Integrating genes and phenotype: a wheat-Arabidopsis-rice glycosyltransferase database for candidate gene analyses

Genome-wide association studies for yield-related traits in soft red winter wheat grown in Virginia

Grain yield is a trait of paramount importance in the breeding of all cereals. In wheat (Triticum aestivum L.), yield has steadily increased since the Green Revolution, though the current rate of increase is not forecasted to keep pace with demand due to growing world population and increasing affluence. While several genome-wide association studies (GWAS) on yield and related component traits have been performed in wheat, the previous lack of a reference genome has made comparisons between studies difficult. In this study, a GWAS for yield and yield-related traits was carried out on a population of 322 soft red winter wheat lines across a total of four rain-fed environments in the state of Virginia using single-nucleotide polymorphism (SNP) marker data generated by a genotyping-by-sequencing (GBS) protocol. Two separate mixed linear models were used to identify significant marker-trait associations (MTAs). The first was a single-locus model utilizing a leave-one-chromosome-out approach to estimating kinship. The second was a sub-setting kinship estimation multi-locus method (FarmCPU). The single-locus model identified nine significant MTAs for various yield-related traits, while the FarmCPU model identified 74 significant MTAs. The availability of the wheat reference genome allowed for the description of MTAs in terms of both genetic and physical positions, and enabled more extensive post-GWAS characterization of significant MTAs. The results indicate a number of promising candidate genes contributing to grain yield, including an ortholog of the rice aberrant panicle organization (APO1) protein and a gibberellin oxidase protein (GA2ox-A1) affecting the trait grains per square meter, an ortholog of the Arabidopsis thaliana mother of flowering time and terminal flowering 1 (MFT) gene affecting the trait seeds per square meter, and a B2 heat stress response protein affecting the trait seeds per head.

A comparison of the transcriptomes between diploid and autotetraploid Paulownia fortunei under salt stress

Paulownia is a tree species grown in many countries. Our previous study reveals that tetraploid Paulownia fortunei is more tolerant to salt stress than its corresponding diploid tree. To investigate the molecular mechanisms of salt stress tolerance in P. fortunei, the transcriptomes of normal and salt-stressed diploid and tetraploid were investigated. After assembling the clean reads, we obtained 130,842 unigenes. The unigenes were aligned against six public databases (Nr, Nt, Swiss-Prot, COG, KEGG, GO) to discover homologs and assign functional annotations. We retrieved 7983 and 15,503 differentially expressed unigenes (DEUs) between the normal and the salt-stressed diploid and tetraploid P. fortunei, respectively. We identified dozens of important DEUs including 3 related to photosynthesis, 10 related to plant growth and development and 11 related to osmolytes. Some of these DEUs were upregulated in tetraploid compared to diploid and others were upregulated under salt stress. Quantitative reverse transcriptase polymerase chain reaction verified the expression patterns of 15 unigenes. Our results provided insights into the molecular aspects why tetraploid is stronger and more energetic than diploid under saline environment. This study provides useful information for further studies on the molecular mechanisms of salt tolerance in other tree plants.

Cloning and characterization of a specific UDP-glycosyltransferase gene induced by DON and Fusarium graminearum

TaUGT5: can reduce the proliferation and destruction of F. graminearum and enhance the ability of FHB resistance in wheat. Deoxynivalenol (DON) is one of the most important toxins produced by Fusarium species that enhances the spread of the pathogen in the host. As a defense, the UDP-glycosyltransferase (UGT) family has been deduced to transform DON into the less toxic form DON-3-O-glucoside (D3G), but the specific gene member in wheat that is responsible for Fusarium head blight (FHB) resistance has been little investigated and proved. In this study, a DON and Fusarium graminearum responsive gene TaUGT5, which is specific for resistant cultivars, was cloned with a 1431 bp open reading frame (ORF) encoding 476 amino acids in Sumai3. TaUGT5 is located on chromosome 2B, which has been confirmed in nulli-tetrasomic lines of Chinese Spring (CS) and is solely expressed among three homologs on the A, B and D genomes. Over-expression of this gene in Arabidopsis conferred enhanced tolerance when grown on agar plates that contain DON. Similarly, the coleoptiles of wheat over-expressing TaUGT5 showed more resistance to F. graminearum, evidencing reduced proliferation and destruction of plant tissue by the pathogen. However, the disease resistance in spikes was not as significant as that on coleoptile compared with wild-type plants. A subcellular localization analysis revealed that TaUGT5 was localized on the plasma membrane of tobacco leaf epidermal cells. It is possible that TaUGT5 could enhance tolerance to DON, protect the plant cell from the pathogen infection and result in better maintenance of the cell structure, which slows down pathogen proliferation in plant tissue.

Potentials, Challenges, and Genetic and Genomic Resources for Sugarcane Biomass Improvement

Lignocellulosic biomass has become an emerging feedstock for second-generation bioethanol production. Sugarcane (Saccharum spp. hybrids), a very efficient perennial C4 plant with a high polyploid level and complex genome, is considered a top-notch candidate for biomass production due to its salient features viz. fast growth rate and abilities for high tillering, ratooning, and photosynthesis. Energy cane, an ideal type of sugarcane, has been bred specifically as a biomass crop. In this review, we described (1) biomass potentials of sugarcane and its underlying genetics, (2) challenges associated with biomass improvement such as large and complex genome, narrow gene pool in existing commercial cultivars, long breeding cycle, and non-synchronous flowering, (3) available genetic resources such as germplasm resources, and genomic and cell wall-related databases that facilitate biomass improvement, and (4) mining candidate genes controlling biomass in genomic databases. We extensively reviewed databases for biomass-related genes and their usefulness in biofuel generation. This review provides valuable resources for sugarcane breeders, geneticists, and broad scientific communities involved in bioenergy production.

The Role of Microsatellites in Streptophyta Gene Evolution

Microsatellites form hotspot regions for recombination. In this research, we investigated whether genic microsatellites can be responsible for generating new genes by enhancing crossover between gene containing microsatellites and other genomic regions. We tested our hypothesis on 33,531 UniGene entries containing microsatellites. Each sequence was divided into microsatellites upstream and downstream fragments, and each pair of sequences was compared to study the microsatellites effect. The candidate pairs of genes are supposed to share a high similar fragment in one side of the microsatellites, while the other fragments should be completely different. This in silico approach detected 448 valid pairs of sequences in which both of them showed semi-resemblance nature. The synteny analysis for the detected sequences against 55 plant genomes indicated low representation of them across plant kingdom. Our results will add a body of knowledge toward understanding the role of microsatellites in gene evolution.

Brachypodium distachyon genotypes vary in resistance to Rhizoctonia solani AG8

Brachypodium distachyon (L.)P.Beauv. (Bd) has previously been developed as a pathosystem model for the wheat root rot pathogen Rhizoctonia solani Kühn anastomosis group 8 (AG8). Here we explore variation in resistance to R. solani AG8 in Bd, to determine whether genomic tools could be used to find Bd genes involved in the grass defence response, with the aim of using this information for the improvement of Rhizoctonia root rot resistance in wheat. We looked for variation in resistance to R. solani AG8 in a diverse Bd natural accession collection and in Bd T-DNA insertion lines selected based on putative mechanisms reported for tagged genes. All lines were susceptible to the pathogen. Repeatable and significant variation in resistance was measured in both groups, with greater variation in resistance found across the natural accessions than in the T-DNA lines. The widest and most repeatable variation in resistance was between lines Koz-3 and BdTR 13a. The ratio of R. solani AG8-inoculated to uninoculated root length for line Koz-3 was 33% greater than the same ratio for line BdTR 13a. The increased resistance of Koz-3 was associated with nodal root initiation in response to the pathogen. A negative correlation between seedling vigour and resistance was observed, but found not to be the sole source of variation in resistance to R. solani AG8. The only T-DNA line with significantly greater resistance to R. solani AG8 than the reference line had an insertion in a putative galactosyltransferase gene; however, this result needs further confirmation. Genetic resistance to Rhizoctonia root rot is not available in wheat cultivars and only a few instances of quantitative resistance to the pathogen have been described within close relatives of wheat. Brachypodium distachyon offers potential for further investigation to find genes associated with quantitative resistance and mechanisms of tolerance to R. solani AG8.

Transcriptional analysis of late ripening stages of grapevine berry

BACKGROUND

The composition of grapevine berry at harvest is a major determinant of wine quality. Optimal oenological maturity of berries is characterized by a high sugar/acidity ratio, high anthocyanin content in the skin, and low astringency. However, harvest time is still mostly determined empirically, based on crude biochemical composition and berry tasting. In this context, it is interesting to identify genes that are expressed/repressed specifically at the late stages of ripening and which may be used as indicators of maturity.

RESULTS

Whole bunches and berries sorted by density were collected in vineyard on Chardonnay (white cultivar) grapevines for two consecutive years at three stages of ripening (7-days before harvest (TH-7), harvest (TH), and 10-days after harvest (TH+10)). Microvinification and sensory analysis indicate that the quality of the wines made from the whole bunches collected at TH-7, TH and TH+10 differed, TH providing the highest quality wines.In parallel, gene expression was studied with Qiagen/Operon microarrays using two types of samples, i.e. whole bunches and berries sorted by density. Only 12 genes were consistently up- or down-regulated in whole bunches and density sorted berries for the two years studied in Chardonnay. 52 genes were differentially expressed between the TH-7 and TH samples. In order to determine whether these genes followed a similar pattern of expression during the late stages of berry ripening in a red cultivar, nine genes were selected for RT-PCR analysis with Cabernet Sauvignon grown under two different temperature regimes affecting the precocity of ripening. The expression profiles and their relationship to ripening were confirmed in Cabernet Sauvignon for seven genes, encoding a carotenoid cleavage dioxygenase, a galactinol synthase, a late embryogenesis abundant protein, a dirigent-like protein, a histidine kinase receptor, a valencene synthase and a putative S-adenosyl-L-methionine:salicylic acid carboxyl methyltransferase.

CONCLUSIONS

This set of up- and down-regulated genes characterize the late stages of berry ripening in the two cultivars studied, and are indirectly linked to wine quality. They might be used directly or indirectly to design immunological, biochemical or molecular tools aimed at the determination of optimal ripening in these cultivars.

wDBTF: an integrated database resource for studying wheat transcription factor families

BACKGROUND

Transcription factors (TFs) regulate gene expression by interacting with promoters of their target genes and are classified into families based on their DNA-binding domains. Genes coding for TFs have been identified in the sequences of model plant genomes. The rice (Oryza sativa spp. japonica) genome contains 2,384 TF gene models, which represent the mRNA transcript of a locus, classed into 63 families.

RESULTS

We have created an extensive list of wheat (Triticum aestivum L) TF sequences based on sequence homology with rice TFs identified and classified in the Database of Rice Transcription Factors (DRTF). We have identified 7,112 wheat sequences (contigs and singletons) from a dataset of 1,033,960 expressed sequence tag and mRNA (ET) sequences available. This number is about three times the number of TFs in rice so proportionally is very similar if allowance is made for the hexaploidy of wheat. Of these sequences 3,820 encode gene products with a DNA-binding domain and thus were confirmed as potential regulators. These 3,820 sequences were classified into 40 families and 84 subfamilies and some members defined orphan families. The results were compiled in the Database of Wheat Transcription Factor (wDBTF), an inventory available on the web http://wwwappli.nantes.inra.fr:8180/wDBFT/. For each accession, a link to its library source and its Affymetrix identification number is provided. The positions of Pfam (protein family database) motifs were given when known.

CONCLUSIONS

wDBTF collates 3,820 wheat TF sequences validated by the presence of a DNA-binding domain out of 7,112 potential TF sequences identified from publicly available gene expression data. We also incorporated in silico expression data on these TFs into the database. Thus this database provides a major resource for systematic studies of TF families and their expression in wheat as illustrated here in a study of DOF family members expressed during seed development.