Cloning and sequence characteristics of the genomic gene of a rice metallothionein

Northern blot analysis showed that a metallothionein gene, ricMT is expressed strongly in the stem of rice with an expression level that could be more than 100-fold stronger than in leaf blades. The results suggest that the 5’ upstream region flanking the coding sequence of the ricMT may contain a fairly strong promoter To elucidatr its regulation and promoter structure, the genomic clones of ricMT were screened out from a rice genomic library and a fragment of about 4084 bp was sequenced. The fragment included a 5’ upstream region of ca. 2970 bp, a transcription region of ca. 690 bp and a 3’ downstream region of ca. 420 bp. Computer analysis of the sequence homology showed that the 5’ upstream region included a putative TATA box, a putative CAAT box, and a typical metal-responsive element TGCGCGCG. The results will promote further understanding of the mechanisms of gene regulation and metal response of plant metallothionein proteins.

Identification of candidate genes for drought stress tolerance in rice by the integration of a genetic (QTL) map with the rice genome physical map

Genetic improvement for drought stress tolerance in rice involves the quantitative nature of the trait, which reflects the additive effects of several genetic loci throughout the genome. Yield components and related traits under stressed and well-water conditions were assayed in mapping populations derived from crosses of Azucena×IR64 and Azucena×Bala. To find the candidate rice genes underlying Quantitative Trait Loci (QTL) in these populations, we conducted in silico analysis of a candidate region flanked by the genetic markers RM212 and RM319 on chromosome 1, proximal to the semi-dwarf (sd1) locus. A total of 175 annotated genes were identified from this region. These included 48 genes annotated by functional homology to known genes, 23 pseudogenes, 24 ab initio predicted genes supported by an alignment match to an EST (Expressed sequence tag) of unknown function, and 80 hypothetical genes predicted solely by ab initio means. Among these, 16 candidate genes could potentially be involved in drought stress response.

Expression and regulatory network of long noncoding RNA in rats after spinal cord hemisection injury

Long noncoding RNAs(lncRNAs)participate in a variety of biological processes and diseases.However,the expression and function of lncRNAs after spinal cord injury has not been extensively analyzed.In this study of right side hemisection of the spinal cord at T10,we detected the expression of lncRNAs in the proximal tissue of T10 lamina at different time points and found 445 lncRNAs and 6522 mRNA were differentially expressed.We divided the differentially expressed lncRNAs into 26 expression trends and analyzed Profile 25 and Profile 2,the two expression trends with the most significant difference.Our results showed that the expression of 68 lncRNAs in Profile 25 rose first and remained high 3 days post-injury.There were 387 mRNAs co-expressed with the 68 lncRNAs in Profile 25.The co-expression network showed that the co-expressed genes were mainly enriched in cell division,inflammatory response,FcγR-mediated cell phagocytosis signaling pathway,cell cycle and apoptosis.The expression of 56 lncRNAs in Profile2 first declined and remained low after 3 days post-injury.There were 387 mRNAs co-expressed with the 56 lncRNAs in Profile 2.The co-expression network showed that the co-expressed genes were mainly enriched in the chemical synaptic transmission process and in the signaling pathway of neuroactive ligand-receptor interaction.The results provided the expression and regulatory network of the main lncRNAs after spinal cord injury and clarified their co-expressed gene enriched biological processes and signaling pathways.These findings provide a new direction for the clinical treatment of spinal cord injury.

水稻基因图谱绘制成功对世界粮食和环境问题的意义

我国科学家率先成功绘制出水稻基因组草图 ,在提供绿色基因资源、加速全球第二次绿色革命———基因革命的前进步伐 ,解决世界粮食安全问题和环境保护方面作出了重要贡献。

水稻子预44和江南香糯基因组比较鉴定稻瘟病抗性相关基因

【目的】子预44是一具有广谱持久稻瘟病抗性的云南地方粳稻品种。为了鉴定子预44中候选稻瘟病抗性相关基因,【方法】本研究利用高通量测序技术(High-throughput sequencing)对子预44和感病水稻江南香糯进行了全基因组测序。而后使用软件GATK(3.4-46)对高质量测序结果进行SNP和InDel的检测和统计,进一步筛选出子预44和江南香糯DNA水平存在SNPs/InDels多态性抗病相关基因。【结果】通过HiseqX10 PE150平台分别获得了4118170045 bp和2995054509 bp子预44和江南香糯的基因组数据,比对到参考基因组(Ensembl release31)的比对率分别为98.56%和98.30%。在抗病水稻子预44和感病水稻江南香糯之间鉴定了922个纯合突变的差异抗病相关基因。结合基因定位结果,在子预44中鉴定了一个新的抗稻瘟病候选基因。【结论】研究结果为子预44中抗稻瘟病新基因的克隆提供了参考,对子预44广谱持久抗瘟分子机制的研究奠定了基础。

水稻特大穗恢复系R1126株叶型性状遗传基础剖析

结合全基因组重测序结果和已克隆基因信息分析了水稻特大穗恢复系R1126株叶型相关基因sd1、IPA1的编码区序列,R1126的sd1基因与低脚乌尖一致,为半矮秆基因型;IPA1基因编码区序列与日本晴一致。利用株叶型差异明显的黄华占和R1126为亲本构建F2群体,对控制株叶型相关性状的QTL进行了初步定位,共定位到21个QTL,分布于第3,4,6,8,9和12染色体的7个区间。其中,第8染色体RM80—RM447区间的贡献率最大,对剑叶宽、倒2叶长、倒2叶宽、倒2叶重、倒3叶长、倒3叶重、茎周长、秆重的贡献率分别为4.34%,19.55%,1.99%,36.41%,13.07%,9.92%,36.53%和8.92%;其次是第4染色体的RM303—RM6748区间,对剑叶宽、倒2叶宽、倒3叶宽、倒3叶重、茎周长、倒2节间长、秆重的贡献率分别为23.8%,31.56%,6.87%,19.25%,1.97%,13.9%和17.13%。这2个区间为主效或多效性QTL聚集区间,其增效QTL均来自R1126。

水稻特大穗恢复系R1126的穗部性状遗传基础剖析

结合全基因组重测序结果和已克隆基因信息分析了水稻特大穗恢复系R1126穗部性状相关基因(Gn1a、LP、Ghd7、Ghd8)的编码区序列,同日本晴相比,R1126的Gn1a基因有1个InDel和3个SNP变异,导致了编码的蛋白产物差异,可增加每穗总粒数,LP基因编码区发生了1个同义突变;R1126的Ghd7、Ghd8基因与明恢63一致。利用穗部性状差异明显的黄华占和R1126为亲本构建F2群体,对R1126穗部性状QTL进行初步定位,定位到4个控制每穗总粒数、3个控制穗长、1个控制一次枝梗数和4个控制二次枝梗数的QTL。其中,第8染色体RM80—RM447区间的贡献率最大,对一次枝梗数、穗长、二次枝梗数和每穗总粒数的贡献率分别达56.67%,49.89%,10.31%和9.67%;其次是第4染色体RM303—RM6748区间,对二次枝梗数和每穗总粒数的贡献率分别为11.95%和7.21%;第3染色体SFP3_3—RM1164区间对二次枝梗数和每穗总粒数的贡献率分别达11.61%和8.09%。

水稻外源DNA导入变异系与受体的农艺性状差异及其基因变异分析

野威B是将小粒野生稻基因组DNA通过穗茎注射法导入杂交水稻保持系V20B后创造的变异系,其在株型、稻米品质和产量相关性状上都发生了明显变化。通过全基因组测序,比较分析了野威B与V20B中27个可能与变异性状有关的基因,发现野威B在与株型相关的基因中存在21个SNP和30个InDel,其中有10个SNP和4个InDel位于编码序列;在稻米品质相关的基因中存在124个SNP和28个InDel,其中25个SNP位于编码序列;在产量相关基因中存在65个SNP和42个InDel,其中有10个SNP和2个InDel位于编码序列。位于编码序列的变异中,有24个SNP为错义突变,导致部分编码氨基酸的极性或电荷状态改变,有4个InDel变异为移码突变,导致编码的氨基酸序列改变。为寻找引起变异系野威B表型变化的关键基因及位点提供依据。

全基因组分析策略应用于水稻抗稻瘟病基因鉴定的研究和进展

水稻是世界上最重要的粮食作物之一。稻瘟病严重危害水稻生产,每年可造成水稻大面积减产。利用水稻抗病基因资源,培育抗病水稻品种,是防治稻瘟病的经济有效、安全的方法。基于遗传定位及图位克隆,已有一百多个抗稻瘟病基因得到鉴定,其中有二十多个基因被克隆。近年来,全基因组分析策略进一步推动了水稻抗稻瘟病基因鉴定的发展。本研究简要总结了水稻抗稻瘟病基因的定位和克隆,并概述了全基因组分析策略应用于水稻抗稻瘟病基因鉴定的研究和进展。