谷子SSR标记研究进展

谷子是一种重要的杂粮作物.谷子是二倍体自花授粉作物,基因组较小,与水稻基因组存在明显的共线性,是开展基因组研究的理想模式植物.SSR标记具有共显性、多态性高、操作简单等优点,广泛应用于遗传多样性研究、品种鉴定、遗传图谱构建、功能基因研究、分子标记辅助选择育种等领域.本文对谷子SSR标记的开发和应用进行总结,提出了谷子分子遗传研究中存在的问题,并对今后的发展趋势作了初步探讨,旨在为谷子分子遗传研究提供参考.     

基因是什么? 分子遗传学教学中的体会和理解

随着分子遗传学的飞速发展,基因概念也在不断更新。笔者从事分子遗传学、分子生物学、遗传学教学以及基因与基因表达调控方面研究多年,对基因的本质和概念有较深的理解和认识。回顾了经典基因概念的形成和发展过程,并讨论了真核生物中的RNA遗传和朊病毒复制现象,提出了新的基因概念。认为基因是携带遗传信息的、可遗传的核酸片段或者多肽分子,它们可以编码具功能的RNA分子或多肽分子。     

谷子逆境相关基因家族研究进展

植物抗逆分子机制是当前的热点研究问题之一,研究目的在于从分子水平上解释植物适应逆境的机制、获得各种抗逆基因并通过遗传工程提高植物抗逆性。介绍了植物响应逆境的分子机制,重点概述了近年来抗旱耐瘠典型作物谷子的抗逆相关基因家族的研究进展,同时展望了谷子基因功能研究的发展前景,以期为今后培育高效抗逆作物新品种提供思路。     

谷子(Setaria italica L.)组蛋白修饰酶类基因的挖掘

组蛋白修饰是表观遗传学领域中一种重要的修饰方式,可经多种组蛋白修饰酶类催化产生.为了研究谷子(Setaria italica L.)基因组中组蛋白修饰酶类基因的特征,本研究利用比较基因组学的方法,以水稻(Oryza sativa)基因组注释信息为参考,对谷子的组蛋白修饰酶类基因进行挖掘,共发现80个谷子组蛋白修饰酶类相关基因,并根据组蛋白乙酰化酶/去乙酰化酶、甲基化酶/去甲基化酶绘制系统进化树,每部分都能根据其行使的功能聚类.组蛋白修饰酶类基因的鉴定是阐明不同生物表观遗传调控机制的重要步骤.本研究为详细探讨这些基因在谷子表观遗传修饰中的功能和作用提供初步的理论依据和参考.     

基因序列在小蜂总科分子系统发育研究中的应用

总结了线粒体基因和核基因在膜翅目小蜂总科分子系统发育研究中的应用.核基因中,28S rDNA序列应用最广泛,探讨的问题从种级到科级不等;其次是ITS序列,主要用于探讨种及种级以下阶元问题;18S rDNA适于探讨科级以上高级阶元的问题.线粒体基因中,16S rDNA和3个蛋白编码基因COⅠ、COⅡ和Cytb,主要用于属种级系统发育关系研究.核基因间、线粒体基因间、核基因和线粒体基因间以及分子数据和形态数据间进行的联合分析,在解决不同层次的问题中均有应用.建议对更多的小蜂类群测定线粒体基因和核基因的序列,不断寻找新的基因对小蜂分子系统发育研究进行充实和拓展.     

谷子bZIP转录因子的全基因组鉴定及其在干旱和盐胁迫下的表达分析

bZIP蛋白是植物转录因子中最大和最保守的一类转录因子, 参与调控植物生长发育等多种生命活动。谷子(Setaria italica)是一种重要的C4杂粮作物, 其bZIP基因家族与功能报道较少。利用生物信息学工具, 从谷子全基因组中鉴定出73个SibZIP转录因子, 划分为A、B、C、D、E、G、H、I和X等亚家族。与已测序的禾谷类作物相比, 谷子SibZIP基因家族在进化中发生缩减。在谷子SibZIP蛋白中检测到25种不同的保守氨基酸基序。RNA-seq和定量PCR检测结果表明, 在干旱和盐胁迫条件下, 多数SibZIPs基因不同程度地被诱导表达, 预示着部分SibZIP成员在谷子干旱和盐胁迫响应中起重要作用。共表达关联性分析进一步揭示19个谷子SibZIP转录因子可通过与蛋白激酶或NPR1相关调节蛋白等互作介导谷子胁迫响应。研究结果为全面解析谷子SibZIPs基因结构与生物学功能、抗旱分子机制以及分子育种提供了新信息。     

谷子光敏色素基因光周期、非生物胁迫响应特性及关键自然变异位点鉴定北大核心CSCD

比较分析光敏色素基因家族成员对光周期、非生物胁迫响应模式并鉴定其有利自然变异类型,为全面了解光敏色素基因家族在光周期调控谷子生长发育及应对非生物胁迫中的作用机制、开展关键性状的分子辅助选择奠定基础。文中利用RT-PCR技术从超晚熟谷子农家种‘毛粟’中克隆了3个光敏色素基因SiPHYA、SiPHYB和SiPHYC;在进行生物信息学分析后,利用荧光定量PCR技术研究了3个基因的光周期调控模式及对聚乙二醇(polyethylene glycol,PEG)模拟干旱、自然干旱、脱落酸(abscisic acid,ABA)、高温、Na Cl五种非生物胁迫的响应特性;最后检测这3个基因在160份谷子材料的突变位点,通过单倍型分析确定基因的功能效应。结果表明,获得了基因SiPHYA、SiPHYB和SiPHYC包含完整编码区的c DNA序列,长度分别为3 981、3 953、3 764 bp,其中基因SiPHYB和SiPHYC具有较近的进化关系。基因SiPHYA、SiPHYB和SiPHYC均受光周期调控,但光周期对SiPHYB、SiPHYC昼夜表达模式的影响要强于SiPHYA;短日照条件临近抽穗SiPHYA、SiPHYB表达水平显著低于长日照,暗示其在谷子长日照抑制抽穗中发挥作用。SiPHYB和SiPHYC共同响应PEG模拟干旱、自然干旱、ABA、高温4种胁迫;SiPHYA和SiPHYB以不同方式响应盐胁迫,SiPHYC没有参与谷子盐胁迫响应过程。基于160份谷子材料重测序数据发现基因SiPHYB高度保守,基因SiPHYA含有两个错义突变:单核苷酸多态性(single nucleotide polymorphism,SNP) 7 034 522;,SNP7 036 657;,导致延迟抽穗、增加株高。基因SiPHYC含有一个错义突变(SNP5 414 823;),导致短日照缩短抽穗期,长日照延长抽穗期,对株高、穗长的增加作用不受光温环境影响。光周期对基因SiPHYA、SiPHYB和SiPHYC具有不同的调控作用,除了盐胁迫,SiPHYB和SiPHYC共同响应多种非生物胁迫,相比参考基因型,SiPHYA、SiPHYC突变延迟抽穗、增加株高和穗长。     

基因的推理设计与改造—体外分子进化的捷径

体外分子进化是改造基因、获得新的功能蛋白质重要手段之一,已经取得了令人瞩目的成就。推理设计是利用序列和结构的比较信息创造新的基因和蛋白质,是研究改造蛋白质功能的有效方法。文章着重介绍了基因推理设计在基因体外分子进化中的应用,从简单实用的基因密码偏爱设计,结合多个不同性状相关功能基因信息的基因推理设计,关键功能区域的简并引物设计,位点直接蛋白质重组4个方面进行描述,并综述了该方法近年来的应用。     

核基因在两栖爬行动物分子系统学中的研究进展

从DNA水平探索生物进化的理论、生物类群的演化历史具有重要的意义,应用DNA序列研究生物的系统发育和进化规律成为当前分子系统学研究的热点,与线粒体DNA相比,核基因由于包含有更加丰富的生物学信息,运用核基因序列或将核基因序列与线粒体基因序列相结合研究两栖爬行动物的系统发育,正成为分子系统学领域的新的发展趋势.Rag-1、Rag-2、tyrosinase、rhodopsin、C-mos等核基因已在两栖爬行动物分子系统学中得到了广泛的应用.由于目前的技术手段等诸多因素,限制了更多的核基因用于两栖爬行动物分子系统学研究.为此简要介绍了目前核基因在两栖爬行动物分子系统学方面的研究进展,并分析了核基因序列在分子系统学应用上面临的问题和应用前景.     

几种可能影响耐力素质的潜在基因

个体间运动能力的差异受多种因素影响,其中环境(运动训练、营养与技术方法)和遗传因素在很大程度上起决定作用。迄今已进行了大量与运动能力有关的基因多态研究,但近年来有关新基因、新位点的探索却渐入瓶颈,限制了优秀运动员分子选材研究的发展。文章着重叙述了几个可能影响耐力素质的潜在基因的运动相关功能和多态研究的结果,以期为研究者提供新的思路和研究的可行性依据。     

Phytolith analysis for differentiating between foxtail millet (Setaria italica) and green foxtail (Setaria viridis)

Foxtail millet (Setaria italica) is one of the oldest domesticated cereal crops in Eurasia, but identifying foxtail millets, especially in charred grains, and differentiating it from its wild ancestor, green foxtail (Setaria viridis), in the archaeobotanical remains, is still problematic. Phytolithic analysis provides a meaningful method for identifying this important crop. In this paper, the silicon structure patterns in the glumes, lemmas, and paleas from inflorescence bracts in 16 modern plants of foxtail millet and green foxtail from China and Europe are examined using light microscopy with phase-contrast and a microscopic interferometer. Our research shows that the silicon structure of ΩIII from upper lemmas and paleas in foxtail millet and green foxtail can be correspondingly divided into two groups. The size of ΩIII type phytolith of foxtail millet is bigger than that from green foxtail. Discriminant function analysis reveals that 78.4% of data on foxtail millet and 76.9% of data on green foxtail are correctly classified. This means certain morphotypes of phytoliths are relatively reliable tools for distinguishing foxtail millet from green foxtail. Our results also revealed that the husk phytolith morphologies of foxtail millets from China and Eastern Europe are markedly different from those from Western Europe. Our research gives a meaningful method of separating foxtail millet and green foxtail. The implications of these findings for understanding the history of foxtail millet domestication and cultivation in ancient civilizations are significant.     

Comparative mapping reveals a complex relationship between the pearl millet genome and those of foxtail millet and rice

Comparative genetic maps were constructed of the pearl millet genome with foxtail millet and used to describe the homoeology between the genomes of pearl millet, foxtail millet and rice. Despite the close taxonomic relationship of pearl and foxtail millet, their genomes were highly, rearranged. A comparison of the millet and rice genomes indicated that most of these rearrangements were likely to have taken place in pearl millet. Two duplications were identified in pearl millet. A duplication between the distal segments of linkage groups 1 and 4 corresponds to the ancient duplication previously identified between rice chromosome arms 11S and 12S and foxtail millet chromosomes VII and VIII. The other putative duplication, also between regions of linkage groups 1 and 4, is likely to be species-specific. The exploitation of the comparative maps in pearl millet research is discussed. Received: 10 February 1999 / Accepted: 6 July 1999     

2,4-D和干燥处理对谷子成熟胚离体再生体系的影响

谷子离体再生体系不够稳定、转化效率低，已成为谷子功能基因研究和品种改良的瓶颈。为了建立谷子成熟胚稳定的离体再生体系，以当地高产优质的6个谷子品种成熟胚为外植体，以不同2,4-二氯苯氧乙酸（2,4-dichlorophenoxyacetic acid，2,4-D）浓度及对胚性愈伤的不同干燥处理时间为变量，通过单因素实验和正交实验考察各因素对谷子愈伤组织分化及成苗的影响。结果表明，晋谷21在2,4-D浓度为9 μmol·L-1、4 h干燥处理的条件下所建立的再生体系最好，分化率为64.35%，成苗率为29.06%。研究通过探索谷子组织培养的最适条件，为谷子高效稳定遗传转化体系的建立和利用基因工程手段进行品质改良提供了依据。     

Genetic structure of landraces in foxtail millet (Setaria italica (L.) P. Beauv.) revealed with transposon display and interpretation to crop evolution of foxtail millet

Although the origin and domestication process of foxtail millet (Setaria italica subsp. italica (L.) P. Beauv.) has been studied by several groups, the issue is still ambiguous. It is essential to resolve this issue by studying a large number of accessions with sufficient markers covering the entire genome. Genetic structures were analyzed by transposon display (TD) using 425 accessions of foxtail millet and 12 of the wild ancestor green foxtail (Setaria italica subsp. viridis (L.) P. Beauv.). We used three recently active transposons (TSI-1, TSI-7, and TSI-10) as genome-wide markers and succeeded in demonstrating geographical structures of the foxtail millet. A neighbor-joining dendrogram based on TD grouped the foxtail millet accessions into eight major clusters, each of which consisted of accessions collected from adjacent geographical areas. Eleven out of 12 green foxtail accessions were grouped separately from the clusters of foxtail millet. These results indicated strong regional differentiations and a long history of cultivation in each region. Furthermore, we discuss the relationship between foxtail millet and green foxtail and suggest a monophyletic origin of foxtail millet domestication.     

谷子全生育期抗旱性鉴定及抗旱指标筛选

作物全生育期抗旱性对发掘和利用抗旱品种和抗旱基因至关重要,但谷子全生育期抗旱鉴定至今未有报道,抗旱鉴定缺乏鉴定指标。本试验在干旱池模拟干旱条件下,对苗期抗旱性表现不同的谷子品种进行了全生育期抗旱性研究,调查分析了根干重等形态和生理性状在干旱胁迫条件下的变化;采用相关和灰色关联度等方法,分析这些指标与抗旱性(DRI)的关系。结果表明,相对根冠比、相对单穗粒重和灌浆期光合速率、蒸腾速率同抗旱性表现极显著相关,可以作为谷子全生育期抗旱性鉴定的指标;而相对根干重、相对单穗重、相对株高和气孔导度则可以作为谷子全生育期抗旱性鉴定的参考指标;在供试的品种中,红根谷和大齐头白表现了良好的综合抗旱性。本文还讨论了抗旱性的复杂性以及不同性状对干旱胁迫的反应,所建立的指标对谷子全生育期抗旱鉴定具有指导意义。     

Genome sequence of foxtail millet (Setaria italica) provides insights into grass evolution and biofuel potential

Foxtail millet (Setaria italica), a member of the Poaceae grass family, is an important food and fodder crop in arid regions and has potential for use as a C(4) biofuel. It is a model system for other biofuel grasses, including switchgrass and pearl millet. We produced a draft genome (～423 Mb) anchored onto nine chromosomes and annotated 38,801 genes. Key chromosome reshuffling events were detected through collinearity identification between foxtail millet, rice and sorghum including two reshuffling events fusing rice chromosomes 7 and 9, 3 and 10 to foxtail millet chromosomes 2 and 9, respectively, that occurred after the divergence of foxtail millet and rice, and a single reshuffling event fusing rice chromosome 5 and 12 to foxtail millet chromosome 3 that occurred after the divergence of millet and sorghum. Rearrangements in the C(4) photosynthesis pathway were also identified.     

Construction and application of EST library from Setaria italica in response to dehydration stress

Foxtail millet is a gramineous crop with low water requirement. Despite its high water use efficiency, less attention has been paid to the molecular genetics of foxtail millet. This article reports the construction of subtracted cDNA libraries from foxtail millet seedlings under dehydration stress and the expression profile analysis of 1947 UniESTs from the subtracted cDNA libraries by a cDNA microarray. The results showed that 95 and 57 ESTs were upregulated by dehydration stress, respectively, in roots and shoots of seedlings and that 10 and 27 ESTs were downregulated, respectively, in roots and shoots. The expression profile analysis showed that genes induced in foxtail millet roots were different from those in shoots during dehydration stress and that the early response to dehydration stress in foxtail millet roots was the activation of the glycolysis metabolism. Moreover, protein degradation pathway may also play a pivotal role in drought-tolerant responses of foxtail millet. Finally, Northern blot analysis validated well the cDNA microarray data.     

运用MSAP技术测定谷子基因组DNA胞嘧啶甲基化水平

DNA甲基化是真核生物一种重要的表观修饰形式。为了探讨谷子基因组DNA胞嘧啶甲基化的水平和模式,以谷子Setaria italica的两个品种朝谷58号和豫谷1号为实验材料,利用Eco RⅠ和HpaⅡ/MspⅠ双酶切建立适合于谷子基因组的甲基化敏感扩增多态性(MSAP)分析体系。结果表明,从100对MSAP选扩引物中,筛选出32对MSAP引物组合,在朝谷58号和豫谷1号中分别扩增产生1 615、1 482条清晰可辨且可重复的DNA条带,其中包括3种类型的甲基化条带,朝谷58号和豫谷1号的基因组中CCGG序列胞嘧啶甲基化水平分别为6.93%和8.77%。这种谷子不同品种间甲基化水平和分布位点的差异为从表观遗传学的角度培育新品种提供了初步的理论依据和参考。     

谷子穗分化的扫描电镜观察

利用扫描电镜对复合品种冀谷１１号的穗分化进行了系统观察,比较了夏谷和春谷穗分化的异同。提出了谷子穗分化划分为穗分化前期、生长锥伸长期、枝梗分化期、小穗和刚毛分化期以及小花分化期共５个时期,就谷子刚毛起源穗分化与栽培育种的关系等问题进行了讨论。