Genetic diversity, population structure, and association mapping of agronomic traits in waxy and normal maize inbred lines

Abstract 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.

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Analysis of Population Structure and Genetic Diversity among Canadian Maize Inbred Lines using SSR Markers

Korean Journal of Breeding Science ◽

10.9787/kjbs.2017.49.2.72 ◽

2017 ◽

Vol 49 (2) ◽

pp. 072-79

Author(s):

Tak Ki Hong ◽

Kyu Jin Sa ◽

Ju Kyong Lee

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Ssr Markers ◽

Inbred Lines ◽

Maize Inbred Lines

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Genetic Diversity and Population Structure of Maize Inbred Lines with Varying Levels of Resistance to Striga Hermonthica Using Agronomic Trait-Based and SNP Markers

Plants ◽

10.3390/plants9091223 ◽

2020 ◽

Vol 9 (9) ◽

pp. 1223

Author(s):

Adekemi Stanley ◽

Abebe Menkir ◽

Agre Paterne ◽

Beatrice Ifie ◽

Pangirayi Tongoona ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Molecular Diversity ◽

Hierarchical Cluster ◽

Molecular Data ◽

Inbred Lines ◽

Striga Hermonthica ◽

Cluster Analyses ◽

Maize Inbred Lines ◽

Hierarchical Cluster Analyses

Striga hermonthica is a serious biotic stress limiting maize production in sub-Saharan Africa. The limited information on the patterns of genetic diversity among maize inbred lines derived from source germplasm with mixed genetic backgrounds limits the development of inbred lines, hybrids, and synthetics with durable resistance to S. hermonthica. This study was conducted to assess the level of genetic diversity in a panel of 150 diverse maize inbred lines using agronomic and molecular data and also to infer the population structure among the inbred lines. Ten Striga-resistance-related traits were used for the phenotypic characterization, and 16,735 high-quality single-nucleotide polymorphisms (SNPs), identified by genotyping-by-sequencing (GBS), were used for molecular diversity. The phenotypic and molecular hierarchical cluster analyses grouped the inbred lines into five clusters, respectively. However, the grouping patterns between the phenotypic and molecular hierarchical cluster analyses were inconsistent due to non-overlapping information between the phenotypic and molecular data. The correlation between the phenotypic and molecular diversity matrices was very low (0.001), which is in agreement with the inconsistencies observed between the clusters formed by the phenotypic and molecular diversity analyses. The joint phenotypic and genotypic diversity matrices grouped the inbred lines into three groups based on their reaction patterns to S. hermonthica, and this was able to exploit a broad estimate of the actual diversity among the inbred lines. The joint analysis shows an invaluable insight for measuring genetic diversity in the evaluated materials. The result indicates that wide genetic variability exists among the inbred lines and that the joint diversity analysis can be utilized to reliably assign the inbred lines into heterotic groups and also to enhance the level of resistance to Striga in new maize varieties.

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Association analysis of agronomic traits with microsatellites in maize inbred lines

Genetika ◽

10.2298/gensr1802379m ◽

2018 ◽

Vol 50 (2) ◽

pp. 379-394

Author(s):

Sanja Mikic ◽

Ankica Kondic-Spika ◽

Ljiljana Brbaklic ◽

Dusan Stanisavljevic ◽

Dragana Trkulja ◽

...

Keyword(s):

Population Structure ◽

Microsatellite Markers ◽

Association Analysis ◽

Agronomic Traits ◽

Inbred Lines ◽

Linkage Disequilibrium Mapping ◽

Heterotic Groups ◽

Local Conditions ◽

Maize Inbred Lines ◽

Trait Associations

Association analysis or linkage disequilibrium mapping is a method for identification of quantitative trait loci (QTLs) in a panel of divergent unrelated individuals based on historical recombinations during a crop?s domestication and selection. It should account for the population structure, which can be the result of adaptation to local conditions or selection, to reduce the possibility of declaring false-positive associations. The aim of this study was to determine potentially significant and consistent associations between markers and agronomic important maize (Zea mays L.) traits using association analysis in a diverse breeding material that can be ultimately implemented in maize selection. To this end, 96 maize inbred lines were evaluated in field trials at three locations in Serbia for eleven agronomic traits and analysed with microsatellite markers. Twenty five microsatellites were used to assess the population structure using Bayesian model-based clustering method and to test the significance of associations between the markers and the traits with general (GLM) and mixed linear (MLM) models. The cluster analysis divided maize inbred lines in four subpopulations, corresponding to the BSSS (Iowa Stiff Stalk Synthetic), LSC (Lancaster Sure Crop), Iodent heterotic groups and exotic and independent germplasm. The models identified associations between twenty five microsatellite markers and eleven agronomic traits, resulting in 133 and 71 associations across the environments for GLM and MLM, respectively. Some of the identified marker-trait associations were significant and consistent in several environments. The associations stable in several environments were identified between the markers bnlg1067 and two flowering traits; nc005 and bnlg434 and plant height, bnlg434 and ear height; bnlg1643 and umc1127 and leaf number, bnlg1360 and ear diameter; umc1019 and umc1506 and number of rows per ear; bnlg2305 and bnlg1451 and ear length, and between bnlg1175 and thousand-kernel weight. The results of this study indicate that these microsatellites could be used in marker-assisted selection of inbred lines, after validation of the marker-trait associations and testing combining abilities of the inbreds during hybrid development.

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Genetic Diversity, Population Structure and Inter-Trait Relationships of Combined Heat and Drought Tolerant Early-Maturing Maize Inbred Lines from West and Central Africa

Agronomy ◽

10.3390/agronomy10091324 ◽

2020 ◽

Vol 10 (9) ◽

pp. 1324

Author(s):

Alimatu Sadia Osuman ◽

Baffour Badu-Apraku ◽

Beatrice E. Ifie ◽

Pangirayi Tongoona ◽

Ebenezer Obeng-Bio ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Polymorphic Information Content ◽

Central Africa ◽

Inbred Lines ◽

Heterotic Groups ◽

Maize Inbred Lines ◽

Wide Range ◽

Early Maturing ◽

West And Central Africa

Adequate knowledge and understanding of the genetic diversity and inter-trait relationships among elite maize inbred lines are crucial for determining breeding strategies and predicting hybrid performance. The objectives of this study were to investigate the genetic diversity of 162 early maturing white and yellow tropical maize inbred lines, and to determine the population structure, heterotic groups and inter-trait relationships among the lines. Using 9684 DArT single nucleotide polymorphism (SNP) markers, a gene diversity (GD) of 0.30 was recorded for the inbred lines with polymorphic information content (PIC) ranging from 0.08 to 0.38. The genetic relatedness among the inbred lines evaluated revealed six different groups based on the history of selection, colour of endosperm and pedigree. The genotype-by-trait (GT) biplot analysis identified inbred 1 (TZEI 935) as outstanding in terms of combined heat and drought (HD) tolerance with the base index analysis identifying 15 superior inbreds in the HD environment. A wide range of genetic variability was observed among the inbred lines, indicating that they are an invaluable resource for breeding for HD tolerance in maize breeding programmes, especially in West and Central Africa.

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