Genomic characterization of Ugandan smallholder farmer-preferred cassava varieties

Development of Methods for Improving Flowering and Seed Set of Diverse Germplasm in Cassava Breeding

Cassava breeding faces obstacles due to late flowering and poor flower and seed set. The acceleration of breeding processes and the reduction in each cycle's duration hinge upon efficiently conducting crosses to yield ample progeny for subsequent cycles. Our primary objective was to identify methods that provide tools for cassava breeding programs, enabling them to consistently and rapidly generate offspring from a wide array of genotypes. In greenhouse trials, we examined the effects of the anti-ethylene silver thiosulfate (STS) and the cytokinin benzyladenine (BA). STS, administered via petiole infusion, and BA, applied as an apical spray, combined with the pruning of young branches, significantly augmented the number of flowers. Controls produced no flowers, whereas treatments with pruning plus either BA or STS alone produced an average maximum of 86 flowers per plant, and the combination of pruning, BA and STS yielded 168 flowers per plant. While STS had its primary effect on flower numbers, BA increased the fraction of female flowers from less than 20% to ≥87%, thus increasing the number of progeny from desired parents. Through field studies, we devised an optimal protocol that maintained acceptable levels of phytodamage ratings while substantially increasing seed production per plant compared to untreated plants. This protocol involves adjusting the dosage and timing of treatments to accommodate genotypic variations. As a result, cassava breeding programs can effectively leverage a diverse range of germplasm to develop cultivars with the desired traits.

Flowering and fruit-set in cassava under extended red-light photoperiod supplemented with plant-growth regulators and pruning

BACKGROUND

Cassava (Manihot esculenta Crantz) is staple food and major source of calories for over 500 million people in sub-Saharan Africa. The crop is also a source of income for smallholder farmers, and has increasing potential for industrial utilization. However, breeding efforts to match the increasing demand of cassava are impeded by its inability to flower, delayed or unsynchronized flowering, low proportion of female flowers and high fruit abortions. To overcome these sexual reproductive bottlenecks, this study investigated the effectiveness of using red lights to extend the photoperiod (RLE), as a gateway to enhancing flowering and fruit set under field conditions.

MATERIALS AND METHODS

Panels of cassava genotypes, with non- or late and early flowering response, 10 in each case, were subjected to RLE from dusk to dawn. RLE was further evaluated at low (LL), medium (ML) and high (HL) red light intensities, at ~  ≤ 0.5; 1.0 and 1.5PFD (Photon Flux Density) in µmol m^-2 s^-1 respectively. Additionally, the effect of a cytokinin and anti-ethylene as plant growth regulators (PGR) and pruning under RLE treatment were examined.

RESULTS

RLE stimulated earlier flower initiation in all genotypes, by up to 2 months in the late-flowering genotypes. Height and number of nodes at first branching, particularly in the late-flowering genotypes were also reduced, by over 50%. Number and proportion of pistillate flowers more than doubled, while number of fruits and seeds also increased. Number of branching levels during the crop season also increased by about three. Earlier flowering in many genotypes was most elicited at LL to ML intensities. Additive effects on flower numbers were detected between RLE, PGR and pruning applications. PGR and pruning treatments further increased number and proportion of pistillate flowers and fruits. Plants subjected to PGR and pruning, developed bisexual flowers and exhibited feminization of staminate flowers. Pruning at first branching resulted in higher pistillate flower induction than at second branching.

CONCLUSIONS

These results indicate that RLE improves flowering in cassava, and its effectiveness is enhanced when PGR and pruning are applied. Thus, deployment of these technologies in breeding programs could significantly enhance cassava hybridizations and thus cassava breeding efficiency and impact.

Long-day photoperiod and cool temperature induce flowering in cassava: Expression of signaling genes

Cassava is a staple food crop in the tropics, and is of particular importance in Africa. Recent development of genomic selection technology have improved the speed of cassava breeding; however, cassava flower initiation and development remains a bottleneck. The objectives of the current studies were to elucidate the effect of photoperiod, temperature and their interactions on the time of flowering and flower development in controlled environments, and to use RNA-sequencing to identify transcriptome expression underlying these environmental responses. Compared to a normal tropical day-length of 12 h, increasing the photoperiod by 4 h or decreasing the air temperature from 34/31 to 22°/19°C (day/night) substantially hastened the time to flowering. For both photoperiod and temperature, the environment most favorable for flowering was opposite the one for storage root harvest index. There was a pronounced treatment interaction: at warm day-time temperatures, percent flowering was low, and photoperiod had little effect. In contrast, at cooler temperatures, percent flowering increased, and long-day (LD) photoperiod had a strong effect in hastening flowering. In response to temperature, many differentially expressed genes in the sugar, phase-change, and flowering-time-integrator pathways had expression/flowering patterns in the same direction as in Arabidopsis (positive or negative) even though the effect of temperature on flowering operates in the reverse direction in cassava compared to Arabidopsis. Three trehalose-6-phosphate-synthase-1 (TPS1) genes and four members of the SPL gene family had significantly increased expression at cool temperature, suggesting sugar signaling roles in flower induction. In response to LD photoperiod, regulatory genes were expressed as in Arabidopsis and other LD flowering plants. Several hormone-related genes were expressed in response to both photoperiod and temperature. In summary, these findings provide insight on photoperiod and temperature responses and underlying gene expression that may assist breeding programs to manipulate flowering for more rapid crop improvement.

Data-driven, participatory characterization of farmer varieties discloses teff breeding potential under current and future climates

In smallholder farming systems, traditional farmer varieties of neglected and underutilized species (NUS) support the livelihoods of millions of growers and consumers. NUS combine cultural and agronomic value with local adaptation, and transdisciplinary methods are needed to fully evaluate their breeding potential. Here, we assembled and characterized the genetic diversity of a representative collection of 366 Ethiopian teff (Eragrostis tef) farmer varieties and breeding materials, describing their phylogenetic relations and local adaptation on the Ethiopian landscape. We phenotyped the collection for its agronomic performance, involving local teff farmers in a participatory variety evaluation. Our analyses revealed environmental patterns of teff genetic diversity and allowed us to identify 10 genetic clusters associated with climate variation and with uneven spatial distribution. A genome-wide association study was used to identify loci and candidate genes related to phenology, yield, local adaptation, and farmers’ appreciation. The estimated teff genomic offset under climate change scenarios highlighted an area around lake Tana where teff cropping may be most vulnerable to climate change. Our results show that transdisciplinary approaches may efficiently propel untapped NUS farmer varieties into modern breeding to foster more resilient and sustainable cropping systems.

Small farms support the livelihoods of about two billion people worldwide. Smallholder farmers often rely on local varieties of crops and use less irrigation and fertilizer than large producers. But smallholdings can be vulnerable to weather events and climate change. Data-driven research approaches may help to identify the needs of farmers, taking into account traditional knowledge and cultural practices to enhance the sustainability of certain crops.

Teff is a cereal crop that plays a critical role in the culture and diets of Ethiopian communities. It is also a super food appreciated on international markets for its nutritional value. Rural smallholder farmers in Ethiopia rely on the crop for subsistence and income and make up the bulk of the country’s agricultural system. Many grow local varieties with tremendous genetic diversity. Scientists, in collaboration with farmers, could tap that diversity to produce more productive or climate-resilient types of teff, both for national and international markets.

Woldeyohannes, Iohannes et al. produced the first large-scale genetic, agronomic and climatic study of traditional teff varieties. In the experiments, Woldeyohannes and Iohannes et al. sequenced the genomes of 366 Ethiopian teff varieties and evaluated their agronomic value in common gardens. The team collaborated with 35 local farmers to understand their preference of varieties and traits. They then conducted a genome-wide association study to assess the crops’ productivity and their adaptations to local growing conditions and farmer preferences. Genetic changes that speed up teff maturation and flowering time could meet small farmers’ needs to secure teff harvest. Woldeyohannes, Iohannes et al. also identified a region in Ethiopia, where local teff varieties may struggle to adapt to climate change. Genetic modifications may help the crop to adapt to frequent droughts that may be a common characteristic of future climates.

The experiments reveal the importance of incorporating traditional knowledge from smallholder farmers into data-driven crop improvement efforts considering genetics and climate science. This multidisciplinary approach may help to improve food security and protect local genetic diversity on small farms. It may also help to ensure that agricultural advances fairly and equitably benefit small farmers.

Environmental responsiveness of flowering time in cassava genotypes and associated transcriptome changes

Cassava is an important food security crop in tropical regions of the world. Cassava improvement by breeding is limited by its delayed and poor production of flowers, such that cassava flowering under field conditions indirectly lengthens the breeding cycle. By studying genotype and environment interaction under two Nigerian field conditions (Ubiaja and Ibadan) and three controlled temperature conditions (22°C/18°C, 28/24°C and 34/30°C (day/night)), we found that while early flowering genotypes flowered at similar times and rates under all growing conditions (unfavorable and favorable field and controlled-temperature environments), late flowering genotypes were environmentally sensitive such that they were substantially delayed in unfavorable environments. On the basis of nodes-to-flower, flowering of late genotypes approached the flowering time of early flowering genotypes under relatively cool Ubiaja field conditions and in growth chambers at 22°C, whereas warmer temperatures elicited a delaying effect. Analysis of transcriptomes from leaves of field and controlled-temperature environments revealed that conditions which promote early flowering in cassava have low expression of the flowering repressor gene TEMPRANILLO 1 (TEM1), before and after flowering. Expression data of field plants showed that the balance between flower stimulatory and inhibitory signaling appeared to correlate with flowering time across the environments and genotypes.

Flower Development in Cassava Is Feminized by Cytokinin, While Proliferation Is Stimulated by Anti-Ethylene and Pruning: Transcriptome Responses

Cassava, a tropical storage-root crop, is a major source of food security for millions in the tropics. Cassava breeding, however, is hindered by the poor development of flowers and a low ratio of female flowers to male flowers. To advance the understanding of the mechanistic factors regulating cassava flowering, combinations of plant growth regulators (PGRs) and pruning treatments were examined for their effectiveness in improving flower production and fruit set in field conditions. Pruning the fork-type branches, which arise at the shoot apex immediately below newly formed inflorescences, stimulated inflorescence and floral development. The anti-ethylene PGR silver thiosulfate (STS) also increased flower abundance. Both pruning and STS increased flower numbers while having minimal influence on sex ratios. In contrast, the cytokinin benzyladenine (BA) feminized flowers without increasing flower abundance. Combining pruning and STS treatments led to an additive increase in flower abundance; with the addition of BA, over 80% of flowers were females. This three-way treatment combination of pruning+STS+BA also led to an increase in fruit number. Transcriptomic analysis of gene expression in tissues of the apical region and developing inflorescence revealed that the enhancement of flower development by STS+BA was accompanied by downregulation of several genes associated with repression of flowering, including homologs of TEMPRANILLO1 (TEM1), GA receptor GID1b, and ABA signaling genes ABI1 and PP2CA. We conclude that flower-enhancing treatments with pruning, STS, and BA create widespread changes in the network of hormone signaling and regulatory factors beyond ethylene and cytokinin.

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.

High density genotype storage for plant breeding in the Chado schema of Breedbase

Modern breeding programs routinely use genome-wide information for selecting individuals to advance. The large volumes of genotypic information required present a challenge for data storage and query efficiency. Major use cases require genotyping data to be linked with trait phenotyping data. In contrast to phenotyping data that are often stored in relational database schemas, next-generation genotyping data are traditionally stored in non-relational storage systems due to their extremely large scope. This study presents a novel data model implemented in Breedbase (https://breedbase.org/) for uniting relational phenotyping data and non-relational genotyping data within the open-source PostgreSQL database engine. Breedbase is an open-source, web-database designed to manage all of a breeder's informatics needs: management of field experiments, phenotypic and genotypic data collection and storage, and statistical analyses. The genotyping data is stored in a PostgreSQL data-type known as binary JavaScript Object Notation (JSONb), where the JSON structures closely follow the Variant Call Format (VCF) data model. The Breedbase genotyping data model can handle different ploidy levels, structural variants, and any genotype encoded in VCF. JSONb is both compressed and indexed, resulting in a space and time efficient system. Furthermore, file caching maximizes data retrieval performance. Integration of all breeding data within the Chado database schema retains referential integrity that may be lost when genotyping and phenotyping data are stored in separate systems. Benchmarking demonstrates that the system is fast enough for computation of a genomic relationship matrix (GRM) and genome wide association study (GWAS) for datasets involving 1,325 diploid Zea mays, 314 triploid Musa acuminata, and 924 diploid Manihot esculenta samples genotyped with 955,690, 142,119, and 287,952 genotype-by-sequencing (GBS) markers, respectively.