Genome-Wide Comparative Analysis of Genetic Diversity of Regular and Specialty Maize Inbred Lines Through Genotyping by Target Sequencing (GBTS)

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

Brazilian Archives of Biology and Technology ◽

10.1590/s1516-89132008000100022 ◽

2008 ◽

Vol 51 (1) ◽

pp. 183-192 ◽

Cited By ~ 11

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.

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

Bangladesh Journal of Agricultural Research ◽

10.3329/bjar.v43i4.39151 ◽

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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