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Winter biotypes of rapeseed (Brassica napus L.) require a vernalization treatment to enter the reproductive phase and generally produce greater yields than spring rapeseed. To find genetic loci associated with freezing tolerance in rapeseed, we first performed genotyping‐by‐sequencing (GBS) on a diversity panel consisting of 222 rapeseed accessions originating primarily from Europe, which identified 69,554 high‐quality single‐nucleotide polymorphisms (SNPs). Model‐based cluster analysis suggested that there were eight subgroups. The diversity panel was then phenotyped for freezing survival (visual damage and Fv/Fo and Fv/Fm) after 2 months of cold acclimation (5°C) and a freezing treatment (−15°C for 4 h). The genotypic and phenotypic data for each accession in the rapeseed diversity panel was then used to conduct a genome‐wide association study (GWAS). GWAS results showed that 14 significant markers were mapped to seven chromosomes for the phenotypes scored. Twenty‐four candidate genes located within the mapped loci were identified as previously associated with lipid, photosynthesis, flowering, ubiquitination, and cytochrome P450 in rapeseed or other plant species. [ABSTRACT FROM AUTHOR]

Abstract: The nature of the vegetative to reproductive transition in the shoot apical meristem of Camelina sativa summer annual cultivar CO46 and winter annual cultivar Joelle was confirmed by treating seedlings with or without 8 weeks of vernalization. True to their life cycle classification, Joelle required a vernalization treatment to induce bolting and flowering, whereas CO46 did not. In this study, whole genome sequence, RNAseq, and resequencing of PCR‐amplified transcripts for a key floral repressor were used to better understand factors involved in the flowering habit of summer and winter biotypes at the molecular level. Analysis of transcriptome data indicated that abundance for one of the three genes encoding the floral repressor FLOWERING LOCUS C (FLC; Csa20 g015400) was 16‐fold greater in Joelle compared to CO46 prior to vernalization. Abundance of this transcript decreased only slightly in CO46 postvernalization, compared to a substantial decrease in Joelle. The results observed in the winter annual biotype Joelle are consistent with repression of FLC by vernalization. Further characterization of FLC at both the genome and transcriptome levels identified a one base deletion in the 5th exon coding for a keratin‐binding domain in chromosome 20 of CO46 and Joelle. The one base deletion detected in chromosome 20 FLC is predicted to result in a frameshift that would produce a nonfunctional protein. Analysis of whole genome sequence indicated that the one base deletion in chromosome 20 FLC occurred at a greater ratio in the summer biotype CO46 (2:1) compared to the winter biotype Joelle (1:4); similar trends were also observed for RNAseq and cDNA transcripts mapping to chromosome 20 FLC of CO46 and Joelle. [ABSTRACT FROM AUTHOR]

• Weeds reduce yield in soybeans (Glycine max) through incompletely defined mechanisms. The effects of weeds on the soybean transcriptome were evaluated in field conditions during four separate growing seasons. • RNASeq data were collected from six biological samples of soybeans growing with or without weeds. Weed species and the methods to maintain weed-free controls varied between years to mitigate treatment effects, and to allow detection of general soybean weed responses. • Soybean plants were not visibly nutrient- or water-stressed. We identified 55 consistently downregulated genes in weedy plots. Many of the downregulated genes were heat shock genes. Fourteen genes were consistently upregulated. Several transcription factors including a PHYTOCHROME INTERACTING FACTOR 3-like gene (PIF3) were included among the upregulated genes. Gene set enrichment analysis indicated roles for increased oxidative stress and jasmonic acid signaling responses during weed stress. • The relationship of this weed-induced PIF3 gene to genes involved in shade avoidance responses in Arabidopsis provide evidence that this gene may be important in the response of soybean to weeds. These results suggest that the weed-induced PIF3 gene will be a target for manipulating weed tolerance in soybean. [ABSTRACT FROM AUTHOR]

Insect diapause (dormancy) synchronizes an insect's life cycle to seasonal changes in the abiotic and biotic resources required for development and reproduction. Transcription analysis of diapause to post-diapause quiescent transition in the alfalfa leafcutting bee Megachile rotundata Fabricius identifies 643 post-diapause up-regulated gene transcripts and 242 post-diapause down-regulated transcripts. The log2 fold change in gene expression levels ranges from −5 to 7. Transcripts from several pivotal diapause-related processes, including chromatin remodelling, cellular signalling pathways, microRNA processing, anaerobic glycolysis, cell cycle arrest and neuroendocrine control, are identified as being differentially expressed during the diapause to post-diapause transition. In conjunction with studies from other insect species, the data indicate that there are several common mechanisms of diapause control and maintenance. [ABSTRACT FROM AUTHOR]

Aim Canada thistle ( Cirsium arvense- Cardueae, Asteraceae) is one of the worst invasive plants world-wide. Native to Eurasia, its unintentional introduction into North America now threatens the native flora and is responsible for enormous agricultural losses. The goals of this study are to: (1) reconstruct the evolutionary history of C. arvense and estimate how often it may have colonized North America, (2) compare the genetic diversity between European and North American populations to detect signs of demographic bottlenecks and/or patterns of population admixture, and (3) conduct bioclimatic comparisons to infer eventual niche shifts following this species' introduction into North America. Location Europe and North America. Methods A total of 1522 individuals from 58 populations were investigated with six microsatellite markers. Estimates of heterozygosity ( HE) and allelic richness ( RS) were quantified for each population, and population structure was inferred via analyses of molecular variance (AMOVAs), principal components analyses (PCAs), Mantel tests and Bayesian clustering analyses. Climatic niche spaces were based on 19 bioclimatic variables extracted from approximately 32,000 locations covering the entire range, and compared using PCA and hierarchical cluster analysis. Results Although there is evidence of multiple introductions from divergent European lineages, North American populations of C. arvense exhibited significantly lower levels of genetic diversity than their putative ancestors. Bioclimatic comparisons pointed to a high degree of niche conservatism during invasion, but indicated that genotypes from the former USSR and Central European mountain chains were probably best adapted to invade North America upon entry into the continent. Main conclusions Genetic and historical data suggest that C. arvense first entered North America from Western Europe with the first European settlers, and was later introduced from Eastern Europe into the prairie states during the agricultural boom. The species went through a significant bottleneck following its introduction into the New World, but the level of genetic diversity remained high owing to admixture between genetically differentiated lineages and to a highly efficient outcrossing breeding system. [ABSTRACT FROM AUTHOR]

* Premise of study: Weeds cause considerable environmental and economic damage. However, genomic characterization of weeds has lagged behind that of model plants and crop species. Here we describe the development of genomic tools and resources for 11 weeds from the Composite family that will serve as a basis for subsequent population and comparative genomic analyses. Because hybridization has been suggested as a stimulus for the evolution of invasiveness, we also analyze these genomic data for evidence of hybridization. * Methods: We generated 22 expressed sequence tag (EST) libraries for the 11 targeted weeds using Sanger, 454, and Illumina sequencing, compared the coverage and quality of sequence assemblies, and developed NimbleGen micro arrays for expression analyses in five taxa. When possible, we also compared the distributions of Ks values between orthologs of congeneric taxa to detect and quantify hybridization and introgression. * Results: Gene discovery was enhanced by sequencing from multiple tissues, normalization of eDNA libraries, and especially greater sequencing depth. However, assemblies from short sequence reads sometimes failed to resolve close paralogs. Substantial introgression was detected in Centaurea and Helianthus, but not in Ambrosia and Lactuca. * Conclusions: Transcriptome sequencing using next-generation platforms has greatly reduced the cost of genomic studies of no model organisms, and the ESTs and micro arrays reported here will accelerate evolutionary and molecular investigations of Composite weeds. Our study also shows how ortholog comparisons can be used to approximately estimate the genome-wide extent of introgression and to identify genes that have been exchanged between hybridizing taxa. [ABSTRACT FROM AUTHOR]

Crown buds of field-grown leafy spurge ( Euphorbia esula L.) were examined to determine relationships between carbohydrate metabolism and gene expression throughout para-, endo-, and eco-dormancy during the transition from summer, autumn, and winter, respectively. The data indicates that endo-dormancy plays a role in preventing new shoot growth during the transition from autumn to winter. Cold temperature was involved in breaking endo-dormancy, inducing flowering competence, and inhibiting shoot growth. An inverse relationship developed between starch and soluble sugar (mainly sucrose) content in buds during the shift from para- to endo-dormancy, which continued through eco-dormancy. Unlike starch content, soluble sugars were lowest in crown buds during para-dormancy but increased over two- to three-fold during the transition to endo-dormancy. Several genes ( AGPase, HK, SPS, SuSy, and UGPase) coding for proteins involved in sugar metabolism were differentially regulated in conjunction with well-defined phases of dormancy in crown buds. Marker genes for S-phase progression, cell wall biochemistry, or responsive to auxin were also differentially regulated during transition from para-, endo-, and eco-dormancy. The results were used to develop a model showing potential signalling pathways involved in regulating seasonal dormancy status in leafy spurge crown buds. [ABSTRACT FROM AUTHOR]

Weed presence early in the life cycle of maize (typically, from emergence through the 8 to 12 leaf growth stage) can reduce crop growth and yield and is known as the critical weed‐free period (CWFP). Even if weeds are removed during or just after the CWFP, crop growth and yield often are not recoverable. We compared transcriptome responses of field‐grown hybrid maize at V8 in two consecutive years among plants grown under weed‐free and two weed‐stressed conditions (weeds removed at V4 or present through V8) using RNAseq analysis techniques. Compared with weed‐free plant responses, physiological differences at V8 were identified in all weed‐stressed plants and were most often associated with altered photosynthetic processes, hormone signaling, nitrogen use and transport, and biotic stress responses. Even when weeds were removed at V4 and tissues sampled at V8, carbon: nitrogen supply imbalance, salicylic acid signals, and growth responses differed between the weed‐stressed and weed‐free plants. These underlying processes and a small number of developmentally important genes are potential targets for decreasing the maize response to weed pressure. Expression differences of several novel, long noncoding RNAs resulting from exposure of maize to weeds during the CWFP were also observed and could open new avenues for investigation into the function of these transcription units. [ABSTRACT FROM AUTHOR]

Summary Expressed sequence tags (EST)-based microarrays are powerful tools for gene discovery and signal transduction studies in a small number of well-characterized species. To explore the usefulness of this technique for poorly characterized species, we have hybridized the 11 522-element Arabidopsis microarrays with labeled cDNAs from mature leaf and shoot apices from several different species. Expression of 23 to 47% of the genes on the array was detected, demonstrating that a large number of genes from distantly related species can be surveyed on Arabidopsis arrays. Differential expression of genes with known functions was indicative of the physiological state of the tissues tested. Genes involved in cell division, stress responses, and development were conserved and expressed preferentially in growing shoots. [ABSTRACT FROM AUTHOR]