荷斯坦奶牛胚胎基因组遗传评估研究

doi:10.11843/j.issn.0366-6964.2024.07.014

畜牧兽医学报 ›› 2024, Vol. 55 ›› Issue (7): 2940-2950.doi: 10.11843/j.issn.0366-6964.2024.07.014

荷斯坦奶牛胚胎基因组遗传评估研究

郭子骄¹(), 郑伟杰¹, 孙伟²^,³, 吴宝江⁴, 包向男²^,³, 张琪¹, 贺巾锋¹, 包斯琴⁴, 赵高平², 王子馨², 韩博¹, 李喜和²^,³^,⁴, 孙东晓¹^,*()

1. 中国农业大学动物科学技术学院，农业农村部动物遗传育种与繁殖重点实验室，动物育种国家工程实验室，畜禽生物育种全国重点实验室，北京 100193
2. 内蒙古赛科星家畜种业与繁育生物技术研究院有限公司，呼和浩特 011517
3. 国家乳业技术创新中心，呼和浩特 010020
4. 内蒙古大学生命科学学院，呼和浩特 010021

收稿日期:2023-10-07 出版日期:2024-07-23 发布日期:2024-07-24
通讯作者: 孙东晓 E-mail:gzijiao@cau.edu.cn;sundx@cau.edu.cn
作者简介:郭子骄(1996-)，女，山西晋中人，硕士生，主要从事分子及数量遗传学研究，E-mail: gzijiao@cau.edu.cn
基金资助:
“国家乳业技术创新中心创建”重点专项(2021—国家乳创中心—3);内蒙古自治区科技计划项目(2021GG0403);国家重点研发计划(2021YFF1000700);教育部创新团队发展计划(IRT_15R62)

Study on Genomic Selection of Embryos in Holstein Cattle

Zijiao GUO¹(), Weijie ZHENG¹, Wei SUN²^,³, Baojiang WU⁴, Xiangnan BAO²^,³, Qi ZHANG¹, Jinfeng HE¹, Siqin BAO⁴, Gaoping ZHAO², Zixin WANG², Bo HAN¹, Xihe LI²^,³^,⁴, Dongxiao SUN¹^,*()

1. National Key Laboratory of Livestock and Poultry Bio-breeding, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
2. Inner Mongolia Saikexing Institute of Breeding and Reproductive Biotechnology in Domestic Animal, Hohhot 011517, China
3. National Center of Technology Innovation for Dairy Industry, Hohhot 010020, China
4. College of Life Sciences, Inner Mongolia University, Hohhot 010021, China

Received:2023-10-07 Online:2024-07-23 Published:2024-07-24
Contact: Dongxiao SUN E-mail:gzijiao@cau.edu.cn;sundx@cau.edu.cn

摘要/Abstract

摘要：

旨在建立一种荷斯坦奶牛胚胎细胞早期基因组检测和遗传评估的方法并筛选优秀种用胚胎，通过胚胎移植技术选育优秀种牛，进一步缩短世代间隔，加快遗传进展。本研究基于4头荷斯坦种公牛克隆细胞，比较分析2细胞、5细胞的微量基因组DNA提取效果、全基因组芯片检出率及错配率；随后提取24枚荷斯坦奶牛早期胚胎5细胞样本的基因组DNA，利用150K芯片进行基因组检测；基于大规模基因组选择参考群体，采用GBLUP方法计算每枚胚胎9个性状的基因组育种值。结果表明，2和5克隆细胞的基因组DNA浓度、纯度和相对完整性均较好；5克隆细胞样品的150K芯片检出率较高(89.54%~95.07%)、错配率较低(1.02%~4.67%)。24枚胚胎的5细胞样品基因组DNA质量、总量和相对完整性均较好，150K芯片数据检出率为92.28%~98.51%，9个性状(产奶、体型和体细胞评分)基因组评估准确性为55%~79%，平均基因组评估准确性不低于65%。综上，本研究优化并建立了奶牛胚胎少量细胞DNA提取及基因组评估技术，胚胎样本基因组检出率不低于90%，平均基因组评估准确性不低于0.65。

关键词: 荷斯坦奶牛, 胚胎, 基因组选择

Abstract:

The present study aimed to establish a method for early genomic detection and genetic evaluation of embryos in Holstein cattle in order to select excellent breeding embryos, and further breed outstanding bulls through embryo transfer technology thereby shortening the generation interval and accelerating genetic progress. Firstly, the cloned somatic cells from 4 Holstein bulls was utilized to compare the efficiency of genomic DNA extraction, and call rate and mismatch rate for genotypic data with genome-wide SNP chip from 2-cell and 5-cell samples. Subsequently, the genomic DNA was extracted from 24 early-stage embryo samples of Holstein cattle with 5 cells in each sample, and then genotyped using 150K chip. Further, the genomic estimated breeding values for 9 traits of each embryo were calculated with the GBLUP method based on a large-scale genomic selection reference population. The results indicated that the concentration, purity and relative integrity of genomic DNA of both 2-cell and 5-cell samples were good. Of them, the call rates of 150K chip genotypic data from 5-cell samples were higher (ranging from 89.54% to 95.07%) than those of 2-cell, the mismatch rates were lower (1.02%-4.67%). The quality, quantity, and relative integrity of the genomic DNA from 5-cell samples of 24 embryos were also usable, which call rate of 150K chip data ranged from 92.28% to 98.51%. The genomic evaluation accuracy for the 9 traits (including milk yield, type and somatic cell score) reached 55%-79%, with an average accuracy of not less than 65%. In conclusion, the present study optimized and established an available method for genomic DNA extraction and genomic selection from a small number of cells in Holstein cattle embryos. The genomic call rate of the embryo samples was not less than 90%, and the average accuracy of genomic evaluation was not less than 0.65.

Key words: Holstein cattle, embryo, genomic selection

中图分类号:

S823.3

郭子骄, 郑伟杰, 孙伟, 吴宝江, 包向男, 张琪, 贺巾锋, 包斯琴, 赵高平, 王子馨, 韩博, 李喜和, 孙东晓. 荷斯坦奶牛胚胎基因组遗传评估研究[J]. 畜牧兽医学报, 2024, 55(7): 2940-2950.

Zijiao GUO, Weijie ZHENG, Wei SUN, Baojiang WU, Xiangnan BAO, Qi ZHANG, Jinfeng HE, Siqin BAO, Gaoping ZHAO, Zixin WANG, Bo HAN, Xihe LI, Dongxiao SUN. Study on Genomic Selection of Embryos in Holstein Cattle[J]. Acta Veterinaria et Zootechnica Sinica, 2024, 55(7): 2940-2950.

图/表 8

表 1

图 1

图 2

表 2

图 3

图 4

图 5

表 3

荷斯坦奶牛胚胎细胞样本基因组遗传评估结果"

胚胎样本号 Sample	检出率 /% Call rate	GCPI	产奶量 Milk yield		乳脂率 Fat percentage		乳蛋白率 Protein percentage		乳脂量 Fat yield		乳蛋白量 Protein yield		体型总分 Total type score		泌乳系统评分 Mammary system		肢蹄评分 Foot & leg		体细胞评分 Somatic cell score
胚胎样本号 Sample	检出率 /% Call rate	GCPI	育种值 DGV	准确性 Accuracy	育种值 DGV	准确性 Accuracy	育种值 DGV	准确性 Accuracy	育种值 DGV	准确性 Accuracy	育种值 DGV	准确性 Accuracy	育种值 DGV	准确性 Accuracy	育种值 DGV	准确性 Accuracy	育种值 DGV	准确性 Accuracy	育种值 DGV	准确性 Accuracy
21	96.78	2 928	2 712.00	0.63	-0.10	0.68	-0.20	0.71	82.21	0.61	57.98	0.61	10.99	0.58	7.26	0.58	13.00	0.67	2.52	0.57
22	98.24	2 849	1 726.26	0.69	0.36	0.72	0.05	0.75	87.35	0.68	54.86	0.67	7.62	0.66	7.41	0.65	3.28	0.72	2.46	0.65
15	96.03	2 819	1 623.14	0.63	0.72	0.67	0.17	0.71	103.71	0.61	61.67	0.61	2.29	0.59	-3.33	0.58	5.28	0.67	2.68	0.58
17	92.28	2 810	1 275.35	0.71	0.25	0.75	0.08	0.78	64.56	0.70	47.08	0.69	12.52	0.67	13.25	0.67	4.43	0.75	2.18	0.67
13	96.56	2 796	1 849.86	0.65	0.48	0.69	0.21	0.72	92.33	0.63	67.07	0.63	2.76	0.61	2.40	0.60	-0.70	0.69	3.19	0.60
23	97.57	2 774	971.56	0.68	0.27	0.72	0.20	0.75	57.42	0.66	50.07	0.66	8.11	0.64	10.44	0.63	4.49	0.72	1.81	0.63
5	97.88	2 673	2 467.47	0.67	0.27	0.71	-0.08	0.74	100.87	0.65	61.89	0.65	-5.76	0.63	0.73	0.63	-8.21	0.71	3.16	0.62
6	97.41	2 665	2 791.03	0.65	-0.11	0.70	-0.11	0.73	86.64	0.64	68.37	0.63	-1.05	0.61	1.96	0.60	-6.77	0.69	3.74	0.60
4	97.56	2 642	889.77	0.66	0.67	0.70	0.28	0.73	83.65	0.64	51.08	0.63	2.22	0.61	-1.64	0.61	-1.70	0.69	2.36	0.60
16	97.28	2 591	2 432.23	0.65	-0.17	0.70	-0.09	0.73	70.52	0.64	62.84	0.63	0.64	0.61	1.59	0.60	-7.59	0.69	3.23	0.60
2	97.13	2 562	632.48	0.63	0.59	0.68	0.23	0.71	73.21	0.61	43.22	0.61	3.48	0.58	5.67	0.58	-6.05	0.67	2.69	0.57
11	98.18	2 544	310.42	0.67	0.98	0.71	0.24	0.74	84.69	0.65	32.77	0.65	2.45	0.63	-0.34	0.62	-2.36	0.71	1.93	0.62
10	98.28	2 537	397.57	0.67	0.85	0.71	0.29	0.74	82.58	0.65	43.06	0.65	2.59	0.63	-0.75	0.62	-1.75	0.71	2.89	0.62
18	97.97	2 499	588.98	0.69	0.40	0.73	0.05	0.76	56.13	0.67	30.40	0.67	11.53	0.65	10.42	0.65	2.62	0.73	3.16	0.64
8	96.90	2 492	1 333.53	0.65	0.39	0.70	0.10	0.73	82.57	0.63	52.33	0.63	-2.50	0.60	-2.79	0.60	-6.78	0.69	3.27	0.59
3	97.12	2 482	996.39	0.64	0.45	0.68	0.19	0.72	73.61	0.62	49.12	0.61	0.11	0.59	-1.85	0.59	-5.11	0.68	3.05	0.58
14	98.07	2 476	1 365.17	0.68	0.69	0.72	0.12	0.75	96.91	0.66	50.50	0.65	-4.48	0.63	-3.79	0.63	-11.15	0.71	3.43	0.63
24	97.76	2 456	1 447.63	0.70	-0.09	0.74	0.01	0.77	53.21	0.68	49.64	0.68	4.23	0.66	1.58	0.66	0.15	0.74	3.46	0.65
12	98.00	2 407	362.47	0.65	0.74	0.69	0.11	0.72	73.41	0.63	29.22	0.62	0.23	0.60	-1.75	0.60	-1.08	0.68	2.34	0.59
1	96.54	2 371	1 103.33	0.60	0.21	0.65	0.04	0.68	60.08	0.58	39.88	0.58	1.46	0.55	-1.41	0.55	-6.32	0.64	2.81	0.55
19	97.63	2 340	-2.52	0.69	0.18	0.73	0.07	0.75	33.77	0.67	22.15	0.66	7.58	0.64	12.70	0.64	-2.79	0.72	2.64	0.63
9	97.99	2 337	397.91	0.66	0.50	0.70	0.19	0.73	62.36	0.64	36.26	0.64	-0.65	0.62	-2.50	0.61	-8.16	0.70	2.55	0.60
20	98.51	2 329	-417.95	0.72	0.45	0.76	0.26	0.79	35.82	0.70	24.04	0.70	11.56	0.68	5.41	0.67	4.05	0.75	2.92	0.67
7	97.28	2 320	1 292.77	0.63	0.25	0.67	-0.03	0.71	65.96	0.61	40.39	0.61	-6.40	0.58	-0.71	0.58	-12.74	0.67	2.79	0.57

表 3

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基因 Gene	染色体 Chromosome	引物名称 Primer name	引物序列(5′→3′) Primer sequence	产物长度/bp Product length	退火温度/℃ Annealing temperature
SESN2	2	F	GAAGTCCCGTTTCATCATGC	465	58
		R	TATCCGCTTGTCTGGCTTCT
RPL11	2	F	CGGGTTAACTGTCCTTCATCC	496
		R	AAGTGTAGGGTAACGGAAGGC
DDIT3	5	F	TCCGGGTCCAACACTAAGTC	481
		R	GACGGGGTGTCTTTCTCGTA
GAPDH	5	F	CAATGCTGAAACCTCCACGC	434
		R	AGCACTGCGGGAGAGTAGTA
DGAT1	14	F	TGTGAAACCAAGTAAGATCGGC	488
		R	CAGGCTGACACCCAACGC

牛号Bulls	样本号Sample	检出率/% Call rate	错配率/% Mismatch rate
1	1-毛囊	99.77
	1-2	91.75	5.90
	1-5	91.60	2.66
2	2-毛囊	99.40
	2-2	87.83	14.06
	2-5	89.54	4.67
3	3-毛囊	99.61
	3-2	92.64	4.49
	3-5	94.37	1.89
4	4-毛囊	99.74
	4-2	90.43	7.99
	4-5	95.07	1.02

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荷斯坦奶牛胚胎基因组遗传评估研究

Study on Genomic Selection of Embryos in Holstein Cattle

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