Phenotypic and molecular characterization of a set of tropical maize inbred lines from a public breeding program in Brazil.

BACKGROUND: The characterization of genetic diversity and population differentiation for maize inbred lines from breeding programs is of great value in assisting breeders in maintaining and potentially increasing the rate of genetic gain. In our study, we characterized a set of 187 tropical maize inbred lines from the public breeding program of the Universidade Federal de Viçosa (UFV) in Brazil based on 18 agronomic traits and 3,083 single nucleotide polymorphisms (SNP) markers to evaluate whether this set of inbred lines represents a panel of tropical maize inbred lines for association mapping analysis and investigate the population structure and patterns of relationships among the inbred lines from UFV for better exploitation in our maize breeding program. RESULTS: Our results showed that there was large phenotypic and genotypic variation in the set of tropical maize inbred lines from the UFV maize breeding program. We also found high genetic diversity (GD = 0.34) and low pairwise kinship coefficients among the maize inbred lines (only approximately 4.00 % of the pairwise relative kinship was above 0.50) in the set of inbred lines. The LD decay distance over all ten chromosomes in the entire set of maize lines with r2 = 0.1 was 276,237 kb. Concerning the population structure, our results from the model-based STRUCTURE and principal component analysis methods distinguished the inbred lines into three subpopulations, with high consistency maintained between both results. Additionally, the clustering analysis based on phenotypic and molecular data grouped the inbred lines into 14 and 22 genetic divergence clusters, respectively. CONCLUSIONS: Our results indicate that the set of tropical maize inbred lines from UFV maize breeding programs can comprise a panel of tropical maize inbred lines suitable for a genome-wide association study to dissect the variation of complex quantitative traits in maize, mainly in tropical environments. In addition, our results will be very useful for assisting us in the assignment of heterotic groups and the selection of the best parental combinations for new breeding crosses, mapping populations, mapping synthetic populations, guiding crosses that target highly heterotic and yielding hybrids, and predicting untested hybrids in the public breeding program UFV.

Optimizing use of U.S. Ex-PVP inbred lines for enhancing agronomic performance of tropical Striga resistant maize inbred lines.

BACKGROUND: Temperate maize inbred lines with expired Plant Variety Protection Act certificates (Ex-PVP) are potential sources of desirable alleles for tropical germplasm improvement. Up to now, the usefulness of the Ex-PVP inbred lines as a potential source of novel beneficial alleles for Striga hermonthica resistance breeding to enhance genetic gain in tropical maize has not been reported. RESULTS: This study was thus conducted to characterize the combining ability of 24 Ex-PVP inbred lines in crosses with two tropical Striga resistant inbred testers under Striga-infested and non-infested conditions and across three locations for 2 years. Many testcrosses between Ex-PVP inbred lines and the first tester (T1) produced competitive or significantly higher grain yields compared to the hybrid between the two resistant testers under Striga infested and non-infested conditions and across multiple test locations. Also, most of the testcrosses with positive heterosis for grain yield and negative heterosis for Striga damage and emerged Striga count involved T1 as a tester. Our study identified six Ex-PVP inbred lines with positive GCA effects for grain yield under Striga infested and non-infested conditions and across multiple test locations. Amongst these, inbred lines HB8229-1 and WIL900-1 also displayed negative GCA effects for emerged Striga count and Striga damage rating. The inbred line HB8229-1 showed positive SCA effects for grain yield with T2, whereas WIL900-1 had positive SCA effects for grain yield with T1. Over 70% of the Ex-PVP inbred lines were consistently assigned to specific heterotic groups using yield-based classifying methods (mean grain yield and SCA effects). CONCLUSIONS: These results could facilitate systematic introgression of the Ex-PVP inbred lines into the existing Striga resistant heterotic groups in IITA. The Ex-PVP inbred lines with positive GCA effects and producing high grain yields in hybrid combinations could be useful parents for enhancing Striga resistance and agronomic performance of tropical maize hybrids.

Understanding the classics: the unifying concepts of transgressive segregation, inbreeding depression and heterosis and their central relevance for crop breeding.

Transgressive segregation and heterosis are the reasons that plant breeding works. Molecular explanations for both phenomena have been suggested and play a contributing role. However, it is often overlooked by molecular genetic researchers that transgressive segregation and heterosis are most simply explained by dispersion of favorable alleles. Therefore, advances in molecular biology will deliver the most impact on plant breeding when integrated with sources of heritable trait variation - and this will be best achieved within a quantitative genetics framework. An example of the power of quantitative approaches is the implementation of genomic selection, which has recently revolutionized animal breeding. Genomic selection is now being applied to both hybrid and inbred crops and is likely to be the major source of improvement in plant breeding practice over the next decade. Breeders' ability to efficiently apply genomic selection methodologies is due to recent technology advances in genotyping and sequencing. Furthermore, targeted integration of additional molecular data (such as gene expression, gene copy number and methylation status) into genomic prediction models may increase their performance. In this review, we discuss and contextualize a suite of established quantitative genetics themes relating to hybrid vigour, transgressive segregation and their central relevance to plant breeding, with the aim of informing crop researchers outside of the quantitative genetics discipline of their relevance and importance to crop improvement. Better understanding between molecular and quantitative disciplines will increase the potential for further improvements in plant breeding methodologies and so help underpin future food security.

Genetic variation for maize root architecture in response to drought stress at the seedling stage.

Although the root system is indispensable for absorption of nutrients and water, it is poorly studied in maize owing to the difficulties of direct measurement of roots. Here, 103 maize lines were used to compare root architectures under well-watered and water-stressed conditions. Significant genetic variation, with medium to high heritability and significant correlations, was observed for root traits. Total root length (TRL) and total root surface area (TSA) had high phenotypical diversity, and TRL was positively correlated with TSA, root volume, and root forks. The first two principal components explained 94.01% and 91.15% of total root variation in well-watered and water-stressed conditions, respectively. Thus, TRL and TSA, major contributors to root variation, can be used as favorable selection criteria at the seedling stage. We found that stiff stalk and non-stiff stalk groups (temperate backgrounds) showed relatively higher mean values for root morphological diversity than the TST group (tropical/subtropical background). Of the tested lines, 7, 42, 45, and 9 were classified as drought sensitive, moderately sensitive, moderately drought tolerant, and highly drought tolerant, respectively. Seven of the 9 extremely drought tolerant lines were from the TST group, suggesting that TST germplasms harbor valuable genetic resources for drought tolerance that could be used in breeding to improve abiotic stress tolerance in maize.

Heterotic grouping of wheat hybrids based on general and specific combining ability from line × tester analysis.

The most important step in plant breeding is the correct selection of parents, and it would be wise to use heterotic groups for this. The purpose of this study is to analyse yield and its components as well as genetic diversity in line × tester wheat populations. It also seeks to present a coherent framework for the isolation of early superior families and the development of heterotic groups in bread wheat. F1 and F2 generations of 51 genotypes, including 36 combinations between 12 lines and three testers and 15 parents, were evaluated for yield and its components in a three-replication experiment according to the randomized block design. Line ×  tester analysis of variance, general and specific combining abilities, heterosis, heterobeltiosis and inbreeding depression were calculated. Heterotic groups created based on general and specific combining abilities were compared with each other. The results showed that there was sufficient genetic variation in the population and that further genetic calculations could be made. The selections made based on general and specific combining abilities, heterosis values and average performance of genotypes without heterotic grouping indicated different genotypes for each feature. The creation of heterotic groups made it possible to select genotypes that were superior in terms of all the criteria listed. It was concluded that heterotic groups created based on specific combining abilities may be more useful for breeding studies.

Heterotic grouping of provitamin A-enriched maize inbred lines for increased provitamin A content in hybrids.

BACKGROUND: The establishment of heterotic groups of inbred lines is crucial for hybrid maize breeding programs. Currently, there is no information on the heterotic patterns of the Provitamin A (PVA) inbred lines developed in the maize improvement program of the International Institute of Tropical Agriculture (IITA) to form productive PVA enriched hybrids for areas affected by vitamin A deficiency. This study assessed the feasibility of classifying PVA-enriched inbred lines into heterotic groups based on PVA content without compromising grain yield in hybrids. Sixty PVA inbred lines were crossed to two testers representing two existing heterotic groups. The resulting 120 testcrosses hybrids were evaluated for two years at four locations in Nigeria. RESULTS: The two testers effectively classified the inbred lines into two heterotic groups. The PVA-based general combining ability and specific combining ability (HSGCA) method assigned 31 and 27 PVA enriched maize inbred lines into HGB and HGA, respectively, leaving two inbred lines not assigned to any group. The yield-based HSGCA method classified 32 inbred lines into HGB and 28 inbred lines into HGA. Both PVA and yield-based heterotic grouping methods assigned more than 40% of the inbred lines into the same heterotic groups. Even though both PVA and yield-based heterotic grouping of the inbred lines differed from the clusters defined by the DArTag SNP markers, more than 40% of the inbred lines assigned to HGA were present in Cluster-1 and 60% of the inbred lines assigned to HGB were present in Cluster-3. Interestingly, the inbred lines assigned to the same heterotic groups based on PVA content and grain yield were distributed across the three Ward's clusters. The PVA-based HSGCA was identified as the most effective heterotic grouping method for breeding programs working on PVA biofortification. CONCLUSIONS: Selecting PVA enriched maize inbred lines with diverse genetic backgrounds from the three marker-based clusters may facilitate the development of productive hybrids with high PVA content and for generating source populations to develop more vigorous maize inbred lines with much higher concentrations of PVA.

On the usefulness of mock genomes to define heterotic pools, testers, and hybrid predictions in orphan crops.

The advances in genomics in recent years have increased the accuracy and efficiency of breeding programs for many crops. Nevertheless, the adoption of genomic enhancement for several other crops essential in developing countries is still limited, especially for those that do not have a reference genome. These crops are more often called orphans. This is the first report to show how the results provided by different platforms, including the use of a simulated genome, called the mock genome, can generate in population structure and genetic diversity studies, especially when the intention is to use this information to support the formation of heterotic groups, choice of testers, and genomic prediction of single crosses. For that, we used a method to assemble a reference genome to perform the single-nucleotide polymorphism (SNP) calling without needing an external genome. Thus, we compared the analysis results using the mock genome with the standard approaches (array and genotyping-by-sequencing (GBS)). The results showed that the GBS-Mock presented similar results to the standard methods of genetic diversity studies, division of heterotic groups, the definition of testers, and genomic prediction. These results showed that a mock genome constructed from the population's intrinsic polymorphisms to perform the SNP calling is an effective alternative for conducting genomic studies of this nature in orphan crops, especially those that do not have a reference genome.

Prediction of additive, epistatic, and dominance effects using models accounting for incomplete inbreeding in parental lines of hybrid rye and sugar beet.

Genomic models for prediction of additive and non-additive effects within and across different heterotic groups are lacking for breeding of hybrid crops. In this study, genomic prediction models accounting for incomplete inbreeding in parental lines from two different heterotic groups were developed and evaluated. The models can be used for prediction of general combining ability (GCA) of parental lines from each heterotic group as well as specific combining ability (SCA) of all realized and potential crosses. Here, GCA was estimated as the sum of additive genetic effects and within-group epistasis due to high degree of inbreeding in parental lines. SCA was estimated as the sum of across-group epistasis and dominance effects. Three models were compared. In model 1, it was assumed that each hybrid was produced from two completely inbred parental lines. Model 1 was extended to include three-way hybrids from parental lines with arbitrary levels of inbreeding: In model 2, parents of the three-way hybrids could have any levels of inbreeding, while the grandparents of the maternal parent were assumed completely inbred. In model 3, all parental components could have any levels of inbreeding. Data from commercial breeding programs for hybrid rye and sugar beet was used to evaluate the models. The traits grain yield and root yield were analyzed for rye and sugar beet, respectively. Additive genetic variances were larger than epistatic and dominance variances. The models' predictive abilities for total genetic value, for GCA of each parental line and for SCA were evaluated based on different cross-validation strategies. Predictive abilities were highest for total genetic values and lowest for SCA. Predictive abilities for SCA and for GCA of maternal lines were higher for model 2 and model 3 than for model 1. The implementation of the genomic prediction models in hybrid breeding programs can potentially lead to increased genetic gain in two different ways: I) by facilitating the selection of crossing parents with high GCA within heterotic groups and II) by prediction of SCA of all realized and potential combinations of parental lines to produce hybrids with high total genetic values.

Selection of Sweetpotato Parental Genotypes Using Simple Sequence Repeat Markers.

Knowledge of the genetic diversity and genetic relationship is important in crop improvement. The objective of this study was to determine the genetic diversity of 31 sweetpotato genotypes and furthermore to select distantly related individuals for breeding of superior parental clones. The genotypes (sourced from the Agricultural Research Council, South Africa) originating from Africa and American continent were genotyped using eight highly polymorphic SSR markers. The SSR markers generated a total of 83 putative alleles. The polymorphic information content (PIC) of the tested simple sequence markers varied from 0.73 to 0.91, with a mean of 0.85. At least 11 different alleles were found in 8 loci within the population, with 7 effective alleles per locus. Although high diversity was found among the genotypes, genetic distances among the genotypes were relatively low. Cluster analysis revealed the existence of three distinct genetic groups, and the clustering patterns follow to some extent the geographic origin and pedigree of the genotypes. High gene flow was observed among different sweetpotato accessions. The selected SSR markers were found to be highly polymorphic with high discriminatory power for genetic characterization studies and are useful genomic tool to complement phenotyping of sweetpotato genotypes. Two heterotic groups were found in the study. The heterotic group A was composed of 14 genotypes mainly of South African origin, while the heterotic group B consisted of 17 genotypes of American origin. The two distinct groups were important for the selection of breeding clones that were distantly related to be used as parental clones in the advancement of traits of interest.

Identification of Heterotic Groups and Patterns Based on Genotypic and Phenotypic Characteristics Among Rice Accessions of Diverse Origins.

Identification of the right parental combinations to maximize heterosis is the major goal of hybrid breeding, which could be achieved through identification of heterotic groups. The main objective of this study was to identify promising heterotic groups for future rice breeding programs. A collection of 359 rice genotypes of diverse origins of China and abroad, composed of inbreds, maintainers, restorers, and temperature-sensitive genic male sterile (TGMS) lines were genotyped using 10K SNP chips. The SNP data set was subjected to genomic analyses for estimation of genetic divergence and diversity. Significant variations were observed in the germplasm with the identification of six different genetic groups. These lines were assigned to the genetic groups independent of their origin. Taking an account of commercially used heterotic groups present in each cluster, three cytoplasmic male sterile (CMS) lines and 14 inbred and restorer lines with moderate to high genetic distances selected from five heterotic patterns were crossed and obtained 42 F1 hybrids. A total of 14 hybrids were found with significant maximum mid- and better-parent heterosis, namely, TaifengA × Guang122, TaifengA × Wushansimiao, and TaifengA × Minghui63 for earliness; Guang8A × Huazhan for dwarf stature; and Guang8A × Huanghuzhan-1, TaifengA × Yuexiangzhan, Guang8A × Minhui3301, TianfengA × Guang122, Guang8A × Yahui2115, TianfengA × Huanghuazhan, TianfengA × Minghui63, TianfengA × Minhui3301, TaifengA × Gui99, and Guang8A × Yuenongsimiao for yield and yield-related traits. Mid-parent and better-parent heterotic F1 hybrids were in positive correlation with the genetic distances as that manifested by commercially used heterotic groups, encouraging the use of genotypic data for identification of heterotic groups. Our study provides an informative strategy for the development of early maturing, lodging resistant and high-yielding commercial hybrids and cultivars in future heterosis breeding programs.

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.

Large-Scale Analysis of Combining Ability and Heterosis for Development of Hybrid Maize Breeding Strategies Using Diverse Germplasm Resources.

Understanding combining ability and heterosis among diverse maize germplasm resources is important for breeding hybrid maize (Zea mays L.). Using 28 temperate and 23 tropical maize inbreds that represent different ecotypes and worldwide diversity of maize germplasm, we first developed a large-scale multiple-hybrid population (MHP) with 724 hybrids, which could be divided into three subsets, 325 temperate diallel hybrids and 136 tropical diallel hybrids generated in Griffing IV, and 263 temperate by tropical hybrids generated in NCD II. All the parental lines and hybrids were evaluated for 11 traits in replicated tests across two locations and three years. Several widely used inbreds showed strong general combining ability (GCA), and their derived hybrids showed strong specific combining ability (SCA). Heterosis is a quantifiable, trait-dependent and environment-specific phenotype, and the response of parental lines and their hybrids to environments resulted in various levels of heterosis. For all the tested traits except plant height and hundred grain weight (HGW), NCD II (temperate × tropical) hybrids showed higher average heterosis than the temperate and tropical diallel hybrids, with higher hybrid performance for ear length, ear diameter, and HGW. Tropical maize germplasm can be used to improve the yield potential for temperate lines. Grain number per row and grain number per ear were two most important traits that determined yield heterosis, which can be used as direct selection criteria for yield heterosis. The hybrids from heterotic groups, Reid × SPT, Reid × LRC, SPT × PA, and Lancaster × LRC, contributed highly significant positive SCA effects and strong heterosis to yield-related traits, and the heterotic patterns identified in this study were potentially useful for commercial maize breeding. Heterosis was more significantly and positively correlated with SCA than GCA, indicating that SCA can be used in heterosis prediction to develop potential hybrids in commercial maize breeding. The results of the present study not only contribute to developing breeding strategies, but also improve targeted breeding efficiency by using both temperate and tropical maize to broaden genetic basis. Large sets of parental lines with available genotypic information can be shared and used in worldwide hybrid breeding programs through an open-source breeding strategy. Potential applications of the reported results in developing hybrid maize breeding strategies were also discussed.

Parental Expression Variation of Small RNAs Is Negatively Correlated with Grain Yield Heterosis in a Maize Breeding Population.

Heterosis refers to a quantitative phenomenon in which F1 hybrid trait values exceed the mean of the parental values in a positive direction. Generally, it is dependent on a high degree of heterozygosity, which is maintained in hybrid breeding by developing parental lines in separate, genetically distinct heterotic groups. The mobility of small RNAs (sRNAs) that mediate epigenetic regulation of gene expression renders them promising candidates for modulating the action of combined diverse genomes in trans-and evidence already indicates their contribution to transgressive phenotypes. By sequencing small RNA libraries of a panel of 21 maize parental inbred lines we found a low overlap of 35% between the sRNA populations from both distinct heterotic groups. Surprisingly, in contrast to genetic or gene expression variation, parental sRNA expression variation is negatively correlated with grain yield (GY) heterosis. Among 0.595 million expressed sRNAs, we identified 9,767, predominantly 22- and 24-nt long sRNAs, which showed an association of their differential expression between parental lines and GY heterosis of the respective hybrids. Of these sRNAs, 3,485 or 6,282 showed an association with high or low GY heterosis, respectively, thus the low heterosis associated group prevailing at 64%. The heterosis associated sRNAs map more frequently to genes that show differential expression between parental lines than reference sets. Together these findings suggest that trans-chromosomal actions of sRNAs in hybrids might add up to a negative contribution in heterosis formation, mediated by unfavorable gene expression regulation. We further revealed an exclusive accumulation of 22-nt sRNAs that are associated with low GY heterosis in pericentromeric genomic regions. That recombinational suppression led to this enrichment is indicated by its close correlation with low recombination rates. The existence of this enrichment, which we hypothesize resulted from the separated breeding of inbred lines within heterotic groups, may have implications for hybrid breeding strategies addressing the recombinational constraints characteristic of complex crop genomes.

Genome-Based Identification of Heterotic Patterns in Rice.

BACKGROUND: Hybrid rice breeding facilitates to increase grain yield and yield stability. Long-term success of hybrid breeding depends on the recognition of high-yielding complementary heterotic patterns, which is lacking in crops like rice. RESULT: The main goal of this study was to evaluate the potential and limits to use genomics for establishing heterotic patterns in rice. For this purpose, data of a commercial hybrid rice breeding program targeted to India was analyzed, including 1,960 phenotyped hybrids from three market segments and 262 genotyped parental lines. Our cross-validation study revealed that grain yield of all potential single-crosses can be accurately predicted. Based on the full matrix of hybrid performances, high-yielding heterotic patterns were identified. These heterotic patterns increased grain yield up to 9% compared to the currently employed groups. Heterotic groups of around 14 individuals reflect a good compromise between long-term and short-term selection response. CONCLUSIONS: Our findings clearly underlined the benefits of a genome-based establishment of heterotic patterns in rice as a requirement for a sustainable long-term success of hybrid rice breeding.

Towards Defining Heterotic Gene Pools in Pearl Millet [Pennisetum glaucum (L.) R. Br.].

Pearl millet is a climate resilient crop and one of the most widely grown millets worldwide. Heterotic hybrid development is one of the principal breeding objectives in pearl millet. In a maiden attempt to identify heterotic groups for grain yield, a total of 343 hybrid parental [maintainer (B-) and restorer (R-)] lines were genotyped with 88 polymorphic SSR markers. The SSRs generated a total of 532 alleles with a mean value of 6.05 alleles per locus, mean gene diversity of 0.55, and an average PIC of 0.50. Out of 532 alleles, 443 (83.27%) alleles were contributed by B-lines with a mean of 5.03 alleles per locus. R-lines contributed 476 alleles (89.47%) with a mean of 5.41, while 441 (82.89%) alleles were shared commonly between B- and R-lines. The gene diversity was higher among R-lines (0.55) compared to B-lines (0.49). The unweighted neighbor-joining tree based on simple matching dissimilarity matrix obtained from SSR data clearly differentiated B- lines into 10 sub-clusters (B1 through B10), and R- lines into 11 sub-clusters (R1 through R11). A total of 99 hybrids (generated by crossing representative 9 B- and 11 R- lines) along with checks were evaluated in the hybrid trial. The 20 parents were evaluated in the line trial. Both the trials were evaluated in three environments. Based on per se performance, high sca effects and standard heterosis, F1s generated from crosses between representatives of groups B10R5, B3R5, B3R6, B4UD, B5R11, B2R4, and B9R9 had high specific combining ability for grain yield compared to rest of the crosses. These groups may represent putative heterotic gene pools in pearl millet.

Genome properties and prospects of genomic prediction of hybrid performance in a breeding program of maize.

Maize (Zea mays L.) serves as model plant for heterosis research and is the crop where hybrid breeding was pioneered. We analyzed genomic and phenotypic data of 1254 hybrids of a typical maize hybrid breeding program based on the important Dent × Flint heterotic pattern. Our main objectives were to investigate genome properties of the parental lines (e.g., allele frequencies, linkage disequilibrium, and phases) and examine the prospects of genomic prediction of hybrid performance. We found high consistency of linkage phases and large differences in allele frequencies between the Dent and Flint heterotic groups in pericentromeric regions. These results can be explained by the Hill-Robertson effect and support the hypothesis of differential fixation of alleles due to pseudo-overdominance in these regions. In pericentromeric regions we also found indications for consistent marker-QTL linkage between heterotic groups. With prediction methods GBLUP and BayesB, the cross-validation prediction accuracy ranged from 0.75 to 0.92 for grain yield and from 0.59 to 0.95 for grain moisture. The prediction accuracy of untested hybrids was highest, if both parents were parents of other hybrids in the training set, and lowest, if none of them were involved in any training set hybrid. Optimizing the composition of the training set in terms of number of lines and hybrids per line could further increase prediction accuracy. We conclude that genomic prediction facilitates a paradigm shift in hybrid breeding by focusing on the performance of experimental hybrids rather than the performance of parental lines in test crosses.

Genomic prediction of northern corn leaf blight resistance in maize with combined or separated training sets for heterotic groups.

Northern corn leaf blight (NCLB), a severe fungal disease causing yield losses worldwide, is most effectively controlled by resistant varieties. Genomic prediction could greatly aid resistance breeding efforts. However, the development of accurate prediction models requires large training sets of genotyped and phenotyped individuals. Maize hybrid breeding is based on distinct heterotic groups that maximize heterosis (the dent and flint groups in Central Europe). The resulting allocation of resources to parallel breeding programs challenges the establishment of sufficiently sized training sets within groups. Therefore, using training sets combining both heterotic groups might be a possibility of increasing training set sizes and thereby prediction accuracies. The objectives of our study were to assess the prospect of genomic prediction of NCLB resistance in maize and the benefit of a training set that combines two heterotic groups. Our data comprised 100 dent and 97 flint lines, phenotyped for NCLB resistance per se and genotyped with high-density single-nucleotide polymorphism marker data. A genomic BLUP model was used to predict genotypic values. Prediction accuracies reached a maximum of 0.706 (dent) and 0.690 (flint), and there was a strong positive response to increases in training set size. The use of combined training sets led to significantly greater prediction accuracies for both heterotic groups. Our results encourage the application of genomic prediction in NCLB-resistance breeding programs and the use of combined training sets.

Genetic distance estimates among single cross hybrids and correlation with specific combining ability and yield in corn double cross hybrids

The objective of the present study was to correlate the genetic distances (GD) of single cross hybrids with yield, heterosis and specific combining ability (SCA) in the double cross hybrid synthesis. For this, 10 single cross commercial hybrids were used from different companies, and all the possible double hybrids were synthesized by a complete dialell. The hybrids were assessed in 15 locations in the 2005/2006 agricultural season, using the randomized complete block design with three repetitions. DNA was extracted from the single cross hybrids and 20 simple sequence repeat primers were used, nine of which were linked to the quantitative trait loci. It was ascertained that the single hybrids were superior in general to the double cross hybrids and that yield was highly correlated with heterosis and SCA (r = 0.75 and 0.82, respectively). There was no significant correlation between yield and GD (r = 0.25), but this index was at the limit of significance. There was a medium correlation between GD and heterosis (r = 0.40) and GD and SCA (r = 0.38). The intergroup hybrids placed by genetic grouping were generally more productive than intragroup hybrids, and the hybrids with GD greater than 0.84 had the maximum heterosis and SCA. It was concluded that the markers were efficient in placing hybrids in different heterosis groups and were also useful in eliminating the most negative heterosis and SCA.