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基因组育种新技术，厉害在哪里？

创建时间：2023-01-03

字号：大中小

今天的育种家拥有大量的创新技术可用于动植物改良。基因芯片技术是分子标记技术方法之一，其将大量的基因片段有序地、高密度地排列在固相载体上，称之为基因芯片。基因芯片技术是融生物学、物理学、化学、计算机科学、微电子学为一体的新技术，是90年代中期以来最重大科技进展之一，已经广泛用于许多物种的功能基因组学研究，具有重大的研究价值及产业化前景。

Breeders today have a wealth of innovations at their disposal for plant and animal improvement.Gene chip technology is one of the methods of molecular marker technology. It arranges a large number of gene fragments on solid carrier in an orderly and high density, which is called gene chip. Gene chip technology is a new technology integrating biology, physics, chemistry, computer science and microelectronics. It is one of the most significant scientific and technological advances since the mid-1990s. It has been widely used in the functional genomics research of many species, and has great research value and industrialization prospects.

由于用该技术可以将极其大量的探针同时固定于支持物上，所以一次可以对大量的生物分子进行检测分析，从而解决了传统核酸印迹杂交自动化程度低、低通量等不足。而且，通过设计不同的探针阵列、使用特定的分析方法可使该技术具有多种不同的应用价值，如基因表达谱测定、突变检测。多态性分析、基因组文库作图及杂交测序（SBH）等，为“后基因组计划”时期基因功能的研究提供了强有力的工具，将会使新基因的发现、基因诊断等方面取得重大突破。

A large number of biomolecules can be detected and analyzed at one time because a large number of probes can be fixed on the support simultaneously by this technique, which solves the shortcomings of traditional nucleic acid imprinting hybridization, such as low automation degree and low throughput. Moreover, by designing different probe arrays and using specific analysis methods, the technology can have a variety of different application values, such as gene expression profiling and mutation detection. Polymorphism analysis, genomic library mapping and hybridization sequencing (SBH), etc., provide powerful tools for the study of gene function in the post-Genome Project period, and will make great breakthroughs in the discovery of new genes and gene diagnosis.

主流：分子标记位点基因芯片技术

Molecular marker loci gene chip technology

利用分子标记位点基因芯片技术对动植物育种方面提供了强大的科学力量，因准确性高而成为国际主流技术。相比杂交等传统方法，该技术大大提高了育种效率，这主要依赖两方面技术突破，一方面，基因芯片能够挖掘到有育种价值的基因组信息；另一方面，通过运用基因组育种值评估算法，能够高效利用收集的基因组、表型组、系谱等信息，准确评估个体育种值。

The use of molecular marker loci gene chip technology provides a powerful scientific force in plant and animal breeding, gene chip breeding has become the international mainstream technology because of its high accuracy. Compared with traditional methods, this technology greatly improves the breeding efficiency, which mainly depends on two technical breakthroughs. On the one hand, gene chip can mine the genome information of breeding value; On the other hand, by using the genome breeding value evaluation algorithm, the collected genome, phenogroup, pedigree and other information can be efficiently used to accurately evaluate the individual breeding value.

由于动物基因组中不同位点携带的有效育种信息含量是不同的，芯片位点设计好坏直接决定了基因组中育种信息的挖掘效率，理论上讲，芯片位点越多、单个位点携带的有效育种信息量越大，芯片能够挖掘的有效育种信息量就越多。分子标记位点基因芯片，每个位点携带的有效育种信息量很少，主要来自与之相连锁的功能突变位点。而且，连锁程度在不同群体、不同世代会发生变化，导致分子标记位点效应不稳定，难以实现数据联合分析，不利于基因组育种效率提升，进而影响了分子标记位点基因芯片的通用性、可持续性，会降低育种效率。

Since the content of effective breeding information carried by different loci in animal genome is different, the design quality of chip loci directly determines the efficiency of breeding information mining in genome. Theoretically, the more chip loci and the more effective breeding information carried by a single loci, the more effective breeding information can be mined by the chip. In conventional molecular marker loci gene chips, each loci carries little effective breeding information, which mainly comes from functional mutation loci linked with it. Moreover, the degree of linkage will change in different populations and generations, resulting in unstable effects of molecular marker sites, difficult to achieve joint analysis of data, which is not conducive to improving the efficiency of genome breeding, thus affecting the universality and sustainability of molecular marker sites gene chips, and reducing the efficiency of breeding.

新秀：功能位点基因芯片

Functional locus microarray

随着NGS技术（高通量测序方法）飞速发展，诞生了数百种经济物种的高质量参考基因组，同时获得了海量的重测序数据，基于这些数据结果，各个物种相继产生了高密度SNP芯片。近几年，功能基因组研究发展迅猛，Hi-C、ATAC-seq、CUT&Tag/ChIP-seq等技术相继在经济物种功能基因组研究中被广泛应用，多个物种基因组启动子、增强子、染色质开放区域等调控元件及活性区域被大规模鉴定，基因组功能注释越来越精细；结合高水平比较基因组、进化等研究，大量能够影响基因表达、蛋白活性的重要功能位点被鉴定。在上述研究成果的基础上，功能位点基因芯片应运而生。

With the rapid development of NGS technology, high-quality reference genomes of hundreds of economic species have been born, and massive resequencing data have been obtained. Based on these data results, each species has produced high-density SNP chips successively. In recent years, functional genome research has developed rapidly. Hi-C, ATAC-seq, CUT&Tag/ChIP-seq and other technologies have been widely used in functional genome research of economic species. Regulatory elements and active regions such as promoters, enhancers and chromatin open regions of genome of several species have been identified on a large scale. The annotation of genome function is becoming more and more refined; Combined with high-level comparative genomic and evolutionary studies, a large number of important functional sites that can affect gene expression and protein activity have been identified. On the basis of the above research results, functional locus microarray emerged.

功能位点基因芯片是指芯片设计所包含的位点全部是能够影响转录水平或蛋白活性的功能突变；相比普通的标记位点基因芯片，功能位点基因芯片在位点选择上更科学，直接影响生命调控过程，位点携带的功能信息含量更高，且位点效应不依赖连锁，在不同群体、不同世代中效应稳定、通用性和可持续更好，育种效率更高，是全新一代基因组育种芯片。同时，配合全新的功能位点加权算法KAML，能够更高效利用基因组、表型组和系谱等信息，对提高基因组育种值评估准确性和育种效率、加快动物改良速度具有重要意义。

Functional site gene chip refers to that all the sites included in the chip design are functional mutations that can affect transcription level or protein activity. Compared with ordinary marker loci gene chips, functional loci gene chips are more scientific in site selection and directly affect the process of life regulation. The functional information carried by loci is higher, and the loci effect is independent of linkage. The effect is more stable, universal and sustainable in different populations and different generations, and the breeding efficiency is higher. At the same time, combined with the new functional site weighting algorithm KAML, it can make more efficient use of genome, phenotype and genealogy information, which is of great significance to improve the accuracy and efficiency of genome breeding value evaluation and accelerate the speed of animal improvement.

参考文献：

1、分子育种研究手段之标记辅助选择[J]

2、影子基因可提供功能位点基因芯片育种整体解决方案

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