Showing papers in "Plant Molecular Biology Reporter in 2013"

AtMYB14 Regulates Cold Tolerance in Arabidopsis

Abstract: Low temperature affects plant growth and crop productivity. The CBF genes are a class of transcription factors that play important roles in cold response. Here we report that AtMYB14 participates in freezing tolerance in Arabidopsis by affecting expression of CBF genes. The AtMYB14 gene was down-regulated by cold treatment. AtMYB14 encodes a nuclear protein that functions as an R2R3-MYB transcription activator. Knock-down of AtMYB14 by artificial microRNA increased the tolerance to freezing stress. Both the CBF genes and the downstream genes were induced to a much higher level in AtMYB14 knock-down plants than in wild type under cold treatment. Our results suggest that AtMYB14 plays an important role in the plant response to cold stress.

Identifying a Carotenoid Cleavage Dioxygenase (ccd4) Gene Controlling Yellow/White Fruit Flesh Color of Peach

Abstract: Peach flesh color is a monogenic trait with the white phenotype being dominant over the yellow; its expression has been reported to be determined by a carotenoid degradative enzyme. In the present study, a carotenoid cleavage dioxygenase (ccd4) gene was analyzed to test whether it can be responsible for the flesh color determinism. The analysis was conducted on chimeric mutants with white and yellow sectors of the fruit mesocarp; it was then extended to a pool of cultivars and a segregating F1 population. A ccd4 functional allele is consistently associated with the ancestral white flesh color; on the other hand, the yellow phenotype originated from at least three independent mutations disrupting ccd4 function, thus preventing carotenoid degradation. In addition, retro-mutations recovering ccd4 function and re-establishing the ancestral white flesh color were detected. Our results show that ccd4 is the gene controlling flesh color in peach; its expression results in the degradation of carotenoids in white-fleshed genotypes, while the yellow color arises as a consequence of its inactivation.

Transferability of Newly Developed Pear SSR Markers to Other Rosaceae Species.

Abstract: A set of 120 simple sequence repeats (SSRs) was developed from the newly assembled pear sequence and evaluated for polymorphisms in seven genotypes of pear from different genetic backgrounds. Of these, 67 (55.8 %) primer pairs produced polymorphic amplifications. Together, the 67 SSRs detected 277 alleles with an average of 4.13 per locus. Sequencing of the amplification products from randomly picked loci NAUPy31a and NAUpy53a verified the presence of the SSR loci. When the 67 primer pairs were tested on 96 individual members of eight species in the Rosaceae family, 61.2 % (41/67) of the tested SSRs successfully amplified a PCR product in at least one of the Rosaceae genera. The transferability from pear to different species varied from 58.2 % (apple) to 11.9 % (cherry). The ratio of transferability also reflected the closer relationships within Maloideae over Prunoideae. Two pear SSR markers, NAUpy43c and NAUpy55k, could distinguish the 20 different apple genotypes thoroughly, and UPGMA cluster analysis grouped them into three groups at the similarity level of 0.56. The high level of polymorphism and good transferability of pear SSRs to Rosaceae species indicate their promise for application to future molecular screening, map construction, and comparative genomic studies among pears and other Rosaceae species.

Differential Expression of Rice Lambda Class GST Gene Family Members During Plant Growth, Development, and in Response to Stress Conditions

Abstract: Glutathione S-transferases (GSTs; EC 2.5.1.18) are members of an isozyme family and catalyze the conjugation of the reduced tripeptide glutathione to a variety of hydrophobic and electrophilic substrates. Though members of different classes of the GST superfamily have been identified and characterized from many plant species including rice, no detailed information is available for the Lambda class gene family in rice. In this study, a genome-wide analysis was carried out to investigate expression patterns of three Lambda class GST members of rice including OsGSTL1, OsGSTL2 and OsGSTL3 in seedlings, at different growth and developmental stages as well as in response to various biotic and abiotic stresses. Expression analysis using microarray datasets and quantitative real-time reverse transcriptase polymerase chain reaction suggests that this gene family express differentially in various tissues, in response to hormones and during different biotic and abiotic stresses including heavy metals, cold, drought and salt stress. Massively Parallel Signature Sequencing (MPSS) analysis also showed differential expression of OsGSTLs during plant growth and development and under different stresses. Out of three members, maximum expression of OsGSTL2 was observed for the MPSS libraries in comparison to other members. We conclude that members of rice Lambda class GST family play an important role in plant growth and development and in combating different biotic and abiotic stresses.

WRKY Transcription Factors in Wheat and Their Induction by Biotic and Abiotic Stress

Abstract: WRKY proteins constitute a large family of transcription factors in higher plants, and are involved in the regulation of development, senescence and stress resistance. However, little is known with respect to the constitution and function of WRKY genes in bread wheat (Triticum aestivum). We identified a set of 92 wheat WRKY genes from publicly available sequence databases, and constructed a phylogeny map based on the conserved WRKY domain peptide sequences. The wheat sequences were classified into the standard set of WRKY groups and sub-groups established from plant model genomes. Our results show the WRKY orthologues of wheat and rice are more similar compared to their Arabidopsis counterparts. Therefore, we argue some expansion of the WRKY family occurred following the divergence of these three species. The induction of sequence variation in a subset of 18 TaWRKY genes via somatic hybridization was studied by comparing the sequences from cv. JN177 and its derivative cv. SR3. We also analyzed the responses of these 18 genes to imposed salinity, PEG, ABA and SA using quantitative real time PCR. Nine of the 18 TaWRKY genes were up-regulated by exogenous SA. Six genes were up-regulated by salinity or PEG treatment, and their expression was also induced by exogenous ABA. Interestingly, induction by salinity or PEG was impaired when ABA biosynthesis was inhibited. The indication was that most of the TaWRKY genes involved in the abiotic stress response acted in an ABA-dependent manner.

An AFLP, SRAP, and SSR Genetic Linkage Map and Identification of QTLs for Fruit Traits in Pear ( Pyrus L.)

Abstract: In this study, a population of 97 F1 seedlings from a cross between the interspecific hybrid (European × Chinese species) pear ‘Bayuehong’ (BYH) and the Chinese pear ‘Dangshansuli’ (DS) was used for establishing linkage maps and for quantitative trait loci (QTL) discovery. Using amplified length polymorphism (AFLP), simple sequence repeat (SSR), and sequence-related amplified polymorphism (SRAP) markers, along with the S locus for self-incompatibility, two parental linkage maps were constructed. The map of BYH consisted of 214 markers (143 AFLPs, 64 SRAPs, 6 SSRs, and S) mapped on all 17 linkage groups of the pear genome with a total length of 1,352.7 cM. The map of DS was comprised of 122 markers (83 AFLPs, 37 SRAPs, 1 SSR, and S) distributed along all 17 linkage groups and covering 1,044.3 cM. Based on phenotypic data from two successive years (2007 and 2008) for six fruit traits, including fruit weight (in grams), fruit diameter (in centimeters), fruit length (in centimeters), soluble solids content, fruit shape index, and maturity date, 19 QTLs were detected. These QTLs were mapped on LG 01, LG 02, LG 05, LG 07, LG 08, LG 10 of the BYH map and LG 02, LG 06, LG 15 of the DS map and accounting for 7.1 to 22.0 % of the observed phenotypic variance. Four QTLs, Pfi-8-1 for fruit shape index, Pfm-8-1 for fruit maturity date, Pfw-7-1 and Pfw-8-1 for fruit weight (in grams), with LOD scores ≥3.5, were deemed as major genes. QTLs Pfi-8-1, Pfm-8-1, and Pfw-8-1 were co-localized on LG 08 of the BYH map, along with Pfl-8-1 for fruit length. It was observed that on LG 07 of the BYH map, QTLs for fruit length, fruit shape index, and fruit weight were clustered. When QTL locations from both years were compared, Pfl-7-1 and Pfl-7-2 for fruit length, Pfi-2-1 and Pfi-2-2 for fruit shape index, and Pfm-8-1 and Pfm-8-2 for fruit maturity date were stably mapped onto the same linkage groups, respectively. Moreover, Pfm-8-1 and Pfm-8-2 were also located within the same region of LG 08 of the BYH map.

Genome-Wide Analysis of Mitogen-Activated Protein Kinase Gene Family in Maize

Abstract: Mitogen-activated protein kinase (MAPK) cascades are universal signal transduction modules in plants. As the last component of the MAPK cascade (MAPKKK–MAPKK–MAPK), MAPK plays important roles in linking upstream kinases and downstream substrates. The MAPK proteins belong to a complex gene family in plants, with 20 MAPK genes in the Arabidopsis genome, 17 in the rice genome, and 21 in the poplar genome. Although the maize genome sequencing has been completed, no comprehensive study has been reported thus far for the MAPK gene family in maize. In this study, we identified 19 MAPK genes in maize. These ZmMPK genes belong to four groups (A–D) found in other plants. The phylogeny, chromosomal location, gene structure, and the functional relevancy of ZmMPK genes were analyzed. Moreover, we discuss the evolutionary divergence of MAPK genes in maize. Furthermore, we analyzed the expression profiles of ZmMPKs using the public microarray data and performed expression analyses in maize seedlings and adult plants. The data obtained from our study contribute to a better understanding of the complexity of MAPKs in plants and provide a useful reference for further functional analysis of MAPK genes in maize.

Transcriptome Profile Analysis of Maize Seedlings in Response to High-salinity, Drought and Cold Stresses by Deep Sequencing

Abstract: To identify the crosstalk between gene expression and metabolism in response to cold, drought and salt stresses, digital gene expression (DGE) analysis was performed on maize (Zea mays L.) seedlings subjected to these stresses. A total of 103,953 (70.79 %), 111,130 (68.62 %), 94,435 (69.33 %) and 94,577 (68.92 %) tags were matched to reference genes. The most differentially regulated tags, with a log2 ratio ≥1 or ≤−1 (P < 0.01 and FDR ≤0.001), were further analysed. Many genes and biological pathways were affected by multiple abiotic stresses. In particular, expression changes for the gibberellin (GA) metabolic genes could improve understanding of the molecular basis of the response of the GA pathway to stress conditions. In addition, a large dataset of tag-mapped transcripts was obtained that provide a strong basis for future research on the response to abiotic stress in maize. And a new list of candidate targets for functional studies on genes involved in cold, drought and salt stresses has been generated. In this study, we revealed complex changes at the transcriptional level in maize seedlings under different abiotic stresses. Such studies could lead to a better understanding of the genetic basis of the maize response to different environmental stimuli and would be essential for improving the abiotic stress tolerance of maize.

De Novo Characterization of Leaf Transcriptome Using 454 Sequencing and Development of EST-SSR Markers in Tea (Camellia sinensis)

Abstract: Although tea leaves are rich in secondary metabolites, not enough transcriptomic information is available to aid understanding of the molecular mechanisms underlying plant growth, development, and secondary metabolite production. In this study, a total of 437,908 reads were generated from the tea leaf transcriptome using 454 sequencing. De novo assembly yielded 25,637 unigenes, 22,872 of which were annotated by BLAST searches against public databases. Most of these unigenes mapped to carbohydrate metabolism, energy metabolism and secondary metabolite biosynthetic pathways. Some abundant transcripts related to photomorphogenesis and development in plants, including ubiquitin/26S proteasome, lipid transfer protein, PPR-containing protein, small GTPase, expansin, transport inhibitor response 1 and thioredoxin, were identified in the transcriptome. Most of the genes encoding the main enzymes involved in flavonoid, caffeine and theanine biosynthesis were also found, and six MYB and two bHLH genes known to regulate flavonoid synthesis were identified. ABC transporter and glutathione S-transferase, generally responsible for secondary metabolite transport, and CYP450, broadly involved in oxidation steps in secondary metabolism, were also present in a large number of unigenes. Additionally, 3,767 EST-SSRs were identified as potential molecular markers in our unigenes. A total of 100 PCR primer pairs used in initial screening tests among 20 tea genotypes successfully identified 36 polymorphic loci. Overall, the tea leaf transcriptome sequences generated in this study reveal novel gene expression profiles and offer important clues for further study of the molecular mechanism of tea leaf growth, development and secondary metabolite synthesis. The thousands of EST-SSR markers identified will facilitate marker-assisted selection in tea breeding.

Overexpression of the ABA-Dependent AREB1 Transcription Factor from Arabidopsis thaliana Improves Soybean Tolerance to Water Deficit

Abstract: Among current strategies for the development of drought-tolerant plants, engineering transcription factors that regulate the expression of genes related to abiotic stress is promising. Soybean plants overexpressing the transcription factor AtAREB1, which is involved in abscisic acid (ABA)-dependent stress responses, were generated using biolistics. Embryos of cultivar BR16, which is considered drought sensitive, were co-transformed with two plant expression vectors, 35S::AtAREB1 and 35S::ahas. Among the lines obtained, the drought tolerance of A24.10 and A2889.12 was assessed because these lines overexpressed the AtAREB1 gene and had a low copy number of the transgene. Another line, A2057.03, was also selected because it had a high copy number of the transgene (more than 100 copies) and low levels of transgene expression. Among the two low-copy lines, the A24.10 plants exhibited a slightly lower number of leaves and a shortening of the internode length; however, no growth retardation was observed for the line A2057.03. Water stress tolerance was particularly improved in the low-copy lines A24.10 and A2889.12. Plants of these lines were able to survive a water stress period of 5 days and exhibited no leaf damage, i.e., dried areas in the leaves 3 days after rewatering. Furthermore, these lines exhibited better growth and physiological performance under water-deficit (higher relative rate of shoot length, stomatal conductance, and photosynthesis) when compared to the wild type. Our results show the potential for improving drought tolerance by overexpressing AtAREB1 in soybean.

The MrWD40-1 Gene of Chinese Bayberry ( Myrica rubra ) Interacts with MYB and bHLH to Enhance Anthocyanin Accumulation

Abstract: Anthocyanins are important for fruits as they contribute not only to fruit color but also to human health Anthocyanin biosynthesis is transcriptionally regulated by the MYB–bHLH–WD40 transcription complex For Chinese bayberry (Myrica rubra), the MYB and bHLH regulating anthocyanin accumulation, named as MrMYB1 and MrbHLH1, respectively, have been isolated previously In this study, by searching and assembling the sequences available in the RNA-Seq database of Chinese bayberry, 60 WD40 members were obtained Through phylogenetic analysis of these members with those related to anthocyanin biosynthesis regulation in other plants, unigenes 803 and 11128, designated as MrWD40-1 and MrWD40-2, respectively, have been isolated as the putative WD40 members regulating anthocyanin biosynthesis However, positive correlation was observed between the anthocyanin accumulation and the expression patterns of MrWD40-1 but not MrWD40-2, both during fruit development, and in different tissues or cultivars of Chinese bayberry Tobacco transient assays indicated that the ternary expression of MrMYB1–MrbHLH1–MrWD40-1 induced anthocyanin accumulation earlier and stronger than with binary expression of MrMYB1–MrbHLH1 in the absence of MrWD40-1 Compared with the enhancement effect on anthocyanin biosynthesis of MrWD40-1, MrWD40-2 could not improve the anthocyanin accumulation even with MrMYB1 and MrbHLH1, although the highly conserved four WD repeat motifs were also present in MrWD40-2 Moreover, it was observed that MrWD40-1 physically interacted with both MrMYB1 and MrbHLH1 according to yeast two-hybrid analysis These results indicated that MrWD40-1, but not MrWD40-2, is the member regulating anthocyanin biosynthesis in Chinese bayberry through the formation of a ternary complex with MrMYB1 and MrbHLH1

Genome-Wide Analysis of the AP2/ERF Gene Family in Prunus mume

Abstract: The APETALA 2/ethylene-responsive element binding factor (AP2/ERF) transcription factors play important roles in plant development and responses to stress. Although the entire genomes of four Rosaceae species have been fully sequenced, no genome-wide analysis of AP2/ERF gene family has yet been reported in the Rosaceae family. In this study, 116 AP2/ERF genes were identified from Chinese plum (Prunus mume). Based on the number of AP2/ERF domains, these PmAP2/ERF genes were classified into three families (AP2, ERF, and RAV) along with a single member. The ERF family was subdivided into 11 groups. Of those, 22 and 41 PmAP2/ERF genes were involved in segmental and tandem duplications, respectively. Putative orthologs in Arabidopsis were identified for 73 PmAP2/ERF genes following synteny analysis. Transcriptome sequencing analysis showed that expression of PmAP2/ERF genes was widely variable.

Overexpression of the GmNAC2 Gene, an NAC Transcription Factor, Reduces Abiotic Stress Tolerance in Tobacco

Abstract: NAC (NAM, ATAF1, 2, and CUC2) proteins play important roles in plant development and stress responses. Glycine max NAC-like gene 2 (GmNAC2) is the first ATAF1-like NAC transcription factor identified in soybean. In this study, GmNAC-2-overexpressing tobacco lines were developed and found to be hypersensitive to drought, high salinity, and cold stress. Under abiotic stress, the transgenic tobacco leaves had higher malondialdehyde (MDA) levels compared with wild-type plants. An elevated MDA level is used frequently as an indicator of reactive oxygen species (ROS) and associated cell membrane degradation or dysfunction. To determine the mechanism of GmNAC2-mediated stress intolerance, leaf transcriptome analyses were performed comparing GmNAC2-overexpressing tobacco with wild-type tobacco. Identified downregulated genes included genes related to ROS scavenging in GmNAC2-overexpressing tobacco. These results indicate that GmNAC2 functions as a negative regulator during abiotic stress, and participates in ROS signaling pathways through modulation of the expression of genes related to ROS-scavenging.

Genetic Diversity and Population Structure Among Oat Cultivars and Landraces

Abstract: In this study, genetic diversity among 177 oat (Avena sativa L.) accessions including both white and red oat landraces and 36 commercial cultivars was studied for simple sequence repeat (SSR) loci. Thirty-one genomic and expressed sequence tags (EST)-derived primer pairs were selected according to high polymorphism from an initial 66 SSR batch. Markers revealed a high level of polymorphism, detecting a total of 454 alleles. The average gene diversity for the whole sample was 0.29. Genetic similarity, calculated using the Dice coefficient, was used for cluster analysis, and principal component analysis was also applied. In addition, population structure using a Bayesian clustering approach identified discrete subpopulation based on allele frequency and showed similar clustering of oat genotypes in four groups. Accessions could be classified into four main clusters that clearly separated the commercial cultivars, the red oat landraces and two clusters of white oat landraces. Cultivars showed less diversity than the landraces indicating a reduction of genetic diversity during breeding, whereas white oat landraces showed higher diversity than red ones. The average polymorphic information content of 0.80 for the SSR loci indicated the usefulness of many of the SSR for genotype identification. In particular, two markers, MAMA5 and AM04, with a total of 50 alleles and a high discrimination power (>0.90), were sufficient to discriminate among all commercial cultivars studied highlighting their potential use for variety identification.

Apple 1-Aminocyclopropane-1-Carboxylic Acid Synthase Genes, MdACS1 and MdACS3a , are Expressed in Different Systems of Ethylene Biosynthesis

Abstract: 1-Aminocyclopropane-1-carboxylic acid synthase (ACS) is one of the key regulatory enzymes involved in the synthesis of ethylene. Climacteric fruit ripening is accompanied by increased ethylene production, in which ethylene biosynthesis is changed from system 1 to system 2. In apple, at least four members of the ACS gene family have been identified, two of which, MdACS1 and MdACS3a, have been studied extensively due to their specific expression in fruit tissue. However, the regulatory role of MdACS1 and MdACS3a in the ethylene biosynthesis system is unknown. Here we addressed this issue by investigating ACS expression in ripening apple fruits. Expression analysis in ‘Golden Delicious’ and ‘Red Fuji’ fruits, in combination with treatments of 1-MCP (1-methylcyclopropene, an ethylene inhibitor) and Ethephon (an ethylene releaser) has demonstrated that MdACS3a and MdACS1operate in system 1 and system 2 ethylene biosynthesis, respectively.

Overexpression of Arabidopsis Dof1 , GS1 and GS2 Enhanced Nitrogen Assimilation in Transgenic Tobacco Grown Under Low-Nitrogen Conditions

Abstract: Nitrogen metabolism is essential for plant growth and development. The glutamine synthetase (GS) enzyme and the Dof transcription factor play important roles in the regulation of nitrogen metabolism. Using expression vectors, transgenic tobacco lines overexpressing each of Dof1 (Dof1.7), GS1 (GLN1;4) and GS2 were developed. cDNA clones of each of these transgenes were derived from Arabidopsis thaliana, and each transgene was under the control of the Rubisco small subunit promoter, PrbcS—a leaf-specific light-inducible promoter. Under low-nitrogen conditions, plant length, leaf surface, total protein, chlorophyll, as well as sucrose and glucose contents in leaves of transgenic tobacco lines were higher than those of wild-type plants. In addition, transgenic plants exhibited increased activities of enzymes involved in carbon and nitrogen metabolism, such as GS, nitrate reductase (NR), phosphoenolpyruvate carboxylase (PEPC) and pyruvate kinase (PK). The contents of most amino acids were significantly higher in transgenic plants than those of wild-type plants, whereas levels of nitrate, malic acid, and citric acid were significantly lower than those of wild-type plants. These findings suggest that Dof1 and GS work together to regulate the nitrogen metabolic pathway in plants, and this enhances nitrogen assimilation in transgenic tobacco plants grown under low-nitrogen conditions.

Identification of Major QTL for Waterlogging Tolerance Using Genome-Wide Association and Linkage Mapping of Maize Seedlings

Abstract: To investigate the genetic basis of maize seedling response to waterlogging, we performed a genome-wide association study in 144 maize inbred lines, measuring length, fresh and dry weight of roots and shoots under normal and waterlogged conditions using 45,868 SNPs. This panel was divided into three subgroups based on the population structure results and the LD decay distance was 180 kb. A biparental advanced backcross (AB) population was also used to detect quantitative trait loci (QTL). In a comparison of 16 different models, principal components analysis (PCA/top PC3) + K was found to be best for reduction of false-positive associations for further analysis. A whole-genome scan detected four strong peak signals (P < 2.18 × 10−5) significantly associated with the waterlogging response on chromosomes 5, 6 and 9. SNP4784, SNP200, SNP298, and SNP6314 showed significant association with corresponding traits under waterlogging and explained 14.99–19.36 %, 15.75–17.64 %, 16.08 % and 15.44 % of the phenotypic variation, respectively. The identified SNPs were located in GRMZM2G012046, GRMZM2G009808, GRMZM2G137108 and GRMZM2G369629 (AGPV1). SNP4784 (GRMZM2G012046) was colocalized with the major QTL that was identified with the same traits in the AB population. Forty-seven SNPs significantly associated (P < 2.18 × 10−4) with six traits in association mapping were identified and, among these, 33 SNPs were already reported in literature as waterlogging-related traits. These results will help elucidate the genetic basis of differential responses and tolerance to waterlogging stress among maize inbred lines, and provide novel loci for improvement of waterlogging tolerance of maize inbred lines using marker-assisted selection.

Proteomic Analysis of Heat Stress Response in Leaves of Radish ( Raphanus sativus L.)

Abstract: High temperature is one of the most important abiotic factors influencing plant growth and development Radish is a cool season vegetable crop sensitive to higher temperatures Heat injuries may affect plant growth, and interfere with formation and thickening of the fleshy taproot To characterize the heat-stress response in radish, 30-day-old radish seedlings were exposed to a temperature of 40 °C Leaf samples were then collected from the seedlings at 0 h, 12 h and 24 h after temperature exposure Proteins extracted from leaves were analyzed with two-dimensional electrophoresis (2-DE), and differentially expressed protein spots were identified by mass spectrometry (MS) In total, 11 differentially expressed proteins were identified successfully by MALDI-TOF MS Of these, four were heat shock proteins (HSPs), four were related to energy and metabolism, two were related to redox homeostasis, and one was related to signal transduction These proteins were analyzed further for mRNA levels, corresponding to differential levels of gene expression The result showed that gene expression profiles at the transcriptional level were not completely consistent with those at translational levels The differentially expressed heat stress response proteins identified, like small heat shock proteins together with energy and metabolism-related proteins, provide new insights into the molecular basis of plant responses to high temperature stresses in radish

Overexpression of TaHSF3 in Transgenic Arabidopsis Enhances Tolerance to Extreme Temperatures

Abstract: Heat shock factors (HSFs) in plants regulate heat stress response by mediating expression of a set of heat shock protein (HSP) genes In the present study, we isolated a novel heat shock gene, TaHSF3, encoding a protein of 315 amino acids in wheat Phylogenetic analysis showed that TaHSF3 belonged to HSF class B2 Subcellular localization analysis indicated that TaHSF3 localized in nuclei TaHSF3 was highly expressed in wheat spikes and showed intermediate expression levels in roots, stems, and leaves under normal conditions It was highly upregulated in wheat seedlings by heat and cold and to a lesser extent by drought and NaCl and ABA treatments Overexpression of TaHSF3 in Arabidopsis enhanced tolerance to extreme temperatures Frequency of survival of three TaHSF3 transgenic Arabidopsis lines was 75–91 % after heat treatment and 85–95 % after freezing treatment compared to 25 and 10 %, respectively, in wild-type plants (WT) Leaf chlorophyll contents of the transformants were higher (052–067 mg/g) than WT (035 mg/g) after heat treatment, and the relative electrical conductivities of the transformants after freezing treatment were lower (from 1756 to 186 %) than those of WT (375 %) The TaHSF3 gene from wheat therefore confers tolerance to extreme temperatures in transgenic Arabidopsis by activating HSPs, such as HSP70

Mapping Architectural, Phenological, and Fruit Quality QTLs in Apricot

Abstract: The F1 population “Harostar” × “Rouge de Mauves” was used to perform a quantitative trait loci (QTL) mapping for tree architecture traits (i.e., tree diameter, total branch number, tree shape); time to initial reproductive bud break; and fruit quality traits (i.e., ground color, fruit form, soluble solid content) using data collected from 2010 to 2012. For architectural traits, interval mapping detected QTLs only in “Rouge de Mauves” on linkage group 1 for trunk diameter in 2010, on LG6 for total branch number in 2010, and on LG1 and LG5 for tree shape for both years 2010 and 2011 combined. QTLs were detected only in “Harostar” for time to initial reproductive bud break on LG1 and LG4 in 2011. For fruit quality traits, data were collected in 2011 and 2012. QTLs were identified on LG1 in 2011 and on LG4 in 2012 for soluble solid content, on LG3 for ground color in both years, on LG7 only in 2011, and on LG3 for fruit form in both years. The QTLs that we identified were compared to those previously identified in other Prunus spp.

Differential Expression of Organic Acid Degradation-Related Genes During Fruit Development of Navel Oranges (Citrus sinensis) in Two Habitats

Abstract: Organic acids as well as soluble sugars contribute highly to flavor and overall quality of citrus fruit. Citric acid level in fruit is influenced by several factors including environmental conditions. In this study, it was observed that different environments in two habitats (Ganzhou, Jiangxi; Songyang, Zhejiang) had minor effects on total soluble solids and citrus color index but had significant effects on organic acids levels, particularly on citric acid level, in fruit of “Newhall” and “SkaggsBonanza” navel oranges (Citrus sinensis). Expression of genes involved in citric acid biosynthesis and degradation (CitCS1, CitCS2, CitAco1, CitAco2, CitAco3, CitIDH1, CitIDH2, CitIDH3, CitGAD4, CitGAD5, and CitGS2) was analyzed in fruit grown in each of the two habitats. Citric acid biosynthesis-related citrate synthase genes were steadily expressed during navel orange fruit development, while degradation-related genes were differentially expressed. These findings suggested that the influence of different environments on fruit quality traits was predominant on the regulation of organic acids level, particularly on the degradation of citric acid. A cascade of CitAco3–CitIDH1–CitGS2 might be involved in citric acid degradation in response to different environments during fruit growth and development.

Development and Characterization of Genomic and Gene-Based Microsatellite Markers in North American Red Oak Species

Abstract: Oaks (Quercus: Fagaceae) are ecological and economic keystones of many forested ecosystems but effective genetic management strategies are hindered by high levels of phenotypic plasticity within species and frequent hybridization among them. These same features, however, make oak communities suited for the study of speciation, hybridization, and genetic adaptation. Efforts to develop new and to adapt existing genomic resources to less-studied members of this genus should not only improve oak conservation and management but also aid the study of fundamental evolutionary processes. Here, we present a suite of 27 highly polymorphic simple sequence repeat (SSR) markers tested in four North American red oak (Quercus section Lobatae) species: Q. rubra, Q. ellipsoidalis, Q. coccinea, and Q. velutina. Five markers are genomic SSRs (gSSRs) — four novel and one previously transferred from Q. petraea — and 22 are gene-based SSRs derived from Q. robur and Q. petraea expressed sequence tags (EST-SSRs). Overall, levels of polymorphism detected with these primer pairs were high, with gene diversity (H e) averaging 0.66 across all loci in natural populations. In addition, we show that EST-SSR markers may have the potential to detect divergent selection at stress-resistance candidate genes among closely related oak species.

Genome-Wide Analysis of Gene Expression in Response to Drought Stress in Populus simonii

Abstract: Drought tolerance varies considerably in different species of Populus, and is a complex trait, involving the interplay of a vast array of genes. Although Populus simonii is one of the most important commercial plantation tree species in China, genes controlling drought-stress tolerance in this organism have not yet been identified. Here, tran- scriptomic changes during drought stress in P. simonii were detected using an Affymetrix GeneChip. In total, 1,028 transcripts were identified as differentially expressed under drought stress, of which 496 transcripts increased and 532 decreased in abundance (two-way ANOVA, fold change >4 and P<0.01). Expression changes of 20 candidate genes were validated by real-time PCR, indicating significant dif- ferences between the controls and water-deficit treatments. Gene annotation demonstrated that the majority of these P. simonii genes encode products involved in phytohormone metabolism, osmoregulation, and oxidative stress. Based on gene ontology (GO) classification, the increased genes were classified into six significantly enriched GO terms involved in 64 pathways, and the decreased genes were classified into 39 significantly enriched GO terms representing 42 path- ways. Bioinformatics analysis showed that the differential expression of plant hormone-related, transcription factor, cytochrome P450 gene superfamily, carbohydrate metabo- lism, and amino acid transporter genes may contribute to drought-stress tolerance in P. simonii. Our study provides global gene expression patterns during drought stress and will be valuable for further study of the molecular mecha- nisms of drought tolerance in P. simonii.

Comparative Analysis of Differentially Expressed Genes in Rice Under Nitrogen and Phosphorus Starvation Stress Conditions

Abstract: Nitrogen (N) and phosphorus (P) are two major mineral nutrients required for plant growth and development. Deficiencies in N or P results in both morphological and molecular changes such that plants develop adaptive responses to low N or P availability. In this study, we applied the Affymetrix Rice Genome array to analyze the overlap between the differentially expressed gene response to N and P starvation conditions. The results showed that a large number of genes were expressed differentially both under N starvation conditions and under P starvation conditions, including genes encoding a sulfate transporter, Fd-glutamate synthase, peroxidases, transcription factors, kinases and cytochrome P450s. In roots, 61, 42 and 159 genes were significantly up-regulated after 1 h, 24 h and 7 days, respectively, under both N and P starvation conditions, whereas 104, 50 and 166 genes, respectively, were significantly down-regulated. In shoots, 56, 104 and 101 genes were significantly up-regulated after 1 h, 24 h and 7 days, respectively, under both N and P starvation conditions, whereas 15, 80 and 59 genes, respectively, were significantly down-regulated. Generally, these differentially expressed genes belonged primarily to six biological process categories: molecular transport, molecular metabolism, regulation and modification, organism development, stress stimuli and electron transport. Our results may indicate some common physiological and genetic mechanisms in plant responses to environmental variations.

Transmission of Fruit Quality Traits in Apricot (Prunus armeniaca L.) and Analysis of Linked Quantitative Trait Loci (QTLs) Using Simple Sequence Repeat (SSR) Markers

Abstract: Twelve important pomological traits related to fruit quality were studied during 3 years in an F1 apricot progeny of 160 seedlings derived from a cross between the Spanish selection ‘Z701-1’ and the South African cultivar ‘Palsteyn’. Results indicated quantitative transmission of most of the fruit quality traits studied. In addition, a clear influence of the genetic background of parents was observed. In some seedlings, values outside the range of the parent were observed due to the influence of this genetic background. No correlations were found among most agronomic traits in apricot during the 3 years of the study. However, high correlations between years were described for most of the evaluated traits, and the environment had limited influence on the expression of the trait. A genetic map was developed using 41 apricot and peach SSR markers. The map obtained showed eight linkage groups (corresponding to the eight chromosomes) covering a total distance of 369.3 cM and an average distance between markers of 9 cM. Fifty-four QTLs associated with different traits were identified, including: blooming date (linkage groups G1, G4 and G7); ripening time (G4 and G6); fruit development (G4 and G6); fruit weight (G1 and G4); stone weight (G1 and G7); flesh color (G1 and G6); pH (G1, G2 and G4); malic acid (G1, G2 and G4); and soluble solids content (G4 and G5). We have highlighted several QTLs in G4 that explain the variability in various traits related to fruit quality such as blooming date, ripening time, and soluble solids content. In addition, we have also highlighted an important QTL on G2 that explains much of the variation in levels of acidity.

Genetic Diversity and Population Structure in Chinese Indigenous Poplar (Populus simonii) Populations Using Microsatellite Markers

Abstract: Populus simonii Carr. is an important ecological and commercial breeding species in northern China; however, human interference during the last few centuries has led to the reduction and fragmentation of natural populations. To evaluate genetic diversity and differentiation within and among existing populations, we used 20 microsatellite markers to examine the genetic variation and structure of 16 natural populations. Our results indicated that the level of genetic diversity differed among populations, with average number of alleles per locus (AR) and expected heterozygosity (He) ranging from 3.7 to 6.11 and 0.589 to 0.731, respectively. A marginal population from Qilian in the Qinghai–Tibetan Plateau showed the highest values (AR = 6.11, He = 0.731), and the Zhangjiakou and Yishui populations showed the lowest values (AR = 4.08, He = 0.589 and AR = 3.7, He = 0.604). The inbreeding coefficient (FIS) values for all populations were positive, which indicated an excess of homozygotes. The microsatellites allowed the identification of a significant subpopulation structure (K = 3), consistent with an isolation by distance model for P. simonii populations. Additionally, molecular variance analysis revealed that 14.2 % of the variation resided among populations, and 85.8 % could be attributed to variation within populations. These data provide valuable information for natural resource conservation and for optimization of breeding programs in the immediate future.

Loss of the Acetyl-CoA Carboxylase (accD) Gene in Poales

Abstract: The loss of a gene is a rare genome-shaping event and as such, contributes important information to our understanding of phylogenetic relationships between genes and between species. Deletion of a gene can help to define a lineage. Here, we utilize the deletion of the chloroplast gene encoding the acetyl-CoA carboxylase subunit D (accD) to help us define lineages based on its presence or absence in monocot plants specifically in Poales. Southern blots were constructed and probed for the presence of the accD gene. The existence of the portion of the accD gene represented by the probe was also verified by PCR and sequencing. Sequences were utilized for assembly of gene trees to link the absence or partial loss of the gene with a particular lineage. Here, we report new information adding accD gene presence in the Xyridaceae, pseudogene presence in the Flagellariaceae, and the absence of accD in Restionaceae and Joinvilleaceae. Based on our findings and the available data for accD sequences in Poales, we propose a model for accD loss beginning with a single event creating a pseudogene in the common ancestor to the restiid and graminid clades within Poales. This model also suggests that this pseudogene is carried as the ancestral state throughout most of the divergence of the Poales, a condition that would explain the highly varied pattern of accD pseudogene presence or gene absence in members of the restiid and graminid clades.

A Novel ABA-Responsive TaSRHP Gene from Wheat Contributes to Enhanced Resistance to Salt Stress in Arabidopsis thaliana

Abstract: A microarray analysis of the salt-resistant wheat mutant, RH8706-49, revealed a salt-induced gene containing a conserved DUF581 domain. The gene was cloned and designated as Triticum aestivum salt-related hypothetical protein (TaSRHP) and submitted to GenBank (accession no. GQ476575). Over-expression of TaSRHP in wild-type Arabidopsis thaliana cv. Columbia resulted in enhanced resistance to both salt and drought stresses. The sensitivity of the transgenic A. thaliana to abscisic acid (ABA) was also increased compared to that of wild-type plants. Furthermore, transgenic plants accumulated more K+ and proline and had a higher osmotic potential and lower Na+ content than untransformed plants. Real-time quantitative PCR analysis indicated that expression of TaSRHP was affected by salt, drought, cold, ABA, and other stresses, and expression of other stress-related genes in the transgenic plants differed from those of the control. Results indicate that the wheat TaSRHP gene may enhance the tolerance of plants to multiple abiotic stresses.

Comparison of Expression Vectors for Transient Expression of Recombinant Proteins in Plants

Abstract: Production of recombinant proteins in plants is of increasing importance for practical applications. However, the production of stable transformed transgenic plants is a lengthy procedure. Transient expression, on the other hand, can deliver recombinant proteins within a week, and many viral vectors have been constructed for that purpose. Each of them is reported to be highly efficient, robust and cost-effective. Here, a variety of expression vectors which were designed for transient and stable plant transformation, including pPZP3425, pPZP5025, pPZPTRBO, pJLTRBO, pEAQ-HT and pBY030-2R, was compared for the expression of green fluorescent protein and β-glucuronidase in Nicotiana benthamiana by Agrobacterium-mediated transient expression. Our results show that pPZPTRBO, pJLTRBO and pEAQ-HT had comparable expression levels without co-infiltration of a RNA-silencing inhibitor. The other vectors, including the non-viral vectors pPZP5025 and pPZP3425, needed co-infiltration of the RNA-silencing inhibitor P19 to give good expression levels.

Discrimination of American Cranberry Cultivars and Assessment of Clonal Heterogeneity Using Microsatellite Markers

Abstract: Cranberries (Vaccinium macrocarpon Ait.) are an economically important fruit crop derived from a North American native species. We report the application of 12 simple sequence repeats (SSR) or microsatellite markers to assess the genetic diversity of cranberry cultivars. We studied 164samplesof21differentcranberry cultivars,11 experimen- tal hybrids, and 6 representative accessions of wild species. Genetic cluster analysis, based on 117 SSR alleles, differenti- ated the major cranberry cultivars. However, some cranberry cultivar subclone variants and mislabeled samples were ob- served. Consensus genetic profiles identified the most likely clonal representatives of several important cranberry cultivars (e.g., "Ben Lear, "" Howes," and "Stevens"). The markers werefurther usedtoconfirm putativeparentsofseveral hybrid progenies. The long-term goal of our studies is to identify, preserve, and utilize unique genetic materials to breed im- proved cranberries. Attaining this goal will help growers maintain sustainability under changing economic and envi- ronmental conditions.