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.

Genetic progress in cowpea [Vigna unguiculata (L.) Walp.] stemming from breeding modernization efforts at the International Institute of Tropical Agriculture.

Genetic gain has been proposed as a quantifiable key performance indicator that can be used to monitor breeding programs' effectiveness. The cowpea breeding program at the International Institute of Tropical Agriculture (IITA) has developed and released improved varieties in 70 countries globally. To quantify the genetic changes to grain yield and related traits, we exploited IITA cowpea historical multi-environment trials (METs) advanced yield trial (AYT) data from 2010 to 2022. The genetic gain assessment targeted short duration (SD), medium duration (MD), and late duration (LD) breeding pipelines. A linear mixed model was used to calculate the best linear unbiased estimates (BLUE). Regressed BLUE of grain yield by year of genotype origin depicted realized genetic gain of 22.75 kg/ha/year (2.65%), 7.91 kg/ha/year (0.85%), and 22.82 kg/ha/year (2.51%) for SD, MD, and LD, respectively. No significant gain was realized in 100-seed weight (Hsdwt). We predicted, based on 2022 MET data, that recycling the best genotypes at AYT stage would result in grain yield gain of 37.28 kg/ha/year (SD), 28.00 kg/ha/year (MD), and 34.85 kg/ha/year (LD), and Hsdwt gain of 0.48 g/year (SD), 0.68 g/year (MD), and 0.55 g/year (LD). These results demonstrated a positive genetic gain trend for cowpea, indicating that a yield plateau has not yet been reached and that accelerated gain is expected with the recent integration of genomics in the breeding program. Advances in genomics include the development of the reference genome, genotyping platforms, quantitative trait loci mapping of key traits, and active implementation of molecular breeding.

Molecular Fingerprinting and Hybridity Authentication in Cowpea Using Single Nucleotide Polymorphism Based Kompetitive Allele-Specific PCR Assay.

Optimization of a breeding program for increased genetic gain requires quality assurance (QA) and quality control (QC) at key phases of the breeding process. One vital phase in a breeding program that requires QC and QA is the choice of parents and successful hybridizations to combine parental attributes and create variations. The objective of this study was to determine parental diversity and confirm hybridity of cowpea F1 progenies using KASP (Kompetitive Allele-Specific PCR)-based single nucleotide polymorphism (SNP) markers. A total of 1,436 F1 plants were derived from crossing 220 cowpea breeding lines and landraces to 2 elite sister lines IT99K-573-1-1 and IT99K-573-2-1 as male parents, constituting 225 cross combinations. The progenies and the parents were genotyped with 17 QC SNP markers via high-throughput KASP genotyping assay. The QC markers differentiated the parents with mean efficiency of 37.90% and a range of 3.4-82.8%, revealing unique fingerprints of the parents. Neighbor-Joining cladogram divided the 222 parents into 3 clusters. Genetic distances between parents ranged from 0 to 3.74 with a mean of 2.41. Principal component analysis (PCA) depicted a considerable overlap between parents and F1 progenies with more scatters among parents than the F1s. The differentiation among parents and F1s was best contributed to by 82% of the markers. As expected, parents and F1s showed a significant contrast in proportion of heterozygous individuals, with mean values of 0.02 and 0.32, respectively. KASP markers detected true hybridity with 100% success rate in 72% of the populations. Overall, 79% of the putative F1 plants were true hybrids, 14% were selfed plants, and 7% were undetermined due to missing data and lack of marker polymorphism between parents. The study demonstrated an effective application of KASP-based SNP assay in fingerprinting, confirmation of hybridity, and early detection of false F1 plants. The results further uncovered the need to deploy markers as a QC step in a breeding program.

Genetic Fine-Mapping of a Quantitative Trait Locus (QTL) Associated with Embryogenic Tissue Culture Response and Plant Regeneration Ability in Maize (Zea mays L.).

Embryogenic and regenerable tissue cultures are widely utilized in plant transformation, clonal propagation, and biological research applications. Germplasm utilized in those applications are limited, however, due to genotype-dependent culture response. The goal of this study was to identify genomic regions controlling embryogenic and regenerable tissue culture response in the globally important crop, maize ( L.), toward the long-term objective of developing approaches for genotype-independent plant genetic engineering and clonal propagation systems. An inbred maize line, WCIC2, nearly-isogenic to reference inbred B73, was developed by phenotypic selection and molecular marker analysis. WCIC2 has over 50x increase in tissue culture response relative to the recurrent parent, B73. This line was used to genetically fine-map a region on chromosome 3 controlling embryogenic and regenerable tissue culture response to a 23.9 Mb region. WCIC2 and derivatives will be useful materials to enable maize research in a genetic background similar to B73, and our genetic mapping results will advance research to identify causal genes controlling somatic embryo formation and plant regeneration in maize.

Whole transcriptome profiling of maize during early somatic embryogenesis reveals altered expression of stress factors and embryogenesis-related genes.

Embryogenic tissue culture systems are utilized in propagation and genetic engineering of crop plants, but applications are limited by genotype-dependent culture response. To date, few genes necessary for embryogenic callus formation have been identified or characterized. The goal of this research was to enhance our understanding of gene expression during maize embryogenic tissue culture initiation. In this study, we highlight the expression of candidate genes that have been previously regarded in the literature as having important roles in somatic embryogenesis. We utilized RNA based sequencing (RNA-seq) to characterize the transcriptome of immature embryo explants of the highly embryogenic and regenerable maize genotype A188 at 0, 24, 36, 48, and 72 hours after placement of explants on tissue culture initiation medium. Genes annotated as functioning in stress response, such as glutathione-S-transferases and germin-like proteins, and genes involved with hormone transport, such as PINFORMED, increased in expression over 8-fold in the study. Maize genes with high sequence similarity to genes previously described in the initiation of embryogenic cultures, such as transcription factors BABY BOOM, LEAFY COTYLEDON, and AGAMOUS, and important receptor-like kinases such as SOMATIC EMBRYOGENESIS RECEPTOR LIKE KINASES and CLAVATA, were also expressed in this time course study. By combining results from whole genome transcriptome analysis with an in depth review of key genes that play a role in the onset of embryogenesis, we propose a model of coordinated expression of somatic embryogenesis-related genes, providing an improved understanding of genomic factors involved in the early steps of embryogenic culture initiation in maize and other plant species.

The genetic architecture of maize flowering time.

Flowering time is a complex trait that controls adaptation of plants to their local environment in the outcrossing species Zea mays (maize). We dissected variation for flowering time with a set of 5000 recombinant inbred lines (maize Nested Association Mapping population, NAM). Nearly a million plants were assayed in eight environments but showed no evidence for any single large-effect quantitative trait loci (QTLs). Instead, we identified evidence for numerous small-effect QTLs shared among families; however, allelic effects differ across founder lines. We identified no individual QTLs at which allelic effects are determined by geographic origin or large effects for epistasis or environmental interactions. Thus, a simple additive model accurately predicts flowering time for maize, in contrast to the genetic architecture observed in the selfing plant species rice and Arabidopsis.

Genetic properties of the maize nested association mapping population.

Maize genetic diversity has been used to understand the molecular basis of phenotypic variation and to improve agricultural efficiency and sustainability. We crossed 25 diverse inbred maize lines to the B73 reference line, capturing a total of 136,000 recombination events. Variation for recombination frequencies was observed among families, influenced by local (cis) genetic variation. We identified evidence for numerous minor single-locus effects but little two-locus linkage disequilibrium or segregation distortion, which indicated a limited role for genes with large effects and epistatic interactions on fitness. We observed excess residual heterozygosity in pericentromeric regions, which suggested that selection in inbred lines has been less efficient in these regions because of reduced recombination frequency. This implies that pericentromeric regions may contribute disproportionally to heterosis.