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International Journal of Plant Genomics

Dmitry V Politov, Maryana M Belokon, Yuri S Belokon, Tatyana A Polyakova, Anna V Shatokhina, Elena A Mudrik, Anna B Azarova, Mikhail V Filippov, Konstantin A Shestibratov
Testing systems for molecular identification of micropropagated elite aspen (Populus tremula L.) genotypes were developed on the base on microsatellite (SSR) loci. Out of 33 tested microsatellite loci, 14 were selected due to sustainable PCR amplification and substantial variability in elite clones of aspen aimed for establishment of fast-rotated forest plantations. All eight tested clones had different multilocus genotypes. Among 114 trees from three reference native stands located near the established plantations, 80 haplotypes were identified while some repeated genotypes were attributed to natural clones which appeared as a result of sprouting...
2015: International Journal of Plant Genomics
Fred Y Peng, Zhiqiu Hu, Rong-Cai Yang
Early flowering is an important trait influencing grain yield and quality in wheat (Triticum aestivum L.) and barley (Hordeum vulgare L.) in short-season cropping regions. However, due to large and complex genomes of these species, direct identification of flowering genes and their molecular characterization remain challenging. Here, we used a bioinformatic approach to predict flowering-related genes in wheat and barley from 190 known Arabidopsis (Arabidopsis thaliana (L.) Heynh.) flowering genes. We identified 900 and 275 putative orthologs in wheat and barley, respectively...
2015: International Journal of Plant Genomics
Hirut Kebede, Paxton Payton, Hanh Thi My Pham, Randy D Allen, Robert J Wright
Cotton exhibits moderately high vegetative tolerance to water-deficit stress but lint production is restricted by the available rainfed and irrigation capacity. We have described the impact of water-deficit stress on the genetic and metabolic control of fiber quality and production. Here we examine the association of tentative consensus sequences (TCs) derived from various cotton tissues under irrigated and water-limited conditions with stress-responsive QTLs. Three thousand sixteen mapped sequence-tagged-sites were used as anchored targets to examine sequence homology with 15,784 TCs to test the hypothesis that putative stress-responsive genes will map within QTLs associated with stress-related phenotypic variation more frequently than with other genomic regions not associated with these QTLs...
2015: International Journal of Plant Genomics
Ehsan Pourabed, Mohammad Reza Jazayeri Noushabadi, Seyed Hossein Jamali, Naser Moheb Alipour, Abbas Zareyan, Leila Sadeghi
Identification and registration of new rice varieties are very important to be free from environmental effects and using molecular markers that are more reliable. The objectives of this study were, first, the identification and distinction of 40 rice varieties consisting of local varieties of Iran, improved varieties, and IRRI varieties using PIC, and discriminating power, second, cluster analysis based on Dice similarity coefficient and UPGMA algorithm, and, third, determining the ability of microsatellite markers to separate varieties utilizing the best combination of markers...
2015: International Journal of Plant Genomics
Ravi Ranjan Kumar, Shailesh Yadav, Shourabh Joshi, Prithviraj P Bhandare, Vinod Kumar Patil, Pramod B Kulkarni, Swati Sonkawade, G R Naik
Pigeonpea (Cajanus cajan (L) Millsp.) is an important food legume crop of rain fed agriculture in the arid and semiarid tropics of the world. It has deep and extensive root system which serves a number of important physiological and metabolic functions in plant development and growth. In order to identify genes associated with pigeonpea root, ESTs were generated from the root tissues of pigeonpea (GRG-295 genotype) by normalized cDNA library. A total of 105 high quality ESTs were generated by sequencing of 250 random clones which resulted in 72 unigenes comprising 25 contigs and 47 singlets...
2014: International Journal of Plant Genomics
Marine Peralta, Marie-Christine Combes, Alberto Cenci, Philippe Lashermes, Alexis Dereeper
High-throughput sequencing is a common approach to discover SNP variants, especially in plant species. However, methods to analyze predicted SNPs are often optimized for diploid plant species whereas many crop species are allopolyploids and combine related but divergent subgenomes (homoeologous chromosome sets). We created a software tool, SNiPloid, that exploits and interprets putative SNPs in the context of allopolyploidy by comparing SNPs from an allopolyploid with those obtained in its modern-day diploid progenitors...
2013: International Journal of Plant Genomics
Mohsen Mohammadi, Davoud Torkamaneh, Hamid-Reza Nikkhah
Vernalization requirement is a key component in determining the overall fitness of developmental patterns of barley to its environment. We have used previously reported markers and spring-sown growth habit nursery to characterize the genotypes of barley germplasm in an applied barley breeding ground to establish a baseline of information required to understand the relationship between adaptation of autumn-sown barley germplasm in diverse regions with warm (W), moderate (M), or cold climates (C). This study revealed that twenty entries were detected with the presence of the vernalization critical region in VRN-H1 locus and complete presence of the three geneclusters ZCCT-Ha, -Hb, and -Hc in VRN-H2 locus represented as genotype vrn-H1/Vrn-H2 (V1w/V2w)...
2013: International Journal of Plant Genomics
Bhupendra Chaudhary
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...
2013: International Journal of Plant Genomics
Subhomoi Borkotoky, Vijayakumar Saravanan, Amit Jaiswal, Bipul Das, Suresh Selvaraj, Ayaluru Murali, P T V Lakshmi
Plants in nature may face a wide range of favorable or unfavorable biotic and abiotic factors during their life cycle. Any of these factors may cause stress in plants; therefore, they have to be more adaptable to stressful environments and must acquire greater response to different stresses. The objective of this study is to retrieve and arrange data from the literature in a standardized electronic format for the development of information resources on potential stress responsive genes in Arabidopsis thaliana...
2013: International Journal of Plant Genomics
Xianting Wu, Jiajie Wu, Yangfan Luo, Jennifer Bragg, Olin Anderson, John Vogel, Yong Q Gu
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...
2013: International Journal of Plant Genomics
Le Hung Linh, Ta Hong Linh, Tran Dang Xuan, Le Huy Ham, Abdelbagi M Ismail, Tran Dang Khanh
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...
2012: International Journal of Plant Genomics
Jafar Mammadov, Rajat Aggarwal, Ramesh Buyyarapu, Siva Kumpatla
The use of molecular markers has revolutionized the pace and precision of plant genetic analysis which in turn facilitated the implementation of molecular breeding of crops. The last three decades have seen tremendous advances in the evolution of marker systems and the respective detection platforms. Markers based on single nucleotide polymorphisms (SNPs) have rapidly gained the center stage of molecular genetics during the recent years due to their abundance in the genomes and their amenability for high-throughput detection formats and platforms...
2012: International Journal of Plant Genomics
Jens Boesger, Volker Wagner, Wolfram Weisheit, Maria Mittag
The green biflagellate alga Chlamydomonas reinhardtii serves as model for studying structural and functional features of flagella. The axoneme of C. reinhardtii anchors a network of kinases and phosphatases that control motility. One of them, Casein Kinase 1 (CK1), is known to phosphorylate the Inner Dynein Arm I1 Intermediate Chain 138 (IC138), thereby regulating motility. CK1 is also involved in regulating the circadian rhythm of phototaxis and is relevant for the formation of flagella. By a comparative phosphoproteome approach, we determined phosphoproteins in the flagellum that are targets of CK1...
2012: International Journal of Plant Genomics
Sivakumar Prasanth Kumar, Saumya K Patel, Ravi G Kapopara, Yogesh T Jasrai, Himanshu A Pandya
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...
2012: International Journal of Plant Genomics
Santosh Kumar, Travis W Banks, Sylvie Cloutier
The decreasing cost along with rapid progress in next-generation sequencing and related bioinformatics computing resources has facilitated large-scale discovery of SNPs in various model and nonmodel plant species. Large numbers and genome-wide availability of SNPs make them the marker of choice in partially or completely sequenced genomes. Although excellent reviews have been published on next-generation sequencing, its associated bioinformatics challenges, and the applications of SNPs in genetic studies, a comprehensive review connecting these three intertwined research areas is needed...
2012: International Journal of Plant Genomics
Erika Asamizu, Kenta Shirasawa, Hideki Hirakawa, Shusei Sato, Satoshi Tabata, Kentaro Yano, Tohru Ariizumi, Daisuke Shibata, Hiroshi Ezura
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...
2012: International Journal of Plant Genomics
K R Gedye, J L Gonzalez-Hernandez, V Owens, A Boe
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...
2012: International Journal of Plant Genomics
Cosette Abdallah, Eliane Dumas-Gaudot, Jenny Renaut, Kjell Sergeant
Two-dimensional gel electrophoresis (2-DE) is widely applied and remains the method of choice in proteomics; however, pervasive 2-DE-related concerns undermine its prospects as a dominant separation technique in proteome research. Consequently, the state-of-the-art shotgun techniques are slowly taking over and utilising the rapid expansion and advancement of mass spectrometry (MS) to provide a new toolbox of gel-free quantitative techniques. When coupled to MS, the shotgun proteomic pipeline can fuel new routes in sensitive and high-throughput profiling of proteins, leading to a high accuracy in quantification...
2012: International Journal of Plant Genomics
Stéphane Deschamps, Kishore Nannapaneni, Yun Zhang, Kevin Hayes
The use of next-generation DNA sequencing technologies has greatly facilitated reference-guided variant detection in complex plant genomes. However, complications may arise when regions adjacent to a read of interest are used for marker assay development, or when reference sequences are incomplete, as short reads alone may not be long enough to ascertain their uniqueness. Here, the possibility of generating longer sequences in discrete regions of the large and complex genome of maize is demonstrated, using a modified version of a paired-end RAD library construction strategy...
2012: International Journal of Plant Genomics
Weifan Gao, Sukumar Saha, Din-Pow Ma, Yufang Guo, Johnie N Jenkins, David M Stelly
A cotton fiber cDNA and its genomic sequences encoding an A-type cyclin-dependent kinase (GhCDKA) were cloned and characterized. The encoded GhCDKA protein contains the conserved cyclin-binding, ATP binding, and catalytic domains. Northern blot and RT-PCR analysis revealed that the GhCDKA transcript was high in 5-10 DPA fibers, moderate in 15 and 20 DPA fibers and roots, and low in flowers and leaves. GhCDKA protein levels in fibers increased from 5-15 DPA, peaked at 15 DPA, and decreased from 15 t0 20 DPA...
2012: International Journal of Plant Genomics
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