基因组学在作物抗逆性研究中的新进展

自然环境中各种生物和非生物胁迫是影响作物产量的巨大威胁。随着现代分子生物学的发展,从分子水平研究作物抵御逆境的机理已成为生态农业研究的一个重要任务,分子遗传学与生态学的整合诞生了生态基因组学即用基因组学的技术和手段研究生态学领域的问题。基因组学按其研究内容分为功能基因组学、结构基因组学和比较基因组学,本文从这3方面分别阐述了作物抵抗生物胁迫和非生物胁迫的生态基因组学研究进展,总结了基因组学在植物抗逆性研究中的一些新技术和新手段,特别是基于近几年发展起来的二代深度测序所带来的一系列高通量的检测方法与结果。①功能基因组学包含转录组学、表观遗传学、蛋白组学、相互作用组学、代谢组学和表型组学,本文侧重从植物抗逆的功能基因表达水平上的研究展开,重点探讨了转录组学和表观遗传学在植物抗逆研究的新进展,介绍了一些转录组学和表观遗传学研究技术,如基因芯片技术、RNA测序技术、SAGE、cDNA-AFLP、SSH、亚硫酸盐法、ChIP-Chip、ChIP-seq等;例举了一些转录因子基因家族在植物抗逆反应中的作用,总结其作用共性,结果表明不少抗逆基因受到胁迫后基因转录激活上有一定相关性,大多受激素信号转导途径所调控,很多抗逆途径最终都涉及到ABA信号传导通路并与衰老相关;植物的抗逆性受多个信号通路调控,对同一逆境响应常常需要不同的转录因子共同参与,而同一转录因子也有可能参与2个以上的不同抗逆反应;表观遗传学则指在不改变基因序列前提下,对DNA甲基化修饰、组蛋白翻译后修饰及小RNA介导的信号传导等,有证据表明其存在遗传印记作用。②结构基因组学主要利用QTL定位和DNA测序技术,确定植物基因组的遗传图谱和物理图谱,二代深度测序平台的建立使许多植物的全基因组测序成为可能。迄今为止,已有超过40种植物完成全基因组测序,越来越多的植物全基因组计划正在实施中或预计实施。③比较基因组学是基于功能基因组学和结构基因组学进而比较不同物种或不同群体间的基因组差异和相关性的研究,可分析逆境响应相关基因在进化过程中及在地理位置分布中的作用和意义,也同时为QTL定位及功能基因组学研究提供丰富信息。此外,还简要介绍并列举了一些网络共享作物抗逆的生物信息资源数据库。虽然基因组学在如何正确处理海量数据等问题上还存在瓶颈,但它提供的大量作物抗逆方面的基因组信息已为植物抗逆研究提供了众多线索与依据,为今后改良作物抗逆性的遗传育种工作带来了新启示。     

杂草基因组学研究进展及策略

本文分析了杂草的特异性和基因组特点,列出杂草基因组学研究的候选模式杂草植物种.论述了分子作图、比较基因组学、RNAi、TILLING、T-DNA插入突变和基因芯片等技术在杂草基因组学研究中的应用现状,以期全面认识和解析控制杂草特异性状的遗传基础和调控机理.重点阐述了杂草基因组学研究进展及加快杂草基因组学研究的技术策略,指出开展杂草基因组学的研究有利于建立科学控制杂草技术体系,改良作物产量和品质,从而提高农业的可持续生产力.     

科学家完成高梁基因组测序工作

美国能源部联合基因组研究所的科学家和几个其他合作伙伴研究所的科研人员发表了主要粮食饲料来源及高价值潜在生物能源作物一高粱,主要为全基因组序列及对其全基因组的分析。基因组数据将帮助科学家不仅在食物和饲料用途方面优化高粱和其他作物,同时也在生物燃料生产方面。高粱基因组的比较分析结果发表在2009年1月29目的“自然”杂志上。     

高粱基因组遗传图谱构建的研究进展

高粱 (Sorghum bicolor L. Moench) 基因组分子遗传连锁图谱的构建始于20世纪90年代。覆盖高粱全基因组的高密度分子遗传连锁图谱已构建完成，正在进行高粱遗传图谱与物理图谱的整合，把遗传连锁群与相应的染色体对应起来, 并已初步确定了染色体着丝粒、长短臂、核仁组织者区域(NOR)等染色体重要结构在遗传连锁图上的位置。随着研究的深入，高粱全基因组完全测序和高粱功能基因组学的研究即将全面启动.     

RNA沉默及其在基因功能研究中的应用

摘要: RNA沉默现象普遍存在于真核生物中，近年来对其作用机理的研究取得了很大的进展，发现并鉴定了一些参与该过程的蛋白和核酸分子。RNA沉默能够抵御病毒和转座子对基因组中重要基因的破坏。RNA沉默技术已经成为功能基因组学研究的重要手段之一。     

粘细菌纤维堆囊菌的基因组学研究现状

纤维堆囊菌（S.cellulosum）属于粘细菌中的堆囊菌属,它们能产生丰富的次级代谢产物,而且是目前基因组最大的原核生物,现已测序的S.cellulosum So ce56和So 0157-2分别拥有13.03 Mb和14.78 Mb的环状染色体。本文阐述了这两株纤维堆囊菌在序列的组装验证和基因组的分析注释等方面的完成情况,以及人们在测序的基础上,对其展开的结构基因组学、比较基因组学和功能基因组学的研究。通过介绍这两株已测序纤维堆囊菌的基因组学研究现状,我们总结了从纤维堆囊菌的全基因组序列中挖掘遗传信息的方法,为发现纤维堆囊菌中新的功能基因提供一些参考。     

高粱淀粉合成酶新基因SSV的鉴定与特征分析

淀粉合成酶(SS)是植物淀粉生物合成过程中的关键酶之一,目前已鉴定并揭示功能的淀粉合成酶有5个亚型。为利用丰富的基因组数据鉴定高粱基因组里的淀粉合成酶新亚型基因,本文利用生物信息学和分子生物学方法,首次鉴定并分离了编码高粱淀粉合成酶的新亚型基因Sb SSV,并对此基因的内含子-外显子结构、表达特性等进行了分析。结果显示,该基因的全长ORF为2 097 bp,其外显子数量、长度及内含子的位置分布等与玉米和水稻的直系同源基因基本一致,推导的蛋白具有细菌糖原合成酶和植物淀粉合成酶特有的糖基催化和糖基转移保守结构域。系统进化分析表明,Sb SSV与已知的SSIV亚型亲缘关系最近,推测本研究鉴定的Sb SSV基因编码高粱淀粉合成酶新亚型。定量PCR分析表达特性结果显示Sb SSV主要在高粱叶片中表达,其表达受光诱导,具有昼夜节律特性。研究结果可为深入揭示和完善植物淀粉合成代谢机制,以及改良植物产量和品质提供理论基础。     

从奶牛的基因组中“挤奶”

驯化的奶牛（Bos taurus）不仅是人类农业文明的一部分,同时在系统进化树中作为一个不同于人类和啮齿类的进化分枝,在比较基因组学中也受到欢迎。两个组装奶牛基因组为进化基因组学和牲畜育种提供了一个有价值的资源,对这些序列数据的分析使我们可以一窥牛奶产生的进化过程及驯化、育种对奶牛基因组的影响。     

科学家完成高粱基因组测序工作

美国能源部联合基因组研究所的科学家和几个其他合作伙伴研究所的科研人员发表了主要粮食饲料来源及高价值潜在生物能源作物—高粱,主要为全基因组序列及对其全基因组的分析。基因组数据将帮助科     

PCR-SSCP技术与比较基因组学结合定位棉花Li1基因

聚合酶链式反应-单链构象多态性(polymerase chain reaction-single strand conformation polymorphism,PCR-SSCP)作为一种能检测基因组间DNA碱基微小差异的技术手段,具有操作简便、快捷且灵敏度高等优点.比较基因组学近年来已经成为研究生物基因组的最主要手段之一;大量基因组序列的产生为通过比较基因组学开发新标记和定位目标基因提供了大量的DNA序列资源.本研究以李氏超短纤维突变体(Ligon lintless-1,Li1)为材料,定位Li1基因,针对PCR扩增产物片段较大的样品(＞400bp)进行PCR-SSCP技术的优化,用己发表的拟南芥(Arabidopsis thaliana)和棉花(Gossypium spp.)D基因组DNA序列为参考,探索PCR-SSCP技术与比较基因组学结合开发新标记应用于棉花基因定位的可能性.结果表明,电压为150V,胶浓度为10％,电泳温度为4℃时电泳结果最好;上样缓冲液与PCR扩增目的片段比例为5∶1为最佳比例.利用上述优化的PCR-SSCP技术将根据棉花与拟南芥同线性区段开发的分子标记构建了一个由28个标记组成的长度为149.6 cM的遗传图,该区域包含4个功能上与Li1位点密切相关的基因.此外,利用D基因组序列开发的标记构建了一个由17个SSCP标记和Li1位点组成,跨越40.3cM的遗传图谱,距其最近的两端标记W058和P095分别为0.6和0.3 cM.本研究为棉花Li1基因的精细定位及其候选基因的克隆提供了理论基础.     

Assessment of farmers’ perceptions of production constraints,and their trait preferences of sorghum in western Ethiopia: implications for anthracnose resistance breeding

Sorghum, Sorghum bicolor (L.) Moench is an important food security crop widely grown by smallholder farmers in sub-Saharan Africa (SSA), including Ethiopia. In SSA, the potential of sorghum production and productivity has not been realised due to an array of constraints. Colletotrichum sublineolum disease is one of the main biotic constraints causing significant yield losses. The objectives of this study were to assess farmers’ perception, preferences and constraints to sorghum production and productivity in western Ethiopia, and to identify key drivers for anthracnose resistance breeding. A participatory rural appraisal study was undertaken in six selected districts in the East Wellega and West Shewa Administrative Zones in Ethiopia. Data were collected through structured questionnaires involving 165 respondent farmers. Further focus group discussions were held with 180 farmers and development agents. Sorghum is the third most preferred cereal crop after Eragrostis tef and Zea mays in western Ethiopia. About 79% of interviewed farmers cultivated sorghum during the study season. Farmers perceived that sorghum production is constrained by anthracnose disease, bird attack, loose smut and covered smut diseases. The most important farmer-preferred traits in sorghum varieties in the study areas were anthracnose resistance and tolerance to bird attack. Breeding sorghum varieties with the farmer-preferred traits is an important consideration to enhance productivity and adoption of improved sorghum cultivars in western Ethiopia.     

Interactions calcium‐magnesium ‐ potassium chez le sorgho‐grain.

Abstract

The interactions of major cations (K,Ca,Mg) are studied in Sorghum (Sorghum dochna F.); the nutritive solutions are deficient or not, in magnesium. The mineral contents of the plants grown on the reference solution are compared to those of two solutions, in which magnesium is replaced by calcium or potassium. The limit threshold of deficiency does not affect the yield of plants, but reduces strongly the content of magnesium. On the other hand, no variation of calcium is observed since the magnesium substitution is effected by potassium. The experiments do not clearly show a Mg/Ca interaction in Sorghum.     

发酵牛粪对苏丹草根系丛枝菌根（AM）真菌侵染及磷吸收效率的影响

通过温室盆栽试验,研究接种苏格兰球囊霉(Glomus caledonium)条件下添加不同比例发酵牛粪(0.33%、0.50%和1.00%)对苏丹草(Sorghum sudanense)根系丛枝菌根(AM)真菌侵染率、土壤孢子密度、植株生物量与根冠比及根系磷(P)吸收效率的影响。结果发现,与对照相比,接种AM真菌处理植株地上部生物量趋于下降、根冠比显著提高(p<0.05),在此基础上添加0.33%或0.50%发酵牛粪处理土壤孢子密度、植株根系生物量和AM真菌侵染率均趋于升高,根冠比没有明显变化,根系P吸收效率显著提高(p<0.05);添加1.00%发酵牛粪显著提高土壤孢子密度、植株生物量和根系AM真菌侵染率(p<0.05),根冠比与仅接种AM真菌处理相同,根系P吸收效率则达到仅接种AM真菌处理的1.83倍。结果表明,添加1.00%发酵牛粪对苏格兰球囊霉扩繁及其宿主植物P吸收均具有突出促进作用。     

Interactions calcium ‐ potassium ‐ magnesium chez le sorgho‐grain

Abstract

Absorption and accumulation of calcium in hydro— ponic solutions, deficient or not in calcium, are studied on whole plants of Sorghum (Sorghum dochna F.), In deficient lots, calcium is replaced either by magnesium (Ca/Mg lot), or by potassium (Ca/K lot). The limit threshold of defiency retained, does not modify, on the 26 day of culture (end of the experience) the yield of different lots compared with the control. The principal modifications in cation content are noted in leaves: plants grown in the Ca/Mg solution show a higher Ca content than plants in a Ca/K solution. As a consequence of saturation with potassium the substitution of Ca in the two deficient lots is effected by magnesium.     

模拟酸雨对杂交苏丹草种子萌芽及幼苗生长的影响

采用不同pH值的模拟酸雨对杂交苏丹草皖草2号进行处理,测定对其种子萌发和幼苗生长的影响。试验结果表明,酸雨会导致土壤酸化,pH值大于4.0的酸雨对杂交苏丹草种子的发芽和幼苗生长无不良影响,pH值低于4.0的酸雨对杂交苏丹草种子的发芽和幼苗生长具有抑制作用,且pH值越低,所产生的不利影响越大。     

An examination of Fe deficiency stress response in relation to Fe uptake in two sorghum hybrids and their parent cultivars

Two sorghum (Sorghum bicolor L. Moench) hybrids CSH‐10 and ‐ 11 and their parent cultivars 296‐A, SB‐1055 and MR‐715 were examined for their tolerance to Fe‐deficiency stress, and also Fe uptake. It was observed that there was greater reduction of pH of the nutrient media and more rapid recovery from chlorosis only in the female parent 296‐A, and to some degree in the hybrids, but not in the male parents. The results indicated that Fe uptake‐translocation were inversely related to their Fe stress tolerance.     

Effects of Soil Alkalization on Osmotic Adjustment and Ion Balance in Sorghum (Sorghum Bicolor L.)

Sorghum (Sorghum bicolor L.) was grown on an alkalinized plot for 90 days. Inorganic ions and compatible solutes were measured to investigate the physiological adaptations by which sorghum tolerates natural alkaline stress. Plant growth was clearly inhibited. The stress led to increased Na⁺ content in roots but had only a small effect on Na⁺ accumulation in leaves; K⁺ content in roots was lower than that in leaves and stems; and Na⁺ content and Na⁺/K⁺ ratio were much higher in roots than in leaves and stems. These suggest that maintaining a substantially higher osmotic potential in roots for greater uptake of water and restricting the spread of Na⁺ to shoots are physiological adaptations to alkalinity. Soluble sugar was the main osmolyte in roots, stems, and leaves; proline, amino acids, and oxalates contributed to osmotic regulation slightly, and it was noteworthy that K⁺ played a major role in osmotic regulation in leaves.     

Phosphate buffer–extractable organic nitrogen as an index of soil‐N availability for sorghum and pearl millet

The availability of soil nitrogen (N) is usually quantified by the amount of mineralized N as determined after several weeks of soil incubation. Various alternative methods using chemical solvents have been developed to extract the available organic N, which is easily mineralized. We compared one such solution, neutral phosphate buffer (NPB), with conventional incubation and 0.01 M–CaCl₂ extraction, as measures of soil N available to two major cereal crops of the semiarid tropics, based on the total N uptake by plants in a pot experiment. Mineralized N had the highest correlation with N uptake by pearl millet (Pennisetum glaucum L., r = 0.979***) and sorghum (Sorghum bicolor [L.] Moench, r = 0.978***). NPB‐extractable N was also highly correlated with N uptake (pearl millet, r = 0.876***; sorghum, r = 0.872***). Only one major peak was detected when NPB extracts were analyzed using size‐exclusion high‐performance liquid chromatography, regardless of soil properties. In addition, the organic N extracted with NPB was characterized by determining the content of peptidoglycan, the main component of bacterial cell walls. Although the characteristics of NPB‐extractable organic N are still unclear, it offers a promising quick assay of available N.     

Sorghum genotype differences to leaf “red‐speckling”; induced by phosphorus 1

Sorghum [Sorghum bicolor (L.) Moench] plants grown in nutrient solutions, sand, and soil under greenhouse or growth chamber conditions developed a lower leaf “red‐speckling”; which was induced by phosphorus (P). As P in solution increased, the intensity of the “red‐speckling”; increased. Although the severity of “red‐speckling”; was not directly related to leaf P concentration, leaves with more severe symptoms had higher P concentrations. KS35, ‘Martin’, and ‘Plainsman’ developed severe symptoms, CK60‐Korgi, SC369–3‐1JB, and TX415 developed intermediate symptoms, and NB9040 developed no symptoms when grown at relatively low levels of P (10 to 20 umol per plant). Organic sources of P induced more severe “red‐speckling”; than inorganic sources. The severity of “red‐speckling”; induced by P compounds followed the sequence of gyceryl > ethyl ammonium = phenyl > potassium dihydrogen > calcium meta > calcium dibasic > calcium tribasic > ferric > calcium pyro = ferrous = aluminum phosphates. “Red‐speckling”; on young sorghum leaves may be caused by excess P. This excess or toxic P “red‐speckling”; occurred at P levels lower than had normally been considered or expected.     

Ultraviolet leaf reflectance of common urban trees and the prediction of reflectance from leaf surface characteristics

The spectral reflectance and transmittance over the wavelength range of 250–700 nm were evaluated for leaves of 20 deciduous tree species and leaf sheaths of five isogenic wax variants of Sorghum bicolor differing in visible reflectance due to cuticular waxes. Using the sorghum sheath reflectance and cuticle surface characteristics as a model, it was concluded that tree leaf reflectance above 0.06 was likely due to the presence of variously-shaped fine epicuticular wax structures on the leaf surface. Increasing the density of sub-micron wax structures corresponded to an enhanced ultraviolet (UV) reflectance over the PAR reflectance of a given leaf surface—either S. bicolor sheath or tree leaf. Amorphous globular epicuticular wax structures did not appear to scatter UV as well as wax filaments or vertical plates in varying patterns even when the dimensions of the structures were similar. Further work is needed to clarify this relationship and the influence of cellular pigments on subsurface contributions to the reflectance.