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Identification of quantitative trait loci (QTL) involved in the variation of hybrid value is of key importance for cross-pollinated species such as maize (Zea mays L.). In a companion paper, we illustrated a new QTL mapping population design involving a factorial mating between two multiparental segregating populations. Six biparental line populations were developed from four founder lines in the Dent and Flint heterotic groups. They were crossed to produce 951 hybrids and evaluated for silage performances. Previously, a linkage analysis (LA) model that assumes each founder line carries a different allele was used to detect QTL involved in General and Specific Combining Abilities (GCA and SCA, respectively) of hybrid value. This previously introduced model requires the estimation of numerous effects per locus, potentially affecting QTL detection power. Using the same design, we compared this “Founder alleles” model to two more parsimonious models, which assume that (i) identity in state at SNP alleles from the same heterotic group implies identity by descent (IBD) at linked QTL (“SNP within-group” model) or (ii) identity in state implies IBD, regardless of population origin of the alleles (“Hybrid genotype” model). This last model assumes biallelic QTL with equal effects in each group. It detected more QTL on average than the two other models but explained lower percentages of variance. The “SNP within-group” model appeared to be a good compromise between the two other models. These results confirm the divergence between the Dent and Flint groups. They also illustrate the need to adapt the QTL detection model to the complexity of the allelic variation, which depends on the trait, the QTL, and the divergence between the heterotic groups.

Heterosis in maize : intermated recombinant inbred lines and their immortalized F2 reveal QTLs with dominant effects but no overdominance. 59. Maize Genetics Conference

Understanding genetic architecture of hybrid performances is important for species showing heterosis. Giraud et al. evaluated an..., Several plant and animal species of agricultural importance are commercialized as hybrids to take advantage of the heterosis phenomenon. Understanding the genetic architecture of hybrid performances is therefore of key importance. We developed two multiparental maize (Zea mays L.) populations, each corresponding to an important heterotic group (dent or flint) and comprised of six connected biparental segregating populations of inbred lines (802 and 822 lines for each group, respectively) issued from four founder lines. Instead of using “testers” to evaluate their hybrid values, segregating lines were crossed according to an incomplete factorial design to produce 951 dent–flint hybrids, evaluated for four biomass production traits in eight environments. QTL detection was carried out for the general-combining-ability (GCA) and specific-combining-ability (SCA) components of hybrid value, considering allelic effects transmitted from each founder line. In total, 42 QTL were detected across traits. We detected mostly QTL affecting GCA, 31% (41% for dry matter yield) of which also had mild effects on SCA. The small impact of dominant effects is consistent with the known differentiation between the dent and flint heterotic groups and the small percentage of hybrid variance due to SCA observed in our design (∼20% for the different traits). Furthermore, most (80%) of GCA QTL were segregating in only one of the two heterotic groups. Relative to tester-based designs, use of hybrids between two multiparental populations appears highly cost efficient to detect QTL in two heterotic groups simultaneously. This presents new prospects for selecting superior hybrid combinations with markers.

Understanding genetic architecture of hybrid performances is important for species showing heterosis. Giraud et al. evaluated an... Several plant and animal species of agricultural importance are commercialized as hybrids to take advantage of the heterosis phenomenon. Understanding the genetic architecture of hybrid performances is therefore of key importance. We developed two multiparental maize (Zea mays L.) populations, each corresponding to an important heterotic group (dent or flint) and comprised of six connected biparental segregating populations of inbred lines (802 and 822 lines for each group, respectively) issued from four founder lines. Instead of using “testers” to evaluate their hybrid values, segregating lines were crossed according to an incomplete factorial design to produce 951 dent–flint hybrids, evaluated for four biomass production traits in eight environments. QTL detection was carried out for the general-combining-ability (GCA) and specific-combining-ability (SCA) components of hybrid value, considering allelic effects transmitted from each founder line. In total, 42 QTL were detected across traits. We detected mostly QTL affecting GCA, 31% (41% for dry matter yield) of which also had mild effects on SCA. The small impact of dominant effects is consistent with the known differentiation between the dent and flint heterotic groups and the small percentage of hybrid variance due to SCA observed in our design (∼20% for the different traits). Furthermore, most (80%) of GCA QTL were segregating in only one of the two heterotic groups. Relative to tester-based designs, use of hybrids between two multiparental populations appears highly cost efficient to detect QTL in two heterotic groups simultaneously. This presents new prospects for selecting superior hybrid combinations with markers.

Plant architecture, phenology and yield components of cultivated plants have repeatedly been shaped by selection to meet human needs and adaptation to different environments. Here we assessed the genetic architecture of 24 correlated maize traits that interact during plant cycle. Overall, 336 lines were phenotyped in a network of 9 trials and genotyped with 50K single-nucleotide polymorphisms. Phenology was the main factor of differentiation between genetic groups. Then yield components distinguished dents from lower yielding genetic groups. However, most of trait variation occurred within group and we observed similar overall and within group correlations, suggesting a major effect of pleiotropy and/or linkage. We found 34 quantitative trait loci (QTLs) for individual traits and six for trait combinations corresponding to PCA coordinates. Among them, only five were pleiotropic. We found a cluster of QTLs in a 5 Mb region around Tb1 associated with tiller number, ear row number and the first PCA axis, the latter being positively correlated to flowering time and negatively correlated to yield. Kn1 and ZmNIP1 were candidate genes for tillering, ZCN8 for leaf number and Rubisco Activase 1 for kernel weight. Experimental repeatabilities, numbers of QTLs and proportion of explained variation were higher for traits related to plant development such as tillering, leaf number and flowering time, than for traits affected by growth such as yield components. This suggests a simpler genetic determinism with larger individual QTL effects for the first category.

Resumen del póster presentado en el Congreso celebrado en Saint-Malo, Francia, entre el 22 y el 25 de marzo de 2018., Comparing and identifying interesting sources of genetic diversity that have been maintained by different genebanks and understanding the global organization of this genetic diversity is an important issue for pre-breeding. We aimed at evaluating how genotyping-by-sequencing (GBS) technologies can address these both issues. We used GBS to compare the genetic diversity of 1191 European Flint lines maintained by INRA and other European institutes (see Gouesnard et al., this meeting) with the USDA collection (Romay et al., 2013, Genome Biology). We first examined the similarity of 68 inbred lines with a same variety name between the two collections, and observed that IBS ranged from 0.775 to 0.997 (with a mean of 0.941). It indicated that GBS can be used for comparing collections and identifying redundancy and illegitimate accessions between genebanks. Based on principal coordinate analysis and structure analysis on 4001 lines, we showed the distinctiveness of flint materials compared to the USDA collection. The structuration analysis in 12 groups confirmed the influence of some historical founder lines in the genetic organization of the dent group (B73, A632, Oh43, Mo17, W182E, PH207 and Wf9). Flint lines were structured in 3 groups (a Sweet-Northern Flint group, an Italian-Argentinan group and a European group formed by Pyrenees Galicia and Lacaune groups). The Tropical and Pop corn groups were distinct. We identified several selective sweeps between Dent, Flint and Tropical inbred lines that co-localized with SNPs associated with flowering time variation identified by association mapping. It suggests that these genomic regions played an important role in adaptation to higher lattitude. The joint analysis of collections by GBS offers opportunities for a global diversity analysis of maize inbred lines., French National Research Agency (Amaizing, ANR-10-BTBR-03)

34 págs., 5 tabl. The definitive version is available at: https://www.crops.org/publications/cs, 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., This research was supported in the framework of the Plant-KBBE program (project acronym “Cornfed”) by the Spanish Ministry of Science and Innovation (proj. EUI2008-03642 and EUI2008-03635), the French National Agency for Research (ANR, Ministry of High Education and Research), and the German Federal Ministry of Education and Research (grant numbers 0315461AD).

General 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. Many 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.

10 Pags.- 3 Tabls.- 3 Figs.- 5 Suppl. Tabls., Background: Breeding for cold tolerance in maize promises to allow increasing growth area and production in temperate zones. The objective of this research was to conduct genome-wide association analyses (GWAS) in temperate maize inbred lines and to find strategies for pyramiding genes for cold tolerance. Two panels of 306 dent and 292 European flint maize inbred lines were evaluated per se and in testcrosses under cold and control conditions in a growth chamber. We recorded indirect measures for cold tolerance as the traits number of days from sowing to emergence, relative leaf chlorophyll content or quantum efficiency of photosystem II. Association mapping for identifying genes associated to cold tolerance in both panels was based on genotyping with 49,585 genome-wide single nucleotide polymorphism (SNP) markers. Results: We found 275 significant associations, most of them in the inbreds evaluated per se, in the flint panel, and under control conditions. A few candidate genes coincided between the current research and previous reports. A total of 47 flint inbreds harbored the favorable alleles for six significant quantitative trait loci (QTL) detected for inbreds per se evaluated under cold conditions, four of them had also the favorable alleles for the main QTL detected from the testcrosses. Only four dent inbreds (EZ47, F924, NK807 and PHJ40) harbored the favorable alleles for three main QTL detected from the evaluation of the dent inbreds per se under cold conditions. There were more QTL in the flint panel and most of the QTL were associated with days to emergence and ΦPSII. Conclusions: These results open new possibilities to genetically improve cold tolerance either with genome-wide selection or with marker assisted selection., This research was supported in the framework of the Plant-KBBE program (project acronym “Cornfed”) by the Spanish Ministry of Science and Innovation (proj. EUI2008-03642 and EUI2008-03635), the Spanish Plan for Research and Development (AGL2013-48852-C3-1-R), the French National Agency for Research (ANR, Ministry of High Education and Research), and the German Federal Ministry of Education and Research (grant number 0315461A-D).

Genomic selection refers to the use of genotypic information for predicting breeding values of selection candidates. A prediction formula is calibrated with the genotypes and phenotypes of reference individuals constituting the calibration set. The size and the composition of this set are essential parameters affecting the prediction reliabilities. The objective of this study was to maximize reliabilities by optimizing the calibration set. Different criteria based on the diversity or on the prediction error variance (PEV) derived from the realized additive relationship matrix–best linear unbiased predictions model (RA–BLUP) were used to select the reference individuals. For the latter, we considered the mean of the PEV of the contrasts between each selection candidate and the mean of the population (PEVmean) and the mean of the expected reliabilities of the same contrasts (CDmean). These criteria were tested with phenotypic data collected on two diversity panels of maize (Zea mays L.) genotyped with a 50k SNPs array. In the two panels, samples chosen based on CDmean gave higher reliabilities than random samples for various calibration set sizes. CDmean also appeared superior to PEVmean, which can be explained by the fact that it takes into account the reduction of variance due to the relatedness between individuals. Selected samples were close to optimality for a wide range of trait heritabilities, which suggests that the strategy presented here can efficiently sample subsets in panels of inbred lines. A script to optimize reference samples based on CDmean is available on request., This research was jointly supported as “Cornfed project” by the French National Agency for Research (ANR), the German Federal Ministry of Education and Research (BMBF), and the Spanish Ministry of Science and Innovation (MICINN). R. Rincent is jointly funded by Limagrain, Biogemma, Kleinwanzlebener Saatzucht AG (KWS), and the Association Nationale de la Recherche et de la Technologie (ANRT)., ANR, BMBF, MICINN, KWS, ANRT

QTL for cell wall digestibility related traits were investigated in maize (Zea mays L.) topcross experiments of 240 RILs obtained from the F838 × F286 early maize hybrid. Genotype effects were highly signifi cant for all agronomic and cell wall related traits and much higher than genotype × environment (GE) interaction effects for cell wall digestibility traits. Eight quantitative trait loci (QTL) for dry matter (DM) yield were observed, out of which only one increasing allele originated from F286. Conversely, three QTL out of four with alleles increasing DM content at silage harvest stage originated from the earliest F286 line. Out of four QTL increasing starch content, two QTL, which originated from F838, did not colocalize with silking date QTL or any other investigated traits. Ten QTL were observed for lignin content and between six and nine QTL were observed for each of the three cell wall digestibility investigated traits. QTL located in bins 1.02 (position 76–80 cM), 1.07 (position 228–230 cM), and 8.07 (position 134–142 cM) are likely of priority interest when it comes to improving maize cell wall digestibility. Candidate genes underlying cell wall digestibility QTL were searched for on the basis of in silico investigations and with maize, Arabidopsis, poplar, and eucalyptus genomic information. In most of QTL positions, transcription factors regulating cell wall lignifi cation were shown to be the currently most plausible candidates involved in genetic variation of maize cell wall digestibility.

The high whole plant biomass productivity of maize makes it a potential source of energy in animal feeding and biofuel production. The variability and the genetic determinism of traits related to biomass are poorly known. We analyzed two highly diverse panels of Dent and Flint lines representing complementary heterotic groups for Northern Europe. They were genotyped with the 50 k SNP-array and phenotyped as hybrids (crossed to a tester of the complementary pool) in a western European field trial network for traits related to flowering time, plant height, and biomass. The molecular information revealed to be a powerful tool for discovering different levels of structure and relatedness in both panels. This study revealed important variation and potential genetic progress for biomass production, even at constant precocity. Association mapping was run by combining genotypes and phenotypes in a mixed model with a random polygenic effect. This permitted the detection of significant associations, confirming height and flowering time quantitative trait loci (QTL) found in literature. Biomass yield QTL were detected in both panels but were unstable across the environments. Alternative kinship estimator only based on markers unlinked to the tested SNP increased the number of significant associations by around 40 % with a satisfying control of the false positive rate. This study gave insights into the variability and the genetic architectures of biomass-related traits in Flint and Dent lines and suggests important potential of these two pools for breeding high biomass yielding hybrid varieties., This research was jointly supported as “Cornfed project” by the French National Agency for Research (ANR), the German Federal Ministry of Education and Research (BMBF), and the Spanish ministry of Science and Innovation (MICINN). R. Rincent is jointly funded by Limagrain, Biogemma, KWS, and the French ANRt. L. Moreau, S. Nicolas and A. Charcosset conducted this research in the framework of Amaizing Investissement d’Avenir program.

International audience; The migration of maize from tropical to temperate climates was accompanied by a dramatic evolution in flowering time. To gain insight into the genetic architecture of this adaptive trait, we conducted a 50K SNP-based genome-wide association and diversity investigation on a panel of tropical and temperate American and European representatives. Eighteen genomic regions were associated with flowering time. The number of early alleles cumulated along these regions was highly correlated with flowering time. Polymorphism in the vicinity of the ZCN8 gene, which is the closest maize homologue to Arabidopsis major flowering time (FT) gene, had the strongest effect. This polymorphism is in the vicinity of the causal factor of Vgt2 QTL. Diversity was lower, whereas differentiation and LD were higher for associated loci compared to the rest of the genome, which is consistent with selection acting on flowering time during maize migration. Selection tests also revealed supplementary loci that were highly differentiated among groups and not associated with flowering time in our panel, whereas they were in other linkage-based studies. This suggests that allele fixation led to a lack of statistical power when structure and relatedness were taken into account in a linear mixed model. Complementary designs and analysis methods are necessary to unravel the architecture of complex traits. Based on linkage disequilibrium (LD) estimates corrected for population structure, we concluded that the number of SNPs genotyped should be at least doubled to capture all QTLs contributing to the genetic architecture of polygenic traits in this panel. These results show that maize flowering time is controlled by numerous QTLs of small additive effect and that strong polygenic selection occurred under cool climatic conditions. They should contribute to more efficient genomic predictions of flowering time and facilitate the dissemination of diverse maize genetic resources under a wide range of environments.

International audience; Remarkable genetic improvement in maize yield, lodging resistance, biotic and abiotic stress tolerance were obtained during the 1955 - 2000 period in Europe. However, a decline in the average cell wall digestibility of maize hybrids has been observed during the 1980 - 2000 period. This trend has now ceased with the breeding of specialized silage varieties. The cell wall degradability of the best current hybrids does not yet equal that of better old types of the 1960s era such as INRA258, mostly because the germplasm currently used in maize breeding corresponds to progenies of resources initially chosen for grain maize breeding. Nearly 110 new lines were thus derived by self-pollination in old or unused landraces and accessions in order to test the interest of this kind of genetic resources in maize breeding for cell wall degradability traits. Based on per se and topcross experiments, several lines representative of different and new germplasm displayed high or medium high cell wall digestibility. F7103 (Argentina-BBC143), F7104 (Argentina-BBC325), F7106 (Gelderland-VC150), F7114 (Zakarpatskaja-Zeltaja-Zubovidnaja), and F7121 (Comptons-Early) are likely among the more romising new resource lines for improvement of cell wall digestibility in elite dent or flint germplasm. These lines covered a large genetic diversity as F7103 and F7104 are mostly lowland tropical, F7106 and F7121 mostly northern flint, F7114 mostly Oh43/Minnesota13 related. Two other lines of medium-high cell wall digestibility, F7101 (St Engrace) and F7112 (Mecklenburger), were shown to be significantly related to lowland tropical germplasm. Several landraces or old varieties also gave lines of low cell wall digestibility such as F7124 (Curaco-de-Velez) or F7126 (Baanbreker), both related to the northern flint group. Average yield of top-crossed lines was nearly 7 t/ha lower than the average value of the three control hybrids and only one hybrid (F7104 x UH002) had yield and earliness equal to those of control hybrids. These low values were related to the fact that investigated lines were derived from old resources that did not get the last 60 years genetic improvements, and also to the only use of a flint male for top-crosses that did not optimize the genetic distance with all top-crossed lines. Allele sequencing and association genetics should give markers for targeted introgression of new alleles of interest originating from this specific set of lines in elite lines.

The aim was to evaluate the influence of (i) cations potentially present in soil solution and (ii) of plant Cd content on apoplastic and symplastic root uptake of Cd. Hydroponically grown maize (Zen mays) roots were exposed to two Cd concentrations together with a cation five times the strength of the Cd. The influence of three pH and four Ca levels was also assessed. In addition, maize and alpine penny-cress (Noccaea caerulescens) were grown so their tissues contained Cd at three levels when their roots were exposed for 1 h to three Cd concentrations. Maize Cd uptake in the 5 mu M Cd solution was reduced by the presence of Pb(2+), Cu(2+), Co(2+), Zn(2+), Mg(2+) or Mn(2+). At a 1 mu M Cd concentration, Cu(2+), as well as Ca(2+) and H(+) reduced the Cd uptake. However, the Ca concentration had to be much higher than that of Cd to restrain its uptake. High plant Cd content was responsible for an increase in the apoplastic Cd uptake and a decrease in the symplastic absorption, for both species. Low plant Cd content neither affected the Cd apoplastic uptake whatever the exposure concentration, nor the symplastic uptake in 0.1 mu M Cd exposure solution. Moreover, the hyperaccumulator symplastic uptake increased when exposed to 10 mu M Cd, but not when exposed to 50 mu M Cd. Maize roots showed a decrease in membrane net flux when exposed to 10 mu M and 50 p,M Cd. Finally, the results suggest that for plants exposed to usual soil solution concentrations, it is mainly calcium and protons which interfere with Cd internalization. (C) 2011 Elsevier B.V. All rights reserved.