Dataset Information

Genetic characterization of a core set of a tropical maize race Tuxpeno for further use in maize improvement.

ABSTRACT: The tropical maize race Tuxpeño is a well-known race of Mexican dent germplasm which has greatly contributed to the development of tropical and subtropical maize gene pools. In order to investigate how it could be exploited in future maize improvement, a panel of maize germplasm accessions was assembled and characterized using genome-wide Single Nucleotide Polymorphism (SNP) markers. This panel included 321 core accessions of Tuxpeño race from the International Maize and Wheat Improvement Center (CIMMYT) germplasm bank collection, 94 CIMMYT maize lines (CMLs) and 54 U.S. Germplasm Enhancement of Maize (GEM) lines. The panel also included other diverse sources of reference germplasm: 14 U.S. maize landrace accessions, 4 temperate inbred lines from the U.S. and China, and 11 CIMMYT populations (a total of 498 entries with 795 plants). Clustering analyses (CA) based on Modified Rogers Distance (MRD) clearly partitioned all 498 entries into their corresponding groups. No sub clusters were observed within the Tuxpeño core set. Various breeding strategies for using the Tuxpeño core set, based on grouping of the studied germplasm and genetic distance among them, were discussed. In order to facilitate sampling diversity within the Tuxpeño core, a minicore subset of 64 Tuxpeño accessions (20% of its usual size) representing the diversity of the core set was developed, using an approach combining phenotypic and molecular data. Untapped diversity represents further use of the Tuxpeño landrace for maize improvement through the core and/or minicore subset available to the maize community.

SUBMITTER: Wen W

PROVIDER: S-EPMC3296726 | biostudies-literature | 2012

REPOSITORIES: biostudies-literature

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Genetic characterization of a core set of a tropical maize race Tuxpeño for further use in maize improvement.

Wen Weiwei W Franco Jorge J Chavez-Tovar Victor H VH Yan Jianbing J Taba Suketoshi S

PloS one 20120307 3

The tropical maize race Tuxpeño is a well-known race of Mexican dent germplasm which has greatly contributed to the development of tropical and subtropical maize gene pools. In order to investigate how it could be exploited in future maize improvement, a panel of maize germplasm accessions was assembled and characterized using genome-wide Single Nucleotide Polymorphism (SNP) markers. This panel included 321 core accessions of Tuxpeño race from the International Maize and Wheat Improvement Center ...[more]

PMID: 22412898

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Project description:BackgroundThe 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.ResultsOur 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.ConclusionsOur 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.

Project description:In sub-Saharan Africa, one of the major challenges to smallholder farmers is soil with low fertility and inability to apply nitrogen fertilizer externally due to the cost. Development of maize hybrids, which perform better in nitrogen depleted soils, is one of the promising solutions. However, breeding maize for nitrogen use efficiency (NUE) is hindered by expensive phenotypic evaluations and trait complexity under low N stress. Genome-wide association study (GWAS) and genomic prediction (GP) are promising tools to circumvent this interference. Here, we evaluated a mapping panel in diverse environments both under optimum and low N management. The objective of this study was to identify SNPs significantly associated with grain yield (GY) and other traits through GWAS and assess the potential of GP under low N and optimum conditions. Testcross progenies of 411 inbred lines were planted under optimum and low N conditions in several locations in Africa and Latin America. In all locations, low N fields were previously depleted over several seasons, and no N fertilizer was applied throughout the growing season. All inbred lines were genotyped with genotyping by sequencing. Genotypic and GxE interaction variances were significant, and heritability estimates were moderate to high for all traits under both optimum and low N conditions. Genome-wide LD decay at r 2 = 0.2 and r 2 = 0.34 were 0.24 and 0.19 Mbp, respectively. Chromosome-specific LD decays ranged from 0.13 to 0.34 Mbps with an average of 0.22 Mbp at r 2 = 0.2. GWAS analyses revealed 38 and 45 significant SNPs under optimum and low N conditions, respectively. Out of these 83 significant SNPs, 3 SNPs on chromosomes 1, 2, and 6 were associated either with different traits or the same trait under different management conditions, suggesting pleiotropic effects of genes. A total of 136 putative candidate genes were associated with the significant SNPs, of which seven SNPs were linked with four known genes. Prediction accuracies were moderate to high for all traits under both optimum and low N conditions. These results can be used as useful resources for further applications to develop hybrids or lines with better performance under low N conditions.

Dataset Information

Genetic characterization of a core set of a tropical maize race Tuxpeno for further use in maize improvement.

Publications

Genetic characterization of a core set of a tropical maize race Tuxpeño for further use in maize improvement.

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