Whole genome resequencing screening of candidate genes for lactation yield in Kazakh horses

doi:10.6048/j.issn.1001-4330.2025.04.024

Xinjiang Agricultural Sciences ›› 2025, Vol. 62 ›› Issue (4): 993-1001.DOI: 10.6048/j.issn.1001-4330.2025.04.024

• Animal Husbandry Veterination · Agricultural Eeconomy • Previous Articles Next Articles

Whole genome resequencing screening of candidate genes for lactation yield in Kazakh horses

MENG Chen¹(), ZENG Yaqi¹^,², WANG Jianwen¹^,², YAO Xinkui¹^,², LUO Penghui³, XIE Xiaoyu³, LI Pengcheng¹, LIU Xiaoxiao¹, WANG Chuankun¹, MENG Jun¹^,²()

1. College of Animal Science, Xinjiang Agricultural University/Institute of Equine Industry, Xinjiang Agricultural University, Urumqi 830052, China
2. Xinjiang Key Laboratory of Horse Breeding and Exercise Physiology, Urumqi 830052, China
3. General Animal Husbandry Station of Xinjiang Uygur Autonomous Region, Urumqi 830000, China

Received:2024-08-11 Online:2025-04-20 Published:2025-06-20
Supported by:
Major Scientific R & D Program Special Project of Xinjiang Uygur Autonomous Region "Construction of the Efficient Breeding Technology System of the Domestic Horse Specialized Strain"(2022A02013-1);Innovation Environment Construction Special Project (Talent, Base) of Xinjiang Uygur Autonomous Region "Key Laboratory Platform Construction for Horse Germplasm Innovation Cultivation and Efficient and Healthy Breeding"(PT2311);Special Project for the Development of Local Science and Technology Guided by the Central Government "Specialized Sports Horse Cultivation Technical Service Support"(ZYYD2023C02)

全基因组重测序筛选哈萨克马泌乳量候选基因

孟晨¹(), 曾亚琦¹^,², 王建文¹^,², 姚新奎¹^,², 罗鹏辉³, 解晓钰³, 李鹏程¹, 刘晓晓¹, 王川坤¹, 孟军¹^,²()

1.新疆农业大学动物科学学院/新疆农业大学马产业研究院,乌鲁木齐 830052
2.新疆马繁育与运动生理重点实验室,乌鲁木齐 830052
3.新疆维吾尔自治区畜牧总站,乌鲁木齐 830000

通讯作者: 孟军(1986-),男,教授,博士,硕士生导师,研究方向为动物生产学,(E-mail)junm86@qq.com
作者简介:孟晨(1998-),男,硕士研究生,研究方向为动物生产学,(E-mail)2900974511@qq.com
基金资助:
新疆维吾尔自治区重大科技专项“国产马专门化品系高效繁育技术体系构建”(2022A02013-1);新疆维吾尔自治区创新环境（人才、基地）建设专项“马种质创新培育与高效健康养殖重点实验室平台建设”(PT2311);中央引导地方科技发展专项资金项目“专门化运动马培育技术服务支撑”(ZYYD2023C02)

Abstract

Abstract:

【Objective】 To perform whole genome resequencing of jugular vein blood of Kazakh horses to identify candidate genes regulating differences in lactation in Kazakh horses and to provide data support for the selection of Kazakh horses for dairy performance. 【Methods】 According to the lactation volume data of 30-105 d of test horses, 12 healthy Kazakh horses with similar age, parity and consistent feeding background, that was, 6 in the high lactation group (HW) and 6 in the low lactation group were selected. Altogether, a total of 288 blood samples were collected during the whole monitoring cycle, and 48 blood samples were selected for whole genome resequencing, 6 blood samples of lactation greater than 2. 26 kg in the HW group and 6 blood samples of lactation less than 1.05 kg in the LW group were selected for whole genome resequencing, and a total of 288 blood samples were obtained. A total of 88 blood samples were collected during the whole monitoring period, and 48 blood samples were collected at the actual peak lactation date. 6 blood samples from the HW group with lactation greater than 2.26 kg and 6 blood samples from the LW group with lactation less than 1.05 kg were selected for whole-genome resequencing, which yielded a total of 20,234,241 mutated sites; 980,491,918 valid sites were obtained after removing the sequences with junctions and low-quality sequences. The loci in the first 0.000,01 of Top were selected, and the threshold value was determined to be 0.000,147,8, with a total of 88 mutation loci located in 40 candidate genes. The candidate genes were analysed for GO and KEGG pathway enrichment, and the significantly enriched pathways were condensed and classified to locate the biological processes affecting high and low lactation in Kazakh horses; the pathway enrichment chordal maps were drawn to further identify the genes related to lactation in Kazakh horses. 【Results】 GO and KEGG enrichment analyses found the largest number in cell development, proliferation, differentiation, adhesion-related and CNS and endocrine system developmental enrichment pathways, and the pathways of cell adhesion molecule binding, morphogenesis of differentiated cells, morphogenesis of cellular components, cellular development, PI3K-Akt signalling pathway, Axon guidance, and ECM receptor interactions affecting lactation. 【Conclusion】 It is determined that KIT, EPHA4, PDGFRA, MYH3, ITGA1, and COL4A1 may be candidate genes affecting lactation in Kazakh horses.

Key words: Kazakh horse; lactation; whole genome resequencing; physiological process

摘要：

【目的】对哈萨克马颈静脉血液进行全基因组重测序,确定调控哈萨克马泌乳量差异的候选基因,为选育乳用性能的哈萨克马提供数据支撑。【方法】根据试验马匹30~105 d泌乳量数据,选取12匹年龄、胎次、体况相近,饲养一致的健康哈萨克马,高泌乳量组(HW)6匹,低泌乳量组(LW)6匹,对12匹哈萨克马颈静脉采血,共采集到48份血样,选择HW组泌乳量大于2.26 kg血样6份和LW组泌乳量小于1.05 kg血样6份进行全基因组重测序,共得到20 234 241个突变位点;去除带接头序列、低质量序列后得到9 804 918个有效位点。选择Top前0.000 01的位点,确定阈值为0.000 147 8,共88个突变位点,位于40个候选基因。对候选基因进行GO和KEGG通路富集分析,并对显著富集通路进行浓缩分类,定位影响哈萨克马高低泌乳量的生物学过程;绘制通路富集弦图,确定哈萨克马泌乳量相关的基因。【结果】GO和KEGG富集分析发现其中细胞发育、增殖、分化、粘附相关和中枢神经系统、内分泌系统发育富集通路数量最多,细胞粘附分子结合、分化的细胞形态发生、细胞成分形态发生、细胞发育、PI3K-Akt信号通路、Axon引导、ECM受体相互作用等通路影响泌乳量。【结论】确定KIT、EPHA4、PDGFRA、MYH3、ITGA1、COL4A1可能是影响哈萨克马泌乳量的候选基因。

关键词: 哈萨克马, 泌乳量, 全基因组重测序, 生理过程

CLC Number:

S821

MENG Chen, ZENG Yaqi, WANG Jianwen, YAO Xinkui, LUO Penghui, XIE Xiaoyu, LI Pengcheng, LIU Xiaoxiao, WANG Chuankun, MENG Jun. Whole genome resequencing screening of candidate genes for lactation yield in Kazakh horses[J]. Xinjiang Agricultural Sciences, 2025, 62(4): 993-1001.

孟晨, 曾亚琦, 王建文, 姚新奎, 罗鹏辉, 解晓钰, 李鹏程, 刘晓晓, 王川坤, 孟军. 全基因组重测序筛选哈萨克马泌乳量候选基因[J]. 新疆农业科学, 2025, 62(4): 993-1001.

Figures/Tables 12

References 38

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分组 Group	24 h平均泌乳量 24 h average lactation(kg)	马匹 Horses	每匹马24 h 泌乳量 Lactation of per horse in 24 h(kg)	10:00泌乳量 10:00 Lactation (kg)	13:00泌乳量 13:00 Lactation (kg)	16:00泌乳量 16:00 Lactation (kg)	19:00泌乳量 19:00 Lactation (kg)
高泌乳量组 HW	15.84±1.13	HW1	16.80	2.20	2.32^*	2.08	1.80
		HW2	16.96	2.48^*	2.00	2.10	1.90
		HW3	15.94	2.25^*	2.00	1.92	1.80
		HW4	16.40	2.30	2.66^*	1.73	1.51
		HW5	14.78	2.26^*	1.87	1.60	1.66
		HW6	14.18	2.26^*	1.50	1.74	1.59
低泌乳量组 LW	9.06±2.16	LW1	11.26	1.51	1.63	1.44	1.05^*
		LW2	10.46	1.96	1.42	0.75^*	1.10
		LW3	9.40	1.74	1.00	1.06	0.90^*
		LW4	10.06	1.57	1.30	1.31	0.85^*
		LW5	7.84	1.24	0.90	1.12	0.66^*
		LW6	5.32	0.75	0.52^*	0.79	0.6

分组 Group	24 h平均泌乳量 24 h average lactation(kg)	马匹 Horses	每匹马24 h 泌乳量 Lactation of per horse in 24 h(kg)	10:00泌乳量 10:00 Lactation (kg)	13:00泌乳量 13:00 Lactation (kg)	16:00泌乳量 16:00 Lactation (kg)	19:00泌乳量 19:00 Lactation (kg)
高泌乳量组 HW	15.84±1.13	HW1	16.80	2.20	2.32^*	2.08	1.80
		HW2	16.96	2.48^*	2.00	2.10	1.90
		HW3	15.94	2.25^*	2.00	1.92	1.80
		HW4	16.40	2.30	2.66^*	1.73	1.51
		HW5	14.78	2.26^*	1.87	1.60	1.66
		HW6	14.18	2.26^*	1.50	1.74	1.59
低泌乳量组 LW	9.06±2.16	LW1	11.26	1.51	1.63	1.44	1.05^*
		LW2	10.46	1.96	1.42	0.75^*	1.10
		LW3	9.40	1.74	1.00	1.06	0.90^*
		LW4	10.06	1.57	1.30	1.31	0.85^*
		LW5	7.84	1.24	0.90	1.12	0.66^*
		LW6	5.32	0.75	0.52^*	0.79	0.6

条件 Prerequisite	位点数(个) Number of bits (pcs)
位点总数 Locus amount	20 234 241
性染色体及非 SNP 位点 Sex chromosomes and non-SNP loci	2 895 788
位点缺失率>10%位点 Sites with a deletion rate>10%	671 958
最小等位基因频率<0.05 的位点 Loci with a minor allete frequency<0.05	6 861 577
质控后位点 Post-quality control loci	9 804 918

条件 Prerequisite	位点数(个) Number of bits (pcs)
位点总数 Locus amount	20 234 241
性染色体及非 SNP 位点 Sex chromosomes and non-SNP loci	2 895 788
位点缺失率>10%位点 Sites with a deletion rate>10%	671 958
最小等位基因频率<0.05 的位点 Loci with a minor allete frequency<0.05	6 861 577
质控后位点 Post-quality control loci	9 804 918

染色体编号 Chromosome number	质控前位点(个) Pre-QC loci (number)	质控后位点(个) Post-quality control loci (number)	平均距离 Average distance (Kb)
1	1 462 880	748 461	0.25
2	985 566	508 520	0.24
3	946 815	503 233	0.24
4	896 098	460 337	0.24
5	733 838	385 880	0.25
6	697 438	370 810	0.24
7	779 343	395 355	0.25
8	821 100	424 122	0.23
9	643 990	343 877	0.25
10	694 774	368 645	0.23
11	447 018	231 209	0.27
12	442 869	239 911	0.15
13	382 072	197 433	0.22
14	715 036	381 070	0.25
15	720 299	370 146	0.25
16	693 328	360 684	0.25
17	677 670	365 359	0.22
18	695 958	359 903	0.23
19	535 407	288 647	0.22
20	736 066	381 982	0.17
21	504 413	268 591	0.22
22	401 656	214 858	0.24
23	425 658	224 460	0.25
24	388 865	209 018	0.23
25	313 103	154 574	0.26
26	396 719	200 791	0.21
27	378 333	205 677	0.2
28	381 997	191 961	0.25
29	326 277	177 428	0.2
30	276 662	145 491	0.22
31	231 274	126 485	0.21

Whole genome resequencing screening of candidate genes for lactation yield in Kazakh horses

全基因组重测序筛选哈萨克马泌乳量候选基因

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Figures/Tables 12

References 38

Related Articles 9

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Metrics

泌乳量 Lactation
总样本数(nbr.val)	12
样本空值数(nbr.null)	0
样本缺失数 (nbr.na)	0
最小值(min)	1
最大值(max)	2
范围(range)	3
总和(sum)	1
中位数(median)	18
平均值(mean)	1.5
标准误 (SE.mean)	1.5
95%置信区间(CI.mean.0.95)	0.331 810 998
方差(var)	0.272 727 273
标准差(std.dev)	0.522 232 968
变异系数(coef.var)	0.348 155 312

序号 Serial number	功能区域 Functional area	基因 Genetics	染色体 Chromosomes	物理位置 Physical location
1	intronic	ENTPD1	1	33528597
2	intronic	HECTD2	1	37498809
3	intergenic	ADGRL3	3	74573413
4	intergenic	KIT,PDGFRA	3	79652994
5	intronic	CORIN	3	82952198
6	intergenic	PCDH7	3	94837131
7	intergenic	LOC102147406	4	5869853
8	intergenic	ATXN7L1	4	5869971
9	intronic	LOC102149526	4	9504887
10	intergenic	SLC4A3	6	9942952
11	intergenic	EPHA2	6	9944478
12	intronic	ARNTL2	6	53590565
13	intergenic	CPNE8,KIF21A	6	59445139
14	intergenic	CTDSP2	6	76335925
15	intergenic	ATP23	6	76336075
16	intronic	GRIP1	6	83402935
17	intronic	RAB3IP	6	85764329
18	intronic	RMDN1	9	2493008
19	intergenic	NKAIN3,ASPH	9	23193863
20	intergenic	UBE2G1,SPNS3	11	48167086
21	intronic	MYBBP1A	11	48304960
22	intergenic	MYH3	11	53491154
23	intronic	LOC100073084	11	53503520
24	intronic	ADPRM	11	53507824
25	intergenic	LOC102149895	12	3158022
26	intergenic	LRRC4C	12	3642716
27	intergenic	LRRC4C	12	5244667
28	intergenic	API5	12	7220509
29	intergenic	NR2C2	12	7220563
30	intronic	TDGF1	16	5223745
31	intergenic	OLFM4	17	31189044
32	intergenic	COL4A1	17	31190347
33	intronic	RNF144B,ID4	17	77524685
34	intergenic	ITGA1,ISL1	20	18074903
35	intergenic	UNC5D	21	20195083
36	intronic	ENTPD1	27	9520032

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