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

Abstract

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

CLC Number:

S823.3

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.

Figures/Tables 8

Table 1

Fig. 1

Fig. 2

Table 2

Fig. 3

Fig. 4

Fig. 5

Table 3

Genetic evaluation results of embryonic cell samples from Holstein cows"

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

Table 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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Study on Genomic Selection of Embryos in Holstein Cattle

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