基因芯片在畜禽遗传育种中的应用及展望

doi:10.16288/j.yczz.23-233

遗传 ›› 2023, Vol. 45 ›› Issue (12): 1114-1127.doi: 10.16288/j.yczz.23-233

基因芯片在畜禽遗传育种中的应用及展望

汪佳豪¹(), 赵卿尧¹, 周月玲¹, 史良玉², 王楚端¹(), 俞英¹()

1.中国农业大学动物科学技术学院，北京 100193
2.武汉轻工大学动物科学与营养工程学院，武汉 430023

收稿日期:2023-09-06 修回日期:2023-10-05 出版日期:2023-12-20 发布日期:2023-11-08
通讯作者: 王楚端,俞英 E-mail:2423280404@qq.com;cdwang@cau.edu.cn;yuying@cau.edu.cn
作者简介:汪佳豪，硕士研究生，专业方向：动物遗传育种与繁殖。E-mail: 2423280404@qq.com.
基金资助:
国家重点研发计划项目(2021YFD1200903);国家重点研发计划项目(2021YFD1200900);国家奶牛产业技术体系项目(CARS-36);国家自然科学基金国际(地区)合作项目(31961143009)

Application and prospect of gene chip in genetic breeding of livestock and poultry

Jiahao Wang¹(), Qingyao Zhao¹, Yueling Zhou¹, Liangyu Shi², Chuduan Wang¹(), Ying Yu¹()

1. College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
2. School of Animal Science and Nutritional Engineering, Wuhan Polytechnic University, Wuhan 430023, China

Received:2023-09-06 Revised:2023-10-05 Published:2023-12-20 Online:2023-11-08
Contact: Chuduan Wang,Ying Yu E-mail:2423280404@qq.com;cdwang@cau.edu.cn;yuying@cau.edu.cn
Supported by:
National Key R&D Program of China(2021YFD1200903);National Key R&D Program of China(2021YFD1200900);National Dairy Industry Technology System Project(CARS-36);National Natural Science Foundation of China-Pakistan Science Foundation Join Project(31961143009)

摘要/Abstract

摘要：

基因芯片是一种通过DNA双链或DNA-RNA互补杂交检测特定DNA序列的高通量技术，其中SNP基因分型芯片已经广泛用于畜禽的遗传育种工作，在牛(Bos taurus)、猪(Sus scrofa)、羊(Caprinae)、鸡(Gallus gallus)等畜禽中取得了重大成就。但是在实际生产中使用的基因组选择仅利用了基因组信息，无法完全解释复杂性状的分子遗传基础，限制了基因组选择的准确性。随着表观遗传学研究的不断深入、商用甲基化芯片的推出、表观基因组关联分析(epigenome-wide association study，EWAS)的提出，DNA甲基化已被广泛用于解释遗传与表型的因果关系。未来，有望开发专门针对畜禽的甲基化芯片，通过EWAS探索与畜禽经济性状显著相关的甲基化位点，深化对复杂性状因果变异的理解。结合甲基化芯片与SNP芯片捕获畜禽表观基因组和基因组信息，更准确地解读遗传变异，提高基因组选择的准确性，推动畜禽分子遗传育种工作的精细化发展。本文综述了SNP芯片在畜禽上的应用，并对甲基化芯片在畜禽上的应用进行了展望，以期为基因芯片在动物育种中的进一步应用提供借鉴和参考。

关键词: 基因芯片, SNPs, DNA甲基化, 畜禽遗传育种

Abstract:

Gene chip is a high-throughput technique for detecting specific DNA sequences by DNA or DNA-RNA complementary hybridization, among which SNP genotyping chips have been widely employed in the animal genetics and breeding, and have made great achievements in cattle (Bos taurus), pigs (Sus scrofa), sheep (Caprinae), chickens (Gallus gallus) and other livestock. However, genomic selection applied in production merely uses genomic information and cannot fully explain the molecular mechanism of complex traits genetics, which limits the accuracy of genomic selection. With the continuous progresses in epigenetic research, the development of commercial methylation chips and the application of the epigenome-wide association study (EWAS), DNA methylation has been extensively used to draw the causal connections between genetics and phenotypes. In the future, it is hopefully expected to develop methylation chips customized for livestock and poultry and explore methylation sites significantly related to economic traits of livestock and poultry through EWAS thereby extending the understanding of causal variation of complex traits. Combining methylation chips and SNP chips, we can capture the epigenomic and genomic information of livestock and poultry, interpret genetic variation more precisely, improve the accuracy of genome selection, and promote the fine evolution of molecular genetic breeding of livestock and poultry. In this review, we summarize the application of SNP chips and depict the prospects of the application of methylation chips in livestock and poultry. This review will provide valuable insights for further application of gene chips in farm animal breeding.

Key words: gene chip, SNPs, DNA methylation, genetic breeding

汪佳豪, 赵卿尧, 周月玲, 史良玉, 王楚端, 俞英. 基因芯片在畜禽遗传育种中的应用及展望[J]. 遗传, 2023, 45(12): 1114-1127.

Jiahao Wang, Qingyao Zhao, Yueling Zhou, Liangyu Shi, Chuduan Wang, Ying Yu. Application and prospect of gene chip in genetic breeding of livestock and poultry[J]. Hereditas(Beijing), 2023, 45(12): 1114-1127.

图/表 4

图1

表1

畜禽上常用的SNP芯片"

物种	芯片名称	类型	开发单位	文献
牛	BovineSNP50 Genotyping BeadChip	固相芯片	美国Illumina公司	[41]
	CCSC-I（奶牛乳房健康分子检测芯片-I）	固相芯片	中国农业大学	[55,56]
	BovineHD Genotyping BeadChip	固相芯片	美国Illumina公司	[59]
	Axiom Genome-Wide BOS 1 Array	固相芯片	美国Affymetrix公司	[59]
	Bovine3K Genotyping BeadChip	固相芯片	美国Illumina公司	[60]
	BovineLD Genotyping BeadChip	固相芯片	美国Illumina公司	[61]
	A2奶牛基因检测液相芯片	液相芯片	山东省农业科学院
	元牛一号	液相芯片	内蒙古元牛繁育科技有限公司
	吉牛一号	液相芯片	吉林省农业科学院
	奶牛126K液相基因组育种芯片	液相芯片	中国农业大学
	家养水牛100K高密度液相芯片	液相芯片	中国农业大学
猪	PorcineSNP60 Genotyping BeadChip	固相芯片	美国Illumina公司	[46]
	GenoBaits Porcine SNP50K	液相芯片	中国农业大学	[53]
	Genomic Profiler 10k BeadChip	固相芯片	美国Neogen公司	[62]
	GGP Porcine 50K	固相芯片	美国Neogen公司
	GGP Porcine 80K	固相芯片	美国Neogen公司
	GenoBaits? Porcine 1K Panel	液相芯片	中国农业大学、山东农业大学
	“Zhongxin-I”Porcine Chip	固相芯片	江西农业大学
羊	OvineSNP50 BeadChip	固相芯片	美国Illumina公司	[49]
	绵羊40K液相芯片	液相芯片	西北农林科技大学	[57]
	绒山羊66K SNP	液相芯片	内蒙古农业大学	[58]
	GoatSNPS0 BeadChip array	固相芯片	美国Illumina公司	[63]
	Ovine HD SNP BeadChip	固相芯片	国际绵羊基因组学联盟(ISGC)	[64,65]
鸡	京芯一号	固相芯片	中国农业科学院北京畜牧兽医研究所	[51]
	60K SNP	固相芯片	荷兰瓦赫宁根大学	[66]
	600K SNP	固相芯片	英国安伟捷公司、英国罗斯林研究所	[67]
	凤芯壹号	固相芯片	中国农业大学	[68]
	酉芯一号	液相芯片	江苏省家禽科学研究所
	神农一号	液相芯片	河南农业大学

表1

图2

图3

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基因芯片在畜禽遗传育种中的应用及展望

Application and prospect of gene chip in genetic breeding of livestock and poultry

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