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.

Combining datasets for maize root seedling traits increases the power of GWAS and genomic prediction accuracies.

The identification of genomic regions associated with root traits and the genomic prediction of untested genotypes can increase the rate of genetic gain in maize breeding programs targeting roots traits. Here, we combined two maize association panels with different genetic backgrounds to identify single nucleotide polymorphisms (SNPs) associated with root traits, and used a genome-wide association study (GWAS) and to assess the potential of genomic prediction for these traits in maize. For this, we evaluated 377 lines from the Ames panel and 302 from the Backcrossed Germplasm Enhancement of Maize (BGEM) panel in a combined panel of 679 lines. The lines were genotyped with 232 460 SNPs, and four root traits were collected from 14-day-old seedlings. We identified 30 SNPs significantly associated with root traits in the combined panel, whereas only two and six SNPs were detected in the Ames and BGEM panels, respectively. Those 38 SNPs were in linkage disequilibrium with 35 candidate genes. In addition, we found higher prediction accuracy in the combined panel than in the Ames or BGEM panel. We conclude that combining association panels appears to be a useful strategy to identify candidate genes associated with root traits in maize and improve the efficiency of genomic prediction.

Relative efficiency of the genotypic value and combining ability effects on reciprocal recurrent selection.

Reciprocal recurrent selection (RRS) has been successfully applied to maize breeding for more than 60 years. Our objective was to assess the relative efficiency of the genotypic value and the effects of general and specific combining abilities (GCA and SCA) on selection. The GCA effect reflects the number of favorable genes in the parent. The SCA effect primarily reflects the differences in the gene frequencies between the parents. We simulated three traits, three classes of populations, and 10 cycles of half- and full-sib RRS. The RRS is a highly efficient process for intra- and interpopulation breeding, regardless of the trait or the level of divergence among the populations. The RRS increases the heterosis of the interpopulation cross when there is dominance, and it decreases the inbreeding depression in the populations and the genetic variability in the populations and in the hybrid. When there is not dominance and the populations are not divergent, the RRS also determines population differentiation. The half-sib RRS, which is equivalent to selection based on the GCA effect, is more efficient than the full-sib RRS based on the genotypic value, regardless of the trait or the level of improvement of the populations. The full-sib RRS based on the SCA effect is not efficient for intra- and interpopulation breeding.

Multi-trait multi-environment Bayesian model reveals G x E interaction for nitrogen use efficiency components in tropical maize.

Identifying maize inbred lines that are more efficient in nitrogen (N) use is an important strategy and a necessity in the context of environmental and economic impacts attributed to the excessive N fertilization. N-uptake efficiency (NUpE) and N-utilization efficiency (NUtE) are components of N-use efficiency (NUE). Despite the most maize breeding data have a multi-trait structure, they are often analyzed under a single-trait framework. We aimed to estimate the genetic parameters for NUpE and NUtE in contrasting N levels, in order to identify superior maize inbred lines, and to propose a Bayesian multi-trait multi-environment (MTME) model. Sixty-four tropical maize inbred lines were evaluated in two experiments: at high (HN) and low N (LN) levels. The MTME model was compared to single-trait multi-environment (STME) models. Based on deviance information criteria (DIC), both multi- and single-trait models revealed genotypes x environments (G x E) interaction. In the MTME model, NUpE was found to be weakly heritable with posterior modes of heritability of 0.016 and 0.023 under HN and LN, respectively. NUtE at HN was found to be highly heritable (0.490), whereas under LN condition it was moderately heritable (0.215). We adopted the MTME model, since combined analysis often presents more accurate breeding values than single models. Superior inbred lines for NUpE and NUtE were identified and this information can be used to plan crosses to obtain maize hybrids that have superior nitrogen use efficiency.

Performance of testers with different genetic structure for evaluation of maize inbred lines / Desempenho de testadores com diferentes estruturas genéticas para avaliação de linhagens endogâmicas de milho

The objective of this study was to evaluate four maize testers for identification of superior inbreed lines in testcross. The four testers evaluated are cultivars with narrow or wide genetic base (single-cross hybrids and open pollinated varieties) and two kernel types (flint or dent). SynD and SynF testers are open pollinated varieties with dent and flint kernels, respectively, and FSH and DSH testers are single-cross hybrids with flint and dent kernels, respectively. SynD tester showed the biggest genetic variance among the maize inbreed lines in crosses. The effects of general combining ability (GCA) for lines and specific combining ability (SCA) for lines x testers were significant, whereas GCA effects for testers were not significant. SynD and SynF testers identified the largest number of lines with higher GCA. The DSH and FSH testers showed suitable to identify lines with high SCA. It was concluded that SynD and SynF testers are adequate to identify inbreed lines with high GCA effects, and it's possible to identify new lines with high heterotic potential in each one of the four testers.

O objetivo deste estudo foi avaliar quatro testadores de milho quanto à capacidade de identificar linhagens superiores em testcross. Os quatro testadores avaliados são cultivares com base genética ampla (variedades de polinização aberta) e estreita (híbridos simples) e dois tipos de grãos (duro e dentado). Os testadores SynD e SynF são populações de milho de polinização aberta com grãos dentados e duros, respectivamente, e FSH e DSH são híbridos simples com grãos duros e dentados, respectivamente. O testador SynD possibilitou a maior expressão de variância genética entre os cruzamentos com as linhagens. A capacidade geral de combinação (CGC) das linhagens e a capacidade específica de combinação (CEC) entre linhagens e testadores foram significativas, enquanto que os efeitos de CGC dos testadores foram não significativos. Concluiu-se que os testadores SynD e SynF mostram-se adequados para identificar linhagens com maiores efeitos de GCA e é possível identificar novas linhagens com alto potencial heterótico com cada um dos quatro testadores utilizados.

Combining ability of tropical maize cultivars in organic and conventional production systems / Capacidade de combinação de milho tropical em sistemas de produção orgânico e convencional

The objectives were to identify maize germplasm for the organic productions system and to compare the genetic effects of the grain yield of maize cultivars in organic and conventional production systems. Diallel crosses were made between six maize cultivars and the hybrid combinations were evaluated in conventional and organic production systems. The hybrid combinations produced different grain yields in the two production systems. The interaction between general combining ability and production systems was significant for grain yield, ear height and number of ears. This indicates that the additive genetic effects differ in organic and conventional production systems. The specific combining abilities (SCA) were significant for grain yield and plant height, indicating a significant difference between the non-additive effects. However, the SCA x production systems interactions were not significant for those traits. It was concluded that for the development of maize cultivars for the organic production system, selection must be made in the specific environment for the expression of favorable alleles that confer advantages for adapting to this system; the general combining ability of genitors is different for the two production systems, but the specific combining ability isn't different in organic and conventional systems.

Os objetivos foram identificar germoplasma de milho para o sistema de produção orgânica e comparar os efeitos genéticos da produtividade de grãos de cultivares de milho em sistemas de produção orgânico e convencional. Para isso, cruzamentos dialélicos foram realizados entre seis cultivares de milho e as combinações híbridas avaliadas em sistemas de produção orgânico e convencional. Os híbridos apresentaram diferentes produtividades de grãos nos dois sistemas de produção. A interação entre a capacidade geral de combinação (CGC) e os sistemas de produção (SP) foi significativa para produtividade de grãos, altura de espiga e número de espigas. Isso indica que os efeitos genéticos aditivos diferem nos sistemas de produção orgânica e convencional. A capacidade de combinação específica (CEC) foi significativa para produtividade de grãos e altura de plantas o que indica a diferença significativa entre os efeitos não aditivos dos genitores. Entretanto, a interação CEC x SP foi não significativa para esses caracteres. Conclui-se que, para o desenvolvimento de cultivares de milho para sistema de produção orgânico, a seleção deve ser feita no ambiente específico para a expressão dos alelos favoráveis que conferem vantagens para adaptar a este sistema; a capacidade geral de combinação dos genitores é diferente nos dois sistemas de produção, mas a capacidade específica de combinação é semelhante nos sistemas orgânico e convencional.

Factor analysis and SREG GGE biplot for the genotype × environment interaction stratification in maize / Análise de fatores e SREG GGE biplot para a estratificação da interação genótipos × ambientes em milho

The objective of this study was to evaluate the use of SREG GGE biplot methodology and factor analysis to stratify the genotype×environment interaction in maize. Forty-nine early maize hybrids were evaluated in nine environments. The experimental design used was a 7×7 square lattice with two replicates. Each plot consisted of two 5m long rows spaced 0.90m apart. Grain yield data were used to perform the analysis. The results indicated the existence of two mega-environments in the State of Minas Gerais, Brazil, for early maize hybrids. The stratification of the environment by factor analysis was more selective to join the similarity the according with cultivar performance. However, this approach did not identify specific genotype x environment interactions, which is possible through SREG GGE biplot analysis.

O objetivo deste estudo foi avaliar a metodologia SREG GGE biplot e a análise de fatores na estratificação da interação genótipos×ambientes em milho. Foram avaliados 49 híbridos comerciais de milho de ciclo precoce em nove ambientes. Foi utilizado o delineamento látice quadrado 7×7, com duas repetições. Cada parcela consistiu de duas linhas de 5m espaçadas por 0,90m. Para a realização das análises, foram utilizados dados de produtividade de grãos. Os resultados indicaram a existência de dois mega-ambientes no Estado de Minas Gerais para híbridos de milho de ciclo precoce. A estratificação de ambientes pela análise de fatores mostrou-se mais seletiva em reunir ambientes pela similaridade de desempenho dos cultivares, mas não evidenciou as interações genótipos x ambientes específicas, o que foi possível pela análise SREG GGE biplot.

Potencial genético da população de milho UFV 7 para o melhoramento em Minas Gerais / Genetic potential of maize population UFV 7 for breeding in Minas Gerais

Neste trabalho, objetivou-se avaliar o potencial genético da população de milho UFV 7 para o melhoramento em Minas Gerais. Foram instalados três experimentos com a população de milho UFV 7, em três regiões de Minas Gerais, na safra 2006/2007. Houve interação genótipos x ambientes para todos os caracteres. Foi verificada variabilidade genética para produtividade de grãos, altura de plantas e altura de espigas na população de milho UFV 7, nas três regiões. Na região Sudeste, a população de milho UFV 7 apresentou as maiores estimativas de parâmetros genéticos. A população UFV 7 apresentou alta produtividade de grãos, 9 112kg ha-1, no Sudeste, média produtividade, 6 510kg ha-1, no Oeste, e baixa, 4 572kg ha-1, na região Central. As estimativas de herdabilidade e CVg/CVe, para produtividade, foram superiores a 60 por cento e 1,00, respectivamente. A produtividade de grãos teve correlação genética significativa e positiva com a altura de planta e altura de espiga, na região Oeste e na Central, e com a prolificidade na região Central e região Sudeste. Conclui-se que a população de milho UFV 7 apresenta potencial para extração de linhagens na região Central; potencial para uso imediato na região Sudeste e para novos ciclos de seleção na região Oeste de Minas Gerais, e a seleção para PG aumenta indiretamente a altura de planta e altura de espiga, nas regiões Oeste e Central.

The objective was to assess the genetic potential of maize population UFV 7 for breeding in Minas Gerais, Brazil. Three experiments were installed with the maize population UFV 7 in the three regions of Minas Gerais, in the harvest of 2006/2007. There was genotype x environment interaction for all characters. It was observed genetic variability for grain yield, plant height and ear height in maize population UFV 7, in the three regions. The Southeast region was where the maize population UFV 7 had the highest parameters. The population UFV 7 presented high grain yield, 9 112kg ha-1 in the Southeast, average grain yield, 6 510kg ha-1 in the West and low, 4 572kg ha-1 in the Central Region. Heritability estimate and CVg / CVe for grain yield were higher than 60 percent and 1.00, respectively. Grain yield had significant and positive genetic correlation with plant height and ear height, in Western and Central, and the prolificacy in Central and Southeast. For maize population UFV 7 it was conclude that it has potential for extraction of lines in the Central Region; it has the potential for immediate use in the Southeast and for new cycles selection in the Western Region of Minas Gerais. The selection for PG provides an indirect increase in plant height and ear height, in the West and Central.