PhenoApp: A mobile tool for plant phenotyping to record field and greenhouse observations

With the ongoing cost decrease of genotyping and sequencing technologies, accurate and fast phenotyping remains the bottleneck in the utilizing of plant genetic resources for breeding and breeding research. Although cost-efficient high-throughput phenotyping platforms are emerging for specific traits and/or species, manual phenotyping is still widely used and is a time- and money-consuming step. Approaches that improve data recording, processing or handling are pivotal steps towards the efficient use of genetic resources and are demanded by the research community. Therefore, we developed PhenoApp, an open-source Android app for tablets and smartphones to facilitate the digital recording of phenotypical data in the field and in greenhouses. It is a versatile tool that offers the possibility to fully customize the descriptors/scales for any possible scenario, also in accordance with international information standards such as MIAPPE (Minimum Information About a Plant Phenotyping Experiment) and FAIR (Findable, Accessible, Interoperable, and Reusable) data principles. Furthermore, PhenoApp enables the use of pre-integrated ready-to-use BBCH (Biologische Bundesanstalt für Land- und Forstwirtschaft, Bundessortenamt und CHemische Industrie) scales for apple, cereals, grapevine, maize, potato, rapeseed and rice. Additional BBCH scales can easily be added. The simple and adaptable structure of input and output files enables an easy data handling by either spreadsheet software or even the integration in the workflow of laboratory information management systems (LIMS). PhenoApp is therefore a decisive contribution to increase efficiency of digital data acquisition in genebank management but also contributes to breeding and breeding research by accelerating the labour intensive and time-consuming acquisition of phenotyping data.

Adaptability, stability and environmental stratification of genetically and nongenetically modified corn in the Cerrado

ABSTRACT Crop yield depends on interaction between genetic and environmental factors, making it essential to study adaptability, stability and environmental stratification in order to mitigate the effects of this interaction. Four experiments were conducted to assess competition between corn cultivars in the 2018/19 growing season, two in Paraíso do Tocantins and two in Palmas, with sowing performed on November 5, 2018 and January 15, 2019. Cultivar-environment interaction was analyzed in genetically modified (GM) and non-GM commercial corn cultivars in the Vale do Araguaia region of Tocantins state (TO), Brazil, A randomized block design was used for all the experiments, in 3 × 12 factorial scheme, with three doses of nitrogen fertilizer as topdressing (50, 100 and 150 kg of N ha-1) and 12 commercial cultivars (six non-GM, 1CHD, 2CV, 3CV, 4CV, 5CTH, 6CDH and six GM, 7GTH, 8GTH, 9GSH, 10GSH, 11GSH, 12GSH. For statistical analysis, the N dose in each experiment represented a different environment. The characteristic studied was grain yield, using the adaptability and stability methods as well as environmental stratification. Different responses were observed between the GM and non-GM cultivars. Most of the GM and non-GM cultivars were better adapted to favorable and unfavorable environments, respectively. All the environments exhibited similar behavior regardless of location, sowing time and the N dose used, demonstrating that fewer environments can be used in future breeding research.

CAN TROIDES HELENA AND PACHLIOPTA ADAMAS CO-EXIST? A PERSPECTIVE FROM THE BUTTERFLY BREEDING FACILITY, CIBINONG SCIENCE CENTER, INDONESIA

Troides helena and Pachliopta adamas utilize the same food plant species: Aristolochia acuminata. For the purpose of captive breeding and conservation, it is desirable to find out whether they can co-exist in captivity. Captive breeding research was conducted on the butterfly species within the period of October 2016 to September 2019. In total, 1,361 individuals were observed. Data on adult emergence of the species is presented to show population trends. Both species co-existed poorly at the facility when food plants were limited. It took 45.9 days for T. helena helena and 32.6 days for Pc. adamas adamas from egg to imago stage. Habitat enrichment can encourage the species to come and establish the population.

Achievements in breeding and main directions for improving black currant adssortment in Federal Horticultural Research Center for Breeding, Agrotechnology and Nursery

The article presents the main results of twenty years of research carried out at the Federal Horticultural Research Center for Breeding, Agrotechnology and Nursery (Kokino Base Station) on the search and creation of various genetic origin genotypes and the possibility of their use in further breeding work on black currants. The created genetic sources of resistance to American powdery mildew, leaf spots (canker, septoria, cercosporosis), large-fruited, berries’ high vitamin С content, fruit strength, plant productivity are presented: 7-37-2 (Litvinovskaya × Dar Smolyaninovoy), 37-27-4/05 (Debryansk, free pollination), 63-35-1 (Lentyay × Debryansk), 68-03-1 (Charodey × Yadryonaya), 5-66-5 (Dobrynya, free pollination), 13-51-1 (Shalunya, free pollination), 33-27-1 (Strelets × Selechenskaya 2) etc. As a result of breeding research, 12 black currant varieties have been created, eight of which (Bryanskiy Agate, Debryansk, Mif, Vera, Gamayun, Strelets, Charodey, Barmaley) are included in the State Register of Breeding Achievements, approved for using.

CottonGen: The Community Database for Cotton Genomics, Genetics, and Breeding Research

Over the last eight years, the volume of whole genome, gene expression, SNP genotyping, and phenotype data generated by the cotton research community has exponentially increased. The efficient utilization/re-utilization of these complex and large datasets for knowledge discovery, translation, and application in crop improvement requires them to be curated, integrated with other types of data, and made available for access and analysis through efficient online search tools. Initiated in 2012, CottonGen is an online community database providing access to integrated peer-reviewed cotton genomic, genetic, and breeding data, and analysis tools. Used by cotton researchers worldwide, and managed by experts with crop-specific knowledge, it continuous to be the logical choice to integrate new data and provide necessary interfaces for information retrieval. The repository in CottonGen contains colleague, gene, genome, genotype, germplasm, map, marker, metabolite, phenotype, publication, QTL, species, transcriptome, and trait data curated by the CottonGen team. The number of data entries housed in CottonGen has increased dramatically, for example, since 2014 there has been an 18-fold increase in genes/mRNAs, a 23-fold increase in whole genomes, and a 372-fold increase in genotype data. New tools include a genetic map viewer, a genome browser, a synteny viewer, a metabolite pathways browser, sequence retrieval, BLAST, and a breeding information management system (BIMS), as well as various search pages for new data types. CottonGen serves as the home to the International Cotton Genome Initiative, managing its elections and serving as a communication and coordination hub for the community. With its extensive curation and integration of data and online tools, CottonGen will continue to facilitate utilization of its critical resources to empower research for cotton crop improvement.

Envisaging an Effective Global Long-Term Agrobiodiversity Conservation System That Promotes and Facilitates Use

Genebanks were established out of a recognised need not just to provide genetic variation to support breeding objectives but to prevent crop diversity from being lost entirely for future users. Such conservation objectives may have led, over the past few decades, to a gradually diminishing connection between genebanks and current users of diversity. While there continues to be large-scale distribution of germplasm from genebanks to recipients worldwide, relatively little is known or published about the detailed trends in the demand for genebank materials. Meanwhile, the rapid expansion of the applications and uses of modern genomic technologies and approaches is, undoubtedly, having a transformational impact on breeding, research and the demand for certain genetic resources and associated data. These trends will require genebanks to be responsive and to adapt. They also provide important opportunities for genebanks to reorganize and become more efficient individually and as a community. Ultimately, future challenges and opportunities are likely to drive more demand for genetic diversity and provide an important basis for genebanks to gear up.

Pre-breeding study for the enhancement of bioactive fruit attributes in strawberry (Fragaria x ananassa Duch.)

The strawberry fruit market increasingly demands new cultivars producing berries with enhanced bioactive attributes. In this research the suitability of twelve strawberry cultivars for effective breeding aimed at the enhancement of bioactive fruit attributes was studied. The group of genotypes with different pedigree was examined in respect of variation, breeding parameters, correlation between the content of bioactive compounds and the antioxidant capacity of fruit. Pre-breeding research showed the highly significant differences between genotypes regarding all traits analysed. Relationship between the bioactive phytochemicals content and antioxidant capacity of fruit were mostly positive and significant. Only correlation between vitamin C and flavonoids was negative (−0.482). Path analysis exhibited the highest positive direct effect of total phenolic content on antioxidant capacity (0.609). Heritability of traits was very high, reaching values above 0.90. The highest genetic advance was observed for flavonoids. Results suggested that the genotype plays the main role in shaping of fruit antioxidant potential. This study indicated that the efficient strawberry breeding focused on obtaining the forms with enhanced bioactive berry properties could be highly possible.

Characterization of wall-associated kinase/wall-associated kinase-like (WAK/WAKL) family in rose (Rosa chinensis) reveals the role of RcWAK4 in Botrytis resistance

Background Wall-associated kinase (WAK)/WAK-like (WAKL) is one of the subfamily of receptor like kinases (RLK). Although previous studies reported that WAK/WAKL played an important role in plant cell elongation, response to biotic and abiotic stresses, there are no systematic studies on RcWAK/RcWAKL in rose. Results In this study, we identified a total of 68 RcWAK/RcWAKL gene family members within rose (Rosa chinensis) genome. The RcWAKs contained the extracellular galacturonan-binding domain and calcium-binding epidermal growth factor (EGF)-like domain, as well as an intracellular kinase domains. The RcWAKLs are missing either calcium-binding EGF-like domain or the galacturonan-binding domain in their extracellular region. The phylogenetic analysis showed the RcWAK/RcWAKL gene family has been divided into five groups, and these RcWAK/RcWAKL genes were unevenly distributed on the 7 chromosomes of rose. 12 of RcWAK/RcWAKL genes were significantly up-regulated by Botrytis cinerea-inoculated rose petals, where RcWAK4 was the most strongly expressed. Virus induced gene silencing of RcWAK4 increased the rose petal sensitivity to B. cinerea. The results indicated RcWAK4 is involved in the resistance of rose petal against B. cinerea. Conclusion Our study provides useful information to further investigate the function of the RcWAK/RcWAKL gene family and breeding research for resistance to B. cinerea in rose.

The feasibility of Indonesian potato’s farming and its global competitiveness

Potato’s farming in Indonesia is thought to be profitable. However, its competitiveness in global production is questionable. The purpose of this study is to analyze the financial feasibility of potato’s farming in Indonesia and its competitiveness in global production. The data used were the results of National Farmers Panel (PATANAS) surveys in 2008, 2011 and 2017. The cost and benefit analysis were used to analyze the financial feasibility. In addition, productivity and producer price were used to measure its global competitiveness. The results showed that potato’s farming during the period of 2008 to 2017 was highly profitable. The R/C ratios were high and continued to increase. These results showed that potato’s farming in the study area is profitable and feasible to be done. In contrast, although potato’s farming in the study area is very profitable, it has no competitiveness in global production, due to the relatively low yield and high cost shown by producer price. The highest cost component was seed. Therefore, there should be a significant effort to find out the efficient use of seed, as well as to increase the capacity of farmers in producing good quality seeds efficiently. It is a challenge for breeding research to produce potato’s varieties with higher yields than currently exist in Indonesia. Another challenge is the research on the use of cut seed into pieces with minimum of two shoots per section.