前沿组学技术创新助力畜禽生物育种

doi:10.13560/j.cnki.biotech.bull.1985.2024-0733

生物技术通报 ›› 2025, Vol. 41 ›› Issue (6): 71-86.doi: 10.13560/j.cnki.biotech.bull.1985.2024-0733

前沿组学技术创新助力畜禽生物育种

李晨莹¹^,²(), 孔大帅², 李若楠²^,³, 张玉波², 阎萍²^,⁴, 李奎², 孔思远²()

^1.青岛农业大学动物科学技术学院，青岛 266109
^2.岭南现代农业科学与技术广东省实验室深圳分中心农业农村部畜禽生物组学重点实验室中国农业科学院深圳农业基因组研究所，深圳 518120
^3.华中农业大学动物科学技术学院、动物医学院，武汉 430070
^4.农业农村部青藏高原畜禽育种重点实验室中国农业科学院兰州畜牧与兽药研究所，兰州 730050

收稿日期:2024-07-12 出版日期:2025-06-26 发布日期:2025-06-30
通讯作者: 孔思远，男，博士，副研究员，研究方向：动物基因组学和分子遗传育种；E-mail: kongsiyuan@caas.cn
作者简介:李晨莹，女，硕士研究生，研究方向：动物遗传育种与繁殖；E-mail: lcy1998102022@163.com
第一联系人：（李晨莹、孔大帅并列第一作者）
基金资助:
中国博士后科学基金博士后创新人才支持计划(BX2021367);中国博士后科学基金面上项目(2021M703543);国家自然科学基金青年科学基金项目(32202653);广东省自然科学基金面上项目(2022A1515010766);深圳市科技创新局可持续发展专项(KCXFZ20201221173205015);畜禽生物育种全国重点实验室开放课题(2024SKLAB6-112)

Cutting-edge Omics Technology Innovations Empower Livestock and Poultry Biological Breeding

LI Chen-ying¹^,²(), KONG Da-shuai², LI Ruo-nan²^,³, ZHANG Yu-bo², YAN ping²^,⁴, LI Kui², KONG Si-yuan²()

^1.College of Animal Science and Technology, Qingdao Agricultural University, Qingdao 266109
^2.Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120
^3.College of Animal Science and Technology, College of Veterinary Medicine, Huazhong Agricultural University (HACAU), Wuhan 430070
^4.Key Laboratory of Livestock and Poultry Breeding on the Qinghai-Tibet Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050

Received:2024-07-12 Published:2025-06-26 Online:2025-06-30

摘要/Abstract

摘要：

全球人口的增长导致对畜禽产品的需求增加，同时气候变化和环境压力对畜禽生存和生产构成挑战，国内自主选育的核心畜禽品种较为缺乏，“生物育种”成为了农业新质生产力的“国家战略”。因此，需要培育出性状优良及适应性强的畜禽新品种。组学与分子生物学技术的不断发展促进了基因组学、转录组学、表观遗传学、三维基因组学、宏基因组学以及单细胞等多组学技术手段的开发和改良，并成功结合应用到全基因组关联分析、标记辅助选择、全基因组选择等畜禽生物育种方法中。随着前沿组学技术的创新和发展，畜禽生物性状功能发生的潜在分子遗传机制也实现了解析。为了更好地利用基因组‒多组学育种技术和理念助力畜禽生物育种，本文对主要的畜禽生物性状形成和分子育种相关组学技术的内容和特点进行总结，阐述了经典组学技术的原理和应用，主要涉及基因组、转录组、蛋白组等。同时也指出这些技术的局限性，由此介绍了一系列新型组学技术，包括三维基因组学技术和肠道微生物组学技术以及单细胞组学技术。并归纳了“基因组‒多组学”育种理念在畜禽重要经济性状解析和分子生物育种研究中的应用，同时概述了这些组学技术的应用场景及存在的挑战。最后，探讨了多组学技术的综合应用，并对未来组学技术的发展趋势进行了展望。本文旨在为畜禽重要性状的研究及育种领域的发展提供新的参考，推动畜禽育种向更精准、更高效、更经济的方向发展。

关键词: 畜禽, 性状, 组学技术, 基因组, 三维基因组, 宏基因组, 生物育种

Abstract:

The growth of the global population has led to an increase in the demand for livestock and poultry products, while climate change and environmental pressures pose challenges to the survival and production of livestock and poultry. The independently selected core livestock and poultry breeds in China is rather lack, and thus "biological breeding" has become a "national strategy" for the New Quality Productivity of Agriculture. Therefore, it is necessary to breed new livestock and poultry breeds with excellent traits and strong adaptability. The continuous development of omics and molecular biology technology has promoted the development and improvement of genomics, transcriptomics, epigenetics, three-dimensional genomics, metagenomics, and single-cell and other multi-omics technologies, and successfully combined and applied to genome-wide association analysis, marker-assisted selection, genome-wide selection and other livestock and poultry bio-breeding methods. With the innovation and development of cutting-edge genomics technologies, the potential molecular genetic mechanisms of livestock and poultry biomorphogenesis have also been realized to be resolved. In order to make better use of Genomic & Multi-omics Breeding techniques and concepts to help livestock and poultry biological breeding, this review summarizes the contents and characteristics of the main livestock and poultry biological trait formation and molecular breeding-related genomics technologies. It firstly describes the principles and applications of classical genomics technologies, which are mainly related to genomes, transcriptomes, proteomes, etc. Meanwhile, it also pointed out the limitations of these technologies, and introduced a series of new omics technologies, including three-dimensional (3D) genomics, gut microbiomics and single-cell omics. It also summarizes the application of the Genomic & Multi-omics Breeding concept in the analysis of economically important traits and molecular biological breeding of livestock and poultry and outlines the application scenarios and challenges of these genomics technologies. Finally, the review discusses the comprehensive application of multi-omics technology, and looks forward to the future development trend of genomics technology. It aims to provide new references for the research of important traits of livestock and poultry and the development of breeding field, and to promote the development of livestock and poultry breeding towards a more precise, efficient, and economical direction.

Key words: livestock and poultry, traits, omics technologies, genomes, three-dimensional genomes, metagenomes, biotechnological breeding

李晨莹, 孔大帅, 李若楠, 张玉波, 阎萍, 李奎, 孔思远. 前沿组学技术创新助力畜禽生物育种[J]. 生物技术通报, 2025, 41(6): 71-86.

LI Chen-ying, KONG Da-shuai, LI Ruo-nan, ZHANG Yu-bo, YAN ping, LI Kui, KONG Si-yuan. Cutting-edge Omics Technology Innovations Empower Livestock and Poultry Biological Breeding[J]. Biotechnology Bulletin, 2025, 41(6): 71-86.

图/表 3

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分类 Classification	技术 Technology	关键流程 Process	优势和局限性 Advantages and limitations	应用场景 Applications	参考文献Reference
经典的组学技术 Classical omics techniques	Sanger sequencing	PCR扩增‒PCR纯化‒循环测序‒测序纯化‒毛细管电泳‒数据分析	优势：读取速度快、高精确度，成本相对很低局限：无法连续测序、测序长度受限制	基因突变检测、基因编辑、微生物鉴定与分型	［13］
	Next-generation sequencing	核酸提取‒文库制备‒上机测序‒数据分析	优势：通量高、速度快、测序成本低、敏感性高、所需样本量少局限：成本高、操作复杂、检测周期长	全基因组测序与全外显子测序、基因变异、基因分型等	［14］
	RNA-seq	总RNA提取‒rRNA去除‒双链合成‒末端修复‒接头连接‒文库扩增‒测序	优势：定量更准确、可重复性更高、检测范围更广、分析更可靠局限：限制其他RNA的读数以及其他RNA表达水平的准确性	基因表达量测量与差异表达分析、新转录本、剪接形式和基因的发现、非编码RNA研究、生物标志物发现等	［30］
	ChIP-seq	甲醛交联‒DNA片段化‒染色质免疫沉淀‒捕获DNA‒蛋白质复合物‒纯化DNA‒测序	优势：大量细胞起始量，挖掘转录因子、蛋白因子全基因组结合位点局限：该技术需要高度特异性抗体、甲醛固定可能是暂时的，甚至是非特异的，可能导致相邻的蛋白形成假阳性信号	转录因子（TF）结合位点和靶基因的全基因组鉴定、组蛋白修饰的全基因组检测、蛋白质- DNA互作研究	［36］
	微生物组16S rDNA测序	细菌基因组提取‒特异引物扩增16S rDNA序列‒纯化PCR产物‒测序获得16S rDNA序列	优势：具有良好的进化保守性、操作速度快、操作简单、成本低局限：可以鉴定到属水平，无法准确到所有物种或亚种水平	微生物群落的多样性、病原菌检测与鉴定、生态系统功能研究	［74］
	宏基因组二代鸟枪法测序 Shotgun sequencing	将DNA序列随机分解成许多小片段‒通过寻找重叠区域来重新组装序列	优势：速度快，简单易行，成本较低局限：会形成大量冗余序列，导致基因组信息的缺失	分析微生物群落的结构、环境微生物群落研究、功能基因发掘、医学诊断与研究、生态与环境保护	［76］
新兴的组学技术 Emerging omics technologies	三代单分子测序 Single-molecule sequencing	DNA片段化‒发夹连接‒获得文库‒文库测序	优势：可以直接进行 cDNA 分析、无需逆转录、测序速度极快局限：单读长错误率高增加测序成本	基因组测序、甲基化研究、突变鉴定	［15］
	CUT&Tag	提取细胞核‒抗体结合‒Tn5结合‒回收DNA‒PCR扩增‒文库测序	优势：背景噪声低、细胞起始量低、信噪比和重复性较好局限：细胞数量要求较高、实验耗时长、数据的重复性较差	蛋白质与DNA互作研究、鉴定转录因子在全基因组上的结合位点、超级增强子鉴定	［38］
	Hi-C	甲醛交联‒限制酶切‒末端补平‒邻近连接‒超声破碎‒biotin富集‒建库测序	优势：高通量测序、Hi-C可以展现出，整个染色体all-to-all的互作关系局限：实验成本高、数据噪声大、实验过程繁琐	研究染色体片段之间的相互作用、基因组组装、单体型图谱构建、辅助宏基因组组装、与其他数据进行联合分析、基因调控网络、表观遗传网络	［58］
	In situ Hi-C	交联‒酶切‒邻近连接‒超声破碎‒生物素下拉‒建库测序	优势：高效、方便、比对率高和低成本局限：暂无法进行单细胞水平	疾病相关基因定位、基因表达调控、识别染色体结构变异、基因组进化与比较基因组学、药物靶点发现	［59］
	In situ exo-Hi-C	交联‒酶切‒邻近连接‒线性DNA消除‒超声破碎‒ 生物素下拉‒建库测序	优势：高效、方便、噪声低、比对率高和低成本局限：暂无法进行单细胞水平	低细胞起始量、下机测序数据少，噪声低，需求有效互作得率高。畜禽发育机制解析，功能基因挖掘等农业、医学应用	［63］
	ChIA-PET	甲醛交联‒DNA片段化‒用特异性蛋白抗体富集DNA和蛋白复合物‒生物素下拉‒限制性内切酶消化‒去除蛋白质‒固定化PET序列‒上机测序	优势：高效、高分辨率、应用范围广泛局限：细胞起始量要求更高、操作相对复杂	基因转录调控、疾病发生机制、生长发育、基因组功能研究、药物研发等	［60-62］
	GutHi-C	微生物分离提纯‒交联裂解‒酶切‒末端补平‒纯化‒片段化‒接头连接‒文库扩增	优势：效率高，便于操作，成本低，数据优局限：如手动裂解破壁步骤需要熟手操作	广泛用于畜禽肠道微生物建库	［78］
高精度的组学技术 Highly accurate omics technology	scRNA-seq	细胞收集‒分选捕获单个细胞‒细胞裂解‒提取DNA‒合成cDNA‒扩增‒测序	优势：高分辨率、可探索未知的细胞类型局限：不同类型的细胞在解离效率上存在差异、对细胞悬液质量的高要求、技术复杂	单细胞分辨率揭示胚胎发育过程、基因表达的动态变化、微生物群落	［90］
	scATAC-seq	细胞收集‒分离单细胞‒裂解‒转座‒扩增酶切割‒扩增‒测序	优势：高通量、低成本、高分辨率局限：技术涉及多个步骤，对实验技术和数据分析要求较高、数据解读和结果分析具有挑战性、不同平台的实验方法和数据分析流程可能存在差异，影响结果的通用性和可比性	单细胞分辨率揭示胚胎发育过程、肿瘤生物学、免疫细胞的基因表达调控、细胞间互作	［88］
	snHi-C	细胞核分离‒交联‒酶切‒末端修复‒连接‒纯化‒建库‒测序	优势：分辨率较高、灵敏度高局限：成本高、实验复杂	单细胞分辨率揭示染色质三维结构、调控网络	［89］
	Dip-C	细胞分离裂解‒交联固定‒染色质片段化‒连接‒标记‒ 构建文库‒测序	优势：高分辨率、可以在单细胞水平上进行基因组三维结构的研究局限：成本高、实验复杂	单细胞分辨率揭示基因组三维结构的动态变化、染色质互作、调控网络	［89］
	scNanoHi-C	交联固定‒Tn5片段化‒连接-扩增-构建文库‒三代单分子Nanopore测序	优势：高阶连接子的效率更高、在单个细胞中检测到更多的接触、捕获更多的杂合SNP位点进行单倍型分析局限：Nanopore错误率高一些	单细胞分辨率揭示染色质高维结构、染色质高阶互作和调控网络	［90］
	MUSIC	分离细胞核‒标记同一细胞核中的所有RNA和片段化DNA‒将RNA和DNA接头连接到RNA和DNA片段上‒构建单个测序文库	优势：分辨率高、能够同时分析单个细胞核内的多重染色质相互作用、基因表达和RNA-染色质关联，提供丰富的单细胞多组学信息局限：成本相对较高	同时检测单细胞染色质三维结构和基因表达的动态变化、基因表达以及RNA-染色质关联的差异	［91］

分类 Classification	技术 Technology	关键流程 Process	优势和局限性 Advantages and limitations	应用场景 Applications	参考文献Reference
经典的组学技术 Classical omics techniques	Sanger sequencing	PCR扩增‒PCR纯化‒循环测序‒测序纯化‒毛细管电泳‒数据分析	优势：读取速度快、高精确度，成本相对很低局限：无法连续测序、测序长度受限制	基因突变检测、基因编辑、微生物鉴定与分型	［13］
	Next-generation sequencing	核酸提取‒文库制备‒上机测序‒数据分析	优势：通量高、速度快、测序成本低、敏感性高、所需样本量少局限：成本高、操作复杂、检测周期长	全基因组测序与全外显子测序、基因变异、基因分型等	［14］
	RNA-seq	总RNA提取‒rRNA去除‒双链合成‒末端修复‒接头连接‒文库扩增‒测序	优势：定量更准确、可重复性更高、检测范围更广、分析更可靠局限：限制其他RNA的读数以及其他RNA表达水平的准确性	基因表达量测量与差异表达分析、新转录本、剪接形式和基因的发现、非编码RNA研究、生物标志物发现等	［30］
	ChIP-seq	甲醛交联‒DNA片段化‒染色质免疫沉淀‒捕获DNA‒蛋白质复合物‒纯化DNA‒测序	优势：大量细胞起始量，挖掘转录因子、蛋白因子全基因组结合位点局限：该技术需要高度特异性抗体、甲醛固定可能是暂时的，甚至是非特异的，可能导致相邻的蛋白形成假阳性信号	转录因子（TF）结合位点和靶基因的全基因组鉴定、组蛋白修饰的全基因组检测、蛋白质- DNA互作研究	［36］
	微生物组16S rDNA测序	细菌基因组提取‒特异引物扩增16S rDNA序列‒纯化PCR产物‒测序获得16S rDNA序列	优势：具有良好的进化保守性、操作速度快、操作简单、成本低局限：可以鉴定到属水平，无法准确到所有物种或亚种水平	微生物群落的多样性、病原菌检测与鉴定、生态系统功能研究	［74］
	宏基因组二代鸟枪法测序 Shotgun sequencing	将DNA序列随机分解成许多小片段‒通过寻找重叠区域来重新组装序列	优势：速度快，简单易行，成本较低局限：会形成大量冗余序列，导致基因组信息的缺失	分析微生物群落的结构、环境微生物群落研究、功能基因发掘、医学诊断与研究、生态与环境保护	［76］
新兴的组学技术 Emerging omics technologies	三代单分子测序 Single-molecule sequencing	DNA片段化‒发夹连接‒获得文库‒文库测序	优势：可以直接进行 cDNA 分析、无需逆转录、测序速度极快局限：单读长错误率高增加测序成本	基因组测序、甲基化研究、突变鉴定	［15］
	CUT&Tag	提取细胞核‒抗体结合‒Tn5结合‒回收DNA‒PCR扩增‒文库测序	优势：背景噪声低、细胞起始量低、信噪比和重复性较好局限：细胞数量要求较高、实验耗时长、数据的重复性较差	蛋白质与DNA互作研究、鉴定转录因子在全基因组上的结合位点、超级增强子鉴定	［38］
	Hi-C	甲醛交联‒限制酶切‒末端补平‒邻近连接‒超声破碎‒biotin富集‒建库测序	优势：高通量测序、Hi-C可以展现出，整个染色体all-to-all的互作关系局限：实验成本高、数据噪声大、实验过程繁琐	研究染色体片段之间的相互作用、基因组组装、单体型图谱构建、辅助宏基因组组装、与其他数据进行联合分析、基因调控网络、表观遗传网络	［58］
	In situ Hi-C	交联‒酶切‒邻近连接‒超声破碎‒生物素下拉‒建库测序	优势：高效、方便、比对率高和低成本局限：暂无法进行单细胞水平	疾病相关基因定位、基因表达调控、识别染色体结构变异、基因组进化与比较基因组学、药物靶点发现	［59］
	In situ exo-Hi-C	交联‒酶切‒邻近连接‒线性DNA消除‒超声破碎‒ 生物素下拉‒建库测序	优势：高效、方便、噪声低、比对率高和低成本局限：暂无法进行单细胞水平	低细胞起始量、下机测序数据少，噪声低，需求有效互作得率高。畜禽发育机制解析，功能基因挖掘等农业、医学应用	［63］
	ChIA-PET	甲醛交联‒DNA片段化‒用特异性蛋白抗体富集DNA和蛋白复合物‒生物素下拉‒限制性内切酶消化‒去除蛋白质‒固定化PET序列‒上机测序	优势：高效、高分辨率、应用范围广泛局限：细胞起始量要求更高、操作相对复杂	基因转录调控、疾病发生机制、生长发育、基因组功能研究、药物研发等	［60-62］
	GutHi-C	微生物分离提纯‒交联裂解‒酶切‒末端补平‒纯化‒片段化‒接头连接‒文库扩增	优势：效率高，便于操作，成本低，数据优局限：如手动裂解破壁步骤需要熟手操作	广泛用于畜禽肠道微生物建库	［78］
高精度的组学技术 Highly accurate omics technology	scRNA-seq	细胞收集‒分选捕获单个细胞‒细胞裂解‒提取DNA‒合成cDNA‒扩增‒测序	优势：高分辨率、可探索未知的细胞类型局限：不同类型的细胞在解离效率上存在差异、对细胞悬液质量的高要求、技术复杂	单细胞分辨率揭示胚胎发育过程、基因表达的动态变化、微生物群落	［90］
	scATAC-seq	细胞收集‒分离单细胞‒裂解‒转座‒扩增酶切割‒扩增‒测序	优势：高通量、低成本、高分辨率局限：技术涉及多个步骤，对实验技术和数据分析要求较高、数据解读和结果分析具有挑战性、不同平台的实验方法和数据分析流程可能存在差异，影响结果的通用性和可比性	单细胞分辨率揭示胚胎发育过程、肿瘤生物学、免疫细胞的基因表达调控、细胞间互作	［88］
	snHi-C	细胞核分离‒交联‒酶切‒末端修复‒连接‒纯化‒建库‒测序	优势：分辨率较高、灵敏度高局限：成本高、实验复杂	单细胞分辨率揭示染色质三维结构、调控网络	［89］
	Dip-C	细胞分离裂解‒交联固定‒染色质片段化‒连接‒标记‒ 构建文库‒测序	优势：高分辨率、可以在单细胞水平上进行基因组三维结构的研究局限：成本高、实验复杂	单细胞分辨率揭示基因组三维结构的动态变化、染色质互作、调控网络	［89］
	scNanoHi-C	交联固定‒Tn5片段化‒连接-扩增-构建文库‒三代单分子Nanopore测序	优势：高阶连接子的效率更高、在单个细胞中检测到更多的接触、捕获更多的杂合SNP位点进行单倍型分析局限：Nanopore错误率高一些	单细胞分辨率揭示染色质高维结构、染色质高阶互作和调控网络	［90］
	MUSIC	分离细胞核‒标记同一细胞核中的所有RNA和片段化DNA‒将RNA和DNA接头连接到RNA和DNA片段上‒构建单个测序文库	优势：分辨率高、能够同时分析单个细胞核内的多重染色质相互作用、基因表达和RNA-染色质关联，提供丰富的单细胞多组学信息局限：成本相对较高	同时检测单细胞染色质三维结构和基因表达的动态变化、基因表达以及RNA-染色质关联的差异	［91］

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前沿组学技术创新助力畜禽生物育种

Cutting-edge Omics Technology Innovations Empower Livestock and Poultry Biological Breeding

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