[Show abstract][Hide abstract] ABSTRACT: Haustoria of biotrophic rust fungi are responsible for the uptake of nutrients from their hosts and for the production of secreted proteins, known as effectors, which modulate the host immune system. The identification of the transcriptome of haustoria and an understanding of the functions of expressed genes therefore hold essential keys for the elucidation of fungus-plant interactions and the development of novel fungal control strategies. Here, we purified haustoria from infected leaves and used 454 sequencing to examine the haustorial transcriptomes of Phakopsora pachyrhizi and Uromyces appendiculatus, the causal agents of soybean rust and common bean rust, respectively. These pathogens cause extensive yield losses in their respective legume crop hosts. A series of analyses were used to annotate expressed sequences, including transposable elements and viruses, to predict secreted proteins from the assembled sequences and to identify families of candidate effectors. This work provides a foundation for the comparative analysis of haustorial gene expression with further insights into physiology and effector evolution.
[Show abstract][Hide abstract] ABSTRACT: Functional markers for Sclerotinia basal stalk rot resistance in sunflower were obtained using gene-level information from the model species Arabidopsis thaliana. Sclerotinia stalk rot, caused by Sclerotinia sclerotiorum, is one of the most destructive diseases of sunflower (Helianthus annuus L.) worldwide. Markers for genes controlling resistance to S. sclerotiorum will enable efficient marker-assisted selection (MAS). We sequenced eight candidate genes homologous to Arabidopsis thaliana defense genes known to be associated with Sclerotinia disease resistance in a sunflower association mapping population evaluated for Sclerotinia stalk rot resistance. The total candidate gene sequence regions covered a concatenated length of 3,791 bp per individual. A total of 187 polymorphic sites were detected for all candidate gene sequences, 149 of which were single nucleotide polymorphisms (SNPs) and 38 were insertions/deletions. Eight SNPs in the coding regions led to changes in amino acid codons. Linkage disequilibrium decay throughout the candidate gene regions declined on average to an r (2) = 0.2 for genetic intervals of 120 bp, but extended up to 350 bp with r (2) = 0.1. A general linear model with modification to account for population structure was found the best fitting model for this population and was used for association mapping. Both HaCOI1-1 and HaCOI1-2 were found to be strongly associated with Sclerotinia stalk rot resistance and explained 7.4 % of phenotypic variation in this population. These SNP markers associated with Sclerotinia stalk rot resistance can potentially be applied to the selection of favorable genotypes, which will significantly improve the efficiency of MAS during the development of stalk rot resistant cultivars.
[Show abstract][Hide abstract] ABSTRACT: Edwardsiella tarda is a Gram-negative facultative anaerobe causing disease in animals and humans. Here, we announce the complete genome sequence of the channel catfish isolate E. tarda strain C07-87, which was isolated from an outbreak of gastrointestinal septicemia on a commercial catfish farm.
[Show abstract][Hide abstract] ABSTRACT: Diacylglycerol acyltransferases (DGAT) catalyze the final and rate-limiting step of triacylglycerol (TAG) biosynthesis in eukaryotic organisms. DGAT genes have been identified in numerous organisms. Multiple isoforms of DGAT are present in eukaryotes. We previously cloned DGAT1 and DGAT2 genes of tung tree (Vernicia fordii), whose novel seed TAGs are useful in a wide range of industrial applications. The objective of this study was to understand the developmental regulation of DGAT family gene expression in tung tree. To this end, we first cloned a tung tree gene encoding DGAT3, a putatively soluble form of DGAT that possesses 11 completely conserved amino acid residues shared among 27 DGAT3s from 19 plant species. Unlike DGAT1 and DGAT2 subfamilies, DGAT3 is absent from animals. We then used TaqMan and SYBR Green quantitative real-time PCR, along with northern and western blotting, to study the expression patterns of the three DGAT genes in tung tree tissues. Expression results demonstrate that 1) all three isoforms of DGAT genes are expressed in developing seeds, leaves and flowers; 2) DGAT2 is the major DGAT mRNA in tung seeds, whose expression profile is well-coordinated with the oil profile in developing tung seeds; and 3) DGAT3 is the major form of DGAT mRNA in tung leaves, flowers and immature seeds prior to active tung oil biosynthesis. These results suggest that DGAT2 is probably the major TAG biosynthetic isoform in tung seeds and that DGAT3 gene likely plays a significant role in TAG metabolism in other tissues. Therefore, DGAT2 should be a primary target for tung oil engineering in transgenic organisms.
PLoS ONE 10/2013; 8(10):e76946. DOI:10.1371/journal.pone.0076946 · 3.53 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Background
Theobroma cacao L. cultivar Matina 1-6 belongs to the most cultivated cacao type. The availability of its genome sequence and methods for identifying genes responsible for important cacao traits will aid cacao researchers and breeders.
We describe the sequencing and assembly of the genome of Theobroma cacao L. cultivar Matina
1-6. The genome of the Matina 1-6 cultivar is 445 Mbp, which is significantly larger than a sequenced Criollo cultivar, and more typical of other cultivars. The chromosome-scale assembly, version 1.1, contains 711 scaffolds covering 346.0 Mbp, with a contig N50 of 84.4 kbp, a scaffold N50 of 34.4 Mbp, and an evidence-based gene set of 29,408 loci. Version 1.1 has 10x the scaffold N50 and 4x the contig N50 as Criollo, and includes 111 Mb more anchored sequence. The version 1.1 assembly has 4.4% gap sequence, while Criollo has 10.9%. Through a combination of haplotype, association mapping and gene expression analyses, we leverage this robust reference genome to identify a promising candidate gene responsible for pod color variation. We demonstrate that green/red pod color in cacao is likely regulated by the R2R3 MYB transcription factor TcMYB113, homologs of which determine pigmentation in Rosaceae, Solanaceae, and Brassicaceae. One SNP within the target site for a highly conserved trans-acting siRNA in dicots, found within TcMYB113, seems to affect transcript levels of this gene and therefore pod color variation.
We report a high-quality sequence and annotation of Theobroma cacao L. and demonstrate its utility in identifying candidate genes regulating traits.
[Show abstract][Hide abstract] ABSTRACT: Camelina (Camelina sativa), a Brassicaceae oilseed, has received recent interest as a biofuel crop and production platform for industrial oils. Limiting wider production of camelina for these uses is the need to improve the quality and content of the seed protein-rich meal and oil, which is enriched in oxidatively unstable polyunsaturated fatty acids that are deleterious for biodiesel. To identify candidate genes for meal and oil quality improvement, a transcriptome reference was built from 2047 Sanger ESTs and more than 2 million 454-derived sequence reads, representing genes expressed in developing camelina seeds. The transcriptome of approximately 60K transcripts from 22 597 putative genes includes camelina homologues of nearly all known seed-expressed genes, suggesting a high level of completeness and usefulness of the reference. These sequences included candidates for 12S (cruciferins) and 2S (napins) seed storage proteins (SSPs) and nearly all known lipid genes, which have been compiled into an accessible database. To demonstrate the utility of the transcriptome for seed quality modification, seed-specific RNAi lines deficient in napins were generated by targeting 2S SSP genes, and high oleic acid oil lines were obtained by targeting FATTY ACID DESATURASE 2 (FAD2) and FATTY ACID ELONGASE 1 (FAE1). The high sequence identity between Arabidopsis thaliana and camelina genes was also exploited to engineer high oleic lines by RNAi with Arabidopsis FAD2 and FAE1 sequences. It is expected that these transcriptomic data will be useful for breeding and engineering of additional camelina seed traits and for translating findings from the model Arabidopsis to an oilseed crop.
[Show abstract][Hide abstract] ABSTRACT: Acyl-CoA binding proteins (ACBPs) have been identified in most branches of life, and play various roles in lipid metabolism, among other functions. Plants contain multiple classes of ACBP genes. The most diverse group is the class III proteins. Tung tree (Vernicia fordii) contains two such genes, designated VfACBP3A and VfACBP3B. The two proteins are significantly different in length and sequence. Analysis of tung ACBP3 genes revealed significant evolution, suggesting relatively ancient divergence of the two genes from a common ancestor. Phylogenetic comparisons of multiple plant class III proteins suggest that this group is the most evolutionarily dynamic class of ACBP. Both tung ACBP3 genes are expressed at similar levels in most tissues tested, but ACBP3A is stronger in leaves. Three-dimensional modeling predictions confirmed the presence of the conserved four α-helix bundle acyl-CoA binding (ACB); however, other regions of these proteins likely fold much differently. Acyl-CoA binding assays revealed different affinities for different acyl-CoAs, possibly contradicting the redundancy of function suggested by the gene expression studies. Subcellular targeting of transiently-expressed plant ACBP3 proteins contradicted earlier studies, and suggested that at least some class III ACBPs may be predominantly targeted to endoplasmic reticulum membranes, with little or no targeting to the apoplast.
[Show abstract][Hide abstract] ABSTRACT: Polyploidy often confers emergent properties, such as the higher fibre productivity and quality of tetraploid cottons than diploid cottons bred for the same environments. Here we show that an abrupt five- to sixfold ploidy increase approximately 60 million years (Myr) ago, and allopolyploidy reuniting divergent Gossypium genomes approximately 1-2 Myr ago, conferred about 30-36-fold duplication of ancestral angiosperm (flowering plant) genes in elite cottons (Gossypium hirsutum and Gossypium barbadense), genetic complexity equalled only by Brassica among sequenced angiosperms. Nascent fibre evolution, before allopolyploidy, is elucidated by comparison of spinnable-fibred Gossypium herbaceum A and non-spinnable Gossypium longicalyx F genomes to one another and the outgroup D genome of non-spinnable Gossypium raimondii. The sequence of a G. hirsutum A(t)D(t) (in which 't' indicates tetraploid) cultivar reveals many non-reciprocal DNA exchanges between subgenomes that may have contributed to phenotypic innovation and/or other emergent properties such as ecological adaptation by polyploids. Most DNA-level novelty in G. hirsutum recombines alleles from the D-genome progenitor native to its New World habitat and the Old World A-genome progenitor in which spinnable fibre evolved. Coordinated expression changes in proximal groups of functionally distinct genes, including a nuclear mitochondrial DNA block, may account for clusters of cotton-fibre quantitative trait loci affecting diverse traits. Opportunities abound for dissecting emergent properties of other polyploids, particularly angiosperms, by comparison to diploid progenitors and outgroups.
[Show abstract][Hide abstract] ABSTRACT: Cotton is the world's primary fiber crop and is a major agricultural commodity in over 30 countries. Like many other global commodities, sustainable cotton production is challenged by restricted natural resources. In response to the anticipated increase of agricultural water demand, a major research direction involves developing crops that use less water or that use water more efficiently. In this study, our objective was to identify differentially expressed genes in response to water deficit stress in cotton. A global expression analysis using cDNA-Amplified Fragment Length Polymorphism was conducted to compare root and leaf gene expression profiles from a putative drought resistant cotton cultivar grown under water deficit stressed and well watered field conditions.
We identified a total of 519 differentially expressed transcript derived fragments. Of these, 147 transcript derived fragment sequences were functionally annotated according to their gene ontology. Nearly 70 percent of transcript derived fragments belonged to four major categories: 1) unclassified, 2) stress/defense, 3) metabolism, and 4) gene regulation. We found heat shock protein-related and reactive oxygen species-related transcript derived fragments to be among the major parts of functional pathways induced by water deficit stress. Also, twelve novel transcripts were identified as both water deficit responsive and cotton specific. A subset of differentially expressed transcript derived fragments was verified using reverse transcription-polymerase chain reaction. Differential expression analysis also identified five pairs of duplicated transcript derived fragments in which four pairs responded differentially between each of their two homologues under water deficit stress.
In this study, we detected differentially expressed transcript derived fragments from water deficit stressed root and leaf tissues in tetraploid cotton and provided their gene ontology, functional/biological distribution, and possible roles of gene duplication. This discovery demonstrates complex mechanisms involved with polyploid cotton's transcriptome response to naturally occurring field water deficit stress. The genes identified in this study will provide candidate targets to manipulate the water use characteristics of cotton at the molecular level.
[Show abstract][Hide abstract] ABSTRACT: Sheath blight (SB), caused by Rhizoctonia solani, is a serious disease of cultivated rice (Oryza sativa L.) for which genetic resistance is in demand by breeders. With the goal of resistance (SBR)-QTL discovery in U. S. japonica breeding material, 197 doubled-haploid lines from a cross between MCR10277 (resistant) and Cocodrie (susceptible) were evaluated
in field and greenhouse assays with U. S. and Colombian pathogen isolates and genotyped at 111 microsatellite marker loci.
Four SBR QTLs from MCR10277 were identified, together accounting for 47% of field genetic variation. In all trials the strongest
effect was provided by a chromosome-9 QTL, qsbr_9.1, but some QTLs differed for U. S. and Colombian R. solani isolates. SBR QTLs coincided with only two of several height or heading-time QTLs, suggesting that the relationship between
these developmental traits and SBR is not simple. For the U. S. isolates, a microchamber greenhouse assay revealed the same
QTLs as did field inoculation.
KeywordsDoubled haploid–Quantitative-trait locus–Sheath blight
[Show abstract][Hide abstract] ABSTRACT: Horntails (Siricidae) are important wood-boring insects with 10 extant genera and about 122 species worldwide. Adults and larvae of Siricidae are often intercepted at ports and are of concern as potential alien invasive species. The family consists of 7 genera and 33 species in the New World: Eriotremex with one species, Sirex with 14 species, Sirotremex with one species, Teredon with one species, Tremex with two species, Urocerus with seven species, and Xeris with seven species. Five of these species have been accidentally introduced from the Old World: Eriotremex formosanus (Matsumura, 1912) into southeastern United States, probably from Vietnam; Sirex noctilio Fabricius, 1793, an important pest of Pinus spp., into eastern North America, Argentina, Brazil, and Uruguay from central Europe; Urocerus gigas (Linnaeus, 1758) into Chile, probably from Europe; Urocerus sah (Mocsáry, 1881) into northeastern North America, probably from southern Europe or North Africa; and Tremex fuscicornis (Fabricius, 1783) into Chile, probably from China. and Xeris spectrum townesi Maa, 1949, n. syn. of X. indecisus (MacGillivray, 1893). Five new lectotypes are designated for: Paururus californicus Ashmead, 1904; P. pinicolus Ashmead, 1898; P. hopkinsi Ashmead, 1904; Sirex torvus M. Harris; and S. taxodii Ashmead 1904. Three changes in rank from subspecies to species level are proposed: Sirex californicus (Ashmead), n. stat., from S. juvencus californicus; Urocerus fl avicornis (Fabricius), n. stat., from U. gigas fl avicornis; and Xeris indecisus (MacGillivray), n. stat., from X. morrisoni indecisus. Two species are excluded from the New World Siricidae: Sirex juvencus (Linnaeus), and Xeris spectrum (Linnaeus); both species have been frequently intercepted in North America, but they are not established. One species is excluded from the Palaearctic Siricidae: Sirex cyaneus Fabricius. The European "Sirex cyaneus" is distinct from the American Sirex cyaneus; Sirex torvus M. Harris is the oldest name for this species. We characterize the family based on all extant genera. The world genera are keyed and a reconstructed phylogeny is proposed. For genera not found in the New World, we provide a synonymic list, a description, and information about diversity with signifi cant references. For genera in the New World, each genus includes the following (if available and/or
Canadian Journal of Arthropod Identification 01/2012; 21:1-305. DOI:10.3752/cjai.2012.21
[Show abstract][Hide abstract] ABSTRACT: Rice (Oryza sativa L.) milling yield is a key export and domestic grain quality trait whose genetic control is poorly understood. To identify genomic regions influencing grain quality, quantitative trait locus (QTL) mapping was performed for quality-related traits including head-rice yield (HR) in 205 recombinant inbred lines (RILs) derived from a cross of L-204, a high-HR long-grain cultivar, with 01Y110, a low-HR advanced breeding line with high yield potential in the temperate U. S. rice-growing region. In replicated trials planted in California during 2007-2008, four QTLs carrying the HR-increasing allele from L204 and three from 01Y110 were consistently expressed. Multi-QTL models accounted for 30% of genetic variation for HR and up to 58% for other quality-related traits. Measures of kernel damage, though correlated with HR, were poor predictors of HR. Heading time, kernel dimension, apparent amylose content, and other highly heritable traits showed no correlation with HR. Stable QTLs for HR are likely to be revealed best by multienvironment experiments employing larger population sizes or more direct measurement of kernel structure and development traits involved in kernel breakage.
[Show abstract][Hide abstract] ABSTRACT: Arias RS, Molin WT, Ray JD, Peel MD & Scheffler BE (2011). Isolation and characterisation of the first microsatellite markers for Cyperus rotundus. Weed Research51, 451–460.SummaryThis is the first report of microsatellite markers for Cyperus rotundus. A total of 191 sequence-specific microsatellite markers were isolated and used to screen 12 accessions of C. rotundus and one accession of Cyperus esculentus collected from 10 different countries. Polymorphisms were observed in 49% of the markers tested, 22% of the markers were monomorphic and 29% had weak or no amplification. The best 57 markers are reported, and cluster analysis was used to analyse their resolving power. BLASTx screening of the contig sequences was also performed. Multiallelic loci over all samples ranged from 24% to 60%. The maximum number of alleles detected by the markers suggests a polyploidy nature of all C. rotundus accessions tested, except for the sample N25-Brazil. Chromosome number was determined for N12-Taiwan and used as an internal flow cytometry standard to estimate the amount of DNA within haploid nuclei of the remaining material. Chromosome numbers estimated for C. rotundus were 16 and 24. The markers identified in this study can be used for the identification of biotypes and detection of potential crosses of C. rotundus, to implement management practices for the effective control of this weed.