Stability evaluation of reference genes for real-time quantitative PCR normalization in Spodoptera frugiperda(Lepidoptera: Noctuidae)

Real-time quantitative PCR(qPCR) is a reliable and widely used technique for analyzing the expression profiles of target genes in different species, and reference genes with stable expressions have been introduced for the normalization of the data. Therefore, stability evaluation should be considered as the initial step for qPCR experiments. The fall armyworm Spodoptera frugiperda(J. E. Smith)(Lepidoptera: Noctuidae) is a polyphagous pest that consumes many plant species and seriously threatens corn production around the world. However, no studies thus far have examined the stability of reference genes in this pest. In this study, the expression profiles of the eight candidate reference genes of Actin, elongation factor 1 alpha(EF1α), elongation factor 2(EF2), glyceraldehyde-3-phosphate dehydrogenase(GAPDH), ribosomal protein L3(RPL3), ribosomal protein L13(RPL13), alpha-tubulin(α-TUB), and beta-1-tubulin(β-1-TUB) were obtained from S. frugiperda in different samples and the stability was evaluated by ΔCt, BestKeeper, geNorm, NormFinder, and RefFinder methods. The results of pairwise variation(V) calculated by GeNorm indicated two reference genes could be selected for normalization. Therefore, the combinations of the most stable reference genes for different experimental conditions of S. frugiperda were shown as follows: EF2 and RPL13 for developmental stages, RPL3 and β-1-TUB for larval tissue samples, EF2 and EF1α for the larval samples treated with different temperatures, RPL3 and EF1α for the larval samples under starvation stress, and RPL13 and EF1α for all the samples. Our results lay the foundation for the normalization of qPCR analyses in S. frugiperda and could help guarantee the accuracy of subsequent research.     

Selection of reference genes for RT-qPCR analysis of Phenacoccus solenopsis (Hemiptera: Pseudococcidae) sex-dimorphic development

Mealybugs, such as Phenacoccus solenopsis, are highly sexually dimorphic. Winged adult males present such remarkable morphological differences from females that, to the untrained eye, conspecific adults of both sexes of P. solenopsis may be considered as two different insect species. A method to investigate sex-dimorphic mechanisms is by evaluating gene expression using RT-qPCR. However, the accuracy and consistency of this technique depend on the reference gene(s) selected. In this study, we analyzed the expression of 10 candidate reference genes in male and female P. solenopsis at different development stages, using common algorithms including the ?Ct method, NormFinder, geNorm, BestKeeper, and a web-based analysis tool, RefFinder. The results showed that EF1-β, RP-L32 and RP-18 S were selected as the most stable genes by both the ?Ct method and NormFinder; TUB-α was the most stable gene identified by BestKeeper; and RP-L40 and RP-L32 were the most stable genes ranked by geNorm. RefFinder, a comprehensive analysis software, ranked the ten genes and determined EF1-β and RP-L32 as the most suitable reference genes for the various developmental stages in male and female P. solenopsis. Furthermore, the two most suitable reference genes were validated by examining expression of the juvenile hormone acid O-methytransferase(JHAMT) gene. Results of the validation portion of the study showed that JHAMT expression was sex-biased towards males and exhibited a dynamic and classic expression pattern among the P. solenopsis developmental stages. The results can help further our knowledge on the molecular mechanisms underlying sexual dimorphic development in P. solenopsis.     

产蛋前期和产蛋期籽鹅组织内参基因的稳定性

【目的】分析比较使用广泛的7个候选内参基因在产蛋前期和产蛋期籽鹅组织中的表达情况,筛选籽鹅组织基因表达分析中最佳的内参基因及其数目。【方法】应用实时定量反转录PCR技术,分别检测28S rRNA、18S rRNA、GAPDH、ACTB、HPRT1、SDH和TUB在产蛋前期与产蛋期健康籽鹅肝脏、肾脏、心脏、腿肌和卵巢组织中的表达情况,采用绝对定量方法确定基因拷贝数,然后分别使用geNorm和NormFinder程序进行数据分析。【结果】产蛋前期籽鹅各组织中7个内参基因表达稳定度的顺序分别为：GAPDH=HRPT1（0.195）＞TUB（0.244）＞28S rRNA（0.414）＞18S rRNA（0.495）＞ACTB（0.541）＞SDH（0.610）;产蛋期籽鹅各组织中7个内参基因表达稳定度的顺序分别为：GAPDH=28S rRNA（0.128）＞TUB（0.181）＞ACTB（0.192）＞SDH（0.221）＞HRPT1（0.316）＞18S rRNA（0.362）,且7个基因的配对差异分析分别为V2/3（产蛋前期）=0.084、V2/3（产蛋期）=0.069,内参基因的最适数目均为2个。【结论】产蛋前期和产蛋期籽鹅组织目的基因的表达分析中相对适合的内参基因分别为GAPDH和HRPT1、GAPDH和28S rRNA。     

Validation of Reference Genes for Quantitative Real-Time PCR in Laodelphax striatellus

The normalization of quantitative real-time PCR （qPCR） is important to obtain accurate gene expression data, and the most common method for qPCR normalization is to use reference genes. However, reference genes can be regulated under different conditions, qPCR has recently been used for gene expression study in Laodelphax striatellus, but there is no study on validation of the reference genes. In this study, five new housekeeping genes （LstrTUB1, LstrTUB2, LstrTUB3, LstrARF and LstrRPL9） in L. striatellus were cloned and deposited in the GenBank with accession numbers of JF728809, JF728810, JF728811, JF728807 and JF728806, respectively. Furthermore, mRNA expressions of the five genes and β-actin were measured by qPCR with insect samples of different instar at nymph stage, and the expression stabilities were determined by the software geNorm and NormFinder. As a result, ARF and RPL9 were consistently more stable than β-actin, while three TUB genes were less stable than β-actin. To determine the optimal number of reference genes used in qPCR, a pairwise variations analysis by geNorm indicated that two references ARF and RPL9 were required to obtain the accurate quantification. These results were fiarther confirmed by the validation qPCR experiment with chitinase gene as the target gene, in which the standard error of the mRNA quantification by using binary reference ARF-RPL9 was much lower than those by ARF, RPL9 or β-actin alone. Taken together, our study suggested that the combination of ARF-RPL9 could replace β-actin as the reference genes for qPCR in L. striatellus.     

平欧杂种榛实时荧光定量PCR内参基因的筛选与体系建立

【目的】构建中国榛属植物主要栽培种平欧杂种榛实时荧光定量PCR内参基因的筛选体系,并筛选稳定的内参基因,为榛属植物的基因表达分析提供内参基因,进而为其植物资源利用和创新育种研究提供理论基础。【方法】利用课题组前期对平欧杂种榛不同亲和性授粉、授粉后不同时间的雌蕊转录组测序数据,结合相关文献搜索,共选取12个候选内参基因;以平欧杂种榛主栽品种‘达维’的盛花期雌蕊、未伸长期雄花序、幼嫩叶片、花粉、一年生枝形成层、嫩茎、根尖、根蘖等8个不同组织器官为研究材料;通过反转录PCR初筛,实时荧光定量PCR检测表达量,并利用ge Norm、Norm Finder、Best Keeper、Delta Ct程序和Ref Finder在线网站评价内参基因的稳定性。【结果】反转录PCR初筛表明,12个候选内参基因引物的特异性良好,Cha STP5和Cha TF在不同组织器官材料中表达存在明显差异,其余候选内参基因在8个组织中均有表达。实时荧光定量PCR的表达谱分析表明,Ch18S r RNA的表达量最高,Cha STP5表达量最低,其余10个候选内参基因均为中等表达量;Cha STP5和Cha TF的稳定性最差,其余10个候选内参基因的稳定性处于中等水平。ge Norm、Norm Finder、Best Keeper和Delta Ct的结果表明,Cha Actin均排名第一,为最稳定的内参基因,Ch18S r RNA的排名均在前五,而其他候选内参基因在不同程序分析结果中的排名存在差异。稳定性综合分析表明,Cha Actin和Ch18S r RNA的稳定性良好,即在8个不同组织器官中表达量均一且在4个稳定性分析程序中均排名靠前,适合作为内参基因;ge Norm程序的变异系数分析则表明,选取6个内参基因便可对RT-q PCR的数据进行精准的标准化处理;相关性分析表明,4个程序均在0.01水平上呈现显著的相关性,Norm Finder和Delta Ct程序的相关性最高,Delta Ct与Best Keeper的相关性最低。【结论】建立了平欧杂种榛实时荧光定量PCR内参基因的筛选体系:以反转录PCR初筛引物,荧光定量PCR分析引物特性及基因表达,4个程序单独评价引物稳定性,Ref Finder综合分析选出最适稳定内参基因,并选出榛属植物8个不同组织器官中最为稳定的2个内参基因Cha Actin和Ch18S r RNA。     

植物乳杆菌Lp基因表达时内参基因的选择

实验以植物乳杆菌Lp为实验材料,用荧光定量PCR技术分析16S rRNA、Glyceraldehyde-3-phosphate dehydrogenas、L-lactate dehydrogenase以及rec A protein四个候选内参基因的表达情况。应用两种软件ge Norm和Norm Finder程序对实验结果进行分析。实验结果显示在植物乳杆菌Lp中,稳定值最小的是16S ribosomal RNA,用Norm Finder软件分析,稳定值最小的也是16S ribosomal RNA。揭示16S ribosomal RNA适合做植物乳杆菌正常生长状态下的内参基因。     

非生物胁迫下青花菜LncRNA内参基因的筛选

长链非编码RNA在植物抵御逆境胁迫中起着重要作用。适宜的内参基因是准确评价其表达水平的基础。本研究利用实时荧光定量PCR技术检测16个青花菜LncRNAs表达水平,并通过geNorm、NormFinder、BestKeerper软件进行表达稳定性分析。结果表明：青花菜的16个LncRNAs在不同逆境胁迫下表达稳定性存在差异。其中在弱光胁迫条件下, XLOC_000400表达最稳定;在低温胁迫条件下 XLOC_030832基因稳定性最好;在干旱和渍水胁迫条件下最稳定表达的内参基因分别是 XLOC_007087和 XLOC_012179;高温和盐胁迫处理下最稳定表达的内参基因均为 XLOC_007980。 XLOC_010342和 XLOC_007980在青花菜不同逆境胁迫下的表达稳定性较好。研究结果可为准确定量青花菜不同逆境胁迫下的LncRNAs提供合适的内参基因。     

甘菊内参基因CITUA的克隆与表达分析

根据前期工作已获得的甘菊α-tubulin基因EST序列，使用RACE技术获得了该基因的全长序列，命名为ClTUA。生物信息学分析表明，ClTUA基因全长cDNA序列为1 580 bp，编码432个氨基酸残基。利用MEGA40软件对推测的氨基酸序列进行系统关系分析发现，其为植物中Ⅰ类α-tubulin基因。RT PCR分析发现:ClTUA基因不仅在盐、干旱、冷、热、脱落酸和水杨酸各种非生物胁迫下稳定表达，而且在不同生长发育阶段的样本中稳定表达；而作为对照的两个内参基因，ClActin和26S rRNA基因在不同非生物胁迫下表达稳定，但在不同生长发育阶段的样本中表达强度不同。这一结果表明，ClTUA基因的表达稳定性优于ClActin和甘菊26S rRNA基因，可以作为内参基因用于甘菊抗逆性和生长发育过程中基因表达规律研究。      

幼龄小鼠小肠组织内参基因的选择

选择B2 M、ACTB、GAPDH、SDHA、HPRT1和ARBP共6个内参基因,研究其在幼龄小鼠小肠组织内的表达情况.结果表明:6个内参基因均可获得特异性扩增产物;经geNorm程序和NormFinder分析,6个内参基因稳定度由高到低为SDHA=HRPT1>ARBP>ACTB>GAPDH>B2 M;基因表达的稳定值分别为0.006(SDHA)、0.006(HRPT1)、0.007(ARBP)、0.018(ACTB)、0.029(GAPDH)、0.111(B2 M),最终筛选出SDHA和HRPT1 2个内参基因适合用于校正目的基因的表达.     

景宁木兰热胁迫下实时荧光定量PCR内参基因的筛选

高温对景宁木兰Magnolia sinostellata生长产生严重影响。通过筛选景宁木兰热胁迫下稳定表达的内参基因,可以为景宁木兰在高温条件下基因表达研究提供准确数据,达到对目的基因进行准确量化的目的。以热胁迫下景宁木兰1年生实生苗的根、茎、叶组织为材料,从转录组数据库中选取13个管家基因ACTIN-7（肌动蛋白基因-7）,CYP（亲环蛋白基因）,EF-1α（延伸因子-1α蛋白基因）,GAPDH（甘油醛-3-磷酸脱氢酶基因）,GTB（GTP结合蛋白基因）,NAC（NAC域蛋白基因）,NADP（异柠檬酸脱氢酶基因）,TEF（翻译延伸因子基因）,UBC（泛素化酶基因）,UBQ（多聚泛素蛋白基因）,α-TUB（α微管蛋白基因）,β-TUB（β微管蛋白基因）和18S（18S核糖体RNA）,通过Primer 5.0进行引物设计,琼脂糖电泳和溶解曲线分析验证引物特异性;利用实时荧光定量聚合酶链式反应（qRT-PCR）技术和geNorm,NormFinder和BestKeeper等3个内参分析软件研究候选内参基因在热胁迫下不同组织中的表达稳定性,并通过CSLD3和KOR 2个目的基因的表达分析验证其可靠性。13个内参基因的电泳结果均显示单一条带,溶解曲线也均显示单一峰,证明引物特异性良好;13对引物的扩增效率均在100%左右;内参软件综合分析得到,UBC,EF-1α和ACTIN-7是景宁木兰在热胁迫下较为稳定的内参基因,以3个单独的内参基因以及内参组合（EF-1α和ACTIN-7）为参照对CSLD3和KOR的表达模式进行校准,也显示了一致的表达水平。通过qRT-PCR技术和内参软件分析,UBC,EF-1α和ACTIN-7等3个内参基因在景宁木兰热胁迫下不同组织中稳定性较高,CSLD3和KOR等2个目的基因的表达也证实了其可靠性。因此,UBC,EF-1α和ACTIN-7可以作为景宁木兰热胁迫下稳定表达的内参基因。     

桂花组织基因表达中荧光定量PCR内参基因的筛选

为了筛选桂花Osmanthus fragrans不同组织基因表达分析中适合的内参基因,以桂花‘堰虹桂’O. fragrans‘Yanhong Gui’花蕾、盛开花序、嫩叶、成熟叶和1年生茎等5个不同组织为材料,利用实时荧光定量聚合酶链式反应（qRT-PCR）检测7个候选内参基因的表达水平,并利用geNorm,NormFinder和BestKeeper软件对各候选内参基因的表达稳定性进行评价,最后利用桂花不同组织中OfCRTISO1基因相对表达水平验证筛选的内参基因的可靠性。结果表明:综合3个软件的评价排序,确定不同组织中最佳内参基因为OfRAN1和OfUBC2,而Of18S是最差内参基因。OfCRTISO1基因相对表达水平分析证实,不同组织中qRT-PCR分析使用OfRAN1和OfUBC2等2个表达最稳定的基因组合,即可获得更为精确的基因表达结果。旨在为桂花组织间重要基因的定量表达分析提供科学依据。图 4 表 4 参34     

中国小麦花叶病毒(CWMV)侵染条件下小麦内参基因的选择

实时定量PCR(qRT-PCR)是分析功能基因表达水平的常用方法之一,qRT-PCR数据统计分析离不开合适内参基因的选择。为了选择中国小麦花叶病毒(Chinese wheat mosaic virus, CWMV)侵染条件下的小麦内参基因,本实验通过PCR扩增效率和扩增特异性分析,从10个持家基因中选择8个候选基因,然后以接种CWMV的小麦样品为材料,利用qRT-PCR技术进一步检测上述8个基因在CWMV侵染条件下小麦样品中的时空表达特性。基于这些数据,通过geNorm、NormFinder程序分析,结果表明,2个小麦基因(即26S和CDC)在CWMV侵染前后以及不同组织中表达最为稳定,26S和CDC组合可选作CWMV与小麦互作过程中功能基因表达分析的内参基因。     

磷胁迫下羊草的响应及磷响应相关基因表达分析

【目的】磷是植物生长发育所必需的大量营养元素,研究无机磷酸盐（inorganic phosphate,Pi）胁迫下羊草的响应,筛选不同浓度Pi胁迫下的内参基因,并分析Pi响应相关基因的表达,为羊草Pi胁迫响应的分子机制研究提供基础数据。【方法】以羊草幼苗为材料,进行不同浓度Pi处理培养,对羊草的株高和根长进行检测,利用钒钼黄比色法检测羊草植株中Pi的含量。根据羊草转录组数据选取7个候选内参基因,从NCBI核酸序列数据库选取1个候选内参基因,对羊草不同处理材料进行总RNA提取和cDNA合成,利用qRT-PCR对候选内参基因的表达进行检测,并通过geNorm、NormFinder和Bestkeeper软件对其稳定性进行评估。根据筛选获得的较稳定内参基因,对Pi响应基因的qRT-PCR检测数据进行相对定量分析。【结果】表型观测结果显示,无论是低Pi还是高Pi胁迫都使得羊草的生长减缓;株高对低Pi或缺Pi胁迫较为敏感,根长对高Pi胁迫较为敏感;并随着处理浓度的增加羊草中Pi的含量也增加。qRT-PCR溶解曲线分析显示8个候选内参基因均具有单一的溶解峰,基因表达谱分析表明8个候选内参基因的CT值范围是17.16—26.61,其中,LcGAPDH的表达丰度最高为17.16—20.22,Lc18SrRNA的表达丰度最低为23.28—26.61,CT值变异系数最小的为LcARPT（2.09%）,最大的为LcTUA（6.8%）。综合geNorm、NormFinder和Bestkeeper稳定性排名,通过计算几何平均数,获得8个候选内参基因综合稳定性排名,其中排名靠前的3个基因分别为Lc18SrRNA、LcCAP和LcEF1α,排名最后的2个基因为LcTUA和LcTUB。分别以Lc18SrRNA、LcCAP和LcEF1α作为内参基因,qRT-PCR相对定量表达分析结果显示,与对照相比,LcPHO1-2的表达受低Pi或者缺Pi诱导;LcPAP2的表达受高Pi诱导;而LcPAP27的表达同时受低Pi和高Pi下调。【结论】低Pi和高Pi胁迫均使羊草生长受阻,羊草地上组织与地下组织对Pi胁迫响应的模式不同。筛选出3个表达较为稳定的内参基因Lc18SrRNA、LcCAP和LcEF1α。LcPHO1-2和LcPAP2分别参与了羊草对低Pi和高Pi的应答响应,LcPAP27同时参与了羊草对低Pi和高Pi的响应进程。     

不同盐度下中华绒螯蟹胁迫相关基因的表达差异

通过对中华绒螯蟹在4个盐度梯度(0、10、20、30)下的胁迫试验,观察了4个类别的10个相关基因,即4个能量代谢相关基因、3个生长相关基因、2个应激性相关基因和1个渗透压调节相关基因的表达情况.结果表明:3个能量代谢相关基因(VATB、UBE、GAPDH)、1个应激性相关基因(GST)和渗透压调节相关基因(NAK)在不同盐度间的表达量存在显著差异(P0.05),而其他基因的表达量差异不显著(P0.05).应用Best Keeper、Norm Finder和Ge Norm 3个软件对各基因的稳定性进行分析发现:应激性相关基因(GST)和渗透压调节相关基因(NAK)对盐度变化的响应程度较高,表达不稳定;3个生长相关基因(S27、β-ACTIN、α-TUB)对盐度变化的响应程度低,表达稳定,可以作为不同盐度处理下基因差异表达的内参基因.     

Construction of a Food-Grade Expression Vector Based on pMG36e by Using an α-Galactosidase Gene as a Selectable Marker

Construction of a food-grade expression vector for application to lactic acid bacteria（LAB） is of importance for dairy fermentation system. An α-galactosidase（aga） gene encoding an enzyme degrading melibiose was amplified by PCR from the plasmid p RAF800 of Lactococcus lactis NZ9000. The aga gene was introduced into pMG36 e to substitute the p rimary antibiotic selectable marker of pMG36 e, resulting in construction of a new food-grade expression vector pMG36-aga. To testify the expression efficiency of exogenous gene in pMG36-aga, a 1.5 kb long α-amylase（amy） gene from Ba cillus li cheniformis was cloned by PCR and introduced into the plasmid pMG36-aga. The resultant plasimd pMG36-aga-amy was transformed into L. lactis ML23 by electroporation. The positive clones were selected with the medium containing melibiose as the sole carbon source. Th e selection efficiency of aga was 8.71×103 CFU with a standard deviation of 9.1×102 CFU ？g-1 DNA of pMG36-aga. Furthermore, the SDS-PAGE analysis showed that the pMG36-aga-amy expressed a 56.4 kDa protein which was the same as the putati ve molecular weight of α-amylase. The starch plate assay also indicated that L. lactis ML23 displayed high activity of α-amylase by expressing of amy gene of pMG36-aga-amy.