International journal of plant genomics最新文献_第2页

Phylogenetic, Molecular, and Biochemical Characterization of Caffeic Acid o-Methyltransferase Gene Family in Brachypodium distachyon. 短叶藻咖啡酸o-甲基转移酶基因家族的系统发育、分子和生化特征。

International journal of plant genomics Pub Date : 2013-01-01 Epub Date: 2013-01-17 DOI: 10.1155/2013/423189

Xianting Wu, Jiajie Wu, Yangfan Luo, Jennifer Bragg, Olin Anderson, John Vogel, Yong Q Gu

{"title":"Phylogenetic, Molecular, and Biochemical Characterization of Caffeic Acid o-Methyltransferase Gene Family in Brachypodium distachyon.","authors":"Xianting Wu, Jiajie Wu, Yangfan Luo, Jennifer Bragg, Olin Anderson, John Vogel, Yong Q Gu","doi":"10.1155/2013/423189","DOIUrl":"https://doi.org/10.1155/2013/423189","url":null,"abstract":"Caffeic acid o-methyltransferase (COMT) is one of the important enzymes controlling lignin monomer production in plant cell wall synthesis. Analysis of the genome sequence of the new grass model Brachypodium distachyon identified four COMT gene homologs, designated as BdCOMT1, BdCOMT2, BdCOMT3, and BdCOMT4. Phylogenetic analysis suggested that they belong to the COMT gene family, whereas syntenic analysis through comparisons with rice and sorghum revealed that BdCOMT4 on Chromosome 3 is the orthologous copy of the COMT genes well characterized in other grass species. The other three COMT genes are unique to Brachypodium since orthologous copies are not found in the collinear regions of rice and sorghum genomes. Expression studies indicated that all four Brachypodium COMT genes are transcribed but with distinct patterns of tissue specificity. Full-length cDNAs were cloned in frame into the pQE-T7 expression vector for the purification of recombinant Brachypodium COMT proteins. Biochemical characterization of enzyme activity and substrate specificity showed that BdCOMT4 has significant effect on a broad range of substrates with the highest preference for caffeic acid. The other three COMTs had low or no effect on these substrates, suggesting that a diversified evolution occurred on these duplicate genes that not only impacted their pattern of expression, but also altered their biochemical properties.","PeriodicalId":73471,"journal":{"name":"International journal of plant genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2013-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2013/423189","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31348427","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 25

Plant domestication and resistance to herbivory. 植物驯化和对食草动物的抵抗力。

International journal of plant genomics Pub Date : 2013-01-01 Epub Date: 2013-03-25 DOI: 10.1155/2013/572784

Bhupendra Chaudhary

{"title":"Plant domestication and resistance to herbivory.","authors":"Bhupendra Chaudhary","doi":"10.1155/2013/572784","DOIUrl":"10.1155/2013/572784","url":null,"abstract":"Transformation of wild species into elite cultivars through \"domestication\" entails evolutionary responses in which plant populations adapt to selection. Domestication is a process characterized by the occurrence of key mutations in morphological, phenological, or utility genes, which leads to the increased adaptation and use of the plant; however, this process followed by modern plant breeding practices has presumably narrowed the genetic diversity in crop plants. The reduction of genetic diversity could result in \"broad susceptibility\" to newly emerging herbivores and pathogens, thereby threatening long-term crop retention. Different QTLs influencing herbivore resistance have also been identified, which overlap with other genes of small effect regulating resistance indicating the presence of pleiotropism or linkage between such genes. However, this reduction in genetic variability could be remunerated by introgression of novel traits from wild perhaps with antifeedant and antinutritional toxic components. Thus it is strongly believed that transgenic technologies may provide a radical and promising solution to combat herbivory as these avoid linkage drag and also the antifeedant angle. Here, important questions related to the temporal dynamics of resistance to herbivory and intricate genetic phenomenon with their impact on crop evolution are addressed and at times hypothesized for future validation.","PeriodicalId":73471,"journal":{"name":"International journal of plant genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2013-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3621290/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31361423","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

SNiPloid: A Utility to Exploit High-Throughput SNP Data Derived from RNA-Seq in Allopolyploid Species. SNiPloid：在全多倍体物种中利用从 RNA-Seq 提取的高通量 SNP 数据的实用工具。

International journal of plant genomics Pub Date : 2013-01-01 Epub Date: 2013-09-12 DOI: 10.1155/2013/890123

Marine Peralta, Marie-Christine Combes, Alberto Cenci, Philippe Lashermes, Alexis Dereeper

引用次数: 0

The Arabidopsis stress responsive gene database. 拟南芥逆境响应基因数据库。

International journal of plant genomics Pub Date : 2013-01-01 Epub Date: 2013-03-17 DOI: 10.1155/2013/949564

Subhomoi Borkotoky, Vijayakumar Saravanan, Amit Jaiswal, Bipul Das, Suresh Selvaraj, Ayaluru Murali, P T V Lakshmi

引用次数: 40

A pair of partially overlapping Arabidopsis genes with antagonistic circadian expression. 一对部分重叠的拟南芥基因与拮抗昼夜表达。

International journal of plant genomics Pub Date : 2012-01-01 Epub Date: 2012-04-03 DOI: 10.1155/2012/349527

Andrea Kunova, Elena Zubko, Peter Meyer

引用次数: 9

Molecular Breeding to Improve Salt Tolerance of Rice (Oryza sativa L.) in the Red River Delta of Vietnam. 越南红河三角洲水稻耐盐性分子育种研究。

International journal of plant genomics Pub Date : 2012-01-01 Epub Date: 2012-12-27 DOI: 10.1155/2012/949038

Le Hung Linh, Ta Hong Linh, Tran Dang Xuan, Le Huy Ham, Abdelbagi M Ismail, Tran Dang Khanh

{"title":"Molecular Breeding to Improve Salt Tolerance of Rice (Oryza sativa L.) in the Red River Delta of Vietnam.","authors":"Le Hung Linh, Ta Hong Linh, Tran Dang Xuan, Le Huy Ham, Abdelbagi M Ismail, Tran Dang Khanh","doi":"10.1155/2012/949038","DOIUrl":"https://doi.org/10.1155/2012/949038","url":null,"abstract":"Rice is a stable food in Vietnam and plays a key role in the economy of the country. However, the production and the cultivating areas are adversely affected from the threats of devastation caused by the rise of sea level. Using marker-assisted backcrossing (MABC) to develop a new salt tolerance rice cultivar is one of the feasible methods to cope with these devastating changes. To improve rice salt tolerance in BT7 cultivar, FL478 was used as a donor parent to introgress the Saltol QTL conferring salt tolerance into BT7. Three backcrosses were conducted and successfully transferred positive alleles of Saltol from FL478 into BT7. The plants numbers IL-30 and IL-32 in BC(3)F(1) population expected recurrent genome recovery of up to 99.2% and 100%, respectively. These selected lines that carried the Saltol alleles were screened in field for their agronomic traits. All improved lines had Saltol allele similar to the donor parent FL478, whereas their agronomic performances were the same as the original BT7. We show here the success of improving rice salt tolerance by MABC and the high efficiency of selection in early generations. In the present study, MABC has accelerated the development of superior qualities in the genetic background of BT7.","PeriodicalId":73471,"journal":{"name":"International journal of plant genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2012-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2012/949038","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31167093","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 103

Advances towards a Marker-Assisted Selection Breeding Program in Prairie Cordgrass, a Biomass Crop. 生物质作物草原草的标记辅助选择育种研究进展

International journal of plant genomics Pub Date : 2012-01-01 Epub Date: 2012-11-26 DOI: 10.1155/2012/313545

K R Gedye, J L Gonzalez-Hernandez, V Owens, A Boe

{"title":"Advances towards a Marker-Assisted Selection Breeding Program in Prairie Cordgrass, a Biomass Crop.","authors":"K R Gedye, J L Gonzalez-Hernandez, V Owens, A Boe","doi":"10.1155/2012/313545","DOIUrl":"https://doi.org/10.1155/2012/313545","url":null,"abstract":"Prairie cordgrass (Spartina pectinata Bosc ex Link) is an indigenous, perennial grass of North America that is being developed into a cellulosic biomass crop suitable for biofuel production. Limited research has been performed into the breeding of prairie cordgrass; this research details an initial investigation into the development of a breeding program for this species. Genomic libraries enriched for four simple sequence repeat (SSR) motifs were developed, 25 clones from each library were sequenced, identifying 70 SSR regions, and primers were developed for these regions, 35 of which were amplified under standard PCR conditions. These SSR markers were used to validate the crossing methodology of prairie cordgrass and it was found that crosses between two plants occurred without the need for emasculation. The successful cross between two clones of prairie cordgrass indicates that this species is not self-incompatible. The results from this research will be used to instigate the production of a molecular map of prairie cordgrass which can be used to incorporate marker-assisted selection (MAS) protocols into a breeding program to improve this species for cellulosic biomass production.","PeriodicalId":73471,"journal":{"name":"International journal of plant genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2012-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2012/313545","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31109057","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 14

Mapping of Micro-Tom BAC-End Sequences to the Reference Tomato Genome Reveals Possible Genome Rearrangements and Polymorphisms. 微tom bac -末端序列与参考番茄基因组的定位揭示了可能的基因组重排和多态性。

International journal of plant genomics Pub Date : 2012-01-01 Epub Date: 2012-11-27 DOI: 10.1155/2012/437026

Erika Asamizu, Kenta Shirasawa, Hideki Hirakawa, Shusei Sato, Satoshi Tabata, Kentaro Yano, Tohru Ariizumi, Daisuke Shibata, Hiroshi Ezura

{"title":"Mapping of Micro-Tom BAC-End Sequences to the Reference Tomato Genome Reveals Possible Genome Rearrangements and Polymorphisms.","authors":"Erika Asamizu, Kenta Shirasawa, Hideki Hirakawa, Shusei Sato, Satoshi Tabata, Kentaro Yano, Tohru Ariizumi, Daisuke Shibata, Hiroshi Ezura","doi":"10.1155/2012/437026","DOIUrl":"https://doi.org/10.1155/2012/437026","url":null,"abstract":"A total of 93,682 BAC-end sequences (BESs) were generated from a dwarf model tomato, cv. Micro-Tom. After removing repetitive sequences, the BESs were similarity searched against the reference tomato genome of a standard cultivar, \"Heinz 1706.\" By referring to the \"Heinz 1706\" physical map and by eliminating redundant or nonsignificant hits, 28,804 \"unique pair ends\" and 8,263 \"unique ends\" were selected to construct hypothetical BAC contigs. The total physical length of the BAC contigs was 495, 833, 423 bp, covering 65.3% of the entire genome. The average coverage of euchromatin and heterochromatin was 58.9% and 67.3%, respectively. From this analysis, two possible genome rearrangements were identified: one in chromosome 2 (inversion) and the other in chromosome 3 (inversion and translocation). Polymorphisms (SNPs and Indels) between the two cultivars were identified from the BLAST alignments. As a result, 171,792 polymorphisms were mapped on 12 chromosomes. Among these, 30,930 polymorphisms were found in euchromatin (1 per 3,565 bp) and 140,862 were found in heterochromatin (1 per 2,737 bp). The average polymorphism density in the genome was 1 polymorphism per 2,886 bp. To facilitate the use of these data in Micro-Tom research, the BAC contig and polymorphism information are available in the TOMATOMICS database.","PeriodicalId":73471,"journal":{"name":"International journal of plant genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2012-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2012/437026","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31109058","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 13

Evolutionary and molecular aspects of Indian tomato leaf curl virus coat protein. 印度番茄卷叶病毒衣壳蛋白的进化和分子方面。

International journal of plant genomics Pub Date : 2012-01-01 Epub Date: 2012-12-11 DOI: 10.1155/2012/417935

Sivakumar Prasanth Kumar, Saumya K Patel, Ravi G Kapopara, Yogesh T Jasrai, Himanshu A Pandya

{"title":"Evolutionary and molecular aspects of Indian tomato leaf curl virus coat protein.","authors":"Sivakumar Prasanth Kumar, Saumya K Patel, Ravi G Kapopara, Yogesh T Jasrai, Himanshu A Pandya","doi":"10.1155/2012/417935","DOIUrl":"10.1155/2012/417935","url":null,"abstract":"Tomato leaf curl disease (ToLCD) is manifested by yellowing of leaf lamina with upward leaf curl, leaf distortion, shrinking of the leaf surface, and stunted plant growth caused by tomato leaf curl virus (ToLCV). In the present study, using computational methods we explored the evolutionary and molecular prospects of viral coat protein derived from an isolate of Vadodara district, Gujarat (ToLCGV-[Vad]), India. We found that the amino acids in coat protein required for systemic infection, viral particle formation, and insect transmission to host cells were conserved amongst Indian strains. Phylogenetic studies on Indian ToLCV coat proteins showed evolutionary compatibility with other viral taxa. Modeling of coat protein revealed a topology similar to characteristic Geminate viral particle consisting of antiparallel β-barrel motif with N-terminus α-helix. The molecular interaction of coat protein with the viral DNA required for encapsidation and nuclear shuttling was investigated through sequence- and structure-based approaches. We further emphasized the role of loops in coat protein structure as molecular recognition interface.","PeriodicalId":73471,"journal":{"name":"International journal of plant genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2012-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3529866/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31151407","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A cotton-fiber-associated cyclin-dependent kinase a gene: characterization and chromosomal location. 棉纤维相关的周期蛋白依赖性激酶A基因:特征和染色体定位。

International journal of plant genomics Pub Date : 2012-01-01 Epub Date: 2012-06-14 DOI: 10.1155/2012/613812

Weifan Gao, Sukumar Saha, Din-Pow Ma, Yufang Guo, Johnie N Jenkins, David M Stelly

引用次数: 7