Towards plant pangenomics

As an increasing number of genome sequences become available for a wide range of species, there is a growing understanding that the genome of a single individual is insufficient to represent the gene diversity within a whole species. Many studies examine the sequence diversity within genes, and this allelic variation is an important source of phenotypic variation which can be selected for by man or nature. However, the significant gene presence/absence variation that has been observed within species and the impact of this variation on traits is only now being studied in detail. The sum of the genes for a species is termed the pangenome, and the determination and characterization of the pangenome is a requirement to understand variation within a species. In this review, we explore the current progress in pangenomics as well as methods and approaches for the characterization of pangenomes for a wide range of plant species

Adapting smartphone app used in water testing, for soil nutrient analysis

Smartphone technology has now penetrated every aspect of modern life. At such high rates of access and utilization, there is today much potential for the development of smartphones as high-performing tools in a number of industries. Traditionally, smartphones have been used as e.g. point-of-care testing devices in developing countries; now a similar approach can be extended to agriculture. This paper assesses the viability of utilizing smartphones in soil analysis. An Android-based smartphone application, in conjunction with commercially available Quantofix® test strips, was employed to analyze 92 soil samples collected across Indonesia. The soils tested encompassed a wide range of different textures (with 13%, 60% and 25% of samples constituting sandy, loamy and clayey soils, respectively), soil organic matter contents (range: 0.8–19.7%) and nutrient concentrations (range for plant-available N: 0.1–137.4 mg kg−1 and P: 1.2 to 64.2 mg kg−1; on dry soil basis). The app utilizes the smartphone as a portable reflectometer, which relates the color of test strips to the concentration of particular nutrients present in the soil medium. Three mobile devices currently available on the market, representing low, mid- and high-end products, were used to test the application. The results obtained via the smartphone were compared against standard methods for determination of extractable nitrate-N and exchangeable phosphorus (Olsen-P) under laboratory conditions. The smartphone-mediated soil analysis was found to have a high degree of agreement with standard methods for nitrate-N determination (87% of samples with nitrate-N differed by less than 10 mg kg−1 from the standard method for the high-end smartphone) but not for phosphorus determination where chemical interferences to test strip colour development were noted. All three mobile devices were shown to be effective as portable reflectometers. However, color perception was found to differ amongst the devices, resulting in a consistent bias between the high-end phone and the remaining appliances. Whereas, it is essential to consider the inter-smartphone variability in readings and environmental factors such as temperature prior to the smartphone-mediated soil analysis, the smartphone-test strip combination might be employed as acceptable screening tool for soil nutrient concentration assessment to enhance crop outcomes, increasing yield, and preventing over-application of inputs, reducing consequent financial and environmental impact. Further enhancements can test the applicability of smartphone-mediated soil analysis in field conditions

The potential for using smartphones as portable soil nutrient analyzers on suburban farms in central East China

Soil testing is frequently conducted to specify nutrient supply recommendations. By adjusting fertilizer type and application rates, farmers can achieve desired crop yields with lower production costs and are thereby less likely to contribute to eutrophication of nearby waterbodies. However, traditional methods of soil testing can be costly, time-consuming and are often impractical in rural and resource-poor regions in China, where rapid population growth and consequent food demand must be balanced against potential environment risks. Smartphones are nearly ubiquitous and offer a ready capability for providing additional support for existing extension advice. In this study, we used an Android-based smartphone application, in conjunction with commercially-available Quantofix test strips, to analyze soil samples with a goal of providing specific fertilizer recommendations. The app transforms the smartphone into a portable reflectometer, relating the reaction color of the test strips to the concentration of soil nutrients available. A 6-month long field study involving two growing seasons of vegetables was conducted in a suburban area of Nanjing, Jiangsu Province of China to evaluate the accuracy and precision of smartphone-mediated soil analysis. Results obtained via the smartphone correlated well with the yield response of the common green vegetable Ipomoea aquatica (water spinach) and could be applied in calculations of necessary off-farm inputs throughout the open-field vegetable growing season. Together, the smartphone and test strip in combination were shown to offer an acceptable screening tool for soil nutrient concentration assessment with the potential to result in substantial monetary savings and reduction of nutrient loss to the environment

Grain dispersal mechanism in cereals arose from a genome duplication followed by changes in spatial expression of genes involved in pollen development

KEY MESSAGE: Grain disarticulation in wild progenitor of wheat and barley evolved through a local duplication event followed by neo-functionalization resulting from changes in location of gene expression. ABSTRACT: One of the most critical events in the process of cereal domestication was the loss of the natural mode of grain dispersal. Grain dispersal in barley is controlled by two major genes, Btr1 and Btr2, which affect the thickness of cell walls around the disarticulation zone. The barley genome also encodes Btr1-like and Btr2-like genes, which have been shown to be the ancestral copies. While Btr and Btr-like genes are non-redundant, the biological function of Btr-like genes is unknown. We explored the potential biological role of the Btr-like genes by surveying their expression profile across 212 publicly available transcriptome datasets representing diverse organs, developmental stages and stress conditions. We found that Btr1-like and Btr2-like are expressed exclusively in immature anther samples throughout Prophase I of meiosis within the meiocyte. The similar and restricted expression profile of these two genes suggests they are involved in a common biological function. Further analysis revealed 141 genes co-expressed with Btr1-like and 122 genes co-expressed with Btr2-like, with 105 genes in common, supporting Btr-like genes involvement in a shared molecular pathway. We hypothesize that the Btr-like genes play a crucial role in pollen development by facilitating the formation of the callose wall around the meiocyte or in the secretion of callase by the tapetum. Our data suggest that Btr genes retained an ancestral function in cell wall modification and gained a new role in grain dispersal due to changes in their spatial expression becoming spike specific after gene duplication. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00122-022-04029-8

An analysis of in‐field soil testing and mapping for improving fertiliser decision‐making in vegetable production in Kenya and Ghana

In‐field soil testing and soil mapping can contribute to addressing the challenge of poor soil fertility and limited fertilizer application across sub‐Saharan Africa. Semi‐quantitative colorimetric methods, such as paper test strips, are frequently employed in soil nutrient assessment across developing countries, especially in South‐East Asia. This research investigated the accuracy of nutrient‐sensitive paper strips and smartphone, which was re‐purposed to act as a reflectometer, to assess soil nitrate‐N, and different methods for mapping soil fertility to identify areas of land that are suitable for human waste‐derived fertilizers (HWDF) application. The study entailed testing soil samples across 42 different farms in Kenya and Ghana and compared it to laboratory results in‐country. It was found that paper strips were capable of assessing available nitrate‐N concentration present in the soil within ±20 kg ha−1 of the standard method for 86% of the farms. Paper strips were less effective in Ghana as they had been calibrated for a method that was not used by local laboratories. Paper strips were not effective for HWDF samples, where chemical interferences and concentration of different forms of nitrates were too high, resulting in overestimation of readings and thus negatively affecting any associated nutrient management advice. Soil mapping has the potential to use open‐source data to inform farmers through mobile technology. For soil mapping two methods were deployed which includes targeting organic matter deficient areas and stakeholder led mapping, with the latter shown to be more effective in identifying areas for HWDF application

Novel procedures for testing of soil field test kits involving paper strips

The need for facilitation of access to soil information has never been greater. Growing human population, shrinking land and water resources, soil pollution, climate change and unequal distribution of agriculture-oriented technology impact negatively on global food security. There has been a long-standing interest in developing low-cost and easily accessible soil field kits to measure different properties of agricultural soils in order to improve their agronomic capacity. Test strips, in particular, have provided a favoured method of obtaining soil nutrient status information since the 1970s. Today there is renewed interest in using semi-qualitative colorimetric methods in soil assessment due to incorporation of modern technological solutions, such as smartphones, which could in turn increase the accuracy and precision of the existing methods. In this paper, we propose streamlined testing procedures based on experience gathered that may be conducted prior to a field kit development involving test strips. Results from laboratory and field experiments are presented, highlighting important factors which ought to be taken into account at the commencement of test-strip oriented studies

Super-Pangenome by Integrating the Wild Side of a Species for Accelerated Crop Improvement

The pangenome provides genomic variations in the cultivated gene pool for a given species. However, as the crop’s gene pool comprises many species, especially wild relatives with diverse genetic stock, here we suggest using accessions from all available species of a given genus for the development of a more comprehensive and complete pangenome, which we refer to as a super-pangenome. The super-pangenome provides a complete genomic variation repertoire of a genus and offers unprecedented opportunities for crop improvement. This opinion article focuses on recent developments in crop pangenomics, the need for a super-pangenome that should include wild species, and its application for crop improvement

Old problem, the Millennial solution: using mobile technology to inform decision making for sustainable fertilizer management

According to the World Bank, as of mid-2000s, more people have access to mobile technologies than clean water. Mobile technologies were quickly recognized as excellent high performing work tools and became adapted early on for use in the agricultural sector. They offer exciting opportunities for improving farming practices, including operating sustainable fertilizer management strategies and related extension support. From assessing potential Nitrogen losses in California to fine-tuning fertilizer recommendations in Thailand — harnessing the potential of mobile technologies was recognized as an essential piece in the worldwide move towards information-driven, efficient, and sustainable agriculture. In this review, mobile technologies designed to augment existing methods of fertilizer management were reviewed and challenges to their adoption together with missing links in their development process were emphasised

The pangenome of hexaploid bread wheat

There is an increasing understanding that variation in gene presence–absence plays an important role in the heritability of agronomic traits; however, there have been relatively few studies on variation in gene pres- ence–absence in crop species. Hexaploid wheat is one of the most important food crops in the world and intensive breeding has reduced the genetic diversity of elite cultivars. Major efforts have produced draft genome assemblies for the cultivar Chinese Spring, but it is unknown how well this represents the genome diversity found in current modern elite cultivars. In this study we build an improved reference for Chinese Spring and explore gene diversity across 18 wheat cultivars. We predict a pangenome size of 140 500 102 genes, a core genome of 81 070 1631 genes and an average of 128 656 genes in each cultivar. Functional annotation of the variable gene set suggests that it is enriched for genes that may be associated with important agronomic traits. In addition to variation in gene presence, more than 36 million intervarietal sin- gle nucleotide polymorphisms were identified across the pangenome. This study of the wheat pangenome provides insight into genome diversity in elite wheat as a basis for genomics-based improvement of this important crop. A wheat pangenome, GBrowse, is available at http://appliedbioinformatics.com.au/cgi-bin/ gb2/gbrowse/WheatPan/, and data are available to download from http://wheatgenome.info/wheat_ge nome_databases.php