scholarly journals TGIF-DB: terse genomics interface for developing botany

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Daisuke Tsugama ◽  
Tetsuo Takano
Keyword(s):  
Pearl Millet ◽  
Pennisetum Glaucum ◽  
Asparagus Officinalis ◽  
Tartary Buckwheat ◽  
Whole Genome Sequence ◽  
Fagopyrum Tataricum ◽  
Crop Species ◽  
Putative Gene ◽  
Functional Annotations ◽  
Garden Asparagus

Abstract Objectives Pearl millet (Pennisetum glaucum) is a staple cereal crop for semi-arid regions. Its whole genome sequence and deduced putative gene sequences are available. However, the functions of many pearl millet genes are unknown. Situations are similar for other crop species such as garden asparagus (Asparagus officinalis), chickpea (Cicer arietinum) and Tartary buckwheat (Fagopyrum tataricum). The objective of the data presented here was to improve functional annotations of genes of pearl millet, garden asparagus, chickpea and Tartary buckwheat with gene annotations of model plants, to systematically provide such annotations as well as their sequences on a website, and thereby to promote genomics for those crops. Data description Sequences of genomes and transcripts of pearl millet, garden asparagus, chickpea and Tartary buckwheat were downloaded from a public database. These transcripts were associated with functional annotations of their Arabidopsis thaliana and rice (Oryza sativa) counterparts identified by BLASTX. Conserved domains in protein sequences of those species were identified by the HMMER scan with the Pfam database. The resulting data was deposited in the figshare repository and can be browsed on the Terse Genomics Interface for Developing Botany (TGIF-DB) website (http://webpark2116.sakura.ne.jp/rlgpr/).

scholarly journals Genome-wide investigation of the heat shock transcription factor (Hsf) gene family in Tartary buckwheat (Fagopyrum tataricum)

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Moyang Liu ◽  
Qin Huang ◽  
Wenjun Sun ◽  
Zhaotang Ma ◽  
Li Huang ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Heat Shock ◽  
Gene Family ◽  
Evolutionary Relationship ◽  
Reference Value ◽  
Heat Shock Transcription Factor ◽  
Tartary Buckwheat ◽  
Whole Genome Sequence ◽  
Functional Characteristics ◽  
Fagopyrum Tataricum

Abstract Background Heat shock transcription factor (Hsfs) is widely found in eukaryotes and prokaryotes. Hsfs can not only help organisms resist high temperature, but also participate in the regulation of plant growth and development (such as involved in the regulation of seed maturity and affects the root length of plants). The Hsf gene was first isolated from yeast and then gradually found in plants and sequenced, such as Arabidopsis thaliana, rice, maize. Tartary buckwheat is a rutin-rich crop, and its nutritional value and medicinal value are receiving more and more attention. However, there are few studies on the Hsf genes in Tartary buckwheat. With the whole genome sequence of Tartary buckwheat, we can effectively study the Hsf gene family in Tartary buckwheat. Results According to the study, 29 Hsf genes of Tartary buckwheat (FtHsf) were identified and renamed according to location of FtHsf genes on chromosome after removing a redundant gene. Therefore, only 29 FtHsf genes truly had the functional characteristics of the FtHsf family. The 29 FtHsf genes were located on 8 chromosomes of Tartary buckwheat, and we found gene duplication events in the FtHsf gene family, which may promote the expansion of the FtHsf gene family. Then, the motif compositions and the evolutionary relationship of FtHsf proteins and the gene structures, cis-acting elements in the promoter, synteny analysis of FtHsf genes were discussed in detail. What’s more, we found that the transcription levels of FtHsf in different tissues and fruit development stages were significantly different by quantitative real-time PCR (qRT-PCR), implied that FtHsf may differ in function. Conclusions In this study, only 29 Hsf genes were identified in Tartary buckwheat. Meanwhile, we also classified the FtHsf genes, and studied their structure, evolutionary relationship and the expression pattern. This series of studies has certain reference value for the study of the specific functional characteristics of Tartary buckwheat Hsf genes and to improve the yield and quality of Tartary buckwheat in the future.

scholarly journals Cover crops on the development of beggar's-tick

2013 ◽  
Vol 43 (2) ◽  
pp. 170-177 ◽  
Author(s):  
Leandro Pereira Pacheco ◽  
Marinete Martins de Sousa Monteiro ◽  
Fabiano André Petter ◽  
Francisco de Alcântara Neto ◽  
Fernandes Antônio de Almeida
Keyword(s):  
Cover Crops ◽  
Weed Management ◽  
Pennisetum Glaucum ◽  
Soil Surface ◽  
Integrated Weed Management ◽  
Fagopyrum Tataricum ◽  
Bidens Pilosa ◽  
Crop Species ◽  
Crambe Abyssinica ◽  
Dry Biomass

Studies to identify potential cover crops species for the no-till system and minimal amounts of biomass required to reduce the emergence and development of weeds in cereal crop areas may represent an important tool in the integrated weed management. Thus, this study aimed at evaluating the inhibition of the emergence and growth of Bidens pilosa plants, using different cover crops biomass levels on the soil surface. The experiment was carried out in a greenhouse located in Bom Jesus, Piauí State, Brazil, from December 2011 to March 2012, in a randomized experimental blocks design with four replications, in a (5x6)+1 factorial scheme, consisting of six cover crop species and five biomass levels on the soil surface, plus a control with no soil cover. The species evaluated were Pennisetum glaucum (ADR 7010 and ADR 300 cultivars), Crotalaria ochroleuca, Urochloa ruziziensis (syn. Brachiaria ruziziensis), Crambe abyssinica and Fagopyrum tataricum, at five biomass levels corresponding to 4.0 t ha-1, 8.0 t ha-1, 12.0 t ha-1, 16.0 t ha-1 and 20.0 t ha-1. Urochloa ruziziensis and Fagopyrum tataricum were considered the best ones for controlling B. pilosa, with 4.0 t ha-1 of their biomass being sufficient to reduce the total number of emerged plants, germination speed index, shoot dry biomass, leaf area, root dry biomass and root volume of B. pilosa.

scholarly journals Discovery and validation of candidate genes for grain iron and zinc metabolism in pearl millet [Pennisetum glaucum (L.) R. Br.]

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Mahesh D. Mahendrakar ◽  
Maheshwari Parveda ◽  
P. B. Kavi Kishor ◽  
Rakesh K. Srivastava
Keyword(s):  
Candidate Genes ◽  
Pearl Millet ◽  
Developmental Stages ◽  
Pennisetum Glaucum ◽  
Gene Families ◽  
Zn Deficiency ◽  
Zinc Metabolism ◽  
Potential Candidate ◽  
Crop Species ◽  
Major Qtl

Abstract Pearl millet is an important crop for alleviating micronutrient malnutrition through genomics-assisted breeding for grain Fe (GFeC) and Zn (GZnC) content. In this study, we identified candidate genes related to iron (Fe) and zinc (Zn) metabolism through gene expression analysis and correlated it with known QTL regions for GFeC/GZnC. From a total of 114 Fe and Zn metabolism-related genes that were selected from the related crop species, we studied 29 genes. Different developmental stages exhibited tissue and stage-specific expressions for Fe and Zn metabolism genes in parents contrasting for GFeC and GZnC. Results revealed that PglZIP, PglNRAMP and PglFER gene families were candidates for GFeC and GZnC. Ferritin-like gene, PglFER1 may be the potential candidate gene for GFeC. Promoter analysis revealed Fe and Zn deficiency, hormone, metal-responsive, and salt-regulated elements. Genomic regions underlying GFeC and GZnC were validated by annotating major QTL regions for grain Fe and Zn. Interestingly, PglZIP and PglNRAMP gene families were found common with a previously reported linkage group 7 major QTL region for GFeC and GZnC. The study provides insights into the foundation for functional dissection of different Fe and Zn metabolism genes homologs and their subsequent use in pearl millet molecular breeding programs globally.

Development of Rutin-rich Noodles Using Trace-rutinosidase Variety of Tartary Buckwheat (Fagopyrum Tataricum Gaertn.) ‘Manten-Kirari’

2019 ◽  
Vol 25 (6) ◽  
pp. 915-920
Author(s):  
Tatsuro Suzuki ◽  
Toshikazu Morishita ◽  
Shigenobu Takigawa ◽  
Takahiro Noda ◽  
Koji Ishiguro
Keyword(s):  
Tartary Buckwheat ◽  
Fagopyrum Tataricum

scholarly journals Constraints to Pearl Millet (Pennisetum glaucum) Production and Farmers’ Approaches to Striga hermonthica Management in Burkina Faso

2021 ◽  
Vol 13 (15) ◽  
pp. 8460
Author(s):  
Armel Rouamba ◽  
Hussein Shimelis ◽  
Inoussa Drabo ◽  
Mark Laing ◽  
Prakash Gangashetty ◽  
...  
Keyword(s):  
Burkina Faso ◽  
Pearl Millet ◽  
Management Practices ◽  
Pennisetum Glaucum ◽  
Control Measures ◽  
Striga Hermonthica ◽  
Soil Conditions ◽  
Management Options ◽  
Central Plateau ◽  
South Central

Pearl millet (Pennisetum glaucum) is a staple food crop in Burkina Faso that is widely grown in the Sahelian and Sudano-Sahelian zones, characterised by poor soil conditions and erratic rainfall, and high temperatures. The objective of this study was to document farmers’ perceptions of the prevailing constraints affecting pearl millet production and related approaches to manage the parasitic weeds S. hermonthica. The study was conducted in the Sahel, Sudano-Sahelian zones in the North, North Central, West Central, Central Plateau, and South Central of Burkina Faso. Data were collected through a structured questionnaire and focus group discussions involving 492 participant farmers. Recurrent drought, S. hermonthica infestation, shortage of labour, lack of fertilisers, lack of cash, and the use of low-yielding varieties were the main challenges hindering pearl millet production in the study areas. The majority of the respondents (40%) ranked S. hermonthica infestation as the primary constraint affecting pearl millet production. Respondent farmers reported yield losses of up to 80% due to S. hermonthica infestation. 61.4% of the respondents in the study areas had achieved a mean pearl millet yields of <1 t/ha. Poor access and the high cost of introduced seed, and a lack of farmers preferred traits in the existing introduced pearl millet varieties were the main reasons for their low adoption, as reported by 32% of respondents. S. hermonthica management options in pearl millet production fields included moisture conservation using terraces, manual hoeing, hand weeding, use of microplots locally referred to as ‘zaï’, crop rotation and mulching. These management techniques were ineffective because they do not suppress the below ground S. hermonthica seed, and they are difficult to implement. Integrated management practices employing breeding for S. hermonthica resistant varieties with the aforementioned control measures could offer a sustainable solution for S. hermonthica management and improved pearl millet productivity in Burkina Faso.

scholarly journals Effects of Cover Crops, Compost, and Vermicompost on Strawberry Yields and Nitrogen Availability in North Carolina

2016 ◽  
Vol 26 (5) ◽  
pp. 604-613 ◽  
Author(s):  
John E. Beck ◽  
Michelle S. Schroeder-Moreno ◽  
Gina E. Fernandez ◽  
Julie M. Grossman ◽  
Nancy G. Creamer
Keyword(s):  
North Carolina ◽  
Pearl Millet ◽  
Cover Crops ◽  
Cover Crop ◽  
Crop Yields ◽  
Pennisetum Glaucum ◽  
Organic Production ◽  
Organic N ◽  
N Availability ◽  
Soil N

Summer cover crop rotations, compost, and vermicompost additions can be important strategies for transition to organic production that can provide various benefits to crop yields, nitrogen (N) availability, and overall soil health, yet are underused in strawberry (Fragaria ×ananassa) production in North Carolina. This study was aimed at evaluating six summer cover crop treatments including pearl millet (Pennisetum glaucum), soybean (Glycine max), cowpea (Vigna unguiculata), pearl millet/soybean combination, pearl millet/cowpea combination, and a no cover crop control, with and without vermicompost additions for their effects on strawberry growth, yields, nutrient uptake, weeds, and soil inorganic nitrate-nitrogen and ammonium-nitrogen in a 2-year field experiment. Compost was additionally applied before seeding cover crops and preplant N fertilizer was reduced by 67% to account for organic N additions. Although all cover crops (with compost) increased soil N levels during strawberry growth compared with the no cover crop treatment, cover crops did not impact strawberry yields in the first year of the study. In the 2nd year, pearl millet cover crop treatments reduced total and marketable strawberry yields, and soybean treatments reduced marketable strawberry yields when compared with the no cover crop treatment, whereas vermicompost additions increased strawberry biomass and yields. Results from this study suggest that vermicompost additions can be important sustainable soil management strategies for transitional and certified organic strawberry production. Summer cover crops integrated with composts can provide considerable soil N, reducing fertilizer needs, but have variable responses on strawberry depending on the specific cover crop species or combination. Moreover, these practices are suitable for both organic and conventional strawberry growers and will benefit from longer-term studies that assess these practices individually and in combination and other benefits in addition to yields.

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