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Genetic gain estimation in a breeding program provides an opportunity to monitor breeding efficiency and genetic progress over a specific period. The present study was conducted to (i) assess the genetic gains in grain yield of the early maturing maize hybrids developed by the International Maize and Wheat Improvement Center (CIMMYT) Southern African breeding program during the period 2000-2018 and (ii) identify key agronomic traits contributing to the yield gains under various management conditions. Seventy-two early maturing hybrids developed by CIMMYT and three commercial checks were assessed under stress and non-stress conditions across 68 environments in seven eastern and southern African countries through the regional on-station trials. Genetic gain was estimated as the slope of the regression of grain yield and other traits against the year of first testing of the hybrid in the regional trial. The results showed highly significant (p< 0.01) annual grain yield gains of 118, 63, 46, and 61 kg ha -1 year -1 under optimum, low N, managed drought, and random stress conditions, respectively. The gains in grain yield realized in this study under both stress and non-stress conditions were associated with improvements in certain agronomic traits and resistance to major maize diseases. The findings of this study clearly demonstrate the significant progress made in developing productive and multiple stress-tolerant maize hybrids together with other desirable agronomic attributes in CIMMYT's hybrid breeding program., Competing Interests: Author ATa, formerly employed by CIMMYT, is currently employed by Zambia Seed Company Limited. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Tarekegne, Wegary, Cairns, Zaman-Allah, Beyene, Negera, Teklewold, Tesfaye, Jumbo, Das, Nhamucho, Simpasa, Kaonga, Mashingaidze, Thokozile, Mhike and Prasanna.)

Estimating genetic gains is vital to optimize breeding programs for increased efficiency. Genetic gains should translate into productivity gains if returns to investments in breeding and impact are to be realized. The objective of this study was to estimate genetic gain for grain yield and key agronomic traits in pre-commercial and commercial maize varieties from public and private breeding programs tested in (i) national performance trials (NPT), (ii) era trial and, (iii) compare the trends with the national average. The study used (i) historical NPT data on 419 improved maize varieties evaluated in 23 trials at 6-8 locations each between 2008 and 2020, and (ii) data from an era trial of 54 maize hybrids released between 1999 and 2020. The NPT data was first analyzed using a mixed model and resulting estimate for each entry was regressed onto its first year of testing. Analysis was done over all entries, only entries from National Agricultural Research Organization (NARO), International Maize and Wheat Improvement Center (CIMMYT), or private seed companies. Estimated genetic gain was 2.25% or 81 kg ha -1 year -1 from the NPT analysis. A comparison of genetic trends by source indicated that CIMMYT entries had a gain of 1.98% year -1 or 106 kg ha -1 year -1 . In contrast, NARO and private sector maize entries recorded genetic gains of 1.30% year -1 (59 kg ha -1 year -1 ) and 1.71% year -1 (79 kg ha -1 year -1 ), respectively. Varieties from NARO and private sector showed comparable mean yields of 4.56 t ha -1 and 4.62 t ha -1 , respectively, while hybrids from CIMMYT had a mean of 5.37 t ha -1 . Era analysis indicated significant genetic gain of 1.69% year -1 or 55 kg ha -1 year -1 , while a significant national productivity gain of 1.48% year -1 (37 kg ha -1 year -1 ) was obtained. The study, thus, demonstrated the importance of public-private partnerships in development and delivery of new genetics to farmers in Uganda., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Asea, Kwemoi, Sneller, Kasozi, Das, Musundire, Makumbi, Beyene and Prasanna.)

Technologies and innovations are critical for addressing the future food system needs where genetic resources are an essential component of the change process. Advanced breeding tools like "genome editing" are vital for modernizing crop breeding to provide game-changing solutions to some of the "must needed" traits in agriculture. CRISPR/Cas-based tools have been rapidly repurposed for editing applications based on their improved efficiency, specificity and reduced off-target effects. Additionally, precise gene-editing tools such as base editing, prime editing, and multiplexing provide precision in stacking of multiple traits in an elite variety, and facilitating specific and targeted crop improvement. This has helped in advancing research and delivery of products in a short time span, thereby enhancing the rate of genetic gains. A special focus has been on food security in the drylands through crops including millets, teff, fonio, quinoa, Bambara groundnut, pigeonpea and cassava. While these crops contribute significantly to the agricultural economy and resilience of the dryland, improvement of several traits including increased stress tolerance, nutritional value, and yields are urgently required. Although CRISPR has potential to deliver disruptive innovations, prioritization of traits should consider breeding product profiles and market segments for designing and accelerating delivery of locally adapted and preferred crop varieties for the drylands. In this context, the scope of regulatory environment has been stated, implying the dire impacts of unreasonable scrutiny of genome-edited plants on the evolution and progress of much-needed technological advances., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Sharma, Palakolanu, Bhattacharya, Shankhapal and Bhatnagar-Mathur.)

Genomic Selection (GS) has allowed the maximization of genetic gains per unit time in several annual and perennial plant species. However, no GS studies have addressed Coffea arabica , the most economically important species of the genus Coffea . Therefore, this study aimed (i) to evaluate the applicability and accuracy of GS in the prediction of the genomic estimated breeding value (GEBV); (ii) to estimate the genetic parameters; and (iii) to evaluate the time reduction of the selection cycle by GS in Arabica coffee breeding. A total of 195 Arabica coffee individuals, belonging to 13 families in generation of F 2 , susceptible backcross and resistant backcross, were phenotyped for 18 agronomic traits, and genotyped with 21,211 SNP molecular markers. Phenotypic data, measured in 2014, 2015, and 2016, were analyzed by mixed models. GS analyses were performed by the G-BLUP method, using the RKHS (Reproducing Kernel Hilbert Spaces) procedure, with a Bayesian algorithm. Heritabilities and selective accuracies were estimated, revealing moderate to high magnitude for most of the traits evaluated. Results of GS analyses showed the possibility of reducing the cycle time by 50%, maximizing selection gains per unit time. The effect of marker density on GS analyses was evaluated. Genomic selection proved to be promising for C. arabica breeding. The agronomic traits presented high complexity for they are controlled by several QTL and showed low genomic heritabilities, evidencing the need to incorporate genomic selection methodologies to the breeding programs of this species.

A comprehensive understanding of the genetic basis of target traits in any crop is critical to design breeding strategies for the development and release of new improved varieties. In this study, 34 cacao families were evaluated for vigor and yield related traits over the course of 6 years in Costa Rica. Linear mixed models provided the variance components for the partitioning of additive and non-additive effects. Heritabilities of yield over time ranged from 0.085 to 0.576, from 0.127 to 0.399 for vigor, and 0.141 to 0.146 for disease resistance traits. Significant ( p < 0.001) general combining abilities were observed for ICS-43 and LcTeen-37 with negative effect on average yield (-0.674, -0.690), respectively. Specific combining abilities for yield had significant ( p < 0.001) positive effect from the cross GU-154-L x UF-273 Type 2 (0.703) and strong negative interaction between ICS-43 and LF-1 (-0.975). A weighted index was used to select the top performers while providing the corresponding genetic gains. At an 1% selection intensity, yield component gains ranged from 17.8 to 331.9%. Agronomic traits such as branch angle, trunk diameter and jorquette height had lower genetic gains and lower heritabilities. In addition, the parents in this study were genotyped with a 96-SNP marker off-typing set and a significant positive correlation of 0.39 ( p = 0.019) was found between genetic distance and specific combining abilities for yield. Preliminary comparison of clonal parents vs. seedlings yield in the family with the highest SCA suggest for the first time presence of heterobeltiosis in cacao.

Breeding programs of cacao ( Theobroma cacao L.) trees share the many challenges of breeding long-living perennial crops, and genetic progress is further constrained by both the limited understanding of the inheritance of complex traits and the prevalence of technical issues, such as mislabeled individuals (off-types). To better understand the genetic architecture of cacao, in this study, 13 years of phenotypic data collected from four progeny trials in Bahia, Brazil were analyzed jointly in a multisite analysis. Three separate analyses (multisite, single site with and without off-types) were performed to estimate genetic parameters from statistical models fitted on nine important agronomic traits (yield, seed index, pod index, % healthy pods, % pods infected with witches broom, % of pods other loss, vegetative brooms, diameter, and tree height). Genetic parameters were estimated along with variance components and heritabilities from the multisite analysis, and a trial was fingerprinted with low-density SNP markers to determine the impact of off-types on estimations. Heritabilities ranged from 0.37 to 0.64 for yield and its components and from 0.03 to 0.16 for disease resistance traits. A weighted index was used to make selections for clonal evaluation, and breeding values estimated for the parental selection and estimation of genetic gain. The impact of off-types to breeding progress in cacao was assessed for the first time. Even when present at <5% of the total population, off-types altered selections by 48%, and impacted heritability estimations for all nine of the traits analyzed, including a 41% difference in estimated heritability for yield. These results show that in a mixed model analysis, even a low level of pedigree error can significantly alter estimations of genetic parameters and selections in a breeding program.

Breeding cassava relies on several selection stages (single row trial-SRT; preliminary; advanced; and uniform yield trials-UYT). This study uses data from 14 years of evaluations. From more than 20,000 genotypes initially evaluated only 114 reached the last stage. The objective was to assess how the data at SRT could be used to predict the probabilities of genotypes reaching the UYT. Phenotypic data from each genotype at SRT was integrated into the selection index (SIN) used by the cassava breeding program. Average SIN from all the progenies derived from each progenitor was then obtained. Average SIN is an approximation of the breeding value of each progenitor. Data clearly suggested that some genotypes were better progenitors than others (e.g., high number of their progenies reaching the UYT), suggesting important variation in breeding values of progenitors. However, regression of average SIN of each parental genotype on the number of their respective progenies reaching UYT resulted in a negligible coefficient of determination (r (2) = 0.05). Breeding value (e.g., average SIN) at SRT was not efficient predicting which genotypes were more likely to reach the UYT stage. Number of families and progenies derived from a given progenitor were more efficient predicting the probabilities of the progeny from a given parent reaching the UYT stage. Large within-family genetic variation tends to mask the true breeding value of each progenitor. The use of partially inbred progenitors (e.g., S1 or S2 genotypes) would reduce the within-family genetic variation thus making the assessment of breeding value more accurate. Moreover, partial inbreeding of progenitors can improve the breeding value of the original (S0) parental material and sharply accelerate genetic gains. For instance, homozygous S1 genotypes for the dominant resistance to cassava mosaic disease (CMD) could be generated and selected. All gametes from these selected S1 genotypes would carry the desirable allele and 100% of their progenies would be resistant. Only half the gametes produced by the heterozygous S0 progenitor would carry the allele of interest. For other characteristics, progenies from the S1 genotypes should be, at worst, similar to those generated by the S0 progenitors.