Data-driven approaches can harness crop diversity to address heterogeneous needs for breeding products.

This perspective describes the opportunities and challenges of data-driven approaches for crop diversity management (genebanks and breeding) in the context of agricultural research for sustainable development in the Global South. Data-driven approaches build on larger volumes of data and flexible analyses that link different datasets across domains and disciplines. This can lead to more information-rich management of crop diversity, which can address the complex interactions between crop diversity, production environments, and socioeconomic heterogeneity and help to deliver more suitable portfolios of crop diversity to users with highly diverse demands. We describe recent efforts that illustrate the potential of data-driven approaches for crop diversity management. A continued investment in this area should fill remaining gaps and seize opportunities, including i) supporting genebanks to play a more active role in linking with farmers using data-driven approaches; ii) designing low-cost, appropriate technologies for phenotyping; iii) generating more and better gender and socioeconomic data; iv) designing information products to facilitate decision-making; and v) building more capacity in data science. Broad, well-coordinated policies and investments are needed to avoid fragmentation of such capacities and achieve coherence between domains and disciplines so that crop diversity management systems can become more effective in delivering benefits to farmers, consumers, and other users of crop diversity.

Breedbase: a digital ecosystem for modern plant breeding.

Modern breeding methods integrate next-generation sequencing and phenomics to identify plants with the best characteristics and greatest genetic merit for use as parents in subsequent breeding cycles to ultimately create improved cultivars able to sustain high adoption rates by farmers. This data-driven approach hinges on strong foundations in data management, quality control, and analytics. Of crucial importance is a central database able to (1) track breeding materials, (2) store experimental evaluations, (3) record phenotypic measurements using consistent ontologies, (4) store genotypic information, and (5) implement algorithms for analysis, prediction, and selection decisions. Because of the complexity of the breeding process, breeding databases also tend to be complex, difficult, and expensive to implement and maintain. Here, we present a breeding database system, Breedbase (https://breedbase.org/, last accessed 4/18/2022). Originally initiated as Cassavabase (https://cassavabase.org/, last accessed 4/18/2022) with the NextGen Cassava project (https://www.nextgencassava.org/, last accessed 4/18/2022), and later developed into a crop-agnostic system, it is presently used by dozens of different crops and projects. The system is web based and is available as open source software. It is available on GitHub (https://github.com/solgenomics/, last accessed 4/18/2022) and packaged in a Docker image for deployment (https://hub.docker.com/u/breedbase, last accessed 4/18/2022). The Breedbase system enables breeding programs to better manage and leverage their data for decision making within a fully integrated digital ecosystem.

A review of varietal change in roots, tubers and bananas: consumer preferences and other drivers of adoption and implications for breeding.

This review of the literature on varietal change in sub-Saharan Africa looks in detail at adoption of new varieties of bananas in Uganda, cassava in Nigeria, potato in Kenya, sweetpotato in Uganda and yams in Côte d'Ivoire. The review explored three hypotheses about drivers of varietal change. There was a strong confirmation for the hypothesis that insufficient priority given to consumer-preferred traits by breeding programmes contributes to the limited uptake of modern varieties (MVs) and low varietal turnover. Lack of evidence meant the second hypothesis of insufficient attention to understanding and responding to gender differences in consumer preferences for quality and post-harvest traits was unresolved. The evidence on the third hypothesis about the informal seed system contributing to slow uptake of MVs was mixed. In some cases, the informal system has contributed to rapid uptake of MVs, but often it appears to be a barrier with inconsistent varietal naming a major challenge.

An interdisciplinary and participatory methodology to improve user acceptability of root, tuber and banana varieties.

Breeding programmes for root, tuber and banana (RTB) crops have traditionally considered consumer demand for quality characteristics as low priority against other considerations such as yield and disease resistance. This has contributed to low levels of adoption of new varieties and its potential benefits. To address these challenges, an interdisciplinary five-step methodology was developed to identify demand for quality characteristics among diverse user groups along the food chain. The methodology includes an evidence review, consultations with key informants and rural communities, processing diagnosis with experienced processors and consumer testing in urban and rural areas. Quality characteristics are then prioritised into a Food Product Profile by user group to inform further work of biochemists and breeders in developing improved selection tools. This initiative presents a new basis to understand consumer preferences for RTB crops. The methodology is currently being applied in projects in sub-Saharan Africa and is applicable globally.

Identification of cassava quality attributes preferred by Ugandan users along the food chain.

This study aimed to identify cassava quality attributes preferred by users along the food chain, in order to provide breeders with criteria for prioritisation. Survey and consumer-testing studies were conducted within Apac and Luwero districts in Uganda. Additionally, sensory evaluation by trained panellists was conducted to determine descriptors for assessing quality of boiled roots. Results revealed softness of boiled roots and in-ground storability as key attributes influencing varietal preference besides high yield, non-bitter roots, disease resistance, early maturity and drought resistance. For some attributes like in-ground storability, preference differed significantly between locations and showed differentiation by gender. Local varieties were found to be superior in quality attributes. From sensory evaluation, twenty-one descriptors associated with appearance, texture, taste and aroma of boiled roots were determined. Findings from this study are vital for breeders to adopt gender-responsive approaches in order to develop varieties that meet the needs and preferences of end users.

Understanding cassava varietal preferences through pairwise ranking of gari-eba and fufu prepared by local farmer-processors.

Within communities in Osun and Imo States of Nigeria, farmer-processors grew and processed a diverse set of improved and landrace cassava varieties into the locally popular foods, gari, eba and fufu. Local and 15 main varieties were grown in a 'mother and baby trials' design in each state. Mother trials with three replications were processed by farmer-processors renown in their community for their processing skills. Baby trials were managed and processed by other farmer-processors. The objective was to identify food quality criteria to inform demand-led breeding to benefit users, especially women, given their key roles in processing. Farmer-processors evaluated the overall quality of fresh roots and derived food products through pairwise comparisons. Improved varieties had higher fresh and dry root yield. Overall, landraces ranked first for quality of gari and eba, but several improved varieties were also appreciated for good quality. Landraces in Osun had higher gari yield and a higher swelling power compared to improved varieties. Colour (browning), bulk density, swelling power, solubility and water absorption capacity were the criteria most related to food product ranking by farmer-processors. Evaluation of varieties under farmer-processors' conditions is crucial for providing guidance to breeders on critical selection criteria.

Assessment of end user traits and physicochemical qualities of cassava flour: a case of Zombo district, Uganda.

Cassava breeding programmes in Uganda do not currently select materials based on flour making quality, explaining in part the low adoption rates of many released varieties. In this study, we describe end user trait preferences, processing qualities and physicochemical properties of cassava flour. We found that higher proportion of women than men showed preference for most attributes of cassava flour quality evaluated in this study. Preference for colour was 66% and 52% among women and men, respectively, while that for stickiness of Kwon was 26% (women) and 15% (men). Ease of peeling and stickiness of Kwon were key processing traits. Heap fermented flour had higher pasting temperatures, but lower viscosities than sun-dried flour, and had lower amylose content compared to fresh root starch. The results demonstrate the importance of gender sensitive participatory evaluation of breeding materials, in tandem with physicochemical evaluation during selection of best possible candidate breeding lines.

A scoping review of adoption of climate-resilient crops by small-scale producers in low- and middle-income countries.

Climate-resilient crops and crop varieties have been recommended as a way for farmers to cope with or adapt to climate change, but despite the apparent benefits, rates of adoption by smallholder farmers are highly variable. Here we present a scoping review, using PRISMA-P (Preferred Reporting Items for Systematic review and Meta-Analysis Protocols), examining the conditions that have led to the adoption of climate-resilient crops over the past 30 years in lower- and middle-income countries. The descriptive analysis performed on 202 papers shows that small-scale producers adopted climate-resilient crops and varieties to cope with abiotic stresses such as drought, heat, flooding and salinity. The most prevalent trait in our dataset was drought tolerance, followed by water-use efficiency. Our analysis found that the most important determinants of adoption of climate-resilient crops were the availability and effectiveness of extension services and outreach, followed by education levels of heads of households, farmers' access to inputs-especially seeds and fertilizers-and socio-economic status of farming families. About 53% of studies reported that social differences such as sex, age, marital status and ethnicity affected the adoption of varieties or crops as climate change-adaptation strategies. On the basis of the collected evidence, this study presents a series of pathways and interventions that could contribute to higher adoption rates of climate-resilient crops and reduce dis-adoption.

Genomic characterization of Ugandan smallholder farmer-preferred cassava varieties.

Understanding the genetic relationships among farmer-preferred cassava (Manihot esculenta Crantz) varieties is indispensable to genetic improvement efforts. In this study, we present a genetic analysis of 547 samples of cassava grown by 192 smallholder farmers, which were sampled at random within four districts in Uganda. We genotyped these samples at 287,952 single nucleotide polymorphisms using genotyping-by-sequencing and co-analyzed them with 349 cassava samples from the national breeding program in Uganda. The samples collected from smallholders consisted of 86 genetically unique varieties, as assessed using a genetic distance-based approach. Of these varieties, most were cultivated in only one district (30 in Kibaale, 19 in Masindi, 14 in Arua, and three in Apac), and only three were cultivated across all districts. The genetic differentiation we observed among farming districts in Uganda (mean fixation index [F ST] = .003) is similar to divergence observed within other countries. Despite the fact that none of the breeding lines were directly observed in farmer fields, genetic divergence between the populations was low (F ST = .020). Interestingly, we detected the presence of introgressions from the wild relative M. glaziovii Müll. Arg. on chromosomes 1 and 4, which implies ancestry with cassava breeding lines. Given the apparently similar pool of alleles in the breeding germplasm, it is likely that breeders have the raw genetic material they require to match the farmer-preferred trait combinations necessary for adoption. Our study highlights the importance of understanding the genetic makeup of cassava currently grown by smallholder farmers and relative to that of plant breeding germplasm.

The utility of NBS-profiling for characterization of yellow rust resistance in an F6 durum wheat population.

Seedling and adult plant (field) resistance to yellow rust in the durum wheat (Triticum turgidum ssp. durum) cross Kunduru-1149 x Cham-1 was characterized using a functionally-targeted DNA marker system, NBS-profiling. Chi-squared analysis indicated a four gene model conferring seedling yellow rust resistance against Puccinia striiformis f. sp. tritici isolate WYR85/22 (virulent on Yr2, Yr6, Yr7 and Yr9). Interval mapping located two QTL for yellow rust resistance on the long arm of chromosome 1B, while Kruskal-Wallis single marker regression identified a number of additional marker loci associated with seedling and/or adult plant, field resistance to yellow rust. These results suggested that much of the yellow rust resistance seen in the field may be due to seedling expressed resistance (R) genes. Characterization of the DNA sequence of three NBS marker loci indicated that all showed significant homology to functionally-characterized R-genes and resistance gene analogues (RGAs), with the greatest homology being NBS-LRR-type R-genes and RGAs from cereal species.

Cassava Trait Preferences of Men and Women Farmers in Nigeria: Implications for Breeding.

Nigeria is the world's largest cassava producer, hosting a diverse array of cassava farmers and processors. Cassava breeding programs prioritize "common denominator" traits in setting breeding agendas, to impact the largest possible number of people through improved varieties. This approach has been successful, but cassava adoption rates are less than expected, with room for improvement by integrating traits in demand by farmers and processors. This paper aims to inform breeding priority setting, by examining trait and varietal preferences of men and women cassava farmer/processors. Men and women in eight communities in Southwest and Southeast Nigeria were consulted using mixed methods. Women and men had significantly different patterns of cassava use in the Southwest. Fifty-five variety names were recorded from the communities demonstrating high genetic diversity maintained by growers, especially in the Southeast. High yield, early maturity, and root size were most important traits across both regions, while traits women and men preferred followed gender roles: women prioritized product quality/cooking traits, while men placed higher priority on agronomic traits. Trait preference patterns differed significantly between the Southeast and Southwest, and showed differentiation based on gender. Patterns of access to stem sources were determined more by region and religion than gender.

Transcriptional response of virus-infected cassava and identification of putative sources of resistance for cassava brown streak disease.

Cassava (Manihot esculenta) is a major food staple in sub-Saharan Africa, which is severely affected by cassava brown streak disease (CBSD). The aim of this study was to identify resistance for CBSD as well as to understand the mechanism of putative resistance for providing effective control for the disease. Three cassava varieties; Kaleso, Kiroba and Albert were inoculated with cassava brown streak viruses by grafting and also using the natural insect vector the whitefly, Bemisia tabaci. Kaleso expressed mild or no disease symptoms and supported low concentrations of viruses, which is a characteristic of resistant plants. In comparison, Kiroba expressed severe leaf but milder root symptoms, while Albert was susceptible with severe symptoms both on leaves and roots. Real-time PCR was used to estimate virus concentrations in cassava varieties. Virus quantities were higher in Kiroba and Albert compared to Kaleso. The Illumina RNA-sequencing was used to further understand the genetic basis of resistance. More than 700 genes were uniquely overexpressed in Kaleso in response to virus infection compared to Albert. Surprisingly, none of them were similar to known resistant gene orthologs. Some of the overexpressed genes, however, belonged to the hormone signalling pathways and secondary metabolites, both of which are linked to plant resistance. These genes should be further characterised before confirming their role in resistance to CBSD.

The ability of cultivars of sweetpotato in East Africa to 'revert' from Sweet potato feathery mottle virus infection.

Asymptomatic field plants are the normal source of the vine cuttings used as sweetpotato planting material in Africa. Previous and new tests of such East African material, mostly using the very sensitive method of graft inoculation to the indicator plant Ipomoea setosa, showed that a majority tested virus-negative. This was despite their never having undergone any science-based therapy. To investigate how this occurs, in a replicated greenhouse experiment, plants of susceptible cultivars from the USA and Peru and three resistant Ugandan cultivars were graft-inoculated with Sweet potato feathery mottle virus (SPFMV), the commonest virus infecting sweetpotato. When the grafts were established, cuttings were taken, rooted and proved to be infected. The health status of each of these new plants was then followed over a 10-week period using a quantitative polymerase chain reaction assay. Most of the plants of the Ugandan cultivars eventually tested SPFMV-negative whereas those of the USA and Peru seldom did. Furthermore, in subsequent graft-inoculations of scions from the tip, top, middle and base of the vine of every plant to I. setosa plants, again, most of the scions of the Ugandan cultivars tested SPFMV-negative whereas those of the USA and Peru seldom did. These tests demonstrate the phenomenon of reversion in the Ugandan cultivars and can explain how most unprotected Ugandan sweetpotato field plants tested SPFMV-negative.

Cardiac progenitor cells engineered with Pim-1 (CPCeP) develop cardiac phenotypic electrophysiological properties as they are co-cultured with neonatal myocytes.

Stem cell transplantation has been successfully used for amelioration of cardiomyopathic injury using adult cardiac progenitor cells (CPC). Engineering of mouse CPC with the human serine/threonine kinase Pim-1 (CPCeP) enhances regeneration and cell survival in vivo, but it is unknown if such apparent lineage commitment is associated with maturation of electrophysiological properties and excitation-contraction coupling. This study aims to determine electrophysiology and Ca(2+)-handling properties of CPCeP using neonatal rat cardiomyocyte (NRCM) co-culture to promote cardiomyocyte lineage commitment. Measurements of membrane capacitance, dye transfer, expression of connexin 43 (Cx43), and transmission of ionic currents (I(Ca), I(Na)) from one cell to the next suggest that a subset of co-cultured CPCeP and NRCM becomes connected via gap junctions. Unlike NRCM, CPCeP had no significant I(Na), but expressed nifedipine-sensitive I(Ca) that could be measured more consistently with Ba(2+) as permeant ion using ramp-clamp protocols than with Ca(2+) and step-depolarization protocols. The magnitude of I(Ca) in CPCeP increased during culture (4-7 days vs. 1-3 days) and was larger in co-cultures with NRCM and with NRCM-conditioned medium, than in mono-cultured CPCeP. I(Ca) was virtually absent in CPC without engineered expression of Pim-1. Caffeine and KCl-activated Ca(2+)-transients were significantly present in co-cultured CPCeP, but smaller than in NRCM. Conversely, ATP-induced (IP(3)-mediated) Ca(2+) transients were larger in CPCeP than in NRCM. I(NCX) and I(ATP) were expressed in equivalent densities in CPCeP and NRCM. These in vitro studies suggest that CPCeP in co-culture with NRCM: a) develop I(Ca) current and Ca(2+) signaling consistent with cardiac lineage, b) form electrical connections via Cx43 gap junctions, and c) respond to paracrine signals from NRCM. These properties may be essential for durable and functional myocardial regeneration under in vivo conditions.

TaWIR1 contributes to post-penetration resistance to Magnaporthe oryzae, but not Blumeria graminis f. sp. tritici, in wheat.

Members of the Wheat-Induced Resistance 1 (TaWIR1) gene family are highly induced in response to a wide range of pathogens. Homologues have been identified in barley, but not in Brachypodium, whereas, in rice, only distant WIR1 candidates are known. Phylogenetic analysis placed TaWIR1a and TaWIR1b within a distinct clade of wheat transcripts, whereas TaWIR1c clustered with HvWIR1 genes. Transcripts of all three TaWIR1 genes were strongly induced by a wheat-adapted isolate of Magnaporthe oryzae. Virus-induced gene silencing of the TaWIR1 gene family had no effect on the initial penetration of epidermal cells by M. oryzae. However, following the establishment of an infection site, the fungus was able to grow more extensively within the leaf tissue, relative to control leaves, indicating a role for the TaWIR1 gene family in the cell-to-cell movement of M. oryzae. In contrast, the silencing of TaWIR1 transcripts had no effect on epidermal cell penetration by a wheat-adapted isolate of Blumeria graminis, or on the subsequent growth of hyphae. Differential transcription of TaWIR1 genes was also seen in epidermal peels, relative to the remaining leaf tissue, following inoculation with M. oryzae.

The Barley stripe mosaic virus system used for virus-induced gene silencing in cereals differentially affects susceptibility to fungal pathogens in wheat.

Barley stripe mosaic virus (BSMV) has emerged as a vector for virus-induced gene silencing (VIGS) in cereals, having been used to study a number of genes involved in resistance in both wheat and barley. However, the effects of the BSMV vector on plant physiology and disease resistance in plants remains unexplored. The BSMV inoculation control vector, BSMV:GFP was shown to cause severe viral symptoms in wheat, displaying chlorosis, leaf curling and growth inhibition typical of the symptoms seen in BSMV-infected barley. These viral symptoms were accompanied by induction of genes implicated in defense against pathogens, namely PR1, PR4, PR5, PR10 and PAL. Subsequent inoculation of BSMV:GFP-infected wheat with a wheat pathotype of Magnaporthe oryzae, the blast pathogen, resulted in decreased susceptibility. Penetration of epidermal cells and subsequent multiple cell colonization by M. oryzae was significantly reduced. This increased restriction of pathogen growth observed for BSMV:GFP infections with and without the viral coat protein gene. However, prior infection with BSMV:GFP had no effect on the development of a compatible isolate of Blumeria graminis f. sp. tritici, the causal agent of powdery mildew.

Wheat blast: histopathology and transcriptome reprogramming in response to adapted and nonadapted Magnaporthe isolates.

* Blast disease (causal agent Magnaporthe oryzae) has presented as a new and serious field disease of wheat in South America. Here, we investigated the responses of wheat to both adapted and nonadapted isolates of the blast fungus Magnaporthe, examining cellular defence and transcriptional changes. * Resistance towards the nonadapted isolate was associated with the formation of appositions, here termed halos, beneath attempted Magnaporthe grisea penetration sites that wheat-adapted, M. oryzae isolates were able to breach. * Transcriptome analysis indicated extensive transcriptional reprogramming following inoculation with both wheat-adapted and nonadapted isolates of Magnaporthe. Functional annotation of many of the differentially expressed transcripts classified into the categories: cell rescue and defence, plant metabolism, cellular transport and regulation of transcription (although a significant number of transcripts remain unclassified). * Defence-related transcripts induced in common by adapted and nonadapted isolates were differentially regulated in response to M. oryzae and M. grisea isolates over time. Differential expression of genes involved in cellular transport indicated the importance of this process in plant defence. Functional characterisation of these transcripts and their role in defence may eventually lead to the identification of broad-spectrum resistance mechanisms in wheat towards Magnaporthe.

An alternative method of using an interpositional silicone sheet in tissue expansion.

To reduce the rate of complications in tissue expansion, we placed a silicone sheet between the expander and the tissue above it in a rat model. In the rats in group 1 (n = 10), the expanders were placed under the dorsal skin. The expanders were inflated with up to 45 mL of saline solution. In group 2 (n = 10), a silicone sheet was inserted between the tissue expander and the skin, after which the procedure used in group 1 was performed. The blood flow was reduced at the dome (center [C]) of the expanders in groups 1C and 2C to a degree greater than that in the expanded skin in groups 1 and 2 far periphery. However, the flow was significantly better in group 2C than in group 1C. Histologic analysis showed that the dermal and capsular tissues were significantly thicker in group 2C than in group 1C. In our opinion, placing a silicone sheet between the expander and the tissue above it seems to be beneficial. This may reduce the incidence of complications, especially the expander extrusion in this model.

Comparison of the protective effects of melatonin and amifostine on radiation-induced epiphyseal injury.

PURPOSE: We compared the effects of amifostine and melatonin in preventing radiation-induced epiphyseal growth plate injury in rats. MATERIALS AND METHODS: Four-week-old (65-85 g), growing male Sprague-Dawley rats were randomly assigned to receive radiation alone, at 25 Gy in three fractions (group R), or this dose of fractionated radiation proceeded by prophylactic amifostine 200 mg/kg i.p. (group A), melatonin 15 mg/kg i.p. (group M), or amifostine + melatonin (group AM). The right rear extremity of each animal was irradiated while the contralateral leg was shielded from radiation, as a control. Bone growth based on the length of the tibia, femur, and overall limb was calculated 6 weeks after the treatment. RESULTS: In groups R, A, M, and AM, the mean growth loss (GL) for the overall limb was 56.9 +/- 8.1%, 46.8 +/- 7.7%, 36.6 +/- 4.3%, and 38.5 +/- 5.1%, respectively. The limb length discrepancies (LLD) in groups R, A, M, and AM were 13.8 +/- 1.4%, 10.5 +/- 0.3%, 7.4 +/- 0.7%, and 8.8 +/- 1.1%, respectively. Differences in LLD were significant between each treatment group and group R (range: p = 0.0001-0.001). Differences in either of mean GL and LLD were not significant between groups M and AM; however both of these groups had significantly less GL and LLD than group A. CONCLUSIONS: We observed a superior radioprotective function of melatonin over amifostine in preventing radiation-induced epiphyseal growth plate injury, without any increase in radioprotective effect by adding amifostine to melatonin.