Pierre Dubreuil

Maize Adaptation to Temperate Climate: Relationship Between Population Structure and Polymorphism in the Dwarf8 Gene

To investigate the genetic basis of maize adaptation to temperate climate, collections of 375 inbred lines and 275 landraces, representative of American and European diversity, were evaluated for flowering time under short- and long-day conditions. The inbred line collection was genotyped for 55 genomewide simple sequence repeat (SSR) markers. Comparison of inbred line population structure with that of landraces, as determined with 24 SSR loci, underlined strong effects of both historical and modern selection on population structure and a clear relationship with geographical origins. The late tropical groups and the early “Northern Flint” group from the northern United States and northern Europe exhibited different flowering times. Both collections were genotyped for a 6-bp insertion/deletion in the Dwarf8 (D8idp) gene, previously reported to be potentially involved in flowering time variation in a 102 American inbred panel. Among-group D8idp differentiation was much higher than that for any SSR marker, suggesting diversifying selection. Correcting for population structure, D8idp was associated with flowering time under long-day conditions, the deletion allele showing an average earlier flowering of 29 degree days for inbreds and 145 degree days for landraces. Additionally, the deletion allele occurred at a high frequency (>80%) in Northern Flint while being almost absent (<5%) in tropical materials. Altogether, these results indicate that Dwarf8 could be involved in maize climatic adaptation through diversifying selection for flowering time.

A comparative study of molecular and morphological methods of describing relationships between perennial ryegrass (Lolium perenne L.) varieties

Abstract A sample set of registered perennial ryegrass varieties was used to compare how morphological characterisation and AFLP® (AFLP® is a registered trademark of Keygene N.V.) and STS molecular markers described variety relationships. All the varieties were confirmed as morphologically distinct, and both the STS and AFLP markers exposed sufficient genetic diversity to differentiate these registered ryegrass varieties. Distances obtained by each of the approaches were compared, with special attention given to the coincidences and divergences between the methods. When correlations between morphological, AFLP and STS distances were calculated and the corresponding scatter-plots constructed, the variety relationships appeared to be rather inconsistent across the methods, especially between morphology and the molecular markers. However, some consistencies were found for closely related material. An implication could be that these molecular-marker techniques, while not yet suited to certain operations in the traditional registration of new varieties, could be suitable methods for investigating disputable distinctness situations or possible EDV (EDV= essentially derived variety. An EDV is a variety being clearly distinct from, but conforming in the expression of the essential characteristics of, an ’initial variety’ (IV) from which it is found to have been predominantly derived) relationships, subject to establishing standardised protocols and statistical techniques. Some suggestions for such a protocol, including a statistical test for distinctness, are given.

Maize introduction into Europe: the history reviewed in the light of molecular data

Abstract.The resolution that can be obtained from molecular genetic markers affords new prospects for understanding the dispersion of agricultural species from their primary origin centres. In order to study the introduction and the dispersion of maize in Europe, we have characterised a large and representative set of maize populations of both American and European origins for their variation at 29 restriction fragment length polymorphism loci. Polymorphism was higher for American populations than for European populations (respectively, 12.3 and 9.6 alleles per locus, on average), and only a few alleles were specific to European populations. Investigation of genetic similarity between populations from both continents made it possible to identify various types of American maize introduced into Europe at different times or in different places and which have given rise to distinctive European races. Beyond confirming the importance of Caribbean germplasm, the first maize type to be introduced into Europe, this research revealed that introductions of Northern American flint populations have played a key role in the adaptation of maize to the European climate. According to a detailed historical investigation, the introduction of these populations must have occurred shortly after the discovery of the New World.

Genetic diversity within and among maize populations : a comparison between isozyme and nuclear RFLP loci

Abstract In order to compare the potential of enzyme and DNA markers to investigate genetic diversity within and among populations, ten maize populations were characterized for (1) 20 isozyme loci and (2) restriction fragment length polymorphism (RFLP) for 35 probe-enzyme combinations. Each population was represented by a sample of at least 30 individuals. The average number of alleles detected per locus was clearly higher for RFLPs (6.3) than for isozymes (2.4). Similarly, total diversity was higher for RFLPs (0.60) than for isozymes (0.23). This difference is consistent with observations on inbred-line collections and can be related to the fact that many variations at the DNA level do not change the amino-acid composition or the global charge of proteins. By contrast, the magnitude of population differentiation, relative to the total diversity, was similar for isozymes (23%) and RFLPs (22%). This suggests that the isozyme and RFLP loci considered in this study are subject to similar evolutionary forces, and that both are mostly neutral. However, RFLPs proved clearly superior to isozymes both to (1) identify the origin of a given individual and (2) reveal a relevant genetic structure among populations. The higher polymorphism observed for RFLP loci and the greater number of these loci contributed to the superior discriminative ability of the RFLP data.

The genetic basis of heterosis: multiparental quantitative trait loci mapping reveals contrasted levels of apparent overdominance among traits of agronomical interest in maize (Zea mays L.).

Understanding the genetic bases underlying heterosis is a major issue in maize (Zea mays L.). We extended the North Carolina design III (NCIII) by using three populations of recombinant inbred lines derived from three parental lines belonging to different heterotic pools, crossed with each parental line to obtain nine families of hybrids. A total of 1253 hybrids were evaluated for grain moisture, silking date, plant height, and grain yield. Quantitative trait loci (QTL) mapping was carried out on the six families obtained from crosses to parental lines following the “classical” NCIII method and with a multiparental connected model on the global design, adding the three families obtained from crosses to the nonparental line. Results of the QTL detection highlighted that most of the QTL detected for grain yield displayed apparent overdominance effects and limited differences between heterozygous genotypes, whereas for grain moisture predominance of additive effects was observed. For plant height and silking date results were intermediate. Except for grain yield, most of the QTL identified showed significant additive-by-additive epistatic interactions. High correlation observed between heterosis and the heterozygosity of hybrids at markers confirms the complex genetic basis and the role of dominance in heterosis. An important proportion of QTL detected were located close to the centromeres. We hypothesized that the lower recombination in these regions favors the detection of (i) linked QTL in repulsion phase, leading to apparent overdominance for heterotic traits and (ii) linked QTL in coupling phase, reinforcing apparent additive effects of linked QTL for the other traits.

Effect of population structure corrections on the results of association mapping tests in complex maize diversity panels.

Association mapping of sequence polymorphisms underlying the phenotypic variability of quantitative agronomical traits is now a widely used method in plant genetics. However, due to the common presence of a complex genetic structure within the plant diversity panels, spurious associations are expected to be highly frequent. Several methods have thus been suggested to control for panel structure. They mainly rely on ad hoc criteria for selecting the number of ancestral groups; which is often not evident for the complex panels that are commonly used in maize. It was thus necessary to evaluate the effect of the selected structure models on the association mapping results. A real maize data set (342 maize inbred lines and 12,000 SNPs) was used for this study. The panel structure was estimated using both Bayesian and dimensional reduction methods, considering an increasing number of ancestral groups. Effect on association tests depends in particular on the number of ancestral groups and on the trait analyzed. The results also show that using a high number of ancestral groups leads to an over-corrected model in which all causal loci vanish. Finally the results of all models tested were combined in a meta-analysis approach. In this way, robust associations were highlighted for each analyzed trait.

Relationships among maize inbred lines and populations from European and North-American origins as estimated using RFLP markers.

Abstract RFLP markers have proven to be a reliable and highly informative tool for characterizing genetic diversity in maize. Joint analysis of inbred lines and populations should provide valuable information with respect to (1) a better understanding of the genetic basis of present elite germplasm and (2) the identification of populations that may prove to be useful sources of genetic diversity for breeding programs. Sixty-two inbred lines of known heterotic groups and ten maize populations, some of them significant contributors to the genetic basis of the heterotic groups, were assayed at 28 RFLP loci. Joint data analyses first underlined that the populations displayed a large number of alleles that were absent in the set of inbred lines. Associations among inbreds and populations further proved consistent with pedigree data of the inbreds and provided new information on the genetical basis of heterotic groups. In particular, European flint inbreds were revealed to be as close to the Northeastern U.S. flint population studied as to the typical European populations. These results advocate the analysis of larger sets of populations by means of molecular markers in order to (1) gain insight into the history of maize germplasm and (2) set up appropriate strategies for the use of genetic resources in breeding programs.

Recovering Power in Association Mapping Panels with Variable Levels of Linkage Disequilibrium

Association mapping has permitted the discovery of major QTL in many species. It can be applied to existing populations and, as a consequence, it is generally necessary to take into account structure and relatedness among individuals in the statistical model to control false positives. We analytically studied power in association studies by computing noncentrality parameter of the tests and its relationship with parameters characterizing diversity (genetic differentiation between groups and allele frequencies) and kinship between individuals. Investigation of three different maize diversity panels genotyped with the 50k SNPs array highlighted contrasted average power among panels and revealed gaps of power of classical mixed models in regions with high linkage disequilibrium (LD). These gaps could be related to the fact that markers are used for both testing association and estimating relatedness. We thus considered two alternative approaches to estimating the kinship matrix to recover power in regions of high LD. In the first one, we estimated the kinship with all the markers that are not located on the same chromosome than the tested SNP. In the second one, correlation between markers was taken into account to weight the contribution of each marker to the kinship. Simulations revealed that these two approaches were efficient to control false positives and were more powerful than classical models.

Analysis of genetic structure in a panel of elite wheat varieties and relevance for association mapping

During the last decades, with the intensification of selection and breeding using crosses between varieties, a very complex genetic structure was shaped in the elite wheat germplasm. However, precise description of this structure with panels and collections is becoming more and more crucial with the development of resource management and new statistical tools for mapping genetic determinants (e.g. association studies). In this study, we investigated the genetic structure of 195 Western European elite wheat varieties using the recent development of high throughput screening methods for molecular markers. After observing that both microsatellites and Diversity Array Technology markers are efficient to estimate the structure of the panel, we used different complementary approaches (Genetic distances, principal component analysis) that showed that the varieties are separated by geographical origin (France, Germany and UK) and also by breeding history, confirming the impact of plant breeding on the wheat germplasm structure. Moreover, by analysing three phenotypic traits presenting significant average differences across groups (plant height, heading date and awnedness), and by using markers linked to major genes for these traits (Ppd-D1, Rht-B1, Rht-D1 and B1), we showed that for each trait, there is a specific optimal Q matrix to use as a covariate in association tests.

General and specific combining abilities in a maize (Zea mays L.) test-cross hybrid panel: relative importance of population structure and genetic divergence between parents

Key messageGeneral and specific combining abilities of maize hybrids between 288 inbred lines and three tester lines were highly related to population structure and genetic distance inferred from SNP data.AbstractMany studies have attempted to provide reliable and quick methods to identify promising parental lines and combinations in hybrid breeding programs. Since the 1950s, maize germplasm has been organized into heterotic groups to facilitate the exploitation of heterosis. Molecular markers have proven efficient tools to address the organization of genetic diversity and the relationship between lines or populations. The aim of the present work was to investigate to what extent marker-based evaluations of population structure and genetic distance may account for general (GCA) and specific (SCA) combining ability components in a population composed of 800 inter and intra-heterotic group hybrids obtained by crossing 288 inbred lines and three testers. Our results illustrate a strong effect of groups identified by population structure analysis on both GCA and SCA components. Including genetic distance between parental lines of hybrids in the model leads to a significant decrease of SCA variance component and an increase in GCA variance component for all the traits. The latter suggests that this approach can be efficient to better estimate the potential combining ability of inbred lines when crossed with unrelated lines, and limits the consequences of tester choice. Significant residual GCA and SCA variance components of models taking into account structure and/or genetic distance highlight the variation available for breeding programs within structure groups.