scholarly journals 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 ◽  
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.

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

BMC Genomics ◽  
2022 ◽  
Vol 23 (1) ◽  
Author(s):  
Sirlene Viana de Faria ◽  
Leandro Tonello Zuffo ◽  
Wemerson Mendonça Rezende ◽  
Diego Gonçalves Caixeta ◽  
Hélcio Duarte Pereira ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Inbred Lines ◽  
Breeding Program ◽  
Tropical Maize ◽  
Maize Breeding ◽  
Breeding Programs ◽  
The Public ◽  
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.

scholarly journals 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 ◽  
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.

Genetic diversity of tropical maize inbred lines combining resistance to Striga hermonthica with drought tolerance using SNP markers

2017 ◽  
Vol 136 (3) ◽  
pp. 338-343 ◽  
Author(s):  
Wende Abera Mengesha ◽  
Abebe Menkir ◽  
Nnanna Unakchukwu ◽  
Silvestro Meseka ◽  
Adetutu Farinola ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Drought Tolerance ◽  
Inbred Lines ◽  
Snp Markers ◽  
Striga Hermonthica ◽  
Tropical Maize ◽  
Maize Inbred Lines

scholarly journals Genetic diversity and population structure of early-maturing tropical maize inbred lines using SNP markers

PLoS ONE ◽  
2019 ◽  
Vol 14 (4) ◽  
pp. e0214810 ◽  
Author(s):  
Gloria Boakyewaa Adu ◽  
Baffour Badu-Apraku ◽  
Richard Akromah ◽  
Ana Luisa Garcia-Oliveira ◽  
Frederick Justice Awuku ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Inbred Lines ◽  
Snp Markers ◽  
Tropical Maize ◽  
Maize Inbred Lines ◽  
Early Maturing

scholarly journals GENOTYPIC DIVERSITY IN 291 MAIZE LINES FROM CIMMYT AND PHENOTYPIC CHARACTERIZATION IN SOUTHERN CORDOBA, ARGENTINA

2019 ◽  
Vol 30 (1) ◽  
pp. 25-33
Author(s):  
E.A. Rossi ◽  
M. Ruiz ◽  
M. Di Renzo ◽  
N.C. Bonamico
Keyword(s):  
Population Structure ◽  
Morphological Traits ◽  
Phenotypic Diversity ◽  
Genotypic Diversity ◽  
Inbred Lines ◽  
Environmental Adaptation ◽  
Procrustes Analysis ◽  
Phenotypic Characterization ◽  
Breeding Programs ◽  
Maize Inbred Lines

CIMMYT maize inbred lines (CMLs) are freely distributed to breeding programs around the world. Better information on phenotypic and genotypic diversity may provide guidance to breeders on how to use more efficiently the CMLs in their breeding programs. In this study a group of 291 CIMMYT maize inbred lines, was phenotyped by nine agro-morphological traits in south Córdoba, Argentina and genotyped using 18,082 SNPs. Based on the geographic information and the environmental adaptation, 291 CMLs were classified into eight subgroups. Anthesis-silking interval (IAE) was the trait with higher phenotypic diversity. A 40% of maize inbred lines, with IAE less than five days, show a good adaptation to growing conditions in south Córdoba, Argentina. The low phenotypic variation explained by environmental adaptation subgroups indicates that population structure is only a minor factor contributing to phenotypic diversity in this panel. Principal component analysis (ACP) allowed us to obtain phenotypic and genotypic orderings. Generalized procrustes analysis (APG) indicated a 60% consensus between both data type from the total panel of maize lines. In each environmental adaptation subgroup, the APG consensus was higher. This result, which might indicate linkage disequilibrium between SNPs markers and the genes controlling these agro-morphological traits, is promising and could be used as an initial tool in the identification of Quantitative Trait Loci (QTL). Information on genetic diversity, population structure and phenotypic diversity in local environments will help maize breeders to better understand how to use the current CIMMYT maize inbred lines group. Key words: broad-sense heritability, multivariate analysis, SNPs, agro-morphological traits.

scholarly journals Comparative analysis of genetic diversity among the maize inbred lines (Zea mays L.) obtained by RAPD and SSR markers

2008 ◽  
Vol 51 (1) ◽  
pp. 183-192 ◽  
Author(s):  
Silvia Graciele Hülse de Souza ◽  
Valéria Carpentieri-Pípolo ◽  
Claudete de Fátima Ruas ◽  
Valdemar de Paula Carvalho ◽  
Paulo Maurício Ruas ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Zea Mays L ◽  
Inbred Lines ◽  
Pedigree Data ◽  
Dice Coefficient ◽  
Quantitative Characters ◽  
Maize Inbred Lines ◽  
Ssr Primers ◽  
Selection Of

The RAPD and SSR markers were used to compare the genetic diversity among the 16 maize inbred lines. Twenty-two primers were used in the RAPD reactions, resulting in the amplification of 265 fragments, while 16 pairs of SSR primers resulted in 75 fragments. The similarity based on Dice coefficient for the RAPD ranged from 53 to 84% and for the SSR from 11 to 82%. The dendrogram obtained by the RAPD showed five groups, while dendrogram obtained by the SSR showed three groups and one isolated line. The association constructed from the markers and the principal coordinate’s analysis separated lines into two groups according to endosperm color, either orange or yellow. The RAPD were effective to validate pedigree data, while the SSR were effective to recognize the differences between the quantitative characters. Because they assess the distinct regions of the genome, the selection of one or other marker would depend on the characteristics of the material used and the objectives of the project.

Molecular assessment of maize inbred lines (Zea mays L.) Using microsatellite markers

2018 ◽  
Vol 43 (4) ◽  
pp. 533-542
Author(s):  
Maniruzzaman ◽  
MG Azam ◽  
S Islam ◽  
MG Hossain ◽  
MM Rohman
Keyword(s):  
Genetic Diversity ◽  
Plant Breeding ◽  
Genetic Relatedness ◽  
Agricultural Research ◽  
Inbred Lines ◽  
The Other ◽  
Diversity Analysis ◽  
Genetic Diversity Analysis ◽  
Maize Inbred Lines ◽  
Maize Genotypes

Genetic diversity analysis and germplasm characterization are essential steps in plant breeding and molecular markers are proved tool to accomplish. The present study was undertaken at the Molecular Breeding Lab of Plant Breeding Division, Bangladesh Agricultural Research Institute (BARI) to determine the genetic relatedness and molecular characterization of 15 maize inbred lines of BARI. In present study, genetic diversity analysis was performed by using 10 SSR primers to evaluate the polymorphisms, among them six primers showed distinct polymorphism between the maize inbred lines. The maize genotypes E81, E144, E08, E167, E102, E142 and E121 were found more diverged (0.9003) compared to other inbred lines. On the other hand, the lowest genetic distance values (0.1501) were found between the genotype E140 and genotype E80 followed by genotype E126 and genotype E140; genotype E140 and genotype E65; genotype E65 and genotype E80 values were identical (0.4502). The genotypes viz. E81, E144, E08, E167, E102, E142 and E121 were found far away from centroid of the cluster and rest of the genotypes were placed around the centroid. The Principal Coordinate Analysis (PCO) helped to visualize four major clusters and showed that seven maize inbred lines (E81, E58, E08, E167, E102, E142 and E121) were far away from the other genotypes. In conclusion, SSR markers enabled discrimination among accessions and provided valuable information for future use in improvement of these genomic resources.Bangladesh J. Agril. Res. 43(4): 533-542, December 2018

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