Flower-inducing technology facilitates speed breeding in cassava

Speed breeding 3.0: mainstreaming light-driven plant breeding for sustainable genetic gains

Advances in photobiological tools are revolutionizing plant breeding by enabling precise control of light parameters, addressing yield stagnation, and mitigating climate challenges. Full-spectrum light-emitting diodes (LEDs) and optimized light protocols have significantly reduced breeding cycles. This review highlights light-driven strategies that are accessible and practical for plant breeders worldwide including the role of light spectrum, intensity, and photoperiod in acceleration of plant growth in both short- and long-day crops. Speed breeding 3.0, with tailored rapid generation advancement (RGA) protocols designed for diverse crop populations, has the potential to significantly sustain genetic gains in a more efficient and targeted manner. These innovative approaches hold the potential to transform global agriculture and secure food systems in the face of rising populations and environmental uncertainties.

Untargeted and targeted metabolomics approaches to characterise, select and advance cassava pre-breeding populations with enhanced whitefly tolerance

Cassava (Manihot esculenta Crantz) provides food security for over 500 million people in Sub-Saharan Africa (SSA). Whitefly (Bemisia tabaci) is a pest in this region that results in ca. 50% crop yield losses. Thus, it is important to develop approaches that will generate new varieties tolerant to this pest to advance food security in the region. Two parental cassava varieties, ECU72 tolerant to whiteflies and COL2246 a susceptible line, have been used to generate bi-parental populations. The F1 generation has been screened for whitefly resistance, and progeny identified displaying enhanced tolerance. From designated F1 tolerant progeny, F2 families have been generated and phenotyped. The tolerance to whiteflies in the F2 population was further enhanced. Untargeted metabolomics was used to characterise whitefly susceptible and tolerant sub-groups. PCA of the molecular features generated clustering of accessions into whitefly resistant and susceptible groups, and differentiating metabolite biomarkers were identified. The most significant metabolite marker for resistance is the chemical feature 316.0924. Although not consistent among all whitefly resistance sub-groups, targeted LC-MS analysis revealed several pathways displaying perturbed levels. These include cyanogenic glycosides, apocarotenoids and the phenylpropanoid super-pathway comprising hydroxycinnamic acids, flavonoids and proanthocyanidins. Thus, the generation of a bi-parental population for whitefly tolerance/susceptibility enabled the identification of quantitative metabolite markers, the pathways contributing to tolerance, the underlying modes of action associated with resistance and the potential for the development of future high-throughput low-cost proxy markers. The approach also provides generic insights into future breeding strategies utilising bi-parental progeny for the enhancement of traits.

The speed breeding technology of five generations per year in cotton

KEY MESSAGE

Developed a speed breeding technique for cotton that enables up to five generations per year using optimized spectral conditions and immature embryo culture, and created new materials with iaaM gene. Shortening the breeding cycle is an effective way to accelerate crop genetic improvement. Previously we developed an integrated breeding technology for cotton that enabled three to four breeding cycles per year. Here, to further shorten the breeding time, we optimized the light spectrum conditions for cotton development and culture conditions for immature embryo developing into seedling. Under optimized spectrum conditions, JSh929 and ND601 plants exhibited the visible flower buds at 19 and 21 days after emergence (DAE), and the first flower bloomed at around 45 and 46 DAE. Using the optimized immature embryo culture technique, immature embryos of 25-30 days after pollination could develop into fertile plants with cotyledon unfolding at 6 days after culture in vitro. The improved speed breeding technique shortened cotton breeding cycle from about 130 days to a range from 71 to 85 days, an average of 79.5 days, achieving up to around five generations per year. Using this optimized system, we transferred iaaM gene into the high-yield and disease-resistant cultivar JND24, and BC4F3 progenies were obtained within 1.5 years. In addition, the JND24-i3 line was selected with increased lint percentage and improved Micronaire value. These results demonstrate that the optimized speed breeding system offers a rapid and effective way to improve traits of cotton.

SpeedyPaddy: a revolutionized cost-effective protocol for large scale offseason advancement of rice germplasm

BACKGROUND

Improving the rate of genetic gain of cereal crop will rely on the accelerated crop breeding pipelines to allow rapid delivery of improved crop varieties. The laborious, time-consuming traditional breeding cycle, and the seasonal variations are the key factor restricting the breeder to develop new varieties. To address these issues, a revolutionized cost-effective speed breeding protocol for large-scale rice germplasm advancement is presented in the present study. The protocol emphasises on optimizing potting material, balancing the double-edged sword of limited nutritional dose, mode and stage of application, plant density, temperature, humidity, light spectrum, intensity, photoperiod, and hormonal regulation to accelerate rice growth and development.

RESULTS

The plant density of 700 plants/m2, cost-effective halogen tubes (B:G:R:FR-7.0:27.6:65.4:89.2) with an intensity of ∼ 750-800 µmol/m2/s and photoperiod of 13 h light and 11 h dark during seedling and vegetative stage and 8 h light and 16 h dark during reproductive stage had a significant effect (P < 0.05) on reducing the mean plant height, tillering, and inducing early flowering. Our results confirmed that one generation can be achieved within 68-75 days using the cost-effective SpeedyPaddy protocol resulting in 4-5 generations per year across different duration of rice varieties. The other applications include hybridization, trait-based phenotyping, and mapping of QTL/genes. The estimated cost to run one breeding cycle with plant capacity of 15,680 plants in SpeedyPaddy was $2941 including one-time miscellaneous cost which is much lower than the advanced controlled environment speed breeding facilities.

CONCLUSION

The protocol offers a promising cost-effective solution with average saving of 2.0 to 2.6 months per breeding cycle with an integration of genomics-assisted selection, trait-based phenotyping, mapping of QTL/genes, marker development may accelerate the varietal development and release. This outstanding cost-effective break-through marks a significant leap in rice breeding addressing climate change and food security.

A cell-based fluorescent system and statistical framework to detect meiosis-like induction in plants

Genetic gains made by plant breeders are limited by generational cycling rates and flowering time. Several efforts have been made to reduce the time to switch from vegetative to reproductive stages in plants, but these solutions are usually species-specific and require flowering. The concept of in vitro nurseries is that somatic plant cells can be induced to form haploid cells that have undergone recombination (creating artificial gametes), which can then be used for cell fusion to enable breeding in a Petri dish. The induction of in vitro meiosis, however, is the largest current bottleneck to in vitro nurseries. To help overcome this, we previously described a high-throughput, bi-fluorescent, single cell system in Arabidopsis thaliana, which can be used to test the meiosis-like induction capabilities of candidate factors. In this present work, we validated the system using robust datasets (>4M datapoints) from extensive simulated meiosis induction tests. Additionally, we determined false-detection rates of the fluorescent cells used in this system as well as the ideal tissue source for factor testing.

Q&A: Methods for estimating genetic gain in sub-Saharan Africa and achieving improved gains

Regular measurement of realized genetic gain allows plant breeders to assess and review the effectiveness of their strategies, allocate resources efficiently, and make informed decisions throughout the breeding process. Realized genetic gain estimation requires separating genetic trends from nongenetic trends using the linear mixed model (LMM) on historical multi-environment trial data. The LMM, accounting for the year effect, experimental designs, and heterogeneous residual variances, estimates best linear unbiased estimators of genotypes and regresses them on their years of origin. An illustrative example of estimating realized genetic gain was provided by analyzing historical data on fresh cassava (Manihot esculenta Crantz) yield in West Africa (https://github.com/Biometrics-IITA/Estimating-Realized-Genetic-Gain). This approach can serve as a model applicable to other crops and regions. Modernization of breeding programs is necessary to maximize the rate of genetic gain. This can be achieved by adopting genomics to enable faster breeding, accurate selection, and improved traits through genomic selection and gene editing. Tracking operational costs, establishing robust, digitalized data management and analytics systems, and developing effective varietal selection processes based on customer insights are also crucial for success. Capacity building and collaboration of breeding programs and institutions also play a significant role in accelerating genetic gains.

SpeedFlower: a comprehensive speed breeding protocol for indica and japonica rice

To increase rice yields and feed billions of people, it is essential to enhance genetic gains. However, the development of new varieties is hindered by longer generation times and seasonal constraints. To address these limitations, a speed breeding facility has been established and a robust speed breeding protocol, SpeedFlower is developed that allows growing 4-5 generations of indica and/or japonica rice in a year. Our findings reveal that a high red-to-blue (2R > 1B) spectrum ratio, followed by green, yellow and far-red (FR) light, along with a 24-h long day (LD) photoperiod for the initial 15 days of the vegetative phase, facilitated early flowering. This is further enhanced by 10-h short day (SD) photoperiod in the later stage and day and night temperatures of 32/30 °C, along with 65% humidity facilitated early flowering ranging from 52 to 60 days at high light intensity (800 μmol m-2 s-1). Additionally, the use of prematurely harvested seeds and gibberellic acid treatment reduced the maturity duration by 50%. Further, SpeedFlower was validated on a diverse subset of 198 rice accessions from 3K RGP panel encompassing all 12 distinct groups of Oryza sativa L. classes. Our results confirmed that using SpeedFlower one generation can be achieved within 58-71 days resulting in 5.1-6.3 generations per year across the 12 sub-groups. This breakthrough enables us to enhance genetic gain, which could feed half of the world's population dependent on rice.

Identification of Genomic Regions for Traits Associated with Flowering in Cassava (Manihot esculenta Crantz)

Flowering in cassava (Manihot esculenta Crantz) is crucial for the generation of botanical seed for breeding. However, genotypes preferred by most farmers are erect and poor at flowering or never flower. To elucidate the genetic basis of flowering, 293 diverse cassava accessions were evaluated for flowering-associated traits at two locations and seasons in Uganda. Genotyping using the Diversity Array Technology Pty Ltd. (DArTseq) platform identified 24,040 single-nucleotide polymorphisms (SNPs) distributed on the 18 cassava chromosomes. Population structure analysis using principal components (PCs) and kinships showed three clusters; the first five PCs accounted for 49.2% of the observed genetic variation. Linkage disequilibrium (LD) estimation averaged 0.32 at a distance of ~2850 kb (kilo base pairs). Polymorphism information content (PIC) and minor allele frequency (MAF) were 0.25 and 0.23, respectively. A genome-wide association study (GWAS) analysis uncovered 53 significant marker-trait associations (MTAs) with flowering-associated traits involving 27 loci. Two loci, SNPs S5_29309724 and S15_11747301, were associated with all the traits. Using five of the 27 SNPs with a Phenotype_Variance_Explained (PVE) ≥ 5%, 44 candidate genes were identified in the peak SNP sites located within 50 kb upstream or downstream, with most associated with branching traits. Eight of the genes, orthologous to Arabidopsis and other plant species, had known functional annotations related to flowering, e.g., eukaryotic translation initiation factor and myb family transcription factor. This study identified genomic regions associated with flowering-associated traits in cassava, and the identified SNPs can be useful in marker-assisted selection to overcome hybridization challenges, like unsynchronized flowering, and candidate gene validation.

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.