Genotype by Environment Interaction by AMMI and GGE Bi-Plot Analysis for Maize (Zea Mays L.) for Transitional High Land Agroecology of Ethiopia.

The current research examined the magnitude of genotype by environment interaction (G x E) and evaluated the adaptability and stability of maize genotypes for grain yield in Ethiopia's transitional highland agroecology using an additive main effects and multiplicative interaction (AMMI) model. The study's goals were to first assess the yield output and stability of maize genotypes in Ethiopia's transitional highlands, and then to investigate the effect of genotype- environment interaction on genotype yield. During the main season of 2017/2018, thirteen advanced maize genotypes which was selected from different observation trials with two commercial check hybrids were evaluated at five representative locations for agroecology. The experiment was set up using an alpha lattice (3*5) with three replications and two rows per plot. AMMI showed highly significant(P < 0.001) variation of grain yield was observed due to the effect of genotype (G), Environment(E) and their interaction (G x E). In fact, all genotypes evaluated in representative locations for this agroecology had higher grain yield advantages than the best commercial check except one genotype. Overall, this study discovered the possibility of fast releasing and overtake of new maize hybrids for transitional high land agroecology of Ethiopia to exploits availability maize germplasm to maximize production. The best candidate genotype, MABK181261 is a stable and high-yielding product. It is recommended for release as a commercial hybrid alternative after national variety verification trial in a high land transitional agroecology of Ethiopia. In addition, the parental lines of this genotypes can be used to enhance germplasm of opposite heterotic group in maize breeding for East Africa.

Heterotic Patterns of Temperate and Tropical Maize by Ear Photometry

As the plant variety protection (PVP) of commercial inbred lines expire, public breeding programs gain a wealth of genetic materials that have undergone many years of intense selection; however, the value of these inbred lines is only fully realized when they have been well characterized and are used in hybrid combinations. Additionally, while yield is the primary trait by which hybrids are evaluated, new phenotyping technologies, such as ear photometry (EP), may provide an assessment of yield components that can be scaled to breeding programs. The objective of this experiment was to use EP to describe the testcross performance of inbred lines from temperate and tropical origins. We evaluated the performance of 298 public and ex-PVP inbred lines and 274 Drought Tolerant Maize for Africa (DTMA) inbred lines when crossed to Iodent (PHP02) and/or Stiff Stalk (2FACC) testers for 25 yield-related traits. Kernel weight, kernels per ear, and grain yield predicted by EP were correlated with their reference traits with r = 0.49, r = 0.88, and r = 0.75, respectively. The testcross performance of each maize inbred line was tester dependent. When lines were crossed to a tester within the heterotic group, many yield components related to ear size and kernels per ear were significantly reduced, but kernel size was rarely impacted. Thus, the effect of heterosis was more noticeable on traits that increased kernels per ear rather than kernel size. Hybrids of DTMA inbred lines crossed to PHP02 exhibited phenotypes similar to testcrosses of Stiff Stalk and Non-Stiff Stalk heterotic groups for yield due to significant increases in kernel size to compensate for a reduction in kernels per ear. Kernels per ear and ear length were correlated (r = 0.89 and r = 0.84, respectively) with and more heritable than yield, suggesting these traits could be useful for inbred selection.

Genomic prediction of hybrid crops allows disentangling dominance and epistasis

We revisited, in a genomic context, the theory of hybrid genetic evaluation models of hybrid crosses of pure lines, as the current practice is largely based on infinitesimal model assumptions. Expressions for covariances between hybrids due to additive substitution effects and dominance and epistatic deviations were analytically derived. Using dense markers in a GBLUP analysis, it is possible to split specific combining ability into dominance and across-groups epistatic deviations, and to split general combining ability (GCA) into within-line additive effects and within-line additive by additive (and higher order) epistatic deviations. We analyzed a publicly available maize data set of Dent × Flint hybrids using our new model (called GCA-model) up to additive by additive epistasis. To model higher order interactions within GCAs, we also fitted “residual genetic” line effects. Our new GCA-model was compared with another genomic model which assumes a uniquely defined effect of genes across origins. Most variation in hybrids is accounted by GCA. Variances due to dominance and epistasis have similar magnitudes. Models based on defining effects either differently or identically across heterotic groups resulted in similar predictive abilities for hybrids. The currently used model inflates the estimated additive genetic variance. This is not important for hybrid predictions but has consequences for the breeding scheme—e.g. overestimation of the genetic gain within heterotic group. Therefore, we recommend using GCA-model, which is appropriate for genomic prediction and variance component estimation in hybrid crops using genomic data, and whose results can be practically interpreted and used for breeding purposes.

De novo identification and targeted sequencing of SSRs efficiently fingerprints Sorghum bicolor sub-population identity

Recent plant breeding studies of several species have demonstrated the utility of combining molecular assessments of genetic distance into trait-linked SNP genotyping during the development of parent lines to maximize yield gains due to heterosis. SSRs (Short Sequence Repeats) are the molecular marker of choice to determine genetic diversity, but the methods historically used to sequence them have been burdensome. The ability to analyze SSRs in a higher-throughput manner independent of laboratory conditions would increase their utility in molecular ecology, germplasm curation, and plant breeding programs worldwide. This project reports simple bioinformatics methods that can be used to generate genome-wide de novo SSRs in silico followed by targeted Next Generation Sequencing (NGS) validation of those that provide the most information about sub-population identity of a breeding line, which influences heterotic group selection. While these methods were optimized in sorghum [Sorghum bicolor (L.) Moench], they were developed to be applied to any species with a reference genome and high-coverage whole-genome sequencing data of individuals from the sub-populations to be characterized. An analysis of published sorghum genomes selected to represent its five main races (bicolor, caudatum, durra, kafir, and guinea; 75 accessions total) identified 130,120 SSR motifs. Average lengths were 23.8 bp and 95% were between 10 and 92 bp, making them suitable for NGS. Validation through targeted sequencing amplified 188 of 192 assayed SSR loci. Results highlighted the distinctness of accessions from the guinea sub-group margaritiferum from all other sorghum accessions, consistent with previous studies of nuclear and mitochondrial DNA. SSRs that efficiently fingerprinted margaritiferum individuals (Xgma1 –Xgma6) are presented. Developing similar fingerprints of other sub-populations (Xunr1 –Xunr182) was not possible due to the extensive admixture between them in the data set analyzed. In summary, these methods were able to fingerprint specific sub-populations when rates of admixture between them are low.

Molecular characterization of a farmer-preferred maize landrace population from a multiple-stress-prone subtropical lowland environment

Makore F, Gasura E, Souta C, Mazamura U, Derera J, Zikhali M, Kamutando CN, Magorokosho C, Dari S. 2021. Molecular characterization of a farmer-preferred maize landrace population from a multiple-stress-prone subtropical lowland environment. Biodiversitas 22: 769-777. The study was conducted to assess genetic diversity of 372 maize lines using 116 single nucleotide polymorphism (SNP) markers. Three hundred and forty-seven lines were S1 lines (coded J lines) from a local maize landrace population and twenty-five were the widely used standard lines. The number of alleles per marker ranged from two to four and the average was three alleles. The average polymorphic information content (PIC) value of 0.405 indicates high genetic diversity for maize lines evaluated in this study. Population structure revealed three distinct sub-populations. Sub-population 1 contained two J lines; sub-population 2 contained five J lines and sub-population 3 contained the rest of the J lines and all the standard lines. Analysis of molecular variance (AMOVA) identified 22% variance among and 78% variance within the three subpopulations, indicating high gene exchange and low genetic differentiation. Hierarchical cluster analysis further divided the lines into nine subgroups placing some of the J lines into known heterotic groups', i.e., J30_3, J393_4, J393_3, and J393_1 in CIMMYT heterotic group B. Allelic variation observed can be a source of allele combination for breeding programs interested in widening their genetic base. The private alleles that were present in the J lines suggest availability of stress-tolerant genes that breeders can incorporate in new hybrids.

Microsatellite marker-based genetic diversity of tropical-adapted shrunken-2 maize inbred lines and its relationship with normal endosperm inbred lines of known heterotic classification

Knowledge of the genetic diversity and relationships among maize inbred lines can facilitate germplasm management and plant breeding programmes. The study investigated the level of genetic diversity among S6 lines developed from a tropical-adapted shrunken-2 (sh-2) maize population and their relationship with normal endosperm tropical inbred lines of known heterotic groups. Ninety-one sh-2 maize inbred lines (UI1-UI91) developed in the University of Ibadan super-sweet Maize Breeding Programme were genotyped at 30 simple sequence repeat (SSR) loci, alongside five normal endosperm maize inbred lines viz. TZi3, TZi4, TZi10, TZi12 and TZi15, four of which belong to two heterotic groups. Twenty-three SSR markers were polymorphic and detected a total of 61 alleles, with a range of 2–7 and an average of 2.65 alleles per locus. The polymorphic information content ranged from 0.12 in bnlg1937 to 0.77 in phi126, with an average of 0.36. The gene diversity (He) averaged 0.43. Cluster analysis resulted in five groups consisting of 16, 36, 17, 23 and 3 inbred lines, with one sh-2 line ungrouped. TZi 12 and TZi 15, both of which are of the same heterotic group, clustered with TZi 3 of another heterotic group. Considerable genetic diversity exists among the 96 inbred lines. Only two of the five normal endosperm lines shared clusters with the sh-2 lines. The clustering of the normal endosperm inbred lines is not related to their established heterotic patterns. Inbred lines in two clusters offer the possibility of guiding the exploitation of heterosis among the sh-2 lines.

Identification of New Single Cross Testers for CIMMYT Heterotic Group B Maize Germplasm Adapted to Mid-Altitudes

The development of higher yielding maize (Zea mays L.) hybrids adapted to low input small-holder farming systems in sub-Saharan Africa is required. Three-way hybrids (i.e. F1 tester crossed to inbred line) can be produced at lower cost for smallholder farmers, but to achieve this it is crucial for CIMMYT-Zimbabwe maize breeding program to identify new high yielding single cross testers with high combining ability to support the development of new high yielding hybrids for this region. Data collected on the performance of F1 and three-way hybrids from a total of 25 multi-environment trials (METs) located in South Africa (three trials), Zambia (four trials) and Zimbabwe (eighteen trials) grown across two seasons during the period from 2015–2018 to: (i) identify new single cross testers for CIMMYT HG-B maize germplasm; (ii) identify stable and high yielding three-way hybrids. Analyses were conducted using a two-stage approach. Clustering based on yield data, grouped sites into three environment types (ET); low (LY) < 3 t ha−1, medium (MY) 3–6 t ha−1 and high (HY) 6–13 t ha−1 yielding groups. Additive genetic effects of both inbred parents and selected F1 crosses used as parents were more important than non-additive genetic effects for grain yield across ETs. Strong genotype x environment interactions on yield and other traits were observed. It was concluded that F1 hybrids (entry 75, 85, 72 and 28) demonstrated high yield across all environment types, and it is recommended that these be also evaluated as potential three-way hybrids. Single crosses CZL15085/CML566 and CZL15085/CZL13102 from heterotic group B to be used as testers for ET 1 and ET 2 respectively.