Using agricultural metadata: a novel investigation of trends in sowing date in on-farm research trials using the Online Farm Trials database [version 2; peer review: 1 approved
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ABSTRACT:
SUBMITTER: Walters J
PROVIDER: S-EPMC8290206 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Background: Date palm (Phoenix dactylifera L.) is a cultivated woody plant with agricultural and economic importance in many countries around the world. With the advantages of next generation sequencing technologies, genome sequences for many date palm cultivars have been released recently. Short sequence repeat (SSR) and single nucleotide polymorphism (SNP) can be identified from these genomic data, and have been proven to be very useful biomarkers in plant genome analysis and breeding. Results: Here, we first improved the date palm genome assembly using 130X of HiSeq data generated in our lab. Then 246,445 SSRs (214,901 SSRs and 31,544 compound SSRs) were annotated in this genome assembly; among the SSRs, mononucleotide SSRs (58.92%) were the most abundant, followed by di- (29.92%), tri- (8.14%), tetra- (2.47%), penta- (0.36%), and hexa-nucleotide SSRs (0.19%). The high-quality PCR primer pairs were designed for most (174,497; 70.81% out of total) SSRs. We also annotated 6,375,806 SNPs with raw read depth≥3 in 90% cultivars. To further reduce false positive SNPs, we only kept 5,572,650 (87.40% out of total) SNPs with at least 20% cultivars support for downstream analyses. The high-quality PCR primer pairs were also obtained for 4,177,778 (65.53%) SNPs. We reconstructed the phylogenetic relationships among the 62 cultivars using these variants and found that they can be divided into three clusters, namely North Africa, Egypt - Sudan, and Middle East - South Asian, with Egypt - Sudan being the admixture of North Africa and Middle East - South Asian cultivars; we further confirmed these clusters using principal component analysis. Moreover, 34,346 SSRs and 4,177,778 SNPs with PCR primers were assigned to shared cultivars for cultivar classification and diversity analysis. All these SSRs, SNPs and their classification are available in our database, and can be used for cultivar identification, comparison, and molecular breeding. Conclusion:DRDB is a comprehensive genomic resource database of date palm. It can serve as a bioinformatics platform for date palm genomics, genetics, and molecular breeding. DRDB is freely available at http://drdb.big.ac.cn/home.
| S-EPMC5701633 | biostudies-literature
Project description:Rice is a major staple food for nearly half of the world's population and has a considerable contribution to the global agricultural economy. While spaceborne Synthetic Aperture Radar (SAR) data have proved to have great potential to provide rice cultivation area, few studies have been performed to provide practical information that meets the user requirements. In rice growing regions where the inter-field crop calendar is not uniform such as in the Mekong Delta in Vietnam, knowledge of the start of season on a field basis, along with the planted rice varieties, is very important for correct field management (timing of irrigation, fertilization, chemical treatment, harvest), and for market assessment of the rice production. The objective of this study is to develop methods using SAR data to retrieve in addition to the rice grown area, the sowing date, and the distinction between long and short cycle varieties. This study makes use of X-band SAR data from COSMO-SkyMed acquired from 19 August to 23 November 2013 covering the Chau Thanh and Thoai Son districts in An Giang province, Viet Nam, characterized by a complex cropping pattern. The SAR data have been analyzed as a function of rice parameters, and the temporal and polarization behaviors of the radar backscatter of different rice varieties have been interpreted physically. New backscatter indicators for the detection of rice paddy area, the estimation of the sowing date, and the mapping of the short cycle and long cycle rice varieties have been developed and assessed. Good accuracy has been found with 92% in rice grown area, 96% on rice long or short cycle, and a root mean square error of 4.3 days in sowing date. The results have been discussed regarding the generality of the methods with respect to the rice cultural practices and the SAR data characteristics.
| S-EPMC5795876 | biostudies-other
Project description:BackgroundAuthority and year information have been attached to taxonomic names since Linnaean times. The systematic structure of taxonomic nomenclature facilitates the ability to develop tools that can be used to explore historical trends that may be associated with taxonomy.ResultsFrom the over 10.7 million taxonomic names that are part of the uBio system 4, approximately 3 million names were identified to have taxonomic authority information from the years 1750 to 2004. A pipe-delimited file was then generated, organized according to a Linnaean hierarchy and by years from 1750 to 2004, and imported into an Excel workbook. A series of macros were developed to create an Excel-based tool and a complementary Web site to explore the taxonomic data. A cursory and speculative analysis of the data reveals observable trends that may be attributable to significant events that are of both taxonomic (e.g., publishing of key monographs) and societal importance (e.g., world wars). The findings also help quantify the number of taxonomic descriptions that may be made available through digitization initiatives.ConclusionTemporal organization of taxonomic data can be used to identify interesting biological epochs relative to historically significant events and ongoing efforts. We have developed an Excel workbook and complementary Web site that enables one to explore taxonomic trends for Linnaean taxonomic groupings, from Kingdoms to Families.
| S-EPMC2408592 | biostudies-literature
Project description:Peanut (Arachis hypogea L.) is an important nut crop extensively grown in rainfed regions of Pakistan. The crop requires low inputs; thus, could grow successfully under diverse environmental conditions. Due to pegging ability, peanut grows aggressively in sandy and sandy-loam soils. However, it has not introduced to Thal region of southern Punjab, Pakistan. A two-year field experiment was conducted to optimize sowing dates for two peanut genotypes ('BARI-2016' and 'NO-334') in Thal region (Layyah). Similarly, a yield trial was conducted at Chakwal where both genotypes are extensively grown. Five sowing dates (10th April, 1st May, 20th May, 10th June and 30th June) were included in the study. The highest seed yield was obtained with early sown crop (10th April) during both years. Pod formation reduced with increasing atmospheric temperature and no pods were formed on the plants sown on 30th June. Decreased pod formation seemed a major reason for low yield in late-sown crop. The highest yield was observed for the crop sown on 10th April, which was decreased by 40% for the crop sown on 1st May. Genotype 'BARI-2016' performed better for seed yield at both locations compared with 'NO-334'. The results suggested that genotype 'BARI-2016' is more adaptive to arid and semi-arid condition under rainfed or irrigated conditions. Sowing peanut at optimum time would increase seed yield in arid and semi-arid regions. Nonetheless, 'BARI-2016' can be grown under rainfed and irrigated conditions successfully.
| S-EPMC8192014 | biostudies-literature
Project description:IntroductionRecurrent P. vivax infections are associated with significant morbidity and mortality. Although radical cure can reduce recurrent infection, it is confounded by antimalarial resistance and the lack of safe and effective hypnozoitocidal treatment. This study documents the available literature of published clinical trials of P. vivax, providing an up to date, online, open access tool to view and download available information.MethodsA systematic review was conducted according to PRISMA guidelines to identify prospective P. vivax therapeutic clinical trials with at least 28 days follow-up published between 1st January 1960 and 12th October 2016. Treatment arms and evidence of chloroquine resistance were mapped to trial sites.ResultsSince 1960, a total of 1152 antimalarial clinical trials with a minimum 28 days follow-up have been published, of which 230 (20.0%) enrolled patients with P. vivax and were included. Trials were conducted in 38 countries: 168 (73.0%) in the Asia-Pacific, 13 (5.7%) in Africa and 43 (18.7%) in the Americas. The proportion of antimalarial trials assessing P. vivax rose from 10.7% (12/112) in 1991-1995, to 24.9% (56/225) in 2011-2015. Overall, 188 (81.7%) P. vivax trials included a chloroquine treatment arm, either alone or in combination with primaquine, and 107 (46.5%) trials included a chloroquine treatment arm with early primaquine to assess radical cure. There has been a recent increase in treatment arms with artemisinin derivatives. Of the 131 sites in which chloroquine resistance could be quantified, resistance was present in 59 (45.0%) sites in 15 endemic countries.ConclusionsOver the last 20 years there has been a substantial increase in clinical research on the treatment of P. vivax, which has generated a greater awareness of the global extent of chloroquine resistance. The WWARN open access, online interactive map provides up to date information of areas where drug resistant P. vivax is emerging.
| S-EPMC5382033 | biostudies-literature
Project description:The BioSamples database at EMBL-EBI provides a central hub for sample metadata storage and linkage to other EMBL-EBI resources. BioSamples has recently undergone major changes, both in terms of data content and supporting infrastructure. The data content has more than doubled from around 2 million samples in 2014 to just over 5 million samples in 2018. Fast, reciprocal data exchange was fully established between sister Biosample databases and other INSDC partners, enabling a worldwide common representation and centralization of sample metadata. The BioSamples platform has been upgraded to accommodate anticipated increases in the number of submissions via GA4GH driver projects such as the Human Cell Atlas and the EGA, as well as from mirroring of NCBI dbGaP data. The BioSamples database is now the authoritative repository for all INSDC sample metadata, an ELIXIR Deposition Database for Biomolecular Data and the EMBL-EBI sample metadata hub. To support faster turnaround for sample submission, and to increase scalability and resilience, we have upgraded the BioSamples database backend storage, APIs and user interface. Finally, the website has been redesigned to allow search and retrieval of records based on specific filters, such as 'disease' or 'organism'. These changes are targeted at answering current use cases as well as providing functionalities for future emerging and anticipated developments. Availability: The BioSamples database is freely available at http://www.ebi.ac.uk/biosamples. Content is distributed under the EMBL-EBI Terms of Use available at https://www.ebi.ac.uk/about/terms-of-use.
| S-EPMC6323949 | biostudies-literature
Project description:Hybrid japonica cultivars, such as the Yongyou series, have shown high yield potential in the field in both the early and late growing seasons. Moreover, understanding the responses of rice flowering dates to temperature and light is critical for improving yield performance. However, few studies have analyzed flowering genes in high-yielding japonica cultivars. Based on the five sowing date experiments from 2019 to 2020, select the sensitive cultivar Yongyou 538 and the insensitive cultivar Ninggeng 4 and take their flag leaves and panicles for transcriptome analysis. The results showed that compared with sowing date 1 (6/16), after the sowing date was postponed (sowing date 5, 7/9), 4480 and 890 differentially expressed genes (DEGs) were detected in the leaves and panicles in Ninggeng 4, 9275 and 2475 DEGs were detected in the leaves and panicles in Yongyou 538, respectively. KEGG pathway analysis showed that both Ninggeng 4 and Yongyou 538 regulated rice flowering through the plant circadian rhythm and plant hormone signal transduction pathways. Gene expression analysis showed that Os01g0566050 (OsELF3-2), Os01g0182600 (OsGI), Os11g0547000 (OsFKF1), Os06g0275000 (Hd1), and Os09g0513500 (FT-1) were expressed higher and Os02g0771100 (COP1-1) was expressed lower in Yongyou 538 compared with Ninggeng 4 as the climate conditions changed, which may be the key genes that regulate the flowering process with the change of temperature and light resources in sensitive cultivar Yongyou 538 in the late season.
| S-EPMC8298600 | biostudies-literature
Project description:Ribosomal DNA (rDNA) loci encoding 5S and 45S (18S-5.8S-28S) rRNAs are important components of eukaryotic chromosomes. Here, we set up the animal rDNA database containing cytogenetic information about these loci in 1343 animal species (264 families) collected from 542 publications. The data are based on in situ hybridisation studies (both radioactive and fluorescent) carried out in major groups of vertebrates (fish, reptiles, amphibians, birds, and mammals) and invertebrates (mostly insects and mollusks). The database is accessible online at www.animalrdnadatabase.com . The median number of 45S and 5S sites was close to two per diploid chromosome set for both rDNAs despite large variation (1-74 for 5S and 1-54 for 45S sites). No significant correlation between the number of 5S and 45S rDNA loci was observed, suggesting that their distribution and amplification across the chromosomes follow independent evolutionary trajectories. Each group, irrespective of taxonomic classification, contained rDNA sites at any chromosome location. However, the distal and pericentromeric positions were the most prevalent (> 75% karyotypes) for 45S loci, while the position of 5S loci was more variable. We also examined potential relationships between molecular attributes of rDNA (homogenisation and expression) and cytogenetic parameters such as rDNA positions, chromosome number, and morphology.
| S-EPMC5818627 | biostudies-literature
Project description:Chickpea is the main legume rotation crop within farming systems in northern New South Wales (NSW), Australia, and is grown mainly under rainfed conditions. Recent expansion of chickpea growing areas in southern and central western NSW expose them to abiotic stresses; however, knowledge about how these stresses affect overall crop development is limited. This study aimed to examine the influence of sowing time on the timing and duration of key chickpea phenological growth phases in southern and central western environments of NSW. Experiments were conducted over two years in southern NSW (Leeton, Wagga Wagga and Yanco (one year)) and central western NSW (Trangie) to identify phenology responses. Climatic, phenology and experimental site data was recorded, and the duration of growth phases and growing degree days calculated. Early sowing (mid-April) generally delayed flowering, extending the crop's vegetative period, and the progressive delay in sowing resulted in shorter vegetative and podding growth phases. All genotypes showed photoperiod sensitivity, and the mean daily temperature at sowing influenced time to emergence and to some extent crop establishment. This study concludes that environmental factors such as temperature, moisture availability and day length are the main drivers of phenological development in chickpea.
| S-EPMC7598726 | biostudies-literature
Project description:Rapidly global urbanization and economic growth in the past several decades have resulted in a sharp contraction of arable areas worldwide. However, food supply requirements are quickly increasing due to higher living standards and larger populations. Therefore, food crises are still a major threat to human society. The conflict between farmland areas and the increasing need for essential supplies is becoming acuter in China. Therefore, we suggest that a novel strategy would address the issue, in which temporal and spatial arrangement of wheat sowing dates would be highly focused.
| S-EPMC10694224 | biostudies-literature