Hsp90 potentiates the rapid evolution of new traits: drug resistance in diverse fungi

Hsp90 is a molecular chaperone for many signal transducers and may influence evolution by releasing previously silent genetic variation in response to environmental change. In fungi separated by approximately 800 million years of evolution, Hsp90 potentiated the evolution of drug resistance in a different way, by enabling new mutations to have immediate phenotypic consequences. Resistance was abrogated by Hsp90 inhibitors and by febrile temperatures, suggesting new therapeutic strategies and a clinical benefit of fever. During selection in a human host, drug resistance that was initially Hsp90-dependent evolved toward independence. Thus, Hsp90 can act in diverse ways to couple environmental contingency to the emergence and fixation of new traits.     

陆地棉叶片叶绿素含量与SSR标记的关联分析及优异等位变异的挖掘

【目的】筛选与陆地棉叶片叶绿素含量性状相关联的分子标记,挖掘其优异等位变异及典型材料,为陆地棉分子标记辅助育种提供技术支持。【方法】在3年6个环境中,对185份陆地棉品种(系)组成的自然群体进行倒4叶叶绿素相对含量(soil and plant analyzer development,SPAD)的测定,每年分3个时期(打顶后0、10和20 d)。采用Power Marker 3.25软件计算各位点的多态性信息含量,以分析群体的遗传多样性。利用STRUCTURE 2.3.4软件计算群体结构矩阵(Q),利用TASSEL 3.0软件计算亲属关系矩阵(K),通过GLM(general linear model,Q)和MLM(mixed linear model,Q+K)2种方法,同时对SPAD与SSR标记进行关联分析。依据计算的等位位点表型效应值,挖掘优异的等位变异及典型材料。【结果】137对SSR多态性引物共扩增出355个等位变异,平均每对引物扩增到2.6个多态性位点,PIC平均值为0.67,变化范围为0.01—0.95,高度多态性引物(PIC0.5)占85%,其中PIC最高的标记为HAU2146(PIC=0.95)和NAU2083(PIC=0.93)。当(35)K取得最大值时,K=2,因此,将185份陆地棉材料划分为2个亚群。通过GLM方法共检测到22个显著性位点(P0.001),表型变异解释率为5.28%—10.85%,平均为7.24%,贡献率最高的等位变异位点是SWU0529a(R2=10.85%)和NAU998c(R2=10.48%);通过MLM方法共检测到17个显著性位点(P0.01),表型变异解释率为3.72%—8.58%,平均为4.72%,贡献率最高的等位变异位点是SWU0923b(R2=8.06%)和SWU0662d(R2=6.74%);2种方法共同检测到的显著性位点有12个,等位变异NAU998c在3个时期2种方法能同时被检测到。通过等位变异的表型效应分析,找到2个增效效应最大的等位变异(HAU3318b和SWU0987b),利用找到的等位变异对材料进行筛选,获得携带2个增效效应等位变异的材料53份,2个增效效应位点都未检测到的材料有46份,统计结果显示,在打顶后10和20 d 2个时期,53份材料的SPAD均值显著高于46份材料的SAPD均值。【结论】检测到12个与SPAD值相关的显著性位点,并挖掘到2个增效效应优异等位变异,获得携带优异等位变异的载体材料53份,获得携带2个优异等位变异的典型材料1份。     

Molecular analysis of FRIGIDA, a major determinant of natural variation in Arabidopsis flowering time

Vernalization, the acceleration of flowering by a long period of cold temperature, ensures that many plants overwinter vegetatively and flower in spring. In Arabidopsis, allelic variation at the FRIGIDA (FRI) locus is a major determinant of natural variation in flowering time. Dominant alleles of FRI confer late flowering, which is reversed to earliness by vernalization. We cloned FRI and analyzed the molecular basis of the allelic variation. Most of the early-flowering ecotypes analyzed carry FRI alleles containing one of two different deletions that disrupt the open reading frame. Loss-of-function mutations at FRI have thus provided the basis for the evolution of many early-flowering ecotypes.     

Unpredictable evolution in a 30-year study of Darwin's finches

Evolution can be predicted in the short term from a knowledge of selection and inheritance. However, in the long term evolution is unpredictable because environments, which determine the directions and magnitudes of selection coefficients, fluctuate unpredictably. These two features of evolution, the predictable and unpredictable, are demonstrated in a study of two populations of Darwin's finches on the Galápagos island of Daphne Major. From 1972 to 2001, Geospiza fortis (medium ground finch) and Geospiza scandens (cactus finch) changed several times in body size and two beak traits. Natural selection occurred frequently in both species and varied from unidirectional to oscillating, episodic to gradual. Hybridization occurred repeatedly though rarely, resulting in elevated phenotypic variances in G. scandens and a change in beak shape. The phenotypic states of both species at the end of the 30-year study could not have been predicted at the beginning. Continuous, long-term studies are needed to detect and interpret rare but important events and nonuniform evolutionary change.     

基于基因组学的作物种质资源研究:现状与展望

作物种质资源工作涉及面很广,包括种质资源的收集、编目、保护、繁种更新、分发利用与信息系统建立等基础性工作,作物起源、驯化与传播、种质分类、民族植物学与传统知识研究等基础研究,遗传多样性评价、重要性状表型鉴定、种质资源基因型鉴定、基因发掘和种质创新等应用基础研究。经过近百年的努力,种质资源的基础性工作已卓有成效,作物种质资源保护与共享利用体系基本建立。但由于主要基于形态学的传统研究思路和方法存在很多先天不足,种质资源基础研究和应用基础研究一直举步维艰,效率低下。随着分子标记技术和第二代测序技术的快速发展,基因组学理论和方法不断深入到种质资源研究的多个层面,使种质资源保护和创新利用发生了研究思路和方法学上的变革。基因组学研究成果为种质资源的有效收集和保护提供了理论指导,也为阐明作物起源和演化、全面评估种质资源结构多样性提供了核心理论和技术,同时大幅度提高了基因发掘和种质创新效率。特别是全基因组测序、重测序和简化基因组测序技术不断成熟,使在全基因组水平上比较不同种质资源基因组变异成为可能;在此基础上,可阐明农作物起源以及驯化、改良和传播对种质资源形成的影响,明确现有种质资源和野外种质资源群体结构和遗传多样性,提出种质资源异地保存和原生境保护的最佳策略;结合表型鉴定数据,利用连锁分析和关联分析等基因组学方法,可高效发掘种质资源中蕴含的新基因和有利等位基因,提出其利用途径和具体方案,并在种质创新过程中充分利用基因组学研究成果提高创新效率。文章评述了基因组学在种质资源研究中的应用现状,特别是在种质资源基因型鉴定、异地保存和原生境保护、作物起源与进化研究、结构多样性分析、新基因发掘和种质创新等方面的应用情况及其发展趋势。提出了今后的发展方向和工作重点,强调把基因组学理论和方法与作物种质资源研究紧密结合,为种质资源的有效保护和高效利用提供强有力的理论、技术、材料与信息支撑。     

栽培大豆农艺性状的关联分析及优异等位变异挖掘

【目的】发掘大豆农艺性状稳定表达的QTL、优异等位变异及其携带优异等位变异的载体材料,为大豆分子标记辅助选择和分子设计育种等后续研究提供重要依据。【方法】利用大豆基因组上均匀分布的135对SSR引物对通过分层随机抽取的6大生态区的257个栽培大豆品种进行全基因组扫描以获得分子标记信息,2009年和2010年在南京农业大学江浦农场对供试群体株高、分枝数、主茎节数、茎粗和单株荚数进行表型鉴定以获得数量性状表型观测值,用广义线性模型、优化压缩混合线性模型和上位性关联分析3种方法,实施农艺性状表型与SSR标记基因型间的关联分析。【结果】供试品种株高、分枝数、主茎节数、茎粗和单株荚数变异系数介于24.62%-52.34%,品种间和品种与环境互作差异极显著;广义线性模型、优化压缩混合线性模型和上位性关联分析3种方法分别检测到年份间稳定表达的上述5性状的47、11和58个QTL,其中,2种方法间和3种方法间分别有34和4个共同QTL,上位性关联分析检测到1对上位性QTL和32个环境互作QTL;检测得到的主效QTL中,有18个主效QTL与前人鉴定的QTL位置一致或紧密连锁;发掘了一批农艺性状的优异等位基因及携带优异等位基因的载体材料,其中,satt669-145bp、satt102-154bp、satt382-395 bp和satt534-161bp分别是主茎节数、分枝数、茎粗和株高的增效效应最大的等位基因,其载体材料分别为白花豆、合肥两塘焦双青豆、油葫芦和浦霞大豆。【结论】检测到年份间或方法间稳定表达的株高、分枝数、主茎节数、茎粗和单株荚数5个农艺性状的107个主效 QTL。     

基于优异等位基因的棉花抗黄萎病性状的分子鉴定

【目的】发掘棉花抗黄萎病相关的优异等位基因,利用优异等位基因对棉花抗黄萎病性状进行分子检测,实现对抗病性的快速鉴定和对抗病基因型的直接选择,有效解决当前抗病性鉴定周期长、抗病性选择效率低的技术难题。【方法】选用125份陆地棉优异种质,分别采用田间黄萎病病圃鉴定和温室接种鉴定对材料进行抗黄萎病鉴定,分析材料的抗病性变异;通过筛选前期获得的与棉花抗黄萎病表型显著关联的优异等位基因位点并计算其效应值,分析不同材料中含有的优异等位基因数目及其优异等位基因效应值之和,研究利用优异等位基因位点进行棉花抗黄萎病预测的可行性,并比较基于优异等位基因位点的抗病性分子鉴定与传统抗病性表型鉴定的相关性。【结果】陆地棉在黄萎病抗性方面表现出广泛的变异,125份种质材料在田间病圃鉴定条件下和温室鉴定条件下的抗黄萎病相对病指变化范围分别为10.10—76.6和17.01—72.63;基于前期的研究结果共筛选到40个抗黄萎病优异等位基因,效应值的变化范围为-8.20—-0.39,每份材料含有的优异等位基因数目为1—24个,每份材料中的优异等位基因效应值之和的变化范围为-92.37—-0.86;相关性分析结果表明,每份材料中含有的优异等位基因效应值之和与材料的抗黄萎病相对病指极显著正相关,病圃鉴定与温室鉴定条件下两者的相关系数分别为0.616和0.566;材料的优异等位基因数目与材料的抗黄萎病相对病指极显著负相关,病圃鉴定与温室鉴定条件下两者的相关系数分别为-0.618和-0.535。【结论】棉花种质材料中含有的优异等位基因数目、优异等位基因效应值之和与材料的抗黄萎病相对病指间存在显著相关性,表明抗黄萎病优异等位基因的累加具有明显提高抗病性的作用,材料所含有的优异等位基因数目和优异等位基因效应值之和在一定程度上可以反映材料抗病性的强弱,从而实现对抗病性的分子鉴定。     

Genes lost and genes found: evolution of bacterial pathogenesis and symbiosis

Traditionally, evolutionary biologists have viewed mutations within individual genes as the major source of phenotypic variation leading to adaptation through natural selection, and ultimately generating diversity among species. Although such processes must contribute to the initial development of gene functions and their subsequent fine-tuning, changes in genome repertoire, occurring through gene acquisition and deletion, are the major events underlying the emergence and evolution of bacterial pathogens and symbionts. Furthermore, pathogens and symbionts depend on similar mechanisms for interacting with hosts and show parallel trends in genome evolution.     

Phenotypic plasticity in the interactions and evolution of species

When individuals of two species interact, they can adjust their phenotypes in response to their respective partner, be they antagonists or mutualists. The reciprocal phenotypic change between individuals of interacting species can reflect an evolutionary response to spatial and temporal variation in species interactions and ecologically result in the structuring of food chains. The evolution of adaptive phenotypic plasticity has led to the success of organisms in novel habitats, and potentially contributes to genetic differentiation and speciation. Taken together, phenotypic responses in species interactions represent modifications that can lead to reciprocal change in ecological time, altered community patterns, and expanded evolutionary potential of species.     

中国玉米地方品种的种族划分及其特点研究

[目的]系统了解中国玉米地方品种多样性及所包括的种族类型,是研究作物生态分化、进一步挖掘优异基因资源、实现育种持续发展的重要基础性工作.[方法]以能代表中国地方品种多样性的核心种质中所包括的730份地方品种为材料,采用随机区组设计,对研究材料进行包括生育期性状在内的31个农艺性状进行了多年鉴定,基于这些表型性状的调查值,进行主成份分析以及聚类分析,依据聚类分析所揭示的表型性状计算730份玉米品种的欧式距离(Euclidean distance),进而对中国玉米地方品种进行种族划分.[结果]主成份分析结果表明,前13个主成份可以囊括所有表型的86.2%遗传信息,基于这13个主成份所揭示的11个表型性状的Neighbor-Joining(NJ)聚类结果表明,中国玉米可以划分为9个种族,即西南黄色硬粒种族、西南白色硬粒种族、北方黄色硬粒种族、北方白色硬粒种族、西南马齿种族、北方马齿种族、衍生种族、南方糯质玉米种族以及爆裂玉米种族.[结论]中国的玉米地方品种对本土具有良好的适应性与自身的特点,基于广泛地理来源的地方品种,所划分的9个玉米种族各自具有不同的表型特征与育种利用价值,但与南美及美国所拥有的玉米多样性相比,中国地方品种的遗传基础显得相对狭窄.引进和利用国外不同类型地方品种,依然具有重要的科学与实践意义.     

Hsp90 and environmental stress transform the adaptive value of natural genetic variation

How can species remain unaltered for long periods yet also undergo rapid diversification? By linking genetic variation to phenotypic variation via environmental stress, the Hsp90 protein-folding reservoir might promote both stasis and change. However, the nature and adaptive value of Hsp90-contingent traits remain uncertain. In ecologically and genetically diverse yeasts, we find such traits to be both common and frequently adaptive. Most are based on preexisting variation, with causative polymorphisms occurring in coding and regulatory sequences alike. A common temperature stress alters phenotypes similarly. Both selective inhibition of Hsp90 and temperature stress increase correlations between genotype and phenotype. This system broadly determines the adaptive value of standing genetic variation and, in so doing, has influenced the evolution of current genomes.     

利用分子标记定位籼稻落粒性QTL

利用2个籼稻品种H359和Acc8558杂交产生的重组自交系群体及相应的分子标记连锁图,采用复合区间定位方法,对籼稻落粒性进行了QTL定位分析.共检测到7个QTL,分别位于第1、2、4、6、7染色体上.这些QTL对表型变异的贡献率在2.49%-9.81%之间,总体可解释39.2%的表型方差.未检测到主效基因.在7个QTL中,有6个来自H359的等位基因均使落粒率降低,这与两亲本间落粒性的差异相吻合.     

Climate-driven range expansion and morphological evolution in a marine gastropod

Little is known about the phenotypic consequences of global climate change, despite the excellent Pleistocene fossil record of many taxa. We used morphological measurements from extant and Pleistocene populations of a marine gastropod (Acanthinucella spirata) in conjunction with mitochondrial DNA sequence variation from living populations to determine how populations responded phenotypically to Pleistocene climatic changes. Northern populations show little sequence variation as compared to southern populations, a pattern consistent with a recent northward range expansion. These recently recolonized northern populations also contain shell morphologies that are absent in extant southern populations and throughout the Pleistocene fossil record. Thus, contrary to traditional expectations that morphological evolution should occur largely within Pleistocene refugia, our data show that geographical range shifts in response to climatic change can lead to significant morphological evolution.     

用高基元微卫星标记分析中国糜子遗传多样性

【目的】开发高基元(4—6)碱基重复微卫星标记,分析种质资源遗传多样性,为糜子遗传和进化研究提供理论基础。【方法】用隶属函数、主成分分析和聚类分析综合评价糜子资源表型多样性,用前期糜子转录组测序获得高基元SSR引物对地理来源差异大的糜子材料进行PCR扩增检测其多态性,用Power Marker 3.25计算遗传多样性参数,用Pop Gen 1.32计算Nei’s遗传距离,用MEGA 5.0进行聚类分析,用Structure 2.2鉴定遗传类群。【结果】96份糜子资源株高和穗长变异最丰富,多样性指数分别为2.08和1.91。PCR扩增发现,占56.29%的85对引物具多态性,其中四、五和六碱基重复引物分别为71对(83.53%)、10对(11.76%)和4对(4.7%)。85个标记扩增产物大小分布为100—450 bp,PIC值平均为0.51,Rp值为1.00—5.75,平均为3.15。四、五和六碱基重复SSR的平均Rp值分别为3.15、2.8和4.0。基于Rp值分析SSR的分布频次,发现85个标记分布区间为0—1、1—2、2—3、3—4、4—5和5—6,分别包含1(1.18%)、15(17.65%)、31(36.47%)、20(23.53%)、12(14.12%)和6(7.06%)个标记,60%(51个)的标记分布在区间2—3和3—4。用85个SSR扩增96份糜子资源,共检测到232个等位变异,每个位点检测到等位变异2—3个,平均2.7294个;62个位点产生3个变异,23个位点产生2个变异;多样性指数为0.2842—1.0633,平均为0.7708;PIC值为0.0400—0.7281,平均为0.4723。不同生态区糜子种质间的遗传距离为0.0093—0.5052(平均为0.1798),遗传一致度为0.6034—0.9907(平均为0.8485)。基于UPGMA将96个糜子基因型聚为4个群组,第一群组主要属于北方春糜子区;第二群主要属于东北春糜子区;第三群组主要属于华北夏糜子区;第四群组主要属于黄土高原春夏糜子区。遗传结构分析将96份试材划分为4个类群,分别代表黄土高原、华北、东北和北方基因库。UPGMA聚类分析和遗传结构分析结果基本一致,均与地理起源相关。【结论】在糜子中构建了85个四、五和六碱基重复微卫星标记,这些高基元SSR的引物分辨率(Rp)高,对不同基因型分辨能力强,PCR扩增多态性好;用其评估中国糜子资源的遗传差异发现,黄土高原春夏糜子区和北方春糜子区资源遗传多样性最丰富。     

Genetic variation in human erythrocyte acetylcholinesterase

A method for solubilization of human erythrocyte membranes was developed and used to survey 70 unselected human blood samples for isozymic variation of stromal acetylcholinesterase. Three variants were observed. Pedigrees of families studied by this method indicated that this variation represented the phenotypic expression of two codominant alleles at a single locus.     

桃(Prunus persica (L.) Batsch.)品种核心种质的构建与评价

为构建桃品种核心种质,通过对56份桃(Prunus persica(L.) Batsch.)初级核心种质的形态农艺性状数据(MOR)和SSR等位基因数据的分析,研究了不同聚类取样方法和完全随机取样方法下9种取样比例的遗传多样性指数、保留比例及各频率段等位基因的丢失比例。结果表明:聚类取样的方法优于完全随机取样,并以在80%的取样比例下MOR结合SSR数据聚类取样的效果最好,利用此方案构建的桃品种核心种质共包括45份材料,该核心种质的基因遗传多样性指数最高,保留了初级核心种质100%的形态农艺性状和96.6%的SSR等位基因,在出现频率低于0.05的等位基因中共丢失了2个等位变异,保留了出现频率在0.05~0.10的所有等位基因;利用6个数量性状对所构建的核心种质的代表性检测表明所构建的核心种质很好地代表558份桃原始种质的遗传变异。     

水稻6个异交相关性状的SSR关联分析

从水稻核心种质和栽培品种中选取95个品种构成品种总群体,调查该群体6个异交相关性状。选用分布在水稻12条染色体上的93个SSR标记对这95个品种进行基因型鉴定。采用TASSEL软件中一般线性模型对标记与性状间的关联进行分析,发掘有利等位变异和相应载体品种。结果表明:品种总群体中6个异交性状的变异系数为9.9%～62.9%。共检测到22个与异交性状相关联的SSR分子标记,其中8个与剑叶角度相关联,2个与花丝长度相关联,4个与花药长度相关联,1个与柱头长度相关联,3个与柱头外露率相关联,9个与开颖角度相关联。发掘了一批携有优良等位变异且效应值较大的载体品种。携有RM480-197 bp和RM535-170 bp条带的‘无芒早稻’分别对增加剑叶角度和花丝长度效应最大。携有RM311-162bp条带的‘敲冰黄’对增加花药长度效应最大。携有RM498-187 bp条带的‘滇屯502选早’对增加柱头长度效应最大。携有RM206-150 bp条带的‘徐稻5号’对提高柱头外露率效应最大。携有RM311-159 bp条带的‘小白野稻’对增加开颖角度效应最大。这些有利等位变异及其载体品种可用作水稻异交性状遗传改良的亲本。     

中国小麦抗穗发芽种质资源的挖掘与创制

根据4年的表型数据,并结合实验室开发和鉴定的13个分子标记,对我国833份小麦种质资源（主要包括278份小麦微核心种质、124份地方品种和431份现代推广品种及高代品系）穗发芽抗性进行鉴定。结果表明,13个分子标记鉴定的抗/感穗发芽等位类型间相对发芽指数（RGI）差异均达显著或极显著水平,其中TaMFT-222和Ta MFT-194标记鉴定的差异最大,U值分别为14.98**和11.30**,均达极显著水平,其优异等位类型可以降低相对发芽指数0.21～0.32。其次是Sdr2A、CNGC2AL、Vp1-b2、Ta MKK3-A、PM19、CAPS-2AL、A17-19和EX06323标记,其等位类型间穗发芽抗性差异也均达极显著水平;Qsd1和Barc321标记也能显著区分穗发芽抗性。共计鉴定出63份穗发芽抗性较好的种质资源,其中达到抗的有41份,多为红皮品种和地方品种;达到中抗的有22份,白皮半冬性居多。利用分子标记辅助选择,并结合杂交聚合,创制出12份穗发芽抗性水平达到中抗和抗的种质资源,至少携带3个抗穗发芽基因/位点。该结果为抗穗发芽新品种选育提供重要遗传资源。     

A single amino acid mutation contributes to adaptive beach mouse color pattern

Natural populations of beach mice exhibit a characteristic color pattern, relative to their mainland conspecifics, driven by natural selection for crypsis. We identified a derived, charge-changing amino acid mutation in the melanocortin-1 receptor (Mc1r) in beach mice, which decreases receptor function. In genetic crosses, allelic variation at Mc1r explains 9.8% to 36.4% of the variation in seven pigmentation traits determining color pattern. The derived Mc1r allele is present in Florida's Gulf Coast beach mice but not in Atlantic coast mice with similar light coloration, suggesting that different molecular mechanisms are responsible for convergent phenotypic evolution. Here, we link a single mutation in the coding region of a pigmentation gene to adaptive quantitative variation in the wild.     

Identification of QTLs for grain size and characterization of the beneficial alleles of grain size genes in large grain rice variety BL129

Grain size is one of the most important agronomic components of grain yield. Grain length, width and thickness are controlled by multiple quantitative trait loci(QTLs). To understand genetic basis of large grain shape and explore the beneficial alleles for grain size improvement, we perform QTL analysis using an F2 population derived from a cross between the japonica variety Beilu 129(BL129, wide and thick grain) and the elite indica variety Huazhan(HZ, narrow and long grain). A total number of eight major QTLs are detected on three different chromosomes. QTLs for grain width(q GW), grain thickness(q GT), brown grain width(q BGW), and brown grain thickness(q BGT) explained 7 7.67, 36.24, 89.63, and 39.41% of total phenotypic variation, respectively. The large grain rice variety BL129 possesses the beneficial alleles of GW2 and q SW5/GW5, which have been known to control grain width and weight, indicating that the accumulation of the beneficial alleles causes large grain shape in BL129. Further results reveal that the rare gw2 allele from BL129 increases grain width, thickness and weight of the elite indica variety Huazhan, which is used as a parental line in hybrid rice breeding. Thus, our findings will help breeders to carry out molecular design breeding on rice grain size and shape.