International Journal of Plant Genomics The latest articles from Hindawi © 2017 , Hindawi Limited . All rights reserved. Transcript Polymorphism Rates in Soybean Seed Tissue Are Increased in a Single Transformant of Glycine max Tue, 29 Nov 2016 09:35:15 +0000 Transgenic crops have been utilized for decades to enhance agriculture and more recently have been applied as bioreactors for manufacturing pharmaceuticals. Recently, we investigated the gene expression profiles of several in-house transgenic soybean events, finding one transformant group to be consistently different from our controls. In the present study, we examined polymorphisms and sequence variations in the exomes of the same transgenic soybean events. We found that the previously dissimilar soybean line also exhibited markedly increased levels of polymorphisms within mRNA transcripts from seed tissue, many of which are classified as gene expression modifiers. The results from this work will direct future investigations to examine novel SNPs controlling traits of great interest for breeding and improving transgenic soybean crops. Further, this study marks the first work to investigate SNP rates in transgenic soybean seed tissues and demonstrates that while transgenesis may induce abundant unanticipated changes in gene expression and nucleotide variation, phenotypes and overall health of the plants examined remained unaltered. Kevin C. Lambirth, Adam M. Whaley, Jessica A. Schlueter, Kenneth J. Piller, and Kenneth L. Bost Copyright © 2016 Kevin C. Lambirth et al. All rights reserved. Application of Microsatellite Loci for Molecular Identification of Elite Genotypes, Analysis of Clonality, and Genetic Diversity in Aspen Populus tremula L. (Salicaceae) Mon, 28 Dec 2015 11:23:26 +0000 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. The selected set of SSR markers showed reliable individual identification with low probability of appearance of identical aspen genotypes (a minimum of and 1 × 10−4 for unrelated and related individuals, resp.). Case studies demonstrating practical applications of the test system are described including analysis of clonal structure and levels of genetic diversity in three natural aspen stands growing in the regions where plantations made of elite clones were established. Dmitry V. Politov, Maryana M. Belokon, Yuri S. Belokon, Tatyana A. Polyakova, Anna V. Shatokhina, Elena A. Mudrik, Anna B. Azarova, Mikhail V. Filippov, and Konstantin A. Shestibratov Copyright © 2015 Dmitry V. Politov et al. All rights reserved. Genome-Wide Comparative Analysis of Flowering-Related Genes in Arabidopsis, Wheat, and Barley Mon, 07 Sep 2015 06:22:37 +0000 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. The annotated flowering-related genes were clustered into 144 orthologous groups with one-to-one, one-to-many, many-to-one, and many-to-many orthology relationships. Our approach was further validated by domain and phylogenetic analyses of flowering-related proteins and comparative analysis of publicly available microarray data sets for in silico expression profiling of flowering-related genes in 13 different developmental stages of wheat and barley. These further analyses showed that orthologous gene pairs in three critical flowering gene families (PEBP, MADS, and BBX) exhibited similar expression patterns among 13 developmental stages in wheat and barley, suggesting similar functions among the orthologous genes with sequence and expression similarities. The predicted candidate flowering genes can be confirmed and incorporated into molecular breeding for early flowering wheat and barley in short-season cropping regions. Fred Y. Peng, Zhiqiu Hu, and Rong-Cai Yang Copyright © 2015 Fred Y. Peng et al. All rights reserved. Toward Coalescing Gene Expression and Function with QTLs of Water-Deficit Stress in Cotton Thu, 18 Jun 2015 09:03:22 +0000 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. Approximately 1,906 of 15,784 TCs were mapped to the consensus map. About 35% of the annotated TCs that mapped within QTL regions were genes involved in an abiotic stress response. By comparison, only 14.5% of the annotated TCs mapped outside these QTLs were classified as abiotic stress genes. A simple binomial probability calculation of this degree of bias being observed if QTL and non-QTL regions are equally likely to contain stress genes was   × 10−15. These results suggest that the QTL regions have a higher propensity to contain stress genes. Hirut Kebede, Paxton Payton, Hanh Thi My Pham, Randy D. Allen, and Robert J. Wright Copyright © 2015 Hirut Kebede et al. All rights reserved. Identification and DUS Testing of Rice Varieties through Microsatellite Markers Sun, 08 Feb 2015 10:38:14 +0000 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. For this research, 12 microsatellite markers were used. In total, 83 polymorphic alleles (6.91 alleles per locus) were found. In addition, the variation of PIC was calculated from 0.52 to 0.9. The results of cluster analysis showed the complete discrimination of varieties from each other except for IR58025A and IR58025B. Moreover, cluster analysis could detect the most of the improved varieties from local varieties. Based on the best combination of markers analysis, five pair primers together have shown the same results of all markers for detection among all varieties. Considering the results of this research, we can propose that microsatellite markers can be used as a complementary tool for morphological characteristics in DUS tests. Ehsan Pourabed, Mohammad Reza Jazayeri Noushabadi, Seyed Hossein Jamali, Naser Moheb Alipour, Abbas Zareyan, and Leila Sadeghi Copyright © 2015 Ehsan Pourabed et al. All rights reserved. Identification and Validation of Expressed Sequence Tags from Pigeonpea (Cajanus cajan L.) Root Tue, 06 May 2014 12:34:36 +0000 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. The ESTs were assigned to 9 functional categories on the basis of their putative function. In order to validate the possible expression of transcripts, four genes, namely, S-adenosylmethionine synthetase, phosphoglycerate kinase, serine carboxypeptidase, and methionine aminopeptidase, were further analyzed by reverse transcriptase PCR. The possible role of the identified transcripts and their functions associated with root will also be a valuable resource for the functional genomics study in legume crop. Ravi Ranjan Kumar, Shailesh Yadav, Shourabh Joshi, Prithviraj P. Bhandare, Vinod Kumar Patil, Pramod B. Kulkarni, Swati Sonkawade, and G. R. Naik Copyright © 2014 Ravi Ranjan Kumar et al. All rights reserved. SNiPloid: A Utility to Exploit High-Throughput SNP Data Derived from RNA-Seq in Allopolyploid Species Thu, 12 Sep 2013 10:08:59 +0000 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. SNiPloid can compare SNPs obtained from a sample to estimate the subgenome contribution to the transcriptome or SNPs obtained from two polyploid accessions to search for SNP divergence. Marine Peralta, Marie-Christine Combes, Alberto Cenci, Philippe Lashermes, and Alexis Dereeper Copyright © 2013 Marine Peralta et al. All rights reserved. Correlation of Vernalization Loci VRN-H1 and VRN-H2 and Growth Habit in Barley Germplasm Tue, 02 Apr 2013 11:48:00 +0000 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). Of these genotypes, 17 entries showed winter growth habit whereas the remaining three revealed facultative growth habit indicating reduced vernalization requirements possibly due to VRN-H3 and photoperiod sensitivity loci as compared to the landmark winter growth habit entries in this group. Twenty-four entries were detected with the lack of vernalization critical region in VRN-H1 locus but complete presence of the three geneclusters ZCCT-Ha, -Hb, and -Hc in VRN-H2 locus represented as genotype Vrn-H1/Vrn-H2 (V1s/V2w). However, only half of these germplasms were identified with spring growth habit in spring-sown nursery, and the rest of the germplasms in this group revealed facultative growth habits due to possible variation in the length of deletion in VRN-H1. Four germplasms showed vernalization insensitive phenotype due to the lack of a functional ZCCT-Ha and/or ZCCT-Hb alleles in VRN-H2 and the deletion in the vernalization critical region of VRN-H1. These germplasms revealed acomplete spring type growth habit. Only one entry showed reduced vernalization requirement solely due to the deletion in functional ZCCT-Hb allele in VRN-H2 and not due to the deletion in the vernalization critical region of VRN-H1. Mohsen Mohammadi, Davoud Torkamaneh, and Hamid-Reza Nikkhah Copyright © 2013 Mohsen Mohammadi et al. All rights reserved. Plant Domestication and Resistance to Herbivory Mon, 25 Mar 2013 18:08:15 +0000 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. Bhupendra Chaudhary Copyright © 2013 Bhupendra Chaudhary. All rights reserved. The Arabidopsis Stress Responsive Gene Database Sun, 17 Mar 2013 09:30:56 +0000 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. This provides a powerful mean for manipulation, comparison, search, and retrieval of records describing the nature of various stress responsive genes in Arabidopsis thaliana. The database is based exclusively on published stress tolerance genes associated with plants. Subhomoi Borkotoky, Vijayakumar Saravanan, Amit Jaiswal, Bipul Das, Suresh Selvaraj, Ayaluru Murali, and P. T. V. Lakshmi Copyright © 2013 Subhomoi Borkotoky et al. All rights reserved. Phylogenetic, Molecular, and Biochemical Characterization of Caffeic Acid o-Methyltransferase Gene Family in Brachypodium distachyon Thu, 17 Jan 2013 14:34:17 +0000 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. Xianting Wu, Jiajie Wu, Yangfan Luo, Jennifer Bragg, Olin Anderson, John Vogel, and Yong Q. Gu Copyright © 2013 Xianting Wu et al. All rights reserved. Molecular Breeding to Improve Salt Tolerance of Rice (Oryza sativa L.) in the Red River Delta of Vietnam Thu, 27 Dec 2012 14:21:19 +0000 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 BC3F1 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. Le Hung Linh, Ta Hong Linh, Tran Dang Xuan, Le Huy Ham, Abdelbagi M. Ismail, and Tran Dang Khanh Copyright © 2012 Le Hung Linh et al. All rights reserved. Application of Phosphoproteomics to Find Targets of Casein Kinase 1 in the Flagellum of Chlamydomonas Tue, 18 Dec 2012 14:45:56 +0000 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. Thereby, we applied the specific CK1 inhibitor CKI-7 that causes significant changes in the flagellum phosphoproteome and reduces the swimming velocity of the cells. In the CKI-7-treated cells, 14 phosphoproteins were missing compared to the phosphoproteome of untreated cells, including IC138, and four additional phosphoproteins had a reduced number of phosphorylation sites. Notably, inhibition of CK1 causes also novel phosphorylation events, indicating that it is part of a kinase network. Among them, Glycogen Synthase Kinase 3 is of special interest, because it is involved in the phosphorylation of key clock components in flies and mammals and in parallel plays an important role in the regulation of assembly in the flagellum. Jens Boesger, Volker Wagner, Wolfram Weisheit, and Maria Mittag Copyright © 2012 Jens Boesger et al. All rights reserved. SNP Markers and Their Impact on Plant Breeding Tue, 18 Dec 2012 08:32:18 +0000 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. Computational approaches dominate SNP discovery methods due to the ever-increasing sequence information in public databases; however, complex genomes pose special challenges in the identification of informative SNPs warranting alternative strategies in those crops. Many genotyping platforms and chemistries have become available making the use of SNPs even more attractive and efficient. This paper provides a review of historical and current efforts in the development, validation, and application of SNP markers in QTL/gene discovery and plant breeding by discussing key experimental strategies and cases exemplifying their impact. Jafar Mammadov, Rajat Aggarwal, Ramesh Buyyarapu, and Siva Kumpatla Copyright © 2012 Jafar Mammadov et al. All rights reserved. Evolutionary and Molecular Aspects of Indian Tomato Leaf Curl Virus Coat Protein Tue, 11 Dec 2012 08:14:05 +0000 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. Sivakumar Prasanth Kumar, Saumya K. Patel, Ravi G. Kapopara, Yogesh T. Jasrai, and Himanshu A. Pandya Copyright © 2012 Sivakumar Prasanth Kumar et al. All rights reserved. Mapping of Micro-Tom BAC-End Sequences to the Reference Tomato Genome Reveals Possible Genome Rearrangements and Polymorphisms Tue, 27 Nov 2012 08:30:13 +0000 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. Erika Asamizu, Kenta Shirasawa, Hideki Hirakawa, Shusei Sato, Satoshi Tabata, Kentaro Yano, Tohru Ariizumi, Daisuke Shibata, and Hiroshi Ezura Copyright © 2012 Erika Asamizu et al. All rights reserved. Advances towards a Marker-Assisted Selection Breeding Program in Prairie Cordgrass, a Biomass Crop Mon, 26 Nov 2012 15:21:16 +0000 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. K. R. Gedye, J. L. Gonzalez-Hernandez, V. Owens, and A. Boe Copyright © 2012 K. R. Gedye et al. All rights reserved. SNP Discovery through Next-Generation Sequencing and Its Applications Thu, 22 Nov 2012 15:15:32 +0000 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. This paper touches upon various aspects of SNP discovery, highlighting key points in availability and selection of appropriate sequencing platforms, bioinformatics pipelines, SNP filtering criteria, and applications of SNPs in genetic analyses. The use of next-generation sequencing methodologies in many non-model crops leading to discovery and implementation of SNPs in various genetic studies is discussed. Development and improvement of bioinformatics software that are open source and freely available have accelerated the SNP discovery while reducing the associated cost. Key considerations for SNP filtering and associated pipelines are discussed in specific topics. A list of commonly used software and their sources is compiled for easy access and reference. Santosh Kumar, Travis W. Banks, and Sylvie Cloutier Copyright © 2012 Santosh Kumar et al. All rights reserved. Gel-Based and Gel-Free Quantitative Proteomics Approaches at a Glance Tue, 20 Nov 2012 16:08:56 +0000 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. Although label-based approaches, either chemical or metabolic, gained popularity in quantitative proteomics because of the multiplexing capacity, these approaches are not without drawbacks. The burgeoning label-free methods are tag independent and suitable for all kinds of samples. The challenges in quantitative proteomics are more prominent in plants due to difficulties in protein extraction, some protein abundance in green tissue, and the absence of well-annotated and completed genome sequences. The goal of this perspective assay is to present the balance between the strengths and weaknesses of the available gel-based and -free methods and their application to plants. The latest trends in peptide fractionation amenable to MS analysis are as well discussed. Cosette Abdallah, Eliane Dumas-Gaudot, Jenny Renaut, and Kjell Sergeant Copyright © 2012 Cosette Abdallah et al. All rights reserved. Local Assemblies of Paired-End Reduced Representation Libraries Sequenced with the Illumina Genome Analyzer in Maize Tue, 09 Oct 2012 17:49:45 +0000 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. Reads are generated from DNA fragments first digested with a methylation-sensitive restriction endonuclease, sheared, enriched with biotin and a selective PCR amplification step, and then sequenced at both ends. Sequences are locally assembled into contigs by subgrouping pairs based on the identity of the read anchored by the restriction site. This strategy applied to two maize inbred lines (B14 and B73) generated 183,609 and 129,018 contigs, respectively, out of which at least 76% were >200 bps in length. A subset of putative single nucleotide polymorphisms from contigs aligning to the B73 reference genome with at least one mismatch was resequenced, and 90% of those in B14 were confirmed, indicating that this method is a potent approach for variant detection and marker development in species with complex genomes or lacking extensive reference sequences. Stéphane Deschamps, Kishore Nannapaneni, Yun Zhang, and Kevin Hayes Copyright © 2012 Stéphane Deschamps et al. All rights reserved. A Cotton-Fiber-Associated Cyclin-Dependent Kinase A Gene: Characterization and Chromosomal Location Thu, 14 Jun 2012 11:15:32 +0000 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. The differential expression of GhCDKA suggested that the gene might play an important role in fiber development. The GhCDKA sequence data was used to develop single nucleotide polymorphism (SNP) markers specific for the CDKA gene in cotton. A primer specific to one of the SNPs was used to locate the CDKA gene to chromosome 16 by deletion analysis using a series of hypoaneuploid interspecific hybrids. Weifan Gao, Sukumar Saha, Din-Pow Ma, Yufang Guo, Johnie N. Jenkins, and David M. Stelly Copyright © 2012 Weifan Gao et al. All rights reserved. A Bayesian Framework for Functional Mapping through Joint Modeling of Longitudinal and Time-to-Event Data Tue, 22 May 2012 10:02:42 +0000 The most powerful and comprehensive approach of study in modern biology is to understand the whole process of development and all events of importance to development which occur in the process. As a consequence, joint modeling of developmental processes and events has become one of the most demanding tasks in statistical research. Here, we propose a joint modeling framework for functional mapping of specific quantitative trait loci (QTLs) which controls developmental processes and the timing of development and their causal correlation over time. The joint model contains two submodels, one for a developmental process, known as a longitudinal trait, and the other for a developmental event, known as the time to event, which are connected through a QTL mapping framework. A nonparametric approach is used to model the mean and covariance function of the longitudinal trait while the traditional Cox proportional hazard (PH) model is used to model the event time. The joint model is applied to map QTLs that control whole-plant vegetative biomass growth and time to first flower in soybeans. Results show that this model should be broadly useful for detecting genes controlling physiological and pathological processes and other events of interest in biomedicine. Kiranmoy Das, Runze Li, Zhongwen Huang, Junyi Gai, and Rongling Wu Copyright © 2012 Kiranmoy Das et al. All rights reserved. Evolutionary History of LTR Retrotransposon Chromodomains in Plants Sun, 29 Apr 2012 10:58:47 +0000 Chromodomain-containing LTR retrotransposons are one of the most successful groups of mobile elements in plant genomes. Previously, we demonstrated that two types of chromodomains (CHDs) are carried by plant LTR retrotransposons. Chromodomains from group I (CHD_I) were detected only in Tcn1-like LTR retrotransposons from nonseed plants such as mosses (including the model moss species Physcomitrella) and lycophytes (the Selaginella species). LTR retrotransposon chromodomains from group II (CHD_II) have been described from a wide range of higher plants. In the present study, we performed computer-based mining of plant LTR retrotransposon CHDs from diverse plants with an emphasis on spike-moss Selaginella. Our extended comparative and phylogenetic analysis demonstrated that two types of CHDs are present only in the Selaginella genome, which puts this species in a unique position among plants. It appears that a transition from CHD_I to CHD_II and further diversification occurred in the evolutionary history of plant LTR retrotransposons at approximately 400 MYA and most probably was associated with the evolution of chromatin organization. Anton Novikov, Georgiy Smyshlyaev, and Olga Novikova Copyright © 2012 Anton Novikov et al. All rights reserved. A Pair of Partially Overlapping Arabidopsis Genes with Antagonistic Circadian Expression Tue, 03 Apr 2012 16:00:16 +0000 A large number of plant genes are aligned with partially overlapping genes in antisense orientation. Transcription of both genes would therefore favour the formation of double-stranded RNA, providing a substrate for the RNAi machinery, and enhanced antisense transcription should therefore reduce sense transcript levels. We have identified a gene pair that resembles a model for antisense-based gene regulation as a T-DNA insertion into the antisense gene causes a reduction in antisense transcript levels and an increase in sense transcript levels. The same effect was, however, also observed when the two genes were inserted as transgenes into different chromosomal locations, independent of the sense and antisense gene being expressed individually or jointly. Our results therefore indicate that antagonistic changes in sense/antisense transcript levels do not necessarily reflect antisense-mediated regulation. More likely, the partial overlap of the two genes may have favoured the evolution of antagonistic expression patterns preventing RNAi effects. Andrea Kunova, Elena Zubko, and Peter Meyer Copyright © 2012 Andrea Kunova et al. All rights reserved. Chromosomal Location of HCA1 and HCA2, Hybrid Chlorosis Genes in Rice Sun, 12 Feb 2012 09:08:42 +0000 Many postzygotic reproductive barrier forms have been reported in plants: hybrid weakness, hybrid necrosis, and hybrid chlorosis. In this study, linkage analysis of the genes causing hybrid chlorosis in F2 generation in rice, HCA1 and HCA2, was performed. HCA1 and HCA2 are located respectively on the distal regions of the short arms of chromosomes 12 and 11. These regions are known to be highly conserved as a duplicated chromosomal segment. The molecular mechanism causing F2 chlorosis deduced from the location of the two genes was discussed. The possibility of the introgression of the chromosomal segments encompassing HCA1 and/or HCA2 was also discussed from the viewpoint of Indica-Japonica differentiation. Katsuyuki Ichitani, Yuma Takemoto, Kotaro Iiyama, Satoru Taura, and Muneharu Sato Copyright © 2012 Katsuyuki Ichitani et al. All rights reserved. Poor Homologous Synapsis 1 Interacts with Chromatin but Does Not Colocalise with ASYnapsis 1 during Early Meiosis in Bread Wheat Mon, 06 Feb 2012 14:50:45 +0000 Chromosome pairing, synapsis, and DNA recombination are three key processes that occur during early meiosis. A previous study of Poor Homologous Synapsis 1 (PHS1) in maize suggested that PHS1 has a role in coordinating these three processes. Here we report the isolation of wheat (Triticum aestivum) PHS1 (TaPHS1), and its expression profile during and after meiosis. While the TaPHS1 protein has sequence similarity to other plant PHS1/PHS1-like proteins, it also possesses a unique region of oligopeptide repeat units. We show that TaPHS1 interacts with both single- and double-stranded DNA in vitro and provide evidence of the protein region that imparts the DNA-binding ability. Immunolocalisation data from assays conducted using antisera raised against TaPHS1 show that TaPHS1 associates with chromatin during early meiosis, with the signal persisting beyond chromosome synapsis. Furthermore, TaPHS1 does not appear to colocalise with the asynapsis protein (TaASY1) suggesting that these proteins are probably independently coordinated. Significantly, the data from the DNA-binding assays and 3-dimensional immunolocalisation of TaPHS1 during early meiosis indicates that TaPHS1 interacts with DNA, a function not previously observed in either the Arabidopsis or maize PHS1 homologues. As such, these results provide new insight into the function of PHS1 during early meiosis in bread wheat. Kelvin H. P. Khoo, Amanda J. Able, and Jason A. Able Copyright © 2012 Kelvin H. P. Khoo et al. All rights reserved. Mutagenesis as a Tool in Plant Genetics, Functional Genomics, and Breeding Sun, 22 Jan 2012 15:19:36 +0000 Plant mutagenesis is rapidly coming of age in the aftermath of recent developments in high-resolution molecular and biochemical techniques. By combining the high variation of mutagenised populations with novel screening methods, traits that are almost impossible to identify by conventional breeding are now being developed and characterised at the molecular level. This paper provides a comprehensive overview of the various techniques and workflows available to researchers today in the field of molecular breeding, and how these tools complement the ones already used in traditional breeding. Both genetic (Targeting Induced Local Lesions in Genomes; TILLING) and phenotypic screens are evaluated. Finally, different ways of bridging the gap between genotype and phenotype are discussed. Per Sikora, Aakash Chawade, Mikael Larsson, Johanna Olsson, and Olof Olsson Copyright © 2011 Per Sikora et al. All rights reserved. Development of New Candidate Gene and EST-Based Molecular Markers for Gossypium Species Tue, 17 Jan 2012 11:02:43 +0000 New source of molecular markers accelerate the efforts in improving cotton fiber traits and aid in developing high-density integrated genetic maps. We developed new markers based on candidate genes and G. arboreum EST sequences that were used for polymorphism detection followed by genetic and physical mapping. Nineteen gene-based markers were surveyed for polymorphism detection in 26 Gossypium species. Cluster analysis generated a phylogenetic tree with four major sub-clusters for 23 species while three species branched out individually. CAP method enhanced the rate of polymorphism of candidate gene-based markers between G. hirsutum and G. barbadense. Two hundred A-genome based SSR markers were designed after datamining of G. arboreum EST sequences (Mississippi Gossypium arboreum  EST-SSR: MGAES). Over 70% of MGAES markers successfully produced amplicons while 65 of them demonstrated polymorphism between the parents of G. hirsutum and G. barbadense RIL population and formed 14 linkage groups. Chromosomal localization of both candidate gene-based and MGAES markers was assisted by euploid and hypoaneuploid CS-B analysis. Gene-based and MGAES markers were highly informative as they were designed from candidate genes and fiber transcriptome with a potential to be integrated into the existing cotton genetic and physical maps. Ramesh Buyyarapu, Ramesh V. Kantety, John Z. Yu, Sukumar Saha, and Govind C. Sharma Copyright © 2011 Ramesh Buyyarapu et al. All rights reserved. Mutations in Lettuce Improvement Wed, 11 Jan 2012 16:18:15 +0000 Lettuce is a major vegetable in western countries. Mutations generated genetic variations and played an important role in the domestication of the crop. Many traits derived from natural and induced mutations, such as dwarfing, early flowering, male sterility, and chlorophyll deficiency, are useful in physiological and genetic studies. Mutants were also used to develop new lettuce products including miniature and herbicide-tolerant cultivars. Mutant analysis was critical in lettuce genomic studies including identification and cloning of disease-resistance genes. Mutagenesis combined with genomic technology may provide powerful tools for the discovery of novel gene alleles. In addition to radiation and chemical mutagens, unconventional approaches such as tissue or protoplast culture, transposable elements, and space flights have been utilized to generate mutants in lettuce. Since mutation breeding is considered nontransgenic, it is more acceptable to consumers and will be explored more in the future for lettuce improvement. Beiquan Mou Copyright © 2011 Beiquan Mou. All rights reserved. POPcorn: An Online Resource Providing Access to Distributed and Diverse Maize Project Data Tue, 27 Dec 2011 13:26:00 +0000 The purpose of the online resource presented here, POPcorn (Project Portal for corn), is to enhance accessibility of maize genetic and genomic resources for plant biologists. Currently, many online locations are difficult to find, some are best searched independently, and individual project websites often degrade over time—sometimes disappearing entirely. The POPcorn site makes available (1) a centralized, web-accessible resource to search and browse descriptions of ongoing maize genomics projects, (2) a single, stand-alone tool that uses web Services and minimal data warehousing to search for sequence matches in online resources of diverse offsite projects, and (3) a set of tools that enables researchers to migrate their data to the long-term model organism database for maize genetic and genomic information: MaizeGDB. Examples demonstrating POPcorn’s utility are provided herein. Ethalinda K. S. Cannon, Scott M. Birkett, Bremen L. Braun, Sateesh Kodavali, Douglas M. Jennewein, Alper Yilmaz, Valentin Antonescu, Corina Antonescu, Lisa C. Harper, Jack M. Gardiner, Mary L. Schaeffer, Darwin A. Campbell, Carson M. Andorf, Destri Andorf, Damon Lisch, Karen E. Koch, Donald R. McCarty, John Quackenbush, Erich Grotewold, Carol M. Lushbough, Taner Z. Sen, and Carolyn J. Lawrence Copyright © 2011 Ethalinda K. S. Cannon et al. All rights reserved.