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A commonly held misconception is that weeds reduce crop yield primarily because of resource competition. Weed presence reduces crop yield regardless of resource availability based on the timing of the critical period for weed control, and resource supplementation, and weed density studies. Weeds alter developmental trajectories of crops early in the growing season that often result in reduced yields. Signals produced by weeds that alter crop growth include light quality alterations, soil-borne chemicals, and/or volatile chemicals. Weed signals elicit a stress response in crops that may suppress growth through repression of the TARGET OF RAPAMYCIN (TOR) signaling system. Identification of weed-inducible genes and promoters will provide tools to investigate mechanisms controlling crop–weed interactions and develop weed-tolerant crops. Direct competition for resources is generally considered the primary mechanism for weed-induced yield loss. A re-evaluation of physiological evidence suggests weeds initially impact crop growth and development through resource-independent interference. We suggest weed perception by crops induce a shift in crop development, before resources become limited, which ultimately reduce crop yield, even if weeds are subsequently removed. We present the mechanisms by which crops perceive and respond to weeds and discuss the technologies used to identify these mechanisms. These data lead to a fundamental paradigm shift in our understanding of how weeds reduce crop yield and suggest new research directions and opportunities to manipulate or engineer crops and cropping systems to reduce weed-induced yield losses. [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]

Reliable reference selection for the accurate quantification of gene expression under various experimental conditions is a crucial step in qRT-PCR normalization. To date, only a few housekeeping genes have been identified and used as reference genes in tea plant. The validity of those reference genes are not clear since their expression stabilities have not been rigorously examined. To identify more appropriate reference genes for qRT-PCR studies on tea plant, we examined the expression stability of 11 candidate reference genes from three different sources: the orthologs of Arabidopsis traditional reference genes and stably expressed genes identified from whole-genome GeneChip studies, together with three housekeeping gene commonly used in tea plant research. We evaluated the transcript levels of these genes in 94 experimental samples. The expression stabilities of these 11 genes were ranked using four different computation programs including geNorm, Normfinder, BestKeeper, and the comparative ?CT method. Results showed that the three commonly used housekeeping genes of CsTUBULIN1, CsACINT1 and Cs18S rRNA1 together with CsUBQ1 were the most unstable genes in all sample ranking order. However, CsPTB1, CsEF1, CsSAND1, CsCLATHRIN1 and CsUBC1 were the top five appropriate reference genes for qRT-PCR analysis in complex experimental conditions. [ABSTRACT FROM AUTHOR]

Some plant species are particularly well adapted to environments disturbed by humans. Often such species are invasive and problematic, and thus are classified as weeds. Despite our best efforts to manage weeds, they continue to interfere with crop production. There is clearly much to learn about weeds, information that could aid in weed management and improve competitiveness in nonweedy species. The tools of molecular biology have been enlisted in ongoing efforts to manage weeds, most notably in the development and commercialization of crop plants tailored to resist certain herbicides. Molecular biology also has been used to gain a better understanding of how weeds compete and interact with neighboring plants, survive harsh environmental conditions, and evolve resistance to the herbicides used to control them. The next generation of molecular biology tools, such as genomic resources, may yield novel weed management strategies and shed new light on what makes plants weedy. [ABSTRACT FROM AUTHOR]

Dormancy regulation in vegetative buds is a complex process necessary for plant survival, development and architecture. Our understanding of and ability to manipulate these processes are crucial for increasing the yield and availability of much of the world''s food. In many cases, release of dormancy results in increased cell division and changes in developmental programs. Much can be learned about dormancy regulation by identifying interactions of signals in these crucial processes. Internal signals such as hormones and sugar, and external signals such as light act through specific, overlapping signal transduction pathways to regulate endo-, eco- and paradormancy. Epigenetic-like regulation of endodormancy suggests a possible role for chromatin remodeling similar to that known for the vernalization responses during flowering. [Copyright &y& Elsevier]

Flowering time is an important agronomic trait for canola breeders, as it provides growers with options for minimizing exposure to heat stress during flowering and to more effectively utilize soil moisture. Plants have evolved various systems to control seasonal rhythms in reproductive phenology including an internal circadian clock that responds to environmental signals. In this study, we used canola cultivar 'Westar' as a recurrent parent and canola cultivar 'Surpass 400' as the donor parent to generate a chromosome segment substitution line (CSSL) and to map a flowering time locus on chromosome A10 using molecular marker-assisted selection. This CSSL contains an introgressed 4.6 mega-bases (Mb) segment (between 13 and 17.6 Mb) of Surpass 400, which substantially delayed flowering compared with Westar. To map flowering time gene(s) within this locus, eight introgression lines (ILs) were developed carrying a series of different lengths of introgressed chromosome A10 segments using five co-dominant polymorphic markers located at 13.5, 14.0, 14.5, 15.0, 15.5, and 16.0 Mb. Eight ILs were crossed with Westar reciprocally and flowering time of resultant 16 F1 hybrids and parents were evaluated in a greenhouse (2021 and 2022). Four ILs (IL005, IL017, IL035, and IL013) showed delayed flowering compared to Westar (P < 0.0001), and their reciprocal crosses displayed a phenotype intermediate in flowering time of both homozygote parents. These results indicated that flowering time is partial or incomplete dominance, and the flowering time locus mapped within a 1 Mb region between two co-dominant polymorphic markers at 14.5–15.5 Mb on chromosome A10. The flowering time locus was delineated to be between 14.60 and 15.5 Mb based on genotypic data at the crossover site, and candidate genes within this region are associated with flowering time in canola and/or Arabidopsis. The co-dominant markers identified on chromosome A10 should be useful for marker assisted selection in breeding programs but will need to be validated to other breeding populations or germplasm accessions of canola. [ABSTRACT FROM AUTHOR]

Winter canola generally produces greater yields than spring canola. However, its range is limited due to its inability to withstand the harsh winter conditions that occur in many northern regions of the U.S.A. To identify loci associated with freezing tolerance in canola, we conducted a genome-wide association study (GWAS) using a genotyped diversity panel containing 399 accessions consisting primarily of winter canola. One-month-old greenhouse grown plants were subsequently cold-acclimated for two months in an environmental growth chamber prior to phenotyping for freezing survival using a visual damage scale and chlorophyll fluorescence (Fv/Fo). There was reasonable correlation observed between visual damage and chlorophyll fluorescence ratings among the top associated loci; the results indicated that some loci contributed to both freezing damage/tolerance and photosynthetic efficiency. The resulting numerical values for phenotypes were used for association analyses with the identified SNPs. Thirteen significant markers were identified on nine chromosomes for the phenotypes scored, with several showing significance for multiple phenotypes. Twenty-five candidate genes were identified as previously associated with freezing tolerance, photosynthesis, or cold-responsive in canola or Arabidopsis. [ABSTRACT FROM AUTHOR]

A diverse population (429 member) of canola (Brassica napus L.) consisting primarily of winter biotypes was assembled and used in genome-wide association studies. Genotype by sequencing analysis of the population identified and mapped 290,972 high-quality markers ranging from 18.5 to 82.4% missing markers per line and an average of 36.8%. After interpolation, 251,575 high-quality markers remained. After filtering for markers with low minor allele counts (count > 5), we were left with 190,375 markers. The average distance between these markers is 4463 bases with a median of 69 and a range from 1 to 281,248 bases. The heterozygosity among the imputed population ranges from 0.9 to 11.0% with an average of 5.4%. The filtered and imputed dataset was used to determine population structure and kinship, which indicated that the population had minimal structure with the best K value of 2–3. These results also indicated that the majority of the population has substantial sequence from a single population with sub-clusters of, and admixtures with, a very small number of other populations. Analysis of chromosomal linkage disequilibrium decay ranged from ~7 Kb for chromosome A01 to ~68 Kb for chromosome C01. Local linkage decay rates determined for all 500 kb windows with a 10kb sliding step indicated a wide range of linkage disequilibrium decay rates, indicating numerous crossover hotspots within this population, and provide a resource for determining the likely limits of linkage disequilibrium from any given marker in which to identify candidate genes. This population and the resources provided here should serve as helpful tools for investigating genetics in winter canola. [ABSTRACT FROM AUTHOR]

Information concerning genes and signals regulating cold acclimation processes in plants is abundant; however, less is known about genes and signals regulating the deacclimation process. A population of primarily winter B. napus varieties was used to conduct a genome-wide association study and to compare the transcriptomes from two winter B. napus varieties showing time-dependent differences in response to cold acclimation and deacclimation treatments. These studies helped to identify loci, candidate genes, and signaling processes impacting deacclimation in B. napus. GWAS identified polymorphisms at five different loci associated with freezing tolerance following deacclimation. Local linkage decay rates near these polymorphisms identified 38 possible candidate genes. Several of these genes have been reported as differentially regulated by cold stress in arabidopsis (Arabidopsis thaliana), including a calcium-binding EF-hand family protein (encoded by BnaCnng10250D) that was also differentially expressed during deacclimation in this study. Thousands of other genes differentially expressed during the acclimation and deacclimation treatments implicated processes involving oxidative stress, photosynthesis, light-regulated diurnal responses, and growth regulation. Generally, responses observed during acclimation were reversed within one week of deacclimation. The primary differences between the two winter B. napus varieties with differential deacclimation responses involved protection from oxidative stress and the ability to maintain photosynthesis. [ABSTRACT FROM AUTHOR]

Highlights • RNAseq data can be a good source for candidate reference genes. • SEC3A , UbOxRed, and RUB are suitable reference genes for qRT-PCR analysis in camelina. • Some summer- and winter-biotypes of camelina are miss-classified. • Allele-specific FLC markers distinguish summer- and winter-biotype of camelina. Abstract Quantitative real-time polymerase chain reaction (qRT-PCR) analysis greatly relies on transcript normalization using stably expressed reference genes. This study identifies reference genes for qRT-PCR analysis in different organs and vernalized tissues of camelina (Camelina sativa). Nineteen stably expressed candidate reference genes from 22,157 genes were identified by RNAseq analysis of pre- and post-vernalized tissues of a summer- (CO46) and winter- (Joelle) biotype. Two additional candidate reference genes were also selected from orthologs of arabidopsis encoding ACTIN2 (ACT2) and NOT INDUCED BY SCLEROTINIA INFECTION (NIS). We also evaluated the transcript levels of three camelina plant genes, SUPPRESSOR OF OVEREXPRESSION OF CO 1 (SOC1), FLOWERING LOCUS C (FLC), and MADS AFFECTING FLOWERING 2 (MAF2), which are known to be differentially-regulated in response to cold temperatures. The stability of transcript abundance was ranked using NormFinder, geNorm, BestKeeper, and Comparative ΔC T software. EXOCYST COMPLEX COMPONENT SEC3A (SEC3A), UBIQUINONE OXIDOREDUCTASE (UbOxRed), and RING-U-BOX domains-containing protein (RUB) were the most suitable reference genes for normalization of gene expression in camelina. In this study, SEC3A was used to normalize qRT-PCR expression data obtained using two sets of allele-specific FLC markers to differentiate summer- and winter-biotypes across 30 accessions of camelina. [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]

Background: Leafy spurge (Euphorbia esula L.) is an herbaceous weed that maintains a perennial growth pattern through seasonal production of abundant underground adventitious buds (UABs) on the crown and lateral roots. During the normal growing season, differentiation of bud to shoot growth is inhibited by physiological factors external to the affected structure; a phenomenon referred to as paradormancy. Initiation of shoot growth from paradormant UABs can be accomplished through removal of the aerial shoots (hereafter referred to as paradormancy release). Results: In this study, phytohormone abundance and the transcriptomes of paradormant UABs vs. shoot-induced growth at 6, 24, and 72 h after paradormancy release were compared based on hormone profiling and RNA-seq analyses. Results indicated that auxin, abscisic acid (ABA), and flavonoid signaling were involved in maintaining paradormancy in UABs of leafy spurge. However, auxin, ABA, and flavonoid levels/signals decreased by 6 h after paradormancy release, in conjunction with increase in gibberellic acid (GA), cytokinin, jasmonic acid (JA), ethylene, and brassinosteroid (BR) levels/signals. Twenty four h after paradormancy release, auxin and ABA levels/signals increased, in conjunction with increase in GA levels/signals. Major cellular changes were also identified in UABs at 24 h, since both principal component and Venn diagram analysis of transcriptomes clearly set the 24 h shoot-induced growth apart from other time groups. In addition, increase in auxin and ABA levels/signals and the down-regulation of 40 over-represented AraCyc pathways indicated that stress-derived cellular responses may be involved in the activation of stress-induced re-orientation required for initiation of shoot growth. Seventy two h after paradormancy release, auxin, cytokinin, and GA levels/signals were increased, whereas ABA, JA, and ethylene levels/signals were decreased. Conclusion: Combined results were consistent with different phytohormone signals acting in concert to direct cellular changes involved in bud differentiation and shoot growth. In addition, shifts in balance of these phytohormones at different time points and stress-related cellular responses after paradormancy release appear to be critical factors driving transition of bud to shoot growth. [ABSTRACT FROM AUTHOR]

Camelina [ Camelina sativa (L.) Crantz] is an annual oilseed crop from the Brassicaceae family. Camelina consists of both spring and winter biotypes with winter biotypes having exceptionally low temperature tolerance. Winter-hardy crops, such as camelina, can be planted in the fall and harvested early in the summer allowing for double- and relay-cropping options in the northern Great Plains of the USA. To enhance double- and relay-cropping systems, early maturing varieties of camelina are desired. The objectives of this study were to evaluate variation in flowering time and identify quantitative trait loci (QTL) in a biparental camelina population developed from crossing a winter (Joelle) and a spring (C046) biotype. An F7 recombinant inbred line (RIL) population consisting of 254 individuals was phenotyped for days to flowering (DTF) under greenhouse conditions after treatment with or without 8-weeks of vernalization. Variation in DTF among two experiments (Exp) was observed in the RIL population and average DTF for non-vernalized plants were 54.6 and 58.1 days after planting (DAP) (Exp 1 and 2 respectively) and 89 and 90.1 DAP in vernalized plants. Broad-sense heritability estimate of DTF across two experiments was 0.79 with and 0.96 without vernalization. The RIL population was genotyped with 2412 SNP markers to create a linkage map and perform QTL analysis. The map consisted of 20 linkage groups representing the 20 chromosomes (Chr) of C. sativa. The QTL analysis of DTF with vernalization identified significant loci on chromosomes 2, 8, 11, 13, and 16 with the highest logarithm of odds (LOD) score of 27.3 in Chr13 that explained 27 % of phenotypic variation. For DTF without vernalization, QTL were identified on chromosomes 7, 8, 12, 13, and 17 with the highest LOD scores of 70.85 on Chr8 and 70.04 on Chr13 that explained 41 and 42 % of phenotypic variation, respectively. Exploring the major QTL regions on chromosomes 8 and 13 of camelina indicated the presence of a MADS-box protein encoded by FLC (FLOWERING LOCUS C). Other candidate genes responsible for flowering time identified in the QTL regions include FLOWERING LOCUS T , TGACG motif-binding factor 4 , AGAMOUS-like MADS-box proteins (AGL17 , AGL71 , AGL72), CONSTANS-like 3 , an RNA-binding protein (HLP1), SHORT VEGETATIVE PHASE (SVP) gene, and a mediator complex subunit (MED18) that affects flowering time and floral organ formation. These RILs provide an important resource for developing early maturing varieties of camelina. • Recombinant Inbred Lines from a winter- x spring-type cross of camelina vary in flowering time. • Quantitative Trait Loci (QTL) for flowering time in camelina are located on chromosomes 2, 7, 8, 11, 12, 13, 16, and 17. • Flowering time regulator FLOWERING LOCUS C is located within major QTL in chromosomes 8 and 13. • This information will help breeders improve flowering time traits in camelina. [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]

Background: Leafy spurge (Euphorbia esula) is a perennial weed that is considered glyphosate tolerant, which is partially attributed to escape through establishment of new vegetative shoots from an abundance of underground adventitious buds. Leafy spurge plants treated with sub-lethal concentrations of foliar-applied glyphosate produce new vegetative shoots with reduced main stem elongation and increased branching. Processes associated with the glyphosate-induced phenotype were determined by RNAseq using aerial shoots derived from crown buds of glyphosate-treated and -untreated plants. Comparison between transcript abundance and accumulation of shikimate or phytohormones (abscisic acid, auxin, cytokinins, and gibberellins) from these same samples was also done to reveal correlations. Results: Transcriptome assembly and analyses confirmed differential abundance among 12,918 transcripts (FDR ≤ 0.05) and highlighted numerous processes associated with shoot apical meristem maintenance and stem growth, which is consistent with the increased number of actively growing meristems in response to glyphosate. Foliar applied glyphosate increased shikimate abundance in crown buds prior to decapitation of aboveground shoots, which induces growth from these buds, indicating that 5-enolpyruvylshikimate 3-phosphate (EPSPS) the target site of glyphosate was inhibited. However, abundance of shikimate was similar in a subsequent generation of aerial shoots derived from crown buds of treated and untreated plants, suggesting EPSPS is no longer inhibited or abundance of shikimate initially observed in crown buds dissipated over time. Overall, auxins, gibberellins (precursors and catabolites of bioactive gibberellins), and cytokinins (precursors and bioactive cytokinins) were more abundant in the aboveground shoots derived from glyphosate-treated plants. Conclusion: Based on the overall data, we propose that the glyphosate-induced phenotype resulted from complex interactions involving shoot apical meristem maintenance, hormone biosynthesis and signaling (auxin, cytokinins, gibberellins, and strigolactones), cellular transport, and detoxification mechanisms. [ABSTRACT FROM AUTHOR]

Camelina (Camelina sativa L. Crantz) is a short-season oilseed crop of the Brassicaceae family that consists of both summer and winter annual biotypes. Winter biotypes require non-freezing cold conditions for acquiring freezing tolerance (cold acclimation) and floral initiation (vernalization). Transcriptome profiles of a summer (CO46) biotype with poor freezing tolerance after acclimation and a winter (Joelle) biotype with excellent freezing tolerance after acclimation were compared prior to and after an 8-week cold treatment to identify key molecular pathways and genes responsive to cold acclimation and vernalization and potentially associated with freezing tolerance. Gene-set enrichment analyses identified AraCyc pathways involved in photosynthesis and lipid and hormone biosynthesis that were different between the two biotypes. Sub-network enrichment analyses identified hubs of molecular networks such as circadian clock, flowering, and hormone and stress responsive genes that were likely involved in vernalization but may also overlap with cold-induced freezing tolerance. A microRNA involved in floral initiation (MIR172A) was identified as a central hub for microRNA targets among upregulated genes for Joelle post-acclimation. Combined results are generally consistent with many previously identified molecular pathways and genes acting together to control vernalization, cold acclimation, and freezing tolerance. Our research provides new insights into the regulation of cold acclimation and molecular genetic mechanisms underlying cold tolerance and floral induction for the winter biotype Joelle. [ABSTRACT FROM AUTHOR]

Camelina (Camelina sativa L., Crantz) is an oilseed crop consisting of both spring- and winter-biotypes. Winter biotypes of camelina need a low-temperature treatment to acquire freezing tolerance and floral competence. However, spring biotypes do not require a low-temperature treatment to initiate flowering and do not cold acclimate to the same extent as winter biotypes. Exposure of the camelina winter biotype 'Joelle' to low temperature (5 °C) for 0-, 1-, 2-, 4-, and 6-weeks resulted in freezing survival rates of ~ 0%, 0%, 20%, 36%, and 72%, respectively, after being exposed to freezing conditions (−15 °C for 4 h). Winter biotype plants that survived the freezing treatment (42 d post-treatment under greenhouse conditions) also flowered; however, time to flowering was dependent on the cold treatment duration. Plants exposed to 5 °C for six weeks flowered first followed in order by plants exposed to 4- and 2-weeks cold. To decipher molecular regulation associated with low-temperature acquired freezing tolerance and floral competence in camelina, we analyzed the transcriptomes of a spring biotype (CO46) and winter biotype (Joelle) exposed to 0-, 1-, 2-, 4-, 6- and 8-weeks low temperature (5 °C). Genes and transcription factors with significant differential abundance (4-fold up or down) in the winter- compared to the spring-biotype of camelina were used to identify those over-represented among gene ontologies. The results highlighted gene ontologies associated with abiotic and biotic defense responses, oxidative stress responses, cell wall modification and cell expansion, biosynthesis of very long chain fatty acids and anthocyanins, as well as processes involving photosynthesis, sugar metabolism, transport, and phytohormone (abscisic acid, auxin, jasmonic acid, and salicylic acid) signaling. Transcripts associated with these processes in the winter biotype of camelina may be regulated by transcription factors similar to Arabidopsis MYB47, MYB75 , MYB90, NF-YA4 and NF-YB2 , HAT1 , GRF7 , CKG , and CBF1 and CBF2. • Freezing tolerance in winter biotypes of Camelina is dependent on duration of cold acclimation. • Cold acclimation-induced freezing tolerance involves additive effects of many genes. • A small number of transcription factors regulate genes associated with cold-induced freezing tolerance in Camelina. [ABSTRACT FROM AUTHOR]

Winter dormancy (WD) is a crucial strategy for plants coping with potentially deadly environments. In recent decades, this process has been extensively studied in economically important perennial eudicots due to changing climate. However, in evergreen monocots with no chilling requirements, dormancy processes are so far a mystery. In this study, we compared the WD process in closely related evergreen (Iris japonica) and deciduous (I. tectorum) iris species across crucial developmental time points. Both iris species exhibit a 'temporary' WD process with distinct durations, and could easily resume growth under warm conditions. To decipher transcriptional changes, full-length sequencing for evergreen iris and short read RNA sequencing for deciduous iris were applied to generate respective reference transcriptomes. Combining results from a multipronged approach, SHORT VEGETATIVE PHASE and FRUITFULL (FUL) from MADS-box was associated with a dormancy- and a growth-related module, respectively. They were co-expressed with genes involved in phytohormone signaling, carbohydrate metabolism, and environmental adaptation. Also, gene expression patterns and physiological changes in the above pathways highlighted potential abscisic acid and jasmonic acid antagonism in coordinating growth and stress responses, whereas differences in carbohydrate metabolism and reactive oxygen species scavenging might lead to species-specific WD durations. Moreover, a detailed analysis of MIKCC MADS-box in irises revealed common features described in eudicots as well as possible new roles for monocots during temporary WD, such as FLOWERING LOCUS C and FUL. In essence, our results not only provide a portrait of temporary WD in perennial monocots but also offer new insights into the regulatory mechanism underlying WD in plants. [ABSTRACT FROM AUTHOR]

Abstract: Seed dormancy is an important stage in the life cycle of many non-domesticated plants, often characterized by the temporary failure to germinate under conditions that normally favor the process. Pre-treating dormant imbibed seeds at a constant temperate accelerated germination of leafy spurge seeds under alternating temperatures. However, dormant seeds will also germinate without a pre-treatment, albeit at a much slower rate, which gives rise to longer periods of imbibition before germination. Transcriptome analyses on seeds exposed to prolonged imbibition highlighted pathways associated with phenylpropanoid biosynthesis and interacting networks of genes involved in plant defense. In addition to the many pathways associated with phenylpropanoid biosynthesis enriched with down-regulated genes upon germination, there were also numerous pathways enriched with up-regulated genes associated with energy metabolism, such as glycolysis. Transcriptome data further suggest that metabolism and signaling by the plant hormones ethylene, gibberellin, and abscisic acid are involved in the developmental transition from dormancy to germination. More specifically, sub-network enrichment analysis identified ABI3 as a central hub of a sub-network at germination including several down-regulated genes such as DELLA (i.e., RGL2), which represses gibberellin signaling processes required for germination. The 595-fold increase in the expression of ACC oxidase (ACO4) at germination also suggests an important role for ethylene biosynthesis in germinating leafy surge seeds. Furthermore, the 10–578-fold difference in expression of many genes such as HY5 and Histone H3 between two populations at germination, which were treated with and without a constant temperature germination-enhancing pretreatment, revealed disparate impacts on various biosynthetic, growth, signaling, and response processes. Overall, our results indicate a constant temperature pretreatment (20°C for 21d) is not required for germination of leafy spurge seeds at an alternating temperature. However, the presence or absence of the pretreatment does affect the rate of germination and the germination transcriptional programs. [Copyright &y& Elsevier]

Seed dormancy has been associated with red grain color in cereal crops for a century. The association was linked to qSD7-1/qPC7, a cluster of quantitative trait loci for seed dormancy/pericarp color in weedy red rice. This research delimited qSD7-1/qPC7 to the Os07g11020 or Rc locus encoding a basic helix-loop-helix family transcription factor by intragenic recombinants and provided unambiguous evidence that the association arises from pleiotropy. The pleiotropic gene expressed in early developing seeds promoted expression of key genes for biosynthesis of abscisic acid (ABA), resulting in an increase in accumulation of the dormancy-inducing hormone; activated a conserved network of eight genes for flavonoid biosynthesis to produce the pigments in the lower epidermal cells of the pericarp tissue; and enhanced seed weight. Thus, the pleiotropic locus most likely controls the dormancy and pigment traits by regulating ABA and flavonoid biosynthetic pathways, respectively. The dormancy effect could be eliminated by a heat treatment, but could not be completely overcome by gibberellic acid or physical removal of the seed maternal tissues. The dormancy-enhancing alleles differentiated into two groups basically associated with tropical and temperate ecotypes of weedy rice. Of the pleiotropic effects, seed dormancy could contribute most to the weed adaptation. Pleiotropy prevents the use of the dormancy gene to improve resistance of white pericarp cultivars against pre-harvest sprouting through conventional breeding approaches. [ABSTRACT FROM AUTHOR]

Expanding the southern range of herbaceous peony (Paeonia lactiflora Pall.) is a meaningful and worthwhile horticultural endeavor in the Northern Hemisphere. However, high temperatures in winter seriously hinder the bud dormancy release and flowering of peony in the more southern areas of subtropical and tropical regions. Resource introduction and hybridization can contribute to creating new cultivars with high adaptability in a warmer winter climate. In this study, three representative cultivars of P. lactiflora were screened for flowering capabilities and their annual growth cycles were observed to provide information needed for hybridization. Among these three cultivars, ‘Hang Baishao’ is the best adapted cultivar for southern growing regions and is unique in its ability to thrive in southern areas of N 30°00’. Pollen viability of ‘Hang Baishao’ was 55.60% based on five measuring methods, which makes it an excellent male parent in hybridization. Hybrid plants among these three cultivars grew well, but all of their flower buds aborted. Additionally, the ability of three growth regulators that advance the flowering of ‘Hang Baishao’ to promote an indoor cultivation strategy for improving peony application as a potted or cut-flower plant was tested. 5-azacytidine could impact the growth of ‘Hang Baishao’ and induce dwarfism and small flowers but not advance the flowering time. Gibberellin A3 promoted the sprouting and growth significantly, but all plants eventually withered. Chilling at 0–4°C for four weeks and irrigation with 300 mg/L humic acid was the optimal combination used to hasten flowering and ensure flowering quality simultaneously. These results can lay the foundation for future studies on the chilling requirement trait, bud dormancy release and key functional gene exploration of herbaceous peony. Additionally, this study can also provide guidance for expanding the range of economically important plants with the winter dormancy trait to the low-latitude regions. [ABSTRACT FROM AUTHOR]

Background Leafy spurge (Euphorbia esula L.) is a herbaceous perennial weed and dormancy in both buds and seeds is an important survival mechanism. Bud dormancy in leafy spurge exhibits three well-defined phases of para-, endo- and ecodormancy; however, seed dormancy for leafy spurge is classified as physiological dormancy that requires after-ripening and alternating temperature for maximal germination. Overlaps in transcriptome profiles between different phases of bud and seed dormancy have not been determined. Thus, we compared various phases of dormancy between seeds and buds to identify common genes and molecular processes, which should provide new insights about common regulators of dormancy. Results Cluster analysis of expression profiles for 201 selected genes indicated bud and seed samples clustered separately. Direct comparisons between buds and seeds are additionally complicated since seeds incubated at a constant temperature of 20°C for 21 days (21d C) could be considered paradormant (Para) because seeds may be inhibited by endospermgenerated signals, or ecodormant (Eco) because seeds germinate after being subjected to alternating temperature of 20:30°C. Since direct comparisons in gene expression between buds and seeds were problematic, we instead examined commonalities in differentially expressed genes associated with different phases of dormancy. Comparison between buds and seeds ('Para to Endo buds' and '21d C to 1d C seeds'), using endodormant buds (Endo) and dormant seeds (1d C) as common baselines, identified transcripts associated with cell cycle (HisH4), stress response/transcription factors (ICE2, ERFB4/ABR1), ABA and auxin response (ABA1, ARF1, IAA7, TFL1), carbohydrate/protein degradation (GAPDH_1), and transport (ABCB2). Comparison of transcript abundance for the 'Eco to Endo buds' and '21d C to 1d C seeds' identified transcripts associated with ABA response (ATEM6), auxin response (ARF1), and cell cycle (HisH4). These results indicate that the physiological state of 21d C seeds is more analogous to paradormant buds than that of ecodormant buds. Conclusion Combined results indicate that common molecular mechanisms associated with dormancy transitions of buds and seeds involve processes associated with ABA and auxin signaling and transport, cell cycle, and AP2/ERF transcription factors or their up-stream regulators. [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]

Quantitative real-time polymerase chain reaction (qRT-PCR) is the most important tool in measuring levels of gene expression due to its accuracy, specificity, and sensitivity. However, the accuracy of qRT-PCR analysis strongly depends on transcript normalization using stably expressed reference genes. The aim of this study was to find internal reference genes for qRT-PCR analysis in various experimental conditions for seed, adventitious underground bud, and other organs of leafy spurge. Eleven candidate reference genes (BAM4, PU1, TRP- like, FRO1, ORE9, BAM1, SEU, ARF2, KAPP, ZTL, and MPK4) were selected from among 171 genes based on expression stabilities during seed germination and bud growth. The other ten candidate reference genes were selected from three different sources: (1) 3 stably expressed leafy spurge genes (60S, bZIP21, and MD-100) identified from the analyses of leafy spurge microarray data; (2) 3 orthologs of Arabidopsis "general purpose" traditional reference genes (GAPDH&lowbar;1, GAPDH&lowbar;2, and UBC); and (3) 4 orthologs of Arabidopsis stably expressed genes (UBC9, SAND, PTB, and F-box) identified from Affymetrix ATH1 whole-genome GeneChip studies. The expression stabilities of these 21 genes were ranked based on the CT values of 72 samples using four different computation programs including geNorm, Normfinder, BestKeeper, and the comparative ΔCT method. Our analyses revealed SAND, PTB, ORE9, and ARF2 to be the most appropriate reference genes for accurate normalization of gene expression data. Since SAND and PTB were obtained from 4 orthologs of Arabidopsis, while ORE9 and ARF2 were selected from 171 leafy spurge genes, it was more efficient to identify good reference genes from the orthologs of other plant species that were known to be stably expressed than that of randomly testing endogenous genes. Nevertheless, the two newly identified leafy spurge genes, ORE9 and ARF2, can serve as orthologous candidates in the search for reference genes from other plant species. [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]

To avoid competing with economical plants, weed control must be implemented with a clean and appropriate strategy. Since the efficiency of leguminous crops in biological fixation of the atmospheric N2 is severely affected when grown under stressful conditions (the soil tested in this study was salt-affected; ECe = 8.99 dS m−1), an appropriate level of N fertilization should also be applied. Two field trials were performed in the 2018 and 2019 seasons to investigate the influences of soil-applied nitrogen (N) levels [48 (N1), 96 (N2), and 144 kg N ha−1 (N3)] and critical timing of weed removal (CTWR) on weed control efficiency, improving weed control, yield traits, and quality attributes in peanut (Arachis hypogaea L.). Each trial was conducted with three replicates and planned according to a split-plot in a completely randomized design. The results revealed that N levels had significant (p ≤ 0.01) variations for the dry weight of all weeds tested (narrow-leaved, broad-leaved, and total annual weeds), pods and seed weight and yields, N use efficiency, and oil and protein yields (t ha−1) in peanut in both seasons. N3 outperformed both N1 and N2 with respect to the above-mentioned traits, however, it decreased N use efficiency and seed oil content compared to N1 and N2, respectively. Dry weight of weeds and seed harvest index were significantly (p ≤ 0.01) increased, while seed oil and protein contents, N use efficiency, and yields of pods, seeds, and protein were decreased, with increased weed interference (with peanut plants) period in both seasons. In both seasons, the interaction effect of N × W (weed removal time) was significant (p ≤ 0.01) on the dry weight of weeds and peanut traits, including seed oil content, N use efficiency, and yields of pods, seeds, and protein, and their highest values were obtained with N3 × W6 (weed-free for the whole season). The CTWR had growing degree days (GDDs) of 221.4 and 189. These two GDDs each corresponded to 2 weeks after emergence (WAE) in both growing seasons. The critical weed-free period (CWFP) had GDDs of 1400 and 1380. These two GDDs corresponded to 9.5 and 10 WAE, respectively. The combination of CTWR and CWFP resulted in a critical period of weed control (CPWC) of 2–9.5 and 2–10 WAE in both growing seasons, respectively, for the peanut crop with an acceptable yield loss of 5%. A high positive (p ≤ 0.01) correlation was noted between oil yield and seed yield (r = 0.999 ** and 0.999 **). However, a high negative (p ≤ 0.01) correlation (r = −0.723 ** and −0.711 **) was found between dry total annual weeds and seed weight in the first and second seasons, respectively. The stepwise regression analysis revealed high significant participation of two traits (i.e., seed yield and oil content) and three traits (i.e., seed yield, oil content, and weight of seeds) in the variations in oil yield in the first and second seasons, respectively. These results recommend the use of N fertilization at a rate of 144 kg N ha−1 in conjunction with keeping the soil free of weeds throughout the season to maximize peanut productivity under saline (8.99 dS m−1) conditions. [ABSTRACT FROM AUTHOR]