Genetic Diversity in CIMMYT Nontemperate Maize Germplasm: Landraces, Open Pollinated Varieties, and 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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Proteomic data from leaves of twenty-four sunflower genotypes underwater deficit

10.1101/2020.06.26.171066 ◽

2020 ◽

Author(s):

Thierry Balliau ◽

Harold Duruflé ◽

Nicolas Blanchet ◽

Mélisande Blein-Nicolas ◽

Nicolas B. Langlade ◽

...

Keyword(s):

Genetic Diversity ◽

Water Deficit ◽

High Throughput ◽

Molecular Basis ◽

Inbred Lines ◽

Vegetative Stage ◽

Valuable Resource ◽

Proteomic Data ◽

High Throughput Phenotyping

AbstractThis article describes how the proteomic data were produced on sunflower plants subjected to water deficit. Twenty-four sunflower genotypes were selected to represent genetic diversity within cultivated sunflower. They included both inbred lines and their hybridsWater deficit was applied to plants in pots at the vegetative stage using the high-throughput phenotyping platform Heliaphen. Here, we provide proteomic data from sunflower leaves corresponding to the identification of 3062 proteins and the quantification of 1211 of them in these 24 genotypes grown in two watering conditions. These data differentiate both treatment and the different genotypes and constitute a valuable resource to the community to study adaptation of crops to drought and the molecular basis of heterosis.

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Phenotypical Variability of “TURDA” Maize Germplasm for Grain Chemical Composition

Bulletin of University of Agricultural Sciences and Veterinary Medicine Cluj-Napoca Agriculture ◽

10.15835/buasvmcn-agr:3737 ◽

1970 ◽

Vol 66 (1) ◽

Author(s):

Voichita HAS ◽

Ioan HAS ◽

Doru PAMFIL ◽

Ana COPANDEAN ◽

Sorin CAMPEAN

Keyword(s):

Grain Quality ◽

Selection Criterion ◽

Quality Attributes ◽

Inbred Lines ◽

Phenotypic Correlation ◽

Starch Concentration ◽

Maize Germplasm ◽

Grain Starch ◽

Food And Feed ◽

Phenotypical Variability

Maize grain has many and diverse uses in the food and feed industry. The diversity of applications requires characteristics of quality in accordance to that. To examine phenotypical diversity in the grain content, it was evaluated a total of 754 maize samples: 265 local populations (landraces); 59 synthetics/composites; 430 “TURDA” inbred lines for their grain quality attributes. Comparison of the inbred lines diversity is on average the most divergent in grain starch concentration (range value 19.9) from landraces (range value 11.8) and synthetics (range value 12.5). The grain oil and ash content showed high variability among the genotypes. The quality attributes in most of the cases showed positive phenotypic correlation except grain starch contents which was negatively correlated at phenotypic levels. The objective of this study was to evaluate the potential of maize “TURDA” germplasm in according to its grain quality content, such as: protein, oil, fiber, ash and starch concentration; to estimate the extent of phenotypical variability and correlation for various quality components to formulate a selection criterion in a breeding program.

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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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Genetic Diversity among Elite Sorghum Inbred Lines Assessed with DNA Markers and Pedigree Information

Crop Science ◽

10.2135/cropsci1996.0011183x003600050049x ◽

1996 ◽

Vol 36 (5) ◽

pp. 1385-1392 ◽

Cited By ~ 24

Author(s):

D. Ahnert ◽

M. Lee ◽

D. F. Austin ◽

C. Livini ◽

W. L. Woodman ◽

...

Keyword(s):

Genetic Diversity ◽

Dna Markers ◽

Inbred Lines ◽

Pedigree Information

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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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High-throughput retrotransposon-based genetic diversity of maize germplasm assessment and analysis

Molecular Biology Reports ◽

10.1007/s11033-020-05246-4 ◽

2020 ◽

Vol 47 (3) ◽

pp. 1589-1603 ◽

Cited By ~ 3

Author(s):

Marwa Ghonaim ◽

Ruslan Kalendar ◽

Hoda Barakat ◽

Nahla Elsherif ◽

Naglaa Ashry ◽

...

Keyword(s):

Genetic Diversity ◽

High Throughput ◽

Genetic Similarity ◽

Maize Genome ◽

Ltr Retrotransposons ◽

Maize Germplasm ◽

Phylogeny Analysis ◽

Generating Method ◽

Polymerase Chain Reaction Primers ◽

Hybrid Lines

AbstractMaize is one of the world’s most important crops and a model for grass genome research. Long terminal repeat (LTR) retrotransposons comprise most of the maize genome; their ability to produce new copies makes them efficient high-throughput genetic markers. Inter-retrotransposon-amplified polymorphisms (IRAPs) were used to study the genetic diversity of maize germplasm. Five LTR retrotransposons (Huck, Tekay, Opie, Ji, and Grande) were chosen, based on their large number of copies in the maize genome, whereas polymerase chain reaction primers were designed based on consensus LTR sequences. The LTR primers showed high quality and reproducible DNA fingerprints, with a total of 677 bands including 392 polymorphic bands showing 58% polymorphism between maize hybrid lines. These markers were used to identify genetic similarities among all lines of maize. Analysis of genetic similarity was carried out based on polymorphic amplicon profiles and genetic similarity phylogeny analysis. This diversity was expected to display ecogeographical patterns of variation and local adaptation. The clustering method showed that the varieties were grouped into three clusters differing in ecogeographical origin. Each of these clusters comprised divergent hybrids with convergent characters. The clusters reflected the differences among maize hybrids and were in accordance with their pedigree. The IRAP technique is an efficient high-throughput genetic marker-generating method.

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