WHAT IS THE IMPACT OF ALLOPOLYPLOIDY ON TRANSPOSABLE ELEMENTS? A STRUCTURAL APPROACH ON NEWLY SYNTHESIZED BRASSICA NAPUS ALLOTETRAPLOIDS

2010 ◽  
pp. 113-118 ◽  
Author(s):  
V. Sarilar ◽  
C. Ridel ◽  
A. Rousselet ◽  
M. Falque ◽  
J.-C. Letanneur ◽  
...  
Author(s):  
Fereshteh Shahoveisi ◽  
Atena Oladzad ◽  
Luis E. del Rio Mendoza ◽  
Seyedali Hosseinirad ◽  
Susan Ruud ◽  
...  

The polyploid nature of canola (Brassica napus) represents a challenge for the accurate identification of single nucleotide polymorphisms (SNPs) and the detection of quantitative trait loci (QTL). In this study, combinations of eight phenotyping scoring systems and six SNP calling and filtering parameters were evaluated for their efficiency in detection of QTL associated with response to Sclerotinia stem rot, caused by Sclerotinia sclerotiorum, in two doubled haploid (DH) canola mapping populations. Most QTL were detected in lesion length, relative areas under the disease progress curve (rAUDPC) for lesion length, and binomial-plant mortality data sets. Binomial data derived from lesion size were less efficient in QTL detection. Inclusion of additional phenotypic sets to the analysis increased the numbers of significant QTL by 2.3-fold; however, the continuous data sets were more efficient. Between two filtering parameters used to analyze genotyping by sequencing (GBS) data, imputation of missing data increased QTL detection in one population with a high level of missing data but not in the other. Inclusion of segregation-distorted SNPs increased QTL detection but did not impact their R2 values significantly. Twelve of the 16 detected QTL were on chromosomes A02 and C01, and the rest were on A07, A09, and C03. Marker A02-7594120, associated with a QTL on chromosome A02 was detected in both populations. Results of this study suggest the impact of genotypic variant calling and filtering parameters may be population dependent while deriving additional phenotyping scoring systems such as rAUDPC datasets and mortality binary may improve QTL detection efficiency.


2019 ◽  
Author(s):  
Michelle C. Stitzer ◽  
Sarah N. Anderson ◽  
Nathan M. Springer ◽  
Jeffrey Ross-Ibarra

Transposable elements (TEs) constitute the majority of flowering plant DNA, reflecting their tremendous success in subverting, avoiding, and surviving the defenses of their host genomes to ensure their selfish replication. More than 85% of the sequence of the maize genome can be ascribed to past transposition, providing a major contribution to the structure of the genome. Evidence from individual loci has informed our understanding of how transposition has shaped the genome, and a number of individual TE insertions have been causally linked to dramatic phenotypic changes. But genome-wide analyses in maize and other taxa have frequently represented TEs as a relatively homogeneous class of fragmentary relics of past transposition, obscuring their evolutionary history and interaction with their host genome. Using an updated annotation of structurally intact TEs in the maize reference genome, we investigate the family-level ecological and evolutionary dynamics of TEs in maize. Integrating a variety of data, from descriptors of individual TEs like coding capacity, expression, and methylation, as well as similar features of the sequence they inserted into, we model the relationship between these attributes of the genomic environment and the survival of TE copies and families. Our analyses reveal a diversity of ecological strategies of TE families, each representing the evolution of a distinct ecological niche allowing survival of the TE family. In contrast to the wholesale relegation of all TEs to a single category of junk DNA, these differences generate a rich ecology of the genome, suggesting families of TEs that coexist in time and space compete and cooperate with each other. We conclude that while the impact of transposition is highly family- and context-dependent, a family-level understanding of the ecology of TEs in the genome can refine our ability to predict the role of TEs in generating genetic and phenotypic diversity.‘Lumping our beautiful collection of transposons into a single category is a crime’-Michael R. Freeling, Mar. 10, 2017


1999 ◽  
Vol 266 (1429) ◽  
pp. 1677-1683 ◽  
Author(s):  
P. T. J. Emery ◽  
T. E. Robinson ◽  
R. Duddington ◽  
J. F. Y. Brookfield

2018 ◽  
Vol 19 (8) ◽  
pp. 2163 ◽  
Author(s):  
Marwa Ismael ◽  
Ali Elyamine ◽  
Yuan Zhao ◽  
Mohamed Moussa ◽  
Muhammad Rana ◽  
...  

Cadmium (Cd) is highly toxic, even at very low concentrations, to both animals and plants. Pollen is extremely sensitive to heavy metal pollutants; however, less attention has been paid to the protection of this vital part under heavy metal stress. A pot experiment was designed to investigate the effect of foliar application of Se (1 mg/L) and Mo (0.3 mg/L) either alone or in combination on their absorption, translocation, and their impact on Cd uptake and its further distribution in Brassica napus, as well as the impact of these fertilizers on the pollen grains morphology, viability, and germination rate in B. napus under Cd stress. Foliar application of either Se or Mo could counteract Cd toxicity and increase the plant biomass, while combined application of Se and Mo solutions on B. napus has no significant promotional effect on plant root and stem, but reduces the seeds’ weight by 10–11%. Se and Mo have decreased the accumulated Cd in seeds by 6.8% and 9.7%, respectively. Microscopic studies, SEM, and pollen viability tests demonstrated that pollen grains could be negatively affected by Cd, thus disturbing the plant fertility. Se and Mo foliar application could reduce the toxic symptoms in pollen grains when the one or the other was sprayed alone on plants. In an in vitro pollen germination test, 500 μM Cd stress could strongly inhibit the pollen germination rate to less than 2.5%, however, when Se (10 μM) or Mo (1.0 μM) was added to the germination medium, the rate increased, reaching 66.2% and 39.4%, respectively. At the molecular level, Se and Mo could greatly affect the expression levels of some genes related to Cd uptake by roots (IRT1), Cd transport (HMA2 and HMA4), Cd sequestration in plant vacuoles (HMA3), and the final Cd distribution in plant tissue at the physiological level (PCS1).


Agronomy ◽  
2019 ◽  
Vol 9 (3) ◽  
pp. 146 ◽  
Author(s):  
Hashem H.A. ◽  
Mansour H.A. ◽  
El-Khawas S.A. ◽  
Hassanein R.A.

The present study aimed to evaluate the potentiality of three seaweeds, which belong to different algal taxa (green alga Ulva lactuca Linnaeus, brown alga Cystoseira spp., and red alga Gelidium crinale (Hare ex Turner) Gaillon) as bio-fertilizers to improve the growth and yield of canola (Brassica napus L.) plants under greenhouse conditions. Furthermore, the impact of seaweeds in alleviating the effects of salt stress (75 and 150 mM NaCl) on canola plants was also investigated. The three examined seaweeds (applied as soil amendments) successfully alleviated the harmful effects of salinity on canola plants by significantly reducing the inhibition of chlorophyll a, b, total carbohydrate accumulation, and growth promoting hormones, while increasing antioxidative compounds, such as phenols, flavonoids, anthocyanin, and osmoprotectants, including total carbohydrates and proline. Phytochemical analysis of the three examined seaweeds suggests that their stimulatory effect on growth and productivity under normal and salinity growth conditions may be linked to their constituents of a wide variety of growth promotive hormones, including indole acetic acid, indole butyric acid, gibberellic acid, cytokinins, total carbohydrates, and phenolic compounds. U. lactuca was found to be the best candidate to be used as a bio-fertilizer to improve canola growth, yield, and salt stress tolerance.


Development ◽  
2016 ◽  
Vol 143 (22) ◽  
pp. 4101-4114 ◽  
Author(s):  
Jose L. Garcia-Perez ◽  
Thomas J. Widmann ◽  
Ian R. Adams

2004 ◽  
Vol 84 (2) ◽  
pp. 463-471 ◽  
Author(s):  
L. V. Gusta ◽  
E. N. Johnson ◽  
N. T. Nesbitt ◽  
K. J. Kirkland

Seedling vigour is a key critical component to produce well-established canola (Brassica napus) seedlings under less than ideal conditions in western Canada. Our objective was to determine if seed lots from late October (fall) or early spring (April) seeding dates improve seed vigour relative to mid-May (May) seeding dates. We compared seed size, seed maturity, germination percentage, and seedling emergence under controlled-environment conditions from six seed lots obtained from fall-sown (1997, 1998), April-sown (1998, 1999) and May-sown canola (1998, 1999) cv. Quest. On average, 80% of fall-derived seed for both years was larger than 1.7 mm compared to only 32% for May-derived canola seed. April-derived seed was intermediate. Fall and April derived seed were considered 40% mature compared to 16% for May-derived seed. In germination tests at 8°C, May derived seed germinated and emerged slower with a lower total germination percentage compared to falland April-derived seed lots. Priming reduced differences in emergence between the seed lots. Field studies at Scott, SK, sown in the fall of 1999 and 2000, and in early May of 2000 demonstrated that seed derived from fall- and April-sown canola produced higher plant densities, higher biomass at bolting, and higher seed yield than seed derived from May-sown canola. Yield was 10 to 45% less from seed derived from May-sown canola than seed derived from fall- and April-sown canola. This study established the impact of seeding date on seed quality and vigour, which in turn affected emergence, seedling vigour and yield. Also, seed vigour slowly declined within 1 yr, primarily with seed derived from the May-sown canola. Key words: Canola, Brassica napus, vigour (seed), seeding (fall), emergence, yield (quality)


Author(s):  
Marisol Domínguez ◽  
Elise Dugas ◽  
Médine Benchouaia ◽  
Basile Leduque ◽  
José Jimenez-Gomez ◽  
...  

ABSTRACTTomatoes come in a multitude of shapes and flavors despite a narrow genetic pool. Here, we leveraged whole-genome resequencing data available for 602 cultivated and wild accessions to determine the contribution of transposable elements (TEs) to tomato diversity. We identified 6,906 TE insertions polymorphisms (TIPs), which result from the mobilization of 337 distinct TE families. Most TIPs are low frequency variants and disproportionately located within or adjacent to genes involved in environmental response. In addition, we show that genic TE insertions tend to have strong transcriptional effects and can notably lead to the generation of multiple transcript isoforms. We also uncovered through genome-wide association studies (GWAS) ~180 TIPs associated with extreme variations in major agronomic traits or secondary metabolites. Importantly, these TIPs tend to affect loci that are distinct from those tagged by SNPs. Collectively, our findings suggest a unique and important role for TE mobilization in tomato diversification, with important implications for future breeding.


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