基于多性状模型内蒙古绒山羊早期生长性状基因组预测准确性研究

doi:10.16288/j.yczz.24-036

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Hereditas(Beijing) ›› 2024, Vol. 46 ›› Issue (5): 421-430.doi: 10.16288/j.yczz.24-036

• Research Article • Previous Articles Next Articles

Comparison of genomic prediction methods for early growth traits of Inner Mongolia cashmere goats based on multi trait models

Linyu Gao¹(), Qi Xu¹, Yuxiao He¹, Haijiao Xi¹, Yifan Liu¹, Tao Zhang¹, Jinquan Li¹^,², Yanjun Zhang¹, Ruijun Wang¹, Qi Lü¹, Bujun Mei⁴, Rui Su¹, Zhiying Wang¹^,³()

1. College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China
2. Key Laboratory of Meat Sheep Genetic Breeding of the Ministry of Agriculture and Rural Affairs, Hohhot 010018, China
3. Key Laboratory of Sheep Genetic Breeding and Reproduction in Inner Mongolia Autonomous Region, Hohhot 010018, China
4. Department of Agriculture, Hetao University, Bayannur 015000, China

Received:2024-01-31 Revised:2024-04-25 Online:2024-05-06 Published:2024-05-06
Contact: Zhiying Wang E-mail:gaolinyu0629@163.com;wzhy0321@126.com
Supported by:
National Key Research and Development Program(2022YFE0113300);National Key Research and Development Program(2022YFD1300201);National Key Research and Development Program(2022YFD1300204);Inner Mongolia Autonomous Region Science and Technology Research Project(2021GG0086);Inner Mongolia Autonomous Region Higher Education Youth Science and Technology Talent Support Program(NJYT22038);Ministry of Finance and the Ministry of Agriculture and Rural Affairs, the National Technical System for Woolen Sheep Industry(CARS-39);High Level Achievement Cultivation Project of Inner Mongolia Agricultural University(QT202201);Inner Mongolia Autonomous Region Higher Education Innovation Team Development Program(NMGIRT2322);Basic Research Expenses of Universities Directly of Inner Mongolia Autonomous Region(BR220112)

Abstract

Abstract:

Inner Mongolia cashmere goat is an excellent livestock breed formed through long-term natural selection and artificial breeding, and is currently a world-class dual-purpose breed producing cashmere and meat. Multi trait animal model is considered to significantly improve the accuracy of genetic evaluation in livestock and poultry, enabling indirect selection between traits. In this study, the pedigree, genotype, environment, and phenotypic records of early growth traits of Inner Mongolia cashmere goats were used to build multi trait animal model., Then three methods including ABLUP, GBLUP, and ssGBLUP wereused to estimate the genetic parameters and genomic breeding values of early growth traits (birth weight, weaning weight, average daily weight gain before weaning, and yearling weight). The accuracy and reliability of genomic estimated breeding value are further evaluated using the five fold cross validation method. The results showed that the heritability of birth weight estimated by three methods was 0.13-0.15, the heritability of weaning weight was 0.13-0.20, heritability of daily weight gain before weaning was 0.11-0.14, and the heritability of yearling weight was 0.09-0.14, all of which belonged to moderate to low heritability. There is a strong positive genetic correlation between weaning weight and daily weight gain before weaning, daily weight gain before weaning and yearling weight, with correlation coefficients of 0.77-0.79 and 0.56-0.67, respectively. The same pattern was found in phenotype correlation among traits. The accuracy of the estimated breeding values by ABLUP, GBLUP, and ssGBLUP methods for birth weight is 0.5047, 0.6694, and 0.7156, respectively; the weaning weight is 0.6207, 0.6456, and 0.7254, respectively; the daily weight gain before weaning was 0.6110, 0.6855, and 0.7357 respectively; and the yearling weight was 0.6209, 0.7155, and 0.7756, respectively. In summary, the early growth traits of Inner Mongolia cashmere goats belong to moderate to low heritability, and the speed of genetic improvement is relatively slow. The genetic improvement of other growth traits can be achieved through the selection of weaning weight. The ssGBLUP method has the highest accuracy and reliability in estimating genomic breeding value of early growth traits in Inner Mongolia cashmere goats, and is significantly higher than that from ABLUP method, indicating that it is the best method for genomic breeding of early growth weight in Inner Mongolia cashmere goats.

Key words: Inner Mongolia cashmere goat, early growth traits, multi trait animal model, accuracy of genomic estimated breeding value

Linyu Gao, Qi Xu, Yuxiao He, Haijiao Xi, Yifan Liu, Tao Zhang, Jinquan Li, Yanjun Zhang, Ruijun Wang, Qi Lü, Bujun Mei, Rui Su, Zhiying Wang. Comparison of genomic prediction methods for early growth traits of Inner Mongolia cashmere goats based on multi trait models[J]. Hereditas(Beijing), 2024, 46(5): 421-430.

Figures/Tables 13

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References 29

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性状	个体数	父本数	母本数	最大值	最小值	平均值	标准差(sd)	变异系数(C.V)
初生重	1811	87	829	4.53	1.00	2.76	0.47	16.96%
断乳重	1809	115	1351	34.77	13.60	21.97	3.34	15.42%
日增重	967	85	789	0.27	0.09	0.17	0.03	17.79%
周岁重	1953	116	1419	80.50	20.50	37.20	7.68	21.04%

方法	方差组分
方法	$\sigma _{a}^{2}$	$\sigma _{m}^{2}$	${{\sigma }_{a,m}}$	$\sigma _{c}^{2}$	$\sigma _{e}^{2}$	$\sigma _{p}^{2}$	h_a²±SE	h_m²	C²	h_T²	r_a,m
ABLUP	0.03	0.01	-3.87×10^-3	0.02	0.14	0.20	0.15±0.07	0.05	0.10	0.15	-0.22
GBLUP	0.02	0.02	-4.31×10^-3	0.02	0.12	0.18	0.11±0.05	0.11	0.11	0.13	-0.22
ssGBLUP	0.02	0.02	-4.63×10^-3	0.02	0.12	0.18	0.11±0.06	0.11	0.11	0.13	-0.23

方法	方差组分
方法	$\sigma _{a}^{2}$	$\sigma _{m}^{2}$	${{\sigma }_{a,m}}$	$\sigma _{c}^{2}$	$\sigma _{e}^{2}$	$\sigma _{p}^{2}$	h_a²±SE	h_m²	C²	h_T²	r_a,m
ABLUP	1.93	0.67	-0.91	0.13	3.12	4.94	0.39±0.13	0.14	0.03	0.18	-0.80
GBLUP	1.62	0.90	-0.83	6.46×10^-5	3.85	5.54	0.29±0.10	0.16	1.17×10^-5	0.20	-0.69
ssGBLUP	1.82	0.94	-1.07	6.94×10^-3	3.68	5.38	0.34±0.05	0.17	1.29×10^-3	0.13	-0.82

方法	方差组分
方法	$\sigma _{a}^{2}$	$\sigma _{m}^{2}$	${{\sigma }_{a,m}}$	$\sigma _{c}^{2}$	$\sigma _{e}^{2}$	$\sigma _{p}^{2}$	h_a²±SE	h_m²	C²	h_T²	r_a,m
ABLUP	3.31×10^-5	2.77×10^-5	-1.95×10^-6	2.93×10^-6	2.51×10^-4	3.13×10^-4	0.11±0.05	0.09	9.36×10^-3	0.14	-0.06
GBLUP	5.50×10^-5	2.96×10^-5	-1.49×10^-5	1.26×10^-5	3.16×10^-4	3.98×10^-4	0.14±0.04	0.07	0.03	0.12	-0.37
ssGBLUP	5.43×10^-5	3.14×10^-5	-1.42×10^-5	3.68×10^-6	3.85×10^-4	4.73×10^-4	0.11±0.05	0.07	7.78×10^-3	0.11	-0.34

方法	方差组分
方法	$\sigma _{a}^{2}$	$\sigma _{m}^{2}$	${{\sigma }_{a,m}}$	$\sigma _{c}^{2}$	$\sigma _{e}^{2}$	$\sigma _{p}^{2}$	h_a²±SE	h_m²	C²	h_T²	r_a,m
ABLUP	6.51	4.98	-4.46	3.35×10^-4	17.32	24.35	0.27±0.09	0.20	1.38×10^-5	0.09	-0.78
GBLUP	4.87	2.38	-2.33	3.80×10^-4	15.52	20.44	0.24±0.07	0.12	1.86×10^-5	0.13	-0.68
ssGBLUP	5.75	2.87	-2.64	3.67×10^-4	17.04	23.02	0.25±0.03	0.12	1.59×10^-5	0.14	-0.65

Comparison of genomic prediction methods for early growth traits of Inner Mongolia cashmere goats based on multi trait models

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性状	初生重	断乳重	日增重	周岁重
初生重	0.15	0.37	0.11	0.31
断乳重	0.23	0.18	0.79	0.47
日增重	0.09	0.53	0.14	0.61
周岁重	0.18	0.37	0.46	0.09

性状	初生重	断乳重	日增重	周岁重
初生重	0.13	0.39	0.17	0.35
断乳重	0.30	0.20	0.77	0.63
日增重	0.12	0.71	0.12	0.56
周岁重	0.21	0.33	0.39	0.13

性状	初生重	断乳重	日增重	周岁重
初生重	0.13	0.44	0.11	0.37
断乳重	0.31	0.13	0.79	0.59
日增重	0.09	0.70	0.11	0.67
周岁重	0.22	0.39	0.48	0.14

性状	方法	准确性	准确性误差	可靠性
初生重	ABLUP	0.5047 (0.5209)	0.1063 (0.1276)	0.2547 (0.2713)
	GBLUP	0.6694 (0.5556)	0.0097 (0.0079)	0.4481 (0.3087)
	ssGBLUP	0.7156 (0.6057)	0.0068 (0.0058)	0.5121 (0.3669)
断乳重	ABLUP	0.6207 (0.6831)	0.1021 (0.1651)	0.3853 (0.4666)
	GBLUP	0.6456 (0.7274)	0.0719 (0.0110)	0.4168 (0.5291)
	ssGBLUP	0.7254 (0.7577)	0.0658 (0.0081)	0.5262 (0.5741)
日增重	ABLUP	0.6110 (0.5857)	0.1146 (0.1604)	0.3733 (0.3430)
	GBLUP	0.6855 (0.6630)	0.0529 (0.0202)	0.4699 (0.4396)
	ssGBLUP	0.7357 (0.7021)	0.0268 (0.0080)	0.5413 (0.4929)
周岁重	ABLUP	0.6209 (0.5965)	0.1231 (0.1494)	0.3855 (0.3558)
	GBLUP	0.7155 (0.6381)	0.0082 (0.0209)	0.5119 (0.4072)
	ssGBLUP	0.7756 (0.6683)	0.0048 (0.0046)	0.6016 (0.4466)