Transcript-derived Fragments Research Articles

Comparative Transcript Profiling and Multiplex qRT-PCR Analysis Between Salt-Tolerant and Sensitive Wheat Genotypes

Identification of candidate genes combined with gene expression profiling carries importance to facilitate the molecular basis of salt stress response in plants. Here, cDNA-AFLP was used to compare the transcribed sequences among two bread and two durum wheat genotypes with different levels of salt tolerance. Transcript derived fragments (TDFs) screened on polyacrylamide gels and 36 salt stress induced unique fragments were detected in salt tolerant bread wheat genotype (Alpu cv.). The fragment size of these 36 TDFs was ranged between 99bp to 252bp. Full sequence information of 14 TDFs were obtained after cloning, then GeXP analyzer-based multiplex qRT-PCR assay was performed on leaf tissue derived from 12 TDFs. Targeted gene expression levels of two TDFs (TDF4-GT066302 and TDF11-GT066301) were showed clear upregulation in salt tolerant bread wheat genotype (Alpu cv.) and they were matched with hypothetical proteins. Especially, gene expression level of GT066301 was increased as 3.28 fold at 27th hours of salt stress for salt tolerant genotype. According to blastx similarity results, out of 14 sequenced fragments, two TDFs were closely matched with “cytochrome P450 monooxygenase” protein while four of them matched with Oryza “hypothetical” and “unknown” proteins. Outputs of this study might ensure comparative data for hypothetical protein gene expression and new useful alleles in response to salt stress in wheat.

Time-course differential expression of transcripts in resistant and susceptible groundnut genotypes challenged with Sclerotium rolfsii Sacc

Groundnut stem rot is one of the most devastating fungal diseases caused by Sclerotium rolfsii, resulting in significant yield loss. A transcriptome approach based on the cDNA-RAPD technique was employed to further understand the specific response of groundnut challenged with S. rolfsii. 35 cDNA-RAPD primers were employed to analyze the expression profiles of ICGV 86590 (resistant) and Narayani (susceptible) genotypes over a time course (0, 24, 48, 72 and 96 h after inoculation). The expression analysis found 3499 Transcript Derived Fragments (TDFs), of which 1431 TDFs with a qualitative difference and 128 quantitative differences (28, 27 up and 30, 43 down-regulated) in resistant and susceptible genotypes. A sharp increase in differentially expressed transcripts (DETs) in ICGV 86590 compared to susceptible Narayani at 24 h after inoculation indicated early recognition and timely activation of defense-related genes. A delayed response to pathogen infection was observed in susceptible genotype and also in the expression of a distinct set of DETs at different time intervals. However, more TDFs were differentially expressed in the resistant genotype compared to the susceptible genotype. As a result, these DETs were the responsible factors for the stem rot resistance and can be employed as functional markers in the development of stem rot resistant groundnut varieties. This study also reveals transcriptome changes before and after stem rot infection in groundnut, signifying the complex nature of stem rot resistance.

The Butterfly Effect: Mild Soil Pollution with Heavy Metals Elicits Major Biological Consequences in Cobalt-Sensitized Broad Bean Model Plants.

Among the heavy metals (HMs), only cobalt induces a polymorphic response in Vicia faba plants, manifesting as chlorophyll morphoses and a ‘break-through’ effect resulting in the elevated accumulation of other HMs, which makes Co-pretreated broad bean plants an attractive model for investigating soil pollution by HMs. In this study, Co-sensitized V. faba plants were used to evaluate the long-term effect of residual industrial pollution by examining biochemical (H2O2, ascorbic acid, malondialdehyde, free proline, flavonoid, polyphenols, chlorophylls, carotenoids, superoxide dismutase) and molecular (conserved DNA-derived polymorphism and transcript-derived polymorphic fragments) markers after long-term exposure. HM-polluted soil induced a significantly higher frequency of chlorophyll morphoses and lower levels of nonenzymatic antioxidants in Co-pretreated V. faba plants. Both molecular markers effectively differentiated plants from polluted and control soils into distinct clusters, showing that HMs in mildly polluted soil are capable of inducing changes in DNA coding regions. These findings illustrate that strong background abiotic stressors (pretreatment with Co) can aid investigations of mild stressors (slight levels of soil pollution) by complementing each other in antioxidant content reduction and induction of DNA changes.

Transcript and Protein Profiling Provides Insights Into the Molecular Mechanisms of Harvesting-Induced Latex Production in Rubber Tree.

Natural rubber, an important industrial raw material with wide applications, is harvested in the form of latex (cytoplasm of rubber-producing laticifers) from Hevea brasiliensis (para rubber tree) by the way of tapping. Conspicuous stimulation on latex production is observed for the first few tappings conducted on virgin (untapped before) or resting (tapped before but no tapping for a period) rubber trees. To understand the underlying mechanisms, an integrative analysis of the latex transcriptome and proteome was conducted on virgin or resting Hevea trees for the first five tappings. A total of 505 non-redundant differentially expressed (DE) transcript-derived fragments (TDFs) were identified by silver-staining cDNA-AFLP, with 217 exhibiting patterns of upregulated, 180 downregulated and 108 irregularly-regulated. Meanwhile, 117 two dimensional gel electrophoresis DE-protein spots were isolated and subjected to mass spectrometry analysis, with 89 and 57 being successfully identified by MALDI-TOF and MALDI-TOF/TOF, respectively. About 72.5% DE-TDFs and 76.1% DE-proteins were functionally annotated and categorized. Noteworthily, most of the DE-TDFs implicated in sugar transport and metabolism as well as rubber biosynthesis were upregulated by the tapping treatment. The importance of sugar metabolism in harvesting-induced latex production was reinforced by the identification of abundant relevant DE-protein spots. About 83.8% of the randomly selected DE-TDFs were validated for expression patterns by semi-quantitative RT-PCR, and an 89.7% consistency for the 29 latex regeneration-related DE-TDFs examined by quantitative RT-PCR analysis. In brief, our results reveal extensive physiological and molecular changes in Hevea laticifers incurred by the tapping treatment, and the vast number of DE genes and proteins identified here contribute to unraveling the gene regulatory network of tapping-stimulated latex production.

CDNA-AFLP analysis reveals altered gene expression profiles involved in juice sac<italic/> granulation in pummelo (<i>Citrus grandis</i>)

Citrus fruits produced in China are often affected by granulation. Granulation is an altered physiological state of citrus fruits occurring usually before harvest but whose underlying mechanisms remain elusive. In this study, cDNA-AFLP technology enabled the identification of 116 granulation-associated genes in pummelo (<italic>C. grandis</italic>) juice sacs. Differentially expressed transcript-derived fragments (TDFs) were shown to be mainly involved in biological regulation and signal transduction, carbohydrate and energy metabolism, nucleic acid, protein metabolism, stress responses, and cell metabolism. Therefore, granulation in pummelo juice sacs seems to involve the following several alterations: (1) changes in hormone levels; (2) activation of metabolic pathways related to ATP and sugar synthesis to produce more energy; (3) nucleic acid accumulation and increased protein degradation; (4) activation of stress-responsive metabolic pathways; (5) accelerated juice sac senescence. Our findings provide an overview of differential responses occurring at the transcriptional level in granulated juice sacs, thus revealing new insights into the adaptive mechanisms underlying this altered physiological state in ‘Guanximiyou’ pummelo (<italic>C. grandis</italic>) juice sacs.

Gene expression profiling by cDNA‐AFLP reveals potential candidate genes for imazapyr‐induced male sterility in sunflower

AbstractChemically induced male sterility (CIMS) is a valuable tool for hybrid breeding in crops. In this context, the acetohydroxyacid synthase (AHAS)‐inhibiting imazapyr has been proposed to induce male sterility in Imisun sunflower (Helianthus annuus L.) when applied during early reproductive development in a two‐fold higher than recommended field dose. This study aimed to perform a comparative transcriptomic analysis to find out the molecular bases of the gametocidal effect of imazapyr on two Imisun genotypes differing in their herbicide resistance level: completely resistant and intermediate resistant. The CIMS of treated plants was confirmed at physiological and anatomical levels. A total of 948 differentially expressed transcript‐derived fragments (TDFs) were identified by complementary DNA amplified fragment‐length polymorphism (cDNA‐AFLP) analysis at the three most informative developmental stages of anther development. Several genes related to xenobiotic metabolism and stress, including cytochrome P450 monooxygenases and ATP‐binding cassette transporters, were identified in the completely resistant genotype. Interestingly, a group of genes, including protein kinases, sulfonylurea receptor 1, aspartic signal peptide‐peptidase, and specific membrane transporters, were recognized from the differential TDFs simultaneously detected in both genotypes. Some of these transcripts were validated by quantitative real‐time polymerase chain reaction (qPCR) in both genotypes. Therefore, these transcripts could be exclusively related to the CIMS in sunflower. Based on the results, we suggest a probable model of action for the gametocidal effect of imazapyr. Our research provides new insights into the molecular mechanisms of male sterility induction in sunflower.

Comparative transcriptomic profiling of susceptible and resistant cultivars of pigeonpea demonstrates early molecular responses during Fusarium udum infection

Vascular wilt caused by Fusarium udum Butler is the most important disease of pigeonpea throughout the world. F. udum isolate MTCC 2204 (M1) inoculated pigeonpea plants of susceptible (ICP 2376) and resistant (ICP 8863) cultivars were taken at invasion stage of pathogenesis process for transcriptomic profiling to understand defense signaling reactions that interplay at early stage of this plant–pathogen encounter. Differential transcriptomic profiles were generated through cDNA-AFLP from M1 inoculated resistant and susceptible pigeonpea root tissues. Twenty five percent of transcript derived fragments (TDFs) were found to be pathogen induced. Among them 73 TDFs were re-amplified and sequenced. Homology search of the TDFs in available databases and thorough study of scientific literature identified several pathways, which could play crucial role in defense responses of the F. udum inoculated resistant plants. Some of the defense responsive pathways identified to be active during this interaction are, jasmonic acid and salicylic acid mediated defense responses, cell wall remodeling, vascular development and pattering, abscisic acid mediated responses, effector triggered immunity, and reactive oxygen species mediated signaling. This study identified important wilt responsive regulatory pathways in pigeonpea which will be helpful for further exploration of these resistant components for pigeonpea improvement.

Analysis of fatty acid compositions and differential gene expression in two Iranian olive cultivars during fruit ripening

Olive is one of the important oil-produce fruit species with long history of cultivation. Despite high economic importance of olive, the molecular mechanisms that are involved in the oil production were not investigated completely in this fruit crop. In this study, the trend of oil accumulation, its composition and the transcriptional profiles of two important olive cultivars of Iran (‘Mari’ and ‘Shenge’) was screened during different fruit developmental stages (60, 90, 120, 150 and 180 days after flowering [DAF]). These cultivars showed the same trend for oil accumulation but a quite different fatty acid composition during the growing season. According to results, 60–120 DAF was identified as the most critical stages for oil biosynthesis in these olive cultivars. A cDNA-AFLP procedure was employed to detect the transcripts with differential expression during the critical stages of fatty acid biosynthesis in the fruit mesocarp. Altogether 195 distinguished fragments were identified as the transcripts with differential expression in these cultivars during the stages that were mostly important for oil biosynthesis. Out of which, twenty high quality clear transcript-derived fragments (TDFs) were cloned, sequenced and subjected to homology search analysis in GenBank database. Based on the homology search results, the entire differentially expressed TDFs in current investigation were classified into four main categories including oil production, carbohydrate metabolism, defense responsive and signaling related transcripts. Altogether, the majority of TDFs that were involved in the fatty acid biosynthesis and carbohydrate metabolism had higher expression in ‘Mari’, the cultivar which is superior in oil percentage and its composition. The expression of these TDFs coincided with the critical stages of oil accumulation (60–120 DAF). On the contrary, most of the defense related TDFs had higher expression in ‘Shenge’, an olive cultivar which is highly tolerant to the environmental stresses but inferior in the oil percentage and its composition. In conclusion, our finding provided primary information about the molecular basis of oil production in olive mesocarp and revealed new insight into the mechanisms that may be involved in the stress resistance in this fruit crop and shed some light on the probable candidate transcripts that may contribute to these two processes.

Differentially expressed genes in resistant and susceptible Pistacia vera L. Cultivars in response to Pseudomonas fluorescens and Phytophthora parsiana

ABSTRACT Gummosis (Phytophthora root and crown rot) is an important and destructive disease that affects fruit trees like pistachio (Pistacia vera L.). Although many studies have been performed on the possibility of biological control of gummosis, up to now few studies have been done on transcriptionally induced resistance genes in pistachio against Phytophthora disease. In the present research, the cDNA-AFLP method was used to analyze the transcriptionally regulated genes during the interaction between susceptible (Sarakhs) and resistant (Badami-Rize Zarandi) pistachio cultivars with Pseudomonas fluorescens and/or Phytophthora parsiana. Using 12 AFLP primer combinations, approximately 740 different cDNA-AFLP fragments with sizes ranged from 50 to 700 bp were generated for susceptible and resistant pistachio cultivars. Forty six TDFs (transcript derived fragments) were then selected for susceptible cultivar and 24 TDFs for resistant cultivar. Accordingly, each one of these TDFs was recognized by similarity search using the BlastX program against the NCBI GenBank nucleotide database. Notably, 18.5% of TDFs were hypothetical or uncharacterized proteins and 1.4% of them indicated no significant similarity to the known genes. Among the TDFs with known function, disease resistance proteins were identified, which were newly regulated in response to pathogen or rhizobacterium. Furthermore, we found that the expression level of different growth-regulatory or defense-related genes was higher after the exposure to Pseudomonas fluorescens and/or Phytophthora parsiana. To better understand the defense mechanism of pistachio plants and recognition of P. fluorescens-activated genes, which induce resistance against P. parsiana, would significantly assist in the development of new resistant pistachio cultivars.

Transcriptomic and proteomic analyses of a new cytoplasmic male sterile line with a wild Gossypium bickii genetic background

BackgroundCotton is an important fiber crop but has serious heterosis effects, and cytoplasmic male sterility (CMS) is the major cause of heterosis in plants. However, to the best of our knowledge,no studies have investigated CMS Yamian A in cotton with the genetic background of Australian wild Gossypium bickii. Conjoint transcriptomic and proteomic analysis was first performed between Yamian A and its maintainer Yamian B.ResultsWe detected 550 differentially expressed transcript-derived fragments (TDFs) and at least 1013 proteins in anthers at various developmental stages. Forty-two TDFs and 11 differentially expressed proteins (DEPs) were annotated by analysis in the genomic databases of G. austral, G. arboreum and G. hirsutum. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses were performed to better understand the functions of these TDFs and DEPs. Transcriptomic and proteomic results showed that UDP-glucuronosyl/UDP-glucosyltransferase, 60S ribosomal protein L13a-4-like, and glutathione S-transferase were upregulated; while heat shock protein Hsp20, ATPase, F0 complex, and subunit D were downregulated at the microspore abortion stage of Yamian A. In addition, several TDFs from the transcriptome and several DEPs from the proteome were detected and confirmed by quantitative real-time PCR as being expressed in the buds of seven different periods of development. We established the databases of differentially expressed genes and proteins between Yamian A and its maintainer Yamian B in the anthers at various developmental stages and constructed an interaction network based on the databases for a comprehensive understanding of the mechanism underlying CMS with a wild cotton genetic background.ConclusionWe first analyzed the molecular mechanism of CMS Yamian A from the perspective of omics, thereby providing an experimental basis and theoretical foundation for future research attempting to analyze the abortion mechanism of new CMS with a wild Gossypium bickii background and to realize three-line matching.

New gene functions are involved in the thermotolerance of the wild wheat relative Aegilops umbellulata

Wheat is one of the most important food crops in the world for human consumption, like all plants it is exposed to environmental stresses including high temperatures. The deleterious effect of high temperatures negatively affects plant growth and development, leading to reduced viability and yield. These effects can be reduced by improvement of thermotolerance through innovative breeding strategies, based on the expansion of the genetic pool available, by exploring important genetic functions from wheat wild progenitors. Improving the genetic thermotolerance characteristics of wheat requires greater understanding of genetic bases of thermotolerance, through identification of high temperature stress related genes. A good source of new useful alleles is given by Aegilops species characterized by thermotolerant habits.In this study we have classified as thermotolerant or thermosensitive, on the basis of physiologic tests, some accessions of wheat wild relative species belonging to Aegilops and Triticum genera. A thermotolerant accession of Aegilops umbellulata (AUM5) was selected, subjected to different thermal treatments and analyzed at transcriptional level. By differential display reverse transcriptase polymerase chain reaction (DDRT-PCR), we investigated modulation of gene expression elicited by heat treatments. This approach allowed the identification of various transcript-derived fragments (TDFs) produced by AUM5 in response to different thermal treatments. The functions of the inducible unique genes in the molecular determination of thermotolerance process are discussed.

Identification of salinity responsive genes in lavender through cDNA-AFLP

Currently, a global demand exists forlavender as a significant medicinal plant and source of essential oils. Freshwater and arable lands are two major factors that inhibit extensive farming of medicinal plants in Iran. Saline water from seas and salty soil may be new resources for agricultural use, especially for medicinal plants. We sought to extend our knowledge of the Lavandula angustifolia genome and molecular basis of its salinity tolerance by using cDNA amplified fragment length polymorphism (cDNA-AFLP) to investigate the changes in plant transcriptomes in response to NaCl. All identified transcript derived fragments (TDF) were assigned as novel L. angustifolia genes related to signal transduction, regulation of gene expression, alternative splicing, autophagy, and secondary metabolite biosynthesis. qRT-PCR analysis of the TDFs in response to different concentrations of NaCl revealed various levels of mRNA of the identified genes in this plant. Our findings provided primary insights into the molecular response of L. angustifolia to salinity.

CDNA-AFLP analysis of differentially expressed genes during microspore embryogenesis in non-heading Chinese cabbage

Stress can induce microspores to change their developmental pathway from the gametophytic to the embryogenic pathway. To explore the molecular mechanisms of microspore embryogenesis, complement DNA-amplified fragment length polymorphism was used to isolate the transcript-derived fragments during microspore embryogenesis of the non-heading Brassica campestris L. ssp. chinensis ‘Wuyueman’. With 256 primer combinations screened, a total of 94 transcript-derived fragments were identified, and 15 were successfully sequenced. Based on a BLAST search in the Brassica database, 12 of the 15 sequenced transcript-derived fragments were homologous to genes with annotations; the remaining three transcript-derived fragments did not match any sequences. Transcript-derived fragments with annotations were involved in cell wall formation, hormones, and resistance. Analysis of cis-elements indicated that there were heat shock-related and stress-related cis-elements in the promoter sequences of 12 transcript-derived fragments. TDF1(Bra040720), TDF6(Bra013664), and TDF15(Bra022587) were selected for validation of complement DNA-amplified fragment length polymorphism expression patterns by real-time quantitative PCR. Results confirmed the altered expression patterns of three genes revealed by the complement DNA-amplified fragment length polymorphism. This study provides novel information on the molecular mechanism of microspore embryogenesis in non-heading Chinese cabbage.

CDNA-AFLP analysis of salicylic acid- and calcium chloride-induced transcript derived fragments under drought in tomato (Solanum lycopersicum)

Drought seriously threatens tomato production worldwide. Despite much research on exogenous salicylic acid (SA) and Ca2+ improving plant resistance to biotic and abiotic stress, the molecular mechanisms of exogenous SA- and Ca2+-mediated drought resistance response in tomato remain unclear. In this study, we analyzed SA- and Ca2+ -induced differentially expressed transcripts under drought in tomato plants using cDNA-amplified fragment length polymorphism (cDNA-AFLP). In total, 34 transcript derived fragments (TDFs) were differentially expressed. The functions identified through NCBI BLAST alignment mainly involved signal transduction, amino acid metabolism, transcription factors, transfer transport and stress response. The quantitative real-time polymerase chain reaction results of 12 TDFs associated with drought response were consistent with the patterns of changes observed with cDNA-AFLP analysis. These differentially expressed transcripts may be used for functional verification, transgenic research and breeding of drought-resistant tomato varieties.

Exploiting Differential Gene Expression to Discover Ionic and Osmotic-Associated Transcripts in the Halophyte Grass Aeluropus littoralis

BackgroundSalinity as a most significant environmental challenges affects the growth and productivity of plants worldwide. In this study, the ionic and iso-osmotic effects of salt stress were investigated in Aeluropus littoralis L., a halophyte grass species from Poaceae family, by cDNA-amplified fragment length polymorphism (cDNA-AFLP) technique. To dissect the two different effects (ionic and osmotic) exerted by salt stress, various ionic agents including 200 and 400 mM sodium chloride (NaCl), 200 and 400 mM potassium chloride (KCl) as well as 280 and 406 gl− 1 (− 0.9 and − 1.4 MPa) polyethylene glycol 6000 (PEG) as their iso-osmotic concentrations were applied.ResultsApplication of KCl and PEG significantly reduced the fresh weight (FW) of A. littoralis seedlings compared to control while NaCl treatment markedly enhanced the FW. At the transcriptome level, different observations of changes in gene expression have been made in response of A. littoralis to ionic and osmotic stresses. Out of 69 transcript derived fragments (TDFs), 42 TDFs belong to 9 different groups of genes involved in metabolism (11.6%), transcription (10.2%), ribosomal protein (8.7%), protein binding (8.7%) transporter (5.8%), translation (5.8%), signal transduction (4.3%), nucleosome assembly protein (2.9%) and catabolism (2.9%). The 44 and 28 percent of transcripts were expressed under ionic stress (NaCl-specific and KCl-specific) and osmotic stress (common with NaCl, KCl and PEG), respectively which indicating a greater response of plants to ionic stress than osmotic stress. Expression pattern of eight candidate TDFs including; SYP81, CAND1, KATN, ISB1, SAMDC, GLY1, HAK18 and ZF30 was evaluated by RT-qPCR at high salinity levels and recovery condition.ConclusionDifferential regulation of these TDFs was observed in root and shoot which confirm their role in salt stress tolerance and provide initial insights into the transcriptome of A. littoralis. Expression pattern of ionic and osmotic-related TDFs at A. littoralis can be taken as an indication of their functional relevance at different salt and drought stresses.

Association between seed yield-related traits and cDNA-AFLP markers in cumin (Cuminum cyminum) under drought and irrigation regimes

Cumin (Cuminum cyminum L.) is an aromatic medicinal herb with beneficial essential oil being used in antibacterial activities and industry of creams, lotions, and perfumes. Use of functional markers expedites breeding cumin for drought tolerance. The objective of this study was to identify association of plant height and several seed yield- related traits with complementary DNA-amplified fragment length polymorphism (cDNA-AFLP) markers in 15 cumin (Cuminum cyminum) accessions under normal irrigation (NI) and drought stress (DS) conditions. Cumin accessions were grown in the field and subjected to NI practice and post-heading DS in two years in Kerman, Iran. The mean seed yield ranged between 448.72 and 994.18 kg/ha in NI and was from 211.05 to 452.05.06 kg/ha in DS. Reduction in plant height and seed yield-related traits ranged 27–28% in the first and 29–50% in the second year in DS compared with NI. Twelve EcoR I-Mse I primer combinations were used to amplify AFLP markers in cDNA fragments isolated from RNA samples. The identified markers were subjected to analysis of marker-trait associations (MTAs) using the generalized linear model (GLM) and mixed linear model (MLM). A number of 239 and 208 reliable transcript-derived fragments (TDFs) were amplified in cumin genotypes tested in NI and DS, respectively. Of the identified TDFs, highly significant markers were used for association analysis, only. Higher number of MTAs was identified for traits in NI compared with DS. Of the identified linked markers, 5 in NI and 3 in DS were significantly associated with more than one trait under two water status conditions. None of markers were identified as common MTAs between the two moisture conditions. Analysis of population structure demonstrated cumin accessions could be divided into 3 and 4 sub-populations. Overall, high variation was identified in cumin with respect to biological yield, seed yield and seed related traits and the identified linked markers can be incorporated into marker-assisted selection programs for the improvement of seed yield in drought condition.

Colinearity of putative flowering gene in both sugarcane and sorghum

Sugarcane (Saccharum spp.) and sorghum (Sorghum spp.) have become increasingly important crops for biofuels production. Sugarcane has an autopolyploid complex genome, whereas sorghum has a diploid simple genome. Flowering is one of the sugar-related agronomic traits in both species. Here, we obtained cDNA of inflorescences at 0–15 cm from S. spontaneum using cDNA-amplified restriction fragment length polymorphisms to develop flower transcriptome profiling with 26 primer combinations. A total of 183 transcript-derived fragments (TDFs) were screened and 96 TDFs were sequenced. Out of 96 TDFs, 26 were selected as putative flowering genes to study collinearity with the sorghum genome. For gene collinearity, a genetic linkage map with 169 SSR co-dominant markers and 12 TDF marker loci were mapped to 14 linkage groups collectively spanning 1077.8 cM and corresponding to the 10 sorghum chromosomes. Interestingly, 9 TDF marker loci could be mapped to 5 linkage groups. In this study, we successfully identified the homologous location of sugarcane flowering TDFs in the sorghum genome and found that 4DS_1X and 2DS_3E TDFs may serve as candidate specific markers linked to flowering in both sorghum and sugarcane.

Genetic and expression differences between putative ecotypes of Sphagnum denticulatum Brid. (Sphagnaceae: Bryophyta) subjected to drought stress and rehydration

Adverse changes in vegetation occur as the effect of the progressive drying of peatlands, leading to the disappearance of peat mosses (Sphagnum), a key component of these ecosystems. We report gene expression divergence for two putative ecotypes of S. denticulatum collected from contrasted habitats under the threat of drought. We used cDNA-amplified fragment length polymorphism (cDNA-AFLP) as the first screening method. We then used real-time, quantitative PCR to identify genes whose transcription changes in response to drought and rehydration treatments. Using 133 of 900 pretested cDNA-AFLP primer combinations, we have identified 949 drought-induced transcript-derived fragments, 6 (0.6%) of which are significantly differentially expressed genes (DEGs) in the putative ecotypes. We cloned and sequenced 378 fragments using designed fragment-specific primers. Transcription patterns were quantified for 21 target genes using qRT-PCR. When upregulated under drought, nine genes showed fold changes in a range of 4.64–150.03. The DEGs represented functional categories including protein/nucleotide binding, catalytic activity, transporter activity, and enzyme regulation activity. These genes are known to be involved in various metabolic pathways and physiological processes which emphasize the complexity of plant response to stress. Most of the significant differences in transcription patterns were evident in the aquatic plants, suggesting induced responses to drought in these plants. The expression was significantly less pronounced in the terrestrial plants, indicating that they are preconditioned to withstand drought stress. We detected positive selection on individual codons for specific branches using the ratio of substitution rates at nonsynonymous and synonymous sites (dN/dS). For the first time, this study provides insight into the genetic basis of the putative adaptive evolution in Sphagnum and allows for the discovery of genes involved in drought stress response.

Xenia in bahiagrass: gene expression at initial seed formation

AbstractXenia is the direct effect of pollen genotype on the development and characteristics of the seed and fruit in the period that spans from fertilization to seed germination. Xenia effects cause phenotypic variations in the seed and fruit, which have importance for seed and fruit production but are not heritable to the progeny. Two hypotheses have been proposed as a mechanism for xenia: the hormonal hypothesis and the mobile mRNAs hypothesis. Although xenia effects have been studied in seeds and fruits in many crops, its effects and mechanism have been poorly studied at the molecular level. The aim of this work was to perform an initial screening of the xenia effect in the hybrid endosperm at the molecular level by differential gene expression among different pollen genotype sources from Paspalum notatum Flüggé. In order to characterize xenia effects and mechanisms, crosses were made between an emasculated mother plant with donors from two different pollen genotypes. RNA was isolated from ovaries 3 h after pollination. Some of the 24 differentially expressed transcript-derived fragments (DETDFs) provided relevant information. Four of those DETDFs were related to germination, pollen tube growth and pollen–pistil interaction. Seven DETDFs were associated with seed development and production. Finally, four DETDFs were predicted to encode for mobile mRNAs. These DETDFs might be involved in xenia effects and mechanisms in P. notatum.

Differentially expressed genes during the transition from early to late development phases in somatic embryo of banana (Musa spp. AAB group, Silk subgroup) cv. Manzano

A cDNA-sequence-related amplified polymorphism (cDNA-SRAP) approach was used to identify relevant genes expressed at the onset of somatic embryo maturation/desiccation in banana (Musa spp. AAB group, Silk subgroup) cv. Manzano. For this, an embryogenic procedure, starting with cell suspensions, was first improved by including a culture period on a free growth-regulator medium for embryo maturation. This produced an up to 95% germination of the coleoptilar embryos. Gene expression patterns were followed through different stages of the process, including immature male flower explants, embryogenic calli, as well as immature, mature and germinated embryos. A total of 151 differentially expressed transcript-derived fragments (TDFs) were detected, sequenced, resulting in the identification of 71 by their similitude to accessions deposited in different data bases. The participation of four of these genes, putatively involved in the banana somatic embryogenesis, was further analyzed by real-time quantitative PCR (q-PCR). This confirmed their preferential expression at the transition from embryo early development to maturation. Noteworthy, tryptophan aminotransferase relate 2 (TAR2), which is involved in the indole-3-pyruvic acid dependent auxin biosynthesis, corresponded to one of the upregulated four genes, suggesting the requirement of this growth regulator at the transition stage. This study opens the path for future in-depth studies of molecular and biochemical events occurring during in vitro somatic embryogenesis in edible bananas.