Mining Candidate Genes for Litter Size Traits in English Springer Spaniel Bitches Based on Whole Genome Resequencing

doi:10.12300/j.issn.1674-5817.2025.149

Abstract

Abstract:

Objective The candidate genes related to the regulation of litter size traits in in English Springer Spaniel were explored, and the genetic mechanism of dog fertility represented by English Springer Spaniel was investigated, in order to lay a foundation for further application of molecular breeding. Method Comparative analysis was conducted on two groups of high and low yielding English Springer Spaniel bitches by using whole genome resequencing, and selection elimination analysis was used to obtain Fst and Pi signal intersection as a high selection region for gene annotation and candidate gene screening. Result The average number of litter size in high yielding group (7.41±1.27) was significantly higher than that in low yielding group (3.82±1.20) (P＜0.05), and the difference in total number of litter size was extremely significant (high yielding group 7.06±1.10 vs low yielding group 3.67±1.11, P＜0.01).A total of 3 155 634 SNPs were found in two groups of samples, 63.09% of which were located in the intergenic region, 33.97％in the intron region, and only 0.38％,0.57％ and 0.09％ in the exon region, non-coding region 3' end, and 5' end, respectively. Among the SNP located in the exon region of the genome, 5 256 were non-synonymous variants, accounting for 43.55%. Extracting SNP loci located in the exon region, intron region, and non-coding regions at the 3' and 5' ends for gene annotation, a total of 1 752 differentially expressed genes were screened between the two groups of samples. KEGG and GO enrichment analysis on differential genes were conducted, and a total of 13 candidate genes that may affect reproductive performance and litter size traits were screened out, including WDR35, SMAD7, RPGR, RERGL, PGRMC2, LOC482182, GIMD1,COX7B2, COX16, BMPR2, BMP6, BICD1 and SLC9C1 . The gene functions mainly involved reproductive hormone regulation, embryonic development, GTPase activation, oocyte apoptosis and so on. Conclusion The English Springer Spaniel bitches have experienced significant artificial selection on the litter size trait, and the candidate genes affecting the litter size trait of these bitches have been preliminarily excavated. These genes play a role in the physiological activities related to dog reproductive performance, and mainly in the period of apoptosis of bitch egg cells and the beginning of pregnancy to particpate in regulation.

Key words: English Springer Spaniel bitches, litter size, genome resequencing, candidate gene, artificial selection

CLC Number:

Q95-33

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. DOI: 10.12300/j.issn.1674-5817.2025.149.

Figures/Tables 8

References 20

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样本号 Sample No.	质控后有效测序段数 Number of effective sequencing segments after quality control	比对数 Comparison quantity	比对率 Comparison rate (%)	平均测序深度 Mean sequencing depth	Q20 (%)	Q30 (%)	GC比例 Proportion of GC (%)
JCS-01	49 701 009	49 495 473	99.59%	3.015 7X	96.84	91.44	40.31
JCS-02	57 569 978	57 424 899	99.75%	3.5008X	96.94	91.66	40.50
JCS-06	50 170 943	50 035 322	99.73%	3.0487X	96.91	91.60	40.44
JCS-11	56 648 593	56 504 709	99.75%	3.4464X	97.01	91.80	40.39
JCS-13	63 501 199	63 282 693	99.66%	3.8588X	97.04	91.79	41.18
JCS-15	67 124 038	66 904 179	99.67%	4.0751X	96.98	91.76	40.54
JCS-17	60 312 575	60 159 920	99.75%	3.6745X	97.05	91.92	40.44
JCS-18	56 651 718	56 505 792	99.74%	3.4491X	97.10	92.02	40.49
JCS-20	52 034 437	51 854 996	99.66%	3.1583X	96.90	91.61	41.38
JCS-25	46 446 939	46 318 986	99.72%	2.8253X	96.89	91.54	40.39
JCS-27	51 579 104	51 417 318	99.69%	3.1311X	96.98	91.77	40.37
JCS-30	57 620 774	57 306 085	99.45%	3.4721X	98.04	94.40	40.97
JCS-32	56 929 134	56 841 636	99.85%	3.4513X	98.01	94.35	40.98
JCS-36	61 621 912	61 516 493	99.83%	3.7334X	98.06	94.47	40.86
JCS-38	59 543 985	59 452 953	99.85%	3.6161X	97.97	94.22	40.01
JCS-41	55 343 670	55 265 057	99.86%	3.3547X	98.03	94.42	40.32
JCS-47	53 077 925	52 998 639	99.85%	3.2192X	98.03	94.39	40.13
JCS-49	47 499 774	47 414 328	99.82%	2.8789X	98.03	94.39	40.06
JCS-50	50 683 884	50 608 669	99.85%	3.0786X	98.02	94.37	40.11
JCS-52	56 492 470	56 374 197	99.79%	3.424X	98.03	94.37	40.03

样本号 Sample No.	质控后有效测序段数 Number of effective sequencing segments after quality control	比对数 Comparison quantity	比对率 Comparison rate (%)	平均测序深度 Mean sequencing depth	Q20 (%)	Q30 (%)	GC比例 Proportion of GC (%)
JCS-01	49 701 009	49 495 473	99.59%	3.015 7X	96.84	91.44	40.31
JCS-02	57 569 978	57 424 899	99.75%	3.5008X	96.94	91.66	40.50
JCS-06	50 170 943	50 035 322	99.73%	3.0487X	96.91	91.60	40.44
JCS-11	56 648 593	56 504 709	99.75%	3.4464X	97.01	91.80	40.39
JCS-13	63 501 199	63 282 693	99.66%	3.8588X	97.04	91.79	41.18
JCS-15	67 124 038	66 904 179	99.67%	4.0751X	96.98	91.76	40.54
JCS-17	60 312 575	60 159 920	99.75%	3.6745X	97.05	91.92	40.44
JCS-18	56 651 718	56 505 792	99.74%	3.4491X	97.10	92.02	40.49
JCS-20	52 034 437	51 854 996	99.66%	3.1583X	96.90	91.61	41.38
JCS-25	46 446 939	46 318 986	99.72%	2.8253X	96.89	91.54	40.39
JCS-27	51 579 104	51 417 318	99.69%	3.1311X	96.98	91.77	40.37
JCS-30	57 620 774	57 306 085	99.45%	3.4721X	98.04	94.40	40.97
JCS-32	56 929 134	56 841 636	99.85%	3.4513X	98.01	94.35	40.98
JCS-36	61 621 912	61 516 493	99.83%	3.7334X	98.06	94.47	40.86
JCS-38	59 543 985	59 452 953	99.85%	3.6161X	97.97	94.22	40.01
JCS-41	55 343 670	55 265 057	99.86%	3.3547X	98.03	94.42	40.32
JCS-47	53 077 925	52 998 639	99.85%	3.2192X	98.03	94.39	40.13
JCS-49	47 499 774	47 414 328	99.82%	2.8789X	98.03	94.39	40.06
JCS-50	50 683 884	50 608 669	99.85%	3.0786X	98.02	94.37	40.11
JCS-52	56 492 470	56 374 197	99.79%	3.424X	98.03	94.37	40.03

序号 No.	分类 Category	SNP 数量 Number of SNP
1	位于基因间区	1 991 050
2	位于基因上游 1kb 区域	27 445
3	位于基因下游 1kb 区域	32 011
4	位于 5'UTR	2 885
5	位于 3'UTR	17 833
6	位于剪切位点	72
7	位于内含子区域	1 071 830
8	外显子非同义变异	5 256
9	外显子同义变异	6 208
10	外显子获得终止密码子变异	73
11	外显子失去终止密码子变异	19
12	外显子	12 068
13	未知	512
14	总数	3 155 634

序号 No.	分类 Category	SNP 数量 Number of SNP
1	位于基因间区	1 991 050
2	位于基因上游 1kb 区域	27 445
3	位于基因下游 1kb 区域	32 011
4	位于 5'UTR	2 885
5	位于 3'UTR	17 833
6	位于剪切位点	72
7	位于内含子区域	1 071 830
8	外显子非同义变异	5 256
9	外显子同义变异	6 208
10	外显子获得终止密码子变异	73
11	外显子失去终止密码子变异	19
12	外显子	12 068
13	未知	512
14	总数	3 155 634

基因 Gene	染色体 Chromosome	基因座位（起始－终止）Locus(Start-End )	SNP变异 SNP variation	基因功能及注释 Gene function and annotation	通路名称 Path name
WDR35	Chr17	15 000 306-15 020 189	Chr17 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（Intraflagellar Transport, IFT）通路、Hedgehog 信号通路
SMAD7	Chr15	31 542 000-31 558 721	Chr15 31,542,000	调控卵巢颗粒细胞增殖与凋亡	MAPK 信号通路
RPGR	ChrX	33 060 949-33 102 418	ChrX: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、GTPase 信号通路
RERGL	Chr27	28 947 686-28 952 314	Chr27:28 947 686	小 GTP 酶编码基因，涉及细胞增殖、分化、信号传导	Ras 信号通路
PGRMC2	Chr19	12 726 628-12 735 981	Chr19:12 726 628	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	Chr13	59 333 984-59 340 152	Chr13:59 333 984	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	Chr32	27 203 619-27 218 453	Chr32:27 203 619	GIMD1编码的蛋白质可能具有 GTP 结合活性和核苷酸结合活性；DKK2参与调控 WNT 信号通路，在胚胎发育、组织稳态	免疫细胞活化与存活调控
COX7B2	Chr13	42 746 234-42 748 911	Chr13:42 746 234	线粒体呼吸链复合体 Ⅳ（细胞色素 c 氧化酶，COX）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	Chr8	44 007 617-44 010 352	Chr8:44 007 617	线粒体 COX 复合体组装的关键辅助因子，通过调控 COX 正确形成维持线粒体呼吸功能	细胞色素c氧化酶复合物组装通路
BMPR2	Chr37	11 386 691-11 420 837	Chr37:11 386 691	骨形态发生蛋白（BMP）受体家族的重要成员，属于丝氨酸 / 苏氨酸激酶受体，在细胞信号传导、胚胎发育、组织稳态及疾病发生中发挥关键作用。	BMP 信号通路
BMP6	Chr35	7 810 492-7 825 638	Chr35:7 810 492	BMP6 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	Chr27	16 534 098-16 548 213	Chr27:16 534 098	BICD1 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
SLC9C1	Chr33	16 824 626-16 838 942	Chr33:16 824 626	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