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Lehermeier C.,TU Munich | Kramer N.,TU Munich | Bauer E.,TU Munich | Bauland C.,French National Institute for Agricultural Research | And 16 more authors.
Genetics | Year: 2014

The efficiency of marker-assisted prediction of phenotypes has been studied intensively for different types of plant breeding populations. However, one remaining question is how to incorporate and counterbalance information from biparental and multiparental populations into model training for genome-wide prediction. To address this question, we evaluated testcross performance of 1652 doubled-haploid maize (Zea mays L.) lines that were genotyped with 56,110 single nucleotide polymorphism markers and phenotyped for five agronomic traits in four to six European environments. The lines are arranged in two diverse half-sib panels representing two major European heterotic germplasm pools. The data set contains 10 related biparental dent families and 11 related biparental flint families generated from crosses of maize lines important for European maize breeding. With this new data set we analyzed genome-based best linear unbiased prediction in different validation schemes and compositions of estimation and test sets. Further, we theoretically and empirically investigated marker linkage phases across multiparental populations. In general, predictive abilities similar to or higher than those within biparental families could be achieved by combining several half-sib families in the estimation set. For the majority of families, 375 half-sib lines in the estimation set were sufficient to reach the same predictive performance of biomass yield as an estimation set of 50 full-sib lines. In contrast, prediction across heterotic pools was not possible for most cases. Our findings are important for experimental design in genome-based prediction as they provide guidelines for the genetic structure and required sample size of data sets used for model training. © 2014 by the Genetics Society of America. Source

Revilla P.,Mision Biologica de Galicia CSIC | Rodriguez V.M.,Mision Biologica de Galicia CSIC | Ordas A.,Mision Biologica de Galicia CSIC | Rincent R.,French National Institute for Agricultural Research | And 14 more authors.
Crop Science | Year: 2014

Maize (Zea mays L.) for northern growing areas requires cold tolerance for extending the vegetative period. Our objectives were to evaluate two large panels of maize inbred lines adapted to Europe for cold tolerance and to estimate the effects of cold-related traits on biomass production. Two inbred panels were evaluated for cold tolerance per se and in testcrosses under cold and control conditions in a growth chamber and under field conditions. Comparisons of inbreds and groups of inbreds were made taking into account the single nucleotide polymorphisms (SNP)-based genetic structure of the panels, and the factors affecting biomass production were studied. Eight flint and one dent inbred with diverse origins were the most cold tolerant. The most cold-tolerant dent and flint groups were the Iodent Ph207 and the Northern Flint D171 groups, respectively. The relationships between inbred per se and testcross performance and between controlled and field conditions were low. Regressions with dry matter yield in the field as dependent variable identified plant height (R2 = 0.285) as the main independent variable, followed by quantum efficiency of photosystem II (R2 = 0.034) and other traits with minor contributions. Cold-tolerance-related traits had low and negative effects on dry matter yield. Models intending the prediction of final performance from traits scored in early developmental stages are not expected to be precise enough for breeding. For improving cold tolerance, inbreds released from crosses among the No Iodent group and the Northern Flint group may show high combining ability, as well as between both groups and the Northern Flint D171 group. © Crop Science Society of America. Source

Bauer E.,TU Munich | Falque M.,University Paris - Sud | Walter H.,TU Munich | Bauland C.,University Paris - Sud | And 17 more authors.
Genome Biology | Year: 2013

Background: In sexually reproducing organisms, meiotic crossovers ensure the proper segregation of chromosomes and contribute to genetic diversity by shuffling allelic combinations. Such genetic reassortment is exploited in breeding to combine favorable alleles, and in genetic research to identify genetic factors underlying traits of interest via linkage or association-based approaches. Crossover numbers and distributions along chromosomes vary between species, but little is known about their intraspecies variation.Results: Here, we report on the variation of recombination rates between 22 European maize inbred lines that belong to the Dent and Flint gene pools. We genotype 23 doubled-haploid populations derived from crosses between these lines with a 50 k-SNP array and construct high-density genetic maps, showing good correspondence with the maize B73 genome sequence assembly. By aligning each genetic map to the B73 sequence, we obtain the recombination rates along chromosomes specific to each population. We identify significant differences in recombination rates at the genome-wide, chromosome, and intrachromosomal levels between populations, as well as significant variation for genome-wide recombination rates among maize lines. Crossover interference analysis using a two-pathway modeling framework reveals a negative association between recombination rate and interference strength.Conclusions: To our knowledge, the present work provides the most comprehensive study on intraspecific variation of recombination rates and crossover interference strength in eukaryotes. Differences found in recombination rates will allow for selection of high or low recombining lines in crossing programs. Our methodology should pave the way for precise identification of genes controlling recombination rates in maize and other organisms. © 2013 Bauer et al.; licensee BioMed Central Ltd. Source

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