丝氨酸/苏氨酸激酶受体，在细胞信号转导、胚胎发育、组织稳态及疾病发生中发挥关键作用	骨形态生成蛋白信号通路
BMP 6	Chr 35:7 810 492	可抑制颗粒细胞凋亡，促进雌激素合成，维持卵泡正常生长	生殖系统调控通路
BICD1	Chr 27:16 534 098	作为细胞内物质运输辅助因子，参与调控卵细胞成熟、受精和早期胚胎形成	参与囊泡介导的运输和高尔基体到内质网的逆向运输等通路
SLC 9C 1	Chr 33:16 824 626	溶质载体基因，与精子的运动和生育能力相关	离子跨膜运输通路

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