Genomics in equine veterinary medicine

Veterinary medicine is marching forward with genomics grasped firmly in one fist. Genomics has been part of our veterinary tool bag for some time in various guises, but the breadth and depth of its ramifications can be daunting. This article is designed to provide toe‐holds for veterinarians to enjoy a better understanding of genomics – a truly fascinating area of science.     

茄科植物比较基因组学研究进展

综述了茄科4种主要蔬菜作物番茄、马铃薯、辣椒和茄子比较基因组学的研究进展,包括其基因组大小、结构、基因重排及演化,R基因在茄科植物中的分布与共线性,花青素基因、果实相关性状QTLs的同源性比较等,并对比较基因组学的发展前景进行了展望。     

胡椒瘟病生防菌 Bacillus subtilis VD18R19 全基因组测序及 比较基因组学分析

Bacillus subtilis VD18R19 具有促进胡椒生长和防治胡椒瘟病的效果,全基因组测序是其分子机理研究和开发 利用的重要基础。本研究采用第二代 Illumina 平台与第三代 PacBio 平台相结合的测序技术,对生防菌 VD18R19 进行 全基因组测序,并进行比较基因组学分析。结果发现,VD18R19 全基因组大小为 4 123 380 bp,GC 含量为 43.80%, 编码基因 4 245 个;含有 tRNA 85 个、rRNA 30 个、sRNA 33 个;含有串联重复序列 60 个,其中小卫星 DNA 43 个、 微卫星 DNA 1 个;共线性分析、core-pan 基因分析及基因家族分析结果均显示 VD18R19 与模式菌株 B. subtilis 168 具 有高度的同源性;antiSMASH 软件预测及同源序列比对结果显示,VD18R19 菌株中含有 6 个抑菌次生代谢产物合成基 因簇,编码 surfactin、plipastatin、bacillibactin、bacilysin、bacillaene、subtilosin A 等抑菌物质,其合成途径涵盖了核 糖体途径、非核糖体途径和聚酮合酶途径。本研究为深入研究生防菌 VD18R19 的分子机理奠定生物信息学基础,有利 于生防菌株及其抑菌次生代谢产物的开发和利用。     

Whole genome sequence analysis to detect signatures of positive selection for high fecundity in sheep

Ovulation rate and prolificacy are the most important reproductive traits that have major impact on the efficiency of lamb meat production. Here, we compared the whole genomes of the Romanov sheep, known as one of the high prolific breeds, and four other sheep breeds namely Assaf, Awassi, Cambridge and British du cher, to identify genetic mechanisms underlying prolificacy in sheep. Selection signature analysis revealed 637 and 477 protein‐coding genes under positive selection from F_ST and nucleotide diversity (Pi) statistics, respectively. Further analysis showed that several candidate genes including LEPR, PDGFRL and KLF5 genes are involved in sheep prolificacy. The identified candidate genes in the selected regions are novel and provide new insights into the genetic mechanisms underlying prolificacy in sheep and can be useful in sheep breeding programmes to develop improved breeds for high reproductive efficiency.     

条斑紫菜基因组Fosmid文库构建

高分子量基因组文库是开展条斑紫菜基因组学研究的必备工具。构建了由23 040个Fosmid克隆组成的条斑紫菜孢子体无偏倚基因组文库。检测分析表明：文库克隆重组率为100%;插入DNA片段长度为28~40 kb,平均长度为35 kb,文库覆盖率约为条斑紫菜基因组的2.78倍;从超级池中筛查条斑紫菜18S rRNA、atpA、h2A、rbcL基因,至少能得到一个阳性克隆,印证了计算所推测的文库覆盖率;随机选取6个Fosmid克隆经100代传代后插入DNA片段未发生丢失或长度变化,表明克隆传代的稳定性。该文库的构建为开展条斑紫菜基因组特性分析和基因克隆奠定了基础。     

微生物药物的研究与开发综述

在临床上,微生物药物是一类应用非常广泛的药物,在抗感染、抗肿瘤、血糖调节、降血脂及器官移植等临床治疗中发挥着重要的作用。该文对微生物药物的发展历程、特点、资源研究及开发等方面进行了论述。     

三维基因组学概述及其在农业生物育种方面的研究进展

真核细胞中染色质以不同层次的三维结构有序的折叠在细胞核中,其空间层次结构对基因的表达调控和细胞发挥正常的生理功能都起着重要的作用,在动物育种方面具有很大潜力,但尚未被完全探索。本文介绍三维基因组的结构单元(染色质疆域、A/B 区室、拓扑关联结构域和染色质环)以及研究三维基因组的主要技术,对三维基因组学在农业中的研究进展和应用前景进行了探讨,旨在深入了解三维基因组学的功能和应用前景,以期为生物育种改良提供部分帮助。     

油菜重要性状功能基因研究进展

为实现从传统育种向以基因（或基因组）信息为依据的分子育种转型,研究油菜功能基因组是重要的基础和前提。本文综述了近几年异源四倍体油菜功能基因组研究进展,重点概述了油菜雄性不育、产量、品质和养分代谢等重要性状的功能基因研究结果,并针对我国油菜功能基因组研究和生产育种现状,提出推进功能基因组研究成果应用于育种体系,培育我国自主的高效型油菜重大品种的有关建议,以增强我国生物技术育种的国际竞争力。     

Genotype disclosure in the genomics era: roles and responsibilities

Disclosure of affected breed without disclosure of major progenitors has been the usual practice in scientific papers reporting recessive heritable disorders of cattle. Before molecular genetics, carrier identity could not be used by breeders to control causal mutations because phenotypically normal heterozygotes among genetically related animals could not be detected other than by test mating. Accurate, low‐cost DNA tests fundamentally changed this situation. Genomics can provide relief from the old problem of emerging recessive disorders in cattle breeding, but greater transparency of genotype data between breeders is necessary to fully exploit the opportunities for cost‐efficient genetic disease control. Effective control of several recessive disorders has been demonstrated in Angus cattle, based entirely on voluntary DNA testing by breeders but mandatory public disclosure of test results and genotype probabilities for all registered animals. When a DNA test is available, major progenitors (particularly bulls from which semen has been distributed) should be identified and disclosed concurrently with the affected breed. As a minimum, whenever possible the closest common ancestors in the pedigrees of the parents of homozygous mutants should be disclosed after confirmation of carrier status. Progenitor disclosure in scientific publications should occur in cooperation with breed societies, which should have the opportunity to advise breeders and initiate management programs before scientific publication. Unless properly managed, genomic enhancement of animal selection using SNP markers may increase inbreeding, co‐ancestry and emergence of recessive disorders. The information systems and genotype disclosure policies of some breed societies will be increasingly challenged, particularly with accelerating mutation discovery using next‐generation sequencing.     

Equine clinical genomics: A clinician's primer

The objective of this review is to introduce equine clinicians to the rapidly evolving field of clinical genomics with a vision of improving the health and welfare of the domestic horse. For 15 years a consortium of veterinary geneticists and clinicians has worked together under the umbrella of The Horse Genome Project. This group, encompassing 22 laboratories in 12 countries, has made rapid progress, developing several iterations of linkage, physical and comparative gene maps of the horse with increasing levels of detail. In early 2006, the research was greatly facilitated when the US National Human Genome Research Institute of the National Institutes of Health added the horse to the list of mammalian species scheduled for whole genome sequencing. The genome of the domestic horse has now been sequenced and is available to researchers worldwide in publicly accessible databases. This achievement creates the potential for transformative change within the horse industry, particularly in the fields of internal medicine, sports medicine and reproduction. The genome sequence has enabled the development of new genome‐wide tools and resources for studying inherited diseases of the horse. To date, researchers have identified 11 mutations causing 10 clinical syndromes in the horse. Testing is commercially available for all but one of these diseases. Future research will probably identify the genetic bases for other equine diseases, produce new diagnostic tests and generate novel therapeutics for some of these conditions. This will enable equine clinicians to play a critical role in ensuring the thoughtful and appropriate application of this knowledge as they assist clients with breeding and clinical decision‐making.