An efficient method for constructing a random insertional mutant library for forward genetics in Nannochloropsis oceanica

Insertional mutation,phenotypic evaluation,and mutated gene cloning are widely used to clone genes from scratch.Exogenous genes can be integrated into the genome during non-homologous end joining(NHEJ)of the double-strand breaks of DNA,causing insertional mutation.The random insertional mutant library constructed using this method has become a method of forward genetics for gene cloning.However,the establishment of a random insertional mutant library requires a high transformation efficiency of exogenous genes.Many microalgal species show a low transformation efficiency,making constructing random insertional mutant libraries difficult.In this study,we established a highly efficient transformation method for constructing a random insertional mutant library of Nannochloropsis oceanica,and tentatively tried to isolate its genes to prove the feasibility of the method.A gene that may control the growth rate and cell size was identified.This method will facilitate the genetic studies of N.oceanica,which should also be a reference for other microalgal species.

Genetic Analysis of a Small Grain Mutant Induced by T-DNA Insertion in Rice

[Objective] The aim of this study is to understand the genetic characteristics of a grain shape mutant and its possible role in genetic improvement of grain yield in rice. [Method] On the basis of the collection of T-DNA tag lines, the progeny of homozygous plants carrying T-DNA insertion were screened for mutants with mutated phenotypes. The genetic analysis of the mutant and test for the linkage between the mutated phenotype and the T-DNA insertion were carried out to determine its genetic characteristics. [Result] In the present study, a grain shape mutant induced by T-DNA insertion in rice was identified, which showed small grain. Genetic analysis of the mutant showed that the two types of phenotype, normal and small grain in the segregating populations derived from the T-DNA heterozygotes, fit the ratio of 3∶1. Test for Basta resistance showed that all the mutants were resistant while the normal plants segregated for resistant and susceptible by the ratio of 2∶1. The results indicated that the mutant phenotype cosegregated with Bar gene. The small grain mutant caused by T-DNA insertion was confirmed by PCR amplification aiming at T-DNA. [Conclusion] The grain shape mutant is useful for isolation of the tagged gene and genetic improvement in rice.

Isolation of T-DNA flanking plant DNA from T-DNAinsertional embryo-lethal mutants of Arabidopsis thaliana by plasmid rescue technique

Three T-DNA insertional embryonic lethal mutants from NASC (The Nottingham Arabidopsis Stock Center)were first checked with their segregation ratio of abortive and normal seeds and the copy number of T-DNA insertion. The N4081 mutant has a segregation ratio of 1:3.04in average and one T-DNA insertion site according to our assay It was therefore chosen for further analysis. To isolate the joint fragment of T-DNA and plan DNA, the plasmid rescue technique waJs used. pEL-7, one of plasmids from left border of T-DNA, which contained pBR322 was selected from ampicillin plate. The T-DNA fragment of pEL-7 was checked by restriction enzyme analysis and Southern Blot. Restriction analysis confirmed the presence of known sites of EcoRI, PstI and PvuII on it.For confirming the presence of flanking plant DNA in this plasmid, pEL-7 DNA was labeled and hybridized with wild type and mutant plant DNA. The Southern Blot indicated the hybridization band in both of them. Furthermore, the junction of T-DNA/plant DNA was subcloned into bluescript SK+ and sequenced by Applied Biosystem 373A Sequencer. The results showed the 822 bp fragment contained a 274 bp sequence, which is 99.6%homolog (273bp/274 bp) to Ti plasmid pTi 15955 DNA.Ten bp of left 25 bp border repeat were also found in the juction of T-DNA and Plant DNA.Taken together, pEL-7 should contain a joint fragment of T-DNA and flanking plant DNA. This plasmid DNA could be used for the isolation of plant gene, which will be helpful to elucidate the relationship between gene function and plant embryo development.

Effort and Contribution of T-DNA Insertion Mutant Library for Rice Functional Genomics Research in China:Review and Perspective

With the completion of the rice （Oryza sativa L.） genome-sequencing project, the rice research community proposed to characterize the func- tion of every predicted gene in rice by 2020. One of the most effective and high-throughput strategies for studying gene function is to employ genetic mutations induced by insertion elements such as T-DNA or transposons. Since 1999, with support from the Ministry of Science and Technology of China for Rice Functional Genomics Programs, large-scale T-DNA insertion mutant populations have been generated in Huazhong Agricultural University, the Chinese Academy of Sciences and the Chinese Academy of Agricultural Sciences. Currently, a total of 372,346 mutant lines have been generated, and 58,226 T-DNA or Tos17 flanking sequence tags have been isolated. Using these mutant resources, more than 40 genes with potential applications in rice breeding have already been identified. These include genes involved in biotic or abiotic stress responses, nutrient metabolism, pollen development, and plant architecture. The functional analysis of these genes will not only deepen our understanding of the fundamental biological questions in rice, but will also offer valuable gene resources for developing Green Super Rice that is high-yielding with few inputs even under the poor growth conditions of many regions of Africa and Asia.

玉米大斑病菌ATMT突变体库的构建及其分析

【目的】利用农杆菌(Agrobacterium tumefaciens)介导的遗传转化技术,对玉米大斑病菌(Setosphaeria turcica)进行转化,构建ATMT突变体库,为从分子水平上揭示病菌的致病机理奠定基础。【方法】以带有重组双元载体的农杆菌对玉米大斑病菌进行转化,利用潮霉素B进行筛选,对抗性稳定的转化子进行PCR检测,构建玉米大斑病菌ATMT突变体库;从突变体库中随机选取一定数量的突变体,对其菌落形态、菌丝及分生孢子发育、致病性等进行分析。【结果】获得了1 265株玉米大斑病菌T-DNA插入突变体;从中随机选取36株突变菌株,对其进行抗性筛选和PCR检测,发现潮霉素磷酸转移酶基因已整合进入野生型菌株的基因组中,且能够稳定遗传;与野生型菌株相比,在供试的菌株中,大部分菌株菌落形态和生长速率没有发生明显改变。生长速率明显减慢的菌株占总数的13.8%,明显加快的菌株占16.7%;发现了2株分生孢子形态发生明显改变的菌株,占菌株总数的5.6%;产孢量明显增大的菌株占5.6%,产孢量减少的菌株占13.5%;分生孢子萌发率发生明显改变的菌株占16.6%;发现了1株致病性明显增强的菌株,占菌株总数的2.8%。【结论】构建了玉米大斑病菌ATMT突变体库,并对突变体库进行了初步分析,将为克隆玉米大斑病菌生长发育和致病性相关基因奠定基础。

棉花黄萎病菌插入突变体库的构建及致病相关基因DVK1的克隆与鉴定

利用ATMT(Agrobacterium tumefaciens-mediated transformation)技术自建Verticillium dahliae强致病力落叶型菌株T-DNA插入突变体库,共获得5000个转化子;随机挑选1000个转化子进行致病力鉴定,筛选获得5株致病力衰退的突变体。挑选致病力下降最为明显的突变体d1,通过TAIL-PCR技术最终获得一段长3237 bp的DVK1全长cDNA序列,编码1079个氨基酸的蛋白。基于DNA序列比对发现,DVK1基因含有2个内含子,分别为52 bp和36 bp。进一步比对发现T-DNA插入到DVK1基因启始密码上游740 bp的启动子中。通过遗传互补实验d1恢复了致病性,进一步证明DVK1基因与黄萎菌致病性相关。

插入突变在功能基因组学研究中的应用

插入突变库的构建是功能基因组学研究的一个重要内容,可为确定基因的功能提供最直接的证据。构建插入突变库的方法有T-DNA插入突变、转座子插入突变和质粒介导的插入突变。本文分别介绍三种方法的原理及其在功能基因组学研究中的应用和研究进展。

TEAseq-based identification of 35,696 Dissociation insertional mutations facilitates functional genomic studies in maize

In plants,transposable element(TE)-triggered mutants are important resources for functional genomic studies.However,conventional approaches for genome-wide identification of TE insertion sites are costly and laborious.This study developed a novel,rapid,and high-throughput TE insertion site identification workflow based on next-generation sequencing and named it Transposable Element Amplicon Sequencing(TEAseq).Using TEAseq,we systemically profiled the Dissociation(Ds)insertion sites in 1606 independent Ds insertional mutants in advanced backcross generation using K17 as background.The Ac-containing individuals were excluded for getting rid of the potential somatic insertions.We characterized 35,696 germinal Ds insertions tagging 10,323 genes,representing approximately 23.3%of the total genes in the maize genome.The insertion sites were presented in chromosomal hotspots around the ancestral Ds loci,and insertions occurred preferentially in gene body regions.Furthermore,we mapped a loss-of-function AGL2 gene using bulked segregant RNA-sequencing assay and proved that AGL2 is essential for seed development.We additionally established an open-access database named MEILAM for easy access to Ds insertional mutations.Overall,our results have provided an efficient workflow for TE insertion identification and rich sequence-indexed mutant resources for maize functional genomic studies.

Comparing Genetic Characteristics of Retrotransposon TOS17 During Different Tissue Culture Processes in the Rice Cultivars Nipponbare and Shishoubaimao

As a retrotransposon, TOS17 was a useful tool for rice genetic and functional genomic research. To ascertain the feasibility of constructing a TOS17 insertion mutation library in the rice cultivar Shishoubaimao, the genetic and expression characteristics of TOS17 were analyzed. We made solid and suspension tissue cultures and confirmed the copy numbers of TOS17 at different time points in both tissue culture processes by real-time quantitative PCR （RT-qPCR）. Three primary copies of TOS17 were detected in naturally grown Shishoubaimao. TOS17 was activated by tissue culture, and the copy numbers of TOSI7 increased along with a prolonged tissue culture time in both the Nipponbare and the Shishoubaimao cultivars. Therefore, Shishoubaimao is a potential candidate for constructing a TOS17 insertion mutant library. Compared with Nipponbare, TOS17 was more active in Shishoubaimao during tissue culture. Higher copy numbers of TOS17 were obtained with the suspension tissue culture process than with the solid tissue culture process over the same time courses. We concluded that 3-4 months of suspension tissue culture time is suitable for constructing a TOS17 insertion mutant library in Shishoubaimao.

黑曲霉纤维素酶突变子T-DNA插入位点的遗传分析及性质鉴定

采用羧甲基纤维素钠筛选培养基,对黑曲霉(Aspergillus niger)T-DNA突变子文库进行筛选,分离到一株纤维素酶分泌水平较低的菌株AN-108,为野生型菌株的83.3%。进一步测定该突变子固体发酵的纤维素酶活力,与野生型菌株相比没有明显差别,推测与固体发酵培养基中含有的天然糖类有关。在添加不同糖类的CMC-Na平板上培养该突变子,菌落周围均出现较明显的水解圈,结果显示糖类可能作为诱导物克服突变带来的影响。为了确定突变子AN-108中何种基因被阻断,采用反向PCR方法分析了T-DNA插入位点的序列,获得序列经过比对分析发现,该序列与黑曲霉An14g03730同源程度达90%,编码富含脯氨酸蛋白(proline-rich protein,PRP)。