基因组选择技术在农业动物育种中的应用

基因组选择(genomic selection, GS)是畜禽经济性状遗传改良的重要方法。随着高密度SNP芯片和二代测序价格的下降,GS技术越来越多被应用于奶牛、猪、鸡等农业动物育种中。然而,降低全基因组SNP分型成本、提高基因组育种值(genomic estimated breeding value,GEBV)估计准确性仍然是GS研究的主要难题。本文从全基因组SNP分型策略和GEBV估计模型两个方面进行了综述,并对目前GS技术在主要畜禽品种中的应用现状进行了介绍,以期为GS在农业动物育种中的深入开展提供借鉴和参考。     

家养食草动物粪便中的花粉及菌孢子类型及其对人类活动的指示意义

考古遗址中动物粪化石中的微体植物遗存是重建过去生态环境以及人类活动的重要材料,然而对于能够指示人类活动的粪化石孢粉组合类型及其特征仍然缺乏清楚的认识。本文研究了山羊(Capra aegagrus)、绵羊(Ovis aries)、牛(Bos taurus)、骆驼(Camelus)、牦牛(Bos grunniens)和马(Equus caballus)等几种中国常见的家养食草类动物粪便中的主要孢粉和真菌孢子类型。通过分析这些动物粪便的花粉组合特征,探讨了花粉和菌孢子等微体植物遗存对生态环境及人类活动的指示意义。花粉种类丰度低、一些特征种属花粉(如禾本科、藜科)含量高是家养食草类动物粪便花粉组合的主要特征,可以用于指示人类的饲养行为。家养食草动物粪便中的粪生真菌孢子类型主要有Sporormiella, Sodaria, Pleospora, Coniochaeta, Thecaphora and Dictyosporium。研究表明真菌孢子的分布主要受到动物活动范围的影响,这使得利用粪生菌孢子(如Sporormiella)并结合其他记录来反映人类的饲养或游牧活动成为可能。     

用模式生物青鳉概观硬骨鱼性别决定及性分化研究进展

鱼类性别决定和性分化呈多元性,既有雌雄同体也有雌雄异体。性腺的雌雄性分化过程受遗传和环境因素(如温度、光照、激素和pH值等)影响,具有可逆可塑性。随着生物技术和基因组学的迅速发展,近年来脊椎动物性别决定和性分化的研究有了重大进展和显著突破。本文通过聚焦青鳉及其他硬骨鱼纲保守存在的dmrt1、gsdf、amh等雄性因子,探讨硬骨鱼普遍存在的雌雄性别可塑可逆信号通路,并介绍了新的基因组编辑和性控育种技术,为单性选育等水产养殖技术的研发提供参考。     

三维基因组学在动物遗传育种中的研究进展*

三维基因组学是近年兴起的研究基因组三维空间和结构的学科,是在基因组序列、基因结构及其调控元件的基础上对基因组序列在细胞核内的三维空间结构,及其对基因复制、转录、修复和调控等生物过程中的功能进行的研究。随着高通量测序技术的出现和改进,三维基因组学相关研究也得到快速发展。重点介绍三维基因组的发展历程、研究技术、结构层次,并总结近年来三维基因组学在动物遗传育种方面的应用。     

是金子无论在何处都发光: 玉米和水稻驯化中的趋同选择

野生植物的驯化为人类定居与文明起源奠定了重要基础。在世界范围内不同地区生活的古人类分别对当地不同的野生植物进行了驯化, 而经过驯化的作物常常表现出相似的驯化综合性状。在基因组层面上对趋同选择规律的解析, 可为作物育种提供重要信息与遗传资源。近日, 中国农业大学杨小红/李建生和华中农业大学严建兵领衔的团队从单基因和全基因组2个层次系统解析了玉米(Zea mays)和水稻(Oryza sativa)趋同选择的遗传基础, 发现玉米KRN2与水稻OsKRN2受到了趋同选择, 并通过相似的途径调控玉米与水稻的粒数与产量。他们还发现玉米与水稻在全基因组范围内存在大量趋同选择同源基因对(gene pair), 这些基因在淀粉代谢、糖及辅酶合成等途径特异富集。该研究不仅克隆了在玉米与水稻中均具有重要育种价值的趋同选择同源基因对KRN2/OsKRN2, 而且在全基因组水平上揭示了玉米与水稻趋同选择的规律, 为进一步解析驯化综合性状形成的分子机理及其在育种中的应用奠定了重要理论基础。     

2017基因组编辑专刊序言

基因组编辑技术,作为一项生物医学领域的革新技术,已经在动物、植物和微生物基因组改造中得到了广泛的应用。以CRISPR/Cas9为主导的基因组编辑技术掀起了基因组编辑的浪潮,在功能基因组学、遗传改良育种、遗传病治疗等研究中展示出其极大的价值与潜力。本专刊报道了基因组编辑技术的总体状况、在相关领域的基础与应用研究、该技术当前存在的优缺点以及未来展望等。     

代谢组学在家养动物遗传育种中的应用

代谢组学是使用分析化学技术对生物样品(如乳液、血浆、血清等)中的大量小分子代谢物进行全面鉴定和定量分析,已经广泛应用于生物医学、营养学、作物学和畜牧学研究中。最初,代谢组学主要应用于畜牧生产中的非遗传学研究。目前,随着生理基因组学、生理遗传学研究的增多,越来越多的研究者开始利用代谢组学的技术和方法开展动物遗传育种研究。本文综述了代谢组学检测技术与平台特点及代谢组学在动物遗传学与基因组中的应用,着重总结了动物代谢分子遗传参数估计、品系(品种)间代谢图谱差异、代谢组全基因组关联分析、筛选影响重要经济性状的生物标记等领域的研究进展,讨论了代谢组学研究还需亟待解决的问题。本文通过综述代谢组学在动物育种中的研究进展,旨在为进一步利用代谢组学技术开展动物重要经济性状的遗传基础研究提供参考。     

大豆基因组解析与重要农艺性状基因克隆研究进展

自2010年大豆(Glycine max)基因组论文在Nature杂志上正式发表以来, 以中国为主的多国科学家已对众多不同地理来源的野生大豆、农家品种及栽培品种进行了基因组重测序, 并通过比较基因组学等技术手段, 揭示了大豆基因组在进化与驯化过程中的基本规律。利用大豆基因组信息, 科学家已成功克隆了调控大豆生育期、生长(结荚)习性、种子形态性状与组分、结瘤与养分利用效率、生物及非生物胁迫抗(耐)性等重要农艺性状的功能基因, 并初步揭示了其相关的作用机理, 取得了一系列突破性进展, 为今后进一步精细解析大豆基因组与相关性状的基因调控网络奠定了坚实的基础, 同时为通过分子(模块)设计育种来培育新品种创造了必要条件。     

一个园艺植物基因组序列和注释的在线批量实时提取平台

目前, 大量园艺植物基因组测序已经完成或接近尾声, 它们的基因组序列和注释数据极大地促进了功能基因组学研究。为给科研人员提供批量下载特定的基因组区段序列和注释平台, 笔者开发了一个称为OBRRP的生物信息学工具。OBRRP具有提取葡萄(Vitis vinifera)、桃(Prunus persica)、草莓(Fragaria vesca)、黄瓜(Cucumis sativus)、西瓜(Citrullus lanatus)、番茄(Solanum lycopersicum)、甜橙(Citrus sinensis)、苹果(Malus x domestica)、猕猴桃(Actinidia chinensis)、马铃薯(Solanum tuberosum)、香蕉(Musa acuminata)和拟南芥(Arabidopsis thaliana) 12种植物基因组序列及注释数据的功能; 同时, 也具有扩展到其它Gbrowser浏览器架构的数据库功能。测试结果表明, OBRRP是一个快捷简便的在线、批量和实时提取工具, 其登录地址为http://bioinfo.jit.edu.cn/OBRRP/。     

360度群体遗传变异扫描——大豆泛基因组研究

大豆(Glycine max)是重要的油料和蛋白作物, 其丰富的遗传变异为生物学性状挖掘和育种改良提供了重要的资源基础。然而, 单个基因组信息无法全面揭示种质资源的遗传变异, 泛基因组研究为解决这一不足提供了新方案。近日, 中国科学院遗传与发育生物学研究所田志喜和梁承志研究团队从2 898份大豆种质中选取26份代表性材料, 并整合已有的3个基因组, 构建了包含野生和栽培大豆的泛基因组和图基因组(graph-based genome), 鉴定了整个群体的绝大多数结构变异数据集, 确定了大豆种质的核心、非必需和个体特异的基因集。利用这些数据系统地揭示了生育期位点E3的等位基因变异和基因融合事件、种皮颜色基因I的单体型和演化关系以及结构变异对铁离子转运基因表达和地区适应性选择的影响。该研究为作物基因组学研究提供了一个新的模式, 同时将加速推动大豆遗传变异的鉴定、性状解析和种质创新。     

Advanced technologies for genomic analysis in farm animals and its application for QTL mapping

Rapid progress in farm animal breeding has been made in the last few decades. Advanced technologies for genomic analysis in molecular genetics have led to the identification of genes or markers associated with genes that affect economic traits. Molecular markers, large-insert libraries and RH panels have been used to build the genetic linkage maps, physical maps and comparative maps in different farm animals. Moreover, EST sequencing, genome sequencing and SNPs maps are helping us to understand how genomes function in various organisms and further areas will be studied by DNA microarray technologies and proteomics methods. Because most economically important traits in farm animals are controlled by multiple genes and the environment, the main goal of genome research in farm animals is to map and characterize genes determining QTL. There are two main strategies to identify trait loci, candidate gene association tests and genome scan approaches. In recent years, some new concepts, such as RNAi, miRNA and eQTL, have been introduced into farm animal research, especially for QTL mapping and finding QTN. Several genes that influence important traits have already been identified or are close to being identified, and some of them have been applied in farm animal breeding programs by marker-assisted selection.     

Novel Genomic Tools and Modern Genetic and Breeding Approaches for Crop Improvement

In recent past, genomic tools especially molecular markers have been extensively used for understanding genome dynamics as well for applied aspects in crop breeding. Several new genomics technologies such as next generation sequencing (NGS), high-throughput marker genotyping, -omics technologies have emerged as powerful tools for understanding genome variation in crop species at DNA, RNA as well as protein level. These technologies promise to provide an insight into the way gene(s) are expressed and regulated in cell and to unveil metabolic pathways involved in trait(s) of interest for breeders not only in model-/major- but even for under-resourced crop species which were once considered “orphan” crops. In parallel, genetic variation for a species present not only in cultivated genepool but even in landraces and wild species can be harnessed by using new genetic approaches such as advanced-backcross QTL (AB-QTL) analysis, introgression libraries (ILs), multi-parent advanced generation intercross (MAGIC) population and association genetics. The gene(s) or genomic regions, responsible for trait(s) of interest, identified either through conventional linkage mapping or above mentioned approaches can be introgressed or pyramided to develop superior genotypes through molecular breeding approaches such as marker-assisted back crossing (MABC), marker assisted recurrent selection (MARS) and genome wide selection (GWS). This article provides an overview on some recent genomic tools and novel genetic and breeding approaches as mentioned above with a final aim of crop improvement.     

Recent progression and future perspectives in cotton genomic breeding

Upland cotton is an important global cash crop for its long seed fibers and high edible oil and protein content.Progress in cotton genomics promotes the advancement of cotton genetics,evolutionary studies,functional genetics,and breeding,and has ushered cotton research and breeding into a new era.Here,we summarize high-impact genomics studies for cotton from the last 10 years.The diploid Gossypium arboreum and allotetraploid Gossypium hirsutum are the main focus of most genetic and genomic studi...     

Genomics for food safety and sustainable animal production

There is a growing concern in society about the safety of animal-derived food, the health and welfare of farm animals and the sustainability of current animal production systems. Along farm animal, breeding genomics may contribute to a solution for these concerns. The use of genomic analysis tools, to achieve genetic progress in typical out-bred populations of farm animals, seems to be more difficult compared to 'model' organisms or plants. However, identification of positional candidate genes may be accelerated by linkage disequilibrium (LD) mapping. Recording of sustainable traits requires a large financial and logistic input and the economic advantages for the market are not as clear as for traditional selection traits. Examples show that the major genes causing variability for similar traits in different species are rarely the same. Therefore, for breeding purposes genomic analysis of the species of interest is needed. The fundamental knowledge obtained on the genetic architecture of complex traits will open new perspectives for the use of DNA tests in selection schemes. For food safety and traceability, DNA-based techniques evolve for monitoring and early warning systems.     

鸡基因组研究新进展

鸡基因组测序草图的完成标志着禽类功能基因组时代的到来。鸡不仅是全世界广泛饲养且有重要经济价值的禽类,而且是极具生命科学研究价值的模式动物。因此,鸡基因组测序草图的完成将对遗传育种和生物学研究有重要的影响。本文综述了近年来鸡基因组研究的最新进展,主要内容包括鸡基因组的有关数据、物理图谱、遗传连锁图谱、比较基因组学、序列表达标签、生物信息学等方面所取得的成绩,同时对鸡基因组研究结果的应用前景进行了展望。     

From genotype to phenotype in bovine functional genomics

In past 5 years, the promise that came with genome sequencing has revolutionized the functional genomics research field at unprecedented manner. It would soon know what all known genes do, particularly genes involved in genetic improvement of animal health and increase food animal production. With the availability of full bovine genomic sequence, yet we still have a lot of daunting tasks on 'genotype-to-phenotype problem' particularly about the phenotypic variations and trying to predict what genes are likely to be involved, and improved integrated interactive database. This article outlined and discussed about the current status of bovine functional genomics, recent development in bovine genome databases particularly in annotation of bovine genome, bovine quantitative trait loci database and its potential impact to unveil the from genotype-to-phenotype problem.     

Resources and transgenesis techniques for functional genomics in Xenopus

Recent developments in genomic resources and high‐throughput transgenesis techniques have allowed Xenopus to ‘metamorphose’ from a classic model for embryology to a leading‐edge experimental system for functional genomics. This process has incorporated the fast‐breeding diploid frog, Xenopus tropicalis, as a new model‐system for vertebrate genomics and genetics. Sequencing of the X. tropicalis genome is nearly complete, and its comparison with mammalian sequences offers a reliable guide for the genome‐wide prediction of cis‐regulatory elements. Unique cDNA sets have been generated for both X. tropicalis and X. laevis, which have facilitated non‐redundant, systematic gene expression screening and comprehensive gene expression analysis. A variety of transgenesis techniques are available for both X. laevis and X. tropicalis, and the appropriate procedure may be chosen depending on the purpose for which it is required. Effective use of these resources and techniques will help to reveal the overall picture of the complex wiring of gene regulatory networks that control vertebrate development.     

Exploring Complex Ornamental Genomes: The Rose as a Model Plant

Despite its high economic importance, little is known about rose genetics, genome structure, and the function of rose genes. Reasons for this lack of information are polyploidy in most cultivars, simple breeding strategies, high turnover rates for cultivars, and little public funding. Molecular and biotechnological tools developed during the genomics era now provide the means to fill this gap. This will be facilitated by a number of model traits as e.g., a small genome, a large genetic diversity including diploid genotypes, a comparatively short generation time and protocols for genetic engineering. A deeper understanding of genetic processes and the structure of the rose genome will serve several purposes: Applications to the breeding process including marker-assisted selection and direct manipulation of relevant traits via genetic engineering will lead to improved cultivars with new combinations of characters. In basic research, unique characters, e.g., the biosynthesis and emission of particular secondary metabolites will provide new information not available in model species. Furthermore comparative genomics will link information about the rose genome to ongoing projects on other rosaceous crops and will add to our knowledge about genome evolution and speciation. This review is intended as a presentation and is the compilation of the current knowledge on rose genetics and genomics, including functional genomics and genetic engineering. Furthermore, it is intended to show ways how knowledge on rose genetics and genomics can be linked to other species in the Rosaceae in order to utilize this information across genera.