scholarly journals De novo super-early progeny in interspecific crosses Pisum sativum L. × P. fulvum Sibth. et Sm

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Hatice Sari ◽  
Duygu Sari ◽  
Tuba Eker ◽  
Cengiz Toker
Keyword(s):  
Wild Species ◽  
Crop Production ◽  
De Novo ◽  
Transgressive Segregation ◽  
Interspecific Crosses ◽  
Vegetable Production ◽  
Agricultural Lands ◽  
Narrow Sense Heritability ◽  
Suitable Climate ◽  
High Level

AbstractEarliness in crop plants has a crucial role in avoiding the stress of drought and heat, which are the most important challenging stressors in crop production and are predicted to increase in the near future due to global warming. Furthermore, it provides a guarantee of vegetable production in the short growing season of agricultural lands in the northern hemisphere and at high altitudes. The growing human population needs super early plant cultivars for these agricultural lands to meet future global demands. This study examined de novo super-early progeny, referred to as much earlier than that of the earlier parent, which flowered in 13–17 days and pod setting in 18–29 days after germination, discovered in F2 and studied up to F5 derived from interspecific crosses between garden pea (P. sativum L.) and the most distant relative of pea (P. fulvum Sibth. et Sm.). De novo super-early progeny were found to be earlier by about one month than P. sativum and two months than P. fulvum under short day conditions in the F5 population. In respect of days to flowering and pod setting, de novo super-early progeny had a relatively high level of narrow sense heritability (h2 = 82% and 80%, respectively), indicating that the selections for earliness in segregating populations was effective for improvement of extreme early maturing varieties. De novo super-early progeny could be grown under heat stress conditions due to the escape ability. Vegetable types were not only high yielding but also free of any known undesirable traits from the wild species, such as pod dehiscence and non-uniform maturity. It could be considered complementary to “speed breeding”, possibly obtaining more than six generations per year in a suitable climate chamber. Not only de novo super-early progeny but also transgressive segregation for agro-morphological traits can be created via interspecific crosses between P. sativum and P. fulvum, a precious unopened treasure in the second gene pool. Useful progeny obtained from crossing wild species with cultivated species reveal the importance of wild species.

Problems and prospects of land reclamation in the non-Chernozem zone of Russia

2020 ◽  
Author(s):  
V.A. Shevchenko ◽  
Keyword(s):  
Agricultural Production ◽  
Land Reclamation ◽  
Agricultural Practice ◽  
Agricultural Crops ◽  
Agricultural Lands ◽  
High Level

The non-black earth zone of Russia is a zone of guaranteed harvest of major agricultural crops. However, at present, the potential of the reclaimed lands of the Non-Black Earth Region remains largely unrealized. In world agricultural practice, land reclamation combined with the use of modern technical means is an important factor in the development of agriculture, a condition for a consistently high level of agricultural production. Therefore, in all countries, reclaimed lands are given a special status, and the necessary amount of reclamation fund of agricultural lands is created.

scholarly journals Genome-Wide Metabolic Reconstruction of the Synthesis of Polyhydroxyalkanoates from Sugars and Fatty Acids by Burkholderia Sensu Lato Species

2021 ◽  
Vol 9 (6) ◽  
pp. 1290
Author(s):  
Natalia Alvarez-Santullano ◽  
Pamela Villegas ◽  
Mario Sepúlveda Mardones ◽  
Roberto E. Durán ◽  
Raúl Donoso ◽  
...  
Keyword(s):  
Fatty Acids ◽  
De Novo ◽  
Reducing Power ◽  
Pentose Phosphate ◽  
Fine Tuning ◽  
Metabolic Reconstruction ◽  
Phylogenetic Groups ◽  
Outlier Group ◽  
Pha Genes ◽  
High Level

Burkholderia sensu lato (s.l.) species have a versatile metabolism. The aims of this review are the genomic reconstruction of the metabolic pathways involved in the synthesis of polyhydroxyalkanoates (PHAs) by Burkholderia s.l. genera, and the characterization of the PHA synthases and the pha genes organization. The reports of the PHA synthesis from different substrates by Burkholderia s.l. strains were reviewed. Genome-guided metabolic reconstruction involving the conversion of sugars and fatty acids into PHAs by 37 Burkholderia s.l. species was performed. Sugars are metabolized via the Entner–Doudoroff (ED), pentose-phosphate (PP), and lower Embden–Meyerhoff–Parnas (EMP) pathways, which produce reducing power through NAD(P)H synthesis and PHA precursors. Fatty acid substrates are metabolized via β-oxidation and de novo synthesis of fatty acids into PHAs. The analysis of 194 Burkholderia s.l. genomes revealed that all strains have the phaC, phaA, and phaB genes for PHA synthesis, wherein the phaC gene is generally present in ≥2 copies. PHA synthases were classified into four phylogenetic groups belonging to class I II and III PHA synthases and one outlier group. The reconstruction of PHAs synthesis revealed a high level of gene redundancy probably reflecting complex regulatory layers that provide fine tuning according to diverse substrates and physiological conditions.

scholarly journals Remote Control of Greenhouse Vegetable Production with Artificial Intelligence—Greenhouse Climate, Irrigation, and Crop Production

Sensors ◽  
2019 ◽  
Vol 19 (8) ◽  
pp. 1807 ◽  
Author(s):  
Silke Hemming ◽  
Feije de Zwart ◽  
Anne Elings ◽  
Isabella Righini ◽  
Anna Petropoulou
Keyword(s):  
Artificial Intelligence ◽  
Crop Production ◽  
Vegetable Production ◽  
Digital Interface ◽  
Greenhouse Climate ◽  
Fresh Food ◽  
Net Profit ◽  
Greenhouse Vegetable ◽  
Process Computer ◽  
Cucumber Yield

The global population is increasing rapidly, together with the demand for healthy fresh food. The greenhouse industry can play an important role, but encounters difficulties finding skilled staff to manage crop production. Artificial intelligence (AI) has reached breakthroughs in several areas, however, not yet in horticulture. An international competition on “autonomous greenhouses” aimed to combine horticultural expertise with AI to make breakthroughs in fresh food production with fewer resources. Five international teams, consisting of scientists, professionals, and students with different backgrounds in horticulture and AI, participated in a greenhouse growing experiment. Each team had a 96 m2 modern greenhouse compartment to grow a cucumber crop remotely during a 4-month-period. Each compartment was equipped with standard actuators (heating, ventilation, screening, lighting, fogging, CO2 supply, water and nutrient supply). Control setpoints were remotely determined by teams using their own AI algorithms. Actuators were operated by a process computer. Different sensors continuously collected measurements. Setpoints and measurements were exchanged via a digital interface. Achievements in AI-controlled compartments were compared with a manually operated reference. Detailed results on cucumber yield, resource use, and net profit obtained by teams are explained in this paper. We can conclude that in general AI performed well in controlling a greenhouse. One team outperformed the manually-grown reference.

scholarly journals Quick and efficient approach to develop genomic resources in orphan species: Application in Lavandula angustifolia

PLoS ONE ◽  
2020 ◽  
Vol 15 (12) ◽  
pp. e0243853
Author(s):  
Berline Fopa Fomeju ◽  
Dominique Brunel ◽  
Aurélie Bérard ◽  
Jean-Baptiste Rivoal ◽  
Philippe Gallois ◽  
...  
Keyword(s):  
Large Scale ◽  
De Novo ◽  
Rapid Development ◽  
Genetic Distances ◽  
Lavandula Angustifolia ◽  
Distance Analysis ◽  
Alternative Medicines ◽  
Dna And Rna ◽  
Snp Development ◽  
High Level

Next-Generation Sequencing (NGS) technologies, by reducing the cost and increasing the throughput of sequencing, have opened doors to generate genomic data in a range of previously poorly studied species. In this study, we propose a method for the rapid development of a large-scale molecular resources for orphan species. We studied as an example the true lavender (Lavandula angustifolia Mill.), a perennial sub-shrub plant native from the Mediterranean region and whose essential oil have numerous applications in cosmetics, pharmaceuticals, and alternative medicines. The heterozygous clone “Maillette” was used as a reference for DNA and RNA sequencing. We first built a reference Unigene, compound of coding sequences, thanks to de novo RNA-seq assembly. Then, we reconstructed the complete genes sequences (with introns and exons) using an Unigene-guided DNA-seq assembly approach. This aimed to maximize the possibilities of finding polymorphism between genetically close individuals despite the lack of a reference genome. Finally, we used these resources for SNP mining within a collection of 16 commercial lavender clones and tested the SNP within the scope of a genetic distance analysis. We obtained a cleaned reference of 8, 030 functionally in silico annotated genes. We found 359K polymorphic sites and observed a high SNP frequency (mean of 1 SNP per 90 bp) and a high level of heterozygosity (more than 60% of heterozygous SNP per genotype). On overall, we found similar genetic distances between pairs of clones, which is probably related to the out-crossing nature of the species and the restricted area of cultivation. The proposed method is transferable to other orphan species, requires little bioinformatics resources and can be realized within a year. This is also the first reported large-scale SNP development on Lavandula angustifolia. All the genomics resources developed herein are publicly available and provide a rich pool of molecular resources to explore and exploit lavender genetic diversity in breeding programs.

scholarly journals Comparative genomics and pangenome-oriented studies reveal high homogeneity of the agronomically relevant enterobacterial plant pathogen Dickeya solani

2020 ◽  
Author(s):  
Agata Motyka-Pomagruk ◽  
Sabina Zoledowska ◽  
Agnieszka Emilia Misztak ◽  
Wojciech Sledz ◽  
Alessio Mengoni ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Large Scale ◽  
De Novo ◽  
Genetic Material ◽  
Soft Rot ◽  
Potato Production ◽  
Core Gene ◽  
Ecological Niches ◽  
Dickeya Solani ◽  
High Level

Abstract Background: Dickeya solani is an important plant pathogenic bacterium causing severe losses in European potato production. This species draws a lot of attention due to its remarkable virulence, great devastating potential and easier spread in contrast to other Dickeya spp. In view of a high need for extensive studies on economically important soft rot Pectobacteriaceae , we performed a comparative genomics analysis on D. solani strains to search for genetic foundations that would explain the differences in the observed virulence levels within the D. solani population. Results: High quality assemblies of 8 de novo sequenced D. solani genomes have been obtained. Whole-sequence comparison, ANIb, ANIm, Tetra and pangenome-oriented analyses performed on these genomes and the sequences of 14 additional strains revealed an exceptionally high level of homogeneity among the studied genetic material of D. solani strains. With the use of 22 genomes, the pangenome of D. solani , comprising 84.7% core, 7.2% accessory and 8.1% unique genes, has been almost completely determined, suggesting the presence of a nearly closed pangenome structure. Attribution of the genes included in the D. solani pangenome fractions to functional COG categories showed that higher percentages of accessory and unique pangenome parts in contrast to the core section are encountered in phage/mobile elements- and transcription- associated groups with the genome of RNS 05.1.2A strain having the most significant impact. Also, the first D. solani large-scale genome-wide phylogeny computed on concatenated core gene alignments is herein reported. Conclusions: The almost closed status of D. solani pangenome achieved in this work points to the fact that the unique gene pool of this species should no longer expand. Such a feature is characteristic of taxa whose representatives either occupy isolated ecological niches or lack efficient mechanisms for gene exchange and recombination, which seems rational concerning a strictly pathogenic species with clonal population structure. Finally, no obvious correlations between the geographical origin of D. solani strains and their phylogeny were found, which might reflect the specificity of the international seed potato market.

scholarly journals 2020–2021 Vegetable Production Handbook: Chapter 6. Cole Crop Production

EDIS ◽  
2020 ◽  
Author(s):  
Lincoln Zotarelli ◽  
Peter J. Dittmar ◽  
Nicholas S. Dufault ◽  
Bonnie Wells ◽  
Johan Desaeger ◽  
...  
Keyword(s):  
Chinese Cabbage ◽  
Crop Production ◽  
Vegetable Production ◽  
Cole Crops ◽  
Cole Crop

This chapter covers production of cole crops and Asian crucifers, including broccoli, cabbage, cauliflower, Chinese broccoli, Chinese cabbage, Chinese mustard (bok choy), kohlrabi, lobok/daikon, collards, kale, mustard, and turnip.

scholarly journals Capture-based enrichment of Theileria parva DNA enables full genome assembly of first buffalo-derived strain and reveals exceptional intra-specific genetic diversity

2020 ◽  
Author(s):  
Nicholas C Palmateer ◽  
Kyle Tretina ◽  
Joshua Orvis ◽  
Olukemi O Ifeonu ◽  
Jonathan Crabtree ◽  
...  
Keyword(s):  
Vaccine Development ◽  
De Novo ◽  
High Specificity ◽  
Theileria Parva ◽  
Nucleotide Polymorphisms ◽  
Specificity And Sensitivity ◽  
Genome Wide ◽  
Dna Capture ◽  
High Level ◽  
Genome Assemblies

AbstractTheileria parva is an economically important, intracellular, tick-transmitted parasite of cattle. A live vaccine against the parasite is effective against challenge from cattle-transmissible T. parva but not against genotypes originating from the African Cape buffalo, a major wildlife reservoir, prompting the need to characterize genome-wide variation within and between cattle- and buffalo-associated T. parva populations. Here, we describe a capture-based target enrichment approach that enables, for the first time, de novo assembly of nearly complete T. parva genomes derived from infected host cell lines. This approach has exceptionally high specificity and sensitivity and is successful for both cattle- and buffalo-derived T. parva parasites. De novo genome assemblies generated for cattle genotypes differ from the reference by ∼54K single nucleotide polymorphisms (SNPs) throughout the 8.31 Mb genome, an average of 6.5 SNPs/kb. We report the first buffalo-derived T. parva genome, which is larger than the genome from the reference, cattle-derived, Muguga strain. The average non-synonymous nucleotide diversity (πN) per gene, between buffalo-derived T. parva and the Muguga strain, was 1.3%. This remarkably high level of genetic divergence is supported by an average FST, genome-wide, of 0.44, reflecting a degree of genetic differentiation between cattle- and buffalo-derived T. parva parasites more commonly seen between, rather than within, species, with clear implications for vaccine development. The DNA capture approach used provides clear advantages over alternative T. parva DNA enrichment methods used previously and enables in-depth comparative genomics in this apicomplexan parasite.

scholarly journals MACHoice: a Decision Support System for agricultural machinery management

2019 ◽  
Vol 4 (1) ◽  
pp. 305-321 ◽  
Author(s):  
M. Cunha ◽  
S.G. Gonçalves
Keyword(s):  
Decision Support ◽  
Decision Support System ◽  
Support System ◽  
Crop Production ◽  
Work Capacity ◽  
Production Costs ◽  
Modern Agriculture ◽  
Level Of Automation ◽  
High Level ◽  
User Friendly

AbstractMechanisation is a key input in modern agriculture, while it accounts for a large part of crop production costs, it can bring considerable farm benefits if well managed. Models for simulated machinery costs, may not replace actual cost measurements but the information obtained through them can replace a farm’s existing records, becoming more valuable to decision makers. MACHoice, a decision support system (DSS) presented in this paper, is a farm machinery cost estimator and break-even analyzer of alternatives for agricultural operations, developed using user-driven expectations and in close collaboration with agronomists and computer engineers. It integrates an innovative algorithm developed for projections of machinery costs under different rates of annual machine use and work capacity processing, which is crucial to decisions on break-even machinery alternatives. A case study based on the comparison of multiple alternatives for grape harvesting operations is presented to demonstrate the typical results that can be expected from MACHoice, and to identify its capabilities and limitations. This DSS offers an integrated and flexible analysis environment with a user-friendly graphical interface as well as a high level of automation of processing chains. The DSS-output consists of charts and tables, evidencing the differences related to costs and carbon emissions between the options inserted by the user for the different intensity of yearly work proceeded. MACHoice is an interactive web-based tool that can be accessed freely for non-commercial use by every known browser.

scholarly journals P1639DEVELOPMENT OF SELF-LIMITED LOW-LEVEL BK VIREMIA/VIRURIA SUGGESTS IDEAL IMMUNOSUPPRESSION TO SUPPRESS T-CELL AND ANTIBODY-MEDIATED REJECTION AND PRESERVE KIDNEY ALLOGRAFT FUNCTION

2020 ◽  
Vol 35 (Supplement_3) ◽  
Author(s):  
Bettina Näf ◽  
Thomas Müller ◽  
Rudolf Peter Wuthrich ◽  
Thomas Schachtner
Keyword(s):  
Lower Incidence ◽  
De Novo ◽  
Allograft Survival ◽  
Kidney Allograft ◽  
Low Level ◽  
Antibody Mediated Rejection ◽  
Maintenance Immunosuppression ◽  
Allograft Function ◽  
High Level ◽  
Egfr Slope

Abstract Background and Aims Polyomavirus BK (BKV) viremia has been suggested as a surrogate marker of overimmunosuppression. Due to recent advances in monitoring strategies and pre-emptive therapy, progression to BKV-associated nephropathy (BKVN) has been reduced. Reduction of maintenance immunosuppression during BKVN, however, has been associated with both T-cell mediated rejection (TCMR), antibody-mediated rejection (ABMR), and inferior kidney allograft outcomes. Although the administration of intravenous immunoglobulins (IVIG) failed to treat BKVN, IVIG may have properties to reduce allosensitization. Method We studied 860 kidney transplant recipients (KTRs) predominantly under tacrolimus-based triple-drug maintenance immunosuppression from 2009 to 2018. We identified 130 KTRs (15.1%) with high-level BK viremia >10,000 copies/mL (presumptive BKVN), 180 KTRs (20.9%) with low-level BK viremia <10,000 copies/mL, 85 KTRs (9.9%) with isolated BK viruria, and 465 KTRs (54.1%) with no BK viruria/viremia. Kidney allograft outcomes with respect to TCMR, ABMR, development of de novo donor-specific antibodies (DSA), kidney allograft survival, and estimated glomerular filtration rate (eGFR) slope were analysed. Due to the increased incidence of TCMR and ABMR among KTRs with presumptive BKVN, 48 of 130 KTRs (36.9%) with high-level BK viremia starting from 2015 received IVIG (0.5 g/kg of body weight) on a biweekly basis during BKV replication. Results Very interestingly, KTRs with low-level BK viremia/viruria showed a significantly lower incidence of TCMR compared to KTRs with no BK viremia/viruria and KTRs with high-level BK viremia (p<0.05). In addition, KTRs with low-level BK viremia/viruria showed a significantly lower incidence of ABMR compared to KTRs with high-level BK viremia (p<0.05). No differences were observed with respect to the development of de novo DSA (MFI>5000) between KTRs with low-level BK viremia/viruria, KTRs with no BK viremia/viruria, and KTRs with high-level BK viremia (p>0.05). KTRs with low-level BK viremia/viruria showed superior kidney allograft survival and lower eGFR slope compared to KTRs with no BK viremia/viruria and KTRs with high-level BK viremia (p<0.05). The administration of IVIG during high-level BK viremia didn’t impact the development of TCMR, ABMR, development of de novo DSA, eGFR slope, and kidney allograft survival (p<0.05). Conclusion Our results show that low-level BK viremia/viruria is associated with suppression of TCMR and ABMR in the early period posttransplantation, and preservation of kidney allograft function in the long-term. The administration of IVIG didn’t prove beneficial to reduce allosensitization among KTRs with high-level BK viremia.

scholarly journals Analysis of Silencing Escape of Tomato leaf curl virus: An Evaluation of the Role of DNA Methylation

2006 ◽  
Vol 19 (6) ◽  
pp. 614-624 ◽  
Author(s):  
Xue-Yu Bian ◽  
M. Saif Rasheed ◽  
Mark J. Seemanpillai ◽  
M. Ali Rezaian
Keyword(s):  
Transgenic Plants ◽  
Rna Silencing ◽  
De Novo ◽  
Tomato Leaf ◽  
Tomato Leaf Curl Virus ◽  
Sense Strand ◽  
High Level ◽  
Tomato Leaf Curl ◽  
Leaf Curl Virus ◽  
Leaf Curl

RNA silencing is a sequence-specific mechanism regulating gene expression and has been used successfully for antiviral defense against RNA viruses. Similar strategies to develop resistance against DNA containing Tomato leaf curl virus (TLCV) and some other geminiviruses have been unsuccessful. To analyze this silencing escape, we transformed tomato plants with a hairpin construct from the TLCV C2 open reading frame (ORF). The transgenic plants showed a strong RNA silencing response, and following TLCV inoculation, their infection was delayed. However, the viral infection was not prevented and TLCV DNA accumulated to the levels found in nontransgenic plants. To determine the fate of a transgene carrying homology to the virus, we used transgenic plants carrying the TLCV C4 gene, which induces a distinct phenotype. Upon TLCV infection, the phenotype was abolished and C4 transcript disappeared. Concurrently, TLCV-specific small interfering RNAs were produced. In situ hybridization showed abundant levels of TLCV DNA in phloem cells of TLCV-infected C4 trans-genic plants. However, the C4 transcripts were no longer detectable in nonvascular cells. Analysis of the transgene by methylation sequencing revealed a high level of de novo methylation of asymmetric cytosines in both the C4 ORF and its 35S promoter. A high level of methylation also was found at both symmetric and asymmetric cytosines of the complementary-sense strand of TLCV double-stranded DNA. Given the previous finding that methylated geminivi-ral DNA is not competent for replication, we provide a model whereby TLCV evades host defense through a population of de novo synthesized unmethylated DNA.

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